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Update the R setup. #500

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Merged
zivy merged 2 commits into from
Feb 10, 2026
Merged

Update the R setup. #500

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5374f1d
Update the R setup.
zivy Feb 5, 2026
234c9b7
Update R to current SimpleITK API.
zivy Feb 10, 2026
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36 changes: 28 additions & 8 deletions R/00_Setup.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,20 +32,32 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# check that all packages are installed (see requirements.txt file)\n",
"required_packages <- c(\"SimpleITK\", \"rPython\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
"required_packages <- c(\"SimpleITK\", \"reticulate\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
"missing_packages <- required_packages[!unlist(lapply(required_packages, require, character.only = TRUE, quietly = TRUE))]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
Expand All @@ -67,8 +79,14 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false,
"simpleitk_error_allowed": "Exception in SITK"
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"simpleitk_error_allowed": "Exception in SITK",
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
Expand All @@ -91,7 +109,9 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
Expand All @@ -111,9 +131,9 @@
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.2.3"
"version": "4.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
16 changes: 11 additions & 5 deletions R/22_Transforms.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -482,7 +482,10 @@
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
"collapsed": true,
"jupyter": {
"outputs_hidden": true
}
},
"source": [
"## Similarity to Affine [3D]\n",
Expand Down Expand Up @@ -935,7 +938,10 @@
{
"cell_type": "markdown",
"metadata": {
"collapsed": true
"collapsed": true,
"jupyter": {
"outputs_hidden": true
}
},
"source": [
"## Writing and Reading\n",
Expand Down Expand Up @@ -980,7 +986,7 @@
"displacement$SetFixedParameters(c(field_size, field_origin, field_spacing, field_direction))\n",
"displacement$SetParameters(runif(length(displacement$GetParameters())))\n",
"\n",
"composite_transform <- Transform(basic_transform)\n",
"composite_transform <- CompositeTransform(basic_transform)\n",
"composite_transform$AddTransform(displacement)\n",
"\n",
"full_file_name <- file.path(OUTPUT_DIR, \"composite.tfm\")\n",
Expand Down Expand Up @@ -1030,9 +1036,9 @@
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.5.3"
"version": "4.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 1
"nbformat_minor": 4
}
48 changes: 27 additions & 21 deletions R/300_Segmentation_Overview.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -35,7 +38,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -61,7 +63,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -76,7 +77,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -101,6 +101,9 @@
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand Down Expand Up @@ -137,6 +140,9 @@
"execution_count": null,
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -148,7 +154,7 @@
"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
"seg$CopyInformation(img_T1)\n",
"seg$SetPixel(seed,1)\n",
"seg <- BinaryDilate(seg, 3)\n",
"seg <- BinaryDilate(seg, c(3,3,3))\n",
"\n",
"Show(LabelOverlay(img_T1_255, seg))"
]
Expand All @@ -164,7 +170,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -187,7 +192,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -212,7 +216,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand Down Expand Up @@ -241,7 +244,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -264,7 +266,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -291,7 +292,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand Down Expand Up @@ -323,17 +323,15 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"metadata": {},
"outputs": [],
"source": [
"seed <- c(132,142,96)\n",
"\n",
"seg <- Image(img_T1$GetSize(), \"sitkUInt8\")\n",
"seg$CopyInformation(img_T1)\n",
"seg$SetPixel(seed, 1)\n",
"seg <- BinaryDilate(seg, 3)"
"seg <- BinaryDilate(seg, c(3,3,3))"
]
},
{
Expand All @@ -347,7 +345,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -365,7 +366,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -376,7 +380,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -396,7 +403,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"simpleitk_error_allowed": "Exception in SITK"
},
"outputs": [],
Expand All @@ -418,9 +424,9 @@
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.2.3"
"version": "4.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 1
"nbformat_minor": 4
}
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