Merge pull request #224 from ntatsisk/notebooks-pixel-types

InsightSoftwareConsortium · May 30, 2023 · 4fbdc9c · 4fbdc9c
2 parents ab0c0c0 + 0a60fc5
commit 4fbdc9c
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Showing 3 changed files with 396 additions and 21 deletions.
diff --git a/.binder/requirements.txt b/.binder/requirements.txt
@@ -1,4 +1,4 @@
-itk-elastix>=0.12.0
+itk-elastix>=0.17.1
 itkwidgets>=0.32.0
 jupyterlab>=2.2.0
 imageio

diff --git a/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb b/examples/ITK_Example09_PointSetAndMaskTransformation.ipynb
@@ -1,13 +1,15 @@
 {
  "cells": [
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## 9. Point set and Mask Transformation"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -19,6 +21,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -57,6 +60,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -65,7 +69,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,6 +81,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -85,25 +90,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import Mask\n",
-    "moving_mask = itk.imread('data/CT_3D_lung_moving_mask.mha', itk.F)"
+    "# Note: Version v0.17.0 and onwards supports various image types for elastix and transformix functions/objects\n",
+    "moving_mask = itk.imread('data/CT_3D_lung_moving_mask.mha', itk.UC)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Mask image is a binary image, therefore the FinalBSplineInterpolationOrder should be 0\n",
-    "result_transform_parameters.SetParameter('FinalBSplineInterpolationOrder','0')\n"
+    "result_transform_parameters.SetParameter('FinalBSplineInterpolationOrder','0')"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -112,7 +119,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -123,6 +130,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -131,7 +139,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -148,13 +156,15 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "### Segmentation Transformation Evaluation"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -163,7 +173,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -180,12 +190,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Import groundtruth segmentation\n",
-    "fixed_mask = itk.imread('data/CT_3D_lung_fixed_mask.mha', itk.F)\n",
+    "fixed_mask = itk.imread('data/CT_3D_lung_fixed_mask.mha', itk.UC)\n",
     "\n",
     "# Cast itk images to numpy arrays and round result image to boolean array.\n",
     "fixed_mask_np = np.asarray(fixed_mask)\n",
@@ -194,23 +204,47 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Dice loss: 0.9862246731348647\n"
+     ]
+    }
+   ],
    "source": [
     "print(\"Dice loss:\",dice_loss(fixed_mask_np, result_mask_np))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "c76e48b027c84e37963cf1e02ee8a702",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "compare(fixed_mask, result_moving_mask)"
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -219,7 +253,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -231,6 +265,7 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -239,7 +274,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,17 +297,32 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "3a044dd051e04f2f92d3dae77639590e",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Viewer(geometries=[], gradient_opacity=0.22, point_set_colors=array([[0.8392157, 0.       , 0.       ]], dtype…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "view(moving_image, point_sets=[result_point_set])"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -286,7 +336,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.0"
+   "version": "3.9.0"
   }
  },
  "nbformat": 4,