Commit f91e2f2
Dev branch pull into master (#442)
* simplified get_frames()
* moved io-bound get_frames() function to io/binary.py
* simplified make_blocks()
* removed unused function shift_data_subpixel()
* fixed docstring and removed unused lines from rigid.shift_data()
* refactored out 'offsets' data structure
* removed redundant nonrigid.make_blocks() call.
* changed print(warning) to warning.warn(), Exception to ValueException,
* pulled 1Preg transformation out of rigid.phasecorr()
* reordered re_1p n phasecorr_refernce()
* split refAndMasks parameter in rigid.phasecorr() into its components and moved numba addmultiply() function to utils.py
* removed unused gpu_phasecorr()
* removed redundant spatial_smooth during nonrigid registration
* refactored non-rigid registration into own function: nonrigid.shift()
* pulled nonrigid.shift() out of compute_motion_and_shift()
* removed commented-out code in compute_crop()
* removed unused imports
* refactored out RefAndMasks and RefAndMasksNR
* refactored out phasecorr_cpu()
* refactored out nonrigid.shift()
* removed unused call to nonrigid.transform_data()
* removed unused vars from nonrigid.phase_corr()
* moved var use closer to declaration
* Detection/Extraction regression tests added along with additional registration tests. (#382)
* Completed 1plane1chan and 2plane2chan tests for detection/extraction. Added pre_registered data for 2plane2chan case.
* Finished adding preprocessing and OASIS to regression tests.
* Added regression test for classification module. Added tailored stat.npy that's used before classifier is called.
* Added np allclose due to sklearn.LogisticRegression's slight differences in output
* Modified tolerance value after checking on another computer.
* removed unused patlib import in classification tests.
* Refactored check_registration_output in test_registration_module.py
* Added input data that requires bidishift.
* Added 1preg regression test for registration module and its test_data
* changed test_register_binary to use input_1500 with metrics
* Removed two pipeline tests. (#383)
* removed unused testcase
* changed setup_and_teardown() to default_ops()
* changed data_dir fixture call to default_ops['data_path'][0]
* refactored TestUtils class/fixture to a utils.py module.
* moved test methods to test functions
* added pipeline Test with sourcery coverage (#385)
* removed unused testcase
* changed setup_and_teardown() to default_ops()
* changed data_dir fixture call to default_ops['data_path'][0]
* refactored TestUtils class/fixture to a utils.py module.
* moved test methods to test functions
* deleted unused test data
* added sourcery test and test data
* re-added necessary test data
* re-added new 1plane2chan verion of sourcery test
* Renamed io.write_tiff to changed io.save_tiff method in io tests.
* split coupled "spatial_hp" ops parameter into "spatial_hp_reg" and "spatial_hp_detect".
* refactored out compute_motion_and_correct()
* removed redundant pre_smooth and spatial_hp value checking
* register_binary() only takes a Dict ops.
* structured nested if statements
* used tuple unpacking on multiple assignment
* removed temporary 'bidi' name and redundant nonrigid.make_blocks() call
* removed unusable utils.split_multiops() line
* removed redudnant np.save(ops) in register_binary()
* moved depgraph scripts to own folder
* added new profiler script (#388)
* refactored out repeated data_smooth conditionals
* moved compute_zpos() back to zalign.py
* cleaned up get_pc_metrics(): collapsed nsamp conditional logic, moved nPC to optional argument
* moved ops-level functions back to their original modules
* fixed paths
* zipped rigid.shift_data()
* pulled single-frame shift_frame() out of shift_data()
* pulled iteration out of rigid.shift_frames(), reducing to simpler rigid.shift_frame()
* pulled memory management out of rigid.shift_frame() into the calling function.
* removed temporary variables from refImg mean shift step
* removed shadow assignment step
* vectorized fft2 and ifft2 steps in rigid.phase_corr()
* used fancy indexing on cmax to vectorize cmax filling
* removed temp variables for lcorr calculation
* refactored out crop() function to remove intermediate vars
* cleaned rigid.phasecorr_reference
* split rigid.phascorr_reference() into independent functions phasecorr_reference() and compute_masks()
* removed extra reference image copying
* split rigid.phasecorr() into independent functions rigid.phasecorr() and rigid.apply_masks()
* created utils.convolve() function to document fft2/ifft2 step and layer math concepts
* removed hard-coded module literals
* removed pre-computed module-level constants, replaced with cached function call.
* spacing
* refactored out nonrigid.clip()
* made cc2 calculation more readable
* cleaned up loop
* cleaned up ymax1, xmax1, cmax1 calculation
* vectorized nested fft2/ifft2 calculation
* removed unused nonrigid.linear_interp() function
* call duplicated addmultiply() in utils instead of nonrigid
* removed extra data copy and unused variables in numba function
* removed inplace parameter modification to rmeove need for guard copying
* removed extra copies
* reordered lines in nonrigid.transform_data()
* shifted array management down from mat_upsample to kernel1d
* refactored nonrigid.make_nblocks(), splitting out two algorithm functions and removed one pipelined argument
* step reduction in nonrigid.phasecorr_reference()
* moved gaussian kernel functions to utils.py
* working in 3D, output in 4D
* reduced preallocation steps in nonrigid.phasecorr_reference()
* refactored getSNR
* replaced fft2/ifft2 call with utils.convolve()
* replace zeros() with empty()
* moved append()
* collapsed two `if ops['1Preg']` into one
* composed rigid registration steps
* removed redundant ops assignment and misleading comment
* merged pre_smooth conditional
* lowered gaussian_filter1d() to utils and replaced it with utils.temporal_smooth()
* removed some squeeze() and newaxis
* added explicit padding step to utils.spatial_smooth, plus a regression test
* renamed intermediate steps
* moved valueerror to algorithmic function, removed unnecessary [newaxis] -> squeeze() around spatial_smooth() calls
* replace concatenate() algorithm with numpy.pad
* removed unused ccsm output of nonrigid.phasecorr()
* changed gaussian_filter1d call to temporal_smooth()
* Added smoothed data for 2 channel test. Removed 1preg test from registration module. (#396)
* Separate detect and extract subpackages. (#394)
* Separated extraction and detection subpackages. Consolidated all of detection's functions to just one call in extraction.
* Removed preclassify code since it doesn't work. Created detection test_module.
* Removed 2plane1chan test_data since we do not have any tests for it.
* Added detection regression tests along with necessary test_data
* Fixed up ops output for main_detect function
* Separate extract and detect from run_s2p and in tests
* Added regression tests for extraction module.
* Checked that separate detection and extraction tests pass. Removing combined tests.
* Added chan2 check for extraction tests. Removed extraction utils and moved to detection utils. source and sparsery now dont depend on extraction module.
* Remove meanImg calculation from extract subpackage.
* Revert "Remove meanImg calculation from extract subpackage."
This reverts commit 241a119.
* Removed meanImg calculations from extract again.
* Moved chan2detect to detection package. Moved chan2detect call to detect. Successfully separated extract and detect subpackages. Added meanImg parameters to both detection/extraction tests.
* Removed redcell from test_pipeline
* changed import in chan2detect.py
* BinaryFile.read() exports indices
* moved batch_size argmument to read() mehtod of BinaryFile
* changed BinaryFile's reg_file and raw_file parameters to read_file and write_file
* removed unused options in BinaryFile
* removed io.get_frames()
* minor cleanup
* simplified filename assignment
* removed temp variable
* refactored bidiphase
* refactored meahgrid_mean_centered() out of gaussian_fft() and spatial_taper()
* simplified convolve()
* reordered import to clean up tuna stack trace
* Refactor registor (#378)
* split write_tiff() into generate_tiff_filename() and save_tiff()
* cleaning register_to_binary()
* removed ops from io.generate_tiff_filename()
* rmeove unused import
* pulled dim keywords out to parameters
* readability
* extracted prepare_ref_and_masks() from register_binary_to_ref()
* pulled mean_img out of register_binary_to_ref()
* minor refactor
* moved file management to context manager
* moved io from register_binary_to_ref to register_binary()
* pulled ops out of init_offets
* uplled print side effects out from register_binary_to_ref() to register_binary().
* pulled unused ops out of getSNR()
* pulled most of ops out of phasecorr
* pull ops out of one_photon_preprocess()
* removed conditional assignment nameerror
* changed if block to conditional assignment
* removed newline
* bugfix: added required parameter
* moved if open/close blocks to context manager
* moved print out to calling function
* pulled ops out of upsample_block_Shifts()
* pulled ops out of nonrigid.transform_data()
* removed redundant calls to filter_gaussian1d()
* extracted ops out of norigid.phasecorr()
* simplified nonrigid check
* pull io out of apply_shifts_to_binary() by changing to generator
* pep8
* pulled ops out of apply_shifts
* removed apply_shifts().
* pulled ops out of apply_shifts_to_binary()
* moved most of ops out of compute_motion_and_shift()
* rmeoved redundant data copying
* made one_photon_preprocess_inplace()
* pass data from inplace
* simplified init_offsets()
* moved register_binary() to main.py
* removed unused variables
* removed unused imports
* move pca functions to pc.py
* moved bin_paths() into register_binary()
* removed unused time module
* removed if branch
* refactored out one_photon_preprocess_inplace()
* one_photon_preprocess raises error instead of modifying its parameters.
* changed ifelse branch to conditional assignment
* moved ops out of get_frames()
* pulled ops out of regid.phasecorr_reference()
* bugfix: have compute_motion_and_shift() use smooth_sigma_time parameter instead of ops key
* moved bidi parameters out of ops
* moved 1p parameters out of ops in compute_motion_and_shift
* seperated name of parameter from name of module.
* pulled ops out of rigid.phasecorr()
* pulled ops out of compute_motion_and_shift()
* stopped yielding ops from register_binary_to_ref()
* moved internal vars closer to used location
* moved mean_img calculation out of register_binairy_to_ref()
* moved progress logging out of register_binary_to_ref()
* moved write functionality closer to read functionality
* exposed offsets data structure by refactoring out init_offsets()
* refactored out offsets assembly out of register_binary_to_ref() and into register_binary().
* removed unnecessary data rounding.
* reduced data copying
* pep8
* pulled ops out of nonrigid.make_blocks()
* pulled ops out of compute_crop()
* pulled ops out of nonrigid.phasecorr_reference()
* refactored out iterative_alignment()
* refactored out compute_reference_image into register_binary()
* refactored out prepare_Refmasks()
* removed docs mention of ops
* removed unused, unworking function subsample_frames()
* minor cleanup
* pulled binary file management details out of register_binary_to_ref()
* minor refactor
* only save lower-resolution data
* refactored meanImg calculation out of apply_shifts_to_binary()
* removed rounding
* removed data clamping
* moved data yielding to mid-function
* refactored out read/writing details from apply_shifts_to_binary()
* regrouped computations in apply_shifts_to_binary()
* moved BinaryFile to io module, refactored out
register_binary_to_ref() and apply_shifts_to_binary() to main.
* passed new tests
* pulled ops out of pc_register()
* removed unused Helper
* pulled maskSlope out of phasecorr_reference()
* pulled one_photon_preproces() out of nonrigid.phasecorr_reference()
* pulled bidiphase.shift() out of compute_motion_and_shift()
* pulled one_photon_preprocess() out of utils.py
* removed unused functions sampled_mean(), sub2ind, and resample_frames()
* removed unused imports
* simplified get_frames()
* moved io-bound get_frames() function to io/binary.py
* simplified make_blocks()
* removed unused function shift_data_subpixel()
* fixed docstring and removed unused lines from rigid.shift_data()
* refactored out 'offsets' data structure
* removed redundant nonrigid.make_blocks() call.
* changed print(warning) to warning.warn(), Exception to ValueException,
* pulled 1Preg transformation out of rigid.phasecorr()
* reordered re_1p n phasecorr_refernce()
* split refAndMasks parameter in rigid.phasecorr() into its components and moved numba addmultiply() function to utils.py
* removed unused gpu_phasecorr()
* removed redundant spatial_smooth during nonrigid registration
* refactored non-rigid registration into own function: nonrigid.shift()
* pulled nonrigid.shift() out of compute_motion_and_shift()
* removed commented-out code in compute_crop()
* removed unused imports
* refactored out RefAndMasks and RefAndMasksNR
* refactored out phasecorr_cpu()
* refactored out nonrigid.shift()
* removed unused call to nonrigid.transform_data()
* removed unused vars from nonrigid.phase_corr()
* moved var use closer to declaration
* Renamed io.write_tiff to changed io.save_tiff method in io tests.
* split coupled "spatial_hp" ops parameter into "spatial_hp_reg" and "spatial_hp_detect".
* refactored out compute_motion_and_correct()
* removed redundant pre_smooth and spatial_hp value checking
* register_binary() only takes a Dict ops.
* structured nested if statements
* used tuple unpacking on multiple assignment
* removed temporary 'bidi' name and redundant nonrigid.make_blocks() call
* removed unusable utils.split_multiops() line
* removed redudnant np.save(ops) in register_binary()
* moved depgraph scripts to own folder
* refactored out repeated data_smooth conditionals
* moved compute_zpos() back to zalign.py
* cleaned up get_pc_metrics(): collapsed nsamp conditional logic, moved nPC to optional argument
* moved ops-level functions back to their original modules
* fixed paths
* zipped rigid.shift_data()
* pulled single-frame shift_frame() out of shift_data()
* pulled iteration out of rigid.shift_frames(), reducing to simpler rigid.shift_frame()
* pulled memory management out of rigid.shift_frame() into the calling function.
* removed temporary variables from refImg mean shift step
* removed shadow assignment step
* vectorized fft2 and ifft2 steps in rigid.phase_corr()
* used fancy indexing on cmax to vectorize cmax filling
* removed temp variables for lcorr calculation
* refactored out crop() function to remove intermediate vars
* cleaned rigid.phasecorr_reference
* split rigid.phascorr_reference() into independent functions phasecorr_reference() and compute_masks()
* removed extra reference image copying
* split rigid.phasecorr() into independent functions rigid.phasecorr() and rigid.apply_masks()
* created utils.convolve() function to document fft2/ifft2 step and layer math concepts
* removed hard-coded module literals
* removed pre-computed module-level constants, replaced with cached function call.
* spacing
* refactored out nonrigid.clip()
* made cc2 calculation more readable
* cleaned up loop
* cleaned up ymax1, xmax1, cmax1 calculation
* vectorized nested fft2/ifft2 calculation
* removed unused nonrigid.linear_interp() function
* call duplicated addmultiply() in utils instead of nonrigid
* removed extra data copy and unused variables in numba function
* removed inplace parameter modification to rmeove need for guard copying
* removed extra copies
* reordered lines in nonrigid.transform_data()
* shifted array management down from mat_upsample to kernel1d
* refactored nonrigid.make_nblocks(), splitting out two algorithm functions and removed one pipelined argument
* step reduction in nonrigid.phasecorr_reference()
* moved gaussian kernel functions to utils.py
* working in 3D, output in 4D
* reduced preallocation steps in nonrigid.phasecorr_reference()
* refactored getSNR
* replaced fft2/ifft2 call with utils.convolve()
* replace zeros() with empty()
* moved append()
* collapsed two `if ops['1Preg']` into one
* composed rigid registration steps
* removed redundant ops assignment and misleading comment
* merged pre_smooth conditional
* lowered gaussian_filter1d() to utils and replaced it with utils.temporal_smooth()
* removed some squeeze() and newaxis
* added explicit padding step to utils.spatial_smooth, plus a regression test
* renamed intermediate steps
* moved valueerror to algorithmic function, removed unnecessary [newaxis] -> squeeze() around spatial_smooth() calls
* replace concatenate() algorithm with numpy.pad
* removed unused ccsm output of nonrigid.phasecorr()
* changed gaussian_filter1d call to temporal_smooth()
* BinaryFile.read() exports indices
* moved batch_size argmument to read() mehtod of BinaryFile
* changed BinaryFile's reg_file and raw_file parameters to read_file and write_file
* removed unused options in BinaryFile
* removed io.get_frames()
* minor cleanup
* simplified filename assignment
* removed temp variable
* refactored bidiphase
* ensured smoothing only alters high-SNR tiff by small amount and removed regression test as it fails due to OG bug
* added smoothed version for non-rigid computation
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Carsen Stringer <[email protected]>
* Separated classification from extraction (#398)
* Initialized classify.py and added classifcation calls.
* Removed classification from extraction subpackage.
* Modified tests to include changes to both extraction and classification. Also, added a regression test to check new classify function.
* Added classifcation section with appropriate classify call.
* moved timing and print out of make_masks
* moved roi_stats to a new stats.py module
* DVC Pull doesn't require authentication anymore. (#400)
* Added dvc authentification for dummy test account
* ensured smoothing only alters high-SNR tiff by small amount and removed regression test as it fails due to OG bug
* added smoothed version for non-rigid computation
Co-authored-by: Carsen Stringer <[email protected]>
* refactored get_stats()
* refactored get_stats()
* seperated mrs normalization
* pulled ops out of roi_stats()
* Fix reg offsets (#407)
* Added dvc authentification for dummy test account
* ensured smoothing only alters high-SNR tiff by small amount and removed regression test as it fails due to OG bug
* added smoothed version for non-rigid computation
* Initialized registration metric benchmark. Moved tests in test_registration to registration_module test.
* add random_state parameter to pc_metrics
* Added registration metrics script
* Changed batch_size to not be 1500 in metrics test.
* Removed unused data dvc files. Added new input tif with 1500 frames and bidi_shift. Added batch_specific reg_tifs.
* Consolidated bidi_shift test with metrics test.
* Revert "Consolidated bidi_shift test with metrics test."
This reverts commit 29221ef.
* Revert "Removed unused data dvc files. Added new input tif with 1500 frames and bidi_shift. Added batch_specific reg_tifs."
This reverts commit 1c18a95.
* Removed registration metrics test.
* Removed registration smoothing output test data
* Removed input_1500 tif used for registration tests.
* Added input1500_bidi_shifted tif
* Removed bidi_shifited 1500 input data
* Add multi-batch test.
* Removed binary files for test_data. Changed test name in pipeline_tests.
* Added 1500 input dataset.
* Added input_1500 dvc file
* io test now only takes in input.tif. Test_pipeline now refers to correct input file.
* corrected test_data name
* Rigid offset shifts fixed for multiple batches.
* Added 2plane2chan test with multiple batches.
* Added missing F.npy test_data
* Added function to combine offsets across batches. Can now combine offset values if batches have different numbers of frames.
Co-authored-by: Carsen Stringer <[email protected]>
* pulled ops and in-place stats assignment our of out of get_overlaps(), added count_overlaps() function.
* removed stats from get_overlaps() and count_overlaps()
* removed parameter tunneling from get_overlaps()
* name fix
* moved distance_kernel() to utils.py
* simplified remove_overlappers()
* removed ops form remove_overlappers()
* changed:
while 1: remove
to:
for(reversed): append
* added bug message
* changed output of remove_overlappers from list[dict] to list[int]
* pulled stats out of remove_overlappers()
* Update nonrigid.py
* Update register.py
* Update zalign.py
* DVC Pull doesn't require authentication anymore. (#400)
* Added dvc authentification for dummy test account
* ensured smoothing only alters high-SNR tiff by small amount and removed regression test as it fails due to OG bug
* added smoothed version for non-rigid computation
Co-authored-by: Carsen Stringer <[email protected]>
* Fix reg offsets (#407)
* Added dvc authentification for dummy test account
* ensured smoothing only alters high-SNR tiff by small amount and removed regression test as it fails due to OG bug
* added smoothed version for non-rigid computation
* Initialized registration metric benchmark. Moved tests in test_registration to registration_module test.
* add random_state parameter to pc_metrics
* Added registration metrics script
* Changed batch_size to not be 1500 in metrics test.
* Removed unused data dvc files. Added new input tif with 1500 frames and bidi_shift. Added batch_specific reg_tifs.
* Consolidated bidi_shift test with metrics test.
* Revert "Consolidated bidi_shift test with metrics test."
This reverts commit 29221ef.
* Revert "Removed unused data dvc files. Added new input tif with 1500 frames and bidi_shift. Added batch_specific reg_tifs."
This reverts commit 1c18a95.
* Removed registration metrics test.
* Removed registration smoothing output test data
* Removed input_1500 tif used for registration tests.
* Added input1500_bidi_shifted tif
* Removed bidi_shifited 1500 input data
* Add multi-batch test.
* Removed binary files for test_data. Changed test name in pipeline_tests.
* Added 1500 input dataset.
* Added input_1500 dvc file
* io test now only takes in input.tif. Test_pipeline now refers to correct input file.
* corrected test_data name
* Rigid offset shifts fixed for multiple batches.
* Added 2plane2chan test with multiple batches.
* Added missing F.npy test_data
* Added function to combine offsets across batches. Can now combine offset values if batches have different numbers of frames.
Co-authored-by: Carsen Stringer <[email protected]>
* Update nonrigid.py
* Update register.py
* Update zalign.py
* removed intermediate var
* elevated some of ops keys out of select_rois()
* removed unused stats argument from select_rois()
* made functions calc_radii() and aspect_ratio()
* minor cleanuip of fitMVGaus
* EllipseData namedtuple output of fitMVGaus(), to make output more readable. Also reduced amount of axis manipulation in function.
* refactored create_neurpil_masks() for readability
* changed for-break to while
* pulled stats out of create_neuropil_masks()
* used from...import to ease function move
* removed code duplication in chan2detect by moving make_masks() to masks.py
* made sparse_mode a parameter of select_rois()(
* pulled high_pass out of ops and refactored out 2 new functions: high_pass_gaussian_filter() and high_pass_rolling_mean_filter().
* minor bin_movie() readability refactor
* used norm()
* added __getitem__() to BinaryFile, resolved merge conflict in register.py
* added crop slicing to BinaryFile
* minor changes
* put BinaryFile in bin_movie()
* used built-in index tracking
* moved timing and logging out of bin_movie
* moved bin_size to parameter of bin_movie
* pulled bad_frames out of bin_movie, added n_frames, shape, and size properties to BinaryFile
* pulled print() out of utils function
* moved ops crop keys out of utils.bin_movie()
* added comments
* pulled ops['reg_file'] out of utils.bin_movie()
* pulled ops out of bin_movie()
* get_sdmov() readability
* moved operations to loop
* removed data copying step
* made functions for reject_frames() and crop() operations
* refactored threshold_reduce()
* vectorized downsample() function
* fixed downsample
* merge conflict resolved, moved fixed downsample() to utils.py
* moved downsample() and threshold_reduce() to utils.py, minor readability refactor for neuropil_subtraction
* refactored square_conv2() for readability
* refactored square_conv2() for readability
* fixed normalization order in sd_mov()
* pulled ops out of make_masks()
* split make_masks()
* split create_cell_masks out into create_Cell_pix()
* removed get_overlaps()
* Added testing page to suite2p wiki and nwb test. (#412)
* Added test setup/run page to suite2p readthedocs
* Fixed up nwb.py. Removed unnecessary import.
* Changes to test util functions. Added functions to retrieve list of output data and test data.
* Added nwb test to 1plane1chan test on pipeline tests.
* added pynwb to test setup
* unpacked dx and dy into roi_stats for nwb test
* minor refactor, create_cell_masks()
* minor refactor
* DRY'd roi stat norming steps with norm_by_average() function
* changed name 'radius' to 'radii' when tuple
* minor type documentation + norm() replacement
* roi stat aggregation dataclass: ROI
* pulled roi_stats() out of detect.py and added PendingDeprecationWarning.
* moved roi calc functions back to stats.py
* added ROI.fit_ellipse interface, with cached-property to keep performance benefits.
* minor: removed rsort from repr
* readability refactor: dict.update() instead of repeated dist.__setitem__()
* whitespace
* moved normailizatoin steps with calculation steps
* renamed remove_overlappers() to filter_overlappers() to reflect its keeping behavior, move overlap assignment to main loop.
* added overlap normalization and filtering interface to ROI as classmethod.
* moved overlaps() calculations to stats.py
* filter in loop
* changed filter_overlappers output from list of indices to list of bools, for simpler logical indexing.
* ROI interface to filtering.
* added type annotation support for docs
* Registration Benchmark script added (#421)
* Implement click package in registration_metrics script
* Moved random_state assignment to ops level.
* Added optional parameters to registration benchmark script
* Included more registration metrics results
* fixed regPC
* Fix import for gui2p error
* Refactored cli script in __main__.py
* Removed dependence of benchmark script on click package. Instead relying on main cli script in suite2p.
* removed npc as a parameter in get_pc_metrics. Rely on ops assignment
* plot avg and max scores of top 10 PCs
* Fixed registration metrics to display statistics on offset scores (not PC weights).
* parallelizing multiplane processing (#423)
* GUI now working on dev branch (tqdm removed + default_ops() function called correctly) #424
* bug with running __main__ script from gui call - reverted to old version
* Renamed default_ops fixture to test_ops. (#429)
* bug with int16 conversion not being forced (#428)
* Fixes reg_tif issue with second channel (#431)
* Removed 2plane2chan test from pipeline tests.
* check_output test util function now compares tifs. Added reg_tif check for 1plane1chan test.
* Added reg_tif data for 1plane1chan1500
* Removed 1plane1chan1500 reg_tifs.
* Removed reg_tif option for 1plane1chan test
* Add test to check reg_tif_chan2 for 2plane2chan_batch test
* reset k for second channel in register.py. Fixed up frame number for batches.
* Added 2plane2chan reg_tifs
* Refactored __main__.py so benchmark script works.
* Update __main__.py
* nbytesread must be an int64 for files longer than ~4000 frames
* speeding up sparsedetect to normal levels
* Refactored registration_metrics into View-Model-Presenter functions and added reg_metrics entry point
* Fixed issue with main script not setting input ops parameter.
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Nicholas A. Del Grosso <[email protected]>
* Cleaner text output
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Nicholas A. Del Grosso <[email protected]>
* removed cached_properties from package. (#434)
* fixing some bugs with keep_movie_raw and classifier without all keys
* Ref det3 (#435)
* ROI interface to overlap location
* reordered mask application, added ROI.ravel_indices()
* minor readability
* moved norm_by_average() to stats.py
* moved repeated appends (xpix, ypix, lam) to single append (stats)
* removed intermediate ops['Vmap'] construction
* removed extra ops['Vmap'] appends and extra copy calls.
* moved high_pass to parameter
* moved bin_movie to io.binary, and moved io operations in detection module to main_datect() function
* moved batch_size and neuropil_high_pass to parameters, abreviated "high-pass" to "hp" in utils functions
* renamed 'rez' to 'mov' for consistency
* moved max_iterations and threshold_scaling to parameters
* moved ops assignments to end of function.
* removed ops input from sparsery(), returns new dict and applies it outside of the function instead of overwriting ops in-place
* added iteration for gxy, refactored out find_best_scale() function and estimate mode message type from sparsery()
* minor whitespace
* changed create_cell_masks() to work on a single ROI at a time.
* refactored out high-level hp_filter selection step as temporal_high_pass_filter(), moved max_proj assignment to select_rois() for sparsery()
* moved temporal_hp back into sparsery() refactored out spatial scale computation into own function.
* minor
* Moved ellipse properties from ROI to EllipseData
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Nicholas A. Del Grosso <[email protected]>
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Carsen Stringer <[email protected]>
* bug in classify import
* adding ops['preclassify'] back into pipeline
* Manual ROI issues fixed. (#439)
* typing changes for stats.py
* Traces now can be extracted from manual_rois. Fix made in drawroi.py
* Overlap is already calculated in roi_stats. Hence, can remove overlap calculation when gui is closed.
* Include MacOS in travis build. (#441)
* Removed tqdm imports
* Add osx to travis. allow for osx failure
* pydrive2 instructions for developers.
* Separated jobs for OSes in .travis.yml
* have different conda installs for OSes in .travis.yml
* changed python version for mac on travis
* modifying setup script
* issue with not rescaling lambda
Co-authored-by: Nicholas A. Del Grosso <[email protected]>
Co-authored-by: Chris Ki <[email protected]>
Co-authored-by: Marius Pachitariu <[email protected]>File tree
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