Render

class Qiber3D.Render(network)

Bases: object

Generate 3D representations

Parameters

network (Qiber3D.Network) –

Variables
  • storage (Qiber3D.helper.NumpyMemoryManager) – storage for rasterized data

  • raster (np.ndarray) – rasterized representation of the network

  • raster_resolution (float) – voxel per length unit

  • raster_offset (tuple(float)) – distance between raster image stack origin and network orgin

animation(out_path='.', overwrite=False, duration=3, fps=30, height=None, color_mode='fiber', color_map='jet', color=None, background=None, object_type=None, segment_list=None, rgba=False, zoom=None)

Animate a network by rotate the camera around it. Saves as h264 .mp4 file by default. Supports also .webm and .gif as target.

Parameters
  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • duration (float) – animation duration in seconds

  • fps (int) – frames per second

  • height (int) – height of the animation (16:9 format)

  • color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]

  • color_map (str) – name of a matplotlib colormap

  • color (tuple(float)) – color if color_mode is ‘flat’

  • background (tuple(float)) – background color

  • object_type (str) – when set to ‘line’ render center line

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

  • rgba (bool) – allow transparency in saved file (for .gif and .webm)

  • zoom (float) – zoom by rendering a larger image and cutting it down afterwards (must be > 1.0)

Returns

path to saved file

Return type

Path

compare(color_mode='flat', color_map='jet', color=None, object_type=None, segment_list=None)

Visualize extraction steps (original image, z-drop image, binary image, reconstruction) at once. The parameter influence just the reconstructed network.

Parameters
  • color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]

  • color_map (str) – name of a matplotlib colormap

  • color (tuple(float)) – color if color_mode is ‘flat’

  • object_type (str) – when set to ‘line’ render center line

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

export_image_stack(out_path='.', overwrite=False, voxel_resolution=None, segment_list=None)

Export a network as TIFF image stack.

Parameters
  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • voxel_resolution (float) – number of voxels per unit length

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

Returns

path to saved file

Return type

Path

export_intensity_projection(image=None, out_path='.', overwrite=False, color_map='bone', mode='max', axis='z', voxel_resolution=None, segment_list=None)

Create a intensity projection of the rasterized network.

Parameters
  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • mode (str) – projection mode, choose between ‘max’ or ‘average’

  • axis (str) – project along this axis (x, y, z)

  • voxel_resolution (float) – number of voxels per unit length

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

Returns

path to saved file

Return type

Path

export_x3d(out_path='.', overwrite=False, color_mode='flat', color_map='jet', color=None, object_type=None, segment_list=None, azimuth=None, elevation=None, roll=None)
Parameters
  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]

  • color_map (str) – name of a matplotlib colormap

  • color (tuple(float)) – color if color_mode is ‘flat’

  • object_type (str) – when set to ‘line’ render center line

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

  • azimuth (float) – change camera azimuth

  • elevation (float) – change camera elevation

  • roll (float) – roll camera

Returns

path to saved file

Return type

Path

overview(out_path='.', overwrite=False, image_resolution=None, color_mode='flat', color_map='jet', color=None, background=None, object_type=None, segment_list=None, azimuth=None, elevation=None, roll=None, rgba=None, axes=0)
Parameters
  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • image_resolution (int) – image width

  • color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]

  • color_map (str) – name of a matplotlib colormap

  • color (tuple(float)) – color if color_mode is ‘flat’

  • background (tuple(float)) – background color

  • object_type (str) – when set to ‘line’ render center line

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

  • azimuth (float) – change camera azimuth

  • elevation (float) – change camera elevation

  • roll (float) – roll camera

  • rgba (bool) – allow transparency in saved file

  • axes – vedo axis selection (Documentation)

Returns

path to saved file

Return type

Path

classmethod save_3d_image(image, out_path='.', overwrite=False, image_resolution=None, binary=False, threshold=None, spacing=None, color=None, background=None, azimuth=None, elevation=None, roll=None, rgba=None)

Render thresholded image stack to file.

Parameters
  • image (np.ndarray) – image stack

  • out_path (str, Path) – file or folder path where to save the network, if None show the plot.

  • overwrite (bool) – allow file overwrite

  • image_resolution (int) – image width

  • binary (bool) – if the image stack is already binary

  • threshold (float) – threshold for volume creation in percent

  • spacing (tuple(float)) – spacing in all three axis

  • color (tuple(float)) – color for rendering (0.0-1.0)

  • background (tuple(float)) – background color

  • azimuth (float) – change camera azimuth

  • elevation (float) – change camera elevation

  • roll (float) – roll camera

  • rgba (bool) – allow transparency in saved file

Returns

path to saved file

Return type

Path

show(color_mode='flat', color_map='jet', color=None, object_type=None, segment_list=None)

Visualize a network interactively.

Parameters
  • color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]

  • color_map (str) – name of a matplotlib colormap

  • color (tuple(float)) – color if color_mode is ‘flat’

  • object_type (str) – when set to ‘line’ render center line

  • segment_list (tuple) – limit the visualisation to certain segment (use sid)

static show_3d_image(image, name, binary=False, spacing=None)

Visualize a image stack interactively. The threshold can be altered in the opened window.

Parameters
  • image (np.ndarray) – image stack

  • name (str) – display name

  • binary (bool) – if the image stack is already binary

  • spacing (tuple(float)) – spacing in all three axis