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Update the R setup.
Move from old style Python wrapping of code in R to new style, rPython replaced by reticulate.
1 parent 959533f commit 5374f1d

15 files changed

+686
-180
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R/00_Setup.ipynb

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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": [
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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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"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": [
@@ -111,9 +131,9 @@
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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

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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",
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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",
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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": "3.5.3"
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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": 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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},
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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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"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": 1
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"nbformat_minor": 4
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}

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