Changelog#

Authors since 5.0.0: Jordi Torrents (jordi.torrentsm@gmail.com)

5.2.12#

  • Works in Python 3.12, 3.11, and 3.10. And NumPy 2.0.

  • Increase and decrease GUI font size with Ctrl++ and Ctrl+-.

  • Fix polavieja_lab/idtrackerai#90

  • Optimized “Connecting coexisting fragments”.

  • The log file copy in session folder contains error tracebacks.

  • Add DEVICE as an optional input parameter.

  • Fix bug occurring when session folder contains non-ASCII characters.

  • Add --no-labels parameter to Video generators (polavieja_lab/idtrackerai!73 by ssfrz)

  • Another fix to “Too many open files” error by disabling pin_memory in Protocol 3 pre-training.

  • Fix the automatic gap detector in Validator’s interpolator when starting the interpolation by double clicking on a centroid.

  • Fix individual videos cropping to keep the centroid of the animal in the center of the video when some padding has to be added.

5.2.11#

  • Fix critical bug making GUI_tools/icon.svg not be included in package build.

  • Set pin_memory=False to non-training DataLoader to avoid “Too many open files” error, pytorch/pytorch#91252.

  • Limit the number of images per animal to use in Idmatcher.ai to 10k.

5.2.10#

  • Added a Length Calibration tool in the Validator and its value length_unit in the trajectory files.

  • Added the parameter bounding_box_images_in_ram to avoid saving bounding box images on disk.

  • Added polavieja_lab/midline to Data analysis.

  • Refactored tracking agent code and merged Protocol 1 into Protocol 2 (no effect on the algorithm).

  • Cleaned Session.accumulation_folder attributes.

  • Add color shuffling action in Validator.

  • Validator interpolates now with splines using scipy.interpolate.make_interp_spline. Previous backend scipy.interpolate.interp1d is now considered legacy by SciPy.

5.2.7#

  • Improved branding design with a new logo and icon.

  • Fix critical bug that was making knowledge transfer crash when tracking videos with different identification image sizes.

  • Change default DATA_POLICY from "all" to "idmatcher.ai".

  • Improved Validator stability.

  • Reallocation of source code files.

  • Catch crash in MacOS when BlockingIOError raises at opening H5FD files in mode “r+”.

5.2.6#

  • Added resilience against corrupted videos avoiding wrongly decoded frames.

  • Added advanced hyper-parameters THRESHOLD_EARLY_STOP_ACCUMULATION, THRESHOLD_ACCEPTABLE_ACCUMULATION and MAXIMAL_IMAGES_PER_ANIMAL in docs and in terminal argument parser.

  • More intelligent automatic zoom in Validator based on animal’s body length.

  • Cleaner logging by not printing the level name if it is DEBUG or INFO.

  • Allow float and infinite values in blob’s area and intensity thresholds.

  • Simplified area widget in Segmentation App.

  • Define default session’s name by double clicking in the session’s name widget in the Segmentation App. The App will save .toml files without names if the widget is empty.

  • THRESHOLD_EARLY_STOP_ACCUMULATION changed from 99.95% to 99.9%.

  • Removed --settings argument from idtrackerai terminal command. Instead, multiple parameters files can be loaded with the --load argument in increasing order of priority.

  • More compact representation of list_of_fragments.json.

  • Merged hyperparameters BATCH_SIZE_PREDICTIONS_IDCNN and BATCH_SIZE_PREDICTIONS_DCD into BATCH_SIZE_PREDICTIONS

5.2.5#

  • Simplified intensity thresholds in Segmentation App.

  • Fixed identity removal in Validator.

  • Deprecate list_of_blobs_validated.pickle. Validated blobs are saved in the same original file list_of_blobs.pickle

  • Added “Autoselect error” option in the Validator.

  • Fix crucial error of not properly shuffling images before splitting into train/validation datasets.

5.2.4#

  • Improved memory efficiency.

  • Removed IDCNN_NETWORK_NAME hyperparameter.

  • Rename class Video to Session and video_object.json to session.json.

  • Rename parameter session to name.

  • Automatic session names made from video paths if no session name is provided.

  • Do not override sessions if their name has been automatically set. Create consecutive names like session_X_1.

  • Add a test step after each training.

5.2.2#

  • Add --size parameter for individual Video generators.

  • The default value for number_of_parallel_workers is limited to 8 maximum.

  • Do not save list_of_blobs_no_gaps.pickle.

  • Merge network architectures for crossings and identification.

  • Simplify video JSON file.

  • Add boolean flag identity_transfer_succeded to video JSON file.

  • Remove accumulation_statistics from video JSON file.

  • Faster training with efficient image normalization.

  • Faster coexisting Fragment connection.

  • Faster “First individual/crossing assignment”.

  • Do not fix identity of small Fragments.

  • More memory efficient network predictions.

5.2.1#

  • Fix crash in the video generator when using --gray.

5.2.0#

  • Add Exclusive Regions of Interest new feature (polavieja_lab/idtrackerai!58).

  • Add a button to remove the selected centroid when double clicking (Validator).

  • Allow loading a TOML parameters file with the Open button in the Segmentation app.

  • More informative logs

  • Fix invalid model predictions when using Metal backend in MacOS machines polavieja_lab/idtrackerai#82.

  • Fix Overflow crash when validation loss is exactly 0.

  • Fix crash of Protocol 3 in Windows because of the default integer type in Numpy.

  • Rename CustomError for IdtrackeraiError.

  • LEARNING_PERCENTAGE_DIFFERENCE_* hyperparameter renamed to LEARNING_RATIO_DIFFERENCE_*

5.1.9#

  • Allow idtrackerai to keep working even if OpenCV fails reading some video frames.

  • Limit framerate option in GUI enabled by default.

  • number_of_parallel_workers=1 disables Python’s Multiprocessing.

  • Fix video generator when dealing with error frames.

  • Add background_subtraction_stat to Segmentation App.

  • More informative logs, specially in the accumulation results.

  • Catch exception when it fails to read the number of frames of a video.

  • Lighter ListOfBlobs and ListOfFragments files, cleaning cached_property before saving.

5.1.8#

  • Fix NumPy integer types.

  • Add defaults values in video_object.json.

  • Improve errors and tracebacks in log.

5.1.7#

  • Works in Python 3.10 and 3.11.

  • Improve error messages.

  • New option to add a time column (in seconds) in the csv trajectory files. Parameter ADD_TIME_COLUMN_TO_CSV (False by default).

  • CONVERT_TRAJECTORIES_TO_CSV_AND_JSON default changed to True.

  • Reorganize trajectories output folder.

  • Change video extension limitation for everything OpenCV can read.

  • Fix output_dir error when it is stated in toml file.

  • Fix Protocol 3 with knowledge transfer

  • Merge and simplify learning_percentage_difference hyper-parameter

  • More stable Validator with unfinished sessions.

  • Clearer code in entry point functions and parameter management.

5.1.6#

  • Fix Validator bugs

  • Zoom un duplicates when clicking this error in Validator.

  • Setup points as integers

  • Fix input parameters effect on segmentation GUI

  • Remove deprecated image blurring parameter

5.1.5#

  • Fix Blob.is_an_individual setting when crossing detection training fails.

  • Fix distorted image visualization in some video formats.

  • Fix crash due to the missing Fragment.P1_vector attribute while validating.

  • Abstract Qt dependencies with qtpy package.

  • Default Qt package downgraded from PyQt6 to PyQt5 because its compatibility issues.

  • Allow running non-GUI idtrackerai parts without any Qt installation.

  • Add identity finder in Validator with Ctrl+F

  • More versatile command line options for idtrackerai_csv

  • (testing) Allowing running idtrackerai in CPU only mode, AMD GPUs and MacOS with or without MPS acceleration.

5.1.4#

  • ListOfGlobalFragments are saved in .json format.

  • ListOfFragments are saved in .json format.

  • Load the penultimate accumulation step if the last one broke.

  • Focus on error when selecting an “No id” error in Validator.

  • Reenable blobs’ contours approximation using less points (lighter blobs objects in RAM and disk).

  • Speed up trining by enabling persistent_workers=True in torch.utils.data.DataLoader.

  • Improve Validator responsiveness when loading a large session.

  • Remove scikit-learn dependency.

  • Fix GUI initialization error in Fedora

  • Fix background view in Segmentation App.

  • Improve logging information.

5.1.3#

  • Fix final compression bug on Windows.

  • Fix idtrackerai_video incompatibility when tracking without identities.

  • Fix GUI theme change malfunctioning.

5.1.2#

  • Disables the first two changes of changelog 5.1.1 (the identification images construction method and the blob’s contour approximation). These will be restored after some more testing.

5.1.1#

  • Maximize the number of relevant pixels inside identification images (faster identification).

  • Approximate blobs’ contours using less points (lighter blobs objects in RAM and disk)

  • Allow a variable number of animals (by setting n_animals=0) when tracking without identities.

  • Removed anti-flickering filter. It improves intensity threshold’s sensitivity and segmentation speed.

  • Using gzip compression on identification images files when finishing a successful session. Optimizing loading times.

  • Added playback speed in a action in the video player menu.

  • Python’s datetime usage in Video timers

  • Free Enter/Return keys from GUI shortcuts.

  • Fix log file issue when more than one session is running.

  • Optimize rescaling when resolution reduction and adapt ROI to scale.

  • Fix bug when validating single animal trackings.

  • Fix “change font size” bug in GUIs.

  • Ctrl+L to toggle playback framerate limitation (GUI).

  • Fix cv2 BRG/RGB color confusion.

  • Fix cv2 error in segmentation app when removing ROI while using background subtraction.

5.1.0#

  • Implement idmatcher.ai

  • ROIs can be reordered in segmentation app by drag and drop

  • ROIs in segmentation app are ordered from bottom to top

  • Select ROI by clicking inside the polygon in the video player (segmentation app)

  • Fix typos

  • Simplify idtrackerai/network file structure and imports

  • Improve v4 compatibility reading video.json/npy

  • Merged crossings/identification NetworkParams as a single dataclass

  • Simplified GetPredictionIdentification converting it into a function

  • Fix gray individual video generation

5.0.0#

  • Full code revision promoting Python built-in libraries, argument type hints and multiples optimizations in terms of code simplicity and structure, RAM usage, lighter output generated data and faster execution.

  • Unify all tools related to idtracker.ai in the same repository/package

  • Works with Python 3.10

  • New graphical apps buildings directly with PyQt6

  • Remove dependency with

    • Pyforms

    • Python-video-annotator

    • Matplotlib

    • Joblib

    • Natsort

    • Tqdm

    • Pandas

    • Gdown

  • Using the last versions of every remaining used dependency

  • Completely new segmentation app, fully responsive, intuitive and faster

  • Completely new validation app to view the session results, navigate through the possible tracking errors, fix them and manipulate the session using other extra tools.

  • idtrackerai_csv tool to convert trajectories after the tracking process finished.

  • Removed local_settings input method.

  • New input methods (more direct and simple) (--load, --settings and terminal declarations).

  • The tool “setup points” moved to the validator.

  • No NUMBER_OF_JOBS_FOR_BACKGROUND_SUBTRACTION, background is computed sequentially.

  • Merged NUMBER_OF_JOBS_FOR_SEGMENTATION and NUMBER_OF_JOBS_FOR_SETTING_ID_IMAGES in the same parameter NUMBER_OF_PARALLEL_WORKERS.

  • Easier background subtraction implementation, with “median” option. It is more robust against difficult tracking intervals/episodes/number of frames.

  • Better and easier parallel episode definitions with optimized parallel distribution (specially with multiple files).

  • Simplified attributes in all idtracker.ai objects.

  • ListOfBlobs reconnects in almost no time after loading from saved .pickle file.

  • Flexibility selecting the number of videos to track.

  • Remove Blob.pixels attribute. Much faster and lighter blob manipulations.

  • Stretch Blob.bounding_box. Much lighter segmentation images.

  • Optimized 80% of the computational time of _process_frame() by properly removing the function binary_fill_holes().

  • Logs more readable, with more useful information and progress bars (using Rich).

  • Faster h5py writing/reading implementation (by not opening and closing the h5py file for every single image, we keep them opened).

  • Python objects are saved as pickle objects and json files when possible (lighter and more standard than .npy files).

  • Removed option save_areas. Now, the statistics of the areas are always printed in the trajectory files.

  • Parallel processing using built-in Multiprocessing, not Joblib.

  • Reorganize internal modules promoting decoupling (fragmentation, tracking and postprocessing modules).

  • Easy video generation with idtrackerai_video.

  • Package is defined using a pyproject.toml file.

  • No git sub-modules used.

  • Faster blob overlapping method (convexHull and point inside contour methods).

4.0.0#

  • Works with Python 3.7.

  • Remove Kivy submodules and stop support for old Kivy GUI.

  • Neural network training is done with Pytorch 1.10.0.

  • Identification images are saved as uint 8.

  • Crossing detector images are the same as the identification images. This saves computing time and makes the process of generating the images faster.

  • Improve data pipeline for the crossing detector.

  • Parallel saving and loading of identification images (only for Linux)

  • Simplify code for connecting blobs from frame to frame.

  • Remove unnecessary execution of the blobs connection algorithm.

  • Background subtraction considers the ROI

  • Allows to save trajectories as csv with the advanced parameter CONVERT_TRAJECTORIES_DICT_TO_CSV_AND_JSON (using the local_settings.py file).

  • Allows to change the output width (and height) of the individual-centered videos with the advanced parameter INDIVIDUAL_VIDEO_WIDTH_HEIGHT (using the local_settings.py file).

  • Horizontal layout for graphical user interface (GUI). This layout can be deactivated using the local_settings.py setting NEW_GUI_LAYOUT=False.

  • Width and height of GUI can be changed using the local_settings.py using the GUI_MINIMUM_HEIGHT and GUI_MINIMUM_WIDTH variables.

  • Add ground truth button to validation GUI.

  • Added “Add setup points” featrue to store landmark points in the video frame that will be stored in the trajectories.npy and trajectories_wo_gaps.npy in the key setup_poitns. Users can use this points to perform behavioural analysis that requires landmarks of the experimental setup.

  • Improved code formatting using the black formatter.

  • Better factorization of the TrackerApi.

  • Some bugs fixed.

  • Better documentation of main idtracker.ai objects (video, blob, list_of_blobs, fragment, list_of_fragments, global_fragment and list_of_global_fragments).

  • Dropped support for MacOS

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