diff --git a/cubids/cubids.py b/cubids/cubids.py index 00d0b76c..e91b2319 100644 --- a/cubids/cubids.py +++ b/cubids/cubids.py @@ -313,7 +313,8 @@ def add_nifti_info(self): Notes ----- - - This method assumes that the NIfTI files are organized in a BIDS-compliant directory structure. + - This method assumes that the NIfTI files are organized in a BIDS-compliant + directory structure. - The method will skip any files in hidden directories (directories starting with a dot). - If a JSON sidecar file does not exist for a NIfTI file, it will be skipped. """ @@ -917,7 +918,8 @@ def get_nifti_associations(self, nifti): Returns ------- associations : list of str - A list of paths to files associated with the given NIfTI file, excluding the NIfTI file itself. + A list of paths to files associated with the given NIfTI file, excluding + the NIfTI file itself. """ # get all assocation files of a nifti image no_ext_file = str(nifti).split("/")[-1].split(".")[0] @@ -1063,15 +1065,19 @@ def create_data_dictionary(self): ---------------------- - ManualCheck: Column where users mark groups to manually check. - Notes: Column to mark notes about the parameter group. - - RenameEntitySet: Auto-generated suggested rename of Non-Dominant Groups based on variant scanning parameters. + - RenameEntitySet: Auto-generated suggested rename of Non-Dominant Groups + based on variant scanning parameters. - Counts: Number of files in the parameter group. - Modality: MRI image type. - MergeInto: Column to mark groups to remove with a '0'. - FilePath: Location of file. - EntitySetCount: Number of participants in an Entity Set. - - EntitySet: A set of scans whose filenames share all BIDS filename key-value pairs, excluding subject and session. - - ParamGroup: The set of scans with identical metadata parameters in their sidecars (defined within an Entity Set and denoted numerically). - - KeyParamGroup: Entity Set name and Param Group number separated by a double underscore. + - EntitySet: A set of scans whose filenames share all BIDS filename key-value + pairs, excluding subject and session. + - ParamGroup: The set of scans with identical metadata parameters in their + sidecars (defined within an Entity Set and denoted numerically). + - KeyParamGroup: Entity Set name and Param Group number separated by a double + underscore. """ sidecar_params = self.grouping_config.get("sidecar_params") for mod in sidecar_params.keys(): @@ -2035,7 +2041,6 @@ def format_params(param_group_df, config, modality): def _order_columns(df): """Organize columns of the summary and files DataFrames. - Parameters ---------- df : pandas.DataFrame