Topographica

* [r4268] external/Python-2.4.2.tgz:
Upgraded from Python 2.4.2 to 2.4.4 to fix libreadline problem

* [r4267] external/Makefile:
Slight change to Python build commands; shouldn't have any
effect, but may work around a build problem

* [r4266] external,
external/.cvsignore,
external/Makefile,
external/Python-2.4.4.tgz:
Upgraded from Python 2.4.2 to 2.4.4 to fix libreadline problem

2006-11-08 jbednar

* [r4265] topo/learningfns/projfns.py:
Cleaned up whitespace

* [r4264]
examples/sullivan_neurocomputing06.ty,
topo/outputfns/homeostatic.py:
Cleaned up sullivan_neurocomputing06.ty; moving TestFn to
topo.outputfns.homeostatic.PiecewiseLinear_debug2 and removing
the initial no-homeostatic plasticity phase

* [r4263] doc/Links/index_text.php:
Added more info on NEST

* [r4262]
examples/Sullivan_homeo_synaptic_SOM.ty,
examples/sullivan_neurocomputing06.ty:
Moved Sullivan_homeo_synaptic_SOM.ty to
sullivan_neurocomputing06.ty

2006-11-08 r_primrose

* [r4261]
examples/sullivan_neurocomputing04.ty:
Added disclaimer

* [r4260] examples/sullivan_nc04.ty,
examples/sullivan_neurocomputing04.ty:
Renamed sullivan_nc04.ty to sullivan_neurocomputing04.ty

2006-11-08 fdemertzis

* [r4259]
examples/Sullivan_homeo_synaptic_SOM.ty:
Initial version, no date of publication

2006-11-08 r_primrose

* [r4258] examples/sullivan_nc04.ty,
topo/learningfns/projfns.py:
*** empty log message ***

2006-11-07 jbednar

* [r4257]
examples/homeo_intrinsic_lissom_or.ty,
examples/lissom_or_homeomaxent.ty:
Moved homeo_intrinsic_lissom_or.ty to lissom_or_homeomaxent.ty

* [r4256] examples/lissom_or_homeoscale.ty:
Moved homeo_synaptic_lissom_or.ty to lissom_or_homeoscale.ty

* [r4255] examples/homeo_synaptic_lissom_or.ty,
examples/lissom_or_homeoscale.ty:
Moved homeo_synaptic_lissom_or.ty to lissom_or_homeoscale.ty

* [r4254]
examples/homeo_intrinsic_lissom_oo_or.ty,
examples/lissom_oo_or_homeomaxent.ty:
Moved homeo_intrinsic_lissom_oo_or.ty to
lissom_oo_or_homeomaxent.ty

* [r4253]
examples/homeo_lissom_or_noshrinking.ty:
No longer needed; moved into lissom_or_noshrinking.ty

* [r4252] examples/lissom_or_noshrinking.ty:
Made homeostatic by default; still usable as non-homeostatic by
adding '-c homeostatic=False' to the command line

* [r4251]
examples/homeo_lissom_or_noshrinking.ty:
Cleaned up imports

* [r4250] examples/lissom_oo_od.ty:
Trivial change to try to remove execute bit

* [r4249] examples/lissom_oo_od.ty:
Trivial change to try to remove execute bit

* [r4248] examples/laminar.ty,
examples/lissom_oo_od.ty:
Trivial change to try to remove execute bit

* [r4247] examples/homeostatic.ty:
Removed unused file

* [r4246]
examples/homeo_intrinsic_lissom_oo_or.ty,
examples/homeo_intrinsic_lissom_or.ty,
examples/homeo_synaptic_lissom_or.ty,
topo/outputfns/homeostatic.py:
Cleaned up homeostatic simulations -- moved OutputFns to
topo.outputfns.homeostatic, removed unused imports

* [r4245] examples/joublin_bc96.ty:
Minor cleanup

2006-11-02 jbednar

* [r4244] doc/shared/index.php:
Added blurb about weave

* [r4243] external/Makefile:
Added re-make when weave.diff changes (or is newer than the weave
target) to force rebuild

* [r4242] external/Makefile,
external/weave.diff:
Added patch to allow weave to work on GCC 4.1.x

* [r4241] doc/Future_Work/current_text.php:
Added FFT plot to-do

2006-10-06 ceball

* [r4240] topo/tests/testlissom_oo_or.py:
Corrected a HACKALERT; added note to myself on how to rnu the
test.

* [r4239] doc,
doc/.cvsignore:
Ignore reference-manual.

* [r4238] topo/tests/testlissom_oo_or.py:
Tests V1 activities at t=1, t=100, and t=210.

* [r4237] topo/tests/testlissom_oo_or.data:
V1 activities from t=1,t=100,t=210 for examples/lissom_oo_or.ty
with Topographica updated just before the time of this commit.

* [r4236] topo/tests/testlissom_oo_or.py:
Initial version.

* [r4235] topo/tests/__init__.py:
Avoid running the slower testlissom_oo_or.py test file. (A future
task is to allow there to be a set of slower tests.)

* [r4234] doc/Future_Work/current_text.php:
Added small clarification.

* [r4233] topo/tests/testlissom.data,
topo/tests/testlissom.ty:
Removed unused and outdated test file, along with its data.

* [r4232] topo/base/cf.py:
Tried to clarify some comments a little. Minor corrections to
docstrings.

2006-10-05 ceball

* [r4231] topo/tests/reference,
topo/tests/reference/.cvsignore:
Initial version.

* [r4230]
topo/tests/reference/retina_lgn_match.ty:
Checks LGN weights.

* [r4229]
topo/tests/reference/lissom_log_parser.py:
get_matrix() (which reads a c++ lissom matrix) always returns an
array. compare_elements() first checks that the two arrays are
the same shape.

* [r4228]
topo/tests/reference/retina_lgn_match.000000.wts.Ganglia00.Afferent0.018_018.matrix:
Initial version

2006-10-04 ceball

* [r4227] topo/tests/reference/lissom5.gz:
Gzip'd lissom5 binary, for generation of reference results.

* [r4226] topo/tests/reference/lissom5:
Adding gzip'd version to repository.

* [r4225]
topo/tests/reference/retina_lgn_match.ty:
Added comment.

* [r4224]
topo/tests/reference/retina_lgn_match.param,
topo/tests/reference/set_thresholds.command:
Initial version.

* [r4223] topo/tests/reference/lissom5:
C++ LISSOM 5 binary, for generation of C++ data.

* [r4222]
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty:
Updated location of lissom_log_parser module to the correct one
(was working before because of pyc file left behind).

* [r4221]
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty:
Removed outdated automatic testing code; the current code is in
retina_lgn_match.ty.

* [r4220]
topo/tests/reference/retina_lgn_match.ty:
Added commented-out code from one of the other reference files.

* [r4219]
topo/tests/reference/lissom_log_parser.py,
topo/tests/reference/retina_lgn_match.ty:
Moved compare_elements() function from retina_lgn_match.ty to
lissom_log_parser.py.

* [r4218]
topo/tests/reference/retina_lgn_match.000001p000.Eye0_Activity.matrix,
topo/tests/reference/retina_lgn_match.000001p000.Ganglia00_Activity.matrix:
Values from C++ LISSOM.

* [r4217]
topo/tests/reference/retina_lgn_match.ty:
Compares retina and cfsheet activities with those from c++.

* [r4216]
topo/tests/reference/lissom_log_parser.py:
Minor clarifications.

* [r4215]
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty,
topo/tests/reference/retina_lgn_match.ty:
Updated path after moving.

* [r4214] doc/Future_Work/current_text.php:
Removed task.

* [r4213] topo/tests/reference/README.txt:
Removed ALERT.

* [r4212]
topo/tests/reference/lissom_log_parser.py,
topo/tests/reference/lissom_oo_or_reference.ty,
topo/tests/reference/lissom_or_reference.ty,
topo/tests/reference/oo_or_map_topo.log,
topo/tests/reference/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
topo/tests/reference/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix,
topo/tests/reference/or_map_topo.000001p000.Eye0_Activity.matrix,
topo/tests/reference/or_map_topo.000001p000.Primary_Activity.matrix,
topo/tests/reference/or_map_topo.log:
Moved here from tests/ directory.

* [r4211] topo/tests/lissom_log_parser.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/oo_or_map_topo.log,
topo/tests/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
topo/tests/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix,
topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
topo/tests/or_map_topo.000001p000.Primary_Activity.matrix,
topo/tests/or_map_topo.log:
Moved to reference/ subdirectory.

* [r4210]
topo/tests/reference/retina_lgn_match.ty:
Some clarifications.

* [r4209] doc/Future_Work/current_text.php:
Minor clean-up.

2006-10-02 jbednar

* [r4208] topo/learningfns/basic.py:
Fixed typos found by Brad Bowman

2006-09-18 jbednar

* [r4207] doc/Makefile:
Added skipping of reference-manual creation if no files have
changed

2006-09-17 jbednar

* [r4206] topo/base/simulation.py:
Cleaned up documentation strings and spacing. Removed unused
state_len().

* [r4205] topo/analysis/featuremap.py,
topo/base/sheet.py,
topo/sheets/lissom.py:
Cleaned up documentation strings and spacing

* [r4204] topo/tests/testsimulation.py:
Removed use of state_len() so that it can be deleted

2006-09-16 jbednar

* [r4203] topo/base/sheet.py:
Clarified state_push and state_pop, and removed apparently unused
functionality from state_pop

* [r4202] topo/base/parameterclasses.py:
Fixed minor typo

2006-09-15 judelaw

* [r4201] topo/base/sheet.py:
changed name of activity_push to state_push

2006-09-14 judelaw

* [r4200] topo/sheets/lissom.py:
added state_push and pop which also ensure the correct iteration
and settling step are saved

* [r4199] topo/base/simulation.py:
rewrote state_push and pop to save state of all event processors
and added event_push and pop which save only the event as before

* [r4198] topo/commands/basic.py:
renamed state_push and pop to event_push and pop in
pattern_present - where these new functions save and reset the
anly the simulation events as before (rather than the state), to
ensure that a map can be calculated

* [r4197] topo/analysis/featuremap.py:
now saves state before and re-instates after
present_input_patterns inMeasureFeatureMap.measure_maps in order
to reset settling count and simulation time properly during map
measurment

* [r4196] topo/tkgui/testpattern.py:
now saves state before and re-instates after pattern_present to
reset activity after a presentation

* [r4195] topo/outputfns/projfns.py:
Added CFPOF_Identity function

2006-09-12 jbednar

* [r4194] topo/patterns/rds.py:
Minor formatting cleanup

* [r4193] topo/misc/patternfns.py,
topo/patterns/rds.py:
Collected RandomDotStereogram code into rds.py for easier
understanding and debugging

* [r4192] doc/Future_Work/current_text.php,
topo/tkgui/testpattern.py:
Fixed bug in Test Pattern window for cases where there are
multiple GeneratorSheets of different sizes or densities -- was
using a single shared test PatternGenerator object for all cases.
Added Sheet Coordinate support to Test Pattern window

2006-09-10 jbednar

* [r4191] doc/Downloads/index_text.php:
Fixed markup errors in previous commit

* [r4190] README.txt,
doc/Downloads/index_text.php:
Added suggestions from Brad Bowman

2006-09-01 chrispalmer

* [r4189] topo/commands/analysis.py:
Corrected so OD, disparity and postion all use the new Feature
class when calling MeasureFeatureMap

* [r4188] topo/tests/testfeaturemap.py:
Altered to test MeasureFeatureMap using newly implemented Feature
class

2006-09-01 jbednar

* [r4187] doc/Reference_Manual/index_text.php:
Fixed links for epydoc; should provide a PHP function for this

* [r4186] topo/base/arrayutils.py,
topo/base/parameterclasses.py,
topo/base/parameterizedobject.py,
topo/misc/keyedlist.py,
topo/patterns/basic.py,
topo/patterns/image.py,
topo/sheets/composer.py:
Trivial tweak to docs to make epydoc happy

* [r4185] topo/analysis/featuremap.py:
Removed outdated comments

* [r4184] doc/User_Manual/overview_text.php:
First complete version; fixed many broken links and filled out
basic descriptions

* [r4183] Makefile,
doc/Makefile:
Changed order of making to avoid clobbering reference manual
first page

2006-08-31 chrispalmer

* [r4182] topo/commands/analysis.py:
Creation of Feature class, whish stores the parameters needed for
generating one map, this polulates empty values and/or range
fields if neccessary

* [r4181] topo/analysis/featuremap.py:
Simplification of MeasureFeatureMap. Determines
__sheets_to_measure_maps_for in more straight forward manner. In
__present_input_patterns determines permutations for presentation
in easier fashion.

2006-08-31 jbednar

* [r4180] topo/misc/patternfns.py:
Fixed the fix() function to work without pylab imported

* [r4179] Makefile:
Changed default targets to avoid rebuilding the Reference_Manual
each time

* [r4178] topo/misc/patternfns.py:
Removed usage of pylab, since that is not available when there is
no GUI

* [r4177]
topo/commands/disp_key_white_vert_small.PNG,
topo/commands/disp_key_white_vert_small.png:
Fixed bogus filename

* [r4176] doc/Reference_Manual,
doc/Reference_Manual/.cvsignore:
Added epydoc outputs to ignore

* [r4175] topo/responsefns/optimized.py:
Minor cleanup of imports

* [r4174] topo/base/patterngenerator.py:
Minor tweaks to documentation

* [r4173] Makefile,
doc/Makefile,
doc/shared/util.php:
Changed Reference_Manual to use epydoc

* [r4172] external,
external/.cvsignore,
external/Makefile,
external/docutils-0.4.tar.gz,
external/epydoc-3.0alpha3.tar.gz,
external/epydoc.diff:
Added Epydoc

2006-08-31 tikesh

* [r4171] topo/patterns/basic.py:
added a small method used in one of the scripts for disparity
project

* [r4170] topo/base/pickle.py,
topo/misc/numbergenerators.py,
topo/misc/patternfns.py,
topo/patterns/basic.py:
*** empty log message ***

* [r4169] examples/disparity_energy.ty,
examples/lissom_oo_disparity_gauss_0.ty,
examples/lissom_oo_disparity_gauss_2_pixel.ty,
examples/lissom_oo_disparity_plus_minus_0.ty,
examples/lissom_oo_disparity_plus_minus_2_pixel.ty,
examples/lissom_oo_phase_disparity.ty,
examples/lissom_oo_position_disparity.ty,
examples/odf_science90.ty,
examples/ohzawa_science90.ty,
topo/analysis/featuremap.py,
topo/commands/analysis.py,
topo/commands/disp_key_white_vert_small.PNG,
topo/patterns/rds.py,
topo/plotting/templates.py,
topo/tkgui/testpattern.py:
*** empty log message ***

2006-08-30 jbednar

* [r4168] doc/User_Manual/overview_text.php:
Minor formatting fix

2006-08-29 vldkr

* [r4167] examples/homeo_synaptic_lissom_or.ty:
Updated version

* [r4166] topo/outputfns/homeostatic.py:
Output functions based on homeostatic plasticity

* [r4165] examples/homeo_lissom_oo_or_image.ty:
*** empty log message ***

* [r4164]
examples/homeo_lissom_or_noshrinking.ty:
Updated version

* [r4163]
examples/homeo_intrinsic_lissom_oo_or.ty,
examples/homeo_intrinsic_lissom_or.ty:
Updated version

2006-08-29 jbednar

* [r4162] external/Makefile:
Made DISPLAY hack for matplotlib be a bit more robust, in case
DISPLAY is already set to something other than :0

2006-08-28 ceball

* [r4161] topo/tests/lissom_oo_or_reference.ty:
Corrected afferent connection strength.

2006-08-28 jbednar

* [r4160] doc/User_Manual/basics_text.php.m4:
Added partially completed Overview section

* [r4159] topo/base/sheet.py:
Minor clarification

* [r4158] doc/User_Manual/parameters_text.php:
Made class links uniform

* [r4157]
doc/User_Manual/introduction_text.php.m4:
Minor clarifications

* [r4156] doc/User_Manual,
doc/User_Manual/.cvsignore,
doc/User_Manual/index_text.php,
doc/User_Manual/overview_text.php:
Added partially completed Overview section

2006-08-26 ceball

* [r4155] topo/tests/lissom_oo_or_reference.ty:
Corrected mistake introduced in some previous commit.

2006-08-25 ceball

* [r4154] topo/tests/lissom_oo_or_reference.ty:
CompositePatternGenerator renamed to Composite.

2006-08-24 jbednar

* [r4153] doc/User_Manual/basics_text.php.m4:
Cleaned up and reformatted

* [r4152] doc/User_Manual/basics_text.php.m4:
Added sketch of list of what Topographica supports

2006-08-21 jbednar

* [r4151]
doc/User_Manual/background_text.php.m4:
Minor cleanup

* [r4150] doc/User_Manual/basics_text.php.m4,
doc/User_Manual/images/060220_topographica_screen_shot_small.png,
doc/User_Manual/images/gaussianrandomweights_dense.png,
doc/User_Manual/index_text.php,
doc/User_Manual/introduction_text.php.m4,
doc/shared/topographica.bib:
Added Introduction section to user manual based on text of paper
that had been in background_text.php.m4

* [r4149] doc/Reference_Manual/index_text.php:
Added targets for intro section to use

* [r4148] doc/User_Manual,
doc/User_Manual/.cvsignore:
More to ignore

* [r4147] topo/tests/testbitmap.py,
topo/tests/testplotgrouppanel.py:
Reduced size of array to speed up tests

* [r4146]
doc/User_Manual/images/fourclassweights.png,
doc/User_Manual/images/gaussian_0.3.png,
doc/User_Manual/images/gaussian_0.5.png,
doc/User_Manual/images/or_gaussian_1.png,
doc/User_Manual/images/or_gaussian_2.png,
doc/User_Manual/images/patterntypes_small.png,
doc/User_Manual/patterns_text.php:
Updated Patterns section images for better resolution

2006-08-19 jbednar

* [r4145] topo/patterns/basic.py:
Minor updates to documentation

2006-08-18 jbednar

* [r4144] doc/User_Manual/images/face.png,
doc/User_Manual/images/patterntypes.png,
doc/User_Manual/images/patterntypes_small.png,
doc/User_Manual/patterns_text.php:
Added more documentation

* [r4143] topo/patterns/basic.py:
Added scale and offset for Composite and Selector patterns, and
fixed x and y positions for rotations.

* [r4142] doc/User_Manual/publishing_text.php:
Minor tweak

* [r4141]
doc/User_Manual/images/fourclassweights.png,
doc/User_Manual/images/gaussian_0.3.png,
doc/User_Manual/images/gaussian_0.5.png,
doc/User_Manual/images/gaussianrandomweights.png,
doc/User_Manual/images/or_gaussian_1.png,
doc/User_Manual/images/or_gaussian_2.png,
doc/User_Manual/index_text.php,
doc/User_Manual/patterns_text.php:
Added section on patterns

* [r4140] doc/User_Manual,
doc/User_Manual/.cvsignore:
More to ignore

* [r4139] doc/Future_Work/current_text.php:
Removed completed tasks

* [r4138] topo/base/patterngenerator.py,
topo/patterns/basic.py:
Added size parameter for all PatternGenerators so that all can be
used with Composite

* [r4137] topo/patterns/basic.py:
Changed lists of PatternGenerators to be ListParameters to
provide better error checking

* [r4136] topo/base/parameterclasses.py:
Added ListParameter

* [r4135] topo/base/parameterclasses.py,
topo/base/patterngenerator.py,
topo/misc/distribution.py:
Removed previous change for now, to avoid breaking existing saved
.typ files

* [r4134] topo/base/parameterclasses.py,
topo/base/patterngenerator.py:
Clarified parameter name

* [r4133] topo/patterns/basic.py:
Added Selector pattern (equivalent to C++ LISSOM's Accum_OneHot)

* [r4132] topo/patterns/basic.py:
Minor clarifications

* [r4131] topo/patterns/basic.py:
Added more extensive documentation for Composite

2006-08-17 jbednar

* [r4130] topo/patterns/basic.py:
Fixed x and y position of Composite patterns so that they don't
depend on the size

* [r4129] topo/patterns/basic.py,
topo/patterns/image.py:
Moved PatternSampler from basic.py to image.py, where it is used

* [r4128] topo/tests/testpatterngenerator.py:
Minor cleanup

* [r4127] examples/lissom_oo_or.ty,
examples/lissom_or_sf.ty,
topo/patterns/basic.py,
topo/tests/testpatterngenerator.py:
Changed name of CompositePatternGenerator to Composite for
consistency

* [r4126] topo/patterns/basic.py:
Added support for scaling size of Composite patterns

* [r4125] topo/patterns/basic.py:
Added support for rotating Composite patterns

* [r4124] topo/patterns/basic.py,
topo/tests/testpatterngenerator.py:
Added support for Composite pattern displacement, and enabled the
corresponding test

2006-08-17 judelaw

* [r4123] topo/commands/analysis.py:
changed cog to take projection as argument instead of sheet

2006-08-17 jbednar

* [r4122] topo/patterns/basic.py:
Removed obsolete comment

* [r4121] topo/patterns/basic.py:
Simplified implementation of Composite by removing
PatternSampler. It does not currently support translation,
rotation, etc. of the whole Composite, but those weren't working
properly before either, and are easier to do without
PatternSampler

2006-08-16 judelaw

* [r4120] topo/commands/analysis.py:
added argument to measure_cog function so that projections from a
chosen sheet can be plotted

2006-08-16 jbednar

* [r4119] doc/User_Manual/about_text.php,
doc/User_Manual/index_text.php,
doc/User_Manual/publishing_text.php:
Added page on how to publish using Topographica

2006-08-15 vldkr

* [r4118]
examples/homeo_lissom_or_noshrinking.ty:
initial version

2006-08-15 judelaw

* [r4117] topo/commands/analysis.py:
Made changes to centre of gravity plotting

2006-08-14 jbednar

* [r4116] topo/base/cf.py,
topo/outputfns/optimized.py:
Changed output_activity argument name to mask to clarify what the
data will be used for. Made all CFPOFs respect the mask, for
consistency.

* [r4115] topo/tests/testpatterngenerator.py:
Enabled some tests of composite patterns

* [r4114] topo/patterns/basic.py:
Cleaned up comments and documentation

* [r4113] topo/outputfns/optimized.py:
Re-enabled optimization that should now be safe again

* [r4112] topo/base/cf.py,
topo/base/projection.py,
topo/sheets/lissom.py:
Changed name of apply_output_fn() to apply_learn_output_fn() to
clarify that it is different from the activity output_fn. (It's
called learn_output_fn instead of weights_output_fn because the
interface is specified at the ProjectionSheet level, and there is
no concept of weights at that level, only learning.) Made
apply_learn_output_fn() accept an explicit mask so that it can be
forced to apply to all units, and made all ones be passed in for
the intial iteration for joint normalization.

* [r4111] topo/base/sheet.py:
Added typedef for activity matrices, to encourage consistency.

* [r4110] examples/lissom_oo_od.ty:
Changed input pattern definition to be a class so that it can be
pickled. Temporarily changed learning rates to match
lissom_oo_or.ty.

2006-08-12 jbednar

* [r4109] examples/lissom_oo_or.ty:
Changed ON and OFF channels to have a single DoG projection,
instead of separate Center/Surround. Switched to joint
normalization. Changed default size of Gaussian for Test Pattern
window. Still needs parameter matching with the book simulations.

2006-08-11 jbednar

* [r4108] topo/outputfns/optimized.py:
Deleted an optimization that was causing problems for joint
normalization

* [r4107] topo/base/cf.py:
Changed __norm_total to _norm_total because hasattr() fails for
names starting with a __ (due to name mangling)

* [r4106] topo/sheets/lissom.py:
Trivial improvement to comment

* [r4105] topo/misc/utils.py:
Added handing for case where an array shape is an empty list; not
sure why this would ever occur, but unpickling was failing until
this was added

* [r4104] topo/sheets/lissom.py:
Removed division by length of joint normalization group

* [r4103] topo/sheets/lissom.py:
Added joint normalization for the first iteration

* [r4102] topo/base/projection.py:
Added default learning method for all ProjectionSheets, to
replace the one no longer in CFSheet

* [r4101] topo/base/cf.py,
topo/sheets/lissom.py:
Moved methods related to joint normalization out of CFSheet and
into JointNormalizingCFSheet (in lissom.py), so that only models
using it will have to deal with that complexity.

* [r4100] topo/outputfns/optimized.py:
Minor clarification

* [r4099] topo/base/cf.py:
Replaced __normalize_joint_projections with
__compute_joint_norm_totals, which only updates the norm_total
property values, without actually doing any normalization

* [r4098] topo/base/cf.py,
topo/learningfns/optimized.py,
topo/outputfns/optimized.py:
Renamed ConnectionField.sum to ConnectionField.norm_total to
emphasize that it is not necessarily always the sum.

* [r4097] examples/joublin_bc96.ty:
Fixed missing import

* [r4096] examples/joublin_bc96.ty:
Removed duplicate specification of weight_type, to ensure that it
is consistent with cf.py

* [r4095] examples/joublin_bc96.ty:
Removed duplicate specification of weight_type, to ensure that it
is consistent with cf.py

2006-08-07 ceball

* [r4094]
topo/tests/reference/retina_lgn_match.ty:
Initial version should have been like this.

* [r4093] topo/tests/reference/README.txt:
Initial version.

* [r4092] topo/tests/reference,
topo/tests/reference/retina_lgn_match.ty:
Script to help matching between c++ lissom and topographica.

2006-08-07 jbednar

* [r4091] doc/Downloads/win32_text.php:
No longer in use

2006-08-04 jbednar

* [r4090] topo/outputfns/optimized.py:
Finished up the code for CFPOF_DivisiveNormalizeL1; mistakenly
checked in earlier

* [r4089] topo/outputfns/basic.py:
Removed outdated comment

* [r4088] topo/outputfns/optimized.py:
Added patch to get old pickled files to work

* [r4087] topo/base/cf.py,
topo/learningfns/optimized.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py,
topo/tests/testoutputfnsoptimized.py:
Renamed _sum to __sum to make it private, and made all external
code use sum instead. This should prevent various problems found
when _sum did not exist, due to mixing optimized and
non-optimized components. Removed use of cached values in
DivisiveNormalizeL1, and instead supported that only in
CFPOF_DivisiveNormalizeL1 to avoid problems when CFPOF_Plugin was
used with anything but DivisiveNormalizeL1. Removed unused
DivisiveNormalizeL1_opt. The changes will affect the numerical
value of each activation pattern, at the six or seventh decimal
place total, due to using Numeric.sum in some cases and other sum
routines in others. This should also fix the various segfaults
that were possible when mixing and matching optimized and
non-optimized components.

* [r4086] doc/User_Manual/parameters_text.php:
Fixed example

* [r4085] doc/Links/index_text.php:
Fixed link

* [r4084] examples/lissom_oo_or.ty:
Made some parameters match those in miikkulainen:book05 better;
not yet tested

2006-08-02 ceball

* [r4083] topo/tests/lissom_oo_or_reference.ty:
Back to Composite for LGN weights, rather than separate
projections.

* [r4082] topo/base/cf.py:
Take the number of connections into account during joint
normalization.

* [r4081] topo/base/cf.py:
Fixed incorrect handling of cf.sum by CFPOF_Plugin; the problem
ultimately comes from elsewhere, probably.

* [r4080] topo/tests/lissom_oo_or_reference.ty:
Changed size parameter of Gaussians for projections to LGN (to
match the different definition of Gaussian in c++ lissom; c++
lissom divides by pi in the argument of exp in
RadialFunction::Gaussian but not in retinalobjs).

* [r4079] topo/tests/lissom_oo_or_reference.ty:
Reverted to separate center and surround projections for
debugging.

2006-08-01 judelaw

* [r4078] examples/lissom_or.ty:
changed mistake in name etc.

2006-08-01 vldkr

* [r4077] examples/homeo_lissom_oo_or_image.ty:
update 2

2006-07-31 judelaw

* [r4076] examples/lissom_or.ty:
matched to C++ version

2006-07-28 ceball

* [r4075] topo/misc/utils.py:
Added function to output an array in a format suitable for Matlab
to read.

2006-07-26 vldkr

* [r4074]
examples/homeo_intrinsic_lissom_oo_or.ty,
examples/homeo_intrinsic_lissom_or.ty,
examples/homeo_lissom_oo_or_image.ty:
Initial version

* [r4073] examples/homeo_synaptic_lissom_or.ty:
*** empty log message ***

2006-07-26 jbednar

* [r4072] examples/joublin_bc96.ty:
Minor cleanup; probably no user-visible effect other than
changing the name of HindpawGaussian to HindpawGaussian2

2006-07-26 cmnglewis

* [r4071] examples/joublin_bc96.ty:
Completed most parts of the implementation

2006-07-24 ceball

* [r4070] doc/Future_Work/current_text.php:
Removed task about display problem on Windows; I'd messed up one
of my copies (by upgrading Python...P.S. good luck for that...)

* [r4069] /trunk/topographica-win/create_python_topo/setup.bat:
Added HACKALERT.

* [r4068] /trunk/topographica-win/util/Y_OR_N.COM:
Removed unused file.

* [r4067] doc/Downloads/cvs_text.php,
doc/Downloads/index_text.php:
Updated instructions for new topographica-win module.

* [r4066] doc/Downloads/cvs_text.php:
No need to download PuTTY since it comes with TortoiseCVS.
Changed note about testing date, and version to current stable
TortoiseCVS.

* [r4065] /trunk/topographica, .cvsignore:
Added back topographica.ico to ignore, since it's present on
windows.

2006-07-23 jbednar

* [r4064] Makefile:
Restored version 1.67 for new post-0.91 changes

2006-07-23 ceball_cvs2svn

* [r4063] /tags/release_0_9_1,
/tags/release_0_9_1/topographica-win,
/tags/release_0_9_1/topographica-win/README.txt,
/tags/release_0_9_1/topographica-win/common/python_topo.tar.gz,
/tags/release_0_9_1/topographica-win/common/topographica.ico,
/tags/release_0_9_1/topographica-win/create_installer/README.txt,
/tags/release_0_9_1/topographica-win/create_installer/prepare_for_installer.bat,
/tags/release_0_9_1/topographica-win/create_python_topo,
/tags/release_0_9_1/topographica-win/setup_cvs_copy,
/tags/release_0_9_1/topographica-win/util,
/tags/release_0_9_1/topographica/Makefile,
/tags/release_0_9_1/topographica/doc/shared,
/tags/release_0_9_1/topographica/external/.cvsignore,
/tags/release_0_9_1/topographica/external/Makefile,
/tags/release_0_9_1/topographica/external/mswin/util,
/tags/release_0_9_1/topographica/external/tcl8.4.13-src.tar.gz,
/tags/release_0_9_1/topographica/external/tcl8.4.9.tgz,
/tags/release_0_9_1/topographica/external/tk8.4.13-src.tar.gz,
/tags/release_0_9_1/topographica/external/tk8.4.9.tgz,
/tags/release_0_9_1/topographica/external/win32/util:
This commit was manufactured by cvs2svn to create tag
'release_0_9_1'.

2006-07-23 jbednar

* [r4062] doc/shared/index.php:
Added 0.9.0 announcement

* [r4061] Makefile:
Temporary checkin for 0.9.1 release only

* [r4060] /trunk/topographica-win/common/setup.py,
/trunk/topographica-win/create_installer/topographica.iss,
Makefile:
Changed version number to 0.9.1 for bugfix release

* [r4059] external,
external/.cvsignore,
external/Makefile,
external/tcl8.4.13-src.tar.gz,
external/tcl8.4.9.tgz,
external/tk8.4.13-src.tar.gz,
external/tk8.4.9.tgz:
Updated tcl/tk to 8.4.13 to fix bug in their configure script for
some platforms. Added DISPLAY variable for matplotlib so that it
builds even in a remote session

2006-07-22 ceball

* [r4058] /trunk/topographica-win/create_python_topo/README.txt:
Added note about weave.

* [r4057] /trunk/topographica-win/create_python_topo/setup.bat:
Removed debugging pause.

* [r4056] /trunk/topographica-win/create_python_topo/setup.bat:
Corrected mistake.

* [r4055] /trunk/topographica-win/create_python_topo/setup.bat:
Initial version.

* [r4054] /trunk/topographica-win/create_python_topo/README.txt:
Updated instructions.

* [r4053]
/trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.py,
/trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.tgz:
Removed confusing archive: replaced with single file (patched in
unix).

* [r4052] /trunk/topographica-win/create_python_topo/setup.py:
Removed unused file.

* [r4051] /trunk/topographica-win/create_python_topo/jpeg-6b-3.exe:
Removed unused package.

* [r4050] /trunk/topographica-win/setup_cvs_copy/setup.bat:
Added HACKALERT.

* [r4049] /trunk/topographica-win/create_installer/README.txt:
Minor update.

* [r4048] /trunk/topographica-win/create_installer/README.txt:
Updates to procedure.

* [r4047]
/trunk/topographica-win/create_installer/prepare_for_installer.bat:
Corrected slash direction.

* [r4046]
/trunk/topographica-win/create_installer/prepare_for_installer.bat:
Remove external/ subdirectory.

* [r4045] /trunk/topographica-win/setup_cvs_copy/setup.bat:
Removed some testing lines.

* [r4044] /trunk/topographica-win/setup_cvs_copy/setup.bat:
Minor update.

* [r4043] /trunk/topographica-win/create_installer/README.txt,
/trunk/topographica-win/create_installer/prepare_for_installer.bat:
Updated for topographica-win

* [r4042] Makefile:
Updated file locations.

* [r4041] Makefile:
Files no longer exist to delete.

* [r4040] /trunk/topographica-win/create_installer/README.txt:
Updated

* [r4039] /trunk/topographica-win/create_python_topo/README.txt:
Added warning that the setup script in this directory does not
yet work.

* [r4038] doc/Future_Work/current_text.php:
Added a task.

* [r4037] /trunk/topographica-win/setup_cvs_copy/setup.bat:
More correction and cleaning.

* [r4036] /trunk/topographica-win/setup_cvs_copy/setup.bat:
Corrected paths.

* [r4035] /trunk/topographica-win/create_python_topo/mingw,
/trunk/topographica-win/create_python_topo/mingw/binutils-2.15.91-20040904-1.tar.gz,
/trunk/topographica-win/create_python_topo/mingw/gcc-core-3.4.2-20040916-1.tar.gz,
/trunk/topographica-win/create_python_topo/mingw/gcc-g++-3.4.2-20040916-1.tar.gz,
/trunk/topographica-win/create_python_topo/mingw/gcc-g77-3.4.2-20040916-1.tar.gz,
/trunk/topographica-win/create_python_topo/mingw/mingw-runtime-3.9.tar.gz,
/trunk/topographica-win/create_python_topo/mingw/w32api-3.6.tar.gz:
Packages currently used for topographica's c compiler. Might not
all be necessary.
Added for my convenience, for the moment.

* [r4034] /trunk/topographica-win/setup_cvs_copy/setup.bat:
Corrected minor mistake with line echoing.

* [r4033] /trunk/topographica-win/README.txt,
/trunk/topographica-win/common/setup.py:
Updated for new topographica-win module.

* [r4032]
/trunk/topographica-win/setup_cvs_copy/create_shortcut.vbs,
/trunk/topographica-win/setup_cvs_copy/setup.bat:
Updated directory locations.

2006-07-21 ceball

* [r4031] doc/Future_Work/current_text.php:
Updated topographica-win task.

* [r4030] /trunk/topographica-win/common/python_topo.tar.gz:
From topographica module.

* [r4029] setup.bat,
topographica.ico:
Moved to topographica-win module or deleted if unused.

* [r4028] external/mswin:
Moved to topographica-win module.

* [r4027] /trunk/topographica-win/create_python_topo,
/trunk/topographica-win/create_python_topo/Numeric-24.2.win32-py2.4.exe,
/trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.4.exe,
/trunk/topographica-win/create_python_topo/README.txt,
/trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.tgz,
/trunk/topographica-win/create_python_topo/jpeg-6b-3.exe,
/trunk/topographica-win/create_python_topo/matplotlib-0.81.win32-py2.4.exe,
/trunk/topographica-win/create_python_topo/python-2.4.2.msi,
/trunk/topographica-win/create_python_topo/setup.py:
From the original topographica module, external/win32

* [r4026] /trunk/topographica-win/common,
/trunk/topographica-win/common/setup.py,
/trunk/topographica-win/common/topographica.ico,
/trunk/topographica-win/util/Y_OR_N.COM,
/trunk/topographica-win/util/patch.exe:
From topographica module.

* [r4025] external/win32:
Moved to topographica-win module.

* [r4024] external/win32/util:
Moved to topographica-win module or deleted if no longer
required.

* [r4023] /trunk/topographica-win/README.txt:
Initial version

* [r4022] /trunk/topographica-win/setup_cvs_copy,
/trunk/topographica-win/setup_cvs_copy/README.txt,
/trunk/topographica-win/setup_cvs_copy/create_shortcut.vbs,
/trunk/topographica-win/setup_cvs_copy/setup.bat:
*** empty log message ***

* [r4021] /trunk/topographica-win/create_installer,
/trunk/topographica-win/create_installer/README.txt,
/trunk/topographica-win/create_installer/prepare_for_installer.bat,
/trunk/topographica-win/create_installer/topographica.iss:
From the original topographica module, external/mswin/

* [r4020] /trunk/topographica-win, /trunk/topographica-win/util,
/trunk/topographica-win/util/README.txt,
/trunk/topographica-win/util/gunzip.exe,
/trunk/topographica-win/util/tar.exe:
*** empty log message ***

2006-07-18 jbednar

* [r4019] topo/tests/README.txt:
Fixed outdated info about running tests

2006-07-18 tikesh

* [r4018]
examples/lissom_oo_position_disparity.py,
examples/lissom_oo_position_disparity.ty:
Moved lissom_oo_position_disparity.py to
lissom_oo_position_disparity.ty

* [r4017]
examples/lissom_oo_phase_disparity.py,
examples/lissom_oo_phase_disparity.ty:
Moved lissom_oo_phase_disparity.py to
lissom_oo_phase_disparity.ty

* [r4016] examples/lissom_oo_od.py,
examples/lissom_oo_od.ty:
Moved lissom_oo_od.py to lissom_oo_od.ty

* [r4015] examples/read_visneuro02.py,
examples/read_visneuro02.ty:
Moved read_visneuro02.py to read_visneuro02.ty

* [r4014] examples/ohzawa_science90.py,
examples/ohzawa_science90.ty:
Moved ohzawa_science90.py to ohzawa_science90.ty

2006-07-11 ceball

* [r4013] topo/tests/lissom_oo_or_reference.ty:
Afferents are jointly normalized; removed strength=0.75 hack.

2006-07-10 tikesh

* [r4012] examples/disparity_energy_Read.py,
examples/lissom_oo_od.ty,
examples/read_visneuro02.py,
examples/read_visneuro02.ty:
*** empty log message ***

* [r4011] examples/disparity_energy_Read.py:
*** empty log message ***

* [r4010] examples/lissom_oo_od.py,
examples/lissom_oo_phase_disparity.py,
examples/lissom_oo_position_disparity.py,
examples/ohzawa_science90.py,
topo/commands/analysis.py,
topo/plotting/templates.py:
*** empty log message ***

2006-07-08 jbednar

* [r4009] topo/base/cf.py:
Added alert

* [r4008] doc/Future_Work/current_text.php:
Added current work

2006-07-07 ceball

* [r4007] topo/tests/lissom_oo_or_reference.ty:
Trivial change: removed names of projections to LGN.

* [r4006] topo/tests/lissom_oo_or_reference.ty:
Uses CompositePatternGenerator for the shared weights, rather
than having two projections.

* [r4005] topo/tests/lissom_oo_or_reference.ty:
Updated out-of-date syntax.

* [r4004] topo/patterns/basic.py:
Corrected typo in the code for CompositePatternGenerator that led
to a bug in the handling of xdensity and ydensity for composite
patterns.

2006-07-04 jbednar

* [r4003] examples/lissom_oo_or.ty:
Added example of joint normalization

* [r4002] topo/base/cf.py:
Replaced commented-out joint normalization code with enabled
version using ports; still needs more cleanup

* [r4001] topo/base/simulation.py:
Added _port_match method to allow the matching rule to be
overridden by subclasses; should not have changed the behavior at
all

2006-07-03 yschoe

* [r4000] examples/leaky_lissom_or.ty,
topo/base/cf.py,
topo/learningfns/projfns.py:
Moved CFPLF_OutstarHebbian from base/cf.py to
learningfns/projfns.py, and
made appropriate changes in leaky_lissom_or.ty.

2006-07-03 jbednar

* [r3999] etc/topographica.el:
Fixed Emacs code for selecting Topographica-mode

2006-07-01 jbednar

* [r3998] doc/Downloads/cvs_text.php:
Added info from Yoonsuck about SSH agent

* [r3997] doc/shared/index.php:
Added news link to the book

2006-06-29 ceball

* [r3996] topo/patterns/basic.py:
The composite pattern generators for a CPG are called with the
same bounds, xdensity, and ydensity as the CPG itself.

* [r3995] topo/tests/testpatterngenerator.py:
Added new test for CompositePatternGenerator. Commented out at
the moment because it fails.

* [r3994] topo/tests/testpatterngenerator.py:
Commented out a test. The test passes when run in isolation, but
I didn't check it also passes when part of the test suite. Added
note about this (should be simple to fix).

2006-06-28 ceball

* [r3993] topo/tests/testpatterngenerator.py:
Added basic test for CompositePatternGenerator.

2006-06-26 ceball

* [r3992] doc/Future_Work/current_text.php:
Added a task.

* [r3991] doc/Future_Work/current_text.php:
Added task about test pattern window.

* [r3990] topo/tkgui/testpattern.py:
Added note of bug.

* [r3989] topo/tests/lissom_oo_or_reference.ty:
Removed unnecessary port specifications.

* [r3988] topo/tests/lissom_or_reference.ty:
Removed unnecessary port specifications.

* [r3987] topo/tkgui/parametersframe.py:
Change to comments.

2006-06-24 yschoe

* [r3986] topo/base/cf.py:
In the process of adding outstar normalization (implementation
is still incomplete). Needs a lot of work.

* [r3985] examples/leaky_lissom_or.ty:
In the process of adding outstar normalization (implementation
is still incomplete).

2006-06-23 jbednar

* [r3984] topo/base/cf.py,
topo/base/simulation.py:
Slight cleanup to documentation

2006-06-23 tikesh

* [r3983] topo/outputfns/basic.py:
topo/outputfns/basic.py

* [r3982] examples/disparity_energy.ty,
examples/lissom_oo_od.ty,
examples/read_visneuro02.ty:
Initial version

2006-06-23 jbednar

* [r3981] examples/Makefile:
Added target for obermayer_pnas90

2006-06-22 jbednar

* [r3980] topo/base/projection.py,
topo/sheets/generatorsheet.py,
topo/sheets/slissom.py:
Made the default src_port and dest_port for Projections be
'Activity' so that incorrect connections can be detected

* [r3979] topo/base/simulation.py:
Added src_ports attribute to provide a roster of what src_ports
are provided

* [r3978] topo/base/projection.py,
topo/base/simulation.py,
topo/sheets/composer.py:
Changed EventProcessor._connect_from to _dest_connect, and
_connect_to to _src_connect, so that it is more obvious at which
end they will be executed

* [r3977] etc/toporename:
Fixed example usage

* [r3976] topo/sheets/generatorsheet.py:
Changed to use a special 'Trigger' port for the self-connection,
to allow error-checking.

* [r3975] topo/tkgui/editortools.py:
Made error message more informative

* [r3974] topo/base/simulation.py,
topo/eps/basic.py,
topo/sheets/composer.py:
Added dest_ports attribute to EventProcessor, and made it accept
connections only those ports

* [r3973] topo/tkgui/editorobjects.py:
Removed duplicate entries in Connections lists

* [r3972] examples/lissom_oo_or.ty,
examples/lissom_or.ty,
topo/patterns/basic.py:
Set default scale for Line in example files instead of pattern
definition

* [r3971] topo/commands/basic.py:
Added handling for case where the class name or location has
changed since a snapshot was created, so that a saved snapshot
can still be loaded

* [r3970] topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Replaced CFPRF_DotProduct with simpler one based on CFPRF_Plugin;
for some reason it's also much faster.

* [r3969] topo/misc/inlinec.py:
Clarified comment

* [r3968] topo/sheets/generatorsheet.py:
Changed default phase to be nonzero so that it will be useful

2006-06-22 ceball

* [r3967] topo/tkgui/parametersframe.py:
Added hackalert plus a break to stop unnecessary looping.

* [r3966] topo/tkgui/parametersframe.py:
Some more simplification and restored an accidentally removed
feature (right clicking on an object allows you to set parameters
for the object being right clicked on).

* [r3965] topo/misc/utils.py:
Changed dict_translator to eval in __main__.__dict__ rather than
calling eval_atof(), which happens (wrongly) just to eval in
__main__.__dict__. (Aiming at being able to make eval_atof() act
as would be expected.

* [r3964] topo/tkgui/parametersframe.py:
Cleaning up (should be no change)...

* [r3963] topo/tkgui/parametersframe.py:
Cleaning up show_parameter_properties()...

* [r3962] topo/tkgui/parametersframe.py:
Removed code that currently never runs. If it were ever to run,
it wouldn't work anyway. Replaced with a NotImplementedError for
the time being.

* [r3961] topo/tkgui/parametersframe.py:
Removed 'object_dictionary' attribute.

* [r3960] topo/misc/utils.py:
Added note.

* [r3959] topo/misc/utils.py:
Renamed dict_sort() to values_sorted_by_key(), plus minor
tidy-up.

2006-06-21 jbednar

* [r3958] topo/tkgui/translatorwidgets.py:
Changed TranslatorWidget to WidgetTranslator to clarify that it
is not itself a Widget. Made get() abstract so that it can be
tested for easily

* [r3957] topo/misc/utils.py,
topo/plotting/templates.py,
topo/tkgui/topoconsole.py:
Cleaned up comments, documentation, imports ordering, alerts, and
spacing.

* [r3956] topo/base/cf.py,
topo/eps/basic.py,
topo/learningfns/__init__.py,
topo/learningfns/optimized.py,
topo/learningfns/som.py,
topo/outputfns/__init__.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py,
topo/outputfns/projfns.py,
topo/patterns/__init__.py,
topo/patterns/basic.py,
topo/patterns/image.py,
topo/patterns/random.py,
topo/projections/__init__.py,
topo/projections/basic.py,
topo/responsefns/__init__.py,
topo/responsefns/projfns.py,
topo/sheets/generatorsheet.py,
topo/sheets/lissom.py,
topo/sheets/slissom.py:
Cleaned up comments, documentation, imports ordering, alerts, and
spacing.

* [r3955] topo/responsefns/basic.py:
Added example ResponseFn

* [r3954] topo/responsefns/optimized.py:
Fixed minor alert

2006-06-20 jbednar

* [r3953] topo/analysis/__init__.py,
topo/base/patterngenerator.py,
topo/commands/__init__.py,
topo/learningfns/__init__.py,
topo/misc/commandline.py,
topo/misc/gendocs.py,
topo/misc/inlinec.py,
topo/misc/keyedlist.py,
topo/plotting/__init__.py,
topo/sheets/generatorsheet.py:
Minor cleanup of documentation and comments

* [r3952] topo/misc/patternfns.py:
Clarified what the problem is for disks and rings

2006-06-20 judelaw

* [r3951] topo/plotting/templates.py:
Changed back unnecessary fix

2006-06-20 jbednar

* [r3950] topo/misc/__init__.py:
Added missing files

* [r3949] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
Cleaned up trailing colon formatting

* [r3948] topo/tkgui/editorobjects.py:
Cleaned up documentation and comments to be closer to
Topographica conventions elsewhere

* [r3947] topo/tkgui/editortools.py:
Cleaned up documentation and comments to be closer to
Topographica conventions elsewhere

* [r3946] topo/tkgui/editorwindow.py:
Cleaned up documentation and comments to be closer to
Topographica conventions elsewhere

* [r3945] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Fixed error when connections have no target object

* [r3944] topo/plotting/bitmap.py:
Clarified documentation

* [r3943] topo/base/parameterizedobject.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/base/simulation.py,
topo/eps/basic.py,
topo/sheets/generatorsheet.py:
Cleaned up verbose messages so that they will be useful; more
esoteric ones are now visible only with a debugging print level

* [r3942] topo/base/cf.py:
Added debugging messages when unsuitable Projection types are
encountered. Simplified update_unit_view

* [r3941] topo/commands/analysis.py:
Fixed trivial typo

* [r3940] external/Makefile:
Removed outdated alert

2006-06-20 judelaw

* [r3939] topo/plotting/templates.py:
Corrected bug in projection activity

* [r3938] examples/laminar.ty:
Most recent version - lots of changes

* [r3937] examples/laminar_or_noshrinking.ty:
Initial version - work in progress

* [r3936] examples/lissom_or_noshrinking.ty:
Initial version - work in progress

2006-06-19 ceball

* [r3935] doc/Future_Work/current_text.php:
Added task about not pickling certain things.

* [r3934] doc/Future_Work/current_text.php:
Added note to a task.

2006-06-17 jbednar

* [r3933] topo/base/cf.py:
Removed unneeded update_projection_view

* [r3932] topo/commands/analysis.py:
Changed update_projectionactivity() to be simpler and
self-contained. Updated doc strings. Made commands check for
appropriate subclasses of Sheet and Projection

2006-06-17 ceball

* [r3931] doc/Downloads/cvs_text.php:
Minor correction.

2006-06-17 jbednar

* [r3930]
topo/tkgui/projectionactivitypanel.py:
Added warning

* [r3929] topo/plotting/plotgroup.py:
Slight cleanup and additional merging into parent class

* [r3928] topo/plotting/plotgroup.py:
Made ConnectionFieldsPlotGroup and ProjectionPlotGroup inherit
shared code from ProjectionSheetPlotGroup

* [r3927] topo/plotting/plotgroup.py:
Pulled out common code from ProjectionActivityPlotGroup to make a
new base class to be used in ConnectionFieldPlotGroup and
ProjectionPlotGroup

2006-06-16 judelaw

* [r3926]
topo/tkgui/projectionactivitypanel.py:
Added Projection Activity Window

* [r3925] topo/base/cf.py,
topo/base/sheetview.py,
topo/commands/analysis.py,
topo/plotting/plotgroup.py,
topo/plotting/templates.py,
topo/tkgui/topoconsole.py:
Added Projection Activity window

2006-06-15 jbednar

* [r3924] doc/Downloads,
doc/Downloads/.cvsignore,
doc/Downloads/cvs_text.php,
doc/Downloads/index_text.php,
doc/shared/index.php:
Revamped Download instructions to simplify instructions for
non-CVS installs

2006-06-13 ceball

* [r3923] doc/Future_Work/current_text.php:
Added task about the command prompt. (Also removed a comment.)

2006-06-12 ceball

* [r3922] doc/shared/index.php:
Added Windows screenshot to 0.9.0 news.

* [r3921]
doc/images/060607_topographica_win_screenshot.png:
Added Windows screenshot.

2006-06-10 ceball_cvs2svn

* [r3920] /tags/release_0_9_0:
This commit was manufactured by cvs2svn to create tag
'release_0_9_0'.

2006-06-10 jbednar

* [r3919] doc/shared/index.php:
Noted that binaries are available

* [r3918] doc/shared/index.php:
Added link to downloads page

2006-06-10 ceball

* [r3917] doc/Downloads/index_text.php:
Minor update to examples for Windows users.

2006-06-08 ceball

* [r3916] doc/Downloads/index_text.php:
Removed duplicate updates mailing list note.

* [r3915] doc/Downloads/index_text.php:
Updated suggested startup example to lissom_oo_or, and the link
to the tutorial.

* [r3914] doc/Downloads/index_text.php:
Slightly altered the 'updating' section to distinguish between
CVS and binary users.

* [r3913] doc/Downloads/index_text.php:
Updated instructions to link to Sourceforge's files section.

* [r3912]
external/mswin/for_binaries/prepare_for_binaries.bat:
Corrected another backslash error.

* [r3911]
external/mswin/for_binaries/prepare_for_binaries.bat:
Corrected a backslash mistake.

* [r3910]
external/mswin/for_binaries/prepare_for_binaries.bat:
Corrections to previous two commits.

* [r3909]
external/mswin/for_binaries/prepare_for_binaries.bat:
Deletes CVS subdirectories.

* [r3908]
external/mswin/for_binaries/prepare_for_binaries.bat:
Updated now I know how to delete files recursively from windows
command prompt.

* [r3907]
doc/Tutorials/images/or_key_horiz_transparent.png:
Updated key.

2006-06-08 jbednar

* [r3906] doc/images/cmvc-cover-icon.jpg:
Copied from computationalmaps.org

* [r3905] ChangeLog.txt:
Updated with current changes

* [r3904] doc/shared/index.php:
Added news item for 0.9.0

* [r3903]
doc/Tutorials/images/som_activity_000000.png,
doc/Tutorials/images/som_activity_000001.png,
doc/Tutorials/images/som_activity_000006.png,
doc/Tutorials/images/som_cog_000000.png,
doc/Tutorials/images/som_cog_000100.png,
doc/Tutorials/images/som_grid_000000.png,
doc/Tutorials/images/som_grid_000100.png,
doc/Tutorials/images/som_grid_010000.png,
doc/Tutorials/images/som_grid_040000.png,
doc/Tutorials/images/som_network_diagram.png,
doc/Tutorials/images/som_projection_000000.png,
doc/Tutorials/images/som_projection_000001.png,
doc/Tutorials/images/som_projection_000006.png,
doc/Tutorials/images/som_projection_040000.png,
doc/Tutorials/som_retinotopy_text.php:
Reverted to full-density simulation; reduced-density version
needs work

* [r3902] doc/Tutorials/lissom_oo_or_text.php:
Fixed the text to match the new simulation

* [r3901] doc/User_Manual/commandline_text.php:
Updated to current syntax

* [r3900] topo/tkgui/plotgrouppanel.py:
Disabled sheet coordinates by default, because it makes V1 be too
tiny to see with any reasonable plot size

2006-06-07 ceball

* [r3899] topo/responsefns/optimized.py:
Added comment to an ALERT.

* [r3898] doc/Future_Work/index_text.php:
Really minor change to wording.

* [r3897] topo/patterns/basic.py:
Changed default scale of Line, for the tutorial.

* [r3896] doc/Tutorials/lissom_oo_or_text.php:
Resized images.

* [r3895]
doc/Tutorials/images/activity_line_oo.png,
doc/Tutorials/images/activity_line_oo_or.png,
doc/Tutorials/images/lissom_network_diagram_oo.png,
doc/Tutorials/images/natural_image_oo_or.png,
doc/Tutorials/images/oo_or_map.png,
doc/Tutorials/images/projection_oo.png,
doc/Tutorials/images/test_pattern_oo.png,
doc/Tutorials/images/topographica_console.png,
doc/Tutorials/images/unit_weights_0_0_oo.png,
doc/Tutorials/images/unit_weights_0_0_oo_or.png:
Updated to match current simulation.

2006-06-07 jbednar

* [r3894] topo/tests/testsheetview.ppm:
Removed unused image

* [r3893] doc/Home,
doc/Home/.cvsignore,
doc/Home/oldnews_text.php:
Added oldnews page

* [r3892] Makefile,
external/mswin/for_binaries/topographica.iss,
external/mswin/setup.py:
Updated to 0.9.0 release

* [r3891] doc/Developer_Manual/index_text.php:
Uncommented Chris's addition

* [r3890] ChangeLog.txt:
Fixed typos

2006-06-07 ceball

* [r3889] topo/base/cf.py:
Mask size set to be that of the weights matrix, rather than the
nominal (user-specified) bounds.

* [r3888] examples/lissom_oo_or.ty:
LGNOnAfferent strength reverted to 0.5 (i.e. removed a hack).

2006-06-07 jbednar

* [r3887] topo/tkgui/testpattern.py:
Restored auto-refresh=True in the Test Pattern window, to make
sure that the preview updates when the PatternGenerator is
changed

* [r3886] README.txt:
Added stronger warnings

* [r3885] ChangeLog.txt:
Updated with recent changes

* [r3884] doc/Future_Work/current_text.php:
Added task

* [r3883] examples/hierarchical.ty:
Changed aspect ratio and density of sheets as an example of doing
so

* [r3882]
doc/Developer_Manual/optimization_text.php:
Updated to match recent changes

* [r3881] doc/Future_Work/current_text.php,
doc/User_Manual/index_text.php,
doc/User_Manual/modeleditor_text.php,
doc/User_Manual/parameters_text.php:
Cleaned up to match recent changes

* [r3880] doc/Tutorials/index_text.php,
doc/Tutorials/lissom_oo_or_text.php:
Commented out lissom_or.ty tutorial so that I don't have to keep
updating it.

* [r3879] topo/tkgui/topoconsole.py:
Removed unnecessary command prompting. Reordered command output
box to look more like a shell

* [r3878] topo/tkgui/plotgrouppanel.py:
Set plots to Sheet coordinates by default. Removed unnecessary
command prompting

* [r3877] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Changed Boolean Checkbutton variables to use an automatically
updated BooleanVar to avoid gratuitous complexity such as the
various toggle_ functions, to allow the default value to be set
easily.

* [r3876] topo/base/cf.py,
topo/base/functionfamilies.py,
topo/base/patterngenerator.py:
Removed unneeded packages lists for ClassSelectorParameters

2006-06-06 jbednar

* [r3875] topo/base/parameterclasses.py,
topo/tkgui/__init__.py:
Removed requirement that ClassSelectorParameters define a
packages attribute now that they use concrete_descendents instead

* [r3874] doc/Reference_Manual/index_text.php,
topo/base/parameterclasses.py,
topo/tkgui/editortools.py:
Replaced find_classes_in_package with concrete_descendents, to
allow classes defined anywhere to be found

* [r3873] examples/joublin_bc96.ty:
Added HindpawGaussian

* [r3872] topo/base/parameterizedobject.py:
Added temporary function for getting access to a parameter
without changing its value

* [r3871] doc/Tutorials/lissom_oo_or_text.php,
doc/Tutorials/lissom_or_text.php:
Updated to match current code

2006-06-05 jbednar

* [r3870] doc/User_Manual/space_text.php:
Updated to match recent changes

2006-06-04 jbednar

* [r3869] doc/Downloads/index_text.php,
doc/Future_Work/current_text.php,
doc/Future_Work/index_text.php,
doc/Home/index_text.php,
doc/Reference_Manual/index_text.php,
doc/Team_Members/index_text.php,
doc/Tutorials/lissom_oo_or_text.php:
Updated with recent changes

* [r3868] topo/tkgui/topoconsole.py:
Moved implementation notes here from Future_Work

2006-06-04 yschoe

* [r3867] examples/leaky_lissom_or.ty:
Tweaking parameters.

2006-06-04 jbednar

* [r3866] topo/base/cf.py:
Added alert

2006-06-04 ceball

* [r3865] topo/tests/lissom_oo_or_reference.ty:
Updated class names.

* [r3864] topo/tests/lissom_or_reference.ty:
Updated class names.

2006-06-04 yschoe

* [r3863] topo/patterns/basic.py:
Added TwoRectangles class. This is really a hack, so it needs to
be replaced
later with a more general version.

* [r3862] examples/leaky_lissom_or.ty:
Testing new pattern generator. Tuning learning rate and decay
parameters.

2006-06-03 ceball

* [r3861] doc/Future_Work/current_text.php:
Added task about allowing min_matrix_rad to be zero; altered task
about problem with examples/joublin_bc96.ty.

* [r3860] doc/Future_Work/current_text.php:
Removed a task.

* [r3859] topo/outputfns/optimized.py:
PyFloat_FromDouble() returns a new reference, so after using it
the reference count should be decremented.

* [r3858] topo/learningfns/optimized.py:
PyFloat_FromDouble() returns a new reference, so after using it
the reference count should be decremented.

* [r3857] examples/lissom_or.ty:
Removed unused import.

* [r3856] examples/lissom_or.ty:
Removed unused imports.

* [r3855] topo/base/cf.py:
Added back line to update the CF's sum (that had been
accidentally removed in the past). If CFPOF_Plugin was being used
in combination with a CFPLF that selectively sets the _sum
attribute (as CFPLF_Hebbian_opt does, setting it only where the
output activity is not 0), then the sum could be out of date
while this line was missing.

* [r3854] topo/outputfns/optimized.py:
Removed unnecessary call to super's init from
CPOF_DivisiveNormalizeL1_opt.

2006-06-02 jbednar

* [r3853] Makefile:
Moved info about specific targets into examples/Makefile

* [r3852] examples/Makefile:
Added more full targets. Added more dependencies.

* [r3851] topo/responsefns/optimized.py:
Cleaned up C variable declarations for
CFPRF_EuclideanDistance_opt

2006-06-02 ceball

* [r3850] topo/outputfns/optimized.py:
No visible change. Removed unnecessary __init__() method and
simplified code in DivisiveNormalizeL1_opt.

2006-06-02 jbednar

* [r3849] topo/learningfns/optimized.py,
topo/outputfns/optimized.py,
topo/responsefns/optimized.py:
Cleaned up memory handling for PyObject calls from C code;
reference counts were increasing with each call, possibly leading
to memory leaks.

2006-06-01 jbednar

* [r3848] topo/tkgui/editorwindow.py:
Fixed Model Editor, broken since
topo.tkgui.topoconsole.dict_console['console'] changed to
topo.guimain

* [r3847] topo/base/arrayutils.py:
Removed confusing return values

* [r3846] topo/outputfns/optimized.py:
Removed now-unnecessary C++ version of PiecewiseLinear

* [r3845] topo/outputfns/basic.py:
Removed outdated alert.

* [r3844] topo/base/sheet.py:
Added explanation from Chris Ball

* [r3843] doc/Future_Work/current_text.php:
Rearranged and reassigned tasks now that Chris Ball is leaving

2006-06-01 judelaw

* [r3842] examples/lissom_or.ty:
corrected errors in naming

2006-06-01 yschoe

* [r3841] examples/leaky_lissom_or.ty:
Changed lateral connections to have LeakyCFProjection. Run this
example, and
use the test pattern generator (gaussian) to observe spiking.

* [r3840] topo/sheets/slissom.py:
Added absolute refractory period to SLISSOM class. Use test
pattern generator
(gaussian) and repeatedly present the input to see the spiking.

2006-06-01 jbednar

* [r3839] topo/base/functionfamilies.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py:
Removed now-unused OutputFn return value

* [r3838] topo/tests/testoutputfnsbasic.py,
topo/tests/testoutputfnsoptimized.py:
Removed tests of OuputFns as functions, in anticipation of
removing the return values

* [r3837] topo/outputfns/basic.py:
Removed unused Spike OutputFn

* [r3836] topo/base/cf.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/patterns/basic.py,
topo/patterns/random.py,
topo/projections/basic.py,
topo/sheets/slissom.py:
Made calls to output_fns consistently use them in place rather
than as functions, which will allow the return value to be
removed

* [r3835] topo/tkgui/parametersframe.py:
Minor documentation cleanup

* [r3834] examples/Makefile:
Added som_retinotopy to standard examples to test with 'make all'

* [r3833]
doc/Tutorials/som_retinotopy_text.php,
examples/som_retinotopy.ty:
Made density be overridable from command line

* [r3832] topo/base/arrayutils.py,
topo/outputfns/basic.py:
At long last, fixed clip_in_place and related functions to use
matrix operations for speed and so that they operate cleanly in
place.

* [r3831] examples/lissom_or.ty:
Fixed typo in commented-out code

2006-05-31 yschoe

* [r3830] topo/responsefns/basic.py,
topo/responsefns/optimized.py:
Removed DynamicThreshold_CFPRF_DotProduct_opt class from
responsefn.basic.
See sheets.slissom for the implementation of spiking.

* [r3829] topo/responsefns/basic.py:
Added hack alert. The stuff here needs to be removed or moved to
optimized.py

* [r3828] examples/leaky_lissom_or.ty:
Moved spiking mechanism from responsefn to sheet (new class
SLISSOM).

* [r3827] topo/sheets/slissom.py:
Spiking LISSOM sheet class, implementing dynamic thresholding.
For leaky
synapses, it needs the LeakyCFProjection class.

2006-05-31 jbednar

* [r3826] topo/tkgui/topoconsole.py:
Made auto-refresh update the actual windows also, so that it
takes effect immediately even when called from a script. Also
made load_snapshot do an auto_refresh() to update any windows
that have auto-refresh enabled.

* [r3825] topo/analysis/featuremap.py,
topo/tkgui/topoconsole.py:
Greatly simplified display of the activity patterns during map
measurement, and now left it uncommented by default.

* [r3824] topo/commands/analysis.py:
Increased size of default pattern for position preference
measurement so that it would be more likely to activate all
neurons; typically improves quality of position preference map.

2006-05-30 jbednar

* [r3823] topo/responsefns/optimized.py:
Removed redundant class

* [r3822] examples/homeostatic.ty:
Fixed thresholds to be applied even on the first call, used
Numeric.sum() for averaging, and allowed bounds to be controlled
by parameters.

* [r3821] examples/homeostatic.ty:
Updated with Veldri's changes: simple example of adjusting
threshold based on the average value in a rectangular window.
Reduced LGNOn density to make debugging easier. Fixed output_fn
for SharedWeightCFProjection.

* [r3820] topo/outputfns/basic.py:
Added BinaryThreshold

* [r3819] topo/base/arrayutils.py:
Clarified alerts

* [r3818] topo/outputfns/basic.py:
Cleaned up spacing

2006-05-30 yschoe

* [r3817] examples/leaky_lissom_or.ty:
Fixed small bug (renamed primitive).

* [r3816] examples/leaky_lissom_or.ty:
Modified a bit to make tsettle=1 and generate spikes using the
dynamic
threshold CFP function.

* [r3815] topo/responsefns/basic.py:
Added DynamicThreshold_CFPRF_DotProduct_opt, a
CFPRF_DotProduct_opt with
dynamic thresholding. Right now, it only has a fixed threshold.
It uses
the optimized __call__ in its parent, while the thresholding part
is plain
Python code.

* [r3814] topo/outputfns/basic.py:
Added a "primitive" Spike output function.

2006-05-29 jbednar

* [r3813] Makefile:
Made examples directory be cleaned up for distributions

* [r3812] examples/README.txt:
Initial version

* [r3811] examples/cfsom_or.ty,
examples/disparity_energy.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/joublin_bc96.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty:
Removed unnecessary run(0) command from examples

* [r3810] examples/disparity_energy.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
topo/learningfns/optimized.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py,
topo/tests/testoutputfnsbasic.py,
topo/tests/testoutputfnsoptimized.py:
Changed DivisiveSumNormalize to DivisiveNormalizeL1

* [r3809] examples/cfsom_or.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty:
Made all examples use a standard delay from retina to V1 so that
the same default would work for measuring orientation maps

* [r3808] examples/laminar.ty:
Trivial change to remove execute bit

* [r3807] examples/lissom_or.ty:
Changed retina->V1 delay so that orientation map can be measured
at the same time as lissom_oo_or_map.ty

* [r3806] topo/commands/analysis.py:
Changed default duration of orientation map measurement to avoid
settling in LISSOM

* [r3805] topo/tkgui/propertiesframe.py:
Reduced width slightly

* [r3804] topo/outputfns/basic.py:
Added HalfRectifyAndSquare output_fn

* [r3803] topo/base/arrayutils.py:
Added (slow) clip_lower function

* [r3802] examples/disparity_energy.ty:
Initial version

* [r3801] topo/learningfns/basic.py:
Added note about original author

* [r3800] doc/Links/index_text.php:
Minor cleanup

* [r3799] doc/Links/index_text.php:
Cleaned up formatting and expanded a bit

* [r3798] doc/shared/util.php:
Added Links to toolbar

2006-05-28 jbednar

* [r3797] doc/Links,
doc/Links/.cvsignore,
doc/Links/index_text.php:
Initial version

2006-05-26 ceball

* [r3796] topo/tkgui/propertiesframe.py:
Set Entry widths.

* [r3795] topo/tkgui/topoconsole.py:
Commented out balloon help binding for 'Go' button because it
prevents simulation time from being printed in the messagebar.

2006-05-26 jbednar

* [r3794] topo/learningfns/projfns.py:
Updated commented code that had gotten stale

2006-05-25 jbednar

* [r3793] topo/tkgui/editorobjects.py:
Fixed bug with help balloons

2006-05-25 ceball

* [r3792] topo/outputfns/basic.py:
Minor change to docstring.

* [r3791] topo/outputfns/basic.py,
topo/patterns/image.py,
topo/tests/testoutputfnsbasic.py:
Changed DivisiveMaxNormalize to DivisiveNormalizeLinf

* [r3790] topo/outputfns/basic.py,
topo/tests/testoutputfnsbasic.py:
Changed DivisiveLpNormalize to DivisiveNormalizeLp

* [r3789] topo/outputfns/optimized.py,
topo/tests/testoutputfnsoptimized.py:
Changed DivisiveSumNormalize_opt1 to DivisiveSumNormalize_opt

* [r3788] topo/outputfns/basic.py,
topo/tests/testoutputfnsbasic.py:
Changed DivisiveLengthNormalize to DivisiveNormalizeL2

* [r3787] examples/tiny.ty,
topo/outputfns/basic.py:
Changed DivisiveL1Normalize to DivisiveNormalizeL1

* [r3786] topo/outputfns/basic.py,
topo/outputfns/optimized.py:
Clarified some alerts.

* [r3785] topo/projections/basic.py:
Minor alteration to comments.

* [r3784] topo/projections/basic.py:
Changed \bSharedWeightCFPOutputFn\b to CFPOF_SharedWeight

* [r3783] external/win32/README.txt:
Added note.

* [r3782] topo/base/cf.py,
topo/projections/basic.py:
Changed IdentityCFPOutputFn to CFPOF_Identity

* [r3781] doc/Future_Work/current_text.php,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
topo/outputfns/optimized.py:
Changed CFPDivisiveSumNormalize_opt1 to
CFPOF_DivisiveSumNormalize_opt

* [r3780] examples/tiny.ty,
topo/base/cf.py,
topo/outputfns/optimized.py,
topo/outputfns/projfns.py:
Changed GenericCFPOutputFn to CFPOF_Plugin

* [r3779] topo/outputfns/optimized.py:
Changed CFPDivisiveSumNormalize to CFPOF_DivisiveSumNormalize

* [r3778] topo/responsefns/optimized.py:
Changed \bDotProduct_opt1\b to DotProduct_opt

* [r3777] examples/lissom_oo_or.ty,
examples/lissom_or_sf.ty,
topo/responsefns/optimized.py:
Changed \bSharedWeightCFPDotProduct_opt1\b to
CFPRF_SharedWeightDotProduct_opt

* [r3776] topo/responsefns/optimized.py:
Changed \bSharedWeightCFPDotProduct\b to
CFPRF_SharedWeightDotProduct

* [r3775] topo/misc/inlinec.py:
Added comment.

* [r3774] topo/projections/basic.py,
topo/responsefns/optimized.py:
Changed SharedWeightCFPResponseFn to CFPRF_SharedWeight

* [r3773] topo/base/cf.py,
topo/base/functionfamilies.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Changed GenericCFPResponseFn to CFPRF_Plugin

* [r3772] examples/som_retinotopy.ty,
topo/responsefns/optimized.py:
Changed \bCFPEuclideanDistance_opt1\b to
CFPRF_EuclideanDistance_opt

* [r3771] topo/responsefns/optimized.py:
Minor change to docstrings.

* [r3770] topo/misc/utils.py:
Changes to comments.

* [r3769] doc/Future_Work/current_text.php:
Update to task.

* [r3768] topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Changed \bCFPEuclideanDistance\b to CFPRF_EuclideanDistance

* [r3767] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/joublin_bc96.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/tiny.ty,
topo/misc/utils.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py,
topo/tests/testplotgroup.py:
Changed \bCFPDotProduct_opt1\b to CFPRF_DotProduct_opt

* [r3766] topo/misc/utils.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Changed CFPDotProduct to CFPRF_DotProduct

* [r3765] topo/learningfns/som.py,
topo/sheets/cfsom.py:
Changed SOMLF to CFPLF_SOM

* [r3764] examples/tiny.ty,
topo/base/cf.py,
topo/base/functionfamilies.py,
topo/learningfns/__init__.py,
topo/learningfns/optimized.py,
topo/learningfns/projfns.py:
Changed \bGenericCFPLearningFn\b to CFPLF_Plugin

* [r3763] topo/base/cf.py,
topo/learningfns/projfns.py,
topo/projections/basic.py:
Changed IdentityCFPLearningFn to CFPLF_Identity

* [r3762] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/joublin_bc96.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/learningfns/som.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py:
Changed \bHebbianSOMLF\b to CFPLF_HebbianSOM

* [r3761] etc/toporename:
Changed example use and added a note.

* [r3760] topo/learningfns/optimized.py:
Changed \bCFPHebbian\b to CFPLF_Hebbian

2006-05-24 jbednar

* [r3759] topo/tkgui/editorobjects.py:
Added class documentation to balloon help for editor objects

* [r3758] topo/misc/utils.py:
Added shortclassname function

2006-05-24 ceball

* [r3757] doc/Future_Work/current_text.php,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/leaky_lissom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
topo/learningfns/optimized.py:
Changed CFPHebbian_opt1 to CFPLF_Hebbian_opt

* [r3756] etc/toporename:
Corrected location of replaceall.

* [r3755] etc/toporename:
Correction to code for whether or not to continue.

2006-05-24 jbednar

* [r3754] doc/Future_Work/current_text.php:
Added task

* [r3753] examples/joublin_bc96.ty:
Initial sketch

* [r3752] topo/base/cf.py,
topo/sheets/lissom.py:
Minor doc cleanup

* [r3751] doc/Future_Work/current_text.php:
Minor addition

2006-05-23 ceball

* [r3750] doc/Future_Work/current_text.php:
Removed a task.

* [r3749] topo/tests/testoutputfnsoptimized.py:
Reduced precision of a test because Numeric sticks with the
Float32s.

* [r3748] topo/projections/basic.py:
The sharedcf has its weights pattern centered on the src sheet,
not the dest shee.

* [r3747] topo/base/cf.py:
Just save the center unit's xcenter and ycenter as attributes
that can be used later. This will be cleaned up.

* [r3746] topo/tkgui/editorobjects.py,
topo/tkgui/parametersframe.py:
Shows balloon help for object over the title.

* [r3745] topo/tkgui/editortools.py:
Added more text to HACKALERT.

* [r3744] doc/Future_Work/current_text.php:
Added some tasks.

* [r3743] topo/tkgui/parametersframe.py:
Checkbuttons are aligned on the left. Removed unused width
specification.

* [r3742] topo/tkgui/propertiesframe.py:
Readonly properties have a readonly Entry.

* [r3741] topo/tkgui/propertiesframe.py:
Removed font specification for read-only entry text.

2006-05-23 jbednar

* [r3740] topo/tkgui/parametersframe.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/topoconsole.py:
Changed balloon help to use inspect.getdoc(x) instead of
x.__doc__ so that leading whitespace would be removed

2006-05-23 ceball

* [r3739] topo/base/parameterizedobject.py:
Added doc string to name Parameter.

2006-05-23 jbednar

* [r3738] topo/base/sheet.py:
Trivial space change

* [r3737] topo/sheets/cfsom.py:
Added docstrings and removed apparently unused rmin and rmax
parameters

* [r3736] topo/base/cf.py,
topo/base/projection.py,
topo/sheets/lissom.py:
Added docstrings

* [r3735] topo/base/cf.py,
topo/sheets/generatorsheet.py:
Added help text

2006-05-23 yschoe

* [r3734] topo/projections/basic.py:
Cleaned up LeakyCFProjection.__init__(), following Jim's
suggestions.

2006-05-22 jbednar

* [r3733] topo/plotting/plotgroup.py,
topo/tkgui/topoconsole.py:
Cleaned up help text

* [r3732] topo/tkgui/connectionfieldspanel.py:
Fixed longstanding bug in error message

* [r3731] topo/projections/basic.py:
Minor cleanup and suggestions

* [r3730] topo/tkgui/plotgrouppanel.py:
Fixed typo that crept into previous version somehow

* [r3729] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Added parameters for normalize, sheetcoords, integerscaling, and
updatecommand so that they can have documentation. Added balloon
help.

* [r3728] etc/replaceall:
Minor note

2006-05-22 ceball

* [r3727] topo/base/cf.py:
CFProjection creates a slice_template and passes it to each CF,
rather than each CF creating its own slice. Reduces
lissom_or.ty's startup time to about 80% of its previous value.

* [r3726] topo/projections/basic.py:
SharedWeightCFProjection initializes its sharedcf to have x and y
'on the grid' - previously it just set them both to 0.

2006-05-22 yschoe

* [r3725] examples/leaky_lissom_or.ty:
Added leaky_lissom_or.ty to the source tree. This is a copy of
lissom_or.ty
with the afferent connections turned into LeakyCFProjection. The
lissom_or.ty
file will be periodically copied to leaky_lissom_or.ty and minor
edits made,
to keep future developments in lissom_or.ty independent of
leaky_lissom_or.ty.

* [r3724] topo/tkgui/plotgrouppanel.py:
Added "kill" hotkey for plot windows (Control-q).

2006-05-22 jbednar

* [r3723] etc/toporename:
Initial version

2006-05-22 yschoe

* [r3722] topo/projections/basic.py:
Fixed bug in LeakyCFProjection, and initialized
leaky_input_activity to a zero matrix.

* [r3721] topo/projections/basic.py:
Added activate() for LeakyCFProjection. A finer time-scale needs
to be
implemented.

2006-05-22 ceball

* [r3720] topo/outputfns/basic.py:
Uses Numeric's sum().

* [r3719] topo/outputfns/optimized.py:
Uses Numeric's sum instead of Python's. This has a big impact on
the performance. Starting lissom_or (which uses
DivisiveSumNormalize_opt1 many times), this gives a the startup
time 65% of the previous time.

* [r3718] topo/tkgui/topoconsole.py:
Shell prints new prompt everytime there simulation is run, as it
did before. Otherwise the prompt does not appear again after
messages are printed.

2006-05-21 ceball

* [r3717] topo/tests/testtopoconsole.py:
Removed test that didn't have much use.

* [r3716] topo/tkgui/topoconsole.py:
Added some sample help messages.

* [r3715] topo/tkgui/topoconsole.py:
Changed layout of 'status' section to match the others.

* [r3714] topo/tkgui/topoconsole.py:
Reduced width of the console. Added HACKALERT.

* [r3713] topo/base/simulation.py:
Corrected typo.

* [r3712] topo/base/parameterclasses.py:
Added ALERT.

* [r3711] topo/tkgui/topoconsole.py:
Changed 'run for' slider.

* [r3710] topo/tkgui/translatorwidgets.py:
Added facility to set slider_width to TaggedSlider.

* [r3709] topo/tkgui/topoconsole.py:
Stopped shell printing a new prompt after every run command from
the GUI.

* [r3708] topo/tkgui/topoconsole.py:
Added '>>>' label to command prompt.

* [r3707] topo/tkgui/topoconsole.py:
'run for' displays 1.0 initially. 'commands' not displayed by
default.

* [r3706] topo/tkgui/topoconsole.py:
'Run for' is a TaggedSlider. String format needs to be adjusted,
and pressing enter should make the simulation run too.

* [r3705] topo/tkgui/translatorwidgets.py:
TaggedSlider seems to assume a method optional_refresh() will
always exist on its parent; I put in a try/catch but the whole
thing (still) needs to be reviewed.

* [r3704] topo/tkgui/topoconsole.py:
Corrected variable name.

* [r3703] topo/tkgui/topoconsole.py:
Altered 'run simulation for group'. Changed how 'commands' group
is hidden. There are still some problems: width changes, not
enough padding in places.

2006-05-21 jbednar

* [r3702] topo/tkgui/editorwindow.py:
Removed debugging print statement

2006-05-21 yschoe

* [r3701] topo/projections/basic.py:
LeakyCFProjection class added (just a place holder, for now).

2006-05-21 ceball

* [r3700] topo/tkgui/topoconsole.py:
Added code to demonstrate showing/hiding the commands box.

2006-05-21 jbednar

* [r3699] etc/pipecap,
etc/replaceall:
Initial version

* [r3698] topo/outputfns/projfns.py,
topo/responsefns/projfns.py:
Added missing imports

* [r3697] topo/base/boundingregion.py,
topo/base/cf.py,
topo/base/simulation.py,
topo/learningfns/som.py,
topo/misc/numbergenerators.py:
Declared abstract classes abstract

* [r3696] topo/learningfns/basic.py,
topo/learningfns/projfns.py:
Moved CFPLearningFns from basic.py to projfns.py

2006-05-20 jbednar

* [r3695] topo/learningfns/basic.py:
Partially debugged BCMCFP; commented it out until fully debugged

* [r3694] topo/learningfns/basic.py:
Added new learning functions; need more testing still

2006-05-20 ceball

* [r3693] topo/tkgui/topoconsole.py:
Minor change: command output box is inside the "Command" frame.

* [r3692] doc/Future_Work/index_text.php:
Added a comment.

* [r3691] topo/tkgui/topoconsole.py:
Added scrollbars to command output textbox.

* [r3690] topo/tkgui/topoconsole.py:
Made command output 10 lines long.

* [r3689] topo/tkgui/topoconsole.py:
'Run simulation for' moved to top of console.

* [r3688] topo/tkgui/topoconsole.py:
Corrected mistake.

* [r3687] topo/tkgui/topoconsole.py:
Command output text is not editable.

* [r3686] topo/tkgui/topoconsole.py:
Output window echos the command.

* [r3685] topo/tkgui/topoconsole.py:
Command output text box scrolls with new text. Added HACKALERT.

* [r3684] topo/tkgui/topoconsole.py:
Updated documentation.

* [r3683] topo/tkgui/topoconsole.py:
Removed unused do_command().

* [r3682] topo/tkgui/topoconsole.py:
Added a Text window to display results of commands.

* [r3681] doc/Future_Work/index_text.php:
Added some notes.

* [r3680] doc/Future_Work/index_text.php:
Updated pickling section.

2006-05-19 ceball

* [r3679] doc/Future_Work/current_text.php:
Added pycheck task and some updates.

* [r3678] doc/Future_Work/index_text.php:
Minor change to wording.

* [r3677] topo/base/cf.py:
Can specify minimum matrix radius for weights of CFProjection;
defaults to 1 for a 3x3 matrix minimum.

* [r3676] doc/Future_Work/current_text.php:
Updated a task.

* [r3675] doc/Future_Work/current_text.php:
Added task about memory usage growing.

* [r3674] doc/Future_Work/current_text.php:
Removed task that was finished recently.

* [r3673] doc/Future_Work/current_text.php:
Removed duplicate task.

* [r3672] doc/Future_Work/current_text.php:
Removed the task about updating documentation before the release,
since it would never be finished and I try to do it continuously
anyway.

* [r3671] doc/Future_Work/current_text.php:
Removed a task.

* [r3670] doc/Tutorials/lissom_oo_or_text.php:
No need to re-run the script when loading a network. Added note
about updating the time estimate for initial training.

* [r3669] doc/Tutorials/lissom_or_text.php:
Don't need to run script before loading snapshot.

* [r3668] doc/Future_Work/current_text.php:
Removed a task. The text I added to the user manual about
xdensity and ydensity should be reviewed.

* [r3667] doc/Future_Work/current_text.php:
Removed a task.

* [r3666] topo/outputfns/optimized.py:
Added comment about the relative performance of all-c vs python/c
vs python/python CFP learning functions.

* [r3665] topo/responsefns/optimized.py:
Added comment about the relative performance of all-c vs python/c
vs python/python CFP response functions.

* [r3664] topo/outputfns/basic.py,
topo/outputfns/optimized.py:
Clarified some hackalerts.

* [r3663] doc/Future_Work/current_text.php:
Removed a task.

* [r3662] topo/base/cf.py:
Added enforce_min_rad BooleanParameter to CFProjection (defaults
to true), which means the weights matrix resulting from the
supplied nominal_bounds_template will be at least 3x3.

* [r3661] topo/tkgui/taggedslider.py:
Renamed to translatorwidgets (was removed in the past but appears
to have resurrected itself.)

* [r3660]
external/mswin/for_binaries/README.txt:
Updated instructions.

* [r3659]
external/mswin/for_binaries/topographica.iss:
Added comments.

* [r3658]
external/mswin/for_binaries/topographica.iss:
Added a HACKALERT.

* [r3657]
external/mswin/for_binaries/topographica.iss:
Corrected syntax.

* [r3656] external/mswin/setup.py:
Corrected mistake in earlier checkin.

* [r3655]
external/mswin/for_binaries/topographica.iss:
Doesn't use batch file to execute setup.py.

* [r3654]
external/mswin/for_binaries/prepare_for_binaries.bat:
Update after removing setup.bat.

* [r3653] external/mswin/setup.py:
Updates to documentation.

* [r3652]
external/mswin/for_binaries/setup.bat:
Removed unnecessary file.

2006-05-19 jbednar

* [r3651] Makefile,
external/mswin/for_binaries/topographica.iss,
external/mswin/setup.py:
Added new-version target and updated the corresponding files

2006-05-19 ceball

* [r3650] topo/base/cf.py:
Corrected a comment.

* [r3649] doc/Future_Work/current_text.php:
Updated.

* [r3648]
external/mswin/for_binaries/setup.bat:
Updated with changes to setup.py.

* [r3647] external/mswin/setup.bat:
Updated with change to setup.py.

* [r3646] external/mswin/setup.py:
Tidied up.

* [r3645]
external/mswin/for_binaries/README.txt:
Updated.

* [r3644]
external/mswin/for_binaries/prepare_for_binaries.bat:
Added comment.

2006-05-18 ceball

* [r3643]
external/mswin/for_binaries/topographica.iss:
Added back in something that got removed by accident.

* [r3642]
external/mswin/for_binaries/topographica.iss:
Removed changing the setup icon file, which didn't seem to work.
Not important.

* [r3641]
external/mswin/for_binaries/topographica.iss:
Shortcuts get topographica.ico

* [r3640]
external/mswin/for_binaries/topographica.iss:
Correction

* [r3639]
external/mswin/for_binaries/topographica.iss:
Minor update (desktop icon's optional).

* [r3638]
external/mswin/for_binaries/topographica.iss:
Added a tip.

* [r3637]
external/mswin/for_binaries/topographica.iss:
Makes desktop shortcut, start menu shortcut, associates ty files
(properly, doesn't
use a vbs script).

* [r3636]
external/mswin/for_binaries/prepare_for_binaries.bat:
Not using create_shortcut.vbs.

* [r3635]
external/mswin/for_binaries/setup.bat,
external/mswin/setup.bat,
external/mswin/setup.py:
Added "cvs" commandline option to setup.py.

2006-05-18 jbednar

* [r3634] topo/base/simulation.py:
Clarified warning

* [r3633] topo/base/patterngenerator.py:
Minor cleanup of documentation and comments

* [r3632] topo/base/parameterizedobject.py:
Cleaned up comments and formatting of warning messages and class
defaults listing

* [r3631] topo/base/functionfamilies.py:
Cleaned up comment

* [r3630] topo/base/__init__.py:
Sorted list in order

2006-05-18 ceball

* [r3629] doc/Future_Work/current_text.php:
Removed a task.

* [r3628] topo/tkgui/editorobjects.py:
Deleting connection actually deletes it from the the simulation.

* [r3627] topo/base/simulation.py:
EPConnection has a remove() method.

2006-05-18 jbednar

* [r3626] topo/base/projection.py:
Minor cleanup of documentation

* [r3625] doc/Downloads/index_text.php:
Updated CVS download instructions

* [r3624] topo/tkgui/editorobjects.py:
Changed default color for Projections from purple to blue to be
more visible. Added alert.

2006-05-18 ceball

* [r3623] topo/base/sheet.py:
Updates to Parameter docstrings.

* [r3622] doc/Future_Work/current_text.php:
Removed a task.

* [r3621] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/sheet.py,
topo/base/sheetcoords.py,
topo/patterns/basic.py,
topo/plotting/plotgroup.py,
topo/sheets/cfsom.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testlissom.ty,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testsheet.py,
topo/tests/testsheetview.py,
topo/tests/testsnapshots.py,
topo/tests/testtemplateplotgrouppanel.py,
topo/tkgui/editorobjects.py:
SheetCoordinateSystem stores the bounds in its bounds attribute,
not a true_bounds attribute. Sheet has Parameters nominal_density
and nominal_bounds; these are what gets set by users of Sheet.
Because Sheet is a SheetCoordinateSystem, it has its true bounds
in its bounds attribute, and its true density in its xdensity or
ydensity attributes (because for a Sheet xdensity=ydensity).

* [r3620] topo/tests/testlissom_cpointer.ty:
Removed test of non-existent classes.

* [r3619] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py:
Removed TopoConsole's active_sim.

* [r3618] topo/tkgui/editorobjects.py:
Simplified getting a connection's bounds.

2006-05-17 ceball

* [r3617] doc/Future_Work/current_text.php:
Added tasks. Fixed typos.

* [r3616] topo/base/simulation.py:
added commented-out code for ensuring all out_connections have a
unique name.

* [r3615] topo/sheets/composer.py:
Made call to EP's _connect_from in a more obvious way.

* [r3614] topo/base/simulation.py:
Corrected a docstring.

* [r3613] topo/base/projection.py:
Removed a HACKALERT: corrected call to EP's _connect_from.

* [r3612] doc/Future_Work/current_text.php:
Updates to tasks.

* [r3611] topo/base/simulation.py:
Modified HACKALERT.

* [r3610] topo/tkgui/editorobjects.py:
Choosing to 'Delete' a sheet actually deletes the sheet from the
simulation.

* [r3609] topo/base/simulation.py:
When adding an EP to the simulation, if one with the same name
already exists, it's overwritten.

* [r3608] topo/base/simulation.py:
EPs can be deleted from the simulation.

* [r3607] topo/tkgui/editorwindow.py:
Removed my HACKALERT about indentation - seems I was wrong. I
don't see how it's working, but it is.

* [r3606] topo/tkgui/editorwindow.py:
Corrected my previous-but-one checkin for iterating through
out_connections.

* [r3605] topo/tkgui/editorwindow.py:
Added HACKALERT.

* [r3604] topo/commands/analysis.py:
Removed HACKALERT that no longer applies (cog plot for
SharedWeightCFProjection is a regular grid).

* [r3603] topo/commands/analysis.py:
Made measure_cog only be called for CFSheets, rather than for all
ProjectionSheets.

* [r3602] topo/commands/analysis.py:
Removed hackalert that doesn't apply since the previous commit.

* [r3601] topo/commands/analysis.py:
Changed how ProjectionSheets are detected by measure_cog().

* [r3600] topo/base/cf.py,
topo/base/projection.py,
topo/base/simulation.py,
topo/commands/analysis.py,
topo/sheets/cfsom.py,
topo/sheets/lissom.py,
topo/tkgui/editorwindow.py,
topo/tkgui/projectionpanel.py:
EventProcessor.out_connections is now a plain list, like
in_connections. A ProjectionSheet does not store a separate
dictionary of in_projections, but it only permits Projections in
its list of in_connections.

* [r3599] doc/Future_Work/current_text.php:
Updates to tasks.

* [r3598] doc/Future_Work/current_text.php:
Updates to tasks. Removed windows binary task.

* [r3597]
external/mswin/for_binaries/topographica.iss:
Minor updates.

* [r3596]
external/mswin/for_binaries/prepare_for_binaries.bat,
external/mswin/for_binaries/setup.bat:
Corrections

2006-05-16 ceball

* [r3595]
external/mswin/for_binaries/prepare_for_binaries.bat:
Uncommented line I commented out by mistake.

* [r3594]
external/mswin/for_binaries/README.txt:
Added note about getting html doc.

* [r3593]
external/mswin/for_binaries/topographica.iss:
Minor updates.

* [r3592]
external/mswin/for_binaries/topographica.iss:
Changed a comment to a HACKALERT.

* [r3591]
external/mswin/for_binaries/prepare_for_binaries.bat:
Forgot to copy a file...

* [r3590]
external/mswin/for_binaries/README.txt:
Further clarifications.

* [r3589]
external/mswin/for_binaries/README.txt:
Clarifications.

* [r3588]
external/mswin/for_binaries/topographica.iss:
Minor updates.

* [r3587] external/mswin/setup.py:
Minot update to comments.

* [r3586]
external/mswin/for_binaries/topographica.iss:
Minor updates.

* [r3585]
external/mswin/for_binaries/prepare_for_binaries.bat:
Corrected initial version.

* [r3584] external/mswin/for_binaries,
external/mswin/for_binaries/README.txt,
external/mswin/for_binaries/prepare_for_binaries.bat,
external/mswin/for_binaries/setup.bat,
external/mswin/for_binaries/topographica.iss:
Initial version.

* [r3583] external/mswin/README.txt:
Initial version to describe files in this directory.

* [r3582] setup.bat:
Added a comment.

2006-05-16 jbednar

* [r3581] etc/toporoot:
Fixed usage info

2006-05-16 ceball

* [r3580] topo/base/simulation.py:
Changed time to a 4 d.p. (FixedPoint) number.

* [r3579] topo/tests/lissom_or_reference.ty:
Made input pattern properties be set on an object, rather than on
the whole Gaussian class.

* [r3578] topo/base/simulation.py:
Re-enabled the repr method of EPConnectionEvent, now that
ParameterizedObject's get_param_values() does not generate a new
DynamicNumber.

* [r3577] topo/base/parameterizedobject.py:
Added a hack to get_param_values to avoid generating new
DynamicNumbers.

* [r3576] topo/base/parameterclasses.py:
Added 'last_value' to DynamicNumber, for storing the last value
that was generated.

* [r3575] topo/base/parameterizedobject.py:
Simplified get_param_values(); I think it still does the same
thing.

* [r3574] topo/base/simulation.py:
Commented out EPConnectionEvent's repr method, because it was
causing new DynamicNumbers to be generated. Added HACKALERT.

2006-05-15 ceball

* [r3573] topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty:
Set GeneratorSheet.phase after changes to Simulation.run().

* [r3572] topo/base/simulation.py:
Added repr() methods to CommandEvent and EPConnectionEvent so
that printing for debugging is easier.

2006-05-15 jbednar

* [r3571] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/simulation.py:
Changed Simulation.run() to complete all events at the stop time,
rather than stopping before the stop time. Shouldn't affect any
long-term simulation results, but scripts have to change
GeneratorSheet.phase to be nonzero so that the plots make sense
at even multiples of the period

2006-05-15 ceball

* [r3570] topo/base/projection.py,
topo/base/simulation.py,
topo/eps/basic.py,
topo/sheets/composer.py,
topo/sheets/lissom.py:
Renamed pre_sleep() to process_current_time().

* [r3569] topo/base/simulation.py,
topo/tests/testcfsom.py,
topo/tests/testsimulation.py:
Removed unimplemented step_mode.

* [r3568] topo/base/simulator.py:
Renamed to simulation.py

* [r3567] topo/base/simulation.py:
Updated some ALERTs.

* [r3566] doc/Future_Work/current_text.php:
Removed a task.

* [r3565] examples/laminar.ty,
examples/laminar_nolearning.ty,
examples/som_retinotopy.ty,
examples/tiny.ty:
Uses UniformRandom instead of RandomWrapper.

* [r3564] examples/homeostatic.ty,
examples/laminar_lissom.ty,
examples/obermayer_pnas90.ty:
Uses UniformRandom instead of RandomWrapper.

* [r3563] examples/lissom_or_sf.ty:
Uses UniformRandom instead of RandomWrapper.

* [r3562] examples/hierarchical.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty:
Reverted orientation's seed to previous value (changed
accidentally in previous commit.

* [r3561] examples/cfsom_or.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty:
Uses UniformRandom instead of RandomWrapper.

* [r3560] topo/base/simulation.py,
topo/base/simulator.py,
topo/eps/basic.py,
topo/sheets/generatorsheet.py:
Renamed enqueue_event_abs() to enqueue_event().

* [r3559] topo/base/simulation.py,
topo/eps/basic.py,
topo/sheets/generatorsheet.py:
Events are first created, and then are passed to Simulation's
enqueue_event_abs().

* [r3558] topo/base/simulation.py:
schedule_command() is always for an absolute time.

* [r3557] topo/base/simulation.py:
Removed sleep(), sleep_window, and sleep_window_violation.

* [r3556] doc/Future_Work/current_text.php:
Removed a task.

* [r3555] topo/base/cf.py,
topo/base/functionfamilies.py,
topo/projections/basic.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Renamed Mdot to DotProduct.

* [r3554] topo/base/connectionfield.py:
Renamed to cf.py

* [r3553] doc/Future_Work/current_text.php:
Updated tasks.

* [r3552] topo/tkgui/propertiesframe.py:
Added HACKALERT about binding return key to combobox widget.

* [r3551] doc/Future_Work/current_text.php:
Removed a task.

* [r3550] examples/hierarchical.ty:
Uses UniformRandom rather than RandomWrapper.

* [r3549] topo/tkgui/editortools.py:
Missing code from previous commit.

* [r3548] topo/tkgui/editortools.py,
topo/tkgui/parametersframe.py:
Allow name to be set on the class but not on an existing object.

* [r3547] topo/base/parameterizedobject.py:
'name' parameter is no longer hidden.

2006-05-15 jbednar

* [r3546] topo/tests/testsimulator.py:
Removed old filename of testsimulation.py

2006-05-14 ceball

* [r3545] topo/base/parameterizedobject.py:
Removed unnecessary deletion of 'initialized' attribute.

* [r3544] topo/misc/numbergenerators.py:
Corrected mistake.

2006-05-14 jbednar

* [r3543] topo/commands/basic.py,
topo/commands/pylabplots.py:
Fixed broken topographic grid plots; had not been updated fully
for topo.sim

* [r3542] examples/lissom_oo_or.ty:
Fixed typo

* [r3541] examples/cfsom_or.ty:
Added missing simulation name

* [r3540] doc/Downloads/index_text.php:
Enabled note about CVS status page

* [r3539] topo/base/boundingregion.py,
topo/base/cf.py:
Added inclusive comparison for bounding boxes to prevent bogus
warning for change_bounds

* [r3538] doc/Future_Work/current_text.php:
Added task for Chris

2006-05-14 ceball

* [r3537] topo/tkgui/parametersframe.py:
Added a HACKALERT.

* [r3536] topo/tests/testsimulation.py:
Made the test slightly more realistic to allow stronger argument
checking in EPConnectionEvent. [jbednar]

* [r3535] topo/tests/testsimulation.py:
Renamed EPEvent to EPConnectionEvent.

* [r3534] topo/sheets/generatorsheet.py:
Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
can be created first then passed to Simulator's
enqueue_event_rel().

* [r3533] topo/sheets/composer.py,
topo/sheets/generatorsheet.py,
topo/sheets/lissom.py,
topo/tests/testcfsom.py,
topo/tests/testsimulation.py:
EPEvent stores conn so no need to pass all of conn's attributes
too.

* [r3532] topo/sheets/composer.py,
topo/sheets/generatorsheet.py,
topo/sheets/lissom.py,
topo/tests/testcfsom.py,
topo/tests/testsimulation.py:
Intermediate checkin (further cleaning to follow). EPEvent stores
the connection. This allows ProjectionSheet to activate the
correct connection. The performance of a LISSOM sheet is now back
to 19 February speed (i.e. approximately twice as fast as it has
been recently).

* [r3531] topo/base/simulation.py:
Cleaned up comments, documentation, and alerts. Changed to
require that input_event is implemented by any subclass.
[jbednar]

* [r3530] topo/base/simulation.py:
Simplified Simulator.connection().

* [r3529] topo/base/simulation.py:
EventProcessor's in_connections must each have a unique name.

* [r3528] topo/base/simulation.py:
Removed a HACKALERT.

* [r3527] topo/base/projection.py:
Fixed typo in commennt

* [r3526] topo/base/projection.py:
No longer check for unique names of Projections because
EventProcessor checks all connections have unique names. Added
HACKALERT about having separate list of in_projections.

* [r3525] topo/base/cf.py:
Minor fix to comment

* [r3524] examples/lissom_or_sf.ty:
Switched to use optimized response function for
SharedWeightCFProjection.

* [r3523] topo/base/simulation.py:
Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
can be created first then passed to Simulator's
enqueue_event_rel().

* [r3522] topo/base/simulation.py:
Renamed EPEvent to EPConnectionEvent.

* [r3521] topo/base/projection.py,
topo/base/simulation.py:
EPEvent stores conn so no need to pass all of conn's attributes
too.

* [r3520] topo/base/projection.py,
topo/base/simulation.py:
Intermediate checkin (further cleaning to follow). EPEvent stores
the connection. This allows ProjectionSheet to activate the
correct connection. The performance of a LISSOM sheet is now back
to 19 February speed (i.e. approximately twice as fast as it has
been recently).

* [r3519] topo/eps/basic.py:
Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
can be created first then passed to Simulator's
enqueue_event_rel().

* [r3518] topo/eps/basic.py:
PulseGenerator must have period>0. EPEvent stores conn so no need
to pass all of conn's attributes too.

* [r3517] topo/eps/basic.py:
Intermediate checkin (further cleaning to follow). EPEvent stores
the connection. This allows ProjectionSheet to activate the
correct connection. The performance of a LISSOM sheet is now back
to 19 February speed (i.e. approximately twice as fast as it has
been recently).

* [r3516] topo/base/simulation.py:
Fixed typo in SimSingleton.__str__; couldn't have been working.
Cleaned up docs and comments, and added ALERTs. [jbednar]

* [r3515] topo/base/utils.py:
Removed empty file.

* [r3514] topo/base/utils.py:
Moved find_classes_in_package() to parameterclasses.py.

2006-05-12 jbednar

* [r3513] etc/toporoot:
Initial version

* [r3512] Makefile:
Updated in preparation for new release

* [r3511] doc/Tutorials/index_text.php:
Trivial update to test CVS

2006-05-07 ceball

* [r3510] doc/Future_Work/current_text.php:
Added another task.

* [r3509] doc/Future_Work/current_text.php:
Added a task.

* [r3508] doc/Future_Work/current_text.php:
Made corrections to previous commit.

* [r3507] doc/Future_Work/current_text.php:
Updated tasks.

2006-05-06 ceball

* [r3506] examples/lissom_oo_or.ty:
Uses c++ response function. Now runs 3.5 times faster than
before.

* [r3505] topo/tests/lissom_oo_or_reference.ty:
Uses c++ shared weight response function.

* [r3504] topo/responsefns/optimized.py:
Added SharedWeightCFPDotProduct_opt1, as a speedier replacement
for SharedWeightCFPResponseFn(single_cf_fn=Mdot()). Also added
untested DotProduct_op1, Mdot in C++; it's not used anywhere, we
might just remove it.

* [r3503] topo/projections/basic.py:
SharedWeightCFProjection needs to wrap its cfs list in a better
way, so we don't need separate response fns etc. But for now,
I've done this enough to allow a C++ replacement of the shared
weight response fn, which we badly need to improve performance.

* [r3502] doc/Future_Work/current_text.php:
Updated tasks.

* [r3501] topo/base/sheet.py:
Altered HACKALERT.

* [r3500] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/cf.py,
topo/projections/basic.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/testlissom.ty,
topo/tkgui/editorobjects.py:
CFProjection has nominal_bounds_template parameter, and
bounds_template attribute.

2006-05-06 jbednar

* [r3499] ChangeLog.txt:
Updated with recent changes

2006-05-05 ceball

* [r3498] topo/base/sheetcoords.py:
Added comment (from JAB) about 'bounds-master' vs
'density-master' approaches.

* [r3497] doc/User_Manual/space_text.php:
Initial attempt at describing 'bounds-master' approach to Sheet
bounds/density.

* [r3496] topo/base/simulation.py:
Made the saved_commands Simulation Parameter be instantiated
(it's specific to one Simulation object); this isn't very
important since most users will not have more than one
Simulation. Removed two HACKALERTs.

* [r3495] topo/base/simulation.py,
topo/eps/basic.py,
topo/sheets/generatorsheet.py:
Cleaned up enqueue_event* methods. This could probably be
simplified further. Events must have a time.

* [r3494] topo/base/simulation.py:
Cleaned up a little.

* [r3493] topo/base/simulation.py,
topo/commands/pylabplots.py:
Removed get_active_sim().

* [r3492] topo/base/sheet.py:
Updates to docstrings and comments.

* [r3491] topo/base/sheet.py,
topo/base/sheetcoords.py:
Simplified creation of SheetCoordinateSystem.

* [r3490] topo/base/sheetcoords.py:
Updated file's docstring.

* [r3489] topo/base/cf.py:
Removed outdated HACKALERT.

* [r3488] topo/base/parameterclasses.py,
topo/tkgui/editortools.py:
Moved find_classes_in_package() to parameterclasses.py.

* [r3487] topo/base/__init__.py:
Updated __all__.

* [r3486] topo/misc/tyimputil.py:
Corrected HACKALERT.

* [r3485] topo/base/arrayutils.py:
Added HACKALERT about savespace and .flat/ravel(), with a note
about upgrading Numeric and a link to Numeric's convertcode.py.

* [r3484] topo/base/arrayutils.py,
topo/base/functionfamilies.py:
Removed mdot() function - there is the Mdot ResponseFn in
topo.responsefns.basic. Moved comment about weave.blitz from mdot
to Mdot.

* [r3483] topo/base/arrayutils.py:
Removed unused and potentially misleading msum() function.

2006-05-04 ceball

* [r3482] topo/patterns/basic.py:
PatternSampler (and hence CompositePatternGenerator and Image) is
based on SheetCoordinateSystem with an activity matrix, rather
than on Sheet.

* [r3481] topo/tests/lissom_or_reference.ty:
Corrected learning rates, added missing scheduled action, and
commented out final weights bounds change.

* [r3480] topo/tests/lissom_oo_or_reference.ty:
Updated for recent changes to code.

* [r3479] doc/Downloads/index_text.php:
Added commented-out section (for JAB to decide whether or not
it's worthwhile to include) about problems with cvs, with a link
to SourceForge's status page.

* [r3478] topo/tests/lissom_or_reference.ty:
Adjusted times which I'd changed by mistake earlier. Altered some
comments. Appears to match c++ lissom after 201 iterations (i.e.
after the first set of scheduled actions).

* [r3477] topo/tests/lissom_or_reference.ty:
Corrected mistake left in previous version by mistake.

* [r3476] topo/tests/lissom_or_reference.ty:
Forget to divide min_exc_rad by BaseN.

* [r3475] topo/base/sheet.py:
Update to a comment.

* [r3474] topo/base/sheet.py,
topo/base/sheetcoords.py:
Moved HACKALERT from sheetcoords to sheet.

* [r3473] topo/base/sheetcoords.py:
Updated HACKALERT.

* [r3472] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/cf.py,
topo/projections/basic.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/testlissom.ty:
For a CFProjection, users specify the BoundingRegionParameter
user_weights_bounds. The actual weights_bounds are stored in the
attribute weights_bounds.

* [r3471] topo/tests/lissom_or_reference.ty:
Added min_exc_rad.

* [r3470] topo/misc/tyimputil.py:
Updated HACKALERT (ty files no longer get compiled to typ).

* [r3469] topo/tests/lissom_or_reference.ty:
Updated learning rates.

2006-05-04 jbednar

* [r3468] topo/base/simulation.py:
Added alert

* [r3467] topo/base/projection.py:
Fixed trivial typo on doc

* [r3466] doc/shared/trailer.php:
Fixed web pages to show the date the page was generated, not a
fixed date from 2005

2006-05-04 ceball

* [r3465] topo/tests/lissom_oo_or_reference.ty:
Corrected mistake in previous commit.

2006-05-04 jbednar

* [r3464] topo/tkgui/parametersframe.py:
Added titles for ParametersFrame windows

2006-05-04 ceball

* [r3463] topo/tests/lissom_or_reference.ty:
Finished previous update.

2006-05-04 jbednar

* [r3462] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py:
Added titles for ParametersFrame windows

2006-05-04 ceball

* [r3461] topo/tests/lissom_or_reference.ty:
Updated for recent changes to code.

* [r3460] doc/Future_Work/current_text.php:
Updated tasks.

* [r3459] topo/tkgui/editortools.py:
For editing sheet and projection classes, a new window opens.
This at least makes the model editor ok for creating sheets and
projections.

* [r3458] doc/Future_Work/current_text.php:
Updates to tasks.

* [r3457] topo/tkgui/parametersframe.py:
Removed unused method.

* [r3456] topo/tkgui/parametersframe.py:
Change to variable name.

* [r3455] topo/tkgui/parametersframe.py:
Added back a modified version of dict_translator use for
add_text_property().

* [r3454] topo/misc/utils.py:
Added comment.

* [r3453] topo/tkgui/translatorwidgets.py:
Minor change to comment.

2006-05-03 ceball

* [r3452] topo/tkgui/parametersframe.py:
Minor changes to notes.

* [r3451] topo/tkgui/parametersframe.py:
Removed some commented-out code about DynamicNumber. If
DynamicNumbers display strangely in ParametersFrames, then it
might be because I commented out this code before - so it may be
necessary to restore it. For now, though, I don't remember what
it was for.

* [r3450] topo/tkgui/parametersframe.py:
Tidied imports.

* [r3449] topo/tkgui/parametersframe.py:
Minor cleanup, with some reminders for myself.

* [r3448] topo/tkgui/parametersframe.py:
Still cleaning: simplified widget creation, corrected some
mistakes.

* [r3447] topo/tkgui/parametersframe.py:
Continued cleaning...

* [r3446] topo/tkgui/editortools.py:
Only ask ParametersFrame to make widgets if something has been
selected.

* [r3445] topo/tkgui/editorobjects.py,
topo/tkgui/parametersframe.py:
Intermediate checkin. Model editor can now set all parameters on
sheet and projection classes before they're instantiated. Not
fully tested, not finished, and might be a regression in some
areas.

* [r3444] topo/misc/utils.py:
Removed some string translation functions.

* [r3443] topo/tkgui/propertiesframe.py,
topo/tkgui/translatorwidgets.py:
Renamed taggedslider.py to translatorwidgets.py.

* [r3442] examples/homeostatic.ty,
examples/lissom_oo_or.ty,
examples/lissom_or_sf.ty,
topo/base/cf.py,
topo/commands/analysis.py,
topo/projections/basic.py,
topo/tests/lissom_oo_or_reference.ty:
Renamed SharedWeightProjection to SharedWeightCFProjection, as
well as the corresponding response and output functions.

* [r3441] examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
topo/learningfns/optimized.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty:
Renamed CFProjectionHebbian to CFPHebbian (along with _opt1
version).

* [r3440] examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
topo/outputfns/optimized.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty:
Renamed CFProjectionDivisiveSumNormalize to
CFPDivisiveSumNormalize (along with _opt1 version).

* [r3439] examples/som_retinotopy.ty,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Renamed CFProjectionEuclideanDistance to CFPEuclideanDistance
(along with _opt1 version).

* [r3438] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/laminar.ty,
examples/laminar_lissom.ty,
examples/laminar_nolearning.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/tiny.ty,
topo/misc/utils.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/testplotgroup.py:
Renamed CFProjectionDotProduct to CFPDotProduct (and the _opt1
version).

2006-05-03 jbednar

* [r3437] topo/tests/testsimulation.py:
Moved testsimulator.py to testsimulation.py

* [r3436] topo/__init__.py,
topo/base/__init__.py,
topo/base/projection.py,
topo/base/sheet.py,
topo/commands/pylabplots.py,
topo/eps/basic.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testsheetview.py,
topo/tests/testsnapshots.py,
topo/tests/testtemplateplotgrouppanel.py,
topo/tests/testtopoconsole.py,
topo/tkgui/topoconsole.py:
Moved topo.base.simulator to topo.base.simulation

* [r3435] topo/base/simulation.py:
Moved topo/base/simulator.py to topo/base/simulation.py

* [r3434] topo/tkgui/testpattern.py:
Added missing import

* [r3433] topo/plotting/plotgroup.py:
Added hack to work around problem with reducing integer
coordinates in the Test Pattern window

* [r3432] topo/base/arrayutils.py:
Removed apparently outdated comments

* [r3431] ChangeLog.txt:
Updated with recent changes

2006-05-03 julienciroux

* [r3430] topo/plotting/plotgroup.py,
topo/tkgui/testpattern.py:
Improved TestPattern so that the reduce, enlarge and sheetcoords
button ar working. There is still a problem remaining for
integerscaling button: when it is on, and that we try to reduce,
we obtain a Division by Zero error.

2006-05-03 ceball

* [r3429] topo/base/parameterizedobject.py:
Removed unused function and the HACKALERT about it.

* [r3428] topo/base/parameterizedobject.py:
Added method to return parameters of a
ParameterizedObjectMetaClass. The object method now just calls
this method.

2006-05-03 jbednar

* [r3427] topo/misc/utils.py:
Added alert

2006-05-03 ceball

* [r3426] topo/tkgui/parametersframe.py:
Added HACKALERT.

2006-05-02 ceball

* [r3425] topo/base/sheet.py:
Set density back to being a Number; it should only ever be a
number.

* [r3424] topo/base/sheetcoords.py:
No visible change - removed duplicate brackets.

* [r3423] examples/cfsom_or.ty,
examples/homeostatic.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/tiny.ty:
Removed unused import statement.

* [r3422] examples/hierarchical.ty:
Removed an import statement that's not currently used.

* [r3421] topo/learningfns/__init__.py,
topo/outputfns/__init__.py,
topo/patterns/__init__.py,
topo/responsefns/__init__.py,
topo/tkgui/__init__.py:
Now the GUI imports all outputfns, patterns, and responsefns
(rather than having a function to allow this in all the separate
packages). Also populates the appropriate ClassSelectorParameter
lists.

2006-05-02 jbednar

* [r3420] topo/tkgui/topoconsole.py:
Removed unused variable

* [r3419] topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
Renamed self.canvas.simulator to self.canvas.simulation

* [r3418] topo/base/simulator.py,
topo/commands/__init__.py,
topo/commands/analysis.py,
topo/commands/basic.py,
topo/eps/__init__.py,
topo/eps/basic.py,
topo/sheets/cfsom.py,
topo/sheets/generatorsheet.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testsheetview.py,
topo/tests/testsimulator.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py:
Renamed self.simulator link for EPs to self.simulation, plus
other instances of the word simulator in documentation and
comments

* [r3417] examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/__init__.py,
topo/base/projection.py,
topo/base/simulator.py:
Renamed self.simulator link for EPs to self.simulation, plus
other instances of the word simulator in documentation and
comments

2006-05-02 judelaw

* [r3416] examples/laminar.ty:
Work in progress - Changed Lateral Excitatory projection to be
one single projection with initial gaussian weights

* [r3415] examples/laminar_nolearning.ty:
Work in progress - contains 2 separate, initially random lateral
excitatory projections - only works for case with afferent
learning or excitatory learning only

* [r3414] examples/laminar_lissom.ty:
Version of Lissom_or with separate excitatory and inhibitory
layers

2006-05-02 ceball

* [r3413] topo/patterns/__init__.py:
Removed outdated HACKALERT.

* [r3412] doc/Future_Work/current_text.php:
Added long-term task of upgrading Numeric.

* [r3411] topo/base/boundingregion.py:
Override __str__() so that the bounds are displayed when printing
a BoundingBox.

2006-05-02 jbednar

* [r3410] topo/base/simulator.py:
Renamed Simulator to Simulation

* [r3409] topo/analysis/featuremap.py,
topo/commands/__init__.py,
topo/eps/__init__.py,
topo/plotting/templates.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testsimulator.py,
topo/tests/testsnapshots.py,
topo/tests/testtemplateplotgrouppanel.py,
topo/tests/testtopoconsole.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py:
Renamed Simulator to Simulation

* [r3408] topo/base/simulator.py:
Temporary: Simulation is an alias for Simulator

2006-05-02 ceball

* [r3407] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py:
Renamed topo/base/connectionfield.py to topo/base/cf.py.

2006-05-02 jbednar

* [r3406] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/obermayer_pnas90.ty,
examples/tiny.ty:
Removed unused import

2006-05-02 ceball

* [r3405] doc/Future_Work/current_text.php:
Removed a task.

* [r3404] topo/base/cf.py:
IdentityCFLearningFn has single_cf_fn=IdentityLF.

* [r3403] topo/base/functionfamilies.py:
Added IdentityLF.

* [r3402] doc/Future_Work/current_text.php:
Removed a task, and split up another.

* [r3401] topo/projections/basic.py:
Renamed SharedWeightOutputFn and SharedWeightResponseFn to
SWPOutputFn and SWPResponseFn. These names might be a bit
cryptic, but for now they are only used in this file.

* [r3400] examples/homeostatic.ty,
examples/lissom_oo_or.ty,
examples/lissom_or_sf.ty,
topo/projections/basic.py,
topo/tests/lissom_oo_or_reference.ty:
Renamed SharedCFProjection to SharedWeightProjection.

* [r3399] topo/base/patterngenerator.py,
topo/base/sheet.py,
topo/patterns/random.py,
topo/plotting/plot.py,
topo/tests/testsheet.py:
Moved SheetCoordinateSystem to sheetcoords.py.

* [r3398] topo/base/sheetcoords.py:
Initial version. SheetCoordinateSystem from sheet.py.

* [r3397] topo/base/cf.py,
topo/base/patterngenerator.py,
topo/base/sheet.py,
topo/patterns/random.py,
topo/plotting/plot.py,
topo/tests/testsheet.py:
Renamed CoordinateTransformer to SheetCoordinateSystem.

* [r3396] topo/tests/testimage.py:
Commented out a test (with an explanation).

* [r3395] doc/Future_Work/current_text.php:
Update to tasks.

* [r3394] doc/Future_Work/current_text.php:
Moved a task.

* [r3393] doc/Future_Work/current_text.php:
Removed a task.

* [r3392] topo/tkgui/editortools.py:
Updated how sheet is added to simulator.

* [r3391] examples/lissom_or_sf.ty:
Import BoundingBox as a Simulator startup action.

2006-05-01 ceball

* [r3390] doc/Future_Work/current_text.php:
Removed a stub. I hope it wasn't about to become an important
task because I've forgotten what it was...

* [r3389] doc/Future_Work/current_text.php:
Restored some text I cut by mistake.

* [r3388] doc/Future_Work/current_text.php:
Updated the task orderings and split some of them up.

* [r3387] doc/Future_Work/current_text.php:
Updated a task.

* [r3386] topo/base/cf.py,
topo/projections/basic.py:
Renamed CFProjectionIdentityOutputFn to IdentityCFPOutputFn.

* [r3385] examples/tiny.ty,
topo/base/cf.py,
topo/outputfns/optimized.py,
topo/outputfns/projfns.py:
Renamed CFProjectionGenericOutputFn to GenericCFPOutputFn.

* [r3384] topo/base/cf.py,
topo/outputfns/optimized.py,
topo/projections/basic.py:
Renamed CFProjectionOutputFn to CFPOutputFn.

* [r3383] examples/tiny.ty,
topo/base/cf.py,
topo/base/functionfamilies.py,
topo/learningfns/optimized.py,
topo/learningfns/projfns.py:
Renamed CFProjectionGenericLearningFn to GenericCFPLearningFn.

* [r3382] topo/base/cf.py,
topo/projections/basic.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Renamed CFProjectionResponseFn to CFPResponseFn.

* [r3381] topo/base/cf.py,
topo/learningfns/projfns.py,
topo/projections/basic.py:
Renamed CFProjectionIdentityLearningFn to IdentityCFPLearningFn.

* [r3380] topo/base/cf.py,
topo/learningfns/__init__.py,
topo/learningfns/optimized.py,
topo/learningfns/som.py,
topo/projections/basic.py:
Renamed CFProjectionLearningFn and
CFProjectionLearningFnParameter to CFPLearningFn and
CFPLearningFnParameter, respectively.

* [r3379] topo/base/cf.py,
topo/base/functionfamilies.py,
topo/projections/basic.py,
topo/responsefns/__init__.py,
topo/responsefns/projfns.py:
Renamed CFProjectionGenericResponseFn to GenericCFPResponseFn.
Renamed CFProjectionResponseFnParameter to
CFPResponseFnParameter.

* [r3378] doc/Future_Work/current_text.php:
Updated a task.

* [r3377] topo/base/cf.py:
Renamed connectionfield.py to cf.py.

* [r3376] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/lissom_oo_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/commands/analysis.py,
topo/learningfns/__init__.py,
topo/learningfns/optimized.py,
topo/learningfns/projfns.py,
topo/learningfns/som.py,
topo/misc/utils.py,
topo/outputfns/optimized.py,
topo/outputfns/projfns.py,
topo/plotting/plotgroup.py,
topo/projections/basic.py,
topo/responsefns/__init__.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py,
topo/sheets/cfsom.py,
topo/sheets/lissom.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py,
topo/tests/testsnapshots.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py:
Renamed connectionfield.py to cf.py

* [r3375] doc/Future_Work/current_text.php:
Updated a task.

* [r3374] topo/base/functionfamilies.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/responsefns/projfns.py:
Moved ResponseFnParameter, Mdot, and ResponseFn to
functionfamilies.

* [r3373] topo/learningfns/optimized.py:
Removed imports of unused classes - the optimized module just has
the optimized classes, and any it needs to use as fall-backs.

* [r3372] topo/base/functionfamilies.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Moved LearningFn, LearningFnParameter, and Hebbian to
functionfamilies.py.

* [r3371] doc/Future_Work/current_text.php:
Removed a task.

* [r3370] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/simulator.py,
topo/eps/basic.py,
topo/sheets/composer.py,
topo/sheets/generatorsheet.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testsimulator.py,
topo/tests/testsnapshots.py,
topo/tkgui/editortools.py:
Renamed Simulator's connect2() to connect().

* [r3369]
topo/tests/testtemplateplotgrouppanel.py:
Added a HACKALERT and commented some code.

* [r3368] topo/base/simulator.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testsimulator.py:
Uses Simulator's connect2() instead of connect().

* [r3367] topo/tests/testcfsom.py:
Uses Simulator's connect2() instead of connect().

* [r3366] topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty:
Uses Simulator's connect2() instead of connect().

* [r3365] topo/sheets/composer.py:
Update to doc string.

* [r3364] topo/eps/basic.py,
topo/sheets/generatorsheet.py:
Uses Simulator's connect2() instead of connect().

* [r3363] topo/tkgui/editortools.py:
Uses Simulator.connect2() rather than .connect(). Before this
change there was an error when making a connection.

* [r3362] doc/Future_Work/current_text.php:
Added task about model editor. Removed schedule_action task.

* [r3361] topo/base/simulator.py:
Removed schedule_action().

* [r3360] examples/lissom_or_sf.ty:
Updated with changes to code, including topo.sim-style access,
and using schedule_command().

2006-05-01 jbednar

* [r3359] examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty:
Added names for the simulations

* [r3358] topo/commands/pylabplots.py:
Added control over window titles

2006-05-01 ceball

* [r3357] examples/laminar.ty:
Changed to use topo.sim-style access to simulator. Tidied up.

* [r3356] examples/homeostatic.ty:
Minor updates, including to use topo.sim rather than s.

* [r3355] examples/som_retinotopy.ty:
Minor tidy.

* [r3354] examples/cfsom_or.ty:
Minor clean up.

* [r3353] examples/obermayer_pnas90.ty:
Tidied up file; uses 'topo.sim' rather than 's'.

* [r3352] topo/base/simulator.py:
If a connection wasn't given a name, it defaults to 'srcTodest'
(e.g. 'RetinaToV1')

* [r3351] doc/Future_Work/current_text.php:
Removed a task; added one to more long-term work.

* [r3350] topo/base/connectionfield.py:
Corrected index order for accessing a list.

* [r3349] topo/misc/tyimputil.py:
Added HACKALERT.

* [r3348] examples/obermayer_pnas90.ty:
Added import of pi; minor reformating of comments.

* [r3347] topo/commands/basic.py:
Minor update to comment.

* [r3346] topo/commands/basic.py:
Warns if there are classes or functions around that were defined
in __main__, since the source won't be found on unpickling.

2006-04-30 ceball

* [r3345] doc/Future_Work/current_text.php:
Updated a task.

* [r3344] examples/obermayer_pnas90.ty:
Input pattern parameters are set on a Gaussian object rather than
on the Gaussian class.

* [r3343] topo/sheets/generatorsheet.py:
Added a HACKALERT about the input_generator bounds.

* [r3342] examples/tiny.ty:
Uses RandomWrapper with separate seed for each stream of number.
Minor tidy.

* [r3341] examples/lissom_or.ty:
Changed to use topo.sim['V1']-style access to simulator.
Scheduled actions changed to strings.

* [r3340] examples/lissom_or.ty:
Finished previous minor cleanup.

* [r3339] examples/lissom_or.ty:
Minor cleanup. Removed commented-out code (it was confusing).

* [r3338] doc/Future_Work/current_text.php:
Corrected date.

* [r3337] doc/Future_Work/current_text.php:
Added task.

* [r3336] examples/hierarchical.ty:
Updated input pattern to use RandomWrapper and have a separate
seed for each stream of random numbers.

* [r3335] examples/cfsom_or.ty:
Updated input pattern to use RandomWrapper, have a separate seed
for each stream of random number, and not set softbounds.

* [r3334] topo/base/sheet.py:
Sheet cannot be created with unequal densities.

* [r3333] doc/Future_Work/current_text.php:
Removed and updated some tasks.

2006-04-28 ceball

* [r3332] topo/tests/lissom_oo_or_reference.ty:
Minor updates to commented-out code. Also set afferent
connections strengths to 0.5 each.

* [r3331] topo/tests/lissom_oo_or_reference.ty:
Removed some commented-out code.

* [r3330] topo/tests/lissom_oo_or_reference.ty:
Added commented-out code for using Composite for center/surround,
rather than two projections.

* [r3329] topo/tests/lissom_oo_or_reference.ty:
Updated to work with current classes.

* [r3328] topo/base/boundingregion.py:
Added reminder that someone should make BoundingRegion display
something useful (like the bounds...) when it's printed.

* [r3327] doc/Future_Work/current_text.php:
Added task.

* [r3326] topo/patterns/basic.py:
Corrected mistake in Composite; now works again for weights
generation.

* [r3325] doc/Future_Work/current_text.php:
Removed erroneous statement in one of the tasks.

* [r3324] topo/base/connectionfield.py:
Changed CFProjection.initialize_bounds() so that it avoids
floating-point representation difficulties. Specifically, it uses
bounds2slice() to get the right and bottom values of the slice,
then mirrors these about the center of the slice to get the left
and top values - ensuring the slice is odd. Updated
CF.offset_bounds() so that it does not assume the bounds it
receives are centered at (0,0) on the Sheet. These alterations
could affect the behaviour of existing networks; the reference
simulations show no change.

* [r3323] topo/base/sheet.py:
Made set_slice be available outside the Slice class, temporarily.

* [r3322] topo/base/boundingregion.py:
Added method to BoundingBox that results the coordinates of the
center of the bounds.

* [r3321] topo/tests/testsheet.py:
Commented out test of bounds2slice() that fails because of the
floating point representation of these particular bounds.

* [r3320] topo/base/connectionfield.py:
Raises a ValueError if the weights matrix ends up with a
zero-sized dimension.

* [r3319] topo/base/connectionfield.py:
Added assert statement (assert that the weights matrix is odd).

2006-04-28 jbednar

* [r3318] topo/tkgui/testpattern.py:
Added ALERTs

* [r3317] topo/tkgui/plotgrouppanel.py:
Minor clarification

* [r3316] topo/tkgui/plotgrouppanel.py:
Added serious HACKALERT

2006-04-28 ceball

* [r3315] topo/tests/testsheet.py:
Updated test.

2006-04-28 jbednar

* [r3314] topo/tkgui/templateplotgrouppanel.py:
Fixed normalize option for ConnectionFieldPanel and
ProjectionPanel -- the button was on, but the plots weren't
normalized

* [r3313] topo/tkgui/projectionpanel.py:
Fixed typo

* [r3312] topo/tkgui/connectionfieldspanel.py:
Removed outdated ALERT

* [r3311] topo/plotting/plotgroup.py:
Improved plot size calculation for projections; still needs work.
Cleaned up comments and documentation.

2006-04-27 ceball

* [r3310] topo/tests/testsheet.py:
Added comment.

* [r3309] topo/tests/testsheet.py:
Added another test of bounds2slice(), currenly failing.

* [r3308] topo/base/connectionfield.py:
Removed the HACKALERT I just added; I was confused.

* [r3307] topo/base/connectionfield.py:
Added HACKALERT about initialize_bounds().

* [r3306] doc/Future_Work/current_text.php:
Updated a task.

* [r3305] examples/lissom_oo_or.ty:
Changed to use 'topo.sim'-style access; tidied up a little.

* [r3304] examples/lissom_oo_or.ty:
Switced to using RandomWrapper.

* [r3303] topo/misc/numbergenerators.py:
Renamed RandomDistributionWrapper to RandomDistribution. Removed
a HACKALERT.

2006-04-27 jbednar

* [r3302] topo/tkgui/testpattern.py:
Minor typo fixed

* [r3301] topo/tkgui/editorobjects.py:
Made default CF representation be more useful

* [r3300] topo/plotting/plotgroup.py,
topo/tkgui/plotgrouppanel.py:
Enforced minimum size on plots, so that no pixels are lost

2006-04-27 ceball

* [r3299] topo/misc/numbergenerators.py:
Added hack to save state of random generators in RandomWrapper.

* [r3298] examples/lissom_or.ty:
Moved RandomWrapper to topo.misc.numbergenerators.

* [r3297] topo/base/parameterclasses.py:
Moved RandomWrapper to topo/misc/numbergenerators.py

* [r3296] topo/misc/numbergenerators.py:
Renamed RandomWrapper to RandomDistributionWrapper. Moved
parameterclasses.py's RandomWrapper into this file.

* [r3295] topo/misc/numbergenerators.py:
Initial version.

* [r3294] topo/tkgui/testpattern.py:
Updated with changes to xdensity and ydensity for
PatternGenerator and Sheet.

* [r3293] doc/Future_Work/current_text.php:
Added some tasks (including one for before release).

2006-04-26 ceball

* [r3292] doc/Future_Work/current_text.php:
Re-inserted a task that got deleted some time back by accident
while rearranging the file.

* [r3291] topo/tests/lissom_or_reference.ty:
Minor update to comment.

* [r3290] topo/tests/lissom_or_reference.ty:
Updated learning rates (before bounds change).

* [r3289] topo/base/connectionfield.py:
Changed CFProjection's initialize_bounds() to move the bounds to
the center of a unit before converting to a slice, thereby
guaranteeing an odd size for the slice.

* [r3288] doc/Future_Work/current_text.php:
Updated a task.

* [r3287] topo/base/parameterclasses.py:
Added note that random streams don't appear to be pickled such
that they resume where they left off.

* [r3286] topo/base/connectionfield.py:
Added HACKALERT.

* [r3285] topo/tests/lissom_or_reference.ty:
Updates to match changes to equivalen C++ lissom example.

* [r3284] doc/Future_Work/current_text.php:
Removed a task! About pickling!

* [r3283] examples/lissom_oo_or.ty:
Added startup command to allow V1 still to be referred to.

* [r3282] topo/commands/basic.py:
Instead of pickle.Pickler and pickle.Unpickler, use our custom
Pickler and Unpickler.

* [r3281] topo/misc/utils.py:
Added new Pickler and Unpickler, used at the moment to save array
savespace setting.

* [r3280] topo/commands/basic.py:
No visible change: switched from using pickle's load() and dump()
functions to using pickle.Pickler and pickle.Unpickler objects
explicitly.

* [r3279] topo/base/patterngenerator.py:
Removed unused import.

2006-04-25 ceball

* [r3278] topo/misc/patternfns.py:
Added deliberate conversion of input to float, in case user
passes an int (for divisions)

2006-04-25 jbednar

* [r3277] doc/Future_Work/current_text.php:
Updated slightly

2006-04-25 ceball

* [r3276] doc/Future_Work/current_text.php:
Finished part of a task.

* [r3275] topo/commands/basic.py:
Removed hack from load_snapshot().

* [r3274] topo/misc/utils.py:
Set class attributes on true class rather than on the name we
might be using for a class.

2006-04-25 jbednar

* [r3273] doc/Developer_Manual/coding_text.php,
doc/Developer_Manual/optimization_text.php,
doc/Reference_Manual/index_text.php:
Minor fixes and clarifications

* [r3272] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore:
Minor fix

2006-04-24 ceball

* [r3271] doc/Future_Work/current_text.php:
Updated a task.

* [r3270] topo/commands/basic.py:
Added a hack to avoid a problem with unpickling when Topographica
was pickled after falling back to non-optimized components.

* [r3269] doc/Future_Work/current_text.php:
Added a task.

* [r3268] topo/tests/testsimulator.py:
Updated test with new class name.

* [r3267] examples/hierarchical.ty,
examples/lissom_oo_or.ty:
Adds a command to the simulator's startup_commands.

* [r3266] topo/base/simulator.py,
topo/commands/basic.py:
Added startup_commands Parameter to Simulator. Altered
topo.commands.basic's save_snapshot() and load_snapshot() so that
these commands are executed before the simulator is unpickled.
Now scheduled actions can be pickled and unpickled without
difficulty.

* [r3265] doc/Future_Work/current_text.php:
Added a task about correcting things causing pickling to fail.
Added task about adding a set of more in-depth tests, distinct
from the quick-to-run tests.

* [r3264] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3263] doc/Future_Work/index_text.php:
Added commented-out optimistic update for pickling section.

* [r3262] topo/commands/basic.py:
Added note for improvement to pickling.

* [r3261] doc/Future_Work/index_text.php:
Updated section about different platforms.

* [r3260] doc/Future_Work/current_text.php:
Updated my tasks, including marking those that need to be
completed before the next release.

* [r3259] examples/lissom_oo_or.ty:
Changed to use schedule_command() instead of schedule_action().

* [r3258] topo/base/simulator.py:
Added more helpful printing in the case of a SyntaxError for
CommandEvent.

* [r3257] topo/base/simulator.py:
Added Event class, and EPEvent and CommandEvent subclasses (as
well as SAEVent class which will be removed when all uses of
schedule_action() in the examples are removed). There is one
change to the logic in Simulator.run(): now did_event is set to
True no matter what type of Event is called (rather than just for
SimulatorEvents without 'fn' attribute, as before). I don't think
this affects the behaviour.

2006-04-24 jbednar

* [r3256] doc/User_Manual,
doc/User_Manual/.cvsignore,
doc/User_Manual/index_text.php,
doc/User_Manual/modeleditor_text.php:
Moved model_editor.html to modeleditor.php and added TOC link

* [r3255] doc/User_Manual/model_editor.html:
Moved to model_editor_text.php

* [r3254] doc/Future_Work/index_text.php:
Fixed stray comment ender that was giving garbage text at the end
of the page

* [r3253] topo/base/connectionfield.py:
Clarified documentation

* [r3252] doc/shared/index.php:
Added more keywords to title

2006-04-24 ceball

* [r3251] examples/hierarchical.ty:
Changed scheduled action example to use schedule_command(), which
allows the network to be pickled before all the scheduled actions
have occurred.

* [r3250] topo/base/simulator.py:
Added ScheduledCommand class and schedule_command() for exec'ing
an arbitrary string in __main__.__dict__ at a specified time.
Added some HACKALERTs (about scheduling commands).

* [r3249] examples/hierarchical.ty:
Added an example scheduled action.

* [r3248] topo/base/simulator.py:
Added comment. Added HACKALERT.

* [r3247] topo/base/simulator.py:
Clarified a HACKALERT.

* [r3246] topo/base/simulator.py:
Added HACKALERT about SimulatorEvent.

* [r3245] topo/tests/lissom_or_reference.ty:
Removed erroneous cropping of rf_radius to an integer.

* [r3244] topo/base/connectionfield.py:
Mask size set from the original, user-specified weights_bounds,
rather than the weights_bounds that may have been adjusted to be
odd-sized. Still need to change to have user-specified
weights_bounds as the Parameter user_weights_bounds.

2006-04-23 jbednar

* [r3243] Makefile:
Added automatic ChangeLog creation

* [r3242] ChangeLog.txt:
Updated with recent changes

2006-04-23 ceball

* [r3241] topo/tests/lissom_or_reference.ty:
Minor clean-up.

* [r3240] topo/tests/lissom_or_reference.ty:
Updated to work with current code, and made some minor
simplifications.

* [r3239]
doc/Developer_Manual/imports_text.php:
Fixed minor typo.

2006-04-22 ceball

* [r3238] topo/base/connectionfield.py,
topo/base/sheet.py:
Added translate() method to Slice.

2006-04-21 ceball

* [r3237] topo/responsefns/optimized.py:
Corrected typo in the code that was stopping Topographica running
without weave.

* [r3236] doc/Future_Work/current_text.php:
Removed a task!

* [r3235] topo/base/connectionfield.py:
Removed a HACKALERT and the corresponding HACK.

* [r3234] topo/base/connectionfield.py:
Removed an assert statement from get_view().

* [r3233] topo/base/connectionfield.py:
get_view() asks for cf's slice directly, rather than getting
bounds and calculating the slice.

* [r3232] topo/projections/basic.py:
Removed get_view() because there is no longer any need to
override the superclass's version.

* [r3231] topo/base/connectionfield.py:
Removed another print statement that I left in by mistake.

* [r3230] topo/projections/basic.py:
SharedWeight's cf(r,c) method now returns the cf with the
appropriate bounds.

* [r3229] topo/base/connectionfield.py:
Removed commented-out print statements left in by mistake.

* [r3228] topo/base/sheet.py:
Corrected typo.

* [r3227] doc/Future_Work/current_text.php:
Updated my tasks; started to put them in some kind of order (in
which I'm doing them).

2006-04-20 ceball

* [r3226] topo/base/sheet.py:
Added HACKALERT about location of CoordinateTransformer.

* [r3225] topo/base/parameterizedobject.py,
topo/base/patterngenerator.py:
Moved _check_params to ParameterizedObject, where I meant to put
it originally.

* [r3224] topo/patterns/random.py:
__call__() checks that its arguments are Parameters.

* [r3223] topo/base/patterngenerator.py:
Moved code that checks arguments of __call__() are Parameters to
its own method; added call to that method to Constant.

* [r3222] topo/base/patterngenerator.py:
PatternGenerator uses a CoordinateTransformer method to get
pattern sampling vectors.

* [r3221] topo/base/sheet.py:
Added method to return the sheet coordinate x-centers and
y-centers of the underlying matrix cells of a
CoordinateTransformer.

2006-04-20 julienciroux

* [r3220] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py:
Fixed projectionpanel and corrected errors in connectionfield
panel. There is still a warning when opening the connectionfield
panel, it has to be sorted.

* [r3219] topo/tkgui/connectionfieldspanel.py:
Corrected display of the sheet_name while looking into history.

2006-04-20 ceball

* [r3218] topo/tests/testsheet.py:
Minor update after change to Sheet.

* [r3217] topo/base/sheet.py:
Continued to update recent work CoordinateTransformer. Equalizing
the densities by adjusting bounds is now an option on creating a
CoordinateTransformer, and is True by default for Sheets.

2006-04-20 julienciroux

* [r3216] topo/tkgui/connectionfieldspanel.py:
Corrected the double call to refresh in the __init__, and got rid
of the FocusOut action for the xy boxes.

* [r3215] topo/tkgui/connectionfieldspanel.py:
Got rid of now unuseful chain import.

2006-04-20 ceball

* [r3214] topo/base/sheet.py:
Minor updates to use of Slice and CoordinateTransformer.

2006-04-20 julienciroux

* [r3213] topo/tkgui/plotgrouppanel.py:
Corrected handling of integerscaling.

* [r3212] topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Added a parameter looking_in_history that indicates if we are
currently looking back in time. Fixed the handling of the
checkbuttons when hitting back and forward.

2006-04-20 ceball

* [r3211] topo/patterns/random.py:
Random generators get shape from CoordinateTransformer, rather
than from a Slice. Removed Slice from imports.

* [r3210] topo/base/patterngenerator.py:
Constant gets shape from CoordinateTransformer, rather than from
a Slice. Removed Slice from imports.

* [r3209] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3208] topo/base/patterngenerator.py:
PatternGenerator uses matrixidx2sheet_array()

* [r3207] topo/tests/testsheet.py:
Added some comments.

* [r3206] topo/base/sheet.py:
Added matrixidx2sheet_array() and updated some comments.

2006-04-20 julienciroux

* [r3205] topo/plotting/plotgroup.py,
topo/tkgui/plotgrouppanel.py:
Added a method restaure_environment in PlotGroup panel to
re-instate the state of the buttons when re-loading a Plotgroup
from the history.

* [r3204] topo/tkgui/plotgrouppanel.py:
Corrected the handling of the history so that it act properly
when hitting refresh or auto-refresh.

* [r3203] topo/tkgui/plotgrouppanel.py:
Corrected the saving of the history so that we do not update a
PlotGroup in the past.

* [r3202] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py:
Changed the handling of the history: now a copy of the plotgroup
is kept in history instead of bitmaps. It still needs more work.

2006-04-20 ceball

* [r3201] topo/base/sheet.py:
Simplified code committed in the last version.

* [r3200] topo/tests/testsheet.py:
Where xdensity==ydensity, CoordinateTransformers are created by
passing just one density.

* [r3199] topo/base/sheet.py:
Can create a CoordinateTransformer by specifying only one density
if xdensity==ydensity.

* [r3198] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3197] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3196] topo/tests/testimage.py,
topo/tests/testpatterngenerator.py:
Uses xdensity and ydensity in the tests, rather than just
density. Only tests cases where they're equal, though.

* [r3195] topo/tests/testcfsom.py,
topo/tests/testsheetview.py:
Commented out the ImageGenerator class. Tests using it will be
resurrected in an equivalent form using the Image class.

* [r3194] topo/tests/testsheet.py:
Updated after changes to sheet.py (introduction of
CoordinateTransformer). Some further changes will be required
when CoordinateTransformer is changed some more...

* [r3193] topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py:
Removed unused import statement.

* [r3192] topo/sheets/generatorsheet.py:
The image generator is passed xdensity and ydensity (both equal,
since for a sheet these are equal).

* [r3191] topo/plotting/plot.py:
Uses Slice and CoordinateTransformer.

* [r3190] topo/patterns/random.py:
Uses xdensity and ydensity, and the Slice object.

* [r3189] topo/patterns/image.py:
Uses xdensity and ydensity.

* [r3188] topo/patterns/basic.py:
PatternSampler uses xdensity and ydensity. This is an
intermediate checkin - needs to be cleaned up.

* [r3187] topo/learningfns/som.py:
Uses xdensity and ydensity in call to pattern generator.

* [r3186] topo/commands/analysis.py:
Calls matrix2sheet() as a method of the sheet being considered.

* [r3185] topo/base/patterngenerator.py:
Part-way checkin. Uses the Slice object, but more of the
calculations in PatternGenerator will move to the Slice object.

* [r3184] topo/base/connectionfield.py:
Uses the Slice and CoordinateTransformer classes. Some of the
calculations in here will move to the Slice object (e.g.
translation of a slice).

* [r3183] topo/base/sheet.py:
Part-way checkin. Created CoordinateTransformer class, which
contains methods that were previously coordinate-transforming
functions in this file. Updated the Slice object. Still have to
move some methods from CoordinateTransformer to Slice, and
finalize other aspects.

2006-04-19 julienciroux

* [r3182] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py:
Deleted the attribute sheet_filter_lam of a PlotGroup in order to
be able to deep copy a PlotGroup.

* [r3181] topo/plotting/plotgroup.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Corrected the _set_height_of_tallest_plot and the scale_images
method for a ProjectionPlotGroup.

2006-04-19 ceball

* [r3180] topo/patterns/basic.py:
Replaced the untested CompositePatternGenerator with a new,
untested CompositePatternGenerator. This one is simpler.

2006-04-19 julienciroux

* [r3179] topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Added a parameter update when calling display_plots (decide
wether re-generating the Sheetviews or not.

* [r3178] topo/plotting/plotgroup.py:
Minor change in doc and comment.

2006-04-19 ceball

* [r3177] topo/commands/analysis.py:
Get cf.slice_array rather than calling cf.slice_tuple(). (This
was part of an earlier change, but does not seem to have been
committed.)

2006-04-18 ceball

* [r3176] topo/sheets/generatorsheet.py:
Removed unnecessary setting of bounds and density. Removed out of
date HACKALERT.

2006-04-15 ceball

* [r3175] topo/tests/testpatterngenerator.py:
File is now a reasonable test of PatternGenerator.

* [r3174] topo/tests/testpatterngenerator.py:
Added more tests.

* [r3173] topo/tests/testpatterngenerator.py:
Updated test.

* [r3172] topo/tests/testpatterngenerator.py:
Changed the test so that it actually does what was intended
(previously the 'assert' statement was not testing anything about
the arrays). Currently it fails but this might be because the
test itself is wrong.

2006-04-14 ceball

* [r3171] topo/base/connectionfield.py,
topo/projections/basic.py,
topo/responsefns/projfns.py:
Removed cf's slice_tuple() method. Going to rename slice_array to
slice_. slice_ being an array does not make it awkward to access
the elements since Python automatically unpacks array values
anyway.

* [r3170] topo/base/sheet.py:
Removed an outdated HACKALERT.

2006-04-14 julienciroux

* [r3169] topo/plotting/plotgroup.py:
Minor re-organization; deleted self.bitmaps.

* [r3168] topo/plotting/bitmap.py,
topo/plotting/plotgroup.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Delete the attribute plot_src_name and name for a Bitmap (Not
needed anymore). Delete the PlotGroup load_images method, now we
explicitly built the bitmap list in PlotGroupPanel
display_plots().

* [r3167] topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py:
Moved the generation of the plot labels to PlotGroup; it will
enable getting rid of the copy of plot_src_name and name from
Plot to Bitmap, and eventually getting rid of the direct use of
Bitmaps objects.

* [r3166] topo/tkgui/plotgrouppanel.py:
Re-organized order in the file, added alert.

* [r3165] topo/tkgui/plotgrouppanel.py:
Deleted unused import statements.

* [r3164] topo/tkgui/plotgrouppanel.py:
Temporary hack to fix back and forward buttons.

* [r3163] topo/tkgui/plotgrouppanel.py:
Minor re-organization of the __init__ method.

* [r3162] topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py:
Added a second control frame for Back, Forward, Sheetcoordinates
and Integerscaling Buttons. Moved the Sheetcoords button from
templateplotgrouppanel to plotgrouppanel. Deleted old comments.

* [r3161] topo/tkgui/plotgrouppanel.py:
Deleted the scale_images() method in PlotGroupPanel. Now the
scaling is done within PlotGroup. Also deleted unused import
statements and old alerts and update doc.

2006-04-13 julienciroux

* [r3160] topo/plotting/plotgroup.py:
Added two ALERTS.

2006-04-13 ceball

* [r3159] topo/base/patterngenerator.py:
No visible change - minor alteration to the code.

2006-04-13 julienciroux

* [r3158] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Deleted the attribute plotgroup_key of a PlotGroup.

2006-04-13 ceball

* [r3157] topo/base/connectionfield.py:
Get sheet's shape from sheet's activity matrix shape.

* [r3156] topo/base/connectionfield.py:
Use sheet methods bounds2slice() and slice2bounds().

* [r3155] topo/base/sheet.py:
Added sheet methods bounds2slice() and slice2bounds().

* [r3154] topo/base/sheet.py:
Minor changes to documentation.

* [r3153] topo/base/sheet.py:
Enforce minimum number of units in each direction to be 1; rename
slice variable to slice_; changes to documentation.

2006-04-13 julienciroux

* [r3152] topo/plotting/plotgroup.py:
Deleted two unused import statement.

* [r3151] topo/plotting/plotgroup.py:
Got rid of the use of dict_sort. Now the ordering of the plot is
performed differently.

* [r3150] topo/plotting/plotgroup.py:
Deleted the import statement for flatten and change the code that
was using it.

2006-04-13 ceball

* [r3149] topo/base/sheet.py:
Small change to documentation.

* [r3148] topo/base/sheet.py:
No visible change - small tidy up.

* [r3147] topo/base/boundingregion.py:
Minor change to documentation.

* [r3146] topo/base/parameterizedobject.py:
Moved __doc__ definition higher up in the Parameter class so it
is a bit more obvious. Added check that subclasses of Parameter
define __slots__.

* [r3145] topo/base/simulator.py:
Added __slots__ and __doc__ to EventProcessorParameter.

* [r3144] topo/base/boundingregion.py:
Added __slots__ and __doc__ to BoundingRegionParameter.

* [r3143] topo/base/sheet.py:
Updated Sheet documentation a bit.

2006-04-13 julienciroux

* [r3142] topo/plotting/plotgroup.py,
topo/tkgui/templateplotgrouppanel.py:
Replaced the import statement for the commands within
templateplotgrouppanel, and import them in __main__.__dict__.
They laso are executed in __main__.__dict__ from the PlotGroups.

2006-04-13 ceball

* [r3141] topo/base/sheet.py:
Removed unused functions slicearray2bounds() and
bounds2slicearray(). All slices will be arrays eventually, but
for now they are Python tuples.

2006-04-13 julienciroux

* [r3140] topo/plotting/plotgroup.py:
Deleted unused import statements.

2006-04-13 ceball

* [r3139] topo/patterns/basic.py:
Removed xdensity and ydensity from current Composite class (which
will be replaced anyway).

2006-04-13 julienciroux

* [r3138] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Deleted the plotgroup_dict variable: now each panel create and
store its own plotgroup attribute and uses it accordingly. Added
a method generate_sheet_views to the PlotGroups: now the command
to update the sheet view is contained in PlotGroups (and still
can be modified from the panel). It is the first version without
plotgroup_dict, it needs some cleaning and improving (in
particular for the projectionpanel and testpattern).

2006-04-13 ceball

* [r3137] topo/base/sheet.py,
topo/tests/testsheet.py:
Removed xdensity and ydensity. Except in the documentation.

* [r3136] topo/base/sheet.py,
topo/tests/testsheet.py:
slice2bounds() does not use xdensity and ydensity.

* [r3135] topo/base/sheet.py,
topo/commands/analysis.py,
topo/tests/testsheet.py:
matrix2sheet() does not use xdensity and ydensity.

* [r3134] topo/base/sheet.py,
topo/tests/testsheet.py:
sheet2matrix() and sheet2matrixidx() don't use xdensity and
ydensity.

* [r3133] topo/tests/testsheet.py:
Altered a test; no visible change.

* [r3132] topo/tests/testsheet.py:
Uncommented a test case that I'd previously left commented out by
mistake.

2006-04-12 ceball

* [r3131] topo/base/sheet.py:
crop_slice_to_sheet() doesn't use xdensity and ydensity.

* [r3130] topo/plotting/plot.py:
Removed unused import.

* [r3129] topo/base/sheet.py:
submatrix() just takes density.

* [r3128] topo/base/sheet.py,
topo/tests/testsheet.py:
bounds2slice() just uses density, not xdensity and ydensity.

* [r3127] topo/tests/testplotfilesaver.py:
Only one line was in the test, so I commented that one too.

* [r3126] topo/plotting/plot.py:
Removed xdensity and ydensity. Adjusted the corresponding
HACKALERT.

* [r3125] topo/base/functionfamilies.py:
Initial version.

* [r3124] topo/base/connectionfield.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/learningfns/som.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py,
topo/patterns/basic.py,
topo/patterns/image.py,
topo/patterns/random.py,
topo/projections/basic.py,
topo/tests/testimage.py:
Moved OutputFn, OutputFnParameter, and Identity to
functionfamilies (from projection). Renamed Identity to
IdentityOF.

* [r3123] topo/responsefns/basic.py:
Import the basic response functions.

* [r3122] topo/responsefns/projfns.py:
Removed unnecessary __init__()s. Use ResponseFnParameter for
single_cf_fn.

* [r3121] topo/responsefns/optimized.py:
Removed unnecessary __init__(). Use ResponseFnParameter.

* [r3120] topo/projections/basic.py:
Use ResponseFnParameter.

* [r3119] topo/base/arrayutils.py,
topo/base/connectionfield.py:
Moved Mdot() to connectionfield.py and made it a LearningFn. Made
ResponseFnParameter.

* [r3118] topo/base/connectionfield.py:
Changed a sum() of the weights to Numeric.sum(). Numeric.sum() is
faster. (Python's sum() and Numeric's sum() appear to give
slightly different results in general, though this particular
change makes no difference at the moment.)

2006-04-12 julienciroux

* [r3117] topo/plotting/plotgroup.py:
Minor re-organization of the __init__.

* [r3116] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py:
Renamed plot_group_key to plotgroup_key for consistency.

* [r3115] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Added arguments sheetcoords and integersaling to the PlotGroup
constructor. Renamed plotgroup() to refresh_plotgroup() in
PlotGroupPanel and subclasses. Now, refresh_plotgroup() is only
called from the refresh method, and I added an attribute
self.plotgroup that stores the current PlotGroup. Also deleted
old code in PlotGroupPanel.

* [r3114] topo/plotting/plotgroup.py:
Deleted old comments; improved two lines of code.

2006-04-12 ceball

* [r3113] doc/Future_Work/current_text.php:
Updated a task.

* [r3112] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3111] topo/base/connectionfield.py:
Removed xdensity and ydensity, just using density now.

* [r3110] topo/base/sheet.py:
Intermediate checkin. Removing xdensity and ydensity gradually.

* [r3109] topo/base/patterngenerator.py,
topo/patterns/random.py:
PatternGenerators only accept density as a single number.

* [r3108] topo/sheets/generatorsheet.py:
Only passes density, not xdensity and ydensity, to
PatternGenerator for creating the input pattern.

* [r3107] topo/tests/testsheet.py:
Removed test of bounds2slice() that deliberately uses different x
and y densities.

* [r3106] topo/tests/testsheet.py:
Added a test for Sheet creation where the specified bounds and
density would not give a sheet with the same density along x as
along y.

2006-04-11 ceball

* [r3105] topo/plotting/plot.py:
Changed a HACKALERT.

2006-04-11 julienciroux

* [r3104] topo/plotting/bitmap.py,
topo/plotting/plot.py:
Got rid of the attribute resize for the bitmap, and added it to
Plot objects.

* [r3103] topo/plotting/plotgroup.py,
topo/tests/testplotfilesaver.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/testpattern.py:
Moved everything not special to the GUI from PlotGroupPanel to
PlotGroup (e.g. sale_images, _set_height_of_tallest_plot). Also
deleted the old do_plot_cmd, by a plotgroup() method that
regenrates the PlotGroup anytime from the panels. It is a first
version that have been committed in order to be further
simplified. Note also that there is a slight bug for the
ProjectionPanel and for the handling of the SheetCoordinates
check_button, but they will be fixed very soon.

2006-04-11 ceball

* [r3102] topo/base/sheet.py:
Sheet has same density in x and y directions (by adjusting height
of BoundingBox if necessary. Intermediate checkin: still have to
removed xdensity and ydensity from the code, and update the
documentation.

* [r3101] examples/Makefile:
Sets default_density to be smaller before running each example.

* [r3100] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty:
Allowed cortical density to be set externally via default_density
variable (otherwise uses the value set in the file).

2006-04-11 alan_lindsay

* [r3099] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
Colours of sheets changed (together) by setting the canvas' mode.
No lateral button in sheet's property panel, just a list of
connections (opens their properties). Auto refresh and normalize
options in the canvas.

* [r3098]
doc/User_Manual/images/editorconnectiondrag.png,
doc/User_Manual/images/editorproperties.png,
doc/User_Manual/images/editorrepresentations.png,
doc/User_Manual/images/editortoolbaritems.png,
doc/User_Manual/model_editor.html:
First draft user guide for the model editor. Does not link to
other sections and does not conform to the style of the other
pages.

2006-04-11 jbednar

* [r3097] topo/tests/testsheet.py:
Fix by Chris -- override default Sheet bounds and density to be
sure it's the ones we expect

* [r3096] /trunk/topographica, .cvsignore:
Added missing newline

2006-04-11 ceball

* [r3095] topo/responsefns/basic.py:
Removed projection-level response functions (they are in
projfns.py.

* [r3094] topo/responsefns/optimized.py:
Updated CFProjectionResponseFn imports to be from projfns.

* [r3093] topo/responsefns/projfns.py:
Renamed basic.py to projfns.py since it contains only
projection-level response functions.

2006-04-10 ceball

* [r3092] topo/tests/testsheet.py:
Re-enabled a test that I disabled. This version, revision 1.25,
is identical to revision 1.23. I disabled the test when I changed
how the tests are run, because it began failing with no change
other than the test-running mechanism (and had not been failing
before). As far as I could tell, the test was running properly
and not failing before I changed the testing mechanism, so I
decided to comment out the test and investigate later on. I am
re-enabling the test because it is legitimately failing. I'm not
sure what is going on: was it not running before? How could it
not have been failing? The functions it is testing have not
changed throughout this process, so I am confused. Maybe we all
had *.pyc files left that were not updated, though that seems
unlikely.

* [r3091] topo/patterns/basic.py:
Added commented-out new version of CompositePatternGenerator.
Corrected import statements (including for when new
CompositePatternGenerator is uncommented.

2006-04-08 ceball

* [r3090] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3089] examples/tiny.ty,
topo/learningfns/__init__.py,
topo/learningfns/basic.py:
Sorted LearningFns into basic and projfns.

* [r3088] topo/learningfns/projfns.py:
Initial version.

* [r3087] topo/base/connectionfield.py:
Removed HACKALERT.

* [r3086] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/homeostatic.ty,
examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/lissom_or_sf.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
examples/tiny.ty,
topo/base/connectionfield.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/learningfns/__init__.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/learningfns/som.py,
topo/outputfns/__init__.py,
topo/outputfns/basic.py,
topo/outputfns/optimized.py,
topo/outputfns/projfns.py,
topo/patterns/image.py,
topo/projections/basic.py,
topo/responsefns/__init__.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/sheets/lissom.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/testplotgroup.py:
Attempting to organize functions that iterate over the CFs of a
CFProjection and those that act on a single array.

(As part of the more general idea that there are e.g. output
functions
which apply to a Projection.)

For output functions, we have the single-array (normal
mathematical) output
functions, e.g.:
OutputFn
Identity
DivisiveSumNormalize
We also have the functions that iterate through a CFProjection's
CFs,
applying an OutputFn to each:
CFProjectionOuputFn
CFProjectionIdentityOutputFn(single_cf_fn=Identity())
CFProjectionDivisiveSumNormalize(single_cf_fn=DivisiveSumNormalize())

OutputFns are in topo.outputfns.basic, and CFProjectionOutputFns
are
in topo.outputfns.projfns. Other Projection-level output
functions
would also go in the projfns module.

The same applies to LearningFns and
CFProjectionLearningFns. ResponseFunctions have been renamed
CFProjectionResponseFunctions where they apply to a CFProjection.
The
reorganization of LearningFns and ResponseFns is not complete
yet.

Along with this reorganization, CFProjectionOutputFnParameter (as
distinct from OutputFnParameter) has been introduced (and
similarly
for LearningFns). Implementation of these is not complete yet;
notably
the __init__.py files in the outputfns, learningfns, and
responsefns
packages need to be cleaned up.

In addition to this, minor cleanups may also have occurred,
including:
skipping calls to __init__() methods if all they do is call the
superclass' __init__()s; documentation strings.

* [r3085] topo/base/parameterclasses.py:
Updated documentation for ClassSelectorParameter.

* [r3084] topo/base/connectionfield.py:
Added CFOutputFunctionParameter class; made weights_output_fn be
a CFOutputFunctionParameter.

* [r3083] topo/base/connectionfield.py:
GenericCFOF: removed __init__() method, since it does nothing but
call the superclass'. Made single_cf_fn parameter be an
OutputFunctionParameter.

* [r3082] topo/base/projection.py:
Minor clean-up of comments.

* [r3081] topo/base/connectionfield.py:
CFOutputFunction is abstract.

* [r3080] topo/outputfns/optimized.py:
Updated docstring.

* [r3079] topo/outputfns/projfns.py:
Initial version.

* [r3078] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3077] topo/misc/utils.py:
No visible change, altered syntax.

* [r3076] topo/commands/basic.py,
topo/misc/utils.py:
Minor changes to pickling - should be no visible change.

* [r3075] topo/tests/__init__.py:
Allowed a test to be ignored easily. Removed testsnapshots from
the automatic tests.

* [r3074] topo/tests/testsnapshots.py:
Initial version.

* [r3073] topo/tests/__init__.py:
Added ability to run a specific list of test modules.

* [r3072] topo/commands/basic.py:
Updated docstrings for save_ and load_snapshot

* [r3071] topo/commands/basic.py:
When being pickled, the simulator has its RELEASE attribute set
to topo.release.

* [r3070]
topo/tests/testtemplateplotgrouppanel.py:
Added missing import statement.

* [r3069] topo/tests/tkgui:
Removing directory.

* [r3068] topo/tests/__init__.py:
Updated doc string, added ALERT about structure of tests/
directory that we might consider in the future.

* [r3067] topo/tests/__init__.py,
topo/tests/testmatplotlibtk.py,
topo/tests/testplotgrouppanel.py,
topo/tests/testpropertiesframe.py,
topo/tests/testtemplateplotgrouppanel.py,
topo/tests/testtopoconsole.py,
topo/tests/tkgui/__init__.py,
topo/tests/tkgui/testmatplotlibtk.py,
topo/tests/tkgui/testplotgrouppanel.py,
topo/tests/tkgui/testpropertiesframe.py,
topo/tests/tkgui/testtemplateplotgrouppanel.py,
topo/tests/tkgui/testtopoconsole.py:
Moved tkgui tests into main test directory.

* [r3066] topo/tests/testcfsom.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py:
Reduced sheet densities.

* [r3065]
topo/tests/tkgui/testplotgrouppanel.py:
Spelt 'density' correctly this time.

* [r3064]
topo/tests/tkgui/testplotgrouppanel.py:
Reduced sheet densities to speed up tests.

* [r3063] topo/analysis/featuremap.py,
topo/commands/analysis.py:
Removed calls to active_sim() and some passing round of
simulators.

* [r3062] topo/analysis/featuremap.py:
Removed a HACKALERT and the corresponding call to active_sim().

* [r3061] topo/tests/testfeaturemap.py:
Reduced density of sheets in test_measurefeaturemap(). It runs a
lot faster now.

2006-04-07 julienciroux

* [r3060] topo/tkgui/cfsheetplotpanel.py:
Deleted cfsheetplotpanel.py: the code is now in both
connectionfield and projection panels.

* [r3059] topo/tkgui/projectionpanel.py:
Added the code of cfsheetplotpanel in projectionpanel and made it
inherit from TemplatePlotGroupPanel instead

* [r3058] topo/tkgui/templateplotgrouppanel.py:
Modified the __init__ method: call refresh only if it is an
instance of TemplatePlotGroupPanel. Allow calling the constructor
for subclasses.

* [r3057] topo/tkgui/connectionfieldspanel.py:
Added the code of cfsheetplotpanel in connectionfieldpanel and
made it inherit from TemplatePlotGroupPanel instead

2006-04-07 ceball

* [r3056] doc/Future_Work/current_text.php:
Updated my tasks.

* [r3055] topo/patterns/image.py:
Removed TopoImage, which I forgot to do on the previous commit.

* [r3054] topo/patterns/image.py:
Removed the TopoImage class and a related HACKALERT. Images are
now loaded only once, rather than every time Image's function()
is called.

2006-04-07 julienciroux

* [r3053] topo/tkgui/cfsheetplotpanel.py:
temporary hack to get the normalize button set properly for a
connectionfieldspanel and a projectionpanel. It will be properly
sorted when getting rid of CFSheetPlotPanel and correcting the
hierarchy of the panels.

2006-04-07 ceball

* [r3052] topo/patterns/image.py:
Added HACKALERT.

* [r3051] topo/patterns/basic.py,
topo/patterns/image.py:
Corrected mistake in PatternSampler where background value was
being calculated before array was normalized.

2006-04-07 julienciroux

* [r3050] topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Renamed _set_initial_master_zoom to _set_eight_of_tallest_plot.

* [r3049] topo/tkgui/projectionpanel.py:
Corrected self.zoom_factor to be self.height_of_tallest_plot and
INITIAL_PLOT_WIDTH to INITIAL_PLOT_HEIGHT. Added a
re-implementation of the _set_initial_naster_zoom for the
projectionpanel (that needs more work).

2006-04-07 ceball

* [r3048] topo/patterns/basic.py,
topo/patterns/image.py:
Moved PatternSampler class from topo/patterns/image.py to
topo/patterns/basic.py in anticipation of using it for Composite.
This might not be the correct final location for PatternSampler.

* [r3047] topo/patterns/image.py:
Created a new class, PatternSampler, which does the sampling of a
pattern that TopoImage did previously. TopoImage is now a
subclass of PatternSampler.

2006-04-07 julienciroux

* [r3046] topo/tkgui/cfsheetplotpanel.py:
Corrected error in cfsheetplotpanel (forgot to change the name of
self.zoom_factor to self.height_of_tallest_plot and
self.min_zoom_factor to self.min_master_zoom); that should fix
the connectionfieldpanel.

* [r3045] topo/tkgui/plotgrouppanel.py:
Replaced self.master_zoom by self.height_of_tallest_plot.

2006-04-07 ceball

* [r3044] topo/tests/__init__.py,
topo/tests/tkgui/__init__.py:
Any file named test*.py that defines the 'suite' attribute will
be included when the tests are run.

* [r3043] topo/tests/testsheet.py:
Commented out a test which is out of date. Will be updated when
sheet.py and connectionfield.py are reviewed.

2006-04-06 julienciroux

* [r3042] topo/tkgui/plotgrouppanel.py:
simplified the function _set_initial_plot_zoom; now there is only
one master_zoom. Deleted the function _compute_max_height.

* [r3041] topo/tkgui/plotgrouppanel.py:
Corrected the function scale image; renamed self.min_zoom_factor
to self.min_master_zoom.

2006-04-06 ceball

* [r3040] /trunk/topographica, .cvsignore:
Added 'topographica.bat' (which exists after installation on
Windows).

* [r3039] topo/tests/testimage.py:
Added more tests.

2006-04-06 julienciroux

* [r3038] topo/tkgui/plotgrouppanel.py:
Implement a master_zoom for both sheet coordinates and matrix
coordinates.

2006-04-06 ceball

* [r3037] topo/patterns/image.py:
User-specified numbers involved in divisions are first turned to
floats in case integer
values are specified.

* [r3036] topo/tests/testimage.py:
Altered HACKALERT.

2006-04-05 ceball

* [r3035] topo/tests/__init__.py:
testimage.py added to the list of tests. Currently one test is
failing, because of a mistake in image.py version 1.40; this will
be corrected in the next version of image.py.

* [r3034] topo/tests/testimage.py:
Continued writing.

* [r3033] topo/patterns/basic.py:
Removed an out-of-date HACKALERT.

* [r3032] topo/patterns/basic.py:
Altered a HACKALERT.

* [r3031] topo/patterns/image.py:
Size scaling of each of the image dimensions is done relative to
the default retinal dimension of 1.0, rather than the current
sheet's dimension.

* [r3030] topo/patterns/image.py:
Corrected typo in documentation.

* [r3029] topo/patterns/image.py:
Changed previous output_fn to 'whole_image_output_fn (needs a
better name), so that there can also be an output_fn to apply to
the section of image that is actually displayed (i.e. the meaning
of output_fn for other PatternGenerators).

* [r3028] topo/patterns/random.py:
Added output_fn to PatternGenerators in random.py. Switched order
of import statements.

* [r3027] topo/base/patterngenerator.py:
Added output_fn to Constant.

* [r3026] topo/base/patterngenerator.py:
PatternGenerators have an OutputFunctionParameter.

* [r3025] topo/base/projection.py:
OutputFunction is an abstract class.

* [r3024] topo/base/patterngenerator.py:
Corrected test for whether or not an argument supplied to
__call__() is a Parameter. Added commented-out code for an
output_fn on PatternGenerator (so this change is separate from
the first one).

* [r3023] topo/base/patterngenerator.py:
Updated some documentation.

* [r3022] topo/base/patterngenerator.py:
Added a warning to __call__() of PatternGenerator if a value is
passed for something that does not exist as a Parameter.

* [r3021] topo/base/patterngenerator.py:
No visible change, just switched order of import statements.

* [r3020] topo/base/patterngenerator.py:
Allowed to specifiy scale and offset when calling
PatternGenerator (altered ConstantGenerator in the same way).

* [r3019] topo/tests/testimage.pgm:
Changed to have one even dimension and one odd dimension.

* [r3018] topo/patterns/image.py:
Simplified the TopoImage class by using a Sheet as the container
for an image. That way, coordinate transforms can work using the
standard sheet.py functions. Also, altered how the initial image
scaling works (it remains to make the initial
scaling relative to the default 1.0 retinal area, rather than the
current retina).

* [r3017] topo/base/sheet.py:
Added a version of sheet2matrixidx() that works for arrays. (All
these functions still
have to be cleaned up into the Slice class.)

* [r3016] topo/base/boundingregion.py:
Added contains_exclusive(), which is the same as contains()
except the right and bottom boundaries of the BoundingBox are
considered exclusive.

2006-04-05 jbednar

* [r3015] ChangeLog.txt:
Updated with recent changes

* [r3014]
topo/tests/tkgui/testplotgrouppanel.py:
Fixed broken test uncovered by better error messages

2006-04-05 ceball

* [r3013] topo/base/projection.py:
Added 'sum' argument to Identity.

* [r3012] topo/tests/testimage.py,
topo/tests/utils.py:
Initial version.

* [r3011] topo/tests/testimage.pgm:
An image to use for testing the image generator in image.py.

2006-03-29 julienciroux

* [r3010] topo/tkgui/plotgrouppanel.py:
Started to re-write scale_images: got rid of the arbitrary factor
10 in the case of sheet coordinate scaling; now the largest
bitmap is scaled to INITIAL_PLOT_HEIGHT in any cases. It remains
to implement a master zoom for each case.

* [r3009] topo/plotting/plotgroup.py,
topo/tkgui/connectionfieldspanel.py:
Corrected label display for connection field panel accordingly to
the new changes in the UnitView plot_src_name attribute.

* [r3008] topo/base/sheetview.py:
Made the plot_src_name attribute beeing set to the src sheet name
for a UnitView as well, (it is a necessary step in order to
implement the sheet coordinates button for the connection field
panel).

2006-03-29 ceball

* [r3007] topo/projections/basic.py:
Removed a line (unused) that I left in by accident one time.

2006-03-29 jbednar

* [r3006] topo/tkgui/plotgrouppanel.py:
Made Integer scaling button refresh automatically

* [r3005] topo/plotting/plotgroup.py:
Fixed typo in comment

2006-03-28 julienciroux

* [r3004] topo/tkgui/plotgrouppanel.py:
Corrected mistake in toogle_normalize (without a call to
scale_images, the Plot are not regenerated.)

* [r3003] topo/tkgui/templateplotgrouppanel.py:
Set the attribute normalize according to the value for the
template (for a TemplatePlotGroupPanel).

* [r3002] topo/tkgui/testpattern.py:
Corrected Plot creation in the TestPattern, according to the new
changes in Plot.

* [r3001] topo/plotting/plot.py,
topo/plotting/plotgroup.py:
Got rid of the situate argument for plot: now it is all
determined by the plot_bounding_box.

* [r3000] topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/tests/testplot.py:
Changed Plot: now that UnitViews shared the same bounds as the
SheetViews, there is no need to slice anymore when combining
SheetViews with UnitViews. Now, a plot_bounding_box is specified,
in which the plot is drawn, or the bounds of the Sheet are taken
if no plot_bounding_box are specified. There is still some
problems for some plot_bounding_box and density values
combinations that will have to be adressed, but no current used
feature is broken.

* [r2999] topo/base/connectionfield.py:
Made UnitView bounds the same as the source Sheet bounds of the
connectionfield; therefore, all SheetViews from a Sheet have the
same bounds.

2006-03-27 jbednar

* [r2998] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py:
Changed PlotGroupPanel to keep track of the plot_time of the
current plot, which may differ from the current simulator time;
this makes the back and forward buttons work with all
PlotGroupPanels. Cleaned up implementation of back and forward in
general.

* [r2997] examples/tiny.ty:
Made it more obvious that the learning_rate is a float

2006-03-27 judelaw

* [r2996] topo/tkgui/plotgrouppanel.py:
Added back and forward buttons - only really currently working
well for activity window

2006-03-27 jbednar

* [r2995] topo/base/connectionfield.py:
Fixed bug -- if users specified the learning rate as an integer,
it was being truncated to an even multiple of the size of the CF,
with surprising results. Now effectively promotes the rate to a
float.

2006-03-27 ceball

* [r2994] topo/base/projection.py:
Removed print statements accidentally left in the previous
version.

* [r2993] topo/base/projection.py:
Altered wording of an error message.

* [r2992] topo/base/projection.py:
Updated documentation for present_input(). Also renamed uses of
the 'dest_port' variable name to just 'port' within the
ProjectionSheet code; before it was confusing. The Projection has
the dest_port and src_port concept (referring to src and dest
EPs), but for a ProjectionSheet should it be more like 'in_port'
and 'out_port'?

2006-03-27 jbednar

* [r2991] topo/tkgui/topoconsole.py:
Added ALERT

* [r2990] topo/tkgui/topoconsole.py:
Improved error message and removed stray unused code

2006-03-27 ceball

* [r2989] topo/base/projection.py:
Removed an outdated HACKALERT.

* [r2988] topo/base/projection.py:
ProjectionSheet raises a TypeError if an attempt is made to
connect anything other than a Projection.

2006-03-27 julienciroux

* [r2987] topo/tkgui/taggedslider.py:
Corrected error in previous commit.

2006-03-27 jbednar

* [r2986] topo/tkgui/topoconsole.py:
Better error message; added ALERT

* [r2985] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py:
Added better checks for whether various plots will be successful
for the current simulation

* [r2984] doc/Future_Work/index_text.php:
More work

2006-03-27 ceball

* [r2983] doc/Future_Work/current_text.php:
Updated my tasks

2006-03-27 chrispalmer

* [r2982] examples/lissom_or_sf.ty:
initial spatial frequency work

2006-03-27 ceball

* [r2981] topo/tests/lissom_oo_or_reference.ty:
Set V1 afferents to normalize together. Set afferent connection
strengths to have
strength 1.

* [r2980] topo/base/connectionfield.py:
Added delattr for _sum attribute. Altered commented-out code.

2006-03-25 jbednar

* [r2979] doc/Tutorials/lissom_oo_or_text.php,
doc/Tutorials/lissom_or_text.php:
Updated estimates of training times based on an actual run!

* [r2978] examples/Makefile:
Changed to put .typ files in this directory

2006-03-23 jbednar

* [r2977] topo/tkgui/plotgrouppanel.py:
Intermediate checkin; still messy. Added integer scaling option,
and sketched eventual cleaned up code for resizing. Turned off
sheetcoords by default so that ConnectionField would work

* [r2976]
topo/commands/or_key_white_vert_small.png,
topo/plotting/templates.py:
Changed default size of OR key to be a smaller image

* [r2975] topo/tkgui/templateplotgrouppanel.py:
Turned off sheetcoords by default so that ConnectionField would
work

2006-03-23 julienciroux

* [r2974] topo/plotting/templates.py:
Corrected mistype.

* [r2973] topo/plotting/plot.py:
Corrected the doc.

* [r2972] topo/tkgui/plotgrouppanel.py:
Started an implementation of the scrollbar that is commented out.
Deleted unused import statement. Cleaned up doc and comments.
Corrected the use of **config by the use of **param in the
__init__ method.

2006-03-23 jbednar

* [r2971] topo/tkgui/plotgrouppanel.py:
Added alert

* [r2970] topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py:
Changed actualsize to sheetcoords for clarity; made on by default

* [r2969] topo/tkgui/topoconsole.py:
Renamed Learning iterations to indicate that it's not necessarily
learning anything and it's not in terms of iterations (!).
Cleaned up time remaining text.

2006-03-22 chrispalmer

* [r2968] topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py:
Added actualsize button; name not yet decided

* [r2967] topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py:
Added the simulator name to window titles to help users keep
multiple simulations straight

2006-03-22 julienciroux

* [r2966] topo/tkgui/plotgrouppanel.py:
Deleted unused attribute self.plots in PlotGroupPanel.Added doc
and comment.

2006-03-22 chrispalmer

* [r2965] topo/tkgui/topoconsole.py:
Added estimate of time remaining

2006-03-22 julienciroux

* [r2964] topo/tkgui/plotgrouppanel.py,
topo/tkgui/testpattern.py:
Changed the argument pgt_name to name for a PlotGroupPanel. There
is no references to template in the PlotGroup class.

* [r2963] topo/tkgui/plotgrouppanel.py,
topo/tkgui/testpattern.py:
Cleaned up reference to a template from PlotGroupPanel. At the
same time, enabled the normalize button for the testpattern. It
recquired to re-implement the toggle_normalize in the
testpattern, but it is only a temporary solution while
re-organizing the panel hierarchy.

2006-03-22 jbednar

* [r2962] topo/base/simulator.py:
Fixed bug in recent checking; scheduled events were failing due
to lack of a src or dest for which to print information

* [r2961] Makefile,
doc/Makefile:
Cleaned up dist package generation

2006-03-22 julienciroux

* [r2960] topo/base/projection.py,
topo/plotting/plotgroup.py,
topo/tests/testcfsom.py:
Deleted the get_in_projection_by_name in ProjectionSheet.
Replaced by using the projections() method now that we ensure a
unique name for projections to the same ProjectionSheet.

* [r2959] topo/plotting/plotgroup.py:
Replaced the use of get_in_projection_by_name() by the use of
projections(). Now that the problem of having a unique name is
solved, we do not need to return a list of projections for a
given name. Deeleted correponding Aletrt. Cleaned up the doc.

2006-03-22 jbednar

* [r2958] Makefile:
More files to clean up for distribution

* [r2957] doc/Future_Work/current_text.php:
Removed completed item

* [r2956] doc/Downloads/win32_text.php:
Added note

* [r2955] Makefile:
First pass at creating dist archive

2006-03-21 julienciroux

* [r2954] topo/misc/commandline.py,
topo/tkgui/taggedslider.py:
Removed global constants Pi and PI. The only syntax is now pi.

* [r2953] topo/misc/commandline.py:
Removed unnecessary exec statements.

* [r2952] topo/misc/commandline.py:
Removed unnecessary in __main__.__dict__ statements.

2006-03-20 julienciroux

* [r2951] topo/misc/commandline.py:
Removed the start function and moved the corresponding code
within process_argv.

2006-03-18 ceball

* [r2950] topo/outputfns/optimized.py:
Corrected DivisiveSumNormalize's test of the current_norm_value.

* [r2949] topo/outputfns/basic.py:
Corrected DivisiveSumNormalize's test of the current_norm_value.

* [r2948] /trunk/topographica, .cvsignore:
Added python_topo directory (which exists on Windows).

* [r2947] topo/plotting/plotfilesaver.py:
Started changing to get simulator from topo.sim.

2006-03-18 ceball_cvs2svn

* [r2946] /tags/CNV_COURSE:
This commit was manufactured by cvs2svn to create tag
'CNV_COURSE'.

2006-03-18 jbednar

* [r2945] topo/tkgui/plotgrouppanel.py:
Hopefully fixed longstanding issues about minimum and initial
plot widths. Plots should now default properly to around 150
pixels wide, or larger if the Sheet has more pixels than that.
The Reduce button will now allow plots to be reduced down to one
pixel per unit, but no further (at the moment)

2006-03-18 ceball

* [r2944] topo/plotting/plotgroup.py,
topo/tkgui/cfsheetplotpanel.py,
topo/tkgui/connectionfieldspanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/templateplotgrouppanel.py:
Started changing to get simulator from topo.sim.

2006-03-18 jbednar

* [r2943] examples/tiny.ty:
Added explanatory note

2006-03-18 ceball

* [r2942] topo/tkgui/connectionfieldspanel.py:
Removed outdated alert.

* [r2941] topo/base/simulator.py:
Altered a comment - no visible change.

* [r2940] topo/base/connectionfield.py:
Altered commented-out code: no visible change.

2006-03-18 jbednar

* [r2939] examples/tiny.ty,
topo/outputfns/basic.py:
Added abs()-using DivisiveL1Normalize

* [r2938] examples/tiny.ty:
Added more example parameters

* [r2937] examples/tiny.ty:
Initial version

* [r2936] topo/learningfns/som.py:
Moved from basic.py

* [r2935] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/learningfns/basic.py,
topo/sheets/cfsom.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py:
Moved SOM learning functions to topo/learningfns/som

* [r2934] topo/base/connectionfield.py:
Added LearningFunction abstract class to establish a family of
objects for use with GenericCFLF

* [r2933] topo/responsefns/basic.py,
topo/responsefns/optimized.py:
Fixed docstrings

* [r2932] topo/outputfns/basic.py:
Added alert

* [r2931] topo/outputfns/basic.py:
Added alert. Removed redundant constructors

* [r2930] topo/base/simulator.py:
Added debugging messages

* [r2929] topo/base/connectionfield.py:
Added alert

* [r2928] topo/learningfns/optimized.py,
topo/projections/optimized.py,
topo/responsefns/optimized.py,
topo/sheets/lissom.py:
Removed out-of-date LISSOM_CPointer, CFDotProduct_CPointer,
CFProjection_CPointer, and DivisiveHebbian_CPointer; may
eventually be resurrected

2006-03-17 jbednar

* [r2927] examples/cfsom_or.ty:
Cleaned up and simplified

* [r2926] examples/cfsom_or.ty:
Changed to Chris's new topo.sim format

* [r2925] examples/hierarchical.ty:
Fixed typo

* [r2924] examples/hierarchical.ty:
Sorted imports

2006-03-17 ceball

* [r2923] doc/Future_Work/current_text.php:
Updates to my tasks.

* [r2922] examples/hierarchical.ty:
Set the simulator name.

* [r2921] topo/base/simulator.py:
Corrected an error in SimSingleton's __setattribute__() method.

* [r2920] topo/base/simulator.py:
Removed a HACKALERT from SimSingleton.

* [r2919] topo/base/simulator.py:
Corrected logic error in SimSingleton.init() that was creating
two Simulators (though it left only one behind).

2006-03-17 jbednar

* [r2918] examples/main.ppm,
topo/tests/testcfsom.py:
Removed unnecessary image

2006-03-17 ceball

* [r2917] topo/base/simulator.py:
Cleaned up code for dictionary-style access to simulator objects.
Doing topo.sim['V1']=EP where EP already exists in the simulator
results in a warning and the object not being added. Doing
topo.sim['V1']=EP2 where topo.sim['V1'] already exists results in
the EP already in topo.sim['V1'] being overwritten with EP2 (as
for dictionaries). Simulator's _event_processors is now a dict
rather than a list to make things simpler.

2006-03-17 jbednar

* [r2916] doc/User_Manual/time_text.php:
Fixed image sizes

2006-03-17 ceball

* [r2915] examples/hierarchical.ty:
Changed to use newer simulator syntax: topo.sim['V1'], etc.

* [r2914] topo/base/simulator.py:
SimSingleton uses the simulator's repr and str methods.

2006-03-17 jbednar

* [r2913]
doc/Developer_Manual/optimization_text.php:
Edited Chris's text slightly

2006-03-17 ceball

* [r2912] doc/Future_Work/current_text.php:
Updated my tasks.

* [r2911] examples/som_retinotopy.ty:
Reduced SOM radius slightly (and random seeds are different).

* [r2910] doc/Developer_Manual/index_text.php,
doc/Developer_Manual/optimization_text.php:
Added some information about how we provide optimized components.
It's commented out for the moment so JAB can review it.

2006-03-16 ceball

* [r2909] examples/som_retinotopy.ty,
topo/responsefns/basic.py,
topo/responsefns/optimized.py:
CFEuclideanDistance is the basic Python version,
CFEuclideanDistance_opt1 is the optimized C version.

* [r2908] examples/som_retinotopy.ty:
Removed unused line of imports.

* [r2907] topo/base/connectionfield.py:
No visible change. Changed commented-out code so it's simpler
(still behaves the
same).

* [r2906] topo/base/connectionfield.py:
Changed sum property's documentation. Apart from that, no visible
change - altered commented-out code.

2006-03-15 ceball

* [r2905] topo/tests/lissom_oo_or_reference.ty:
Update after recent class changes.

* [r2904] topo/base/connectionfield.py:
Removed duplicate import statement.

* [r2903] topo/base/connectionfield.py:
Removed optimization from GenericCFOF.

* [r2902] topo/learningfns/basic.py:
Removed unused references to output_fn.

* [r2901] topo/outputfns/optimized.py:
DivisiveSumNormalizeCFOF sets the cfs' sum attribute after
normalizing. (Currently has no visible effect.)

* [r2900] topo/learningfns/optimized.py,
topo/outputfns/optimized.py:
Modified documentation.

* [r2899] examples/lissom_oo_or.ty:
Reverted names of projections - changes which I accidentally left
in.

* [r2898] examples/laminar.ty,
examples/lissom_oo_or.ty:
Uses DivisiveSumNormalizeCFOF_opt1 instead of GenericCFOF with
single_cf_fn=DivisiveSumNormalize_opt1.

* [r2897] topo/projections/basic.py:
Corrected location of single_cf_fn for weight initialization.

* [r2896] topo/base/connectionfield.py:
Removed output_fn Parameter accidentally left behind in
CFLearningFunction.

* [r2895] examples/lissom_or.ty:
Uses DivisiveSumNormalizeCFOF_opt1 instead of GenericCFOF with
single_cf_fn=DivisiveSumNormalize_opt1.

* [r2894] topo/outputfns/optimized.py:
Corrected mistake in non-optimized wrapper for
DivisiveSumNormalizeCFOF.

* [r2893] topo/responsefns/basic.py:
Corrected call to super(), must have been missed from a previous
set of commits.

* [r2892] topo/outputfns/optimized.py:
Corrected typo (in the code).

* [r2891] topo/outputfns/optimized.py:
Uncommented code for DivisiveSumNormalizeCFOF and added
non-optimized fallback to
GenericCFOF(single_cf_fn=DivisiveSumNormalize).

* [r2890] topo/tkgui/topoconsole.py:
Added return statement so all the possible locations aren't
opened in open_location().

* [r2889] topo/tkgui/topoconsole.py:
Windows users are unlikely to have the locally built
documentation. Therefore, locations on the web are tried if the
local copies fail. Also, fixed 'about' text,
since the ABOUT_TEXT variable in topo/__init__ had been moved
into a function.

* [r2888] topo/__init__.py:
'About' text can be returned or printed. Default is to print, as
before.

2006-03-14 ceball

* [r2887] doc/Future_Work/current_text.php:
Update to a task.

* [r2886] topo/base/connectionfield.py:
learn() split tp learn() and apply_output_fn(). No visible
change. Also committed commented-out code in CFSheet's learn().

* [r2885] topo/misc/inlinec.py:
Reverted to previous version (mistakenly committed).

* [r2884] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/misc/inlinec.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/tests/testplotgroup.py:
Changed response_fns.optimized.CFDotProduct to CFDotProduct_opt1.
If inline-optimized components aren't available, falls back to
basic's CFDotProduct.

* [r2883] examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
topo/learningfns/optimized.py:
Changed learningfns.optimized.Hebbian to Hebbian_opt1. If
inline-optimized components aren't available, falls back to
Hebbian.

* [r2882] topo/base/projection.py:
Added 'norm_value' Parameter to OutputFunction(). This is a hack
while ConnectionField assumes all OutputFunctions have a
norm_value.

* [r2881] examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
topo/outputfns/optimized.py,
topo/tests/testoutputfnsoptimized.py:
Changed ouputfns.optimized.DivisiveSumNormalize to
DivisiveSumNormalize_opt1. If inline-optimized components aren't
available, falls back to DivisiveSumNormalize.

* [r2880] examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty:
Removed cache_sum attribute from CFProjection.

* [r2879] topo/learningfns/optimized.py:
Hebbian sets cf._sum, allowing the sum of the weights to be
cached without using the slower Python property.

* [r2878] topo/base/connectionfield.py:
Removed cache_sum; if _sum attribute exists, it is assumed that
the value is always current.

* [r2877] examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/projections/basic.py:
Split output_fns from learning_fns. Introduced CFOuputFunction
class to apply the output_fn to all CFs. Some ways things have
been done are a little confusing and could be simplified (notably
caching the sum of a CF's weights), but at the moment the example
networks should all behave the same.

* [r2876] topo/outputfns/optimized.py:
Committed some commented-out classes (the CF output function
doesn't belong here).

* [r2875] examples/homeostatic.ty:
Removed apparently unused code.

2006-03-13 ceball

* [r2874] topo/tests/__init__.py:
Test of optimized output functions runs automatically.

* [r2873] topo/outputfns/optimized.py:
Added return statements to match other output functions.

* [r2872] topo/outputfns/optimized.py:
Corrected DivisiveSumNormalize for when the desired norm_value is
not 1.

2006-03-12 ceball

* [r2871] topo/outputfns/basic.py:
Changed DivisiveSumNormalize so that it can accept a
pre-calculated norm_value for the array, if one is known. If the
pre-calculated value is equal to the current value, no
normalization operation need occur.

2006-03-11 ceball

* [r2870] topo/outputfns/optimized.py:
Initial version. DivisiveSumNormalize intended to be equivalent
but faster version of that in outputfns/basic.py

* [r2869] topo/learningfns/optimized.py:
The previous commit was a mistake (it was supposed to be
outputfns/optimized that I committed, not learningfns/optimized).
This is the code from version 1.39.

* [r2868] topo/learningfns/optimized.py,
topo/tests/testoutputfnsoptimized.py:
Initial version. DivisiveSumNormalize intended to be equivalent
but faster version of that in outputfns/basic.py

2006-03-10 ceball

* [r2867] topo/learningfns/optimized.py:
DivisiveHebbian's normalization happens every time, whether or
not the output activity is zero.

* [r2866] topo/base/connectionfield.py:
Added sum of cf's initial weights.

2006-03-09 ceball

* [r2865] external/mswin/setup.bat,
external/mswin/setup.py:
Installation creates a desktop shortcut with the Topographica
icon.

* [r2864] external/mswin/create_shortcut.vbs:
Creates a desktop shortcut.

2006-03-08 ceball

* [r2863] external/mswin/setup.py:
Fixed typo.

* [r2862] external/mswin/setup.py:
Removed comment left in by accident.

* [r2861] topo/misc/commandline.py:
Filename arguments are enclosed in repr() so that bits of Windows
paths that look like control characters don't turn into control
characters. (Note: I don't know that the slashes around the
string were for originally.)

* [r2860] external/mswin/setup.py:
Batch file: changes to Topographica path before running, so that
the current path variable is correct.

* [r2859] topo/responsefns/optimized.py:
Changed syntax in CFDotProduct: no visible change.

* [r2858] topo/learningfns/optimized.py:
Moving to c++ syntax for clarity...no visible change.

* [r2857] topo/learningfns/optimized.py:
Moving to c++ syntax for clarity...no visible change.

* [r2856] topo/learningfns/optimized.py:
Moving to c++ syntax for clarity...no visible change.

* [r2855] topo/misc/inlinec.py:
Added verbose=0 to the inline() arguments. I'm not sure it
actually makes any difference. Developers can set it to 2 to see
more output for debugging; 0 should result in less garbage output
for users. See the weave documentation (but good luck finding
it...try old.scipy.org).

* [r2854] topo/misc/commandline.py:
Removed apparently redundant try/catch block (there is already
one in inlinec.py; in any case, if something other than an
ImportError occurs I think a user should see it).

* [r2853] topo/learningfns/optimized.py:
Cleanup in DivisiveHebbian - no visible change.

* [r2852] topo/learningfns/optimized.py:
Intermediate checkin: DivisiveHebbian has learning in one chunk
of C, and normalization in another. No visible change.

* [r2851] topo/learningfns/optimized.py:
Intermediate checkin: store sum of cf's weights in cf.sum, and
retrieve. No visible change.

* [r2850] topo/base/connectionfield.py:
Intermediate checkin: added sum attribute to connectionfield.

* [r2849] topo/learningfns/optimized.py:
Normalization factor is calculated as the sum of the weights each
time, rather than accumulating the differences and assuming they
summed to 1 in the previous iteration. This has a very small
effect; after 20000 iterations, the weights are different in
about the 6th decimal place, and a sum over the activity in V1
differs in about the fifth decimal place.

2006-03-07 ceball

* [r2848] topo/misc/commandline.py:
No visible change: minor change to import statement.

* [r2847] doc/Downloads/index_text.php:
Minor correction to text.

* [r2846] doc/Future_Work/current_text.php:
Updated with my current tasks.

* [r2845] doc/Downloads/index_text.php:
Changed Windows installation instructions.

* [r2844] setup.bat:
Just calls external\mswin\setup.bat

* [r2843] external/mswin/setup.bat,
external/mswin/setup.py:
Minor changes, plus associates '.ty' files with Topographica.

* [r2842] external/mswin/setup.bat:
Minor change - pauses at the end in case launched by double
clicking.

* [r2841] external/mswin/setup.py:
Now generates a script that looks more like the one on unix.
Fixed a problem with quotation marks.

* [r2840] topo/__init__.py:
Added 'release' attribute, which is set by the topographica
script. Moved ABOUT_TEXT into the about() function so that the
release value is filled in once it's been set, rather than
before.

* [r2839] Makefile:
Removed setting of TOPORELEASE environment variable, and replaced
it by setting topo.release.

* [r2838] Makefile:
Removed PYTHONPATH.

* [r2837] Makefile:
Removed TOPOGRAPHICAPATH.

2006-03-07 jbednar

* [r2836] external/mswin/setup.py:
Hopefully fixes the backslash problem for the generated
topographica.py script

2006-03-07 ceball

* [r2835] topo/learningfns/optimized.py,
topo/projections/optimized.py,
topo/responsefns/optimized.py,
topo/sheets/lissom.py:
Commented out cpointer code.

2006-03-06 ceball

* [r2834] external/mswin/setup.py:
Corrected another mistake.

* [r2833] external/mswin/setup.py:
Corrected an error with quotation marks.

* [r2832] external/mswin/setup.bat,
external/mswin/setup.py,
external/mswin/topographica.bat:
Various changes to the scripts.

* [r2831] Makefile,
topo/base/parameterclasses.py:
Filename parameter gets the path by going up a level from the
directory of the binary, which works on Windows and unix. There
might be a better way.

2006-03-06 jbednar

* [r2830] topo/tkgui/editorwindow.py:
Clarified what the snapshot is, to distinguish it from the
network snapshot

2006-03-06 ceball

* [r2829] external/mswin/python242_topo.tar.gz,
external/mswin/python242_topo_weave.tar.gz,
external/mswin/python_topo.tar.gz:
Removed previous versions of Python directories and added one
back. The new one has weave and the mingw c compiler, and is
configured to use this c compiler by default so it will work on
windows without any extra work.

* [r2828] external/mswin/setup.bat,
external/mswin/setup.py,
external/mswin/topographica.bat:
Updated to work with new python_topo.tar.gz

* [r2827] Makefile,
external/Makefile:
Instead of setting the LD_LIBRARY_PATH environment variable after
python has started, we hard-code the lib/ as the path when we
make the python binary.

2006-03-04 ceball

* [r2826] topo/base/parameterclasses.py:
Added a HACKALERT and corrected a typo in the code.

* [r2825]
external/mswin/python242_topo_weave.tar.gz:
Python with weave from scipy. Unfortunately includes other things
for the moment that take up space and could be removed.

* [r2824] external/mswin/setup.bat:
Added note on how to get weave.

* [r2823] topo/base/parameterclasses.py:
Removed a HACKALERT.

* [r2822] external/mswin/python242_topo.tar.gz:
Python 2.4.2 with Numeric, PIL, matplotlib, Pmw, Fixedpoint

* [r2821] external/mswin/topographica.bat:
Starts python with the topographica.py script. INitial version.

* [r2820] external/mswin/setup.py:
Creates topographica.py script. Initial version.

* [r2819] external/mswin/setup.bat:
Simple windows batch file to install ready-made python. Initial
version.

* [r2818] external/mswin,
external/mswin/util,
external/mswin/util/gunzip.exe,
external/mswin/util/tar.exe:
Utilities for extracting archives.

* [r2817] Makefile,
topo/base/parameterclasses.py:
Added TOPOGRAPHICAPATH to environment variables.

2006-03-03 ceball

* [r2816]
external/win32/Numeric-24.2.win32-py2.4.exe:
New version (added binary)

* [r2815]
external/win32/Numeric-24.2.win32-py2.4.exe:
Removed apparently-corrupt file. It wasn't added as binary and
isn;t the same size as the original.

* [r2814] doc/Future_Work/current_text.php:
Updated my tasks.

* [r2813] external/win32/python-2.4.2.msi:
Added as a binary file.

* [r2812] external/win32/python-2.4.2.msi:
Not in binary format. Two Windows machines I tried it on said it
is invalid; it worked on another.

* [r2811] external/win32/python-2.4.msi:
Removed Python 2.4 since it's not used any more (we have 2.4.2).

* [r2810] Makefile:
Topograpgica script: no longer uses os.getenv() - instead
accesses the os.environ dictionary itself.

* [r2809] Makefile:
For topographica script: ignore PYTHONPATH environment variable
and just use our own Python's path.

2006-03-03 jbednar

* [r2808] examples/lissom_or_20000.typ:
Removed saved .typ files, to speed up CVS downloads

* [r2807] examples/lissom_oo_or_20000.typ:
Removed saved .typ files, to speed up CVS downloads

* [r2806] doc/Tutorials/lissom_oo_or_text.php,
doc/Tutorials/lissom_or_text.php:
Changed tututorial instructions to ask users to build a map
rather than assuming it is in CVS

* [r2805] Makefile,
examples/Makefile:
Added code to generate saved example files

* [r2804] doc/Future_Work/index_text.php:
Added note about filenames as window titles

* [r2803] ChangeLog.txt:
Updated with recent changes

* [r2802] examples/Makefile:
Added one iteration of execution

* [r2801] Makefile:
Changed exec_argv to process_argv to match change in
commandline.py

* [r2800] Makefile:
Changed exec_argv to process_argv to match change in
commandline.py

* [r2799] topo/misc/commandline.py:
Cleaned up and simplified

* [r2798] Makefile:
Minor cleanup to topographica script

2006-03-02 ceball

* [r2797] Makefile:
Removed 'rm topographica' and put back '> topographica' instead
of '>> topographica' on first line. (I didn't realize there was a
difference...)

* [r2796] Makefile:
Removed TOPO variable from generated topographica script code.

* [r2795] Makefile:
Changed generated code for topographica script. (1) Environment
variables are set before any imports of Topographica things. (2)
Environment variables are not set with putenv() (see
http://www.python.org/doc/2.4.2/lib/os-procinfo.html). (3)
Removed extra slash in first line. (4) Sorted out ':' between
paths. (3) and (4) might be wrong and need to be checked.

* [r2794] topo/__init__.py:
No visible change - moved import statemtements to the top.

* [r2793] topo/misc/commandline.py:
If topographica is started with no scripts or commands to run, it
opens interactively (i.e. './topographica' is the same as
'./topographica -i').

* [r2792] topo/base/parameterclasses.py,
topo/plotting/templates.py:
Simplified Filename Parameter, so it has just one search list.

2006-03-02 jbednar

* [r2791] topo/base/patterngenerator.py:
Moved an alert here from learningfns/basic.py. (Chris)

* [r2790] topo/learningfns/basic.py:
Removed an irrelevant alert and moved another to
patterngenerator. (Chris)

* [r2789] topo/learningfns/basic.py:
Modified commented-out print statement to include simulation
time. (Chris)

* [r2788] Makefile:
Added control over test verbosity

* [r2787] topo/misc/commandline.py:
Fixed scripts to run in main (e.g. to get the value of pi
defined); not sure why the previous syntax was not signalling an
error

2006-03-02 ceball

* [r2786] runtests:
No longer required: tests can be run like this:\n./topographica
-c 'import topo.tests; topo.tests.run()'

* [r2785] Makefile:
Changed how tests are run (no longer uses runtests script).

* [r2784] topo/tests/__init__.py:
Added run() function to allow tests to be run like
this:\n./topographica -c 'import topo.tests; topo.tests.run()'

* [r2783] topo/base/parameterclasses.py:
Added HACKALERT: think about Parameter class attributes,
remembering they won't pickle because Parameter isn't a
TopoObject (in most cases that's likely to be fine, but some
class attributes are designed to be set by the user). Moved
Filename's topographica_path to be an instance attribute for the
moment, because trying to set it on unpickling wasn't possible
since it's read-only. This will be investigated at the same time
as the alert.

* [r2782] topo/tkgui/topoconsole.py:
Removed a line that should have been removed in the previous
version.

* [r2781] topo/base/simulator.py,
topo/tkgui/topoconsole.py:
Got rid of some uses of 'active_sim', and got rid of
'objects_to_notify_of_active_sim' concept, since the current
simulator is always in topo.sim.

2006-03-01 jbednar

* [r2780] topo/__init__.py:
Reduced amount imported

* [r2779] topo/learningfns/basic.py:
Moved aspect_ratio into the default Gaussian neighborhood,
because it's conceivable to use a non-unity aspect ratio

* [r2778] topo/commands/analysis.py:
Fixed bogus assumption that all projections will have a cfs
variable, and made it respect the measure_maps declaration. It
should now work with lissom_oo_or.ty, but it still needs work
because it doesn't seem to measure any useful map for a
SharedWeightProjection

* [r2777] topo/misc/commandline.py:
Clarified help message

* [r2776] runtests:
Added ALERT

* [r2775] topo/tkgui/editorwindow.py:
Added alert

2006-03-01 ceball

* [r2774] topo/tkgui/topoconsole.py:
Removed uses of get_active_sim().

* [r2773] topo/commands/basic.py:
Replaced get_active_sim() with topo.sim

* [r2772] topo/base/parameterclasses.py:
No visible change - changed a variable name.

* [r2771] topo/base/simulator.py,
topo/tests/tkgui/testtopoconsole.py:
Removed topo.base.simulator.set_active_sim().

* [r2770] topo/tkgui/editorwindow.py:
Just uses topo.sim to get the simulator.

* [r2769] examples/hierarchical.ty:
Added some temporary demonstration lines for how access to the
simulator might work.

* [r2768] topo/base/simulator.py:
Simulator supports dictionary-like assignment. Temporary method
connect2() added to work with this.

* [r2767] topo/tkgui/topoconsole.py:
On initialization, gets self.simulator from topo.sim. There is
always a simulator now. Some plotting menu options need to be
updated to check there are sheets of the right type to do
whatever it is they're supposed to do.

* [r2766] topo/__init__.py,
topo/base/simulator.py,
topo/commands/basic.py,
topo/tkgui/topoconsole.py:
Added SimSingleton class. Added variable topo.sim=SimSingleton(),
so there is simulator (empty) on startup. SimSingleton() keeps
one Simulator() object and allows almost-transparent access to
it, so topo.sim['V1'] etc is possible. Begun changing calls to
get_active_sim etc.

2006-03-01 jbednar

* [r2765] examples/homeostatic.ty:
Initial version for Veldri to work with

2006-02-28 ceball

* [r2764] runtests:
Commented out argument-processing to allow runtests (and 'make
all') to work.

* [r2763] examples/som_retinotopy.ty:
Uses indepedent streams for input pattern parameters.

* [r2762] topo/plotting/templates.py:
Made image_path be a parameter; a path can be 'put through' this
to ensure it's valid for the OS and that the correct locations
are searched.

* [r2761] topo/base/parameterclasses.py:
Filename searches prefixes specified for this particular
parameter first, then common ones.

* [r2760] topo/base/parameterclasses.py:
Filename can be declared with None as the path (i.e. no default
path). Changed path searching method, to allow relative and
absolute prefix paths.

* [r2759] topo/patterns/image.py:
Removed path left in by mistake, updated doc string.

* [r2758] topo/base/parameterclasses.py,
topo/patterns/image.py:
For relative paths, Filename now searches both the
Filename.common_search_paths list and any specific list of
search_paths an instance is given. Currently common_search_paths
includes sys.exec_prefix (Topographica base directory.

* [r2757] doc/Future_Work/current_text.php:
Updated with current work.

2006-02-28 julienciroux

* [r2756] Makefile,
topo/misc/commandline.py:
Changed the generate_params and generate_prefixes so that they
execute commands as they find them instead of creating a string.
They have been re-named exec_argv and exec_prefixes.

2006-02-28 ceball

* [r2755] examples/lissom_or.ty:
Uses RandomWrapper, so x, y, and orientation are independent
random streams, and resume where they left off on pickling.

* [r2754] topo/base/parameterclasses.py:
Added RandomWrapper, a modified version of Wrapper, that creates
a new Random() instance. Gives independent random streams, and
allows the state of the stream to be saved when pickling.

2006-02-28 julienciroux

* [r2753] Makefile,
topo/misc/commandline.py:
Modified the generate_params and generate_prefixes function in
commandline.py so that to work with the first copy of python,
instead of having to re-open a new one. Python options are now
directly set on the corresponding environment variable, and the
string of command is then executed with the exec command. There
is one problem for the verbose option: the variable PYTHONVERBOSE
is only read during startup, and cannot be re-set afterwards.
Therefore, the verbose option is currently disabled.

2006-02-28 jbednar

* [r2752] topo/misc/commandline.py:
Added alert

2006-02-27 julienciroux

* [r2751] topo/misc/commandline.py:
Replaced old topographica_script code by the new version that
uses Optparse.

* [r2750] topographica_script.py:
Deleted the topographica_script.py file; the code has been moved
to topo.misc.commandline.py.

* [r2749] Makefile:
Modified the Makefile to take into account that the code of
topographica_script has been moved to topo/misc/commandline.py;
also inserted the variable TOPO into the environment. People will
have to do a make after the update to get a version that works.

* [r2748] topo/misc/commandline.py:
Moved the topographica_script code to topo/misc/commandline.py.

* [r2747] topo/learningfns/basic.py:
Set the x and y to 0 when creating the Gaussian instead of when
calling it. That allows more flexibility for the user.

2006-02-27 ceball

* [r2746] topo/base/simulator.py:
Added more helpful error to __getattribute__(), for if a string
is not given.

* [r2745] topo/base/simulator.py:
Added dictionary-like object access for Simulator: for a
Simulator s, s['V1'] does s.objects()['V1'].

2006-02-27 jbednar

* [r2744] topo/base/simulator.py:
Fixed typo

* [r2743] topo/base/parameterizedobject.py:
Minor comment cleanup

* [r2742] doc/Future_Work,
doc/Future_Work/.cvsignore:
Added current page

2006-02-26 ceball

* [r2741] examples/hierarchical.ty:
Input pattern parameters set on objects, rather than the class. I
use two independent objects here, though for the moment they
aren't really independent because everything shares one stream of
random numbers.

* [r2740] doc/Future_Work/current_text.php:
Updated my tasks.

* [r2739] examples/laminar.ty,
examples/lissom_or.ty:
Input pattern parameters set on a Gaussian object rather than the
Gaussian class.

* [r2738] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/laminar.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/base/connectionfield.py,
topo/base/parameterclasses.py,
topo/patterns/basic.py:
Some things will not deepcopy, such as Numeric's ufuncs. Added a
Wrapper class (which will be renamed and will probably be changed
to operate differently) that allows these things to be
deepcopied. CompositePatternGenerator used a ufunc, so is changed
to use a Wrapper. Lambdas will also not deepcopy; Wrapper does
not support them, but does offer an alternative. Examples files
that used lambdas are changed accordingly.

* [r2737] topo/commands/basic.py:
save_snapshot and load_snapshot are changed to include pickling
of class attributes.

* [r2736] topo/misc/utils.py:
Added a function (which could be simplified) to search modules
and retrieve class' states.

* [r2735] topo/base/parameterizedobject.py:
ParameterizedObject has __getstate__() that only returns instance
data (before it also returned class data). Also, it deep copies
any instance attribute that is a Parameter. Parameter has support
for deepcopy and pickle with its own __getstate__ and
__setstate__ (required because Parameter uses __slots__, and does
not have a __dict__).

2006-02-25 jbednar

* [r2734] doc/Future_Work/index_text.php:
More to do

* [r2733] topo/tkgui/topoconsole.py:
Added indication of why the GUI is exiting

2006-02-24 ceball

* [r2732] topo/base/parameterizedobject.py:
No visible change: commented-out code for new __getstate__().

* [r2731] topo/commands/basic.py:
No visible change: new commented-out code for replacement
snapshot functions.

* [r2730] topo/misc/utils.py:
No visible change: new commented-out code for a recursive module
search. Might not belong here.

* [r2729] topo/base/parameterclasses.py:
No visible change: a commented-out Wrapper class.

* [r2728] topo/base/parameterizedobject.py:
No visible change: commented-out code for __getstate__() and
__setstate__() of Parameter.

* [r2727] doc/Future_Work/current_text.php:
Updated what I'm working on.

* [r2726] topo/__init__.py:
ABOUT text includes the Topographica release number.

2006-02-24 julienciroux

* [r2725] topo/plotting/templates.py:
Made normalize be a BooleanParameter, and corrected the templates
where it was passed in as a string. Cleaned up ALERTS.

* [r2724] topo/plotting/bitmap.py:
Cleaned up doc and ALERTS.

2006-02-24 ceball

* [r2723] topo/tkgui/topoconsole.py:
Updates to 'Help' menu options.

* [r2722] doc/Future_Work/current_text.php:
Added a task.

2006-02-23 julienciroux

* [r2721] examples/som_retinotopy.ty:
Corrected to the right density (which has been changed by mistake
in the previous commit.

* [r2720] topo/learningfns/basic.py:
Ensured that the neighborhood matrix is defined with x=0 and y=0.

* [r2719] examples/som_retinotopy.ty:
Corrected the som_retinotopy example such as not setting x,y and
orientation directly on the Gaussian class, but rather creating a
Gaussian object and assigning it to the GeneratorSheet.

2006-02-23 ceball

* [r2718] doc/Future_Work/current_text.php:
Added task, moved another to current work section.

* [r2717] topo/projections/basic.py:
Projection imported to projections/basic.py so that it's part of
the projections package.

* [r2716] topo/base/projection.py:
Projection is an abstract class.

* [r2715] doc/Future_Work/current_text.php:
Added a task, changed some others round.

2006-02-23 alan_lindsay

* [r2714] topo/tkgui/editorobjects.py:
Fixed a wee typo(Ta Chris).

2006-02-23 ceball

* [r2713] topo/base/parameterclasses.py,
topo/base/utils.py:
find_classes_in_package() returns the base class, but does not
return any abstract classes.

* [r2712] topo/base/sheet.py:
Sheet is declared to be an abstract class.

* [r2711] topo/base/sheet.py:
Continued to write Slice class. Added methods sheet2matrix() and
matrix2sheet() to Sheet. This is still a work in progress - there
won't be so many functions by the end.

* [r2710] topo/patterns/image.py:
Tidied up import statements.

2006-02-23 jbednar

* [r2709] topo/base/parameterizedobject.py:
Changed ParameterizedObject.__repr__ to use __repr__ for
attribute values also, to get closer to a valid Python expression

2006-02-23 ceball

* [r2708] doc/Future_Work/current_text.php:
Corrected html tag error.

* [r2707] doc/Future_Work/current_text.php:
Removed a task and added another to the doing next section.

* [r2706] topo/base/connectionfield.py,
topo/base/parameterclasses.py,
topo/base/patterngenerator.py,
topo/base/projection.py:
ClassSelectorParameter subclasses have packages attribute that
works properly.

* [r2705] topo/base/parameterclasses.py:
Corrected mistake introduced in the previous-but-one version.

* [r2704] topo/base/parameterclasses.py:
Minor updates

* [r2703] topo/base/connectionfield.py,
topo/base/parameterclasses.py,
topo/base/patterngenerator.py,
topo/base/projection.py:
ClassSelectorParameter and subclasses use __slots__.

* [r2702] topo/tkgui/editortools.py:
Removed duplicate import statement.

* [r2701] topo/base/parameterclasses.py:
Tidying ClassSelectorParameter; no visible change.

2006-02-23 jbednar

* [r2700] examples/Makefile:
Made default LISSOM test be oo_or instead of or to test more code

* [r2699] doc/Future_Work/current_text.php:
Cleaned up and reworded

2006-02-22 ceball

* [r2698] topo/base/parameterizedobject.py:
__repr__() returns almost-runnable expression.

* [r2697] doc/Future_Work/current_text.php:
Removed a task; moved another to currently-working-on section.

* [r2696] topo/base/sheet.py,
topo/base/simulator.py:
No longer overrides __repr__().

* [r2695] topo/base/parameterizedobject.py:
ParameterizedObject's __repr__() returns <classname name> and a
list of all Parameters. __str__() returns <classname name>.

* [r2694] topo/base/parameterclasses.py:
ClassSelectorParameter's suffix_to_lose defaults to empty string
rather than None (which it did before I accidentally changed it).

* [r2693] topo/base/parameterclasses.py,
topo/tkgui/testpattern.py:
ClassSelectorParameter doesn't list abstract_classes.

* [r2692] topo/patterns/random.py:
RandomGenerator declared to be an abstract class.

* [r2691] topo/tkgui/parametersframe.py:
Moved topo/base/utils.py to topo/misc/utils.py

* [r2690] topo/base/parameterizedobject.py,
topo/base/patterngenerator.py:
Classes now have an 'abstract' attribute which is True if the
class declares an _abstract_class_name equal to its name and
False otherwise (i.e. if it doesn't declare _abstract_class_name,
or it's set to False. Abstract classes can be instantiated.

2006-02-22 julienciroux

* [r2689] topo/base/parameterclasses.py:
Added the possibility to change the default value for instantiate
when creating a ClassSelectorParameter.

2006-02-22 ceball

* [r2688] topo/analysis/featuremap.py,
topo/base/utils.py,
topo/commands/pylabplots.py,
topo/misc/distribution.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/sheets/composer.py,
topo/sheets/generatorsheet.py,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testsheetview.py,
topo/tkgui/parametersframe.py:
Moved contents of topo/base/utils.py to topo/misc/utils.py

* [r2687] topo/misc/utils.py:
Moved topo/base/utils.py to topo/misc/utils.py.

2006-02-22 jbednar

* [r2686] examples/laminar.ty:
Made afferent learning match over the first few iterations. Fixed
bug in tsettle. Removed cortical edge buffers.

2006-02-22 ceball

* [r2685] topo/base/arrayutils.py,
topo/base/utils.py,
topo/outputfns/basic.py:
Moved clip_in_place() from utils.py to arrayutils.py

* [r2684] topo/base/parameterizedobject.py:
Minor edit of comments.

* [r2683] topo/base/parameterizedobject.py:
Removed HACKALERT

* [r2682] topo/base/parameterclasses.py,
topo/base/utils.py:
classname_repr() moved to be a method of ClassSelectorParameter.

* [r2681] topo/base/parameterclasses.py,
topo/base/patterngenerator.py,
topo/tkgui/testpattern.py:
Added suffix_to_lose to ClassSelectorParameter, allowing that
siffix to be removed when the class name is displayed.
PatternGeneratorParameter removes 'Generator' by default.

* [r2680] topo/base/utils.py:
Cleaned up documentation and removed unused import for
classname_repr().

* [r2679] topo/base/sheet.py,
topo/base/simulator.py:
__repr__() is overridden to print more useful information.

* [r2678] topo/base/utils.py:
classname_repr() no longer inserts spaces before capital letters.

* [r2677] topo/base/parameterizedobject.py:
Made __str__() use __repr__() (both previously contained the same
code).

* [r2676] topo/base/parameterizedobject.py:
Removed HACKALERT about name-sharing; added a HACKALERT about
printing more useful info at the commandline.

* [r2675] doc/Future_Work/current_text.php:
Added task (CB).

* [r2674] doc/Future_Work/current_text.php:
Initial version, biased towards my work.

2006-02-21 jbednar

* [r2673] topo/sheets/lissom.py:
Changed tsettle into a positive Integer parameter instead of a
plain attribute

* [r2672] topo/sheets/lissom.py:
Fixed for cases where there are multiple sheets in the model --
it had been counting the number of times pre_sleep was called,
which happens whenever any input event occurs. Now it counts the
number of actual activations for this sheet instead. Should not
change the results for lissom_or.ty, but should change the
results for lissom_oo_or.ty (which should do one less settling
step now)

2006-02-21 ceball

* [r2671] topo/patterns/basic.py:
Minor alterations to CompositePatternGenerator.

* [r2670] topo/patterns/basic.py:
Composite is now in a state where it can be tried out usefully in
the test pattern window (to see better how it should finally
work). But the implementation is temporary.

2006-02-20 ceball

* [r2669] topo/base/parameterizedobject.py,
topo/base/patterngenerator.py:
Example of how we could prevent instantiation of abstract
classes, PatternGenerator in this case. Since the super() call
requires the class itself inside the call anyway, putting it in
there again is not too much trouble...

* [r2668] topo/base/parameterclasses.py:
Change to a HACKALERT.

* [r2667] topo/base/utils.py:
Added to documentation.

2006-02-20 ceball_cvs2svn

* [r2666] /tags/release_0_8_2:
This commit was manufactured by cvs2svn to create tag
'release_0_8_2'.

2006-02-20 ceball

* [r2665] topo/base/parameterizedobject.py:
Changed __param_inheritance() to look up the classlist
(superclasses) itself, rather than having it passed in. Renamed
uses of 'base_classes' to 'superclasses'; previously there was
confusion between 'bases' returned from classlist() and bases as
passed to the metaclass' __init__() method.

* [r2664] topo/base/parameterizedobject.py:
__param_inheritance() changed to look at all slots, not just
those in the immediate class (so e.g. a Number parameter does
inheritance for bounds,softbounds and all the slots of its
superclasses (Parameter in this case)).

* [r2663] topo/base/parameterizedobject.py:
Moved classlist() and descendents() to beginning of file.

2006-02-20 julienciroux

* [r2662] topo/plotting/plot.py:
Cleaned up the doc.

* [r2661] topo/plotting/plot.py:
Corrected mistake in Plot.

* [r2660] topo/analysis/featuremap.py:
Deleted old Alert in FeatureMap.

2006-02-20 jbednar

* [r2659] doc/shared/index.php:
Updated release date

* [r2658] topo/patterns/basic.py,
topo/patterns/image.py:
Updated doc strings

2006-02-20 ceball

* [r2657] doc/Team_Members/index_text.php:
Updated link.

* [r2656] topo/base/parameterclasses.py:
Cleaned up ClassSelectorParameter a little.

* [r2655] topo/base/connectionfield.py:
Cleaned up ResponseFunctionParameter and
LearningFunctionParameter.

* [r2654] topo/base/patterngenerator.py:
Cleaned up PatternGeneratorParameter a little.

* [r2653] topo/base/projection.py:
Cleaned up OutputFunctionParameter a little.

* [r2652] topo/patterns/basic.py,
topo/patterns/image.py:
Added some doc strings

* [r2651] topo/tkgui/parametersframe.py:
Removed out-of-date hackalert.

2006-02-20 jbednar

* [r2650] doc/User_Manual/parameters_text.php:
Changed get_paramobj_dict to params

* [r2649]
doc/images/060220_model_editor_screen_shot.png,
doc/images/060220_topographica_screen_shot.png,
doc/shared/index.php:
Added screenshots

2006-02-20 ceball

* [r2648] topo/base/parameterizedobject.py:
Removed unused argument from params().

* [r2647] topo/base/parameterizedobject.py,
topo/tkgui/parametersframe.py,
topo/tkgui/testpattern.py:
Re-named get_paramobj_dict() to params().

2006-02-20 jbednar

* [r2646] doc/shared/index.php:
Updated release date

* [r2645] examples/lissom_or_20000.typ:
Retrained map

* [r2644] examples/lissom_oo_or_20000.typ:
Retrained map

* [r2643] doc/User_Manual,
doc/User_Manual/.cvsignore,
doc/User_Manual/index_text.php,
doc/User_Manual/parameter_text.php,
doc/User_Manual/parameters_text.php:
Added link to Parameters documentation

* [r2642] doc/User_Manual/parameter_text.php:
Cleaned up

2006-02-19 jbednar

* [r2641] topo/base/simulator.py:
Changed schedule_action to accept only callable values. Changed
step_mode and register to be BooleanParameters, and added ALERT
about step_mode.

* [r2640] topo/tests/testcfsom.py,
topo/tests/testsimulator.py:
Fixed step_mode to be Boolean to allow that parameter to be a
BooleanParameter

* [r2639] topo/base/parameterclasses.py:
Added CallableParameter

* [r2638] topo/plotting/templates.py:
Added OrientationSelectivity subplot to avoid confusion for
Sheets that are not orientation selective but still sometimes
have a map measured

* [r2637] topo/plotting/bitmap.py:
Removed unused normalize parameter

* [r2636] topo/learningfns/basic.py:
Made SOM neighborhood function into a PatternGeneratorParameter

* [r2635] topo/eps/basic.py:
Replaced Parameters with Numbers

* [r2634] topo/base/patterngenerator.py:
Changed density into a Number with a lower bound

* [r2633] topo/base/parameterizedobject.py:
Added ALERT

2006-02-19 alan_lindsay

* [r2632] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Activity toggle for all now too.

* [r2631] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Right click in the canvas to bring up menu, allows save snapshot
of canvas (saved to postscript) and all sheet densities to be
toggled on/off.

2006-02-19 jbednar

* [r2630] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py,
topo/base/sheet.py,
topo/learningfns/optimized.py:
Removed Constant Parameter, since it is the same as
Parameter(constant=True).

* [r2629] topo/projections/basic.py:
Changed Constant to a LearningFunctionParameter(constant=True)

2006-02-19 julienciroux

* [r2628] topo/sheets/generatorsheet.py:
Made period and phase parameter be Number instead of Parameter.

* [r2627] topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Moved the declaration of the ouput_fn parameter in the superclass
CFLearningFunction, instead of re-declaring it in all
sub-classes.

* [r2626] topo/learningfns/optimized.py:
Cleaned up parameter doc string, changed output_fn for for
DivisiveHebbian and DivisiveHebbian_Cpointer to be
OutputFunctionParameter rather than Constant.

* [r2625] topo/learningfns/basic.py:
Cleaned up parameters doc string.

* [r2624] topo/base/connectionfield.py:
Added period to doc strings.

* [r2623] topo/base/simulator.py:
Added alert about not being able to decalrestep_mode and register
Parameter as BooleanParameter.

* [r2622] topo/base/patterngenerator.py:
Declared BoundingBox parameters as BoundingRegionParameter rather
than Parameter.

* [r2621] topo/base/connectionfield.py:
Declared BoundingBox parameters as BoundingRegionParameter rather
than Parameter. Added some parameter doc string. Transformed
CFProjection learning_rate parameter to be a Number. Transformed
CF x and y parameters to be Numbers as well.

* [r2620] examples/lissom_or.ty:
Deleted ommitted code added for testing purpose.

2006-02-19 jbednar

* [r2619] topo/base/connectionfield.py:
Cleaned up doc strings

2006-02-19 julienciroux

* [r2618] topo/base/connectionfield.py:
Added a doc string for the learning_fn parameter of a
CFProjection.

* [r2617] topo/projections/optimized.py:
Declared the CFProjection_Cpointer learning_fn parameter as a
LearningFunctionParameter rather than a Parameter.

* [r2616] topo/projections/optimized.py:
Declared the CFProjection_Cpointer response_fn parameter as a
ResponseFunctionParameter rather than a Parameter.

* [r2615] topo/base/connectionfield.py:
Added a doc string for the response_fn parameter of a
CFProjection.

* [r2614] topo/base/connectionfield.py,
topo/base/projection.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/projections/basic.py:
Changed the output_fn declared as Parameters to be declared as
OutputFunctionParameter. I added a doc string when needed, that
might need to be reviewed. I tried to see in which case this doc
string was already inherited, and not added it ?\004in such case.

2006-02-19 jbednar

* [r2613] topo/base/boundingregion.py:
Made BoundingRegionParameter instantiate by default

2006-02-19 julienciroux

* [r2612] examples/lissom_oo_or.ty,
examples/lissom_or.ty:
Deleted the dest_port setting when creating a CFProjection. Now,
it is possible for different projections to the same sheet to
share the same dest_port (as soon as they are named differently).

* [r2611] topo/base/projection.py:
Solved the problem of the port for Projection: first, ensure that
all the projection to the same ProjectionSheet are named
differently by raising an error if intenting to do so; second,
allow all the projection sharing the same ports to be?\004
activated (by removing the break in the activate method).

2006-02-19 jbednar

* [r2610] topo/base/sheet.py:
Made bounds be a BoundingRegionParameter, and density be a
constant Parameter

2006-02-19 julienciroux

* [r2609] topo/base/connectionfield.py,
topo/base/sheet.py,
topo/plotting/plot.py,
topo/plotting/plotgroup.py:
Replaced the old bounds.aarect().lbrt() syntax by bounds.lbrt().

2006-02-19 jbednar

* [r2608] topo/base/boundingregion.py:
Added BoundingRegionParameter

* [r2607] topo/base/simulator.py:
Added EventProcessorParameter for src and dest of an EPConnection

* [r2606] topo/base/projection.py:
Added docstring

* [r2605] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py:
Added ALERT

2006-02-19 julienciroux

* [r2604] topo/base/boundingregion.py:
Added a lbrt() method to the BoundingBox. It should make Chris
happy by allowing him to to do bounds.lbrt().

* [r2603] examples/lissom_or.ty:
Corrected the Retina edge buffer.

2006-02-19 jbednar

* [r2602] topo/base/parameterclasses.py:
Fixed exceptions to be classes

* [r2601] topo/base/boundingregion.py:
Added Cartesian2DPoint parameter, and changed BoundingCircle to
use it and Number instead of Parameter

* [r2600] ChangeLog.txt:
Added new entries

2006-02-18 jbednar

* [r2599] topo/base/connectionfield.py,
topo/base/simulator.py:
Made a few more parameters constant

2006-02-18 julienciroux

* [r2598] topo/base/parameterizedobject.py:
Corrected a doc referring to topo.base.parameter.

* [r2597] topo/tkgui/parametersframe.py:
Corrected a doc referring to topo.base.parameter.

2006-02-18 alan_lindsay

* [r2596] topo/tkgui/editorobjects.py:
Line view bounds check sorted.

* [r2595] topo/tkgui/editortools.py:
Updates class parameters without update button

2006-02-18 ceball

* [r2594] doc/User_Manual/parameter_text.php:
Tried to break text up a little.

* [r2593] doc/User_Manual/parameter_text.php:
Continued writing...

2006-02-18 alan_lindsay

* [r2592] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
Added Refresh, Enlarge, Reduce buttons and an error message for
when connections don't happen.

2006-02-18 ceball

* [r2591] doc/User_Manual/parameter_text.php:
Continued writing; still incomplete.

2006-02-18 jbednar

* [r2590] doc/User_Manual/commandline_text.php,
doc/User_Manual/images/matrixvectorplot.png,
doc/User_Manual/images/sine_plot.png:
Added plot screenshots

* [r2589] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py:
Cleaned up and generalized the documentation. Renamed methods and
variables that referred to Topographica, since the classes are
now fully general

* [r2588] doc/Downloads/index_text.php:
Added note about make -k

2006-02-18 ceball

* [r2587] topo/base/parameterizedobject.py:
Removed get_param_dict() because it simply returns attributes of
the TopoObject (and its superclasses) that are Parameters.

* [r2586] topo/base/parameterizedobject.py:
Tidied comments.

* [r2585] topo/base/parameterizedobject.py:
Moved two functions to the end of the file.

* [r2584] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py:
Moved a HACKALERT

* [r2583] topo/tkgui/parametersframe.py:
Parameters with attribute constant==True are set non-editable for
an object, and editable for a class (i.e. no visible change, just
updated for constant attribute of Parameter).

* [r2582] topo/base/connectionfield.py:
weights_shape is set to be a constant Parameter.

* [r2581] topo/tkgui/parametersframe.py:
Corrected import for classlist. There might be other files with
this mistake?

* [r2580] topo/base/parameterclasses.py:
Removed HACKALERT.

* [r2579] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py:
Moved Constant to parameterclasses.py

* [r2578] topo/base/parameterizedobject.py:
Parameters can have a 'constant' attribute. If this is True, they
cannot be set on an initialized TopoObject (and they are also
instantiated). The Constant Parameter is now simply a Parameter
with constant=True. Constant parameters are now no longer
excluded from pickling - they are pickled like everything else.
Such changes go together because deepcopy uses __getstate__ and
__setstate__, as does pickling.

2006-02-17 ceball

* [r2577] topo/projections/basic.py:
All SharedWeightCFProjections were sharing the same
cf_slice_and_bounds list because it was declared as a class
attribute.

* [r2576] topo/base/parameterizedobject.py:
Removed print statement accidentally left behind.

* [r2575] topo/base/parameterizedobject.py:
Corrected mistake in previous commit.

* [r2574] topo/base/parameterizedobject.py:
get_name() doesn't just look in the immediate class for the
parameter, but in the whole class hierarchy. Before, None was
being returned sometimes. That had broken pickling.

2006-02-17 julienciroux

* [r2573] topo/base/parameterclasses.py,
topo/base/parameterizedobject.py:
Moved Parameter (and associated functions class_list() and
descendents()) in parameterizedobject.py. I also momentarily
moved Constant, until the use of this class in Parameter is
deleted (Chris should fix that). Parameter and Constant are?\004
still imported in parameterclasses.py, so that we can still
import any Parameter class from parameterclasses.py.

* [r2572] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/base/__init__.py,
topo/base/boundingregion.py,
topo/base/connectionfield.py,
topo/base/parameter.py,
topo/base/parameterclasses.py,
topo/base/parameterizedobject.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/base/sheet.py,
topo/base/simulator.py,
topo/eps/basic.py,
topo/learningfns/__init__.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/outputfns/__init__.py,
topo/outputfns/basic.py,
topo/patterns/__init__.py,
topo/patterns/basic.py,
topo/patterns/image.py,
topo/patterns/random.py,
topo/plotting/bitmap.py,
topo/plotting/palette.py,
topo/plotting/plot.py,
topo/plotting/templates.py,
topo/projections/basic.py,
topo/projections/optimized.py,
topo/responsefns/__init__.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/sheets/cfsom.py,
topo/sheets/generatorsheet.py,
topo/sheets/lissom.py,
topo/tests/lissom_oo_or_reference.ty,
topo/tests/lissom_or_reference.ty,
topo/tests/testcfsom.py,
topo/tests/testlissom.ty,
topo/tests/testlissom_cpointer.ty,
topo/tests/testpatternpresent.py,
topo/tests/testsheetview.py,
topo/tests/tkgui/testplotgrouppanel.py,
topo/tkgui/parametersframe.py:
Renamed parameter.py to parameterclasses.py.

* [r2571] topo/base/parameter.py:
Re-implemented the __get__ method for Number, so that not having
to know about DynamicNumber from the Parameter class (will
eventually allow to move the Parameter class to
parameterizedobject.py.

2006-02-17 alan_lindsay

* [r2570] topo/tkgui/editorobjects.py:
Added density grid view for sheets

2006-02-17 julienciroux

* [r2569] examples/hierarchical.ty,
topo/analysis/featuremap.py,
topo/base/__init__.py,
topo/base/boundingregion.py,
topo/base/connectionfield.py,
topo/base/parameterizedobject.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/base/sheetview.py,
topo/base/simulator.py,
topo/base/topoobject.py,
topo/base/utils.py,
topo/commands/basic.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/outputfns/basic.py,
topo/patterns/image.py,
topo/plotting/bitmap.py,
topo/plotting/palette.py,
topo/plotting/plot.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/plotting/templates.py,
topo/projections/basic.py,
topo/projections/optimized.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/sheets/lissom.py,
topo/tests/testcfsom.py,
topo/tests/testpatternpresent.py,
topo/tests/testplot.py,
topo/tests/testplotfilesaver.py,
topo/tests/testsheet.py,
topo/tests/tkgui/testplotgrouppanel.py,
topo/tests/tkgui/testtemplateplotgrouppanel.py,
topo/tests/tkgui/testtopoconsole.py,
topo/tkgui/__init__.py,
topo/tkgui/parametersframe.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/topoconsole.py:
Re-named topoobject.py to parameterizedobject.py.

* [r2568] topo/base/parameter.py,
topo/base/topoobject.py:
Renamed TopoMetaclass to ParameterizedObjectMetaclass.

* [r2567] topo/analysis/featuremap.py,
topo/base/arrayutils.py,
topo/base/boundingregion.py,
topo/base/connectionfield.py,
topo/base/parameter.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/base/sheetview.py,
topo/base/simulator.py,
topo/base/topoobject.py,
topo/base/utils.py,
topo/commands/basic.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py,
topo/outputfns/basic.py,
topo/patterns/image.py,
topo/plotting/bitmap.py,
topo/plotting/palette.py,
topo/plotting/plot.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/plotting/templates.py,
topo/projections/basic.py,
topo/projections/optimized.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/sheets/generatorsheet.py,
topo/sheets/lissom.py,
topo/tests/testplot.py,
topo/tkgui/parametersframe.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/topoconsole.py:
Renamed TopoObject to ParameterizedObject.

2006-02-17 ceball

* [r2566] topo/tkgui/parametersframe.py:
Added HACKALERT.

2006-02-17 julienciroux

* [r2565] topo/base/connectionfield.py:
Added comment and ALERT.

2006-02-17 ceball

* [r2564] topo/base/parameter.py,
topo/base/topoobject.py:
bounds and softbounds are None when not set so that parameter
inheritance works.

2006-02-17 julienciroux

* [r2563] topo/base/connectionfield.py,
topo/sheets/cfsom.py:
Moved the test on the input_buffer from CFSheet learn() to
CFProjection learn().

2006-02-17 ceball

* [r2562] topo/tkgui/parametersframe.py:
set_obj_params() only sets the value on an object if the value is
different from the one already in the object.

2006-02-17 jbednar

* [r2561] topo/sheets/cfsom.py:
Moved alert here from som_retinotopy.ty

* [r2560] examples/som_retinotopy.ty:
Simplified slightly

2006-02-17 ceball

* [r2559] topo/base/connectionfield.py:
Added wrapper around hebbian() so deepcopy works. TopoObject
needs to have its support for deepcopy corrected.

* [r2558] topo/base/topoobject.py:
Renamed __set_name() to __generate_name().

* [r2557] topo/base/topoobject.py:
If a Parameter is a TopoObject, and it's deepcopied for a new
TopoObject, it's renamed.

* [r2556] topo/base/topoobject.py:
No visible change: created a simple __set_name() method from the
original line of code in topoobject. (Done because it will be
used when Parameters are deepcopied to new objects.)

* [r2555] topo/base/topoobject.py:
Added HACKALERT about the possibility of TopoObjects sharing the
same name.

* [r2554] topo/base/connectionfield.py,
topo/base/topoobject.py,
topo/projections/basic.py:
Added wrapper around mdot so deepcopy works. TopoObject needs to
have its support for deepcopy corrected.

* [r2553] topo/base/arrayutils.py:
Added temporary wrapper class around mdot.

2006-02-16 ceball

* [r2552] topo/base/topoobject.py:
Had to add a HACK - some things don't seem to deepcopy.

* [r2551] topo/sheets/lissom.py:
A Parameter has an 'instantiate' attribute (previously
'value_semantics') that indicates whether or not a TopoObject
should copy the Parameter into its own __dict__. instantiate
defaults to False for Parameter, but True for certain subclasses
(e.g. ClassSelectorParameter, Constant).

* [r2550] topo/base/sheet.py:
topo/sheets/lissom.py

* [r2549] topo/base/parameter.py,
topo/base/topoobject.py:
topo/sheets/lissom.py

2006-02-15 jbednar

* [r2548] examples/laminar.ty:
Initial version from Judith

2006-02-15 julienciroux

* [r2547] topo/base/connectionfield.py,
topo/sheets/cfsom.py:
Added a mysterious test (if proj.input_buffer), that I previously
deleted in CFSheet abd CFSOM learn() function, but that happens
to be needed. This will be solved tomorrow.

* [r2546] topo/sheets/cfsom.py:
Modified the CFSOM learning function so that it calls the learn()
function on the projections, instead of re-implementing it.

* [r2545] topo/base/connectionfield.py,
topo/base/projection.py:
Added a learn() function for Projections, which is called from
the CFSheet learn() function.

2006-02-15 ceball

* [r2544] examples/lissom_oo_or.ty,
examples/lissom_oo_or_20000.typ:
Increased ON connection strength to 0.75. C++ LISSOM normalizes
all its afferent weights to 1 so the ON and OFF channel can have
different effects; topographica doesn't so we compensate by
increasing the ON connection strength until we sup?\004port joint
normalization.

* [r2543] topo/tests/lissom_oo_or_reference.ty:
density and output_fn set on V1 rather than on LISSOM.

* [r2542] topo/tests/lissom_oo_or_reference.ty:
Various changes to help match c++ lissom (adding edge buffers)
and to make the file clearer.

2006-02-14 ceball

* [r2541] topo/base/boundingregion.py:
min_radius is deleted from the args if it's passed in, so that
it's not passed to the superclass. Removed a hackalert.

* [r2540] topo/tests/lissom_oo_or_reference.ty:
SharedWeightCFProjection.learning_fn.output_fn set to
DivisiveSumNormalize, rather than being set on the Projections
separately.

2006-02-14 jbednar

* [r2539] topo/commands/or_key_white_vert.png:
Flipped to fix

2006-02-14 julienciroux

* [r2538] topo/plotting/plotgroup.py:
Added the possibility of passing SheetView plot_template to a
ConnectionField PlotGroupTemplate. If the plot_template uses the
keyword 'Weights' for the Strength, we request a UnitView,
otherwise we create a normal plot with Strength specifying a
SheetView. This not at all effective so far, because no such
template are declared (also the displaying of labels is not
exactly consistent between a connection field plot, and a normal
SheetView plot, but still it looks alright).

* [r2537] topo/tkgui/connectionfieldspanel.py:
Corrected a typo mistake in the label display.

2006-02-14 ceball

* [r2536] doc/User_Manual/parameter_text.php:
Beginnings of Parameter documentation. Committed while I change
locations...

* [r2535] topo/base/topoobject.py:
Added HACKALERT about parameter inheritance.

* [r2534] examples/lissom_oo_or.ty:
SharedWeightCFProjection.learning_fn.output_fn set to
DivisiveSumNormalize, instead of setting the projections'
learning_fn.output_fns separately.

2006-02-14 alan_lindsay

* [r2533] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Changed the way you change the view of connectioons and sheets.
Radius' are represented, though, it seems like connections might
not be reporting the truth..

2006-02-13 jbednar

* [r2532]
doc/Tutorials/som_retinotopy_text.php:
Minor cleanup

2006-02-13 julienciroux

* [r2531] topo/plotting/plotgroup.py:
Deleted the added_list attribute and the add() function in
PlotGroup. It was an unused concept, and we can still add Plots
to a PlotGroup since its plot_list attribute is public.

* [r2530] topo/plotting/plotgroup.py:
Added a function _ordering_plots in PlotGroup. It is called by
plots() before returning the plot_list. It allows to only have to
re-implement this simple function in ProjectionPlotGroup, instead
of the whole plots() function.

2006-02-13 ceball

* [r2529] doc/User_Manual/space_text.php:
Minor changes.

2006-02-13 julienciroux

* [r2528] topo/plotting/plotgroup.py:
Deleted a unused attribute self.all_plots.

2006-02-13 ceball

* [r2527] doc/Tutorials/lissom_oo_or_text.php:
Changed Afferent0 that was left over to LGNOnAfferent.

2006-02-13 julienciroux

* [r2526] topo/tkgui/projectionpanel.py:
Modified the sorting of the projections in the projection_menu:
now they are first sorted with the precedence number of there
source Sheet and then by alphabetical order. Also added a comment
about re-writing the function _create_projection_dict(), which is
quite messy.

* [r2525] topo/base/sheetview.py:
Made the UnitView precedence parameter to be set to the value of
the projection.src.precedence parameter (the precedence number of
the source Sheet). That allows the plot in the
connectionfieldpanel to be sorted accordingly.

2006-02-13 ceball

* [r2524] examples/lissom_oo_or_20000.typ:
Same map, but with updates to code in the pickle.

* [r2523] topo/base/parameter.py,
topo/base/sheet.py,
topo/base/topoobject.py:
Parameter has a 'value_semantics' attribute. TopoObject copies
the Parameter into its own dictionary if this is set True. This
is just a demonstration of how we could do explicit value
semantics: setting value_semantics=True on any paramet?\004er
means a copy of its default value is always given to a new
TopoObject. So for a Constant parameter, setting
value_semantics=True makes the Constant truly constant. There is
one example of this for demonstration: Sheet's bounds. Presumably
the attribut?\004e shouldn't actually be called value_semantics.

2006-02-13 jbednar

* [r2522] doc/Tutorials/lissom_oo_or_text.php:
Fixes and cleanup

* [r2521]
doc/Tutorials/images/natural_image_oo_or.png,
doc/Tutorials/lissom_oo_or_text.php:
Fixes and cleanup

2006-02-13 ceball

* [r2520] topo/patterns/image.py:
Updated to take account of patterngenerator being passed the true
xdensity and ydensity rather than just the density. Added
hackalert.

2006-02-13 jbednar

* [r2519]
doc/Tutorials/images/or_key_vert_transparent_topo.png:
Unused

* [r2518] topo/commands/or_key_white_vert.png,
topo/plotting/templates.py:
Updated color key

* [r2517]
doc/Tutorials/images/activity_line_oo.png,
doc/Tutorials/images/activity_line_oo_or.png,
doc/Tutorials/images/lissom_network_diagram_oo.png,
doc/Tutorials/images/oo_or_map.png,
doc/Tutorials/images/or_key_horiz_transparent.png,
doc/Tutorials/images/projection_oo.png,
doc/Tutorials/images/test_pattern_oo.png,
doc/Tutorials/images/unit_weights_0_0_oo.png,
doc/Tutorials/images/unit_weights_0_0_oo_or.png,
doc/Tutorials/lissom_oo_or_text.php:
Updated lissom_oo_or tutorial

* [r2516] examples/lissom_oo_or.ty:
Adjusted model editor coordinates due to edge buffer change

* [r2515] doc/Reference_Manual/index_text.php:
Added caveat

* [r2514] doc/Downloads/index_text.php:
Updated Mac and Windows instructions

* [r2513] doc/Tutorials/index_text.php:
Added link to lissom_oo_or tutorial

* [r2512] doc/User_Manual/commandline_text.php:
Reorganized

* [r2511] doc/shared/index.php:
Added news item

* [r2510] README.txt:
Minor bugfix

* [r2509] doc/User_Manual/commandline_text.php,
doc/User_Manual/index_text.php:
Added command line examples

* [r2508] doc/User_Manual,
doc/User_Manual/.cvsignore:
More to ignore

* [r2507] doc/Future_Work/index_text.php:
Updates; some items actually completed!

* [r2506] Makefile:
Bumped version number in anticipation of release

* [r2505] doc/Downloads/index_text.php:
Added Windows disclaimer

* [r2504]
external/win32/Numeric-23.7.win32-py2.4.exe,
external/win32/Numeric-24.2.win32-py2.4.exe,
external/win32/setup.py:
Upgraded to Numeric 24

2006-02-13 ceball

* [r2503] topo/base/connectionfield.py:
Minor change to hackalert.

* [r2502] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty:
BoundingBox can be created by specifying a radius.

2006-02-13 jbednar

* [r2501] doc/Developer_Manual,
doc/Developer_Manual/.cvsignore,
doc/Developer_Manual/parameters_text.php,
doc/Developer_Manual/python_text.php:
Reorganized developer manual to be grouped more reasonably

2006-02-13 ceball

* [r2500] examples/lissom_oo_or.ty,
topo/base/boundingregion.py,
topo/base/connectionfield.py,
topo/tests/lissom_oo_or_reference.ty:
BoundingBox can be created by passing a radius or points. This
takes the place of the previous radial_bounds() function.

2006-02-13 jbednar

* [r2499] doc/Tutorials,
doc/Tutorials/.cvsignore:
More to ignore

2006-02-12 jbednar

* [r2498] doc/Developer_Manual/alerts_text.php,
doc/Developer_Manual/coding_text.php,
doc/Developer_Manual/communication_text.php,
doc/Developer_Manual/gui_text.php,
doc/Developer_Manual/imports_text.php,
doc/Developer_Manual/index_text.php,
doc/Developer_Manual/naming_text.php,
doc/Developer_Manual/ood_text.php,
doc/Developer_Manual/optimization_text.php,
doc/Developer_Manual/revisioncontrol_text.php:
Reorganized developer manual to be grouped more reasonably

2006-02-12 ceball

* [r2497] topo/base/parameter.py:
Changed variable name in Constant to make the code clearer. The
previous version does appear to work - I appear to have been
confusing myself while testing it.

* [r2496] topo/base/parameter.py:
Simple version of Constant that ought to work, but appears not
to.

2006-02-12 jbednar

* [r2495] topo/responsefns/optimized.py:
Simplified CFDotProduct C++ code by moving declarations to where
they are needed

2006-02-12 ceball

* [r2494] topo/base/parameter.py:
Changed Constant's attepted set error to a TypeError.

* [r2493] topo/base/parameter.py:
Removed a HACKALERT that should have been removed a while back.

* [r2492] topo/base/parameter.py:
Constant parameter is now constant (i.e. doesn't inherit changes
once it's been created).

* [r2491] topo/base/sheet.py:
Removed 'default=' from Constant declarations.

* [r2490] topo/sheets/lissom.py:
The LISSOM sheet output_fn Parameter is set in the constructor,
rather than being re-declared at the class level. This means that
each LISSOM sheet object has its own output_fn by default, rather
than all LISSOM sheets sharing one object.?\004

2006-02-12 julienciroux

* [r2489] topo/tkgui/cfsheetplotpanel.py:
Changed the sorting of the region_menu, so that to start by high
area instead of low area.

* [r2488] topo/tkgui/cfsheetplotpanel.py:
Sorted the region_menu for a CFSheetPlotPanel, according to the
precedence parameter of the sheets.

* [r2487] topo/plotting/plotgroup.py:
Changed the sort_plots function (and introduced a new cmp_plot
function) to sort according to bith the precedence and the
alphabetical order.

* [r2486] topo/base/connectionfield.py:
Forgotten CFSheet precedence default value in previous commit.

* [r2485] topo/plotting/plot.py:
Added an attribute precedence to a Plot, that is 0.0 by default,
and a copy of the SheetViews used for making the plot (set at the
same time as the src_name).

* [r2484] topo/analysis/featuremap.py,
topo/base/sheetview.py,
topo/commands/analysis.py:
Added a precedence attribute to the SheetView, which is a copy of
the sheet precedence parameter, passed when creating a SheetView.

* [r2483] topo/base/sheet.py,
topo/sheets/cfsom.py,
topo/sheets/lissom.py:
Added a parameter precedence to the Sheet objects. It gives a
sorting information for plot display.

2006-02-12 jbednar

* [r2482] topo/plotting/bitmap.py:
Fixed bug when plotting selectivities higher than 1.0; now crops
h,s,v before calling hsv2rgb. Silenced warning from PIL.

* [r2481] doc/Downloads/index_text.php:
Cleanup of Windows instructions in progress

* [r2480]
doc/Developer_Manual/testing_text.php:
Minor clarification

* [r2479] examples/lissom_oo_or_20000.typ:
Retrained the map

2006-02-12 ceball

* [r2478] topo/base/sheet.py:
Initializes activity matrix correctly. Added HACKALERT: here and
elsewhere there is duplication of code.

* [r2477] topo/sheets/generatorsheet.py:
Now uses PatternGenerator correctly.

2006-02-12 jbednar

* [r2476] README.txt:
Simplified so that it will stay up to date; just points to doc/

2006-02-12 ceball

* [r2475] topo/patterns/basic.py,
topo/patterns/image.py:
Removed 'precedence constants' since we have decided on an
ordering for the parameters.

2006-02-12 julienciroux

* [r2474] topo/tkgui/plotgrouppanel.py:
Corrected an error in load_image.

2006-02-12 ceball

* [r2473] topo/base/connectionfield.py,
topo/projections/basic.py:
Initialization of the cfs in CFProjection.__init__() can be
disabled. SharedWeightCFProjection uses this to avoid
initializing the cfs (since it only requires a single, shared cf
- that it was previously initializing all the cfs was an error,
causing its initialization time to be much longer than
necessary).

2006-02-12 jbednar

* [r2472] ChangeLog,
ChangeLog.txt:
Moved ChangeLog to ChangeLog.txt to make it readable under
Windows

* [r2471] models:
Not used anymore

2006-02-12 alan_lindsay

* [r2470] topo/tkgui/editorobjects.py:
Fixed a rounding error

* [r2469] topo/tkgui/editorobjects.py:
Fixed a delete update bug

2006-02-12 jbednar

* [r2468] topo/tkgui/topoconsole.py:
Fixed error in percentage calculation

* [r2467] examples/lissom_oo_or.ty:
Changed Retina's edge buffer to match wt_bounds

2006-02-12 julienciroux

* [r2466] examples/lissom_oo_or.ty:
Set the retina and LGN edge buffer.

2006-02-12 jbednar

* [r2465] ChangeLog:
Added recent changes

* [r2464] examples/lissom_oo_or.ty:
Updated gui attribute names to match Alan's recent changes

2006-02-12 alan_lindsay

* [r2463] topo/tkgui/parametersframe.py:
Allows class constants to be set, crudely. A dictionary of
dictionaries, holding only the objects changed by the user is
used to allow values to be mainained after closing the
parameterframe.

* [r2462] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
Changed method and variable names to coincide with the rest of
Topographica. Activity plots are now mapped correctly onto sheets
and the shape and size of a sheets bounding box is represented by
the editor sheet.

* [r2461] topo/base/utils.py:
Added extra translator functions for features in ParameterFrame.

* [r2460] examples/hierarchical.ty:
ModelEditor uses gui_x instead of guiX, same fory.

2006-02-12 jbednar

* [r2459] examples/lissom_oo_or_20000.typ:
New version from Chris

2006-02-11 jbednar

* [r2458] topo/tkgui/topoconsole.py:
Added simple progress reporting (just a sketch)

2006-02-10 ceball

* [r2457] examples/lissom_oo_or_20000.typ:
Removed - something went wrong with the previous commit. Will
replace.

* [r2456] examples/lissom_oo_or_20000.typ:
Slied in measure_maps code and change to input_generator.

* [r2455] doc/Tutorials/lissom_oo_or_text.php:
Initial version - unchecked.

* [r2454]
doc/Tutorials/images/activity_line_oo.png,
doc/Tutorials/images/activity_line_oo_or.png,
doc/Tutorials/images/lissom_network_diagram_oo.png,
doc/Tutorials/images/natural_image_oo_or.png,
doc/Tutorials/images/oo_or_map.png,
doc/Tutorials/images/projection_oo.png,
doc/Tutorials/images/test_pattern_oo.png,
doc/Tutorials/images/unit_weights_0_0_oo.png,
doc/Tutorials/images/unit_weights_0_0_oo_or.png,
doc/Tutorials/images/unit_weights_0_0_or.png:
New image for oo_or tutorial.

* [r2453] examples/lissom_oo_or.ty:
Positioned network for model editor. Replaced lambda functions
for getting random.uniform value with a class (to allow
pickling); this class will be moved.

* [r2452] examples/lissom_oo_or.ty:
LGN declared with measure_maps=False.

* [r2451] topo/analysis/featuremap.py:
Sheets with a measure_maps attribute, and with it set True, get
their maps measured - others do not.

* [r2450] topo/base/connectionfield.py:
Added a 'measure_maps' attribute to CFSheet.

* [r2449] examples/lissom_oo_or.ty:
No longer have afferent_weight_bounds, lgn_weight_bounds, and
input_bounds. Instead, bounds are just created by
radial_bounds().

2006-02-10 jbednar

* [r2448] doc/User_Manual/space_text.php:
Minor clarification

2006-02-10 ceball

* [r2447] examples/lissom_oo_or.ty:
Eliminated inhibitory_ and excitatory_weight_bounds variables,
instead just creating the bounds where the projection is defined.

* [r2446] examples/lissom_oo_or.ty,
topo/base/connectionfield.py:
Renamed wt_bounds() to radial_bounds().

* [r2445] examples/lissom_oo_or.ty:
Gaussian class' parameters are not now set; instead, parameters
on the Retina's input_generator are set.

* [r2444] topo/base/parameter.py:
Added a hack to allow DynamicNumbers to work when they are set on
an object.

* [r2443] topo/commands/basic.py:
Hacked the hack in load_snapshot to allow
examples/lissom_oo_or_20000.typ to keep its dynamic input pattern
numbers. Because the unpickleable lambda functions for generating
random numbers are used in two different ways now, there are two
different hacks here. Once we eliminate those lambda functions,
it should all be ok.

2006-02-10 jbednar

* [r2442] topo/base/sheet.py,
topo/base/simulator.py:
Added ALERTs

2006-02-10 ceball

* [r2441] examples/lissom_oo_or_20000.typ:
Initial version.

2006-02-09 ceball

* [r2440] examples/lissom_oo_or.ty:
Updates to match lissom_oo_or_reference.ty.

* [r2439] examples/lissom_oo_or.ty:
Updates to match lissom_oo_or_reference.ty.

* [r2438] topo/tests/lissom_oo_or_reference.ty:
delta and beta values corrected.

2006-02-09 julienciroux

* [r2437] topo/plotting/templates.py:
Added the color_key to the Orientation Preference
PlotGroupTemplate.

* [r2436] topo/tkgui/plotgrouppanel.py:
Changed the function load_image; now, all topographica plot are
resized to be the close as possible to the height of the biggest
topographica plot; then, the static_images are resized to be of
this height. There is still a warning about using the
image.resize function with floats that we need to take care
about.

* [r2435] topo/plotting/plotgroup.py:
Set the resize parameter to False when creating static image
plot.

* [r2434] topo/plotting/bitmap.py:
Added a resize attribute for a bitmap; it is set to True by
default. It is a flag that allows distinguishing between
topographica plot and static external images when resizing them.

* [r2433] doc/images/color_key.png:
Added the color_key png file in doc/images.

2006-02-09 ceball

* [r2432] topo/tests/lissom_oo_or_reference.ty:
Corrected setting LGN's density - I probably re-introduced
accidentally setting it on the CFSheet class.

* [r2431] topo/tests/lissom_oo_or_reference.ty:
Removed bounds change that has no effect at this density. Updated
learning rates.

* [r2430] examples/lissom_oo_or.ty:
Updated parameters to match the ones in
lissom_oo_or_reference.ty. There are more to go...

* [r2429] examples/lissom_oo_or.ty:
Simplified weights bounds specification with wt_bounds().

* [r2428] topo/tests/lissom_oo_or_reference.ty:
Removed last change_bounds for lateral excitatory connection
because it wouldn't occur anyway for this density.

* [r2427] topo/tests/lissom_or_reference.ty:
Added note to myself.

* [r2426] examples/lissom_or.ty:
Added a HACAKLERT about missing scheduled events.

* [r2425] topo/tests/lissom_oo_or_reference.ty:
Use wt_bounds() function to set weight bounds. Included
min_exc_rad parameter.

* [r2424] topo/base/connectionfield.py:
Removed print statement accidentally left in previous commit.

* [r2423] topo/base/connectionfield.py:
Added wt_bounds(), which allows a bounding box to be created with
simple syntax from a radius. Also allows specification of a
minimum radius. Added a HACKALERT about the change_bounds
warning.

* [r2422] topo/tests/oo_or_map_topo.log:
About 20000 iterations from the equivalent c++ lissom simulation.

* [r2421] topo/tests/lissom_oo_or_reference.ty:
Learning rates set on correct projections.

2006-02-09 jbednar

* [r2420] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore:
More to ignore

* [r2419]
doc/User_Manual/images/connection_field.fig,
doc/User_Manual/images/matrix_coords.fig,
doc/User_Manual/images/matrix_coords_hidensity.fig,
doc/User_Manual/images/sheet_coords.fig,
doc/User_Manual/images/sheet_coords_-0.275_-0.0125_0.025_0.2885.fig,
doc/User_Manual/images/sheet_coords_-0.2_0.4.fig:
Made images line up; added some missing elements and removed some
stray ones, and added markings for similar features in different
plots

* [r2418]
doc/User_Manual/background_text.php.m4,
doc/User_Manual/basics_text.php.m4,
doc/User_Manual/features_text.php.m4,
doc/User_Manual/images/Makefile,
doc/User_Manual/space_text.php,
doc/User_Manual/time_text.php:
Reduced image sizes to allow two side by side, and added such
plots where appropriate

* [r2417] doc/Future_Work/index_text.php:
More work

2006-02-08 jbednar

* [r2416] topo/tests/lissom_oo_or_reference.ty:
LGNOn and LGNOff to V1 connection strengths halved. LGNOn and
LGNOff sheet bounds adjusted. (Chris)

2006-02-08 julienciroux

* [r2415] topo/plotting/plotgroup.py:
Added a function _add_static_images() in TemplatePlotGroup. It
creates the Plot specified by the static_images attribute of the
PlotGroupTemplate, and add them to the added_list of Plot (This
will still need some clean up).

* [r2414] topo/plotting/templates.py:
Added an attribute static_images to the PlotGroupTemplate and a
method add_static_image; static_images is a KeyedList of tuple
(name,file_path) specifying a Plot from an image file. It will
enable specifying additional static plots to a
Pl?\004otGroupTemplate (e.g. color key for Orientation
Preference). There is no images added to a template yet, because
the re-sizing needs to be fixed in PlotGroupPanel; therefore, the
line is commented out for the moment.

* [r2413] topo/plotting/plot.py:
Added a missing import statement; added a call to the super class
in the Plot __init__.

* [r2412] topo/plotting/bitmap.py,
topo/plotting/plot.py:
Deleted the unuseful FileBitmap class.

* [r2411] topo/plotting/plot.py,
topo/plotting/plotgroup.py,
topo/tests/testplot.py,
topo/tkgui/testpattern.py:
Renamed make_plot() to make_template_plot().

* [r2410] topo/plotting/plot.py:
Changed the Plot hierarchy: now the Plot class is really simple
and just creates its bitmap from an image; the former Plot class
has been renamed TemplatePlot, and others sub-classes inherit
from it. It remains to re-name the make_plot fun?\004ction to
make_template_plot. Also deleted the BitmapPlot class which is
now replaced by the simple Plot class.

2006-02-08 ceball

* [r2409] topo/tests/lissom_or_reference.ty:
Change to a comment.

* [r2408] topo/tests/lissom_oo_or_reference.ty:
Updates to parameters and learning rates.

* [r2407] topo/tests/lissom_oo_or_reference.ty:
Initial version; parameters don't yet match the equivalent c++
simulation.

* [r2406] topo/tests/oo_or_map_topo.log:
log file from oo_or_map_topo.param c++ simulation.

* [r2405] topo/tests/lissom_or_reference.ty:
Added some comments.

* [r2404] examples/lissom_oo_or.ty:
Corrected typo in afferent_weight_bounds.

2006-02-07 julienciroux

* [r2403] topo/responsefns/optimized.py:
Simplified the CFEuclideanDistance function; got rid of the
optimization in the code.

2006-02-07 ceball

* [r2402] examples/lissom_oo_or.ty:
Updated alpha and beta (V1.outputfn bounds).

2006-02-07 julienciroux

* [r2401] topo/responsefns/optimized.py:
Continued to clean up the CFDotProduct() code, using C++ syntax.

2006-02-07 ceball

* [r2400] examples/lissom_oo_or.ty:
Changed bounding boxes for circular rfs.

2006-02-07 julienciroux

* [r2399] topo/responsefns/optimized.py:
Simplified version of CFDotProduct().It still needs some clean up
(e.g using C++ syntax). It seems to perform a bit better than the
previous optimized version; in any case it does not do worse
(most of the times, the profiling statistics are better for the
new version).

2006-02-07 ceball

* [r2398] examples/lissom_or.ty:
Last commit contained an error - switched commented
afferent_weights_bounds with uncommented.

* [r2397] examples/lissom_or.ty:
No visible change. Committed commented-out code for circular
connection fields (including adjustments to input_bounds.

* [r2396] topo/tests/lissom_or_reference.ty:
Undid previous changes. I didn't notice that in c++ lissom the
changes to e.g. exc_radius were accumulating.

* [r2395] topo/tests/lissom_or_reference.ty:
Altered to match equivalent c++ lissom simulation: scheduled
lateral excitatory bounds changes, scheduled lateral excitatory
learning rates, scheduled afferent learning rates.

* [r2394] topo/tests/or_map_topo.log:
20001 iterations from c++ lissom's or_map_topo.param

* [r2393] examples/lissom_oo_or.ty:
Added learning rates and scheduled changes to them for LGN ON/OFF
afferents. Added some comments.

2006-02-06 jbednar

* [r2392] doc/User_Manual/simulator.html:
Not sure why this was checked in

* [r2391] doc/User_Manual,
doc/User_Manual/.cvsignore:
More to ignore

* [r2390] doc/User_Manual/coordinates_text.php,
doc/User_Manual/index_text.php,
doc/User_Manual/simulator_text.php,
doc/User_Manual/space_text.php,
doc/User_Manual/time_text.php:
Renamed files to reflect their contents

* [r2389] doc/User_Manual/coordinates_text.php,
doc/User_Manual/index_text.php,
doc/User_Manual/simulator_text.php:
Clarified distinction between time and space topics

* [r2388] doc/User_Manual/coordinates_text.php:
Fixed Sheet coordinate errors found by Julien

2006-02-06 ceball

* [r2387] topo/tests/lissom_or_reference.ty:
Removed a HACKALERT - clarified why scheduled events are at one
time-step less than the equivalent or_map_topo's.

2006-02-06 jbednar

* [r2386]
doc/Tutorials/som_retinotopy_text.php:
Fixed typos; clarified SOM algorithm

2006-02-06 ceball

* [r2385] topo/responsefns/optimized.py:
Same change to CFEuclideanDistance as to CFProjection (i.e. same
changes as were made to CFProjection in the previous two
commits).

* [r2384] topo/responsefns/optimized.py:
Removed the variables or and oc (that were having no effect and
should have been removed in the previous version).

* [r2383] topo/responsefns/optimized.py:
Removed an apparently problematicoptimization from CFProjection,
but it needs to be done properly. Julien is going to do this, and
make the same change to CFEuclideanDistance.

2006-02-06 jbednar

* [r2382] doc/User_Manual/simulator_text.php:
Minor clarification

* [r2381] doc/User_Manual/coordinates.html:
Not sure why this generated file was ever checked in

2006-02-06 julienciroux

* [r2380] topo/plotting/plot.py:
New class BitmapPlot that is just a Plot constructed by
specifying a file path.

* [r2379] topo/plotting/bitmap.py:
New class FileBitmap that just creates a Bitmap from a file path.

2006-02-06 jbednar

* [r2378] doc/User_Manual/simulator.html:
Clarification

* [r2377] doc/User_Manual/coordinates.html,
doc/User_Manual/simulator.html,
doc/User_Manual/simulator_text.php:
Initial version

* [r2376] doc/User_Manual/basics_text.php.m4:
Removed items now implemented elsewhere

* [r2375] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore:
More to ignore

* [r2374] doc/User_Manual/index_text.php:
Added link to simulator.html

* [r2373]
doc/User_Manual/images/clocked-timeline.fig,
doc/User_Manual/images/connection_field.fig,
doc/User_Manual/images/connection_field_master.fig,
doc/User_Manual/images/event-driven-timeline.fig,
doc/User_Manual/images/matrix_coords.fig,
doc/User_Manual/images/matrix_coords_hidensity.fig,
doc/User_Manual/images/sheet_coords.fig,
doc/User_Manual/images/sheet_matrix_master.fig,
doc/User_Manual/images/sheet_matrix_master_hidensity.fig:
Sorted labels in order for easier editing

* [r2372] doc/User_Manual/coordinates_text.php,
doc/shared/util.php:
Moved classref function to shared utils file

* [r2371] doc/User_Manual/coordinates_text.php,
doc/User_Manual/index_text.php:
Added coordinates page

* [r2370]
doc/User_Manual/images/connection_field.fig,
doc/User_Manual/images/matrix_coords.fig,
doc/User_Manual/images/sheet_matrix_master.fig,
doc/User_Manual/images/sheet_matrix_master_hidensity.fig:
Fixed bogus labels

* [r2369] doc/Makefile:
Added automatic making of images

* [r2368] doc/User_Manual/features_text.php.m4:
Fixed path

* [r2367] doc/User_Manual/background_text.php,
doc/User_Manual/background_text.php.m4,
doc/User_Manual/basics_text.php,
doc/User_Manual/basics_text.php.m4,
doc/User_Manual/features_text.php,
doc/User_Manual/features_text.php.m4:
Moved .php files to .m4 files for now

* [r2366] doc,
doc/.cvsignore,
doc/Makefile,
doc/shared/topographica.bib:
Added m4 preprocessing and bib2html support for .php.m4 files

2006-02-05 jbednar

* [r2365] doc/shared/bib2html.m4:
Copied from lib/nn/tex/bib2html/bib2html.m4

* [r2364] doc/shared/bib2html,
doc/shared/bib2html/.cvsignore,
doc/shared/bib2html/README,
doc/shared/bib2html/bib2html,
doc/shared/bib2html/bib2html.m4,
doc/shared/bib2html/bib2html.man,
doc/shared/bib2html/bibsearch,
doc/shared/bib2html/gen-bst,
doc/shared/bib2html/html-btxbst.doc,
doc/shared/bib2html/makefile:
Initial version

2006-02-05 alan_lindsay

* [r2363] topo/tkgui/parametersframe.py:
Allows the current value to belong to a class that is not one of
the usual classes for a given parameter. This allows
CFProjections to be manipulated.

* [r2362] topo/tkgui/parametersframe.py:
Seems to allow updating of connections and sheets and selected
classes within fields of these.

* [r2361] topo/tkgui/parametersframe.py:
Allows a dictionary, with a list entry for fields of the object,
to be passed in; these lists are searched for object covers for
each of the possible classes of a class selector item. Works for
sheets.

2006-02-05 ceball

* [r2360] topo/tests/or_map_topo.log:
About 200 iterations from current c++ reference.

* [r2359] topo/tests/lissom_or_reference.ty:
Use only integer part of rf_radius, as c++ LISSOM does.

* [r2358] topo/responsefns/optimized.py:
Added missing import statement.

2006-02-04 alan_lindsay

* [r2357] topo/base/utils.py:
a method that takes a dictionary and a key and returns
dictionary[key] or key if it doesn't exist.

* [r2356] topo/tkgui/parametersframe.py:
First attempt at allowing a translator dictionary to be passed to
parameter frame, has broken embedded class property windows
though.

* [r2355] topo/tkgui/editorwindow.py:
Displays activity as soon as you set it. Does not need refreshed
anymore.

* [r2354] topo/tkgui/parametersframe.py:
Class selector fields can have there properties modified. These
are lost as soon as the original object is updated. Works for
TestPatterns.

2006-02-03 jbednar

* [r2353]
doc/Tutorials/som_retinotopy_text.php:
Fixed paths

2006-02-03 alan_lindsay

* [r2352] topo/tkgui/parametersframe.py:
The object's current value is now selected in ComboBox.

2006-02-03 jbednar

* [r2351] examples/som_retinotopy.ty:
Fixed typo in last checkin

* [r2350] doc/Downloads/index_text.php:
Clarified issue found by Yoonsuck

2006-02-03 chrispalmer

* [r2349] topo/patterns/basic.py:
Added initial version of CompositePatternGenerator. There seems
to be a problem with Parameter, which needs to be investigated.

2006-02-03 julienciroux

* [r2348] topo/tkgui/connectionfieldspanel.py:
Renamed unitweightspanel to connectionfieldspanel.

* [r2347] topo/tkgui/topoconsole.py,
topo/tkgui/unitweightspanel.py:
topo/tkgui/connectionfieldspanel.py

* [r2346]
topo/tests/tkgui/testtemplateplotgrouppanel.py:
Forgotten assert line in previous commit.

* [r2345] topo/tests/tkgui/__init__.py,
topo/tests/tkgui/testtemplateplotgrouppanel.py:
Corrected a strange bug in testtemplateplotgrouppanel.py. The
'case' notation was not working there.. maybe because the
tests/tkgui/ directory is a sub-directory?

2006-02-03 ceball

* [r2344] topo/tests/tkgui/__init__.py:
Commented out import of test that doesn't seem to run properly.
It's not clear why it doesn't run.

2006-02-03 julienciroux

* [r2343] topo/tkgui/plotgrouppanel.py,
topo/tkgui/topoconsole.py,
topo/tkgui/unitweightspanel.py:
Renamed the class UnitWeightsPanel to ConnectionFieldsPanel.

2006-02-03 jbednar

* [r2342] doc/User_Manual/about_text.php,
doc/User_Manual/background_text.php,
doc/User_Manual/basics_text.php,
doc/User_Manual/features_text.php,
doc/User_Manual/index_text.php:
Moved material in comments into other unlinked files

* [r2341] doc/User_Manual,
doc/User_Manual/.cvsignore:
More to ignore

* [r2340] doc/User_Manual/images/Makefile:
Added special handling for one PDF->PNG conversion

2006-02-03 ceball

* [r2339] examples/lissom_oo_or.ty:
Still not tested. Changed LGN connections.

2006-02-03 jbednar

* [r2338] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore:
More to ignore

* [r2337] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore:
Ignore PNG too

* [r2336] doc/User_Manual/images,
doc/User_Manual/images/.cvsignore,
doc/User_Manual/images/Makefile,
doc/User_Manual/images/connection_field.fig,
doc/User_Manual/images/connection_field_master.fig,
doc/User_Manual/images/epstopdf,
doc/User_Manual/images/generic-cortical-hierarchy-model.fig,
doc/User_Manual/images/matrix_coords.fig,
doc/User_Manual/images/retina_edge_buffer.fig,
doc/User_Manual/images/sheet_coords.fig,
doc/User_Manual/images/sheet_matrix_master.fig,
doc/User_Manual/images/sheet_matrix_master_hidensity.fig,
doc/User_Manual/images/toplevel.fig,
doc/User_Manual/images/toplevel_bare.fig:
Initial version

* [r2335] doc/User_Manual/images,
doc/User_Manual/images/face-blurred-off-stretched-sheared.gif,
doc/User_Manual/images/face-blurred-on-stretched-sheared.gif,
doc/User_Manual/images/face-blurred-stretched-sheared.gif,
doc/User_Manual/images/measuring-map.v3.pdf:
Version from book

2006-02-03 ceball

* [r2334] topo/tests/or_map_topo.log:
Updated for changes to c++ lissom's params file.

* [r2333] topo/tests/lissom_or_reference.ty:
Changed rf_radius, inh_rad, and exc_rad. Changed
retina_edge_buffer and RN. Altered layout at start of file to
look more like equivalent c++ lissom params file. The input
pattern is identical to C++ lissom, but the activity in V1 has
not y?\004et been matched (the parameters aren't all being used
correctly).

2006-02-03 jbednar

* [r2332] topo/commands/pylabplots.py:
Added simple vector and matrix plots for the command line

* [r2331] topo/commands/lineplotting.py,
topo/commands/pylabplots.py,
topo/tkgui/templateplotgrouppanel.py:
Renamed lineplotting.py to pylabplots.py in anticipation of new
non-line-based plot

* [r2330] doc/Downloads/index_text.php,
doc/Home/index_text.php,
doc/Reference_Manual/index_text.php,
doc/shared/index.php,
doc/shared/util.php:
Moved Tutorial to Tutorials now that there are more than one

* [r2329] doc/Tutorial,
doc/Tutorials,
doc/Tutorials/.cvsignore,
doc/Tutorials/images,
doc/Tutorials/images/activity_gaussian.png,
doc/Tutorials/images/activity_gaussian_or.png,
doc/Tutorials/images/activity_line.png,
doc/Tutorials/images/activity_line_or.png,
doc/Tutorials/images/lissom_network_diagram.png,
doc/Tutorials/images/or_key_horiz_transparent.png,
doc/Tutorials/images/or_key_vert_transparent_topo.png,
doc/Tutorials/images/or_map.png,
doc/Tutorials/images/projection.png,
doc/Tutorials/images/som_activity_000000.png,
doc/Tutorials/images/som_activity_000001.png,
doc/Tutorials/images/som_activity_000006.png,
doc/Tutorials/images/som_cog_000000.png,
doc/Tutorials/images/som_cog_000100.png,
doc/Tutorials/images/som_grid_000000.png,
doc/Tutorials/images/som_grid_000100.png,
doc/Tutorials/images/som_grid_010000.png,
doc/Tutorials/images/som_grid_040000.png,
doc/Tutorials/images/som_network_diagram.png,
doc/Tutorials/images/som_projection_000000.png,
doc/Tutorials/images/som_projection_000001.png,
doc/Tutorials/images/som_projection_000006.png,
doc/Tutorials/images/som_projection_040000.png,
doc/Tutorials/images/test_pattern.png,
doc/Tutorials/images/topographica_console.png,
doc/Tutorials/images/unit_weights_0.2_0.0.png,
doc/Tutorials/images/unit_weights_0.2_0.0_or.png,
doc/Tutorials/images/unit_weights_0_0.png,
doc/Tutorials/images/unit_weights_0_0_or.png,
doc/Tutorials/index_text.php,
doc/Tutorials/lissom_or_text.php,
doc/Tutorials/som_retinotopy_text.php:
Moved Tutorial to Tutorials now that there are more than one

2006-02-02 julienciroux

* [r2328] examples/obermayer_pnas90.ty:
Corrected the initial and final learning rate value, according to
the new changes in learning rate computation in HebbianSOMLF().

* [r2327] topo/plotting/plotgroup.py:
Fixed sort_plot() according to the new changes in Plot. Cleaned
up comments and doc.

* [r2326] topo/tests/tkgui/__init__.py,
topo/tests/tkgui/testactivitypanel.py,
topo/tests/tkgui/testbasicplotgrouppanel.py,
topo/tests/tkgui/testtemplateplotgrouppanel.py:
Renamed testbasicplotgrouppanel.py to
testtemplateplotgrouppanel.py. Also deleted testactivitypanel.py
and put the code that was in it into
testtemplateplotgrouppanel.py.

* [r2325]
topo/tests/tkgui/testbasicplotgrouppanel.py:
Forgotten in previous commit.

* [r2324]
topo/tests/tkgui/testactivitypanel.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/templateplotgrouppanel.py,
topo/tkgui/topoconsole.py:
Renamed basicplotgrouppanel.py to templateplotgrouppanel.py.

2006-02-02 ceball

* [r2323] examples/lissom_oo_or.ty:
Rearranged file to make more sense - no visible change.

* [r2322] topo/learningfns/optimized.py:
Added HACKALERT about C pointer version of DivisiveHebbian.

* [r2321] topo/tests/testlissom_cpointer.ty:
Cleaned up connecitions (removed connection_params, but also
sharedweight projection code). Added a HACKALERT.

* [r2320] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_oo_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/base/simulator.py,
topo/tests/lissom_or_reference.ty,
topo/tests/testcfsom.py,
topo/tests/testfeaturemap.py,
topo/tests/testlissom.ty,
topo/tests/testpatternpresent.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py:
Made syntax to specificy connections simpler by removing
'connection_params' and using a dictionary of keywords. Left a
note by Simulator.connect() about adding a dictionary back in for
extra parameters should they later be required.

2006-02-02 jbednar

* [r2319] doc/Tutorial,
doc/Tutorial/.cvsignore:
More to ignore

* [r2318] topo/commands/lineplotting.py:
Reduced default topographic grid figure size

* [r2317]
doc/Tutorial/images/som_activity_000000.png,
doc/Tutorial/images/som_activity_000001.png,
doc/Tutorial/images/som_activity_000006.png,
doc/Tutorial/images/som_cog_000000.png,
doc/Tutorial/images/som_cog_000100.png,
doc/Tutorial/images/som_grid_000000.png,
doc/Tutorial/images/som_grid_000100.png,
doc/Tutorial/images/som_grid_010000.png,
doc/Tutorial/images/som_grid_040000.png,
doc/Tutorial/images/som_network_diagram.png,
doc/Tutorial/images/som_projection_000000.png,
doc/Tutorial/images/som_projection_000001.png,
doc/Tutorial/images/som_projection_000006.png,
doc/Tutorial/images/som_projection_040000.png,
doc/Tutorial/som_retinotopy_text.php:
Initial version

* [r2316] doc/shared/util.php:
Added alert

* [r2315] topo/plotting/plot.py,
topo/tkgui/projectionpanel.py:
Added an alert

* [r2314] topo/base/sheet.py:
Fixed typo

* [r2313] doc/Reference_Manual/index_text.php:
Added explanation of why to read or avoid this manual

* [r2312] doc/Future_Work/index_text.php:
Added notes from meetings, etc.

* [r2311] doc/Downloads/index_text.php:
Added note about CVS

2006-02-01 julienciroux

* [r2310] topo/tests/testplotgroup.py,
topo/tests/tkgui/testactivitypanel.py,
topo/tests/tkgui/testbasicplotgrouppanel.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/cfsheetplotpanel.py,
topo/tkgui/topoconsole.py:
Renamed BasicPlotGroupPanel to TemplatePlotGroupPanel.

2006-02-01 alan_lindsay

* [r2309] topo/tkgui/editorwindow.py:
Tidied and some of the methods written a little nicer.

2006-02-01 julienciroux

* [r2308] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/unitweightspanel.py:
Renamed UnitWeightsPlotGroup to ConnectionFieldsPlotGroup, for
consistency with the template name. Nevertheless, I realised that
it might be confusing from a developper point of view: the
concept of CF is different that the weights of a unit, i.e. we
can have sheets with no CF and still vizualize the weights of a
unit.

* [r2307] topo/plotting/templates.py,
topo/tkgui/topoconsole.py:
Renamed the Connection Field template to Connection Fields
(plural).

* [r2306] topo/tkgui/testpattern.py:
Deleted two old ALERTS and wrote a new one.

* [r2305] topo/plotting/bitmap.py,
topo/plotting/plot.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/unitweightspanel.py:
Replaced the Bitmap's view_info attribute by a name and
plot_src_name attributes; they are copies of the plot's
attributes of the same name. Now, the string that has to be
displayed is built from these two attributes in PlotGroupPanel's
display_labels(). The UnitWeightPanel() display_labels method has
to be modified: connection fields panel and projection's panel do
not handle labels as a normal BasicPlotGroupPanel.

2006-02-01 ceball

* [r2304] examples/lissom_oo_or.ty:
Changed V1's density to 48. Changed CFSheet's density to 24.
Connected on and off LGN sheets to V1, though not properly.

* [r2303] topo/projections/basic.py:
If a unit is near the sheet edge, the shared weights matrix will
not necessarily be the right matrix - the correct submatrix is
needed. Added code to do that.

* [r2302] topo/base/connectionfield.py:
Changed the function that was for slicing the mask matrix to one
that returns the slice.

2006-02-01 julienciroux

* [r2301] topo/plotting/plot.py,
topo/plotting/plotgroup.py:
Replaced the Plot attribute view_info (a dict) by a single
plot_src_name. It has still to be changed in future commit.

* [r2300] topo/base/connectionfield.py,
topo/base/sheetview.py,
topo/commands/analysis.py,
topo/plotting/plot.py,
topo/projections/basic.py,
topo/tests/testplot.py,
topo/tests/testsheet.py,
topo/tests/testsheetview.py:
Deleted the attribute view_info of a SheetView, replaced by a
single src_name attribute. Deleted the parameter view_type that
wasn't of any use. Also added two ALERT in sheetview.py that will
have to be examined.

2006-02-01 ceball

* [r2299] topo/tests/lissom_or_reference.ty:
Added performance profiling code examples back in (they're
commented out).

2006-02-01 julienciroux

* [r2298] examples/cfsom_or.ty,
examples/hierarchical.ty:
Corrected the learning rate now that the HebbianSOMLF function
does not use the constant_sum_connection_rate() anymore.

* [r2297] examples/som_retinotopy.ty:
Adapted the min radius to be set like in the book (0.5/40 in
sheet coordinates), now that there is a crop_radius. It gives a
good result (with the same parameters than in the book: 40 units
and so on...), but I did not compared it with our previous result
with a radius of 1.25/40.

* [r2296] examples/som_retinotopy.ty:
Made the simulation use the new C coded CFEuclideanDistance()
function; also corrected the generator sheet density to be 24 (it
has been committed with a value of 40, by mistake). Also got rid
of unused commented out code.

* [r2295] topo/responsefns/optimized.py:
C version of the CFEuclideanDistance reponse function. It is
mostly based on the C version of CFDotProduct().It does seem to
be about 1.5 times faster (when it took 1mn it now takes 40s). It
could probably be even faster (as well as the CFDotProduct() C
version, I think) but would need more work.

2006-01-31 julienciroux

* [r2294] topo/plotting/palette.py:
Started an implementation of the String-Based Palette class. It
is just committed for my convenience, but there is nothing
finished at all; it shouldn't affect anything to commit it
though.

* [r2293] examples/som_retinotopy.ty,
topo/learningfns/basic.py:
Fixed afferent learning rate scaling for SOMs; i.e, don't need
scaling at all for this learning function. Changed the
crop_radius for the neighborhood function to have a minimum
radius, to ensure that it covers at least a neighboring unit in
each direction

2006-01-31 ceball

* [r2292] examples/lissom_oo_or.ty:
Initial version - incomplete. Based on lissom_or.ty, but with
circular connectionfields.

* [r2291] topo/projections/basic.py:
Updated SharedWeightCFProjection to match changes in
connectionfield and cfprojection. Not yet tested.

* [r2290] topo/tests/or_map_topo.log:
20009 iterations from c++ lissom.

* [r2289] topo/tests/lissom_or_reference.ty:
Updated learning rates to correct ones from lissom_or.ty before
it was split into lissom_or.ty and lissom_or_reference.ty. THey
were lost when lissom_or_reference was reverted to 21st December
2005 code.

2006-01-30 ceball

* [r2288] topo/tests/lissom_or_reference.ty:
Back to the previous network size (BaseN=72).

* [r2287] topo/tests/or_map_topo.log:
200 iterations from c++ lissom

* [r2286] topo/tests/lissom_or_reference.ty:
Using a smaller network.

* [r2285] topo/base/connectionfield.py,
topo/tests/lissom_or_reference.ty:
Altered some hackalerts.

* [r2284] topo/base/connectionfield.py:
Mask centered on matrixidx center.

* [r2283] topo/tkgui/testpattern.py:
Added hack to remove Random Generator from the list of
PatternGenerators in the test pattern window. But it will still
appear in other menus.

2006-01-30 jbednar

* [r2282] ChangeLog:
Updated with recent changes

2006-01-30 julienciroux

* [r2281] topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Renamed the single_connection_learning_rate() to
constant_sum_connection_rate(); it indicates that the learning
rate is scaled based on keeping the sum constant,which leaving it
open for adding other types of connection_rate() functions.

* [r2280] topo/analysis/featuremap.py,
topo/plotting/bitmap.py:
Modified featuremap so that in the case of a cyclic value the
preference matrix is normalized, but not in the case of a
non-cyclic value. It solves the problem of the position
preference plot shrinking when increasing the range of values.
Though it might be an alright reasoning, an hack alert has been
added in FeatureMap and in bitmap.py, because it made me realised
that if this normalization is not performed for a sheetview that
will be used as the hue key in an HSV plot, an error will occur
in bitmap. Therefore, we should think about this case, and decide
what to do to avoid unexpected errors in the future.

* [r2279] topo/commands/analysis.py:
Corrected a mistyped parenthesis.

2006-01-30 ceball

* [r2278] topo/base/connectionfield.py:
Mask is resized by change_bounds() in a way that is consistent
with how it's generated in the first place. Not sure if it's the
right way though - these changes have not yet been verified (but
the resizing is better than before, in any cas?\004e).

* [r2277] topo/base/connectionfield.py:
ConnectionField.__init__()'s mask creation code is moved to a
subroutine.

* [r2276] topo/base/connectionfield.py:
Moved CFProjection's mask creation code to a subroutine.

* [r2275] topo/base/connectionfield.py:
weight_type no longer an attribute of CFProjection (and no longer
passed to ConnectionField). Instead, it's a global variable.

* [r2274] topo/base/connectionfield.py:
Corrected variable name error in previous commit. Updated a
HACKALERT.

* [r2273] topo/tests/lissom_or_reference.ty:
Changed to circular ConnectionFields.

* [r2272] topo/base/connectionfield.py:
Mask pattern is generated in CFProjection and passed to each
ConnectionField. A ConnectionField takes the correct submatrix of
this mask (which is all of the mask, unless it is near an edge.
The way this is done needs to be simplified, but?\004 is
currently working. The size calculated for a mask that is e.g. a
Disk does not appear to be correct.

2006-01-30 jbednar

* [r2271] topo/patterns/random.py:
Made RandomGenerator base class to make it simpler to add other
Random classes. Added GaussianRandom

2006-01-29 jbednar

* [r2270] examples/som_retinotopy.ty:
Cleaned up comments

* [r2269] examples/som_retinotopy.ty:
Changed density to match lissombook

* [r2268] topo/learningfns/basic.py:
Changed crop_radius_multiplier to match fm2d; will make
simulations much slower but much more likely to work. Also added
commented-out print function printing parameters in the format of
fm2d

* [r2267] topo/learningfns/basic.py:
Added radius_crop_multiplier. Shouldn't have changed the behavior
at all yet.

2006-01-29 ceball

* [r2266] topo/base/connectionfield.py:
Corrected mistake in previous version.

* [r2265] examples/hierarchical.ty,
topo/base/connectionfield.py:
Masks are setup with the size of the weights_bounds_template.
This is an intermediate checkin for how it will work, but the
specification of the weights_shape at the user level code won't
change. hierarchical contains a commented-out example.

2006-01-29 jbednar

* [r2264] examples/som_retinotopy.ty:
Cleaned up comments and documentation

* [r2263] topo/learningfns/basic.py:
Fixed to match recent change in definition of Gaussian
PatternGenerator size

* [r2262] topo/plotting/templates.py:
Added CoG plot

* [r2261] topo/commands/lineplotting.py:
Added user-controllable sheet_view names for x and y preferences
in topographic_grid. Suppressed annoying plotting display glitch.

* [r2260] topo/commands/analysis.py:
Added measure_cog function. Added user-controllable x_range and
y_range parameters to measure_position_pref.

* [r2259] topo/base/arrayutils.py:
Added centroid function written by Julien

* [r2258] topo/responsefns/basic.py:
Improved CFEuclideanDistance_Py

* [r2257] topo/base/sheet.py:
Added alert

2006-01-29 ceball

* [r2256] topo/base/connectionfield.py:
initialize_slice_array() changed to initialize_bounds().
initialize_bounds() takes the centered bounds, converts them to a
slice at the origin of the sheet, then translates that slice to
the cf's location, and finally stores the correspond?\004ing
bounding box (and slice_array for access by C). Removed
set_slice_array().

* [r2255] topo/base/patterngenerator.py:
Removed a CEBHACKALERT, which was out of date.

2006-01-29 jbednar

* [r2254] topo/misc/patternfns.py,
topo/patterns/basic.py:
Changed name of height and width for gaussian and gabor to xsigma
and ysigma, to avoid confusion (since they are radii and not
actual widths and heights)

* [r2253] doc/Reference_Manual/index_text.php:
Minor updates

2006-01-29 julienciroux

* [r2252] topo/plotting/plotfilesaver.py:
Added a class TemplateFile to plotfilesaver. It is just a first
try for implementing plotfilesaver. Just committed for my
convenience (i.e. beeing able to work on it at the office.)

2006-01-28 ceball

* [r2251] doc/Downloads/win32_text.php:
Corrected scipy install command.

2006-01-28 julienciroux

* [r2250] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tests/testplotgroup.py,
topo/tkgui/basicplotgrouppanel.py:
Renamed BasicPlotGroup to TemplatePlotGroup.

* [r2249] topo/patterns/basic.py:
Changed the default size value for the Gaussian to be 0.5 (to
match recent changes in Gaussian size definition).

* [r2248] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/unitweightspanel.py:
Changed the hierarchy of the PlotGroup classes: now PlotGroup is
a simpler class that works by passing it a plot_list of plots,
while BasicPlotGroup (soon to be renamed TemplatePlotGroup)
implements the generation of the plot_list according to a
template specification; others PlotGroup classes now inherit from
BasicPlotGroup.

* [r2247] examples/cfsom_or.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/patterns/basic.py,
topo/tests/lissom_or_reference.ty,
topo/tests/testlissom.ty,
topo/tests/testlissom_cpointer.ty:
Modified the size parameter for a Gaussian so that it corresponds
to the real size (and it is consistent with the definition of the
size for,e.g. a disk or rectangle). The width of the Gaussian
(sigma) corresponds to half the size.

* [r2246] topo/base/sheet.py:
Updated doc for slice2bounds().

* [r2245] examples/som_retinotopy.ty:
Added some commentary; working version for switching from
CFDotProduct to CFEuclideanDistance_Py response function. Left
with a density of 10, used during testing.

* [r2244] topo/responsefns/basic.py:
First version of an euclidean-distance response function. This is
supposed to be used by the som_retinotopy example, but did not
allow to achieve the expected result yet.

2006-01-28 ceball

* [r2243] topo/base/connectionfield.py:
Removed line left in by mistake in the previous commit.

2006-01-28 jdepaula

* [r2242] doc/Downloads/index_text.php:
Changed line about Windows install to use CVS

* [r2241] doc/Downloads/win32_text.php:
added that scipy_core is already in external

2006-01-28 ceball

* [r2240] topo/plotting/plot.py:
Restored situate, but haven't checked it's correct.

* [r2239] topo/base/sheet.py:
Added initial version of Slice object; currently unused and
untested.

* [r2238] topo/patterns/basic.py:
Simplified a little - nobody would be passing in pattern_x and
pattern_y as parameters.

* [r2237] topo/base/parameter.py,
topo/base/topoobject.py:
A TopoObject is 'uninitialized' until its __init__() method
completes. A Constant Parameter can be set on an uninitialized
TopoObject.

2006-01-27 ceball

* [r2236] topo/plotting/plot.py:
slice2matrixshape() removed and replaced with current functions
from sheet (bounds2slice() with crop_slice_to_sheet_bounds),

* [r2235] topo/base/connectionfield.py,
topo/base/patterngenerator.py,
topo/base/sheet.py,
topo/patterns/image.py,
topo/patterns/random.py,
topo/tests/testsheet.py:
PatternGenerator no longer takes slice_array from
ConnectionField. Now, it is passed the ConnectionField's bounds
and x and y location. PatternGenerator still evaluates the
pattern in the center rather than at the ConnectionField's
location. bounds2slice()-type functions are tidied up a bit in
sheet. lissom_or_reference behavior is unchanged.

* [r2234] topo/tests/lissom_or_reference.ty:
Updated to current Topographica code (had been setup for
2005/12/21 code). Actual tests commented out.

* [r2233] topo/plotting/plot.py:
Accidentally checked in a half-finished version previously.

* [r2232] topo/plotting/plot.py:
Changed to work with different functions in sheet.py. The changes
will probably need updating after work on sheet.py is finished.

* [r2231] topo/base/connectionfield.py,
topo/base/sheet.py:
No visible changes. Removed bounds2shape(). Temporary
modification to bounds2slice() allowing it to skip cropping the
slice to the sheet. Temporarily added slice2matrixshape().
ConnectionField temporarily modified so its behavior is
unchanged.

* [r2230] topo/patterns/image.py:
Removed use of bounds2shape() function. Image is now broken, but
does not cause errors. To be fixed after modification of sheet.py
is finished.

* [r2229] topo/tests/testsheet.py:
Commented-out bounds2shape() tests. They will be replaced with an
equivalent test.

* [r2228] topo/tests/testlissom.ty:
CFDotProduct moved to topo/responsefns/optimized.py

2006-01-27 jbednar

* [r2227] doc/Downloads/win32_text.php:
Added Id tag

* [r2226] doc/Downloads/win32_text.php:
Minor updates

2006-01-26 ceball

* [r2225] topo/tkgui/editorwindow.py:
Removed an import that was preventing the tests from running.

* [r2224] topo/base/sheet.py:
Temporary hack (I'm sorry) in bounds2shape() to get round a
problem (which only occurs for some bounds and densities) in
bounds2slice() - I think it's a floating point issue.

2006-01-26 jdepaula

* [r2223] doc/Downloads/win32_text.php:
Extensive revision to directions, turned into steps, and Weave is
now more of a natural part of the installation process.

2006-01-26 ceball

* [r2222] topo/tests/testsheet.py:
Added a test that involves the kind of situation that exists in
creating a connection field. The test fails because
bounds2shape() returns the wrong shape. Is the problem a floating
point issue?

2006-01-26 alan_lindsay

* [r2221] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Activity of a sheet can be displayed in the Editor, upsidedown..

2006-01-26 jbednar

* [r2220] topo/commands/lineplotting.py:
Added ALERT

* [r2219] examples/lissom_or_20000.typ:
This version was self-organized again, instead of just editing
the file to change the path (though that seemed to work fine)

* [r2218] examples/lissom_or_20000.typ:
Moved inlinec-dependent functions from responsefns/basic.py to
responsefns/optimized.py

2006-01-26 julienciroux

* [r2217] topo/plotting/plot.py:
Added doc for _normalize() and _situate_plot().

* [r2216] topo/plotting/plot.py:
Corrected normalize again: in case of a negative or zero
constant, a zero matrix is returned; in case of a positive value,
a one matrix is returned.

2006-01-26 jbednar

* [r2215] topo/commands/analysis.py:
Fixed docstring

2006-01-26 julienciroux

* [r2214] topo/plotting/plot.py:
Corrected _normalize() so that it returns a one matrix in case of
a constant.

2006-01-26 jbednar

* [r2213] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
examples/som_retinotopy.ty,
topo/projections/optimized.py,
topo/responsefns/basic.py,
topo/responsefns/optimized.py,
topo/tests/testplotgroup.py:
Moved inlinec-dependent functions from basic.py to optimized.py

* [r2212] topo/learningfns/optimized.py:
Minor documentation cleanup

2006-01-25 jbednar

* [r2211] ChangeLog:
Updated with recent changes

* [r2210] topo/commands/lineplotting.py:
Enforced minimum size of topographic map plots

2006-01-25 julienciroux

* [r2209] topo/commands/analysis.py,
topo/plotting/templates.py:
Changed the name of the template CoG Preference to be Position
Preference. Also changed measure_cog() to be named
measure_position_pref().

2006-01-25 jbednar

* [r2208] topo/learningfns/basic.py:
Added question about proper scaling for a SOM learning rate

* [r2207] topo/sheets/lissom.py:
Added tsettle alert

* [r2206] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
examples/som_retinotopy.ty:
Changed all parameter files to remove initial iteration so that
the user can inspect an untrained network

* [r2205] topo/base/parameter.py:
Added alert

* [r2204] doc/shared/util.php:
Minor tweak

2006-01-25 ceball

* [r2203] topo/base/sheet.py:
bounds2shape() uses bounds2slice() to get the matrix shape.

* [r2202] topo/base/connectionfield.py,
topo/base/patterngenerator.py,
topo/patterns/random.py:
PatternGenerator no longer uses bounds2shape(); instead, it uses
bounds2slice(). If the slice is already known, it can be passed
in (as an optimization, like rows and cols could be passed in
before). There should be no visible changes.

2006-01-25 julienciroux

* [r2201] examples/som_retinotopy.ty:
Corrected an error in last commit.

* [r2200] examples/som_retinotopy.ty:
Version that appears to match the parameter in the book, but
still does not give the expected results with Topographica.

* [r2199] topo/commands/analysis.py:
Improved the code in PatternPresenter: now use the __setattr__
method rather than an exec to update the pattern generator
attributes.

* [r2198] examples/som_retinotopy.ty:
Adjusted the parameters to match the simulation in the book.

* [r2197] topo/plotting/plotgroup.py:
Minor cleaning.

2006-01-24 jdepaula

* [r2196] doc/Downloads/index_text.php,
doc/Downloads/win32_text.php:
Updated documentation for Windows port

2006-01-24 julienciroux

* [r2195] topo/plotting/__init__.py:
Deleted plotengine from the plotting/__init__.py file.

* [r2194] topo/plotting/templates.py:
Cleaned up old alerts.

* [r2193] topo/tkgui/plotgrouppanel.py:
Cleaned up comments and old alerts.

2006-01-24 jdepaula

* [r2192] external/win32/setup.py:
Added header information about the different steps within
setup.py

* [r2191] external/win32/README.txt:
Moved what the code in setup.py does, into setup.py

2006-01-24 julienciroux

* [r2190] topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/cfsheetplotpanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py,
topo/tkgui/unitweightspanel.py:
Deleted the parameter plotgroup_type and plotgroup_key when
creating a PlotGroupPanel.

2006-01-24 jdepaula

* [r2189] topo/misc/inlinec.py,
topographica_script.py:
Changed direction of importing. Lowercased variable.

2006-01-24 julienciroux

* [r2188] topo/tkgui/plotgrouppanel.py:
Re-organized import statements.

* [r2187] topo/plotting/plot.py:
Added the normalizing for the RGBPlot.

* [r2186] topo/tkgui/cfsheetplotpanel.py:
Got rid of unused default value.

* [r2185] topo/plotting/templates.py:
Deleted the normalize field in the plot_templates. Now, normalize
is only specified for a PlotGroupTemplate.

* [r2184] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/unitweightspanel.py:
Added a parameter normalize to be passed to a PlotGroup. Now the
information normalize is no longer passed through the template
but rather by modifying the PlotGroup.normalize attribute.

2006-01-24 ceball

* [r2183] topo/base/sheet.py:
bounds2slice() always returns int values.

2006-01-24 julienciroux

* [r2182] topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/unitweightspanel.py:
Renamed the PlotGroupPanel attribute plot_group to
plot_group_title.

* [r2181] topo/tkgui/plotgrouppanel.py:
Started a re-organization of the file. Moved code around to made
it clearer. Added alert about how to improve the file, and take
the normalize information from the template rather than the first
plot_template. (This has been tested with version 1.42 of
sheet.py because the new version 1.43 has introduced an error in
the slicing of the sheetviews.)

2006-01-24 ceball

* [r2180] topo/base/sheet.py:
bounds2slice() returns the slice that includes all units whose
centres are within the specified bounds (and within the sheet's
bounds).

2006-01-24 julienciroux

* [r2179] topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/plotting/templates.py,
topo/tkgui/projectionpanel.py:
Got rid of the now un-used Density and Projection_name fields in
the Projection PlotGroupTemplate.

* [r2178] topo/commands/analysis.py:
Omitted in previous commit: changed the name of update_weights()
to update_connectionfields().

* [r2177] topo/plotting/templates.py,
topo/tkgui/topoconsole.py,
topo/tkgui/unitweightspanel.py:
Renamed the Unit Weights template to Connection Field; made the
corresponding change in topoconsole. Also modified the way labels
is display from the UnitWeightsPanel to display the name of the
template (as it is defined in templates.py). I think we might
renamed UnitWeightsPanel to ConnectionFieldPanel, it has to be
decided.

* [r2176] topo/plotting/templates.py:
Added a function new_plotgroup_template to create and store a
PlotGroupTemplate. Renamed add_plot_template() to add_plot(), and
re-write all the template creation using new_plotgroup_template()
and add_plot().

2006-01-23 ceball

* [r2175] examples/lissom_or.ty:
Added a note about the input_bounds.

2006-01-23 julienciroux

* [r2174] examples/cfsom_or.ty:
Added a comment to explain how to find the learning rate.

* [r2173] examples/som_retinotopy.ty:
Added the skeleton for the retinotopic map simulation. It has to
be modifiedf
so that the parameters exactly match the simulation published in
the book.

2006-01-23 alan_lindsay

* [r2172] topo/tkgui/editorobjects.py:
1st receptive field in centre and labels are closer to middle.

2006-01-23 ceball

* [r2171] topo/tests/testlissom.ty:
Added test for activity matrix size.

* [r2170] topo/base/connectionfield.py:
No visible change for networks that use weight generators like
COnstat() or UniformRandom(): weights patterns drawn at the
center of the sheet rather than at the ConnectionField's x and y
location (as used to be the case).

* [r2169] topo/base/sheet.py:
No visible change. Removed redundant 'maxrow+1', clarified
'toprow+1'. Cleaned up docstring.

* [r2168] topo/base/sheet.py:
No visible change. Altered variable names in bounds2slice().

2006-01-22 jbednar

* [r2167] examples/obermayer_pnas90.ty:
Made initial state be clean

* [r2166] topo/commands/lineplotting.py:
Minor tweaks

* [r2165] topo/commands/analysis.py:
Removed temporary plot_cog() command

* [r2164] topo/commands/lineplotting.py,
topo/plotting/templates.py,
topo/tkgui/basicplotgrouppanel.py:
Added topographic_grid plot

* [r2163] topo/commands/analysis.py:
Temporary commit to preserve octave-based topographic-grid
plotting; requires external command topogrid in ./external/

* [r2162] topo/analysis/updatecommands.py,
topo/commands/analysis.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/unitweightspanel.py:
Moved topo/analysis/updatecommands to topo/commands/analysis

* [r2161]
doc/Developer_Manual/imports_text.php:
Minor tweak

* [r2160] topo/base/arrayutils.py:
Added octave_str and octave_output commands

* [r2159] doc/Future_Work/index_text.php:
Added link to pymat

* [r2158] topo/plotting/templates.py:
Added a few notes

2006-01-20 julienciroux

* [r2157] topo/base/sheet.py:
Added a comment about a JABALERT./topographica -g
examples/cfsom_or.ty I need Jim's advise before getting rid of
it.

* [r2156] topo/plotting/templates.py:
Wrote an add_plot_template() function in PlotGroupTemplate in
order to create them more conveniently. I did not change the
current way templates are defined because I am waiting for Jim
reviewing the function and confirming it is OK.

* [r2155] topo/base/sheet.py,
topo/tests/testplotgroup.py,
topo/tests/testsheet.py,
topo/tests/testsheetview.py,
topo/tests/tkgui/testactivitypanel.py:
Got rid of add_sheet_view() in Sheet now that the sheet_view_dict
is public.

* [r2154] topo/tests/testsheet.py:
Wrote a slice2bounds test. Now there is a pretty heavy testing
of: bounds2slice,slice2bounds and also
slice2bounds_to_bounds2slice (that test that both function
combined together provide an identity function).

2006-01-20 alan_lindsay

* [r2153] topo/tkgui/editorwindow.py:
Fixed a few wee bugs in the popup menu.

* [r2152] topo/tkgui/editorobjects.py,
topo/tkgui/editorwindow.py:
Add order to objects drawn in the canvas. Allow for order to be
changed, in popup menu.

2006-01-20 julienciroux

* [r2151] topo/tests/testsheet.py:
Finished to write the test for bounds2slice. I think it is enough
testing for this function now.

* [r2150] topo/base/connectionfield.py,
topo/base/sheet.py:
Modified slice2bounds and bounds2slice so that the bounds
returned by slice2bounds do not have any additional margins; the
margin is now built internally to bounds2slice, and therefore
slice2bounds return the exact bounds. I had to slightly (and
temporarily, because Chris is still working on it) modified
connectionfield.py.

2006-01-19 alan_lindsay

* [r2149] topo/tkgui/editorobjects.py,
topo/tkgui/editortools.py,
topo/tkgui/editorwindow.py:
All possible import * occurrences omitted

* [r2148] topo/tkgui/editorobjects.py:
Ok button added to objects properties window. Updates and closes.

2006-01-19 ceball

* [r2147] topo/base/connectionfield.py:
No visible change. Altered call to ConnectionField.__init__().

2006-01-18 alan_lindsay

* [r2146] topo/tkgui/editorobjects.py:
Lateral Connections colour when they have the focus.

* [r2145] topo/tkgui/editorobjects.py:
Connections from a sheet from one neuron. Lateral connection
ovals can be selected and their properties obtained. Labels
highlight when their object is selected and they sit (right
justified) on the left of their object.

* [r2144] topo/tkgui/editorwindow.py:
Order of boundary search changed to allow lateral connections to
be selected.

* [r2143] topo/tkgui/editortools.py:
More distinct display of focus

2006-01-18 jdepaula

* [r2142] topo/misc/inlinec.py,
topographica_script.py:
Make loading weave on Windows non-default

* [r2141] external/win32/setup.py:
Now uses Python 2.4.2

* [r2140] external/win32/python-2.4.2.msi:
Upgrade Python 2.4 to 2.4.2

* [r2139] setup.bat:
Upgrade Python 2.4.2 for Windows

2006-01-18 jbednar

* [r2138] topo/tkgui/parametersframe.py:
Added ALERT

* [r2137] CONVENTIONS,
doc/Developer_Manual,
doc/Developer_Manual/.cvsignore,
doc/Developer_Manual/communication_text.php,
doc/Developer_Manual/gui_text.php,
doc/Developer_Manual/imports_text.php,
doc/Developer_Manual/index_text.php,
doc/Developer_Manual/naming_text.php,
doc/Developer_Manual/ood_text.php,
doc/Developer_Manual/optimization_text.php,
doc/Developer_Manual/parameters_text.php,
doc/Developer_Manual/python_text.php,
doc/Developer_Manual/refactoring_text.php,
doc/Developer_Manual/revisioncontrol_text.php,
doc/Developer_Manual/testing_text.php,
doc/shared/util.php:
Converted CONVENTIONS into a developer manual

* [r2136] doc/Future_Work/index_text.php:
Added Judith's suggestion

2006-01-18 julienciroux

* [r2135] topo/tkgui/plotgrouppanel.py:
Changed the code for toggle normalize so that it just regenerate
the normalized plots but not re-run the do_plot command.

* [r2134] topo/plotting/plot.py:
Changed the code for normalizing, introduced an offset so that
the minimum value of the matirx is zero.

2006-01-18 ceball

* [r2133] topo/base/connectionfield.py:
Weight (and mask) patterns are setup using the bounds as
calculated by initialize_slice_array(). This corrects the weights
near the edges of sheets. There should be no visible change to
simulations that were using a weights_generator or
w?\004eights_shape that was a pattern such as UniformRandom() or
Constant() (as opposed to a Disk() or Gaussian(), which were
being incorrectly calculated at the edge of Sheets).

2006-01-18 louisem

* [r2132] examples/obermayer_pnas90.ty:
Cleaned up alpha and radius; might work now. Enabled
DivisiveSumNormalize

2006-01-18 ceball

* [r2131] topographica_script.py:
Undid previous change - commandline.py is in topo/misc/, not
topo/base/.

2006-01-18 jdepaula

* [r2130] topographica_script.py:
Someone missed this file when they moved commandline.py

2006-01-17 ceball

* [r2129] topo/tests/testsheet.py:
Added a partial test of bounds2slice(). I think bounds2slice()
might be incorrect - needs to be investigated (I might be
confused).

2006-01-17 jbednar

* [r2128] topo/plotting/templates.py:
Replaced testing version of RGB plot with a real RGB CoG plot

* [r2127] topo/analysis/featuremap.py:
Cleaned up imports and minor spelling errors. Cleaned up
commented-out display functions, and Julien made them work with
the current version of the GUI (though they still aren't clean
enough to leave uncommented). Fixed non-cyclic features to use an
inclusive frange.

* [r2126] topo/analysis/updatecommands.py:
Added measure_cog command

* [r2125] topo/base/utils.py:
Added inclusive option to frange

* [r2124] topo/tkgui/topoconsole.py:
Added hack useful for MeasureFeatureMap

* [r2123] topo/analysis/updatecommands.py:
Expanded HACKALERT description

* [r2122] topo/analysis/updatecommands.py:
Changed SineGratingPresenter to be a general PatternPresenter
class that accepts any PatternGenerator

* [r2121] topo/analysis/updatecommands.py:
Changed measure_or_pref to accept a presenter object instead of a
presenter class

* [r2120] topo/analysis/featuremap.py,
topo/analysis/updatecommands.py:
Moved sim argument out of SineGratingPresenter __init__ and put
it in __call__ instead

* [r2119] external/Makefile:
Fixed bug in previous commit

* [r2118] topo/analysis/updatecommands.py,
topo/commands/basic.py,
topo/tkgui/testpattern.py:
Removed unused sim argument in pattern_present

* [r2117] external/Makefile:
Forced matplotlib to be remade when Python changes, because it
seems to require that

* [r2116] ChangeLog:
Up-to-date version of changes

2006-01-17 ceball

* [r2115] topo/tests/lissom_or_reference.ty:
Minor correction plus put back RN=32.0 in case that's the
problem.

2006-01-16 julienciroux

* [r2114]
topo/tests/tkgui/testplotgrouppanel.py:
Directly access the Sheet.sheet_view_dict, instead of the
add_sheet_view function the SheetViews. The function
add_sheet_view will be soon deleted when all similar calls (in
other files) will have been replaced.

* [r2113] topo/analysis/updatecommands.py:
Directly access the Sheet.sheet_view_dict, instead of the
add_sheet_view function to store the Activity sheetviews. The
function add_sheet_view will be soon deleted when all similar
calls (in other files) will have been replaced.

* [r2112] topo/analysis/featuremap.py:
Directly access the Sheet.sheet_view_dict, instead of the
add_sheet_view function to store the feature preference and
selectivity sheetviews. The function add_sheet_view will be soon
deleted when all similar calls (in other files) will hav?\004e
been replaced.

2006-01-16 ceball

* [r2111] topo/tests/lissom_or_reference.ty:
Added test for weights.

* [r2110]
topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
topo/tests/or_map_topo.000001p000.Primary_Activity.matrix:
For or_map_topo.param v.1.6

* [r2109]
topo/tests/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
topo/tests/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix:
C++ LISSOM values from or_map_topo.param version 1.6

2006-01-16 julienciroux

* [r2108] topo/analysis/updatecommands.py,
topo/tkgui/projectionpanel.py:
Added a parameter proj_name to set before calling
update_projection(), so that we only request UnitView for a given
projection.

* [r2107] topo/base/connectionfield.py:
Corrected Unit_View in CFSheet so that it only installs UnitView
in the sheet_view_dict but does not do any look_up or does not
return any UnitView object. Also added a test for making sure
that we request UnitView from CFProjections only,?\004 and added
the possibility to pass a projection name to only request
UnitViews from the requested projection (or for all of them if
projection_name == None).

* [r2106] topo/plotting/plotfilesaver.py:
Got rid of the call to PlotGroup do_plot_cmd that no longer
exists. It has to be replaced by a call to update_projection, but
it will be done when re-writing entirely PlotFileSaver.

* [r2105] topo/tkgui/projectionpanel.py:
Got rid of the now un-used attribute shape and corresponding
ALERT! (It has been forgotten in the last commit.)

* [r2104] topo/plotting/plotgroup.py:
Cleaned up old ALERTS: got rid of the unused FLAT constant and
PlotGroup shape attribute, deleted PlotGroup do_plot_cmd() that
is now unused.

* [r2103] topo/plotting/plotgroup.py,
topo/tkgui/projectionpanel.py:
Replaced generate_coords() in ProjectionPlotGroup and made it
non-private so that it is callable from the projectionpanel.py.
It enables to keep executing the
updatecommands.update_projection() from the projectionpanel.

2006-01-16 jbednar

* [r2102] doc/Future_Work/index_text.php:
Minor clarifications, plus added Eyal notes

* [r2101] doc/Downloads/index_text.php:
Fixed the explanation of upgrading to the very latest release

* [r2100] CONVENTIONS:
Added section about ALERTs

2006-01-15 ceball

* [r2099] topo/tests/lissom_or_reference.ty:
To match C++ LISSOM's samples/or_map_topo.param version 1.6. This
version is for Topographica as of 2005/12/21 00:00. It will be
updated for the current version of Topographica as testing
proceeds from that date in December.

* [r2098]
topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
topo/tests/or_map_topo.000001p000.Primary_Activity.matrix:
From C++ LISSOM's samples/or_map_topo.param version 1.6

* [r2097] topo/tests/lissom_log_parser.py:
Added function to read in C++ LISSOM .matrix file.

* [r2096] topo/tests/or_map_topo.log:
Values from C++ LISSOM's or_map_topo.param version 1.6

2006-01-14 julienciroux

* [r2095] examples/lissom_or.ty:
Added a scheduled action deleted by mistake on a previous commit.

2006-01-14 jbednar

* [r2094] examples/lissom_or.ty:
Minor cleanup; shouldn't have affected results

2006-01-14 julienciroux

* [r2093] examples/lissom_or.ty:
Rounded the value assigned to the input learning rate for the
scheduled actions (left temporary comments with original values).

* [r2092] examples/lissom_or.ty:
Rounded the value assigned to the excitatory learning rate for
the scheduled action (left temporary comment with original
values).

* [r2091] examples/lissom_or.ty:
Rounded the initial values of the three learning rates (input,
exc, inh).

* [r2090] examples/lissom_or.ty:
Got rid of a scheduled action that had no effect on the
simulation.

* [r2089] examples/lissom_or.ty:
Rounded the numerical value for declaring the inhibitory weights
bounding box.

* [r2088] examples/lissom_or.ty:
Rounded the numerical value for declaring the afferent weights
bounding box.

* [r2087] examples/lissom_or.ty:
Rounded the numerical value for declaring the Gaussian size
parameter.

* [r2086] examples/lissom_or.ty:
Rounded the value for declaring the input_bounds. Also replaced
the fraction for declaring the Gaussian size by its numerical
expression.

* [r2085] examples/lissom_or.ty:
Changed expression written as fraction to replace them by the
numerical expression as they are calculated by Python. Next step
is to round these values and still have a valid simulation.

2006-01-13 ceball

* [r2084] topo/tests/lissom_or_reference.ty:
Skips first C++ LISSOM input pattern...which C++ LISSOM skips
also?

* [r2083] topo/tests/lissom_or_reference.ty:
Corrected conversion from C++ LISSOM's cx and cy.
retina_edge_buffer set to match C++ LISSOM's - might not be
correct.

2006-01-13 alan_lindsay

* [r2082] topo/tkgui/editorobjects.py:
Lateral projections represented as dotted circles; labels appear
when hovered over and properties set through the projection's
sheet. In bounds calculations are determined using full extent of
parallelogram or receptive field. Multiple connections have a
representation, however labels need sorted.

* [r2081] topo/tkgui/editorwindow.py:
Correction to the import code (doesn't connect connections
twice).

2006-01-13 ceball

* [r2080] topo/tests/lissom_or_reference.ty:
weights_generator is Constant().

* [r2079] topo/tests/lissom_or_reference.ty:
Takes input pattern parameters from a C++ lissom log file.

* [r2078] topo/tests/lissom_log_parser.py:
Used to parse .log files from lissom and return input parameters.

* [r2077] topo/tests/or_map_topo.log:
Initial verison of log file from C++ LISSOM's or_map_topo.params.
This initial version is just to setup the testing.

* [r2076] examples/lissom_or_reference.ty,
topo/tests/lissom_or_reference.ty:
Moved from examples/ to topo/tests/

2006-01-12 ceball

* [r2075] topo/tests/testlissom.data:
Data from 2006/01/09 1315

* [r2074] topo/tests/testlissom.ty:
Added comment about changing the reference data.

* [r2073] topo/tests/testlissom.data:
Added as binary

* [r2072] topo/tests/testlissom.data:
Removed - file should have been added as binary.

* [r2071] topo/tests/testlissom.ty:
Made afferent_weights_bounds larger. Test cases bound to fail
right now until the test activities are updated.

2006-01-12 julienciroux

* [r2070] examples/lissom_or_reference.ty:
Commented what are the number added to match the old simulation
now that the learning rate is divided by the number of unit of
the CF at the center.

* [r2069] topo/base/connectionfield.py:
Deleted old JCALERT.

* [r2068] topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Delered the parameter rows and cols that were passed to
CFLearningFunction.single_connection_learning_rate(), they are
now retrieved from the cfs parameter instead of being passed.

* [r2067] topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Changed the name of set_learning_rate() to
single_connection_learning_rate() in CFLearningFunction, and
wrote the documentation for this function. Also changed the
parameter single_cf_learning_rate to be
single_connection_learning_rate in all sub-classes of
CFLearningFunction. Got rid of old JABALERT about the learning
rate handling.

2006-01-12 ceball

* [r2066] topo/tests/testlissom.ty:
Updated to use pickled data file testlissom.data.

* [r2065] topo/tests/testlissom.data:
Pickled data for use with the test file. Data from release_0_8_1.

* [r2064] topo/tests/testlissom.ty:
Was running with slightly different results each time. I have no
idea why - the random and RandomArray seeds were set. I replaced
all the lissom code again and it seems to run with the same
results every time now. Test values to follow...?\004

2006-01-12 julienciroux

* [r2063] examples/lissom_or.ty:
Cleaned up the new lissom_or.ty.

2006-01-12 ceball

* [r2062] topo/tests/testlissom.ty:
The previous commit contained incorrect activity arrays.

* [r2061] topo/tests/testlissom.ty:
Test values come from release_0_8_1.

2006-01-12 julienciroux

* [r2060] examples/lissom_or.ty:
New version of lissom_or.ty without any old Lissom parameters
explicilty declared. This version matches exactly the old one
(which is now saved as lissom_or_reference.ty.

* [r2059] examples/lissom_or_reference.ty:
The former lissom_or.ty file has been renamed
lissom_or_reference.ty.The former lissom_or.ty will be replaced
by a simpler version that won't declare any of the old Lissom
parameters.

2006-01-12 ceball

* [r2058] topo/tests/testlissom.ty:
Rough initial version.

* [r2057] topo/learningfns/optimized.py:
Had to add a hack for detection of zero in the mask values.
Removed a stray '*' (that was having no effect).

* [r2056] topo/learningfns/optimized.py:
Corrected a mistake in the previous version of DivisiveHebbian
where even unmasked values were used to calculate the total
weight change. Made application of the mask simpler and more
efficient by doing it in the same loop as the weight
mo?\004dification. Added HACKALERT about how to make the code
clearer.

2006-01-12 jbednar

* [r2055] topo/tests/tkgui/testmatplotlibtk.py:
Tried to make the test be skipped when there is no display, but
without any apparent effect

* [r2054] doc/User_Manual/index_text.php:
Added note about citations

* [r2053] doc/Downloads/index_text.php:
Cleaned up Mac instructions

* [r2052] topo/base/connectionfield.py:
Cleaned up comments

2006-01-11 ceball

* [r2051] topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Added HACKALERT; changed order of output_fn and mask as a
temporary solution.

* [r2050] topo/outputfns/basic.py:
Added HACKALERT

* [r2049] topo/learningfns/optimized.py:
Removed code accidentally left behind.

* [r2048] topo/learningfns/optimized.py:
Minor change to DivisiveHebbian_CPointer C code to improve speed.

* [r2047] topo/tests/testlissom_cpointer.ty:
Initial version, based on examples/lissom_or.ty version 1.42.

* [r2046] topo/learningfns/optimized.py,
topo/projections/optimized.py,
topo/sheets/lissom.py:
LISSOM_CPointer and its various optimized functions now respects
the mask of the weights.

* [r2045] topo/learningfns/optimized.py:
Corrected learning_rate setting in DivisiveHebbian_CPointer.

* [r2044] topo/learningfns/optimized.py:
Minor alteration to DivisiveHebbian C code to improve speed.

* [r2043] topo/learningfns/optimized.py:
The DivisiveHebbian C code now respects the mask. Added a
hackalert about the name, and slightly changed 1 another
hackalert.

* [r2042] topo/base/connectionfield.py:
Made cf's mask array be the same type as the weights array, and
made it savespace(1). Had to do the same on change_bounds because
it appears that using Numeric.where() causes these attributes to
be lost.

* [r2041] topo/base/connectionfield.py:
Removed apparently redundant use of savespace(). The savespace
and typecode attributes of the weights matrix appear to be kept
anyway. If they weren't, typecode would need to be set again
anyway.

2006-01-11 julienciroux

* [r2040] external,
external/.cvsignore:
Ignore Python-2.4.2 directory.

2006-01-11 ceball

* [r2039] topo/projections/basic.py:
Added missing import statement.

2006-01-10 julienciroux

* [r2038] topo/analysis/updatecommands.py,
topo/plotting/plotgroup.py,
topo/plotting/templates.py,
topo/tkgui/projectionpanel.py:
Moved the function _generate_coords() from ProjectionPlotGroup to
ProjectionPanel. Wrote the function update_projections in
analysis/updatecommands.py. Now this command is executed instead
of do_plot_cmd() in ProjectionPlotGroup (that has been deleted).

* [r2037] topo/plotting/plotengine.py,
topo/plotting/plotfilesaver.py,
topo/plotting/plotgroup.py,
topo/tests/__init__.py,
topo/tests/testplotengine.py,
topo/tests/testplotfilesaver.py,
topo/tests/testplotgroup.py,
topo/tests/tkgui/testactivitypanel.py,
topo/tests/tkgui/testbasicplotgrouppanel.py,
topo/tests/tkgui/testplotgrouppanel.py,
topo/tests/tkgui/testtopoconsole.py,
topo/tkgui/basicplotgrouppanel.py,
topo/tkgui/cfsheetplotpanel.py,
topo/tkgui/plotgrouppanel.py,
topo/tkgui/projectionpanel.py,
topo/tkgui/testpattern.py,
topo/tkgui/topoconsole.py,
topo/tkgui/unitweightspanel.py:
Deleted plotengine.py (and testplotengine.py). Now, the PlotGroup
objects are stored in a variable plotgroup_dict declared in
plotgroup.py. From the panel, the plotgroup_dict is accessed, and
if the requested PlotGroup is not found, it is directly created
from the panel. Corresponding changes have been made in some test
files and in PlotFileSaver.

2006-01-10 ceball

* [r2036] topo/base/connectionfield.py:
Removed line I left in by accident at some time in the past.

2006-01-10 julienciroux

* [r2035] topo/plotting/plotgroup.py:
Got rid of now unused do_plot_cmd() function in
UnitWeightPlotGroup() (replaced by update_weights in
analysis/updatecommands.py). Simplified the do_plot_cmd in
ProjectionPlotGroup: the goal is too soon replace it by an
update_projection command in analysis/updatecommands.py.

2006-01-10 ceball

* [r2034] topo/base/connectionfield.py:
Removed unused import statement.

* [r2033] examples/lissom_or.ty,
topo/base/connectionfield.py,
topo/projections/basic.py:
Moved SharedWeightProjection and SharedWeightCFResponseFunction
from topo/base/connectionfield.py to topo/projections/basic.py.
Renamed SharedWeightProjection to SharedWeightCFProjection.

* [r2032] examples/lissom_or.ty:
No visible changes (only changed commented-out code). LGNOn
projections' output_fns set to DivisiveSumNormalize(). Added
LGNOff. Called DivisiveSumNormalize() with norm_value=-1.0 where
projections' strengths are -1.0 so that activities' signs aren't
reversed. On and Off channels appear to work (which you can see
if you normalize the activity in the GUI).

* [r2031] topo/outputfns/basic.py:
Added HACKALERT to DivisiveSumNormalize.

* [r2030] topo/outputfns/basic.py:
Removed HACKALERT. I realize now that although the syntax for
Numeric.clip() implies it is an in-place operation, the array
must really be copied.

* [r2029] topo/outputfns/basic.py:
Undid change in previous commit. Why doesn't Numeric.clip() work
here?

* [r2028] topo/learningfns/basic.py:
No visible changes. Changed use of output_fn() so the syntax
matches the in-place operation.

* [r2027] topo/outputfns/basic.py:
Used Numeric's clip() rather than utils.clip_in_place(). See the
hackalert.

* [r2026] topo/base/connectionfield.py:
No visible changes. Used xrange() to generate a loop instead of
range(), and inside large loops that will run often avoided some
evaluations.

2006-01-09 ceball

* [r2025] topo/base/connectionfield.py:
Added HACKALERT about already-known masking problem.

* [r2024] examples/lissom_or.ty:
Added dest_port to connections for LGNOn (change is to
commented-out code, so no visible effect).

* [r2023] topo/base/projection.py:
Added HACKALERT about ports.

2006-01-09 julienciroux

* [r2022] doc/Downloads/index_text.php:
Added instructions for building Topographica on Mac OS X 10.4
(Tiger), in the Downloads section of the /doc/ directory. It may
have to reviewed by a native english speaker.

* [r2021] external/Python-2.4.tgz:
remove Python-2.4.tgz from external/.

* [r2020] external/Makefile,
external/Python-2.4.2.tgz:
Replaced Python-2.4 by Python-2.4.2 in the external packages, and
made the corresponding changes to the external/Makefile. This
upgrade allows to get rid of a warning appearing in the Mac
version of Python-2.4.

* [r2019] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty,
topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
Changed the handling of the learning rate: now the learning rate
(as it is applied when passing to connectionfield.hebbian()) has
been divided by the number of unit in the receptive field of the
unit at the center of the sheet. The learning rate is set by a
function set_learning_rate in CFLearningFunction, and has to be
called by the subclasses of CFLearningFunction. Changes have been
made to the simulation scripts in order to match the former
situation, these changes have been heavily tested.

2006-01-08 jbednar

* [r2018] topo/base/connectionfield.py:
Removed apparently unneeded set_cfs function. Changed base class
of SharedWeightProjection to be CFProjection instead of
Projection. Added ALERTs.

* [r2017] examples/lissom_or.ty:
Fixed radius/diameter confusion for circular RF masks

* [r2016] topo/base/simulator.py,
topo/tkgui/unitweightspanel.py:
Added ALERTs

* [r2015] topo/tkgui/editorobjects.py:
Changed Update to Apply, and added ALERT

* [r2014] examples/lissom_or.ty:
Changed commented-out example SharedWeightProjection to a
prototype of an ON channel

2006-01-07 jbednar

* [r2013] topo/base/connectionfield.py:
Corrections to messages and documentation

* [r2012] topo/analysis/updatecommands.py:
Added ALERTs

* [r2011] topo/__init__.py:
Updated list for import *

2006-01-07 julienciroux

* [r2010] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
examples/obermayer_pnas90.ty:
Added control of the input stream seed and weight stream seed for
all the examples currently implemented. That way, the simulation
are always similar, which enables easy testing.

* [r2009] topo/tests/testplotengine.py:
Got rid of old commented out code in testplotengine.

2006-01-07 ceball

* [r2008] examples/lissom_or.ty:
Added note about the radius of the afferent projection's
connecttionfields.

* [r2007] examples/cfsom_or.ty:
No visible change - removed some commented-out code.

* [r2006] examples/lissom_or.ty:
No visible change: checked in commented-out code. The code is an
example SharedWeightProjection. (Also added another note.)

* [r2005] topo/base/connectionfield.py:
SharedWeightProjection stores the slice indexes and bounds of
units (and still just the single set of weights). This allows
shared weight response functions to use the correct
activity_matrix slice, and SharedWeightProjection.get_view() to
get the correct bounds for a unit. The slices and bounds are
stored to avoid having to calculate them each time e.g. a
response function is called. Also added some hackalerts
(including minor ones about code unrelated to that being
committed here).

2006-01-06 julienciroux

* [r2004] topo/plotting/templates.py,
topo/tkgui/cfsheetplotpanel.py,
topo/tkgui/unitweightspanel.py:
Changed templates.py, unitweightpanel.py and cfsheetpanel.py so
that now it executes the command update_weight defines in
updatecommands.py and declared in the UnitWeight template,
instead of using the do_plot_cmd in UnitWeightPlotGroup.

* [r2003] topo/analysis/featuremap.py,
topo/analysis/updatecommands.py,
topo/tkgui/basicplotgrouppanel.py:
Moved the updatecommands (e.g. update_activity), from
featuremap.py to a new file updatecommands.py in the analysis
directory. Made the corresponding change in the import in
BasicPlotGroupPanel.

2006-01-06 jbednar

* [r2002] topo/projections/basic.py:
Cleaned up documentation

* [r2001] topo/base/connectionfield.py,
topo/base/sheet.py,
topo/plotting/plotgroup.py:
Added alerts

2006-01-06 ceball

* [r2000] examples/lissom_or.ty:
No visible change. Added commented-out code to allow the shape of
the weights to be specified.

* [r1999] topo/base/connectionfield.py:
ConnectionField's mask (for weights) has a threshold (temporarily
hard-coded rather than being user-definable).

2006-01-06 julienciroux

* [r1998] topo/plotting/plot.py,
topo/plotting/plotgroup.py:
Got rid of the unused function release_sheetviews both in Plot
and PlotGroup. It has ot be re-defined if we want to re-implement
this functionnality.

2006-01-06 ceball

* [r1997] topo/base/connectionfield.py:
Corrected a mistake (changed Int to Numeric.Int32).

2006-01-05 ceball

* [r1996] topo/base/parameter.py:
Added HACKALERT about inheritance of default values for
Parameters.

* [r1995] topo/base/connectionfield.py:
Added weights_shape to SharedWeightProjection.

* [r1994] examples/obermayer_pnas90.ty:
Temporarily commented line that sets default
PatternGeneratorParameter.

* [r1993] examples/cfsom_or.ty,
examples/hierarchical.ty,
examples/lissom_or.ty,
topo/base/connectionfield.py,
topo/learningfns/basic.py,
topo/learningfns/optimized.py:
No visible change (I hope) (except the example files temporarily
do not default to a particular PatternGenerator for e.g. the test
pattern window) , although simulations will run a little slower.
Added code to allow ConnectionFields to have a shape
(CFProjection has a weights_shape Parameter). The default shape
is Constant (i.e. the same rectangular shape as before).

* [r1992] topo/base/connectionfield.py:
Changed references to topo.base.patterngenerator to
patterngenerator.

* [r1991] topo/base/connectionfield.py:
No visible change - small alteration to code.

2006-01-04 ceball

* [r1990] topo/tkgui/__init__.py:
Imported all LearningFunctions and ResponseFunctions for the GUI.

* [r1989] topo/responsefns/__init__.py:
Code to populate ResponseFunctionParameter's range().

* [r1988] topo/learningfns/__init__.py:
Code to populate LearningFunctionParameter's range().

* [r1987] topo/base/utils.py:
Added HACKALERT about classname_repr().

* [r1986] topo/base/connectionfield.py:
Added LearningFunctionParameter and ResponseFunctionParameter.
Made response_fn and learning_fn attributes into
ResponseFunctionParameters and LearningFunctionParameters.

* [r1985] topo/learningfns/optimized.py:
Added a comment about using xrange() instead of range().

* [r1984] topo/learningfns/basic.py:
Changed height and width to size and aspect ratio (I missed when
I made the change from height and width to size and aspect_ratio.
Added notes about (1) specifying size and aspect_ratio here in
the first place and (2) there being no warnin?\004g when the
non-parameter attributes height and width were being set (I spent
a long, long time finding this bug).

2006-01-02 ceball

* [r1983] topo/base/patterngenerator.py,
topo/base/sheet.py:
Added a HACKALERT noting problems in the unlikely case of
zero-sized or very small density matrices being specified.

* [r1982] topo/tkgui/parametersframe.py:
Added HACKALERT.

* [r1981] topo/base/projection.py:
Changed output_fn to be an OutputFunctionParameter.

2005-12-31 ceball

* [r1980] topo/sheets/lissom.py:
Made the output_fn be an OutputFunctionParameter.

* [r1979] topo/__init__.py:
Added HACKALERT.

* [r1978] topo/base/parameter.py,
topo/base/patterngenerator.py,
topo/base/projection.py,
topo/outputfns/__init__.py,
topo/patterns/__init__.py,
topo/sheets/generatorsheet.py,
topo/tkgui/__init__.py:
Part-way checkin. ClassSelectorParameters (such as
PatternGeneratorParameter) can now be declared in the correct
file (topo.base.patterngenerator in this example) because the
list of available classes (PatternGenerators in this case) is
added to in the relevant __init__.py file
(topo/patterns/__init__.py in this case). The list of available
classes comes from the imported modules in the package, so the
GUI does e.g. 'from topo.patterns import *' to make all options
available. There are other ClassSelectorParameters still to add,
and the documentation is incomplete.

* [r1977] topo/outputfns/__init__.py,
topo/patterns/__init__.py,
topo/patterns/basic.py,
topo/tkgui/parametersframe.py:
Changed name of PackageParameter to ClassSelectorParameter.

* [r1976] topo/base/parameter.py:
Changed name of PackageParameter to ClassSelectorParameter. Made
DynamicNumber's setting error message slightly more informative.

* [r1975] topo/tkgui/parametersframe.py:
Commented out some currently unused code.

2005-12-30 ceball

* [r1974] topo/tkgui/parametersframe.py:
Continued cleaning - no visible change.

* [r1973] topo/tkgui/parametersframe.py,
topo/tkgui/propertiesframe.py:
Cleaned method arguments.

* [r1972] topo/tkgui/taggedslider.py:
Added ALERT about TaggedSlider widths.

* [r1971] topo/tkgui/propertiesframe.py,
topo/tkgui/taggedslider.py:
Some simplifications.

* [r1970] topo/tkgui/parametersframe.py:
Now uses a dictionary to map parameters to widgets.

2005-12-29 ceball

* [r1969] topo/tkgui/taggedslider.py:
Cleaned up TaggedSlider (no visible change).

* [r1968] topo/tkgui/parametersframe.py,
topo/tkgui/propertiesframe.py,
topo/tkgui/taggedslider.py:
Continued to cleaned up widgets in taggedslider.py (not yet
finished). Gave the idea of 'string_translator' widgets an
existence with a TranslatorWidget base class. We might want to
change the name.

2005-12-28 ceball

* [r1967] topo/tkgui/parametersframe.py,
topo/tkgui/propertiesframe.py,
topo/tkgui/taggedslider.py:
Read-only properties are displayed with a label rather than a
read-only entry box. The label text needs to be fixed - there's
an alert about that.

2005-12-22 jbednar

* [r1966] doc/Downloads/index_text.php:
Clarified updating

* [r1965] doc/Downloads/index_text.php:
Clarified updating

* [r1964] doc/shared/trailer.php:
Updated web site date; not sure why it is not set up to update
automatically

2005-12-22 ceball_cvs2svn

* [r1963] /tags/release_0_8_1:
This commit was manufactured by cvs2svn to create tag
'release_0_8_1'.

2005-12-22 jbednar

* [r1962] Makefile,
doc/Downloads/index_text.php:
Fixed problem with LATEST_STABLE tagging

* [r1961] doc/Downloads/index_text.php,
doc/Future_Work/index_text.php,
doc/Home/index_text.php,
doc/Reference_Manual/index_text.php,
doc/Team_Members/index_text.php,
doc/Tutorial/index_text.php,
doc/User_Manual/index_text.php,
doc/shared/index.php,
topo/misc/__init__.py:
Updated documentation to match latest release

* [r1960] Makefile:
Minor fix

* [r1959] Makefile:
Made web site depend on doc

* [r1958] Makefile: