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jcschaffjcschaff
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added fvsolver_demo.ipynb notebook and run_notebook.sh script
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‎.gitignore‎

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.python-version
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**/.DS_Store
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/.venv_jupyter/
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examples/test_output/SimID_*
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‎examples/fvsolver_demo.ipynb‎

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{
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"cells": [
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{
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:01:54.750649Z",
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"start_time": "2025-01-23T23:01:53.532205Z"
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}
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},
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"cell_type": "code",
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"source": [
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"import tempfile\n",
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"import os\n",
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"import requests\n",
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"import tarfile\n",
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"\n",
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"temp_dir = tempfile.mkdtemp(prefix='pyvcell_test_data_')\n",
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"filename = os.path.join(temp_dir, 'SimID_946368938_simdata.tgz')\n",
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"url = 'https://github.com/virtualcell/pyvcell/blob/main/tests/test_data/SimID_946368938_simdata.tgz?raw=true'\n",
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"response = requests.get(url)\n",
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"\n",
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"with open(filename, 'wb') as f:\n",
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" f.write(response.content)\n",
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"\n",
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"with tarfile.open(filename, 'r:gz') as tar:\n",
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" tar.extractall(temp_dir)\n",
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"print(f\"Files extracted to {temp_dir}\")"
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],
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"id": "5e183b4a68315dfe",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Files extracted to /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/pyvcell_test_data_i35r8_br\n"
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]
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}
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],
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"execution_count": 1
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},
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{
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"cell_type": "code",
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"source": [
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"import shutil\n",
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"from pathlib import Path\n",
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"\n",
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"test_data_dir = Path(temp_dir)\n",
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"fv_input_file = test_data_dir / \"SimID_946368938_0_.fvinput\"\n",
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"vcg_file = test_data_dir / \"SimID_946368938_0_.vcg\"\n",
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"functions_file = test_data_dir / \"SimID_946368938_0_.functions\"\n",
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"test_output_dir = Path(os.getcwd()) / \"test_output\"\n",
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"\n",
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"shutil.copy(functions_file, test_output_dir)\n",
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"\n",
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"from pyvcell.solvers.fvsolver import solve\n",
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"try:\n",
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" ret_code = solve(input_file=fv_input_file, vcg_file=vcg_file, output_dir=test_output_dir)\n",
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" print(f\"Return code: {ret_code}\")\n",
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"except ValueError as e:\n",
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" print(f\"Error: {e}\")\n",
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"\n"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:19:41.486252Z",
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"start_time": "2025-01-23T23:19:40.386826Z"
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}
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},
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"id": "902c6d3a8dc70af",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"initializing mesh\n",
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"Return code: 0\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"Simulation Complete in Main() ... \n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"numVolume=126025\n",
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"\n",
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"CartesianMesh::computeNormalsFromNeighbors(), compute normals from neighbors\n",
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"Membrane Elements -> N=7817\n",
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"==============================================\n",
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"--------Num of points that have zero neighbors 0\n",
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"--------Num Neighbors before symmetrize 46161\n",
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"--------Num Neighbors after symmetrize 51016\n",
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"Total volume=5824.650822\n",
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"Total FluxArea =36.79383373\n",
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"Total FluxAreaXM =0\n",
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"Total FluxAreaXP =0\n",
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"Total FluxAreaYM =21.43445916\n",
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"Total FluxAreaYP =15.35937457\n",
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"Total FluxAreaZM =0\n",
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"Total FluxAreaZP =0\n",
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"mesh initialized\n",
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"preprocessing finished\n",
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"pdeCount=4, odeCount=0\n",
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"error opening log file </Users/jimschaff/Documents/workspace/pyvcell/examples/test_output/SimID_946368938_0_.log>\n",
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"simulation [SimID_946368938_0_] started\n",
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"temporary directory used is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/\n",
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"sim file name is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/SimID_946368938_0_0000.sim\n",
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"**This is a little endian machine.**\n",
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"[[[data:0]]]\n",
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"numVolRegions=6\n",
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"Region 0: size=110800, offset=0\n",
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"Region 1: size=12207, offset=110800\n",
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"Region 2: size=1, offset=123007\n",
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"Region 3: size=1, offset=123008\n",
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"Region 4: size=1, offset=123009\n",
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"Region 5: size=3015, offset=123010\n",
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"# of active points = 126025\n",
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"Constant diffusion/advection in region cytosol1\n",
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"Constant diffusion/advection in region cytosol2\n",
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"Constant diffusion/advection in region cytosol3\n",
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"Constant diffusion/advection in region cytosol4\n",
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"Constant diffusion/advection in region Nucleus5\n",
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"numUnknowns = 39645\n",
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"\n",
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"****** using Sundials CVode with PREC_LEFT, relTol=1e-07, absTol=1e-09, maxStep=0.1\n",
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"\n",
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"----------------------------------\n",
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"sundials pde solver is starting from time 0\n",
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"----------------------------------\n",
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"temporary directory used is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/\n",
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"sim file name is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/SimID_946368938_0_0001.sim\n",
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"[[[data:0.25]]]temporary directory used is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/\n",
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"sim file name is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/SimID_946368938_0_0002.sim\n",
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"[[[data:0.5]]]temporary directory used is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/\n",
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"sim file name is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/SimID_946368938_0_0003.sim\n",
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"[[[data:0.75]]]\n",
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"Final Statistics.. \n",
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"\n",
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"lenrw = 396539 leniw = 50\n",
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"lenrwLS = 396496 leniwLS = 10\n",
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"nst = 63\n",
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"nfe = 76 nfeLS = 87\n",
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"nni = 72 nli = 87\n",
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"nsetups = 22 netf = 0\n",
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"npe = 2 nps = 147\n",
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"ncfn = 0 ncfl = 0\n",
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"last step = 0.017509\n",
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"\n",
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"temporary directory used is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/\n",
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"sim file name is /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/SimID_946368938_0_0004.sim\n",
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"[[[data:1]]][[[progress:100%]]]"
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]
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}
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],
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"execution_count": 4
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},
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{
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"cell_type": "code",
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"id": "ed266f9194abb748",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:22:08.523252Z",
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"start_time": "2025-01-23T23:22:08.520883Z"
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}
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},
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"source": [
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"import os\n",
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"with os.scandir(test_output_dir) as entries:\n",
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" for entry in entries:\n",
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" print(entry.name)"
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],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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".placeholder\n",
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"SimID_946368938_0_.hdf5\n",
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"SimID_946368938_0_.mesh\n",
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"SimID_946368938_0_.log\n",
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"SimID_946368938_0_.meshmetrics\n",
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"SimID_946368938_0_00.zip\n",
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"SimID_946368938_0_.functions\n"
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]
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}
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],
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"execution_count": 7
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.2"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎examples/test_output/.placeholder‎

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‎examples/vcell_publications.ipynb‎

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{
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"cell_type": "code",
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"source": [
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"from IPython.display import display\n",
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"from pyvcell.api.vcell_client import ApiClient, Configuration, PublicationResourceApi\n",
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"from pyvcell.api.vcell_client.auth.auth_utils import login_interactive\n",
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"from pyvcell.api.vcell_client.models import Publication"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:37.703710Z",
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"start_time": "2025-01-23T07:43:37.701027Z"
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"start_time": "2025-01-23T23:24:17.359245Z"
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}
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},
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"id": "5e183b4a68315dfe",
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"outputs": [],
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"execution_count": 2
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"execution_count": 1
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"start_time": "2025-01-23T07:43:37.723335Z"
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"end_time": "2025-01-23T23:24:18.612189Z",
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"start_time": "2025-01-23T23:24:18.610330Z"
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}
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},
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"id": "902c6d3a8dc70af",
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"outputs": [],
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"execution_count": 2
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},
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"cell_type": "markdown",
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{
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"cell_type": "code",
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"source": [
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"from IPython.display import display\n",
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"\n",
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"public_publication_api = PublicationResourceApi(public_client)\n",
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"pubs: list[Publication] = public_publication_api.get_publications()\n",
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"display(pubs[0])"
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],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"start_time": "2025-01-23T07:43:37.735773Z"
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"end_time": "2025-01-23T23:24:19.365418Z",
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"start_time": "2025-01-23T23:24:18.663169Z"
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}
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},
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"id": "9ba5b1ac2df17231",
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"outputs": [
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{
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"data": {
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"text/plain": [
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"Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"cell_type": "markdown",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T23:24:20.900935Z",
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"start_time": "2025-01-23T23:24:19.375651Z"
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}
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"authenticated_client = login_interactive(api_base_url=api_url, client_id=client_id, issuer_url=issuer_url)\n",
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"display(\"may loose focus to the browser window for login, switch back to this notebook after login.\")"
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],
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"outputs": [
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"data": {
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"'may loose focus to the browser window for login, switch back to this notebook after login.'"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"start_time": "2025-01-23T07:43:46.852654Z"
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"end_time": "2025-01-23T23:24:21.114730Z",
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"start_time": "2025-01-23T23:24:20.912950Z"
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}
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},
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"source": [
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"publication_api = PublicationResourceApi(authenticated_client)\n",
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"pubs: list[Publication] = publication_api.get_publications()\n",
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"display(pubs[0])"
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],
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"outputs": [
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{
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"data": {
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"text/plain": [
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"Publication(pub_key=279906235, title='A continuum model of mechanosensation based on contractility kit assembly', authors=['Dolgitzer', ' D.', ' Plaza-Rodríguez', ' A. I.', ' Iglesias', ' M. A.', ' Jacob', ' M. A. C.', ' Todd', ' B.', ' Robinson', ' D. N.', ' & Iglesias', ' P. A.'], year=2024, citation='Biophys J. 2024 Nov 8:S0006-3495(24)00708-2', pubmedid='39521955', doi='https://doi.org/10.1016/j.bpj.2024.10.020', endnoteid=0, url='url', wittid=0, biomodel_refs=[BiomodelRef(bm_key=279851639, name='Dolgitzer 2025 A Continuum Model of Mechanosensation Based on Contractility Kit Assembly', owner_name='Dolgitzer', owner_key=259537152, version_flag=3)], mathmodel_refs=[], var_date=datetime.date(2024, 11, 26))"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"execution_count": 6
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"outputs": [],
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"execution_count": 5
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},
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"id": "ed266f9194abb748",
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"metadata": {
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"collapsed": false,
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"ExecuteTime": {
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"end_time": "2025-01-23T07:43:47.026801Z",
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"start_time": "2025-01-23T07:43:47.025477Z"
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"end_time": "2025-01-23T23:24:21.125418Z",
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"start_time": "2025-01-23T23:24:21.123871Z"
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}
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},
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"source": [],

‎scripts/run_notebook.sh‎

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#!/bin/bash
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set -ex
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ROOT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && cd .. && pwd )"
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cd ${ROOT_DIR} || (echo "Failed to cd into ${ROOT_DIR}" && exit 1)
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python -m venv .venv_jupyter
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source .venv_jupyter/bin/activate
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pip install jupyter ipython
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poetry install
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jupyter notebook

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