trx.workflows#

Attributes#

`convert_dsi_studio`(in_dsi_tractogram, in_dsi_fa, ...)
`convert_tractogram`(in_tractogram, out_tractogram, ...)
`tractogram_simple_compare`(in_tractograms, reference)
`verify_header_compatibility`(in_files)
`tractogram_visualize_overlap`(in_tractogram, reference)
`validate_tractogram`(in_tractogram, reference, ...[, ...])
`_load_streamlines_from_csv`(positions_csv)	Load streamlines from CSV file.
`_load_streamlines_from_arrays`(positions, offsets)	Load streamlines from position and offset arrays.
`_apply_spatial_transforms`(streamlines, reference, ...)	Apply spatial transforms and verify streamlines.
`_write_header`(tmp_dir_name, reference, streamlines)	Write header file.
`_write_streamline_data`(tmp_dir_name, streamlines, ...)	Write streamline position and offset data.
`_normalize_dtype`(dtype_str)	Normalize dtype string format.
`_write_data_array`(tmp_dir_name, subdir_name, args[, ...])	Write data array to file.
`generate_trx_from_scratch`(reference, out_tractogram[, ...])	Generate TRX file from scratch using various input formats.
`manipulate_trx_datatype`(in_filename, out_filename, ...)

trx.workflows.convert_dsi_studio(in_dsi_tractogram, in_dsi_fa, out_tractogram, remove_invalid=True, keep_invalid=False)[source]#

trx.workflows.convert_tractogram(in_tractogram, out_tractogram, reference, pos_dtype='float32', offsets_dtype='uint32')[source]#

trx.workflows.tractogram_simple_compare(in_tractograms, reference)[source]#

trx.workflows.tractogram_visualize_overlap(in_tractogram, reference, remove_invalid=True)[source]#

trx.workflows.validate_tractogram(in_tractogram, reference, out_tractogram, remove_identical_streamlines=True, precision=1)[source]#

trx.workflows._load_streamlines_from_csv(positions_csv)[source]#: Load streamlines from CSV file.

trx.workflows._load_streamlines_from_arrays(positions, offsets)[source]#: Load streamlines from position and offset arrays.

trx.workflows._apply_spatial_transforms(streamlines, reference, space_str, origin_str, verify_invalid, offsets)[source]#: Apply spatial transforms and verify streamlines.

trx.workflows._write_header(tmp_dir_name, reference, streamlines)[source]#: Write header file.

trx.workflows._write_streamline_data(tmp_dir_name, streamlines, positions_dtype, offsets_dtype)[source]#: Write streamline position and offset data.

trx.workflows._normalize_dtype(dtype_str)[source]#: Normalize dtype string format.

trx.workflows._write_data_array(tmp_dir_name, subdir_name, args, is_dpg=False)[source]#: Write data array to file.

trx.workflows.generate_trx_from_scratch(reference, out_tractogram, positions_csv=False, positions=False, offsets=False, positions_dtype='float32', offsets_dtype='uint64', space_str='rasmm', origin_str='nifti', verify_invalid=True, dpv=None, dps=None, groups=None, dpg=None)[source]#: Generate TRX file from scratch using various input formats.

trx.workflows.manipulate_trx_datatype(in_filename, out_filename, dict_dtype)[source]#