Changelogs » Paintera

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Paintera

0.27.2


        

0.27.1


        

0.27.0


        

0.26.2


        

0.26.1


        

0.26.0

Changelog
  
  Paintera is now compatible with Java 11+
  
  Other
  - Merge pull request 400 from saalfeldlab/add-compatibility-with-java-13
  
  
  Pull Requests
  
  400
  Merge pull request 400 from saalfeldlab/add-compatibility-with-java-13

0.25.0

Changelog
  
  New Features
  - Add ability to export meshes for intersecting sources (synapses) (409)
  - Add menu item for creating a thresholding source (416)
  - Update authentication mechanism for Google Cloud (415)
  
  Bug Fixes
  - Fix opening project with label sources in deprecated LabelSourceState format (408)
  - Fix race conditions at startup in multi-resolution renderer (413)
  - Fix UI in shape interpolation mode (417)
  
  Other
  - Merge pull request 406 from saalfeldlab/unable-to-deserialize-project-show-error: Show stack trace if an error occurs while trying to open a project
  
  
  Pull Requests
  
  406
  Merge pull request 406 from saalfeldlab/unable-to-deserialize-project-show-error
  
  Show stack trace if an error occurs while trying to open a project
  
  408
  Merge pull request 408 from saalfeldlab/fix-opening-labelsourcestate
  
  [BUGFIX] Fix opening project with label sources in deprecated LabelSourceState format
  
  413
  Merge pull request 413 from saalfeldlab/fix-intermittent-startup-exceptions
  
  [BUGFIX] Fix race conditions at startup in multi-resolution renderer
  
  415
  Merge pull request 415 from saalfeldlab/update-google-cloud
  
  Update Google Cloud authentication mechanism
  
  409
  Merge pull request 409 from saalfeldlab/export-synapse-meshes
  
  [FEATURE] Add ability to export meshes for intersecting sources (synapses)
  
  416
  Merge pull request 416 from saalfeldlab/create-thresholded-source-menu
  
  Add menu item for creating a thresholded raw source
  
  417
  Merge pull request 417 from saalfeldlab/fix-ui-shape-interpolation
  
  [BUGFIX] Fix UI while in shape interpolation mode

0.24.0


        

0.23.3

Changelog
  
  Bug Fixes
  - Very slow painting and 2D navigation (395)
  
  Pull Requests
  
  396
  Merge pull request 396 from saalfeldlab/optimize-orthoslice-textures
  
  Optimize orthoslice texture updates

0.23.2

Changelog
  
  Bug Fixes
  - Fix memory leak when meshes are refreshed (393)
  
  Pull Requests
  
  394
  Merge pull request 394 from saalfeldlab/fix-mesh-memory-leak
  
  Fix memory leak when meshes are refreshed

0.23.1


        

0.23.0

Changelog
  
  New Features
  - Adaptive level of detail for meshes in 3D view. (267)
  - New settings for changing transparency and shading of the orthoslices in the 3D viewer (382)
  - Add 3d mesh visualization for thresholded sources. By default, 3d meshes are disabled for thresholded sources but they can be enabled with the checkbox at the Meshes section in the thresholded source preferences. In order to unify 3d mesh generation, the label-centric `MeshManager` interface was removed and replaced with the `AdaptiveResolutionMeshManager`. Source-specific mesh menagers simply wrap around and translate and forward requests to the `AdaptiveResolutionMeshManager`. This simplifies the code a lot and reduces code duplication. In the course of this refactoring, cancellation of tasks does not need to be controlled at the level of iteration of a tight loop, which makes the `Interruptible` and similar interfaces obsolete. Use the `LabeLBlockLookup` directly instead, which may be cached, anyways. (377)
  
  Bug Fixes
  - Committing canvas failed for new n5 label block lookup backends (374). Initialize lookup properly when committing to fix this issue. (377)
  
  Pull Requests
  
  267
  Merge pull request 267 from saalfeldlab/adaptive-mesh-resolution
  
  [FEATURE] Adaptive level of detail for meshes in 3D view.
  * Only blocks that are visible inside the 3D viewer screen will now be rendered, and the order in which meshes are generated is now determined by the distance between a block and the camera (closest blocks will be rendered first).
  * The blocks are quickly re-prioritized every time the user turns the camera with respect to the new orientation. The delay with which the blocks are updated can be changed in the 3D Viewer settings tab (Update delay).
  * The appropriate resolution for a block is also chosen based on the distance from the camera and can be controlled with the new settings (Level of detail, Finest scale level, Coarsest scale level). For instance, when the user zooms in or rotates the camera such that some of the blocks are closer to the camera, the resoluton for them is gradually increased. When the user zooms out, the resolution is decreased again.
  * To reduce variations in mesh appearance between several scale levels, there is a new setting 'Min label ratio'. It allows to control the thickness of the binary mask used to generate the meshes. For example, 0.25 means that at least 25% of all labels in a given pixel must be occurrences of this particular label in order for a pixel in the mask to be set to 'true'. 0.0 would mean that a pixel in the mask is set to 'true' if the pixel contains any number of occurrences of this particular label.
  * The block size for generating meshes is now independent from the block size of the data source and can be controlled via the new setting in the 3D Viewer settings tab (Renderer block size). Smaller blocks help to increase the granularity of the 3D scene and make individual meshes smaller so that there is less visible lag when a mesh is being uploaded onto the scene.
  * Additionally, there is now a throttling queue for uploading meshes onto the scene. It aims to solve the following problem: when the meshes are initially generated, the speed with which the meshes are produced is limited by the marching cubes algorithm. The generated meshes are memory-cached then, and on subsequent requests they are quickly retrieved from the cache. This leads to trying to add hundreds of meshes to the scene at the same time, which implicitly blocks the main thread and the application freezes. The new throttling queue limits the number of meshes added a a time and helps to keep the application responsive. Its parameters can be tweaked in the 3D Viewer settings tab (Elements per frame, Frame delay).
  
  382
  Merge pull request 382 from saalfeldlab/orthoslices-transparency
  
  [FEATURE] New settings for changing transparency and shading of the orthoslices in the 3D viewer
  
  377
  Merge pull request 377 from saalfeldlab/3d-visualize-masks
  
  [FEATURE] Add 3d mesh visualization for thresholded sources. By default, 3d meshes are disabled for thresholded sources but they can be enabled with the checkbox at the Meshes section in the thresholded source preferences. In order to unify 3d mesh generation, the label-centric `MeshManager` interface was removed and replaced with the `AdaptiveResolutionMeshManager`. Source-specific mesh menagers simply wrap around and translate and forward requests to the `AdaptiveResolutionMeshManager`. This simplifies the code a lot and reduces code duplication. In the course of this refactoring, cancellation of tasks does not need to be controlled at the level of iteration of a tight loop, which makes the `Interruptible` and similar interfaces obsolete. Use the `LabeLBlockLookup` directly instead, which may be cached, anyways.
  [BUGFIX] Committing canvas failed for new n5 label block lookup backends (374). Initialize lookup properly when committing to fix this issue.

0.22.0


        

0.21.0


        

0.20.1


        

0.20.0


        

0.19.3


        

0.19.2


        

0.19.1


        

0.19.0


        

0.18.1


        

0.18.0

- New Features
  - Add support for importing CATMAID json mesh format (263 265)
  - Label data rendering speed increased (264 269, thanks to axtimwalde)
  - Improved Readme:
  - Installation Instructions (274)
  - `paintera-conversion-helper` (275)
  - non-scalar label-multiset label data representation (275)
  - Added zenodo tag (277)
  - Serialize 3D viewer transform into Paintera project (244 272)
  - Select all label ids  (278, thanks to igorpisarev)
  - within data set, or
  - within current field of view.
  - Background label id (`id=0`) cannot be selected anymore.
  - Add CLI options to add data at startup and make `PainteraShowContainer`/`paintera-show-container` obsolete (176 179 273)
  - Bug Fixes
  - Threading in shape interpolation (282, thanks to igorpisarev)
  - Update outdated label multiset and n5 dependencies (281, thanks to igorpisarev)

0.17.0

- New Features
  - Bookmarks for global and 3D viewer transforms (255 140)
  - Load arbitrary meshes (currently only from .obj, 262 254)
  - Bug Fixes
  - Update coordinate in status display when navigating with keyboard controls (260 204)

0.16.0

- New features:
  - Configurable scale bar (238, 247):
  - font size
  - scale bar size
  - foreground color
  - background color
  - Bug fixes:
  - Draw overlays when transformation changes (21bdeac57401706e1a4004534bc8ac4bdb351db7)
  - Store correct alpha channel in `Colors.toHTML` (909c065891de65f1e4505fab52fcf996cd47269f)

0.15.0

- New features:
  - Merge all selected fragments (237)
  - Add logo/icon draft (240)

0.14.1

- Bug fixes:
  - Toggle interpolation globally instead of per source (214 222)

0.14.0

- new features:
  - shape interpolation mode (228)
  - bug fixes:
  - remove delay setting for ortho-views (236 227)
  - fix crosshair update issues (235)

0.13.0

- New Features:
  - Loading indicator when applying mask in status bar
  - Color indicator for last selected label id in status bar (with label id in tooltip)
  - Add generic source display status support
  - Progress indicator for 3d flood-fill
  - No waiting cursor during flood-fill
  - Unify flood-filling for label multi-sets and primitive types
  - Toggle appending ids to current selection with ctrl+left click
  - Auto-detect data type in opener dialog (172)
  - Bug Fixes:
  - Concurrent modification exception when clicking on labels (208)
  - Label block lookup that considers all entire dataset is not serialized properly (232)

0.10.0

- different rendering modes for navigation and painting (200)
  - experimental features:
  - caching recently opened containers at `~/.cache/paintera/${class.getName()}/recent`
  - paintera config file at `~/.config/paintera.yml`
  - select from favorites or recent when opening N5/HDF5 datasets with fuzzy matching or browse for container
  - fuzzy matching for dataset
  - fuzzy matching for type
  - introduce mnemonics for buttons in opener dialog -- can now open dataset without touching mouse!
  - example `~/.config/paintera.yml`:
  yaml
  data:
  defaultDirectory: "/data/hanslovskyp"
  loadTypeAs:
  has no effect yet
  int64: label
  uint8: raw
  uint64: label
  n5:
  defaultDirectory: "/data/hanslovskyp"
  favorites:
  - "/data/hanslovskyp/sample_A_padded_20160501-bs=64.n5"
  hdf5:
  favorites:
  - "/home/hanslovskyp/Downloads/sample_A_padded_20160501.hdf"
  - "/home/hanslovskyp/Downloads"

0.9.7

Bug Fixes
  
  - Fragment-segment-assignment LUT (de-)serialization (198, 199)

0.9.5

Bug Fixes
  
  - out of bounds error when painting outside viewer window (196, 197)