nireports.interfaces.mosaic module

Visualization of n-D images with mosaics cutting through planes.

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

Bases: nipype.interfaces.base.core.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.mosaic.PlotMosaic(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.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.mosaic.PlotSpikes(from_file=None, resource_monitor=None, **inputs)[source]

Bases: nipype.interfaces.base.core.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.