Interfaces¶

class PipelineQC.interfaces.AssembleReport(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:	in_files (a legal value) – Reportlet files title (a string) – Title of final report out_file (a pathlike object or string representing a file) – Output file relative_dir (a pathlike object or string representing an existing directory or None) – None

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of AssembleReportInputSpec

output_spec¶: alias of AssembleReportOutputSpec

class PipelineQC.interfaces.Compare(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:

name1 (a string) – Name of first image
name2 (a string) – Name of second image
image1 (a pathlike object or string representing an existing file or None) – None
image2 (a pathlike object or string representing an existing file or None) – None
slice_to_image2 (a boolean) – If true, calculated slices based on non zero extent of image2
max_intensity_fraction_image1 (a float) – The intensity display range is 0, max where max is calculated as: vals = np.sort(niimg.get_fdata()).ravel() vals = vals[vals > 0] max = vals[int(len(vals) * max_intensity_fraction)]
max_intensity_fraction_image2 (a float) – The intensity display range is 0, max where max is calculated as: vals = np.sort(niimg.get_fdata()).ravel() vals = vals[vals > 0] max = vals[int(len(vals) * max_intensity_fraction)]
image_width (a float) – Image width (in inches)
image_height (a float) – Image height (in inches)
nslices (an integer) – Number of slices to plot
affine_absolute_tolerance (a float) – atol parameter of np.allclose when comparing affines
affine_relative_tolerance (a float) – atol parameter of np.allclose when comparing affines
relative_dir (a pathlike object or string representing an existing directory or None) – None
description (a string) – Longer description of reportlet

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of CompareInputSpec

class PipelineQC.interfaces.Contour(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:

name (a string) – Name of image
image (a pathlike object or string representing an existing file or None) – None
labelimage (a pathlike object or string representing an existing file or None) – None
contour_width (a float) – Contour line width (in pts)
slice_to_label (a boolean) – If true, calculated slices based on non zero extent of labelimage
max_intensity_fraction (a float) – The intensity display range is 0, max where max is calculated as: vals = np.sort(niimg.get_fdata()).ravel() vals = vals[vals > 0] max = vals[int(len(vals) * max_intensity_fraction)]
contour_levels (a legal value or None) – Levels at which to draw contours. If none assume label image is integers.
threshold_above_zero (a boolean) – If true, threshold lable image above zero and draw a single contour separating 0 and 1
image_width (a float) – Image width (in inches)
image_height (a float) – Image height (in inches)
nslices (an integer) – Number of slices to plot
affine_absolute_tolerance (a float) – atol parameter of np.allclose when comparing affines
affine_relative_tolerance (a float) – atol parameter of np.allclose when comparing affines
relative_dir (a pathlike object or string representing an existing directory or None) – None
description (a string) – Longer description of reportlet

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of ContourInputSpec

class PipelineQC.interfaces.Crash(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:	name (a string) – Name of reportlet crashfiles (a legal value) – List of nipype crash files (can be empty) relative_dir (a pathlike object or string representing an existing directory or None) – None

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of CrashInputSpec

class PipelineQC.interfaces.Distributions(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:

name (a string) – Name of distributions
distsfile (a pathlike object or string representing an existing file or None) – None
labelfile (a pathlike object or string representing an existing file or None) – None
relative_dir (a pathlike object or string representing an existing directory or None) – None
description (a string) – Longer description of reportlet

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of DistributionsInputSpec

class PipelineQC.interfaces.IndexReport(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:	in_files (a legal value) – QC pages out_file (a pathlike object or string representing a file) – Name of output index file

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of IndexReportInputSpec

output_spec¶: alias of IndexReportOutputSpec

class PipelineQC.interfaces.Rating(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:

name (a string) – Name of first image
widgets (a legal value) – List of discriptions for each widget. Each widget must have a “name” key and a “type” key, with string values. “type” determines the type of widget. It can be radio: Description of the radio buttons for the reportlet. The an “options” key, where the value of options is a list of dictionaries, each with “name” and “value” checkbox: Description of the checkboxes for the reportlet. Must have “fields” key, which is a list of names for different checkboxes. text: Description of the text field. Only requires “name”.

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of RatingInputSpec

class PipelineQC.interfaces.Single(from_file=None, resource_monitor=None, **inputs)¶

Inputs:

Parameters:

name (a string) – Name of image
image (a pathlike object or string representing an existing file or None) – None
max_intensity_fraction (a float) – The intensity display range is 0, max where max is calculated as: vals = np.sort(niimg.get_fdata()).ravel() vals = vals[vals > 0] max = vals[int(len(vals) * max_intensity_fraction)]
image_width (a float) – Image width (in inches)
image_height (a float) – Image height (in inches)
nslices (an integer) – Number of slices to plot
affine_absolute_tolerance (a float) – atol parameter of np.allclose when comparing affines
affine_relative_tolerance (a float) – atol parameter of np.allclose when comparing affines
relative_dir (a pathlike object or string representing an existing directory or None) – None
description (a string) – Longer description of reportlet

Outputs:

Parameters:	out_file (a pathlike object or string representing an existing file) – None

input_spec¶: alias of SingleInputSpec