Mrestimator

Latest version: v0.1.6

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27.11.2018

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* __Changed__: `coefficients()` with `trialseparate` method calculates `rk` differently (now strictly linear regression). This should enable `m>1` estimates.
* __Changed__: builtin fitfunctions now use absolute values of the amplitude of the exponential term
* __Changed__: fits drawn above data (again), otherwise, they get hidden if data is noisy
* __Fixed__: maximum steps `k` in `coefficients` cannot exceed half the trial length any longer. this could lead to strong fluctuations in `r_k` and fits would fail
* __Fixed__: Crashes when providing custom fitfunctions to `fit()` due to unhandled request of default parameters
* __New__: Rasterization of plots in the `OutputHandler`. Especially timeseries grow large quickly. Now, if OutputHandlers create their own figures/axes elements (`ax`-argument not given on construction) all elements with `zorder<0` are rastered. Per default, `add_ts()` uses a `zorder` of `-1` but `add_coefficients()` and `add_fit()` have values above one so they stay vectorized. Call `ax.set_rasterization_zorder(0)` on your custom `ax` axes element if you want the same effect on customized figures.
* __New__: export as png option for `OutputHandler.save_plot()`

24.09.2019

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* __Changed__: One-file spaghetti code was separated into submodules.
* __Fixed__: `stationarymean` method for coefficients should work for `m>1` (Note that this is a non-standard case. A detailed discussion will follow.)
* __New__: Optional Numba dependency to parallelize and precompile the computation of the correlation coefficients. To install numby along with mrestimator, `pip install -U mrestimator[numba]`
* __New__: Uploading pre-release versions to pypi. To switch run `pip install -U --pre mrestimator[full]` and to go back to stable `pip install mrestimator==0.1.5`.
* __New__: Basic unit tests. `python -m unittest mrestimator.test_suite`

19.09.2018

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* __Changed__: Check for old numpy versions in `fit()`
* __Changed__: Per default, fits are drawn solid (dashed) over the fitted (remaining) range
* __Fixed__: Typos

16.01.2019

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This is a bugfix version in preparation for the wrapper rewrite in 0.1.4.

* __Changed__: If no `steps` are provided to `coefficients()`, the default maxstep is (for now) 1/10 of the trial length. (Was hard coded to 1500 before)
* __Changed__: Default logs are less verbose to be clearer. The new function `mre._enable_detailed_logging()` enables fully detailed output to console and logfile. This also calls the two new switches, see next point. `mre._enable_detailed_logging()` also enables console display of runtime warnings that are usually only printed into the log.
* __Fixed__: Crash due to logfiles. If the toolbox was used by more than one user on one machine, the logfile created in the temporary directory could not be overwritten by other users. We now try to set file permissions of the logfile and target directory to `777` if they are not subfolders of the user folder. Also, per default, each user gets their own directory `/tmp/mre_username`. Logfilehandler is now rotating and creates a maximum of 10 logfiles, 50mb each.
* __Fixed__: `full_analysis()` no longer crashes with `substracttrialaverage=True` when the provided input is of integer type.
* __Fixed__: `fit()` now returns a (mostly empty) `FitResult` when no fit converged instead of raising an exception. Helps with scripts that run multiple fits. The returned FitResult works with the OutputHandler in default settings and a note about the failed fit is added to the description and meta data.
* __Fixed__: Calling `coefficients()` with custom steps e.g. `steps=np.arange(0,100,5)` is more robust and does not crash due to `steps < 1`. Incorrect entries are replaced.
* __Fixed__: `OutputHandler` now has a deconstructor that closes the matplotlib figure if it was not provided as an arugment. Hence, opening many handlers (e.g. by reassigning a variable in a loop `o = mre.OutputHandler()`) does not keep the figure after reusing the variable. This used to cause a warning: `More than 20 figures have been opened.`
* __New__: Enable logging of function arguments to console _and_ logfile with `mre._log_locals = True`. Enable logging of stack traces to logfile via `mre._log_trace = True`. (Avoiding the console printout of stack traces on exceptions is not feasible at the moment). Per default, both options are `False`.

14.09.2018

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* __New__: CoefficientResult constructor now has some default arguments. Still required: `steps` and `coefficients`. Also added the `dt, dtunit` attributes.
* __New__: FitResult constructor now has some default arguments. Still required: 'tau, mre, fitfunc'. Also added the `dt, dtunit, steps` attributes.
* __New__: `fit()` takes argument `steps=(minstep, maxstep)` to specify a custom fitrange. `OutputHandler` plots the fitted range opaque (excluded range has less alpha).
* __Changed__: `dt` is no longer an argument for `fit()`. Setting `dt` (the step size) and its units `dtunit` is done via the equally named parameters of `coefficients()`. It is added to the `CoefficientResult`, so `fit` and the `OutputHandler` can rely on it.

13.09.2018

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* Renamed: module from `mre` to `mrestimator`, use `import mrestimator as mre`
* Renamed: `correlation_coefficients()` to `coefficients()`
* Renamed: `correlation_fit()` to `fit()`
* Renamed: `CorrelationFitResult` to `FitResult`

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