trx.utils#

Attributes#

dipy_available

Functions#

`close_or_delete_mmap`(obj)	Close the memory-mapped file if it exists, otherwise set the object to None.
`split_name_with_gz`(filename)	Returns the clean basename and extension of a file.
`get_reference_info_wrapper`(reference)	Will compare the spatial attribute of 2 references.
`is_header_compatible`(reference_1, reference_2)	Will compare the spatial attribute of 2 references.
`get_axis_shift_vector`(flip_axes)	Parameters:
`get_axis_flip_vector`(flip_axes)	Parameters:
`get_shift_vector`(sft)	When flipping a tractogram the shift vector is used to change the origin
`flip_sft`(sft, flip_axes)	Flip the streamlines in the StatefulTractogram according to the
`load_matrix_in_any_format`(filepath)	Load a matrix from a txt file OR a npy file.
`get_reverse_enum`(space_str, origin_str)	Convert string representation to enums for the StatefulTractogram.
`convert_data_dict_to_tractogram`(data)	Convert a data from a lazy tractogram to a tractogram
`append_generator_to_dict`(gen, data)
`verify_trx_dtype`(trx, dict_dtype)	Verify if the dtype of the data in the trx is the same as the one in

Module Contents#

trx.utils.dipy_available = True[source]#

trx.utils.close_or_delete_mmap(obj)[source]#: Close the memory-mapped file if it exists, otherwise set the object to None.

trx.utils.split_name_with_gz(filename)[source]#

Returns the clean basename and extension of a file. Means that this correctly manages the “.nii.gz” extensions.

Parameters:

filename: str: The filename to clean

Returns:

base, exttuple(str, str)
Clean basename and the full extension

trx.utils.get_reference_info_wrapper(reference)[source]#

Will compare the spatial attribute of 2 references.

Parameters:

referenceNifti or Trk filename, Nifti1Image or TrkFile, Nifti1Header or

trk.header (dict), TrxFile or trx.header (dict) Reference that provides the spatial attribute.

Returns

——-

outputtuple

affine ndarray (4,4), np.float32, tranformation of VOX to RASMM
dimensions ndarray (3,), int16, volume shape for each axis
voxel_sizes ndarray (3,), float32, size of voxel for each axis
voxel_order, string, Typically ‘RAS’ or ‘LPS’

trx.utils.is_header_compatible(reference_1, reference_2)[source]#

Will compare the spatial attribute of 2 references.

Parameters:

reference_1Nifti or Trk filename, Nifti1Image or TrkFile,: Nifti1Header or trk.header (dict) Reference that provides the spatial attribute.
reference_2Nifti or Trk filename, Nifti1Image or TrkFile,: Nifti1Header or trk.header (dict) Reference that provides the spatial attribute.
Returns
——-
outputbool: Does all the spatial attribute match

trx.utils.get_axis_shift_vector(flip_axes)[source]#

Parameters:

flip_axeslist of str: String containing the axis to flip. Possible values are ‘x’, ‘y’, ‘z’
Returns
——-
flip_vectornp.ndarray (3,): Vector containing the axis to flip. Possible values are -1, 1

trx.utils.get_axis_flip_vector(flip_axes)[source]#

Parameters:

flip_axeslist of str: String containing the axis to flip. Possible values are ‘x’, ‘y’, ‘z’
Returns
——-
flip_vectornp.ndarray (3,): Vector containing the axis to flip. Possible values are -1, 1

trx.utils.get_shift_vector(sft)[source]#

When flipping a tractogram the shift vector is used to change the origin of the grid from the corner to the center of the grid.

Parameters:

sftStatefulTractogram: StatefulTractogram object
Returns
——-
shift_vectorndarray: Shift vector to apply to the streamlines

trx.utils.flip_sft(sft, flip_axes)[source]#

Flip the streamlines in the StatefulTractogram according to the flip_axes. Uses the spatial information to flip according to the center of the grid.

Parameters:

sftStatefulTractogram: StatefulTractogram to flip
flip_axeslist of str: Axes to flip. Possible values are ‘x’, ‘y’, ‘z’
Returns
——-
sftStatefulTractogram: StatefulTractogram with flipped axes

trx.utils.load_matrix_in_any_format(filepath)[source]#

Load a matrix from a txt file OR a npy file.

Parameters:

filepathstr: Path to the matrix file.
Returns
——-
matrixnumpy.ndarray: The matrix.

trx.utils.get_reverse_enum(space_str, origin_str)[source]#

Convert string representation to enums for the StatefulTractogram.

Parameters:

space_strstr: String representing the space.
origin_strstr: String representing the origin.
Returns
——-
outputstr: Space and Origin as Enums.

trx.utils.convert_data_dict_to_tractogram(data)[source]#

Convert a data from a lazy tractogram to a tractogram

Keyword arguments:: data – The data dictionary to convert into a nibabel tractogram
Returns:: A Tractogram object

trx.utils.append_generator_to_dict(gen, data)[source]#

trx.utils.verify_trx_dtype(trx, dict_dtype)[source]#

Verify if the dtype of the data in the trx is the same as the one in the dict.

Parameters:

trxTractogram: Tractogram to verify.
dict_dtypedict: Dictionary containing all elements dtype to verify.
Returns
——-
outputbool: True if the dtype is the same, False otherwise.