Fix symmetric skeletons (via table input) #1136
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roomrys
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Codecov Report
@@ Coverage Diff @@
## develop #1136 +/- ##
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+ Coverage 69.95% 69.96% +0.01%
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Files 130 130
Lines 22475 22476 +1
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+ Hits 15723 15726 +3
+ Misses 6752 6750 -2
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roomrys
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Feb 24, 2023
* GUI Training: Use hidden params from loaded config (#1053) * Add optional unragging arg to model export (#1054) * Fix config option to `split_by_inds` (#1060) * Convert training, validation, and test to Labels object * Add test for split_by_inds * Use Labels.extract instead of Labels(List[LabeledFrames]) * Tracking: robust assignment of the best score to an instance (#1062) * Set max instances for top down models (#1070) * Add optional unragging arg to model export * Add option to set max instances for multi-instance models * Fix test * Don't create instances during inference if no points were found (#1073) * Don't create instances during inference if no points were found * Add points check for all predictors * Fix single instance predictor logic and test * Add tests for all predictors Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> * Add one-line fix to VideoWriterSkyvideo (#1082) * Fix parser for sleap-export (#1085) * Refactor commands to load project as `AppCommand`s (#1098) * Add working Proof of Concept * Create command class for loading project * Split `LoadProjectFile` as a subclass of `LoadLabelsObject` * Reroute last existing reference * Remove debugging code * Flexibly resize input layer of `tf.keras.Model` upon loading trained model (#1084) * Add initial implementation (auto output stride problematic) * Add to load_predictor test (error when auto-compute output stride) * Use output stride from config instead of auto-computing * Fix output-stride/padding modulo error and do not resize on export * Fix resizing bug in multi-class predictors * Non-functional clean-up * Rename new input layer to original name * Add inference integration test * Minimize config surgery, generalize layer iteration Co-authored-by: Talmo Pereira <talmo@salk.edu> * Add Option to Make Trail Shade Darker/Lighter (#1103) * Make trails 60% darker than track color * Add menu option for shade of trails * Remove unexpected indent (fat-fingered) * Create signal that updates plot instead of removing and replotting items (#1134) * Create signal that updates plot instead of redrawing * Remove debug code * Non-functional self-review changes * Fix symmetric skeletons (via table input) (#1136) Ensure variable initialized before calling it * Nix export of tracking results (#1068) * [io] export tracking results to NIX file * [io] nix added to export filter only if available * [nixio] refactor, add scores link data as mtag * [nixio] speeding up export by chunked writing * [nixio] rename point score to node score * [nixio] fix missing dimension descriptor for node scores * [export analysis] support multiple formats also for bulk export * [nixio] export centroid, some documentation * [nixio] fix double dot before filename suffix * [nixio] fix bug when not all nodes were found * [nixio] housekeeping * [nix] add nix analyis output format to convert * [nix] tiny fix, catch file write error and properly close file * [inference] main takes optional args. Can be imported to run inference form scripts * [convert] simplify if else structure and outfile handling for analysis export * [nix] use pathlib instead of os * [nix] catch if there are instances with a None frame_idx ... not sure why this occurred. The nix adaptor cannot save instances that are not related to a frame. * [nix] move checks to top of write function * [nix] use absolute imports * [nix] use black to reformat * [commands] revert qtpy import and apply code style * [convert] use absolute imports, apply code style * [commands]fix imports * [inference/nix]fix linter complaint, adjust nix types for scores * [nix] add test case for nix export format * [nix] extended testing, some modifications of adaptor * [skeleton] add __eq__ to Skeleton ... make Node.name and Node.weight instance variables instead of class variables * [nix] add nixio to requirements, remove unused nix_available, ... allow for non-unique entries in node, track and skeleton. Extend node map to store the skeleton it is part of * [nix] make the linter happy * [Node] force definition of a name Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [nix] use getattr for getting grayscale information Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [nix] fixes according to review * [convert] break out of loop upon finding the video Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [commands.py] use pathilb instead of splitting filename Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * [dev requirements] remove linebreak at last line * [skeleton] revert attribute creation back to original * [nix] break lines in class documentation * Ensure all file references are closed * Make the linter happy * Add tests for ExportAnalysis and (docs for) sleap-convert Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Fix body vs symmetry subgraph filtering (#1142) Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Handle changing backbones in training editor GUI (#1140) Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Added scaling functionality for both the instances and bounding box. (#1133) * Create VisibleBoundingBox class. * Added instance scaling functionality in addition to bounding box scaling functionality. * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Update sleap/gui/widgets/video.py Co-authored-by: Talmo Pereira <talmo@salk.edu> * Added new testing for scaling operation and simplified VisibleBoundingBox class code. * Added type hinting to the scaling padding and removed erroneous bounding rect initialization. Co-authored-by: Talmo Pereira <talmo@salk.edu> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Add better error message for top down (#1121) * Add better error message for top down * Add test for error message * Raise different error, fix test * Hotfix for video save #1098 (#1148) * Add a hotfix for #1098 * WIP: Add test for detecting changes on load * Finialize change on load test * Remove unused imports * Skip test if on windows since files are being used in parallel * Add central padding to SizeMatcher (#1129) * add center padding to size matcher * add test for center padding * add ensure_float option to inference layer * reformat resizing and test_resizing * Remove redundant operation * Replace existing constants with fixtures --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Added MoveNet as an external model reference (#1141) * add center padding to size matcher * add test for center padding * add ensure_float option to inference layer * reformat resizing and test_resizing * add MoveNet as an external model inference * add the movenet to the from_model_paths * add tests * add comments to movenet predictor * add tensorflow_hub to the requirements.txt * modified default video path * resolved most of the comments except expanding the predictor * expanded Predictor.from_model_paths function to include any pre-trained models. * add test_load_model * added from_trained_models in class Predictor and modified test_load_model for it. * modified test_load_model to be more generalized. * moved pretrained model from Predictor.from_trained_model to Predictor.from_model_paths and added a test for it. * Fix Predictor.from_model_paths and tests * Rename load_movenet_model to make_model_movenet * minor clean-up * Remove redundant operation * Replace existing constants with fixtures * Handle loading movenet models via load_model API * Clean-up doc strings --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Resumable Training (#1130) * add resume training functionality * add testing function for resume training functionality * linting black * Resumable Training 2 - CLI Options (#1131) * add cli options for resumable training * add test for cli resume training * black linting for cli resumable training * simplify resumable checkpoint CLI fn to a single CLI arg (#1132) * simplify resumable checkpoint CLI fn to a single CLI arg * Adam/resumable training 3 (#1150) * correct path of labels_path for test_training * add resume training to gui * add train from scratch message * Add finishing touches to resumable training PR (#1150) (#1168) * Refactor/update 'use trained' and 'resume training' checkbox logic * Simplify checkbox logic and reset model field when resume training * Reset checkboxes upon changing config selection * Handle case for updating TrainingEditor when sender is not a checkbox * Add complete state space GUI test for checkboxes * Finish combobox test * Test that form is reset * Remove straggling TODO --------- Co-authored-by: roomrys <38435167+roomrys@users.noreply.github.com> Co-authored-by: jimzers <jimzersml@gmail.com> --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Return trainer from sleap-train and check that trainer configured correctly * Add CLI documentation for website --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Small (final?) revisions and fix test * Revert changes to fixture --------- Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * GenericTableModel/View improvements (#1163) * [dataviews] GenericTableModel/View improvements ... * GenericTableView got a new argument specifying whether the ellipsis for long cell content should be right (old behavior, default) or left useful for long content such as the filenames in the video table. * GenericTableView uses all the space that available to the table. * The model's data function returns the full cell content to be shown as tool tip text. * [gui/app] set the ellipsis to be on the left for long table contents --------- Co-authored-by: Liezl Maree <38435167+roomrys@users.noreply.github.com> * Add Skeleton Templates (#1122) * Update docs: change 'M1' to 'Apple Silicon' (#1188) * Bump to 1.3.0a0 (#1189) --------- Co-authored-by: sheridana <asheridan@salk.edu> Co-authored-by: getzze <getzze@gmail.com> Co-authored-by: Talmo Pereira <talmo@salk.edu> Co-authored-by: Jan Grewe <jngrewe@googlemail.com> Co-authored-by: Sean Afshar <84047864+sean-afshar@users.noreply.github.com> Co-authored-by: Jiaying Hsu <72051972+jiayinghsu@users.noreply.github.com> Co-authored-by: Adam Lee <38634441+jimzers@users.noreply.github.com> Co-authored-by: jimzers <jimzersml@gmail.com> Co-authored-by: Jan Grewe <jan.grewe@g-node.org> Co-authored-by: Aaditya Prasad <78439225+aaprasad@users.noreply.github.com>
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Description
In #1022 we conditionally set a variable
item_value, but always compared the variable downstream. This isn't a problem if theitemalready exists, but when trying to set new symmetries for example,item_valuewas never being set.This PR runs through a conditional chain ending in an
elsewhich always intializeditem_value.Types of changes
Does this address any currently open issues?
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