scilpy.viz package

scilpy.viz.chord_chart module

scilpy.viz.gradient_sampling module

scilpy.viz.scene_utils module

scilpy.viz.screenshot module

scilpy.viz.screenshot.compose_image(img_scene, img_size, slice_number, corner_position=(0, 0), transparency_scene=None, image_alpha=1.0, labelmap_scene=None, labelmap_overlay_alpha=0.7, overlays_scene=None, overlays_alpha=0.7, overlays_colors=None, peaks_overlay_scene=None, peaks_overlay_alpha=0.7, display_slice_number=False, display_lr=False, lr_labels=['L', 'R'], canvas=None)[source]

Compose an image with the given scenes, with transparency, overlays, labelmap and annotations. If no canvas for the image is given, it will be automatically created with sizings to fit.

Parameters:

  • img_scene (np.ndarray) – Image scene data.

  • img_size (array-like) – Image size (pixels) (width, height).

  • slice_number (int) – Number of the current slice.

  • corner_position (array-like) – Image corner (pixels) (left, top).

  • transparency_scene (np.ndarray, optional) – Transaprency scene data.

  • image_alpha (float) – Alpha value for the image in range [0, 1].

  • labelmap_scene (np.ndarray, optional) – Labelmap scene data.

  • labelmap_alpha (float) – Alpha value for labelmap overlay in range [0, 1].

  • overlays_scene (np.ndarray, optional) – Overlays scene data.

  • overlays_alpha (float) – Alpha value for the overlays in range [0, 1].

  • overlays_colors (list, optional) – Colors for the overlays as a list of 3 integers in range [0, 255].

  • peaks_overlay_scene (np.ndarray, optional) – Peaks overlay scene data.

  • peaks_overlay_alpha (float) – Alpha value for peaks overlay in range [0, 1].

  • display_slice_number (bool) – If true, displays the slice number in the upper left corner.

  • display_lr (bool or int) – If 1 or -1, annotates the left and right sides on the image. -1 flips left and right positions.

  • lr_labels (list) – Labels used to annotate the left and right sides of the image.

  • canvas (PIL.Image, optional) – Base canvas into which to paste the scene.

Returns:

canvas – Canvas containing the pasted scene.

Return type:

PIL.Image

scilpy.viz.screenshot.compose_mosaic(img_scene_container, cell_size, rows, cols, slice_numbers, overlap_factor=None, transparency_scene_container=None, image_alpha=1.0, labelmap_scene_container=None, labelmap_overlay_alpha=0.7, overlays_scene_container=None, overlays_alpha=0.7, overlays_colors=None, display_slice_number=False, display_lr=False, lr_labels=['L', 'R'])[source]

Create the mosaic canvas for given number of rows and columns, and the requested cell size and overlap values.

Parameters:

  • img_scene_container (list) – Image scene data container.

  • cell_size (array-like) – Cell size (pixels) (width, height).

  • rows (int) – Row count.

  • cols (int) – Column count.

  • overlap_factor (array-like) – Overlap factor (horizontal, vertical).

  • transparency_scene_container (iterable) – Transaprency scene data container.

  • image_alpha (float) – Alpha value for the image in range [0, 1].

  • labelmap_scene_container (iterable) – Labelmap scene data container.

  • overlays_scene_container (iterable) – Overlays scene data container.

  • overlays_alpha (float) – Alpha value for the overlays in range [0, 1].

  • overlays_colors (list, optional) – Color for the overlays as a list of 3 integers in range [0, 255].

  • display_slice_number (bool) – If true, displays the slice number in the upper left corner.

  • display_lr (bool or int) – If 1 or -1, annotates the left and right sides on the image. -1 flips left and right positions.

  • lr_labels (list) – Labels used to annotate the left and right sides of the image.

Returns:

mosaic – Canvas containing the mosaic scene.

Return type:

PIL.Image

scilpy.viz.screenshot.screenshot_contour(bin_img, orientation, slice_ids, size, bg_opacity=0.0)[source]

Take a screenshot of the given binary image countour with the appropriate slice data at the provided slice indices.

Parameters:

  • bin_img (nib.Nifti1Image) – Binary volume image.

  • orientation (str) – Slicing axis name.

  • slice_ids (array-like) – Slice indices.

  • size (array-like) – Size of the screenshot image (pixels).

  • bg_opacity (float) – Background opacity in range [0, 1].

Returns:

snapshots – Scene screenshots generator.

Return type:

generator

scilpy.viz.screenshot.screenshot_peaks(img, orientation, slice_ids, size, mask_img=None)[source]

Take a screenshot of the given peaks image at the provided slice indices.

Parameters:

  • img (nib.Nifti1Image) – Peaks volume image.

  • orientation (str) – Slicing axis name.

  • slice_ids (array-like) – Slice indices.

  • size (array-like) – Size of the screenshot image (pixels).

Returns:

snapshots – Scene screenshots generator.

Return type:

generator

scilpy.viz.screenshot.screenshot_volume(img, orientation, slice_ids, size, labelmap=None)[source]

Take a screenshot of the given volume at the provided slice indices.

Parameters:

  • img (nib.Nifti1Image) – Volume image.

  • orientation (str) – Slicing axis name.

  • slice_ids (array-like) – Slice indices.

  • size (array-like) – Size of the screenshot image (pixels).

Returns:

snapshots – Scene screenshots generator.

Return type:

generator

scilpy.viz.utils module

scilpy.viz.utils.affine_from_offset(orientation, offset)[source]

Create an affine matrix from a scalar offset in given orientation, in RPS coordinates for imaging.

Parameters:

  • orientation (str) – Name of the axis to visualize. Choices are axial, coronal and sagittal.

  • offset (float) – The offset of the texture image.

Returns:

affine – The affine transformation.

Return type:

np.ndarray

scilpy.viz.utils.check_mosaic_layout(img_count, rows, cols)[source]

Check whether a mosaic can be built given the image count and the requested number of rows and columns. Raise a ValueError if it cannot be built.

Parameters:

  • img_count (int) – Image count to be arranged in the mosaic.

  • rows (int) – Row count.

  • cols (int) – Column count.

scilpy.viz.utils.compute_cell_topleft_pos(idx, cols, offset_h, offset_v)[source]

Compute the top-left position of a cell to be drawn in a mosaic.

Parameters:

  • idx (int) – Cell index in the mosaic.

  • cols (int) – Column count.

  • offset_h – Horizontal offset (pixels).

  • offset_v – Vertical offset (pixels).

Returns:

  • top_pos (int) – Top position (pixels).

  • left_pos (int) – Left position (pixels).