add support for image-based field data

.editorconfig

@@ -1,3 +1,4 @@
+[*.py]
 max_line_length = 120
 
 [*.json]

examples/scripts/fielddata_workflow.py

@@ -1,52 +1,53 @@
 import os
 import shutil
+import tempfile
 from pathlib import Path
 
 from pyvcell.vcml import Simulation, VcmlReader
 from pyvcell.vcml.vcml_simulation import VcmlSpatialSimulation as Solver
 
-# ----- make a workspace
-workspace_dir = Path(os.getcwd()) / "workspace"
-sim1_dir = workspace_dir / "sim1_dir"
-if sim1_dir.exists():
-    shutil.rmtree(sim1_dir)
-sim2_dir = workspace_dir / "sim2_dir"
-if sim2_dir.exists():
-    shutil.rmtree(sim2_dir)
-
-# ---- read in VCML file
-model_fp = Path(os.getcwd()).parent / "models" / "SmallSpatialProject_3D.vcml"
-bio_model1 = VcmlReader.biomodel_from_file(model_fp)
-
-# ---- get the application and the species mappings for species "s0" and "s1"
-app = bio_model1.applications[0]
-s1_mapping = next(s for s in app.species_mappings if s.species_name == "s1")
-s0_mapping = next(s for s in app.species_mappings if s.species_name == "s0")
-
-# ---- add a simulation to the first application in the biomodel (didn't already have a simulation in the VCML file)
-new_sim = Simulation(name="new_sim", duration=10.0, output_time_step=0.1, mesh_size=(20, 20, 20))
-app.simulations.append(new_sim)
-
-# ---- set the initial concentration of species "s0" and "s1" in the first application
-s0_mapping.init_conc = "3+sin(x)+cos(y)+sin(z)"
-s1_mapping.init_conc = "3+sin(x+y+z)"
-
-# ---- run simulation, store in sim1_dir, and plot results
-# >>>>> This forms the data for the "Field Data" identified by 'sim1_dir' <<<<<<
-sim1_result = Solver(bio_model=bio_model1, out_dir=sim1_dir).run(new_sim.name)
-print([c.label for c in sim1_result.channel_data])
-print(sim1_result.time_points[::11])
-sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
-sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
-sim1_result.plotter.plot_concentrations()
-
-
-# ----- use field data from sim1_dir to set initial concentration of species "s0"
-s0_mapping.init_conc = "vcField('sim1_dir','s0',0.0,'Volume') * vcField('sim1_dir','s1',0.0,'Volume')"
-s1_mapping.init_conc = "5.0"
-# ---- re-run simulation and store in sim2_dir
-# note that the solution of s0 draws from the data from sim1_dir
-sim2_result = Solver(bio_model=bio_model1, out_dir=sim2_dir).run(new_sim.name)
-sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
-sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
-sim2_result.plotter.plot_concentrations()
+with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir:
+    # ----- make a workspace
+    workspace_dir = temp_dir / "workspace"
+    sim1_dir = workspace_dir / "sim1_dir"
+    if sim1_dir.exists():
+        shutil.rmtree(sim1_dir)
+    sim2_dir = workspace_dir / "sim2_dir"
+    if sim2_dir.exists():
+        shutil.rmtree(sim2_dir)
+
+    # ---- read in VCML file
+    model_fp = Path(os.getcwd()).parent / "models" / "SmallSpatialProject_3D.vcml"
+    bio_model1 = VcmlReader.biomodel_from_file(model_fp)
+
+    # ---- get the application and the species mappings for species "s0" and "s1"
+    app = bio_model1.applications[0]
+    s1_mapping = next(s for s in app.species_mappings if s.species_name == "s1")
+    s0_mapping = next(s for s in app.species_mappings if s.species_name == "s0")
+
+    # ---- add a simulation to the first application in the biomodel (didn't already have a simulation in the VCML file)
+    new_sim = Simulation(name="new_sim", duration=10.0, output_time_step=0.1, mesh_size=(20, 20, 20))
+    app.simulations.append(new_sim)
+
+    # ---- set the initial concentration of species "s0" and "s1" in the first application
+    s0_mapping.init_conc = "3+sin(x)+cos(y)+sin(z)"
+    s1_mapping.init_conc = "3+sin(x+y+z)"
+
+    # ---- run simulation, store in sim1_dir, and plot results
+    # >>>>> This forms the data for the "Field Data" identified by 'sim1_dir' <<<<<<
+    sim1_result = Solver(bio_model=bio_model1, out_dir=sim1_dir).run(new_sim.name)
+    print([c.label for c in sim1_result.channel_data])
+    print(sim1_result.time_points[::11])
+    sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
+    sim1_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
+    sim1_result.plotter.plot_concentrations()
+
+    # ----- use field data from sim1_dir to set initial concentration of species "s0"
+    s0_mapping.init_conc = "vcField('sim1_dir','s0',0.0,'Volume') * vcField('sim1_dir','s1',0.0,'Volume')"
+    s1_mapping.init_conc = "5.0"
+    # ---- re-run simulation and store in sim2_dir
+    # note that the solution of s0 draws from the data from sim1_dir
+    sim2_result = Solver(bio_model=bio_model1, out_dir=sim2_dir).run(new_sim.name)
+    sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s0")
+    sim2_result.plotter.plot_slice_3d(time_index=0, channel_id="s1")
+    sim2_result.plotter.plot_concentrations()