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Recent Releases of NeuroCAPs

NeuroCAPs - 0.35.2

🐛 Fixes

  • Fixes an error message not providing valid number of nodes when fetching parcellation approaches.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.35.1...0.35.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.35.1

🐛 Fixes

  • Properly set data type in nifti image header to address floating point issues for certain atlases when converting CAP vectors to niftis and saving image.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.35.0...0.35.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.35.0

  • JOSS Version ### 🐛 Fixes
  • Ensures mutability by using deepcopy in CAP and TimeseriesExtractor to not bypass validation
  • Accounts for case when duration is coded as 0 in event timing files as 0 in BIDS can indicate impulse.

New Contributors

  • @yibeichan made their first contribution in https://github.com/donishadsmith/neurocaps/pull/63

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.34.3...0.35.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.34.3

🚀 New/Added

  • Added n_cores and progress_bar parameters to simulate_bids_dataset. ### 🐛 Fixes
  • Incorrect session ID also raises a BIDSQueryError.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.34.2...0.34.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.34.2

🐛 Fixes

  • Type hint fixes and fix undocumented parameter.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.34.1...0.34.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.34.1

🚀 New/Added

  • Added new utility functions to make tutorials easier.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.34.0...0.34.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.34.0

♻ Changed

  • PlotDefaults is now apart of the public API and has a new method (available_methods).
  • Documentation for plot related parameters moved to PlotDefaults.
  • For correlation and transition matrices plot, "annot" is now True by default.
  • Renamed "plottingutils.py" to "plotutils.py".

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.33.1...0.34.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.33.1

🐛 Fixes

  • Fix in knn_dict that always defaulted to "Schaefer"

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.33.0...0.33.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 5 months ago

NeuroCAPs - 0.33.0.post1

📖 Documentation

  • Updates to remove old information in parameters (type hints and strings).

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.33.0...0.33.0.post1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.33.0

🚀 New/Added

  • plot_output_format parameter added to replace as_pickle, as_json, and as_html
  • This parameter is added under output_dir, which changes signature ordering ### ♻ Changed
  • Significant changes in ordering of signature parameters for better grouping
  • Removal of certain parameters to clean up signatures:
    • flush (in TimeseriesExtractor): remnant of print but logging is used now
    • fwhm (in CAP.caps2niftis and CAP.caps2surf, parameter still available in TimeseriesExtractor to apply smoothing during timeseries extraction; however smoothing is not needed for statistical maps)
    • fslr_giftis_dict (in CAP.caps2surf)
  • Changed default in CAP.caps2plot from "outer_product" to "heatmap" ### 📖 Documentation
  • Only version specifiers from >= 0.33.0 are shown. Previous specifiers are archived in the 0.32.4 readthedocs.io

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.32.4...0.33.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.32.4

🐛 Fixes

  • Get fslr atlas of the correct density to prevent error.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.32.3...0.32.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.32.3

🚀 New/Added

  • Add "Gordon" to preset

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.32.2...0.32.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.32.2

🚀 New/Added

  • Create fetch_preset_parcel_approach to retrieve preset parcellations (HCPex and 4S) from OSF
  • Parcel approaches have informational metadata keys ### 🐛 Fixes
  • Fixed blank figure issue when saving the cluster performance

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.32.1...0.32.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.32.1

🐛 Fixes

  • Return type hint for generate_custom_parcel_approach.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.32.0...0.32.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.32.0

🚀 New/Added

  • Created "generatecustomparcelapproach" to help create a "Custom" `parcelapproach` for a parcellations metadata file. ### 🔧 Refactoring
  • "_utils" is now "utils". Private file in the "utils" folder now start with "underscore".
  • ".utils.parcellation.py" now "utils.parcellationvalidation.py" ### 📖 Documentation
  • If checking documentation from an IDE, links are provided for the typing definition.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.31.1...0.32.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.31.1

🐛 Fixes

  • When computing metrics in CAP.calculate_metrics, internally, the dataframes are no longer built one row at a time. All data is collected and the dataframe is created once.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.31.0...0.31.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.31.0

🔧 Refactoring

  • Significant internal refactoring to clean the code in the public API, changes include:
    • Moving files in neurocaps._utils.extraction and neurocaps._utils.analysis to internal folders in neurocaps.extraction and neurocaps.analysis
    • Changing internal function names to be more descriptive
    • Moving certain internal functions in TimeseriesExtractor and CAP into separate internal modules
    • Changing internal file names ### ♻ Changed
  • Improved the default region names (changing how nodes are grouped) for the AAL atlas to improve granularity.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.30.0...0.31.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 6 months ago

NeuroCAPs - 0.30.0

🚀 New/Added

  • Added support for parcellations with non-lateralized nodes in the custom parcel_approach.
  • Added the addcustomnode_names keyword argument to CAP.caps2plot() to control the display of node labels. ### ♻ Changed
  • Removed the hemisphere_labels keyword argument from CAP.caps2plot(). This is replaced by add_custom_node_names.
  • Node labels on heatmaps and outer product plots are now disabled by default. add_custom_node_names=True to can be used to display them. ### 🐛 Fixes
  • Fixed an issue where whitespace in plot filenames was not correctly replaced with underscores.
  • Improved the node labeling logic for heatmaps and outer product plots. Labels are now applied correctly even when the input parcellation has all nodes of one hemisphere ordered before the other.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.7...0.30.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 7 months ago

NeuroCAPs - 0.29.7

🐛 Fixes

  • For TimeseriesExtractor, check and filtering added for confound_names when wildcard for prefix is used to ensure only that the asterisk is at the end since only prefix wildcards are supported. Also checks for case when only "*" is used since it would select all columns.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.6...0.29.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 7 months ago

NeuroCAPs - 0.29.6

🚀 New/Added

  • method parameter added to CAP.caps2corr to allow spearman or pearson correlation to be computed. By default pearson is computed for backwards compatibility.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.5...0.29.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 7 months ago

NeuroCAPs - 0.29.5

🚀 New/Added

  • Adds "method" key to knn_dict, which defaults to majority vote KNN approach but allows for distance weighted KNN to be used.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.4...0.29.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 7 months ago

NeuroCAPs - 0.29.4

🐛 Fixes

  • Fixes and improve type hints for public API and some private functions
  • Updates plotly restriction to allow 6.1.1 to be downloaded

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.3...0.29.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 7 months ago

NeuroCAPs - 0.29.3

♻ Changed

  • Restricts kaleido version to less than 1.0.0, which will have to be tested to ensure it is compatible on Windows and works similarly on non-Windows machines.
  • Stays with plotly versions less than 6.1.0 since versions greater than 6.1.0 may require kaleido versions >= 1.0.0.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.2...0.29.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.29.2

📖 Documentation

  • Adds documentation to properties to be viewed in IDEs instead of the definitions only being in the public class. ### 🐛 Fixes
  • Adds a small check for parallel_log_config, since the queue key is mandatory.
  • Changes plotly version to "!=6.1.0" instead of "<6.1.0" as there are several issues raised about the write_image issue.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.29.1...0.29.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.29.1

🐛 Fixes

  • Adds a small check to ensure required attributes are available before return_cap_labels can run to issue an error and guide user towards the expected workflow.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.29.0

🚀 New/Added

  • Adds return_cap_labels function to public API, which used to be an internal function. This allows CAP assignments to be returned directly. ### 🐛 Fixes
  • Adds temporary version restriction for plotly to not install 6.1.0 since it currently breaks image saving function. Once fixed, will allow versions after 6.1.0.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.6...0.29.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.6

♻ Changed

  • Backwards compatible change for CAP.calculate_metrics, which changes the default metrics from None to ("temporal_fraction", "persistence", "counts", "transition_frequency"), Still retains the same behavior where None defaults to "temporalfraction", "persistence", "counts", and "transitionfrequency". Change done to enhance clarity ### 📖 Documentation
  • Minor language fixes. Fix to example in CAP.caps2radar, which had low_amp = high_amp = np.where(cap_1_cluster_centroid < 0, -cap_1_cluster_centroid, 0) instead of low_amp = np.where(cap_1_cluster_centroid < 0, -cap_1_cluster_centroid, 0) ### 🐛 Fixes
  • If fslr_giftis_dict in CAP.caps2surf is supplied, then caps is not a required attribute
  • Stops invalid kwargs warning in CAP.get_caps for S and max_nbytes

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.5...0.28.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.5

🚀 New/Added

  • Add clear_groups function to CAP
  • Add max_nbytes kwarg to CAP.get_caps. ### ♻ Changed
  • Removes private _IO class

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.4...0.28.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.4

🐛 Fixes

  • More robust handling of certain edge cases for event timing conversion. Instead of having

Old Computation: python adjusted_onset = onset - slice_time_ref * tr adjusted_onset = max([0, adjusted_onset]) start_scan = int(adjusted_onset / tr) + condition_tr_shift end_scan = math.ceil((adjusted_onset + duration) / tr) + condition_tr_shift scans.extend(range(onset_scan, end_scan)) scans = sorted(list(set(scans)))

New Computation: ```python adjustedonset = conditiondf.loc[i, "onset"] - data.slice_ref * data.tr

Int is always the floor for positive floats

onsetscan = int(adjustedonset / data.tr) + data.trshift endscan = math.ceil((adjustedonset + conditiondf.loc[i, "duration"]) / data.tr) + data.tr_shift

Avoid accidental negative indexing

onsetscan = max([0, onsetscan]) endscan = max([0, endscan]) scans.extend(range(onsetscan, endscan)) ```

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.3...0.28.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.3

🐛 Fixes

  • Use "all" to ensure all figures are closed for matplotlib objects and prevent unnecessary memory consumption whenever show_figs is False.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.2...0.28.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.2

♻ Changed

  • Changes and refactors for internal functions and classes related to plotting and IO:
    • "plottingdefaults.py" changed to "plottingutils.py"
    • "heatmaputils.py" deleted and functions are now stored in _MatrixVisualizer class in "plottingutils.py"
    • Shared plotting function now stored in PlotFuncs to increase reusability
    • "pickle_utils.py" changed to "io.py"
    • Created IO class to store IO operations
    • Removed some internal methods in CAP that are either generalized IO operations or generalized plotting functions
    • Logged IO related warnings about not specifying an output directory when specifying a filenames only comes from "io.py" instead of various modules ### 🐛 Fixes
    • Support compressed serialized files
    • Fix serialization of timeseries dict to use Joblib instead of standard pickle

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.1...0.28.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.1

  • Primarily refactoring to improve readability. Also includes internal functions that can be used independently for implementation purposes or unit testing. ### 🐛 Fixes
  • Guarantees the returned dictionary from CAP.calculate_metrics, will have keys in the same order as listed in metrics.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.28.0...0.28.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.28.0

  • Backwards compatible default changes (same default behavior):
    • Changed default of parcel_approach to None in TimeseriesExtractor, which defaults to Schaefer when None
    • Changed default of metrics in CAP.calculate_metrics to None, which computes the transition frequency, temporal fraction, counts, and persistence when None
  • In pyproject.toml:
    • The typing_extension package is no longer restricted to versions less than 3.11
    • Python version restricted to 3.9 to 3.12 for now since only VTK >= 9.4 works with Python 3.13 and above and brainspace is currently only compatible with VTK < 9.4.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.27.0...0.28.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.27.0

🚀 New/Added

  • To the QC report, added the number of dummy volumes, which is useful if the "auto" option is used ### ♻ Changed
  • To the QC report, if either fd_threshold or dummy_scans is None
  • 0 is now treated as Falsy for fd_threshold since this is an impractical value anyway

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.10...0.27.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.26.10

  • Final round to address mutability

♻ Changed

  • For TimeseriesExtractor, certain mutable parameters such as confound_names, fd_threshold, and dummy_scans are copied to prevent un-intentional user changes that mutate these parameters without validation.
  • Also for TimeseriesExtractor and CAP certain properties return a deep copy. However, large properties such as subject_timeseries and concatenated_timeseries return just a reference to prevent excessive memory usage.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.9...0.26.10

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 8 months ago

NeuroCAPs - 0.26.9

✨ Enhancement

  • Improves stacking in merge_dicts to make less memory intensive for larger datasets.
  • IO operations when pickles are given in subject_timeseries_list for merge_dicts is only done once per call. Consequently, fixes issue if strings are given in subject_timeseries_list but doesn't have the "pkl" extension since ".pkl", ".pickle", and ".joblib" are recognized.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.8...0.26.9

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.8

♻ Changed

  • Exceptions no longer require message ### 🐛 Fixes
  • In the merge_dicts function, fixes issue a mutability issue where if a subject only has a single run, the memory address of the numpy array in the merged dict would be the same as the original input dict. Now deepcopy used to safeguard against any unintended side effects to the original input dictionaries.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.7...0.26.8

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.7

🐛 Fixes

  • Adds the py.typed file

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.6...0.26.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.6

♻ Changed

  • For str method, changed "Metadata" to "Current Object State" and made other minor tweaks. ### 🐛 Fixes
  • Fixed a logged warning about condition event windows being out of bounds when condition_tr_shift is not used. Previously, the log message would never actually be logged. ### 📖 Documentation
  • Improved documentation about how the default class in CAP is handles and added a logged message about this behavior.
  • Added doc string to str method.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.5...0.26.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.5

  • Updates related to plotting and pickling

🚀 New/Added

  • Several functions now include a as_pickle parameter to save figures as pickle files. For CAP.cas2radar, an as_json file is added to saved plotly files in json format as opposed to pickle. This allows for further modifications of the plots outside of the functions. ### ♻ Changed
  • For parameters that except files as strings such as subject_timeseries and parcel_approach, recognized extensions are now ".pkl", ".pickle", and ".joblib", instead of just ".pkl". ### 🐛 Fixes
  • For file names in TimeseriesExtractor.visualize_bold, the default file name saved with an additional "run-", this has been removed.
  • For file names in CAP.caps2plot, groups with spaces saved with whitespace, now this whitespace is replaced with underscores ("_").

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.4...0.26.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.4

🐛 Fixes

  • Fix for upcoming use of clean_args in NiftiLabelsMasker.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.3...0.26.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.3

  • Dependency fixes ### 🐛 Fixes
  • Updates minimum dependencies in pyproject toml for functions to work
  • Fixes error if using knn_dict with nilearn version < 0.11.0 due to using a parameter introduced in that version
  • Accounts for upcoming nilearn changes that add "Background" to the labels list to ensure proper plotting
  • Accounts for future deprecation in NiftiLabelsMasker that will transition from using kwargs to cleanargs in order to use `clean_extrapolate=False`

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.2...0.26.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.2

  • Updates for CAP ### 🐛 Fixes
  • Reverse the mean and standardize properties returning None unless standardized to allow them to be cleared any time CAP.get_caps function is called since this can be an issue if standardizing is first requested, then CAP.get_caps is ran again without standardizing and then the CAP metrics are computed. This would result in incorrect scaling for predicting CAP assignment for that particular scenario. Affected version 0.26.1.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.1...0.26.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.1

  • Updates for CAP ### 🐛 Fixes
  • Fixed performance bottleneck when stacking large timeseries by only calling NumPy's vstack once per group instead of once per subject and run pair. Consequently, updates to the progress bar were made to reflect this.
  • If an invalid cluster selection method is called, the error now comes before concatenation instead of after.
  • The mean and stdev properties now return None unless standardized is True or truthy instead of returning empty dictionaries when standardization is False.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.26.0...0.26.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.26.0

  • Full source repository now archived on Zenodo, instead of just the pure source code ### 🚀 New/Added
  • Added mean and standard deviation of framewise displacement of QC report, which are added at the beginning of the QC report. ### ♻ Changed
  • In, TimeseriesExtractor, default for detrend changed from True to False to avoid redundancy since the default behavior for confound_names includes the cosine-basis regressors. This is also the default for NiftiLabelsMasker.
  • Now skips timeseries extraction if the number of confound regressors are equal to or greater than the length of the timeseries.
  • For CAP.caps2radar, the default for fill changed from "none" to "toself" so that the traces of the radar plot are always filled in by default.
  • For CAP, the region_means property now fully replaces the region_caps property. The only difference is that region_means includes the region names themselves and better describes what it represents.
  • Version directives under 0.25.0 have been removed to clean the docs. These directives can still be viewed on 0.25.1 documentation.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.25.1...0.26.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.25.1

  • Simple internal change, to explicitly change scaling to False for NiftiLabelsMasker, in case the scaling approach changes in a future version or has been changed in a past version.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.25.0...0.25.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.25.0.post1

📖 Documentation

  • Added documentation note

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.25.0...0.25.0.post1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.25.0

♻ Changed

  • For TimeseriesExtractor, standardize is no longer passed to Nilearn. Since standardizing is the final step in signal cleaning, it is now done within this package. Only standardizing using Bessel's correction (sample standard deviation) is used. This removes having to do external standardizing with neurocaps.analysis.standardize when censoring or extracting conditions and standardizing is True.
  • For CAP, tqdm progress bar is now also displayed for the concatenation step when progress_bar is True.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.7...0.25.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.7

  • Minor refactoring ### 🚀 New/Added
  • dummy_scans now accepts "auto" for convenience so that {"auto": True} does not need to be used.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.6...0.24.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.6

🚀 New/Added

  • Added "MeanHighMotionLength" and "StdHighMotionLength" to qc report. ### ♻ Changed
  • Qc report only produced when fd_threshold is specified, a valid and a confounds tsv file with "framewise displacement" column is found. Done since qc currently only focuses on framewise displacement. ### 🐛 Fixes Errors that could arise for some edge cases that usually won't be used
  • Setting fd_threshold and "outlier_percentage" to 0 are now recognized.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.5

  • Some Internal refactoring done to clean code
  • Adds all to exceptions module for star import ### 🐛 Fixes
  • Issue introduced in 0.24.3 specifically for condition, where if interpolation is requested and outlier percentage is used, the computation would only consider frames not being interpolated instead of all frames flagged for high motion. Added test too test suite to confirm behavior. ### 📖 Documentation
  • Adds clarifications in documentation
  • Adds links to docs for the type hints
  • Adds basic docstring for many internal functions in _utils

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.4...0.24.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.4.post0

🐛 Fixes

  • Broken zenodo badge.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.4...0.24.4.post0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.4

  • Simply adds an additional conditional as a safeguard when passing sample mask to nilearn.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.3...0.24.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.3

  • Internal refactoring ### 🚀 New/Added
  • Added the qc property and the report_qc function in TimeseriesExtractor ### 🐛 Fixes
  • Type hint for output_dir in TimeseriesExtractor.timeseries_to_pickle ### 📖 Documentation
  • Some docs cleaning.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.2...0.24.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.2

[0.24.2] - 2025-03-25

  • Some internal refactoring and name changes to internal functions for clarity ### 🐛 Fixes
  • Removes wheel in requirements since it is no longer needed for bdist_wheel since setuptools v70.1.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.1...0.24.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.1

🐛 Fixes

  • Update license field to comply with PEP 639 and avoid deprecation.
  • Upgraded to setuptools to 77.0.1, since this expression is supported in version 77.0.0 (which was yanked) ### 📖 Documentation
  • Added some additional information in docs for user guiding.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.24.0...0.24.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.24.0

  • Minor internal refactoring for private functions to improve readability.
  • Some general improvements for better use of this package by others. ### 🚀 New/Added
  • Added NoElbowDetectedError for instances where elbow method fails to detect elbow. ### ♻ Changed
  • Uses default for mask_img for NiftiLabelsMasker, which is None, as opposed to using masks queried from data. This better aligns with standard usage of the class and the parcellation serves as a mask already and is redundant especially when atlas and data are registered to the same space.
  • In TimeseriesExtractor.visualize_bold(), run no longer needs to be specified if the given subject only has a single run.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 9 months ago

NeuroCAPs - 0.23.8.post1

📖 Documentation

  • Adds additional documentation clarity and emphasis.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.8.post0...0.23.8.post1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.8.post0

📖 Documentation

  • Fixes improper documentation rendering in IDE's
  • Streamlines documentation

To tag significant documentation change

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.8...0.23.8.post0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.8

🐛 Fixes

  • Added all to neurocaps.typing module so that the star import only restricts to public types.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.7...0.23.8

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.7

  • Fixes an incorrect return typehint for a CAP.caps2corr function.
  • Add optional type hint for certain parameter.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.6...0.23.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.6

🚀 New/Added

  • Add type hints to all internal classes; minor code cleaning.
  • Use new types for subject timeseries and parcellations throughout docs.

♻ Changed

  • Change some internal parameters for the private _Data class such as scrub_lim -> out_percent, fd -> fd_thresh, and shift -> tr_shift. Done for clarity.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.5...0.23.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.5

🐛 Fixes

  • Updated type hints for class methods that return self from None to Self.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.4...0.23.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.4

  • Primarily some internal refactoring and API docs updates:
    • Some refactoring to reduce some code complexity.
    • Internal code for public classes only use private attributes to separate it from public properties. Exception for private getter classes that are inherited public classes.

♻ Changed

  • Internal function changed from _create_regions to compute_region_means.
  • Internal CAP._raise_error function changed slightly to accept attribute names, which are preceded by the underscore instead of properties. Done so that their is a separation between the internal private attributes and public properties.
  • Property change from region_caps to region_means and now includes "Regions" key. For backward compatibility, the old region_caps behavior is still available.

📖 Documentation

  • Name change from "neurocaps" to "NeuroCAPs" in documentation only. Package name to remain "neurocaps" for compliance with PEP 8.
  • Additional documentation fixes to enhance clarity.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.3...0.23.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.3

✨ Enhancement

  • Improved error handling for custom parcel approaches. The structure of the sub-keys are validated to prevent errors due to incorrect structure down the pipeline.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.2...0.23.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.2

♻ Changed

  • Minor improvements to str call for clarity.
  • Added optional dependencies for benchmarking and cleaned repeating optional dependencies.
  • Created separate static internal function for computing cosine similarity between the 1D region mask and high/low amplitude of the CAP vector.

What's Changed

  • Update codecov/codecov-action action to v5.4.0 by @renovate in https://github.com/donishadsmith/neurocaps/pull/15
  • Update codecov/codecov-action action to v5.4.0 by @renovate in https://github.com/donishadsmith/neurocaps/pull/17

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.1...0.23.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.1

  • Minor improvements in how run IDs are intersected to prevent errors in rare cases. ### 🐛 Fixes
  • Added pytest-cov and pre-commit as optional dependencies
  • Fix case in version 0.23.0 when confound_names is None but n_acompcor_separate is specified, which resulted in the no acompcor components being included for nuisance regression.
  • Also, add warning is no cosine regressors are included in confound_names but the following is detected:
    • n_acompcor_separate specified
    • "acompcor" or "tcompcor" included in confound_names

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.23.0...0.23.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.23.0

  • Updates pertain to TimeseriesExtractor ### 🚀 New/Added
  • Added a new key to fd_threshold for optional cubic spline interpolation of censored volumes not at the beginning or end of the timeseries and is only done after nuisance regression and parcellation. By default, interpolation is not done and must explicitly be set to True. ### ♻ Changed
  • Default for confounds_names changed from None to "basic". The "basic" option now performs the same functionality as confound_names=None did in previous versions.
  • Ordering of some self.signal_clean_info parameters changed. ### 🐛 Fixes
  • Raises ValueError when use_confounds=False but fd_threshold, n_acompcor_separate, or ``dummy_scans = {"auto": True} is specified. IMPORTANT:
  • Fixed issue that occured only when n_acompcor_separate is None (default), which resulted in all acompcor regressors are selected from the confounds metadata due to list slicing issue [0:None]. Not an issue when n_acompcor_separate is not None or the preproccesing pipeline directory did not have a confounds json file.
  • Overall improved error handling.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.22.2...0.23.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.22.2

🚀 New/Added

  • Added new "exceptions" module containing the BIDSQueryError. ### 📖 Documentation
  • BIDSQueryError now documented.
  • Updated doc strings to redirect to documentation about directory structure/entities.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.22.1...0.22.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 10 months ago

NeuroCAPs - 0.22.1

♻ Changed

  • More efficient computation of transition probability

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.22.0...0.22.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.22.0

♻ Changed

  • Change in internal logic for condition to not add plus one to the duration scan index (scans = range(start, end + 1) -> scans = range(start, end)) to reduce potential condition spillover in certain task designs such as rapid events. ### 📖 Documentation
  • Remove version change directives under 0.19.0 to clean up docs.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.8...0.22.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.8

🚀 New/Added

  • CAP and TimeseriesExtractor classes now have defined string dunder methods that return specific metadata.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.7...0.21.8

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.7

🐛 Fixes

  • Fixed documentation rendering issues in VSCode. ### 📖 Documentation
  • Cleaned documentation in some functions. ### 🐳 Docker
  • Updated image in DockerHub to latest version.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.6...0.21.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.6

🐛 Fixes

  • CAP.outer_products property now no longer returns None when it is not None. ### 🐳 Docker
  • Updated image in DockerHub to latest version.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.5...0.21.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.5

🚀 New/Added

  • Added new progress_bar parameter to CAP.calculate_metrics, CAP.caps2niftis, CAP.caps2surf, CAP.get_caps, and TimeseriesExtractor.get_bold to display tqdm progress bars. ### 📖 Documentation
  • Cleans version change/version added directives and references for versions under 0.19.0 to clean up documentation.
  • Additional minor documentation cleaning. ### 🐳 Docker
  • Updated image in DockerHub to latest version.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.4...0.21.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.4

🐛 Fixes

  • Fix issue in "counts" computation in CAP.calculate_metrics for case where no TRs are assigned to a specific label/CAP. Instead of "counts" being 0 in this case, it would be a 1. Issue did not affect the other metrics ("temporal fraction", "persistence", etc), which would correctly be 0 in such cases.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.3...0.21.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 11 months ago

NeuroCAPs - 0.21.3

🐛 Fixes

  • Added ipywidgets in optional dependencies for a better experience with the "openneuro_demo" Jupyter notebook.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.2...0.21.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 12 months ago

NeuroCAPs - 0.21.2

🐛 Fixes

  • Fixes warning about ignoring mandatory keys in fd_threshold and dummy_scans.
  • Also adds check to ensure that the "outlier_percentage" key is a float between 0 and 1.
  • - Setuptools version pinned to 64.0 or greater.

What's Changed

  • Configure Renovate by @renovate in https://github.com/donishadsmith/neurocaps/pull/2
  • Update codecov/codecov-action action to v5 by @renovate in https://github.com/donishadsmith/neurocaps/pull/4
  • Update actions/setup-python action to v5 by @renovate in https://github.com/donishadsmith/neurocaps/pull/10
  • Update actions/checkout action to v4 by @renovate in https://github.com/donishadsmith/neurocaps/pull/9

New Contributors

  • @renovate made their first contribution in https://github.com/donishadsmith/neurocaps/pull/2

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.1...0.21.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 12 months ago

NeuroCAPs - 0.21.1

🐛 Fixes

  • Better type validation for fd_threshold and dummy_scans. ### 📖 Documentation
  • Slightly clearer documentation on the criteria used for fd_threshold.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.21.0...0.21.1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 12 months ago

NeuroCAPs - 0.21.0

🚀 New/Added

  • Added a new parameter, slice_time_ref in TimeseriesExtractor.get_bold to allow onset to be subtracted by slice_time_ref * tr if desired.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.20.0...0.21.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 12 months ago

NeuroCAPs - 0.20.0

🚀 New/Added

  • Added new log message specifying the condition being extracted if condition is not None.
  • Added a new parameter, condition_tr_shift in TimeseriesExtractor.get_bold to allow a shift in the the starting and ending scan in TR units for a condition.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.19.4...0.20.0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith 12 months ago

NeuroCAPs - 0.19.4

📖 Documentation

  • Links are fixed in the documentation. ### 🐛 Fixes
  • Fix indexing error for visualize_bold if parcel_approach["Custom"]["nodes"] is a NumPy array instead of list. ### ♻ Changed
  • Internally, the verbose parameter is set to 0 for nilearn's fetch_atlas_aal and fetch_atlas_schaefer. and the behavior is stated in the documentation. Cosine similarity in this case is assigned np.nan
  • When creating "regions" for the "Custom" parcel approach, both a list and range can be accepted. Previously, only lists were accepted.

List method:

python parcel_approach["Custom"]["regions"] = { "Primary Visual": {"lh": [0], "rh": [180]}, "Early Visual": {"lh": [1, 2, 3], "rh": [181, 182, 183]}, "Dorsal Stream Visual": {"lh": list(range(4, 10)), "rh": list(range(184, 190))}, "Ventral Stream Visual": {"lh": list(range(10, 17)), "rh": list(range(190, 197))}, "MT+ Complex": {"lh": list(range(17, 26)), "rh": list(range(197, 206))}, "SomaSens Motor": {"lh": list(range(26, 31)), "rh": list(range(206, 211))}, "ParaCentral MidCing": {"lh": list(range(31, 40)), "rh": list(range(211, 220))}, "Premotor": {"lh": list(range(40, 47)), "rh": list(range(220, 227))}, "Posterior Opercular": {"lh": list(range(47, 52)), "rh": list(range(227, 232))}, "Early Auditory": {"lh": list(range(52, 59)), "rh": list(range(232, 239))}, "Auditory Association": {"lh": list(range(59, 67)), "rh": list(range(239, 247))}, "Insula FrontalOperc": {"lh": list(range(67, 79)), "rh": list(range(247, 259))}, "Medial Temporal": {"lh": list(range(79, 87)), "rh": list(range(259, 267))}, "Lateral Temporal": {"lh": list(range(87, 95)), "rh": list(range(267, 275))}, "TPO": {"lh": list(range(95, 100)), "rh": list(range(275, 280))}, "Superior Parietal": {"lh": list(range(100, 110)), "rh": list(range(280, 290))}, "Inferior Parietal": {"lh": list(range(110, 120)), "rh": list(range(290, 300))}, "Posterior Cingulate": {"lh": list(range(120, 133)), "rh": list(range(300, 313))}, "AntCing MedPFC": {"lh": list(range(133, 149)), "rh": list(range(313, 329))}, "OrbPolaFrontal": {"lh": list(range(149, 158)), "rh": list(range(329, 338))}, "Inferior Frontal": {"lh": list(range(158, 167)), "rh": list(range(338, 347))}, "Dorsolateral Prefrontal": {"lh": list(range(167, 180)), "rh": list(range(347, 360))}, "Subcortical Regions": {"lh": list(range(360, 393)), "rh": list(range(393, 426))}, }

List and range method: python parcel_approach["Custom"]["regions"] = { "Primary Visual": {"lh": [0], "rh": [180]}, "Early Visual": {"lh": [1, 2, 3], "rh": [181, 182, 183]}, "Dorsal Stream Visual": {"lh": range(4, 10), "rh": range(184, 190)}, "Ventral Stream Visual": {"lh": range(10, 17), "rh": range(190, 197)}, "MT+ Complex": {"lh": range(17, 26), "rh": range(197, 206)}, "SomaSens Motor": {"lh": range(26, 31), "rh": range(206, 211)}, "ParaCentral MidCing": {"lh": range(31, 40), "rh": range(211, 220)}, "Premotor": {"lh": range(40, 47), "rh": range(220, 227)}, "Posterior Opercular": {"lh": range(47, 52), "rh": range(227, 232)}, "Early Auditory": {"lh": range(52, 59), "rh": range(232, 239)}, "Auditory Association": {"lh": range(59, 67), "rh": range(239, 247)}, "Insula FrontalOperc": {"lh": range(67, 79), "rh": range(247, 259)}, "Medial Temporal": {"lh": range(79, 87), "rh": range(259, 267)}, "Lateral Temporal": {"lh": range(87, 95), "rh": range(267, 275)}, "TPO": {"lh": range(95, 100), "rh": range(275, 280)}, "Superior Parietal": {"lh": range(100, 110), "rh": range(280, 290)}, "Inferior Parietal": {"lh": range(110, 120), "rh": range(290, 300)}, "Posterior Cingulate": {"lh": range(120, 133), "rh": range(300, 313)}, "AntCing MedPFC": {"lh": range(133, 149), "rh": range(313, 329)}, "OrbPolaFrontal": {"lh": range(149, 158), "rh": range(329, 338)}, "Inferior Frontal": {"lh": range(158, 167), "rh": range(338, 347)}, "Dorsolateral Prefrontal": {"lh": range(167, 180), "rh": range(347, 360)}, "Subcortical Regions": {"lh": range(360, 393), "rh": range(393, 426)}, }

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.19.3...0.19.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.19.3.post0

📖 Documentation

  • Additional documentation for standardize function.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.19.3...0.19.3.post0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.19.3

🚀 New/Added

  • Method chaining for several methods in the CAP and TimeseriesExtractor class.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.19.2...0.19.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.19.2

🐛 Fixes

  • Add type hints to properties.
  • Improve accuracy of type hints for the properties.
  • Fixes type hints for certain parameters that included numpy.ndarray.
  • Replaces any returns that implies a plot object is returned and replaces with None for clarity.
  • Raise type error when self.subject_table in CAP is set but is not a dictionary.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.19.1...0.19.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.19.1

  • Primarily to ensure all the latest distributions have the correct documentation links.
  • Includes some internal code changes that won't change results.
  • TODO for future version is to support Python 3.13.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.19.0

  • Cleaning some of the API, specifically parameter names and properties, no defaults have been changed in this update.

🚀 New/Added

  • suffix_filename added to CAP.caps2plot, CAP.caps2surf, CAP.caps2radar, and transition_matrix. This addition was done to allow the suffix_title parameter in each of the previously listed methods to only be responsible for the title of the plots. The suffix filename will also be appended to the end of the default filename.

  • CAP class now has a cluster_scores property to consolodate the inertia, davies_bouldin, silhouette, and "varianceratio" scores into a property instead of separate properties. Consequently, the inertia, ``daviesbouldin,silhouette``, and "variance_ratio" have been removed.

The structure of this property is:

{ "Cluster_Selection_Method": str, # e.g., "elbow", "davies_bouldin", "silhouette", or "variance_ratio" "Scores": { "GroupName": { 2: float, # Score for 2 clusters 3: float, # Score for 3 clusters 4: float, # Score for 4 clusters }, } }

♻ Changed

  • Any instance of file_name in a parameter name has been changed to the more conventional parameter name filename. For instance, suffix_file_name now becomes suffix_filename and file_names becomes filenames. This change effects the following functions: merge_dicts, standardize, change_dtypes, CAP.calculate_metrics, CAP.caps2niftis, TimeseriesExtractor.timeseries_to_pickle, and TimeseriesExtractor.visualize_bold.
  • Warning logged whenever file name parameter is used but output_dir is not specified.

📖 Documentation

  • Fix doc parameter error for CAP.caps2niftis that used suffix_title instead of suffix_file_name, which is now suffix_filename.
  • In documentation, version labels restricted to changes or additions make from 0.18.0 and above for less clutter.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.11

🐛 Fixes

  • An error in a setter method that did not use raise.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.10...0.18.11

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.10

🚀 New/Added

- Added deleter method for subject_timeseries and concatenated_timeseries properties

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.9...0.18.10

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.9

🚀 New/Added

  • Custom error to warn about querying issues
  • Add optional dependency for demo ### 🐛 Fixes
  • Documentation rendering issues
  • Restrict from downloading the latest vtk 9.4.0 for caps2surf to work.

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.8.post0

📖 Documentation

  • Update to documentation to show example directory structure.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.8...0.18.8.post0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.8

🚀 New/Added

  • Added "usesamplemask" key for fd_threshold parameter, which if set to True, generates a sample mask to pass to nilearn's NiftiLabelsMasker for censoring prior to nuisance regression. Internally, the clean__extrapolate parameter is used to set extrapolate to False. If condition filtering is requested, when "usesamplemask" key for fd_threshold parameter is True, then the truncated timeseries is temporarily padded to ensure the correct indices corresponding to the condition are obtained.
  • Added new property.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.7...0.18.8

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.7

🐛 Fixes

  • Fixes projection of CAPs onto NiFTI atlas by preventing in-place modification. Previously, if a new CAP value matched a subsequent atlas label ID, it could cause incorrect coordinate assignments.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.6...0.18.7

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.6

  • Minor code cleaning ### 📖 Documentation
  • Readme example fix

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.5...0.18.6

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.5

♻ Changed

  • Updated Dependencies:
    • NumPy: version 2.0 and above can be installed.
    • BrainSpace: requires version 0.1.16 and above.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.4...0.18.5

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.4

🐛 Fixes

  • Corrected region names for version "3v2" of the AAL atlas. ## ♻ Changed
  • Added a specific logged warning when no confound names are found. If some confound names are missing, they will still be listed accordingly.
  • Added a specific logged warnings for methods in CAP that use the runs parameter. Warnings are issued if a subject is missing any requested run, with an additional warning if all runs are missing.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.3...0.18.4

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.3.post1

📖 Documentation

  • Added reference for merge_dicts.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.3.post0...0.18.3.post1

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.3.post0

📖 Documentation

  • Significant documentation revisions for clarity and precision.
  • Also, updates outdated documentation for CAP.get_caps to clarify that figure generation and saving parameters can be used with any cluster_selection_method, not just specific ones as previously implied.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.3...0.18.3.post0

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.3

🐛 Fixes

  • More conservative maxsizes for @lru_cache, change @cache in TimeseriesExtractor to @lru_cache.
  • Clean unused import.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.2...0.18.3

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago

NeuroCAPs - 0.18.2

  • A simple pre commit hook added to remove a few trailing whitespace, add new lines, etc.

♻ Changed

  • Add's _get_target_indices and _build_tree to the init file for a shorter import path if cache needs to be cleared or assessed. essentially allows:

New import: python from neurocaps._utils import _build_tree, _get_target_indices

Previous import: python from neurocaps._utils.analysis.cap2statmap import _build_tree, _get_target_indices

📖 Documentation

  • Very minor doc fix.

Full Changelog: https://github.com/donishadsmith/neurocaps/compare/0.18.1...0.18.2

Scientific Software - Peer-reviewed - Python
Published by donishadsmith about 1 year ago