CHANGELOG

0.25.6
 - maintenance release
0.25.5
 - enh: support unnamed table data in `HDF5Data`
 - setup: pin scipy<1.15 due to https://github.com/scipy/scipy/issues/22333
0.25.4
 - enh: support passing a single file to `concatenated_hdf5_data`
0.25.3
 - enh: request single threaded operations when going into mp.Process (#17)
 - enh: new module `dcnum.single_thread_osenv`
0.25.2
 - setup: officially support numpy 2
 - setup: pin dependencies
0.25.1
 - fix: catch ValueError when computing relative path on different anchors
 - ref: replace np.string_ with np.bytes_
 - ref: remove unused `data` argument to QueueCollectorThread
 - ref: minor speed-up for QueueCollectorThread
0.25.0
 - feat: identify flickering in raw data via dcnum.read.detect_flickering
 - fix: handle out-of-bounds slice indexing for BaseImageChunkCache
 - fix: np.bool_ and np.floating not recognized in PPID parsing
0.24.0
 - feat: add support for internal basins
 - feat: "image_bg" as internal basin for "sparsemed" background computer
 - fix: "sparsmed" background computer attributed background images with
   an offset of `split_time` (the fist event obtained the background image
   of the first event of the first second and so on)
 - enh: support numpy indexing for mapped basins
 - enh: add new `write.copy_basins` method
 - ref: return `h5py.Group` in `HDF5Data.get_basin_data` instead of
   a basin `HDF5Data` instance
 - ref: perform "plumbing" before "cleanup" in pipeline
 - ref: increment DCNUM_PPID_GENERATION to 11
0.23.4
 - enh: run set_num_interop_threads(1) for torchmpo segmenter
0.23.3
 - fix: ignore non-file-type-like basins
 - fix: workaround for slow reading from HDF5 (don't use index arrays)
 - fix: avoid excessive stalling when writer is slow
0.23.2
 - enh: add DCNumPipelineJob.validate method
 - enh: list Python libraries used in job log
 - setup: change required pytorch version from 2.3 to 2.2 (hardware support)
0.23.1
 - enh: support passing custom default arguments to get_class_method_info
 - tests: fix torch preprocessing tests
0.23.0
 - feat: implement segmentation using PyTorch models
 - fix: always compute image_bg if it is not in the input file
 - enh: introduce `Segmenter.validate_applicability` method
0.22.1
 - fix: compute pipeline identifier of origin dataset for basin mapping
0.22.0
 - fix: GPUSegmenter did not perform mask postprocessing
   (this was not actually fixed in 0.21.0)
 - tests: implement mock STO segmenter for testing (#3)
 - tests: add tests for bg_off in segmentation
 - ref: increment DCNUM_PPID_GENERATION to 10
 - ref: renamed CPUSegmenter to MPOSegmenter
 - ref: renamed GPUSegmenter to STOSegmenter
0.21.4
 - fix: division by zero error when computing stall time
0.21.3
 - fix: negative stall time in log messages
0.21.2
 - fix: negative argument for time.sleep
0.21.1
 - enh: support boolean images in mask postprocessing
0.21.0
 - ref: enable mask postprocessing by default for all segmenters
 - ref: increment DCNUM_PPID_GENERATION to 9
0.20.4
 - fix: slot_chunks were not performed in increasing order, making it
   impossible for writer to continue writing and consequent OOM
 - enh: reserve one CPU for writer thread and control logic
 - enh: disentangle logging and debugging keyword arguments
 - enh: do not initialize slot_chunks and slot_states with lock
0.20.3
 - enh: improve strategy for stalling for slow writer
0.20.2
 - ref: remove __init__ from SegmentThresh
0.20.1
 - fix: relative basin locations not written correctly
 - enh: increase deque size threshold for waiting for writer
0.20.0
 - feat: support reading mapped basins
 - feat: support writing mapped-basin-based output files
 - fix: copy "bg_off" data to output file when copying background data
 - enh: allow to slice BaseImageChunkCache
 - enh: sort logs, tables and basins for reproducible access
 - enh: add more timing information in logs
 - ref: background progress value is now a double between 0 and 1
0.19.1
 - enh: support steps when specifying data slices in `index_mapping`
0.19.0
 - enh: elevate `HDF5Data`s `index_mapping` to pipeline identifier status
   (this changes the pipeline identifier)
 - enh: improve sanity checks for `BackgroundRollMed`
0.18.0
 - BREAKING CHANGE: mask postprocessing did a morphological opening instead
   of a morphological closing, failing to remove spurious noise
 - BREAKING CHANGE: perform first fill_holes and then closing_disk in mask
   postprocessing
 - feat: allow to specify ranges when creating an HDF5Data instance to
   enable e.g. processing only a portion of an input file
 - feat: volume computation via contour revolve algorithm (#23)
 - feat: background offset (flickering) correction via the
   "offset_correction" keyword for the "sparsemed" background computer
   and "bg_off" everywhere else
 - enh: allow creating HDF5Writer from h5py.File
 - fix: mask postprocessing did a morphological opening instead
   of a morphological closing, failing to remove spurious noise
 - fix: remove mask ppid part for segmenters that do not use it
 - fix: mask postprocessing with "fill_holes" using `cv2.floodFill`
   sometimes segmented the entire frame if the upper left pixel was not
   set to background
 - enh: perform first fill_holes and then closing_disk in mask
   postprocessing
 - enh: pop read-cache items before adding a new one
 - enh: allow to request the raw contour from `moments_based_features`
 - ref: increment DCNUM_PPID_GENERATION to 8
 - ref: added new super class `BaseImageChunkCache`
 - ref: use HDF5Writer in Background class
 - ref: minor cleanup
 - ref: rename submodule `feat_moments` to `feat_contour`
 - ref: remove unused `name` property from `Background` class
0.17.2
 - fix: make sure unsupported features are not propagated in
   `concatenated_hdf5_data` (#27)
0.17.1
 - ref: remove "bg_med" and "index_online" from protected scalar features,
   because "bg_med" may change due to a different background computation
   method and "index_online" enumerates events from online segmentation
0.17.0
 - feat: allow to register topical search paths
 - ref: remove deprecated `get_ppid_from_kwargs` methods
 - ref: remove deprecated `preselect` and `ptp_median` keyword
   arguments from `QueueEventExtractor`
 - ref: remove deprecated "key" from `get_class_method_info` info dict
 - ref: issue UserWarning instead of DeprecationWarning when checking
   segmenter keyword arguments
 - ref: remove pixel size check for HDF5 data
 - ref: remove unused `_get_model_file` from GPUSegmenter
0.16.8
 - fix: correctly set number of workers for CPUSegmenter
 - enh: update list of environment variables that should be set to
   disable multithreading in subprocesses
0.16.7
 - fix: if the writer dequeue fills up, stall the feature extractor
 - enh: optimize DequeWriterThread loop
 - enh: minor optimization in HDF5Writer.require_feature
0.16.6
 - fix: correctly handle mask images with no background on border
 - fix: enforce user-defined features in concatenated_hdf5_data
 - fix: Gate.features returned duplicate entries
 - ref: cache empty border image creation for clear_border
 - ref: rename internal background worker classes
 - ref: simplify Gate initialization
 - ref: Gate instance does not have to keep a reference to the data
 - ref: better box_gates management for Gate class
 - tests: increase coverage
0.16.5
 - fix: replace unreliable Queue.empty and Queue.qsize (macOS support)
0.16.4
 - fix: there was no progress for background copying
 - enh: detect data files that contain no events
 - tests: add test for sparsemed bg worker
 - tests: add test for logic json encoder
0.16.3
 - enh: define valid DCNumJobRunner state
 - enh: more robust computation of progress
 - enh: use HDF5Data when loading input data for background computation
 - enh: automatically split segmenters and extractors equally
 - ref: reduce default image cache size from 5 to 2
 - ref: move dataset generation default kwargs to writer submodule
 - ref: warn above 0.5% of discarded events in EventExtractorManagerThread
0.16.2
 - fix: ignore empty HDF5 datasets when copying metadata
 - fix: logging from subprocesses did not work as expected
 - enh: warn user about total number of invalid masks
 - enh: introduce DCNumJobRunner.error_tb for errors happening in threads
 - enh: improve logging verbosity
 - enh: append job information as log entry in DCNumJobRunner output file
 - enh: set chunk size for all feature data to 1MiB in HDF5Writer
 - ref: removed close_queues argument from EventExtractor init
 - ref: rename event_count with image_count in background computation
 - ref: do not print anything to stdout when computing background data
 - ref: use data from background computer in DCNumJobRunner.get_status
0.16.1
 - fix: when checking for ppid kwargs, allow kwargs defined in `__init__`
 - ref: use kwonly arguments for segmenter `__init__` method
 - tests: set environment variables so that libraries use one thread only
0.16.0
 - feat: implement "copy" background class
 - fix: handle small kernel size before background computation (#16)
 - fix: update experiment:run identifier for dclab-user convenience
 - fix: make sure output directory exists for pipeline job
 - fix: forward debugging flag to SegmenterManagerThread
 - ref: reduced minimum frame count for rolling median background
   computation to kernel size
0.15.0
 - BREAKING CHANGE: Remove preselection capabilities, because it is not
   well integrated into the pipeline. For more information, please see
   issue #15.
 - feat: introduce logic submodule for running pipelines
 - feat: implement HDF5Writer.store_log
 - enh: add Segmenter.hardware_processor property
 - enh: introduce pipeline identifier for data pixel size
 - enh: reduce pixel_size accuracy to 8 digits after the decimal point
   for pipeline reproducibility
 - enh: warn the user when creating a basin-based file without basin paths
 - ref: deprecate pixel size correction in HDF5Data
 - ref: increment DCNUM_PPID_GENERATION to 7
 - ref: several changes and deprecations in the PPID helper functions
 - build: change flat-layout to src-layout (issues with editable installs)
0.14.0
 - fix: protected features (e.g. time, frame) were not included in ouptut
   files when the input file was basin-based
 - ref: increment DCNUM_PPID_GENERATION to 6
0.13.3
 - fix: correctly raise KeyError for missing image-based feature from
   HDF5Data._image_cache
0.13.2
 - fix: properly convert variable-length string logs in `copy_metadata`
0.13.1
 - fix: wrong event count in logs
 - ref: np.product is deprecated in numpy 2.0
0.13.0
 - feat: support writing file-based HDF5 basins (#11)
 - feat: support reading file-based HDF5 basins (#11)
 - feat: implement `create_with_basins` convenience method (#11)
 - fix: correctly support passing an ndarray to BackgroundSparseMed
   instead of an input file path
 - fix: BackgroundSparseMed did not work for datasets of length < 100
 - fix: bad f-string in BackgroundSparseMed
 - enh: create a default basin-based output file for background computation
 - ref: unite initialization code of background comptuers in base class
 - ref: define context managers of background comptuers in base class
 - ref: remove functools.cache decorator from HDF5Data
 - tests: add tests for BackgroundSparseMed
0.12.3
 - fix: background computation with sparsemed did not work
 - enh: support passing paths as strings to Background class
0.12.2
 - enh: more efficient computation of inert_ratio_prnc feature (#6)
 - enh: more efficient computation of tilt feature (#6)
 - enh: feature computation for area_um_raw, deform_raw, eccentr_prnc,
   per_ratio, and per_um_raw
 - ref: increment DCNUM_PPID_GENERATION to 5
0.12.1
 - fix: avoid NaN-valued features due to invalid contours (#9)
 - ref: increment DCNUM_PPID_GENERATION to 4
0.12.0
 - ref: always use "spawn" for creating new processes to avoid race
   conditions with Python threading.Lock upon forking on POSIX
 - enh: some multiprocessing values in CPUSegmenter can be raw
0.11.13
 - enh: wait for event queue to empty before attempting to join
   QueueEventExtractor processes
0.11.12
 - enh: explicitly close event queue in QueueEventExtractor
0.11.11
 - fix: QueueCollectorThread hangs indefinitely because of a missing
   EventStash.is_complete check
 - tests: increase coverage for queue_collector_thread submodule
0.11.10
 - fix: GPUSegmenter does not remove model_file from passed kwargs anymore
0.11.9
 - fix: properly support table data of length 1
 - tests: make sure all segmenters have clear type definitions
0.11.8
 - reg: do not close the background thread of the event queue
0.11.7
 - enh: add more debugging messages for feature extraction workers
0.11.6
 - enh: add more debugging messages for feature extraction workers
0.11.5
 - setup: fix bad package discovery
0.11.4
 - fix: properly handle empty logs
0.11.3
 - fix: make sure values in tables dictionary are one-dimensional
0.11.2
 - meta: increment pipeline ID (texture feature computation)
 - fix: HDF5Data was not pickable
 - fix: HDF5Data did not properly handle tables
 - enh: add context manager for CPUSegmenter
 - enh: record and log execution time of segmentation and feature extraction
 - enh: properly handle border case for computing contour-moments
 - enh: properly handle empty images/masks in haralick texture features
 - tests: do not use numba's JIT during testing (coverage)
0.11.1
 - fix: fix GPUSegmenter labeling
0.11.0
 - feat: introduce GPUSegmenter base class
 - fix: handle bytes-values in HDF5 attributes
 - ref: correctly introduce `requires_background_correction` for segmenters
 - setup: don't requrie cibuildwheel
0.10.0
 - enh: some minor improvements in efficiency
 - ref: increment DCNUM_PPID_GENERATION for the sake of clarity
 - ref: unify dealing with num_workers and debugging
0.0.9
 - fix: properly propagate event extraction keyword arguments
 - fix: QueueCollectorThread used uint16 for enumerating indices
 - fix: handle case where number of events is not multiple of chunk_size
 - enh: reduce thread waiting times
 - enh: add bounds check for image cache
0.0.8
 - feat: introduce QueueCollectorThread
 - feat: introduce SegmenterManagerThread
 - feat: instroduce EventExtractorManagerThread and corresponding workers
 - enh: minor improvements for HDF5ImageCache and ImageCorrCache
 - enh: use data size as cache size if smaller than requested chunk size
 - enh: return dictionary for brightness feature computation
 - enh: allow to pass a single image for brightness feature computation
 - enh: allow to pass a single image for texture feature computation
 - enh: make sure that masks are written as uint8 to HDF5 files
 - ref: haralick texture computation now returns dict instead of recarray
 - ref: renamed HDF5WriterThread to DequeWriterThread
 - ref: renamed feature submodules (prepended "feat_")
0.0.7
 - enh: dataset keyword arguments and mode HDF5WriterThread
 - enh: speed-up of brightness feature computation
0.0.6
 - feat: add HDF5Writer and HDF5WriterThread classes in write submodule
 - feat: segmenters compute labeled images instead of masks
 - enh: introduce iter_chunks for cached image data
 - ref: do not filter for contour length
 - ref: rename feat.background.get_available_background_methods
 - ref: store PPID information in dataset metadata instead of "user" section
0.0.5
 - enh: allow to set image_cache_size in HDF5Data
 - enh: allow to easily register new custom segmenters
 - ref: CPUSegmenter has its own submodule now
0.0.4
 - feat: introduce HDF5 virtual dataset path concatenator
 - enh: allow to pass h5py.File object to HDF5Data
 - fix: typo in logging statement for sparse median bg computation
0.0.3
 - feat: introduce median background computation
 - feat: introduce data reader
 - feat: introduce thresholding segmenter
 - feat: introduce brightness, haralick texture, and moments-based features
0.0.2
 - first automated release
0.0.1
 - stub release