.. _scil_viz_volume_screenshot:

scil_viz_volume_screenshot
==========================

::

	usage: __main__.py [-h] [--volume_cmap_name VOLUME_CMAP_NAME]
	                   [--volume_opacity VOLUME_OPACITY]
	                   [--transparency TRANSPARENCY] [--slices SID [SID ...]]
	                   [--axis {sagittal,coronal,axial}] [--size WIDTH HEIGHT]
	                   [--display_slice_number] [--display_lr]
	                   [--labelmap LABELMAP]
	                   [--labelmap_cmap_name LABELMAP_CMAP_NAME]
	                   [--labelmap_opacity LABELMAP_OPACITY]
	                   [--overlays OVERLAYS [OVERLAYS ...]]
	                   [--overlays_as_contours]
	                   [--overlays_colors R G B [R G B ...]]
	                   [--overlays_opacity OVERLAYS_OPACITY]
	                   [--peaks PEAKS [PEAKS ...]] [--peaks_width PEAKS_WIDTH]
	                   [--peaks_opacity PEAKS_OPACITY]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   volume out_fname
	
	Take screenshot(s) of one or more slices in a given image volume along the
	requested axis. If slice indices are not provided, all slices in the volume
	are used. The name of the output images are suffixed with _slice_{id}, with
	id being the slice number in the volume. If a labelmap image is provided (e.g.
	a tissue segmentation map), it is overlaid on the volume slices. Same goes if
	a mask is provided, with the difference that it can be rendered as a
	transparency overlay as well as a contour.
	
	A labelmap image can be provided as the image volume, without requiring it as
	the optional argument if only the former needs to be plot.
	
	Example:
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_annotated.png
	    --display_slice_number --display_lr
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_masked.png
	    --transparency brainmask.nii.gz
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial.png
	    --slices 30 40 50 60 70 80 90 100
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_sagittal.png --axis sagittal
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_plasma_cmap.png
	    --slices 30 40 50 60 70 80 90 100 --volume_cmap_name plasma
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_mask_overlay.png
	    --slices 30 40 50 60 70 80 90 100 --overlays brain_mask.nii.gz
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_mask_contour.png
	    --slices 30 40 50 60 70 80 90 100
	    --overlays brain_mask.nii.gz --overlays_as_contours
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_tissue_map.png
	    --slices 30 40 50 60 70 80 90 100 --labelmap tissue_map.nii.gz
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_tissue_viridis_cmap.png
	    --slices 30 40 50 60 70 80 90 100
	    --labelmap tissue_map.nii.gz --labelmap_cmap_name viridis
	
	>>> scil_viz_volume_screenshot t1.nii.gz t1_axial_peaks.png
	    --slices 30 40 50 60 70 80 90 100 --peaks peaks.nii.gz --volume_opacity 0.5
	
	positional arguments:
	  volume                Input 3D Nifti file (.nii/.nii.gz).
	  out_fname             Name of the output image(s). If multiple slices areprovided (or none),
	                        their index will be appended to the name (e.g. volume.jpg, volume.png 
	                        become volume_slice_0.jpg, volume_slice_0.png).
	
	options:
	  -h, --help            show this help message and exit
	  --transparency TRANSPARENCY
	                        Transparency Nifti image (.nii/.nii.gz). Can either be a 
	                        binary mask or a scalar image in the range [0, 1].
	  --size WIDTH HEIGHT   Size of the output image. [(768, 768)]
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  -f                    Force overwriting of the output files.
	
	Slicing:
	  --slices SID [SID ...]
	                        Slice indices to screenshot. If None are supplied, 
	                        all slices inside the transparency mask are selected.
	  --axis {sagittal,coronal,axial}
	                        Name of the axis to visualize. [axial]
	
	Input overlays:
	  --labelmap LABELMAP   Input labelmap file (.nii/.nii.gz).
	  --overlays OVERLAYS [OVERLAYS ...]
	                        3D Nifti image(s) to overlay (.nii/.nii.gz).
	  --peaks PEAKS [PEAKS ...]
	                        Peaks Nifti image (.nii/.nii.gz).
	
	Volume rendering:
	  --volume_cmap_name VOLUME_CMAP_NAME
	                        Colormap name for the 3D Nifti image data. [None]
	  --volume_opacity VOLUME_OPACITY
	                        Opacity value for the 3D Nifti image data. [1.0]
	  --labelmap_cmap_name LABELMAP_CMAP_NAME
	                        Colormap name for the labelmap image data. [viridis]
	  --labelmap_opacity LABELMAP_OPACITY
	                        Opacity value for the labelmap image data. [0.5]
	
	Peaks rendering:
	  --peaks_width PEAKS_WIDTH
	                        Width of the peaks lines. [3.0]
	  --peaks_opacity PEAKS_OPACITY
	                        Opacity value for the peaks overlay. [1.0]
	
	Overlay rendering:
	  --overlays_as_contours
	                        Display overlays contours and reduce the opacity of their 
	                        inner region (see the `--overlays_opacity` argument).
	  --overlays_colors R G B [R G B ...]
	                        Colors for the overlays or contours. You may provide a single color, 
	                        for all overlays/contours, or one color for each. Each color is given 
	                        as three values: R G B
	  --overlays_opacity OVERLAYS_OPACITY
	                        Opacity value for the masks overlays. When combined with `--overlays_as_contours`,
	                        this will be the opacity of the region inside the computed contours. [0.5]
	
	Annotations:
	  --display_slice_number
	                        If true, displays the slice number in the upper left corner.
	  --display_lr          If true, add left and right annotations to the images.
	
	2.2.2