oursin.volumes
Volumetric datasets (x*y*z matrix)
Functions
Create an empty volume data matrix in the renderer. |
|
Delete a volume data matrix. |
|
Set the colormap for a volume, maximum of 254 values |
|
Set the data for a volume using uint8 values from 0->254 (255 is reserved for transparent). |
|
Set a single slice of data in a volume |
|
Change the visibility of a volume |
|
Set the visibility of the Allen CCF annotation volume |
- create(volume_name)[source]
Create an empty volume data matrix in the renderer.
Note: you must call create_volume and set_volume_colormap before setting data.
Parameters
- volume_namestring
volume name
Examples
>>> urn.create('histology')
- delete(volume_name)[source]
Delete a volume data matrix.
Parameters
- volume_namestring
volume name
Examples
>>> urn.delete('histology')
- set_colormap(volume_name, colormap)[source]
Set the colormap for a volume, maximum of 254 values
Note: index 255 is reserved by the renderer for transparency.
Parameters
- volumeNamestring
volume name
- volumeDatalist of string
list of hex colors, values can be RGB or RGBA
Examples
>>> urn.set_colormap('histology',['#800000','#FF0000'])
- set_visibility(volume_name, volume_visibility)[source]
Change the visibility of a volume
Parameters
- volumeNamestring
Volume name
- volumeVisibilitybool
New visibility setting
Examples
>>> urn.set_visibility('histology', True)
- set_data(volume_name, volumeData)[source]
Set the data for a volume using uint8 values from 0->254 (255 is reserved for transparent). Sending your data as any type other than np.uint8 is potentially unsafe. Data will be remapped in the renderer according to the active colormap. nan values will be set to transparent.
Note: this function slices the data by depth and sends data slice-by-slice, it may take a long time to run.
Parameters
- volumeData[string, numpy matrix]
Name of the volume and the volume itself. Volume should be [528, 320, 456] with +x = posterior, +y = ventral, +z = right
- set_slice_data(volume_name, slice, volume_bytes, override_gpu_apply=False)[source]
Set a single slice of data in a volume
Parameters
- volumeNamestring
name of volume
- sliceint
depth slice in volume (on lr dimension)
- volume_bytesbytes
flattened bytes array from slice
- override_gpu_applybool, optional
immediately set the GPU texture data after this slice is sent, by default False