algorithms.diagnostics.commands¶
Module: algorithms.diagnostics.commands
¶
Implementation of diagnostic command line tools
Tools are:
- nipy_diagnose
- nipy_tsdiffana
This module has the logic for each command.
The command script files deal with argument parsing and any custom imports.
The implementation here accepts the args
object from argparse
and does
the work.
Functions¶
-
nipy.algorithms.diagnostics.commands.
diagnose
(args)¶ Calculate, write results from diagnostic screen
Parameters: args : object
object with attributes:
- filename : str - 4D image filename
- time_axis : str - name or number of time axis in filename
- slice_axis : str - name or number of slice axis in filename
- out_path : None or str - path to which to write results
- out_fname_label : None or filename - suffix of output results files
- ncomponents : int - number of PCA components to write images for
Returns: res : dict
Results of running
screen()
on filename
-
nipy.algorithms.diagnostics.commands.
parse_fname_axes
(img_fname, time_axis, slice_axis)¶ Load img_fname, check time_axis, slice_axis or use default
Parameters: img_fname : str
filename of image on which to do diagnostics
time_axis : None or str or int, optional
Axis indexing time-points. None is default, will be replaced by a value of ‘t’. If time_axis is an integer, gives the index of the input (domain) axis of img. If time_axis is a str, can be an input (domain) name, or an output (range) name, that maps to an input (domain) name.
slice_axis : None or str or int, optional
Axis indexing MRI slices. If slice_axis is an integer, gives the index of the input (domain) axis of img. If slice_axis is a str, can be an input (domain) name, or an output (range) name, that maps to an input (domain) name. If None (the default) then 1) try the name ‘slice’ to select the axis - if this fails, and fname refers to an Analyze type image (such as Nifti), then 2) default to the third image axis, otherwise 3) raise a ValueError
Returns: img :
Image
instanceImage as loaded from img_fname
time_axis : int or str
Time axis, possibly filled with default
slice_axis : int or str
Slice axis, possibly filled with default
-
nipy.algorithms.diagnostics.commands.
tsdiffana
(args)¶ Generate tsdiffana plots from command line params args
Parameters: args : object
object with attributes
- filename : str - 4D image filename
- out_file : str - graphics file to write to instead of leaving graphics on screen
- time_axis : str - name or number of time axis in filename
- slice_axis : str - name or number of slice axis in filename
- write_results : bool - if True, write images and plots to files
- out_path : None or str - path to which to write results
- out_fname_label : None or filename - suffix of output results files
Returns: axes : Matplotlib axes
Axes on which we have done the plots.