cmtklib.util module¶
Module that defines CMTK Utility functions.
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class
cmtklib.util.
BColors
[source]¶ Bases:
object
Utility class for color unicode.
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BOLD
= '\x1b[1m'¶
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ENDC
= '\x1b[0m'¶
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FAIL
= '\x1b[91m'¶
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HEADER
= '\x1b[95m'¶
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OKBLUE
= '\x1b[94m'¶
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OKGREEN
= '\x1b[92m'¶
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UNDERLINE
= '\x1b[4m'¶
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WARNING
= '\x1b[93m'¶
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cmtklib.util.
bidsapp_2_local_bids_dir
(local_dir, path, debug=True)[source]¶ Replace all path prefixes /bids_dir by the real local directory path.
- Parameters
local_dir (string) – Local path to BIDS root directory
path (string) – Path where the prefix should be replaced
debug (Boolean) – If True, print the new path after replacement
- Returns
new_path – Output path with prefix replaced
- Return type
string
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cmtklib.util.
bidsapp_2_local_output_dir2
(local_dir, path, debug=True)[source]¶ Replace all path prefixes /output_dir by the real local directory path.
- Parameters
local_dir (string) – Local path to output / derivatives directory
path (string) – Path where the prefix should be replaced
debug (Boolean) – If True, print the new path after replacement
- Returns
new_path – Output path with prefix replaced
- Return type
string
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cmtklib.util.
create_results_plkz_local
(plkz_file, local_output_dir, debug=True)[source]¶ Update path in pickle files generated by Nipype nodes.
- Parameters
plkz_file (zipped pickle) – Pickle file generated by Nipype node
local_output_dir (string) – Local output / derivatives directory
debug (Boolean) – If True, print extra information
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cmtklib.util.
extract_freesurfer_subject_dir
(reconall_report, local_output_dir=None)[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
- Returns
fs_subject_dir – Freesurfer subject directory
- Return type
string
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cmtklib.util.
force_decode
(string, codecs=None)[source]¶ Force decoding byte string with a specific codec.
- Parameters
string (bytes) – String in bytearray format to be decoded
codecs (list) – List of codecs to try to decode the encoded string
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cmtklib.util.
get_node_dictionary_outputs
(node_report, local_output_dir=None)[source]¶ Read the Nipype node report and return a dictionary of node outputs.
- Parameters
node_report (string) – Path to node report
local_output_dir (string) – Local output / derivatives directory
- Returns
dict_outputs – dictionary of outputs extracted from node execution report
- Return type
dict
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cmtklib.util.
get_pipeline_dictionary_outputs
(datasink_report, local_output_dir=None)[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
- Returns
dict_outputs – Dictionary of pipeline outputs
- Return type
dict
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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 ifalong
== 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])
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cmtklib.util.
load_graphs
(output_dir, subjects, parcellation_scheme, weight)[source]¶ Return a dictionary of connectivity matrices (graph adjacency matrices).
Still in development
- Parameters
output_dir (string) – Output/derivatives directory
subjects (list) – List of subject
parcellation_scheme (['NativeFreesurfer','Lausanne2008','Lausanne2018']) – Parcellation scheme
weight (['number_of_fibers','fiber_density',..]) – Edge metric to extract from the graph
- Returns
connmats – Dictionary of connectivity matrices
- Return type
dict
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cmtklib.util.
magn
(xyz, n=1)[source]¶ Returns the vector magnitude
- Parameters
xyz (vector) – Input vector
n (int) – Tile by
n
ifn>1
before return
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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
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