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thewtexthewtex
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BUG: Fix available colormaps
Improved for multi-component volume rendering.
1 parent 06a6e41 commit 19842cc

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-39
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6 files changed

+55
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‎README.rst‎

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@@ -129,7 +129,7 @@ Recipes:
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- `Binder: Record a video <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/RecordAVideo.ipynb>`_
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- `Binder: Restore a volume opacity transfer function <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/VolumeOpacityTransferFunction.ipynb>`_
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- `Binder: Select a region of interest <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SelectRegionOfInterest.ipynb>`_
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- `Binder: Specify camera parameters <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SpecifyCameraParameters.ipynb>`_
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- `Binder: Specify camera parameters <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/CameraParameters.ipynb>`_
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- `Binder: Specify a colormap <https://mybinder.org/v2/gh/InsightSoftwareConsortium/itkwidgets/master?urlpath=lab/tree/examples/SpecifyAColormap.ipynb>`_
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Installation
@@ -294,7 +294,7 @@ or how to:
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- `Record a video <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/RecordAVideo.ipynb>`_
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- `Restore a volume opacity transfer function <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/VolumeOpacityTransferFunction.ipynb>`_
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- `Select a region of interest <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SelectRegionOfInterest.ipynb>`_
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- `Specify camera parameters <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SpecifyCameraParameters.ipynb>`_
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- `Specify camera parameters <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/CameraParameters.ipynb>`_
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- `Specify a colormap <https://github.com/InsightSoftwareConsortium/itkwidgets/blob/master/examples/SpecifyAColormap.ipynb>`_
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‎examples/SpecifyCameraParameters.ipynb‎ renamed to ‎examples/CameraParameters.ipynb‎

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@@ -2,19 +2,29 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Requirement already satisfied: itk-io in /home/matt/bin/miniconda3/envs/itkwidgets/lib/python3.7/site-packages (5.1.0.post3)\r\n",
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"Requirement already satisfied: vtk in /home/matt/bin/miniconda3/envs/itkwidgets/lib/python3.7/site-packages (8.1.2)\r\n",
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"Requirement already satisfied: itk-core==5.1.0.post3 in /home/matt/bin/miniconda3/envs/itkwidgets/lib/python3.7/site-packages (from itk-io) (5.1.0.post3)\r\n"
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]
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}
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],
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"source": [
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"# Install dependencies for this example\n",
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"# Note: This does not include itkwidgets, itself\n",
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"import sys\n",
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"!{sys.executable} -m pip install itk-io"
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"!{sys.executable} -m pip install itk-io vtk"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -23,13 +33,14 @@
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"\n",
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"import itk\n",
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"import numpy as np\n",
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"import vtk\n",
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"\n",
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"from itkwidgets import view"
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"from itkwidgets import view, cm"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
@@ -42,18 +53,18 @@
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "32285f355d8d42658c6f163f43c6eda1",
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"model_id": "6e4bf6b5d5524c27ab58325155a4b859",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"Viewer(cmap='Reds', geometries=[], gradient_opacity=0.5, point_sets=[], rendered_image=<itkImagePython.itkImag…"
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"Viewer(cmap=['BkRd'], geometries=[], gradient_opacity=0.5, point_sets=[], rendered_image=<itk.itkImagePython.i…"
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]
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},
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"metadata": {},
@@ -62,7 +73,7 @@
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],
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"source": [
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"image = itk.imread(file_name)\n",
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"viewer = view(image, vmax=150, gradient_opacity=0.5, cmap='Reds', ui_collapsed=True)\n",
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"viewer = view(image, vmax=150, gradient_opacity=0.5, cmap=cm.BkRd, ui_collapsed=True)\n",
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"viewer"
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]
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},
@@ -81,18 +92,32 @@
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"# To store / restore camera parameters:\n",
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"camera = np.array([[ 3.6606824e+02, 1.4895028e+00, 1.0029479e+02],\n",
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" [ 1.5009012e+02, 1.2883676e+02, -1.1309737e+01],\n",
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" [-4.5256451e-01, 1.3861613e-02, 8.9162391e-01]], dtype=np.float32)\n",
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"\n",
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"viewer.camera = camera"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"array([[ 518.88116, -479.65298, 454.602 ],\n",
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" [ 149. , 161. , 27.5 ],\n",
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" [ 0. , 0. , 1. ]], dtype=float32)"
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"array([[ 3.6606824e+02, 1.4895028e+00, 1.0029479e+02],\n",
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" [ 1.5009012e+02, 1.2883676e+02, -1.1309737e+01],\n",
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" [-4.5256451e-01, 1.3861613e-02, 8.9162391e-01]], dtype=float32)"
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]
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},
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"execution_count": 4,
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -103,17 +128,10 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# To store / restore camera parameters:\n",
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"camera = np.array([[ 3.6606824e+02, 1.4895028e+00, 1.0029479e+02],\n",
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" [ 1.5009012e+02, 1.2883676e+02, -1.1309737e+01],\n",
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" [-4.5256451e-01, 1.3861613e-02, 8.9162391e-01]], dtype=np.float32)\n",
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"\n",
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"viewer.camera = camera"
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]
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"source": []
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}
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],
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"metadata": {

‎itkwidgets/cm.py‎

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@@ -1,5 +1,7 @@
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# Some aliases similar to matplotlib.cm
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Blues = "Blues"
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BkRd = "BkRd"
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BkGn = "BkGn"
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BkBu = "BkBu"
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BkCy = "BkCy"
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BkMa = "BkMa"
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BrBG = "BrBG"
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GnRP = "GnRP"
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GnYlRd = "GnYlRd"
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grayscale = "Grayscale"
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Greens = "Greens"
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GyRd = "GyRd"
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Haze = "Haze"
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inferno = "Inferno (matplotlib)"
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RdOr = "RdOr"
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RdOrYl = "RdOrYl"
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RdPu = "RdPu"
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Reds = "Reds"
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viridis = "Viridis (matplotlib)"
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xray = "X Ray"
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blot = "blot"

‎itkwidgets/trait_types.py‎

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@@ -603,8 +603,8 @@ class Colormap(traitlets.Unicode):
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'Magma (matplotlib)',
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'Grayscale',
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'X Ray',
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'magenta',
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'blue2cyan',
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'BkMa',
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'BkCy',
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'gray_Matlab',
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'bone_Matlab',
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'pink_Matlab',
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'Green-Blue Asymmetric Divergent (62Blbc)',
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'Muted Blue-Green',
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'BkCy',
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'BkMa',
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'Reds',
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'Greens',
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'Blues',
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'BkRd',
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'BkGn',
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'BkBu',
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'Purples',
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'Oranges',
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'PuBu',

‎itkwidgets/widget_viewer.py‎

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@@ -819,7 +819,7 @@ def view(image=None, # noqa: C901
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default:
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- single component: 'viridis', 'grayscale' with a label map,
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- two components: 'BkCy', 'BkMa'
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- three components: 'Reds', 'Greens', 'Blues'
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- three components: 'BkRd', 'BkGn', 'BkBu'
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Colormap for each image component. Some valid values available at itkwidgets.cm.*
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select_roi: bool, default: False

‎js/lib/viewer.js‎

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@@ -1488,9 +1488,9 @@ const ViewerView = widgets.DOMWidgetView.extend({
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const cmap = this.model.get('cmap')
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if (cmap !== null && this.model.hasOwnProperty('itkVtkViewer')) {
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for (let index = 0; index < cmap.length; index++) {
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const lutProxies = this.model.itkVtkViewer.getLookupTableProxies()
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const lutProxy = lutProxies[index]
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if (cmap[index].startsWith('Custom')) {
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const lutProxies = this.model.itkVtkViewer.getLookupTableProxies()
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const lutProxy = lutProxies[index]
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const customCmap = this.model.get('_custom_cmap')
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const numPoints = customCmap.shape[0]
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const rgbPoints = new Array(numPoints)

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