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Update the R setup.
Move from using the IRKernel (R 3.x) to RKernel (R 4.x) Jupyter kernel. Move from old style Python wrapping of code in R to new style, rPython replaced by reticulate.
1 parent 959533f commit a21af16

16 files changed

+695
-185
lines changed

‎R/00_Setup.ipynb‎

Lines changed: 35 additions & 11 deletions
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@@ -32,20 +32,32 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
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"# check that all packages are installed (see requirements.txt file)\n",
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"required_packages <- c(\"SimpleITK\", \"rPython\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
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"required_packages <- c(\"SimpleITK\", \"reticulate\", \"scatterplot3d\", \"tidyr\", \"ggplot2\", \"xtable\", \"purrr\")\n",
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"missing_packages <- required_packages[!unlist(lapply(required_packages, require, character.only = TRUE, quietly = TRUE))]"
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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": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -67,8 +79,14 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"simpleitk_error_allowed": "Exception in SITK"
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK",
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -91,7 +109,13 @@
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"vscode": {
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"languageId": "r"
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}
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},
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"outputs": [],
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"source": [
@@ -103,17 +127,17 @@
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"kernelspec": {
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"display_name": "R",
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"language": "R",
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"name": "ir"
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"name": "rkernel"
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},
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"language_info": {
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"codemirror_mode": "r",
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"file_extension": ".r",
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"codemirror_mode": "R",
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"file_extension": ".R",
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"mimetype": "text/x-r-source",
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"name": "R",
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"pygments_lexer": "r",
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"version": "3.2.3"
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"version": "4.5.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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"nbformat_minor": 4
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}

‎R/22_Transforms.ipynb‎

Lines changed: 10 additions & 4 deletions
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@@ -482,7 +482,10 @@
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{
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"cell_type": "markdown",
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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}
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},
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"source": [
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"## Similarity to Affine [3D]\n",
@@ -935,7 +938,10 @@
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{
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"cell_type": "markdown",
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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}
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},
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"source": [
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"## Writing and Reading\n",
@@ -1022,7 +1028,7 @@
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"kernelspec": {
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"display_name": "R",
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"language": "R",
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"name": "ir"
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"name": "rkernel"
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},
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"language_info": {
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"codemirror_mode": "r",
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

‎R/300_Segmentation_Overview.ipynb‎

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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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"outputs": [],
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": false
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"collapsed": false,
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"jupyter": {
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"outputs_hidden": false
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}
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},
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"outputs": [],
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"source": [
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"execution_count": null,
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"metadata": {
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"collapsed": true,
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"jupyter": {
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"outputs_hidden": true
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},
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"simpleitk_error_allowed": "Exception in SITK"
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},
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"outputs": [],
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"kernelspec": {
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"display_name": "R",
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"language": "R",
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"name": "ir"
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"name": "rkernel"
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},
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"language_info": {
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"codemirror_mode": "r",
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}
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},
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"nbformat": 4,
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"nbformat_minor": 1
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"nbformat_minor": 4
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}

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