update examples

_templates/my_header.html

@@ -17,6 +17,15 @@
   </span>
 </button>
 
+<button class="btn btn-sm" id="github-button" style="display: inline-block;"
+          data-bs-placement="bottom" data-bs-toggle="tooltip" title="Open on GitHub">
+    <span class="btn__icon-container">
+      <a id="github-link" href="https://github.com/OpenTPS/examples.git" target="_blank" style="color: inherit;">
+        <i class="fa-brands fa-github"></i>
+      </a>
+    </span>
+  </button>
+
 
 <button onclick="toggleFullScreen()"
   class="btn btn-sm btn-fullscreen-button"

auto_community/CommunityExample/SimpleDoseComputationAndOptOnCT.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_community/Template/run_template.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/create3DSeqFromDicom.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/create3DSeqFromImages.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/createDynamic3DModelFromDicomFields.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/createModelWithROIsFromDicomImages.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/crop3DDataAroundROI.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/exampleImageResampling.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/generateDRRAndGTVMasks.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DICOMExample/run_generateRandomSamplesFromModel.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseComputation/run_SimpleDoseCalculation.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseComputation/run_UseOfRangeShifterForProtonPlan.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseComputation/run_photonPlanCreationAndDoseCalculation.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseComputation/run_protonPlanCreationAndDoseCalculation.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseDeliverySimulation/PlanDeliverySimulation.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/DoseDeliverySimulation/run_PBSDeliveryTimings.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {

auto_examples/PlanOptimization/run_4DProtonOptimization.ipynb

@@ -11,7 +11,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "## Setting up the environment in google collab\n First you need to change the type of execution in the bottom left from processor to GPU. Then you can run the example.\n\n"
+        "## Setting up the environment in google collab\n\n"
       ]
     },
     {
@@ -22,7 +22,7 @@
       },
       "outputs": [],
       "source": [
-        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    get_ipython().system('pip install cupy-cuda12x')\n    import opentps"
+        "import sys\nif \"google.colab\" in sys.modules:\n    from IPython import get_ipython\n    get_ipython().system('git clone https://gitlab.com/openmcsquare/opentps.git')\n    get_ipython().system('pip install ./opentps')\n    get_ipython().system('pip install scipy==1.10.1')\n    import opentps"
       ]
     },
     {