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BUG: Fix masked registration notebook #215

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merged 1 commit into from
May 16, 2023
Merged

BUG: Fix masked registration notebook #215

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31 changes: 21 additions & 10 deletions ...03_Masked_3D_Registration.ipynb.needtofix → ...TK_Example03_Masked_3D_Registration.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -56,6 +56,10 @@
"parameter_object = itk.ParameterObject.New()\n",
"parameter_object.AddParameterFile('data/parameters.3D.NC.affine.ASGD.001.txt')\n",
"\n",
"# \"WriteResultImage\" needs to be set to \"true\" so that the image is resampled at the end of the registration\n",
"# and the result_image is populated properly\n",
"parameter_object.SetParameter(0, \"WriteResultImage\", \"true\")\n",
"\n",
"# Import Mask Images\n",
"fixed_mask = itk.imread('data/CT_3D_lung_fixed_mask.mha', itk.UC)\n",
"moving_mask = itk.imread('data/CT_3D_lung_moving_mask.mha', itk.UC)\n",
Expand Down Expand Up @@ -89,7 +93,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "e77f22d8efb043b2afc8933a519a20cd",
"model_id": "9e0ed89550c043a29bef90625e1cb58e",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -113,7 +117,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "a25e8065b1af425ea0f055ef6f327dfc",
"model_id": "3e093036b3be428389dcebe081bb587b",
"version_major": 2,
"version_minor": 0
},
Expand Down Expand Up @@ -145,7 +149,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -199,13 +203,13 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "fb1b24b4266543f6a1acc897adfc0f85",
"model_id": "94d279f136cc48b3983cc60458776d58",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -223,13 +227,13 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "bbad23662da64e76a9d94c57fc252c28",
"model_id": "b68308d4d978479789642fe885a49896",
"version_major": 2,
"version_minor": 0
},
Expand All @@ -244,11 +248,18 @@
"source": [
"compare(fixed_image, result_image, label_image= [fixed_image, result_image],link_cmap=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -262,7 +273,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.0"
"version": "3.11.0"
}
},
"nbformat": 4,
Expand Down