cellmap_flow.viewer.raw
=======================
.. py:module:: cellmap_flow.viewer.raw
.. autoapi-nested-parse::
The raw data's neuroglancer layer, and the shaders of the viewer's layers.
``get_raw_layer`` shows a zarr, N5 or precomputed volume. By default it is
served from this process: a multiscale pyramid (an OME-Zarr group's
levels, a precomputed volume's scales) as one ``ScalePyramid`` (each level
a ``LocalVolume``, served as a power-of-two downsampling of the finest; a
level that is not one is left out), a single array
as a ``LocalVolume``, both read through ImageDataInterface so that the
input chain applies to what is drawn (never to a segmentation's ids), and
placed by a source transform that puts voxel 0's lower corner where the
metadata says. With ``wrap_raw=False`` neuroglancer reads the
files itself. ``RAW_SHADER`` and ``prediction_shader`` are the layers'
shaders, their contrast windows sampled from the data where it can be read.
``ScalePyramid`` is adapted from funlib.show.neuroglancer's scale_pyramid.py
(https://github.com/funkelab/funlib.show.neuroglancer).
Attributes
----------
.. autoapisummary::
cellmap_flow.viewer.raw.logger
cellmap_flow.viewer.raw.RAW_SHADER
cellmap_flow.viewer.raw.PREDICTION_SHADER
cellmap_flow.viewer.raw.PREDICTION_COLORS
cellmap_flow.viewer.raw.FLOW_SHADER
Classes
-------
.. autoapisummary::
cellmap_flow.viewer.raw.ScalePyramid
Functions
---------
.. autoapisummary::
cellmap_flow.viewer.raw.prediction_shader
cellmap_flow.viewer.raw.flow_shader
cellmap_flow.viewer.raw.neuroglancer_source
cellmap_flow.viewer.raw.get_raw_layer
Module Contents
---------------
.. py:data:: logger
.. py:data:: RAW_SHADER
:value: Multiline-String
.. raw:: html
Show Value
.. code-block:: python
"""#uicontrol invlerp normalized(range=[{lo:.6g}, {hi:.6g}], window=[{wlo:.6g}, {whi:.6g}]);
#uicontrol vec3 color color(default="white");
void main(){{emitRGB(color * normalized());}}"""
.. raw:: html
Show Value
.. code-block:: python
"""#uicontrol invlerp normalized(range=[{lo:.6g}, {hi:.6g}], window=[{wlo:.6g}, {whi:.6g}]);
#uicontrol vec3 color color(default="{color}");
void main(){{emitRGB(color * normalized());}}"""
.. raw:: html
Show Value
.. code-block:: python
"""#uicontrol bool flows checkbox(default=true);
#uicontrol float flow_length slider(min=0.5, max=10, default=5);
{cell_control}#uicontrol vec3 color color(default="{color}");
void main(){{
float shown = {cell};
if (!flows) {{ emitRGB(color * shown); return; }}
vec2 flow = vec2(toNormalized(getDataValue({flow_x})), toNormalized(getDataValue({flow_y})));
float len = length(flow);
vec2 dir = flow / max(len, 1e-6);
// cos(angle + 0, -120, 120 degrees), from the direction without atan.
vec3 hue = 0.5 + 0.5 * (dir.x * vec3(1.0, -0.5, -0.5) - dir.y * vec3(0.0, -0.866, 0.866));
emitRGB(hue * clamp(len / flow_length, 0.0, 1.0) * shown);
}}"""
.. raw:: html