cmtklib.util module

Module that defines CMTK Utility functions.

class cmtklib.util.BColors[source]

Bases: object

Utility class for color unicode.

BOLD = '\x1b[1m'

ENDC = '\x1b[0m'

FAIL = '\x1b[91m'

HEADER = '\x1b[95m'

OKBLUE = '\x1b[94m'

OKGREEN = '\x1b[92m'

UNDERLINE = '\x1b[4m'

WARNING = '\x1b[93m'

cmtklib.util.check_directory_exists(mandatory_dir)[source]

Makes sure the mandatory directory exists.

Raises: FileNotFoundError – Raised when the directory is not found.

cmtklib.util.convert_list_to_tuple(lists)[source]

Convert list of files to tuple of files.

(Duplicated with preprocessing, could be moved to utils in the future)

Parameters: lists ([bvecs, bvals]) – List of files containing bvecs and bvals
Returns: out_tuple – Tuple of files containing bvecs and bvals
Return type: (bvecs, bvals)

cmtklib.util.extract_freesurfer_subject_dir(reconall_report, local_output_dir=None, debug=False)[source]

Extract Freesurfer subject directory from the report created by Nipype Freesurfer Recon-all node.

Parameters

reconall_report (string) – Path to the recon-all report
local_output_dir (string) – Local output / derivatives directory
debug (bool) – If True, show printed outputs

Returns

fs_subject_dir – Freesurfer subject directory

Return type

string

cmtklib.util.extract_reconall_base_dir(file)[source]

Extract Recon-all base directory from a file.

Parameters: file (File) – File generated by Recon-all
Returns: out_path – Recon-all base directory
Return type: string

cmtklib.util.get_basename(path)[source]

Return os.path.basename() of a path.

Parameters: path (os.path) – Path to extract the containing directory
Returns: path – Path to the containing directory
Return type: os.path

cmtklib.util.get_freesurfer_subject_id(file)[source]

Extract Freesurfer subject ID from file generated by recon-all.

Parameters: file (str) – File generated by recon-all
Returns: out – Freesurfer subject ID
Return type: str

cmtklib.util.get_pipeline_dictionary_outputs(datasink_report, local_output_dir=None, debug=False)[source]

Read the Nipype datasink report and return a dictionary of pipeline outputs.

Parameters

datasink_report (string) – Path to the datasink report
local_output_dir (string) – Local output / derivatives directory
debug (bool) – If True, print output dictionary

Returns

dict_outputs – Dictionary of pipeline outputs

Return type

dict

cmtklib.util.isavailable(file)[source]

Check if file is available and return the file if it is.

Used for debugging.

Parameters: file (File) – Input file
Returns: file – Output file
Return type: File

cmtklib.util.length(xyz, along=False)[source]

Euclidean length of track line.

Parameters

xyz (array-like shape (N,3)) – array representing x,y,z of N points in a track
along (bool, optional) – If True, return array giving cumulative length along track, otherwise (default) return scalar giving total length.

Returns

L – scalar in case of along == False, giving total length, array if along == True, giving cumulative lengths.

Return type

scalar or array shape (N-1,)

Examples

>>> xyz = np.array([[1,1,1],[2,3,4],[0,0,0]])
>>> expected_lens = np.sqrt([1+2**2+3**2, 2**2+3**2+4**2])
>>> length(xyz) == expected_lens.sum()
True
>>> len_along = length(xyz, along=True)
>>> np.allclose(len_along, expected_lens.cumsum())
True
>>> length([])
0
>>> length([[1, 2, 3]])
0
>>> length([], along=True)
array([0])

cmtklib.util.magn(xyz, n=1)[source]

Returns the vector magnitude

Parameters

xyz (vector) – Input vector
n (int) – Tile by n if n>1 before return

cmtklib.util.mean_curvature(xyz)[source]

Calculates the mean curvature of a curve.

Parameters: xyz (array-like shape (N,3)) – array representing x,y,z of N points in a curve
Returns: m – float representing the mean curvature
Return type: float

Examples

Create a straight line and a semi-circle and print their mean curvatures

>>> from dipy.tracking import metrics as tm
>>> import numpy as np
>>> x=np.linspace(0,1,100)
>>> y=0*x
>>> z=0*x
>>> xyz=np.vstack((x,y,z)).T
>>> m=tm.mean_curvature(xyz)  # mean curvature straight line
>>> theta=np.pi*np.linspace(0,1,100)
>>> x=np.cos(theta)
>>> y=np.sin(theta)
>>> z=0*x
>>> xyz=np.vstack((x,y,z)).T
>>> m=tm.mean_curvature(xyz)  # mean curvature for semi-circle

cmtklib.util.print_blue(message)[source]

Print blue-colored message

Parameters: message (string) – The string of the message to be printed

cmtklib.util.print_error(message)[source]

Print red-colored error message

Parameters: message (string) – The string of the message to be printed

cmtklib.util.print_warning(message)[source]

Print yellow-colored warning message

Parameters: message (string) – The string of the message to be printed

cmtklib.util.return_button_style_sheet(image, image_disabled=None, verbose=False)[source]

Return Qt style sheet for QPushButton with image

Parameters

image (string) – Path to image to use as icon when button is enabled
image_disabled (string) – Path to image to use as icon when button is disabled
verbose (Bool) – Print the style sheet if True Default: False

Returns

button_style_sheet – Qt style sheet for QPushButton with image

Return type

string

cmtklib.util.unicode2str(text)[source]

Convert a unicode to a string using system’s encoding.

Parameters: text (bytes) – Unicode bytes representation of a string
Returns: out_str – Output string
Return type: str