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updated notebooks, using pygemc from latest image
1 parent bc4980b commit 00e2710

9 files changed

Lines changed: 111 additions & 184 deletions

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‎Dockerfile‎

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Original file line numberDiff line numberDiff line change
@@ -1,14 +1,16 @@
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FROM ghcr.io/gemc/src:dev-ubuntu-24.04
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FROM ghcr.io/gemc/src:dev-ubuntu-26.04
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USER root
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RUN apt-get update && apt-get install -y --no-install-recommends \
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python3-pip \
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&& rm -rf /var/lib/apt/lists/*
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RUN pip install --no-cache-dir --break-system-packages \
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RUN DOCKER_ENTRYPOINT_SOURCE_ONLY=1 . /usr/local/bin/docker-entrypoint.sh \
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&& python3 -m pip install --no-cache-dir \
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'jupyterlab>=3' \
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ipywidgets \
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ipykernel \
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'pyvista[all,trame]' \
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jupyter-server-proxy \
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pandas \
@@ -24,4 +26,4 @@ WORKDIR /home/ubuntu
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COPY --chown=ubuntu:ubuntu notebooks/ /home/ubuntu/notebooks/
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CMD ["jupyter", "lab", "--ip=0.0.0.0", "--no-browser"]
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CMD ["python3", "-m", "jupyter", "lab", "--ip=0.0.0.0", "--no-browser"]

‎README.md‎

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@@ -4,7 +4,7 @@ GEMC Jupyter Notebooks Tutorials on Binder
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# Build and run:
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```shell
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docker pull ghcr.io/gemc/src:dev-ubuntu-24.04
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docker pull ghcr.io/gemc/src:dev-ubuntu-26.04
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docker build -t gemc-binder .
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docker run --rm -p 8888:8888 gemc-binder
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```

‎notebooks/basic/b1.ipynb‎

Lines changed: 12 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -29,18 +29,19 @@
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"# │ dosimeter digitization to store the accumulated dose on a detector. │\n",
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"# │ │\n",
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"# │ │\n",
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"# │ import PyVista and editor │\n",
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"# │ Import notebook helpers │\n",
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"# │ Copy basic/b1 example to local directory │\n",
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"# └────────────────────────────────────────────────────────────────────────┘\n",
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"\n",
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"import subprocess, warnings, sys, vtk\n",
37-
"import pyvista as pv\n",
38-
"vtk.vtkObject.GlobalWarningDisplayOff() # suppress warnings\n",
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"\n",
40-
"from pygemc.api.run_geometry import run_geometry\n",
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"import subprocess\n",
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"import sys\n",
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"from pathlib import Path\n",
39+
"from IPython.display import Image, display\n",
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"\n",
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"sys.path.insert(0, str(Path.cwd().parent))\n",
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"from notebook_tools import edit, setup_example\n",
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"\n",
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"from pygemc.api.run_geometry import run_geometry\n",
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"setup_example(\"examples/basic/b1\")\n"
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],
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"id": "70c84bea9eb56292"
@@ -76,9 +77,6 @@
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"# │ - Display generated screenshot if present │\n",
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"# └─────────────────────────────────────────────────────────┘\n",
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"\n",
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"from pathlib import Path\n",
80-
"from IPython.display import Image, display\n",
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"\n",
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"yaml='b1.yaml'\n",
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"driver='-g4view=[{driver: TOOLSSG_OFFSCREEN}]'\n",
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"camera='-g4camera=[{phi: -10*deg, theta: 250*deg}]'\n",
@@ -98,15 +96,7 @@
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" display(Image(filename=str(image_file)))\n",
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"else:\n",
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" print(f\"No GEMC image found: {image_file}\")\n",
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" \n",
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" \n",
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"result = subprocess.run(\n",
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"\t[\"ls\", \"-l\"],\n",
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"\tcapture_output=True,\n",
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"\ttext=True,\n",
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")\n",
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"\n",
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"print(result.stdout)\n"
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"\n"
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],
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"id": "289ce146d178545c"
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},
@@ -123,7 +113,8 @@
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"# │ histogram. │\n",
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"# └───────────────────────────────────────────────────────────────────────┘\n",
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"\n",
126-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"dose\", data=\"digitized\", bins=50, logy=False, show=True)\n"
116+
"from pygemc import read_output, plot_variable\n",
117+
"plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"dose\", data=\"digitized\", bins=50, logy=False, show=True)\n"
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],
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"id": "b1-plot-totEdep-code"
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},
@@ -140,7 +131,8 @@
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"# │ histogram. │\n",
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"# └───────────────────────────────────────────────────────────────────────┘\n",
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"\n",
143-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"etot\", data=\"digitized\", bins=50, logy=True, show=True)\n"
134+
"from pygemc import read_output, plot_variable\n",
135+
"plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"etot\", data=\"digitized\", bins=50, logy=True, show=True)\n"
144136
],
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"id": "b1-plot-pid-code"
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},

‎notebooks/basic/b2.ipynb‎

Lines changed: 13 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -30,18 +30,19 @@
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"# │ output. │\n",
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"# │ │\n",
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"# │ │\n",
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"# │ import PyVista and editor │\n",
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"# │ Import notebook helpers │\n",
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"# │ Copy basic/b2 example to local directory │\n",
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"# └────────────────────────────────────────────────────────────────────────┘\n",
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"\n",
37-
"import subprocess, warnings, sys, vtk\n",
38-
"import pyvista as pv\n",
39-
"vtk.vtkObject.GlobalWarningDisplayOff() # suppress warnings\n",
40-
"\n",
41-
"from pygemc.api.run_geometry import run_geometry\n",
37+
"import subprocess\n",
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"import sys\n",
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"from pathlib import Path\n",
40+
"from IPython.display import Image, display\n",
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"\n",
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"sys.path.insert(0, str(Path.cwd().parent))\n",
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"from notebook_tools import edit, setup_example\n",
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"\n",
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"from pygemc.api.run_geometry import run_geometry\n",
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"setup_example(\"examples/basic/b2\")\n"
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],
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"id": "eefd95102f38a3f2"
@@ -77,14 +78,11 @@
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"# │ - Display generated screenshot if present │\n",
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"# └─────────────────────────────────────────────────────────┘\n",
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"\n",
80-
"from pathlib import Path\n",
81-
"from IPython.display import Image, display\n",
82-
"\n",
8381
"yaml='b2.yaml'\n",
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"driver='-g4view=[{driver: TOOLSSG_OFFSCREEN}]'\n",
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"camera='-g4camera=[{phi: -10*deg, theta: 250*deg}]'\n",
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"light='-g4light=[{phi: 160*deg, theta: 120*deg}]'\n",
87-
"nevents=\"-n=1000\"\n",
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"nevents=\"-n=50\"\n",
8886
"nthreads=\"-nthreads=1\"\n",
8987
"\n",
9088
"result = subprocess.run([\"gemc\", yaml, driver, camera, light, nevents, nthreads], capture_output=True, text=True)\n",
@@ -99,15 +97,7 @@
9997
" display(Image(filename=str(image_file)))\n",
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"else:\n",
10199
" print(f\"No GEMC image found: {image_file}\")\n",
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" \n",
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" \n",
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"result = subprocess.run(\n",
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"\t[\"ls\", \"-l\"],\n",
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"\tcapture_output=True,\n",
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"\ttext=True,\n",
108-
")\n",
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"\n",
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"print(result.stdout)\n"
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"\n"
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],
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"id": "d4569ba806553c65"
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},
@@ -124,7 +114,8 @@
124114
"# │ histogram. │\n",
125115
"# └───────────────────────────────────────────────────────────────────────┘\n",
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"\n",
127-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"totEdep\", data=\"digitized\", bins=50, logy=False, show=True)\n"
117+
"from pygemc import read_output, plot_variable\n",
118+
"plot_variable(read_output(\"CO2_t0_digitized.csv\"), \"totEdep\", data=\"digitized\", bins=50, logy=True, show=True)\n"
128119
],
129120
"id": "b2-plot-totEdep-code"
130121
},
@@ -141,7 +132,8 @@
141132
"# │ histogram. │\n",
142133
"# └───────────────────────────────────────────────────────────────────────┘\n",
143134
"\n",
144-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"CO2_t0_true_info.csv\"), \"vz\", data=\"true_info\", bins=50, logy=False, show=True)\n"
135+
"from pygemc import read_output, plot_variable\n",
136+
"plot_variable(read_output(\"CO2_t0_true_info.csv\"), \"vz\", data=\"true_info\", bins=50, logy=False, show=True)\n"
145137
],
146138
"id": "b2-plot-pid-code"
147139
},

‎notebooks/basic/materials.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -25,18 +25,19 @@
2525
"# │ molecular and fractional-mass materials, and optical material │\n",
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"# │ properties. │\n",
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"# │ │\n",
28-
"# │ import PyVista and editor │\n",
28+
"# │ Import notebook helpers │\n",
2929
"# │ Copy basic/material example to local directory │\n",
3030
"# └────────────────────────────────────────────────────────────────────────┘\n",
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"\n",
32-
"import subprocess, warnings, sys, vtk\n",
33-
"import pyvista as pv\n",
34-
"vtk.vtkObject.GlobalWarningDisplayOff() # suppress warnings\n",
35-
"\n",
36-
"from pygemc.api.run_geometry import run_geometry\n",
32+
"import subprocess\n",
33+
"import sys\n",
3734
"from pathlib import Path\n",
35+
"from IPython.display import Image, display\n",
36+
"\n",
3837
"sys.path.insert(0, str(Path.cwd().parent))\n",
3938
"from notebook_tools import edit, setup_example\n",
39+
"\n",
40+
"from pygemc.api.run_geometry import run_geometry\n",
4041
"setup_example(\"examples/basic/material\")\n"
4142
],
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"id": "29a4af82943c7d2"
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7273
"# │ - Display generated screenshot if present │\n",
7374
"# └────────────────────────────────────────────────────────┘\n",
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"\n",
75-
"from pathlib import Path\n",
76-
"from IPython.display import Image, display\n",
77-
"\n",
7876
"yaml='materials.yaml'\n",
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"driver='-g4view=[{driver: TOOLSSG_OFFSCREEN}]'\n",
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"camera='-g4camera=[{phi: -10*deg, theta: 250*deg}]'\n",
@@ -94,52 +92,10 @@
9492
" display(Image(filename=str(image_file)))\n",
9593
"else:\n",
9694
" print(f\"No GEMC image found: {image_file}\")\n",
97-
" \n",
98-
" \n",
99-
"result = subprocess.run(\n",
100-
"\t[\"ls\", \"-l\"],\n",
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"\tcapture_output=True,\n",
102-
"\ttext=True,\n",
103-
")\n",
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"\n",
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"print(result.stdout)\n"
95+
"\n"
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],
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"id": "2bd23d4e8b022c78"
10898
},
109-
{
110-
"cell_type": "code",
111-
"execution_count": null,
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"metadata": {},
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"outputs": [],
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"id": "materials-plot-totEdep-code",
115-
"source": [
116-
"# ┌───────────────────────────────────────────────────────────────────┐\n",
117-
"# │ Cell 6 · Plot totEdep (Shift+Enter to run) │\n",
118-
"# │ │\n",
119-
"# │ Use the analyzer API on the digitized CSV file with a log-scale │\n",
120-
"# │ 50-bin histogram. │\n",
121-
"# └───────────────────────────────────────────────────────────────────┘\n",
122-
"\n",
123-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"material_t0_digitized.csv\"), \"totEdep\", data=\"digitized\", bins=50, logy=True, show=True)\n"
124-
]
125-
},
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{
127-
"cell_type": "code",
128-
"execution_count": null,
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"metadata": {},
130-
"outputs": [],
131-
"id": "materials-plot-energy-code",
132-
"source": [
133-
"# ┌───────────────────────────────────────────────────────────────────┐\n",
134-
"# │ Cell 7 · Plot E (Shift+Enter to run) │\n",
135-
"# │ │\n",
136-
"# │ Use the analyzer API on the digitized CSV file with a log-scale │\n",
137-
"# │ 50-bin histogram. │\n",
138-
"# └───────────────────────────────────────────────────────────────────┘\n",
139-
"\n",
140-
"from pygemc import read_output, plot_variable; plot_variable(read_output(\"material_t0_digitized.csv\"), \"E\", data=\"digitized\", bins=50, logy=True, show=True)\n"
141-
]
142-
},
14399
{
144100
"cell_type": "code",
145101
"execution_count": null,

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