nireports.interfaces package

NiPype interfaces to generate reportlets.

class nireports.interfaces.CompCorVariancePlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot the number of components necessary to explain the specified levels of variance.

Mandatory Inputs:

metadata_files (a list of items which are a pathlike object or string representing an existing file) – List of files containing component metadata.

Optional Inputs:

  • metadata_sources (a list of items which are a string) – List of names of decompositions (e.g., aCompCor, tCompCor) yielding the arguments in metadata_files.

  • out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value: None)

  • variance_thresholds (a tuple of the form: (a float, a float, a float)) – Levels of explained variance to include in plot. (Nipype default value: (0.5, 0.7, 0.9))

Outputs:

out_file (a pathlike object or string representing an existing file) – Path to saved plot.

class nireports.interfaces.ConfoundsCorrelationPlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot the correlation among confound regressors.

Mandatory Inputs:

confounds_file (a pathlike object or string representing an existing file) – File containing confound regressors.

Optional Inputs:

  • columns (a list of items which are a string) – Filter out all regressors not found in this list.

  • ignore_initial_volumes (an integer) – Number of non-steady-state volumes at the beginning of the scan to ignore. (Nipype default value: 0)

  • max_dim (an integer) – Maximum number of regressors to include in plot. Regressors with highest magnitude of correlation with reference_column will be selected. (Nipype default value: 20)

  • out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value: None)

  • reference_column (a string) – Column in the confound file for which all correlation magnitudes should be ranked and plotted. (Nipype default value: global_signal)

Outputs:

out_file (a pathlike object or string representing an existing file) – Path to saved plot.

class nireports.interfaces.FMRISummary(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Prepare an fMRI summary plot for the report.

Mandatory Inputs:

in_func (a pathlike object or string representing an existing file)

Optional Inputs:

  • drop_trs (an integer) – Dummy scans. (Nipype default value: 0)

  • dvars (a pathlike object or string representing an existing file)

  • fd (a pathlike object or string representing an existing file)

  • fd_thres (a float) – (Nipype default value: 0.2)

  • in_segm (a pathlike object or string representing an existing file)

  • in_spikes_bg (a pathlike object or string representing an existing file)

  • outliers (a pathlike object or string representing an existing file)

  • tr (a float or None) – The TR. (Nipype default value: None)

Outputs:

out_file (a pathlike object or string representing an existing file) – Written file path.

class nireports.interfaces.PlotContours(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot contours

Mandatory Inputs:

  • in_contours (a pathlike object or string representing an existing file) – File to pick the contours from.

  • in_file (a pathlike object or string representing an existing file) – File to be plotted.

Optional Inputs:

  • colors (a list of items which are a string) – Colors to be used for contours. (Nipype default value: ['r'])

  • cut_coords (an integer) – Number of slices. (Nipype default value: 8)

  • display_mode (‘ortho’ or ‘x’ or ‘y’ or ‘z’ or ‘yx’ or ‘xz’ or ‘yz’) – Visualization mode. (Nipype default value: ortho)

  • levels (a list of items which are a float) – Add a contour per level. (Nipype default value: [0.5])

  • out_file (a string or os.PathLike object) – Output file name.

  • saturate (a boolean) – Saturate background. (Nipype default value: False)

  • vmax (a float) – Maximum intensity.

  • vmin (a float) – Minimum intensity.

Outputs:

out_file (a pathlike object or string representing an existing file) – Output svg file.

class nireports.interfaces.PlotMosaic(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plots slices of a 3D volume into a pdf file

Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – File to be plotted.

Optional Inputs:

  • annotate (a boolean) – Annotate left/right. (Nipype default value: True)

  • bbox_mask_file (a pathlike object or string representing an existing file) – Brain mask.

  • cmap (a string) – (Nipype default value: Greys_r)

  • dpi (an integer) – Desired DPI of figure. (Nipype default value: 300)

  • figsize (a tuple of the form: (a float, a float)) – Figure size. (Nipype default value: (11.69, 8.27))

  • only_noise (a boolean) – Plot only noise. (Nipype default value: False)

  • out_file (a pathlike object or string representing a file) – Output file name. (Nipype default value: mosaic.svg)

  • title (a string) – A title string for the plot.

  • view (a list of from 1 to 3 items which are ‘axial’ or ‘sagittal’ or ‘coronal’) – (Nipype default value: ['axial', 'sagittal'])

Outputs:

out_file (a pathlike object or string representing an existing file) – Output pdf file.

class nireports.interfaces.PlotSpikes(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot slices of a dataset with spikes.

Mandatory Inputs:

  • in_fft (a pathlike object or string representing an existing file) – Nifti file with the 4D FFT.

  • in_file (a pathlike object or string representing an existing file) – File to be plotted.

  • in_spikes (a pathlike object or string representing an existing file) – Tsv file of spikes.

Optional Inputs:

  • annotate (a boolean) – Annotate left/right. (Nipype default value: True)

  • cmap (a string) – (Nipype default value: Greys_r)

  • dpi (an integer) – Desired DPI of figure. (Nipype default value: 300)

  • figsize (a tuple of the form: (a float, a float)) – Figure size. (Nipype default value: (11.69, 8.27))

  • out_file (a pathlike object or string representing a file) – Output file name. (Nipype default value: mosaic.svg)

  • title (a string) – A title string for the plot.

Outputs:

out_file (a pathlike object or string representing an existing file) – Output svg file.

class nireports.interfaces.RaincloudPlot(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Plot a raincloud of values.

Mandatory Inputs:

  • data_file (a pathlike object or string representing an existing file) – File containing the data.

  • feature (a string) – Feature of interest.

  • group_name (a string) – Group name of interest.

Optional Inputs:

  • density (a boolean) – True to plot the density. (Nipype default value: True)

  • limit_offset (a float) – Offset to plot the values over/under the upper/lower limit values. (Nipype default value: None)

  • lower_limit_color (a string) – Color name to represent values under lower_limit_value. (Nipype default value: gray)

  • lower_limit_value (a float) – (Nipype default value: None)

  • mark_nans (a boolean) – True to plot NaNs as dots. nans_values must be provided if True. (Nipype default value: True)

  • nans_color (a string) – Color name to represent NaN values. (Nipype default value: black)

  • nans_value (a float) – Value to use for NaN values`. (Nipype default value: None)

  • orient (a string) – Orientation. (Nipype default value: v)

  • out_file (a pathlike object or string representing a file or None) – Path to save plot. (Nipype default value: None)

  • palette (a string) – Color palette name. (Nipype default value: Set2)

  • upper_limit_color (a string) – Lower limit value under which any value in the data will be styled with a different style. (Nipype default value: gray)

  • upper_limit_value (a float) – Upper limit value over which any value in the data will be styled with a different style. (Nipype default value: None)

Outputs:

out_file (a pathlike object or string representing an existing file) – Path to saved plot.

Subpackages

Submodules