cardiac-geometriesx 0.1.2__tar.gz → 0.2.0__tar.gz

cardiac_geometriesx-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Computational Physiology at Simula Research Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

cardiac_geometriesx-0.2.0/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.1
+Name: cardiac-geometriesx
+Version: 0.2.0
+Summary: A python library for cardiac geometries
+Author-email: Henrik Finsberg <henriknf@simula.no>
+License: MIT
+Project-URL: Homepage, https://github.com/finsberg/cardiac-geometriesx
+Keywords: cardiac,geometry
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fenics-dolfinx>=0.8.0
+Requires-Dist: structlog
+Requires-Dist: cardiac-geometries-core
+Requires-Dist: rich-click
+Requires-Dist: adios4dolfinx
+Provides-Extra: dev
+Requires-Dist: bump-my-version; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Requires-Dist: wheel; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: jupyter-book; extra == "docs"
+Requires-Dist: jupytext; extra == "docs"
+Requires-Dist: jupyter; extra == "docs"
+Requires-Dist: pyvista[all]>=0.43.0; extra == "docs"
+Requires-Dist: trame-vuetify; extra == "docs"
+Requires-Dist: ipywidgets; extra == "docs"
+Requires-Dist: fenicsx-ldrb; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pre-commit; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: gui
+Requires-Dist: streamlit; extra == "gui"
+Requires-Dist: stpyvista; extra == "gui"
+Requires-Dist: pyvista[all]>=0.43.0; extra == "gui"
+Requires-Dist: trame-vuetify; extra == "gui"
+Requires-Dist: ipywidgets; extra == "gui"
+Requires-Dist: fenicsx-ldrb; extra == "gui"
+
+![_](docs/_static/logo.png)
+
+[![Create and publish a Docker image](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/docker-image.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/docker-image.yml)
+[![Test package](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test.yml)
+[![Test package MPI](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test-mpi.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test-mpi.yml)
+[![Pre-commit](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/pre-commit.yml)
+[![PyPI version](https://badge.fury.io/py/cardiac-geometriesx.svg)](https://badge.fury.io/py/cardiac-geometriesx)
+
+# Cardiac geometries
+
+Cardiac geometries is a software package built on top of [`cariac-geometries-core`](https://github.com/ComputationalPhysiology/cardiac-geometries-core) that adds support for creating idealized cardiac geometries for dolfinx.
+
+There are two ways you can use `cardiac-geomtries`, either using the command line interface, e.g
+```
+geox lv-ellipsoid --create-fibers lv-mesh --fiber-space P_2
+```
+
+or using the python API e.g
+```python
+geo =  cardiac_geometries.mesh.lv_ellipsoid(outdir="lv-mesh", create_fibers=True, fiber_space="P_2")
+```
+
+## Install
+
+To install the package you can use `pip`
+```
+python3 -m pip install cardiac-geometriesx
+```
+however, this assumes that you already have `dolfinx` pre-installed. You can also use the provided docker image e.g
+```
+docker pull ghcr.io/computationalphysiology/cardiac-geometriesx:latest
+```
+To start a new container interactive you can do
+```
+docker run --name geox -v $PWD:/home/shared -w /home/shared -it ghcr.io/computationalphysiology/cardiac-geometriesx:latest
+```
+or if you just want to create a mesh and exit you can run the command line interface directly e.g
+```
+docker run --rm -v $PWD:/home/shared -w /home/shared -it ghcr.io/computationalphysiology/cardiac-geometriesx:latest geox lv-ellipsoid --create-fibers lv-mesh --fiber-space P_2
+```
+
+## Authors
+Henrik Finsberg (henriknf@simula.no)
+
+## License
+MIT
+
+## Contributing

cardiac_geometriesx-0.2.0/README.md

@@ -0,0 +1,48 @@
+![_](docs/_static/logo.png)
+
+[![Create and publish a Docker image](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/docker-image.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/docker-image.yml)
+[![Test package](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test.yml)
+[![Test package MPI](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test-mpi.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/test-mpi.yml)
+[![Pre-commit](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/pre-commit.yml/badge.svg)](https://github.com/ComputationalPhysiology/cardiac-geometriesx/actions/workflows/pre-commit.yml)
+[![PyPI version](https://badge.fury.io/py/cardiac-geometriesx.svg)](https://badge.fury.io/py/cardiac-geometriesx)
+
+# Cardiac geometries
+
+Cardiac geometries is a software package built on top of [`cariac-geometries-core`](https://github.com/ComputationalPhysiology/cardiac-geometries-core) that adds support for creating idealized cardiac geometries for dolfinx.
+
+There are two ways you can use `cardiac-geomtries`, either using the command line interface, e.g
+```
+geox lv-ellipsoid --create-fibers lv-mesh --fiber-space P_2
+```
+
+or using the python API e.g
+```python
+geo =  cardiac_geometries.mesh.lv_ellipsoid(outdir="lv-mesh", create_fibers=True, fiber_space="P_2")
+```
+
+## Install
+
+To install the package you can use `pip`
+```
+python3 -m pip install cardiac-geometriesx
+```
+however, this assumes that you already have `dolfinx` pre-installed. You can also use the provided docker image e.g
+```
+docker pull ghcr.io/computationalphysiology/cardiac-geometriesx:latest
+```
+To start a new container interactive you can do
+```
+docker run --name geox -v $PWD:/home/shared -w /home/shared -it ghcr.io/computationalphysiology/cardiac-geometriesx:latest
+```
+or if you just want to create a mesh and exit you can run the command line interface directly e.g
+```
+docker run --rm -v $PWD:/home/shared -w /home/shared -it ghcr.io/computationalphysiology/cardiac-geometriesx:latest geox lv-ellipsoid --create-fibers lv-mesh --fiber-space P_2
+```
+
+## Authors
+Henrik Finsberg (henriknf@simula.no)
+
+## License
+MIT
+
+## Contributing

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "cardiac-geometriesx"
-version = "0.1.2"
+version = "0.2.0"
 description = "A python library for cardiac geometries"
 authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
 license = {text = "MIT"}
@@ -38,12 +38,28 @@ dev = [
     "wheel",
 ]
 docs = [
+    "jupyter-book",
+    "jupytext",
+    "jupyter",
+    "pyvista[all]>=0.43.0",
+    "trame-vuetify",
+    "ipywidgets",
+    "fenicsx-ldrb",
 ]
 test = [
     "pre-commit",
     "pytest",
     "pytest-cov",
 ]
+gui = [
+    "streamlit",
+    "stpyvista",
+    "pyvista[all]>=0.43.0",
+    "trame-vuetify",
+    "ipywidgets",
+    "fenicsx-ldrb",
+
+]
 
 [project.scripts]
 geox = "cardiac_geometries.cli:app"
@@ -80,6 +96,7 @@ exclude = [
 
 # Exclude a variety of commonly ignored directories.
 exclude = [
+    "demos/*.py",
     ".bzr",
     ".direnv",
     ".eggs",
@@ -156,7 +173,7 @@ tag = true
 sign_tags = false
 tag_name = "v{new_version}"
 tag_message = "Bump version: {current_version} → {new_version}"
-current_version = "0.1.2"
+current_version = "0.2.0"
 
 
 [[tool.bumpversion.files]]

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/src/cardiac_geometries/cli.py

@@ -8,8 +8,10 @@ from . import mesh
 
 meta = metadata("cardiac-geometriesx")
 __version__ = meta["Version"]
-__author__ = meta["Author"]
+__author__ = meta["Author-email"]
 __license__ = meta["License"]
+__email__ = meta["Author-email"]
+__program_name__ = meta["Name"]
 
 
 @click.group()
@@ -867,8 +869,20 @@ def slab_in_bath(
     geo.save(outdir / "slab_in_bath.bp")
 
 
+@click.command("gui")
+def gui():
+    # Make sure we can import the required packages
+    from . import gui  # noqa: F401
+
+    gui_path = Path(__file__).parent.joinpath("gui.py")
+    import subprocess as sp
+
+    sp.run(["streamlit", "run", gui_path.as_posix()])
+
+
 app.add_command(lv_ellipsoid)
 app.add_command(biv_ellipsoid)
 app.add_command(biv_ellipsoid_torso)
 app.add_command(slab)
 app.add_command(slab_in_bath)
+app.add_command(gui)

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/src/cardiac_geometries/fibers/lv_ellipsoid.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 
-import basix
 import dolfinx
 import numpy as np
 
+from ..utils import space_from_string
 from . import utils
 
 
@@ -82,14 +82,9 @@ def compute_system(
     s0 = np.cross(f0, n0, axis=0)
     s0 = utils.normalize(s0)
 
-    el = basix.ufl.element(
-        element.family_name,
-        mesh.ufl_cell().cellname(),
-        degree=element.degree,
-        discontinuous=element.discontinuous,
-        shape=(mesh.geometry.dim,),
+    Vv = space_from_string(
+        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
     )
-    Vv = dolfinx.fem.functionspace(mesh, el)
 
     fiber = dolfinx.fem.Function(Vv)
     norm_f = np.linalg.norm(f0, axis=0)
@@ -131,10 +126,13 @@ def create_microstructure(
     )
 
     if outdir is not None:
-        with dolfinx.io.VTXWriter(
-            mesh.comm, Path(outdir) / "laplace.bp", [t], engine="BP4"
-        ) as file:
-            file.write(0.0)
+        try:
+            with dolfinx.io.VTXWriter(
+                mesh.comm, Path(outdir) / "laplace.bp", [t], engine="BP4"
+            ) as file:
+                file.write(0.0)
+        except RuntimeError:
+            pass
 
     system = compute_system(
         t,

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/src/cardiac_geometries/fibers/slab.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 
-import basix
 import dolfinx
 import numpy as np
 
+from ..utils import space_from_string
 from . import utils
 
 
@@ -59,14 +59,9 @@ def compute_system(
     n0 = np.cross(f0, s0, axis=0)
     n0 = utils.normalize(n0)
 
-    el = basix.ufl.element(
-        element.family_name,
-        mesh.ufl_cell().cellname(),
-        degree=element.degree,
-        discontinuous=element.discontinuous,
-        shape=(mesh.geometry.dim,),
+    Vv = space_from_string(
+        space_string=f"{element.family_name}_{element.degree}", mesh=mesh, dim=mesh.geometry.dim
     )
-    Vv = dolfinx.fem.functionspace(mesh, el)
 
     fiber = dolfinx.fem.Function(Vv)
     norm_f = np.linalg.norm(f0, axis=0)
@@ -134,10 +129,13 @@ def create_microstructure(
         function_space=function_space,
     )
     if outdir is not None:
-        with dolfinx.io.VTXWriter(
-            mesh.comm, Path(outdir) / "laplace.bp", [t], engine="BP4"
-        ) as file:
-            file.write(0.0)
+        try:
+            with dolfinx.io.VTXWriter(
+                mesh.comm, Path(outdir) / "laplace.bp", [t], engine="BP4"
+            ) as file:
+                file.write(0.0)
+        except RuntimeError:
+            pass
 
     system = compute_system(
         t,

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/src/cardiac_geometries/fibers/utils.py

@@ -7,6 +7,8 @@ import numpy as np
 import ufl
 from dolfinx.fem.petsc import LinearProblem
 
+from ..utils import space_from_string
+
 
 class Microstructure(NamedTuple):
     f0: dolfinx.fem.Function
@@ -20,17 +22,20 @@ def save_microstructure(
     from ..utils import element2array
 
     # Save for paraview visualization
-    with dolfinx.io.VTXWriter(
-        mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
-    ) as file:
-        file.write(0.0)
+    try:
+        with dolfinx.io.VTXWriter(
+            mesh.comm, Path(outdir) / "microstructure-viz.bp", functions, engine="BP4"
+        ) as file:
+            file.write(0.0)
+    except RuntimeError:
+        pass
 
     # Save with proper function space
     filename = Path(outdir) / "microstructure.bp"
     for function in functions:
         adios4dolfinx.write_function(u=function, filename=filename)
 
-    attributes = {f.name: element2array(f.ufl_element().basix_element) for f in functions}
+    attributes = {f.name: element2array(f.ufl_element()) for f in functions}
     adios4dolfinx.write_attributes(
         comm=mesh.comm,
         filename=filename,
@@ -73,10 +78,10 @@ def laplace(
     uh = problem.solve()
 
     if function_space != "P_1":
-        family, degree = function_space.split("_")
-        W = dolfinx.fem.functionspace(mesh, (family, int(degree)))
+        W = space_from_string(function_space, mesh, dim=1)
         t = dolfinx.fem.Function(W)
-        t.interpolate(uh)
+        expr = dolfinx.fem.Expression(uh, W.element.interpolation_points())
+        t.interpolate(expr)
     else:
         t = uh
 

{cardiac_geometriesx-0.1.2 → cardiac_geometriesx-0.2.0}/src/cardiac_geometries/geometry.py

@@ -15,9 +15,11 @@ from . import utils
 @dataclass  # (frozen=True, slots=True)
 class Geometry:
     mesh: dolfinx.mesh.Mesh
-    markers: dict[str, tuple[str, str]] = field(default_factory=dict)
-    ffun: dolfinx.mesh.MeshTags | None = None
+    markers: dict[str, tuple[int, int]] = field(default_factory=dict)
     cfun: dolfinx.mesh.MeshTags | None = None
+    ffun: dolfinx.mesh.MeshTags | None = None
+    efun: dolfinx.mesh.MeshTags | None = None
+    vfun: dolfinx.mesh.MeshTags | None = None
     f0: dolfinx.fem.Function | None = None
     s0: dolfinx.fem.Function | None = None
     n0: dolfinx.fem.Function | None = None
@@ -25,8 +27,7 @@ class Geometry:
     def save(self, path: str | Path) -> None:
         path = Path(path)
 
-        if path.exists() and self.mesh.comm.rank == 0:
-            shutil.rmtree(path)
+        shutil.rmtree(path, ignore_errors=True)
         self.mesh.comm.barrier()
         adios4dolfinx.write_mesh(mesh=self.mesh, filename=path)
 
@@ -37,15 +38,37 @@ class Geometry:
             attributes={k: np.array(v, dtype=np.uint8) for k, v in self.markers.items()},
         )
 
+        if self.cfun is not None:
+            adios4dolfinx.write_meshtags(
+                meshtags=self.cfun,
+                mesh=self.mesh,
+                filename=path,
+                meshtag_name="Cell tags",
+            )
         if self.ffun is not None:
             adios4dolfinx.write_meshtags(
                 meshtags=self.ffun,
                 mesh=self.mesh,
                 filename=path,
+                meshtag_name="Facet tags",
+            )
+        if self.efun is not None:
+            adios4dolfinx.write_meshtags(
+                meshtags=self.efun,
+                mesh=self.mesh,
+                filename=path,
+                meshtag_name="Edge tags",
+            )
+        if self.vfun is not None:
+            adios4dolfinx.write_meshtags(
+                meshtags=self.vfun,
+                mesh=self.mesh,
+                filename=path,
+                meshtag_name="Vertex tags",
             )
 
         if self.f0 is not None:
-            el = self.f0.ufl_element().basix_element
+            el = self.f0.ufl_element()
             arr = utils.element2array(el)
 
             adios4dolfinx.write_attributes(
@@ -60,26 +83,49 @@ class Geometry:
         if self.n0 is not None:
             adios4dolfinx.write_function(u=self.n0, filename=path, name="n0")
 
+        self.mesh.comm.barrier()
+
     @classmethod
     def from_file(cls, comm: MPI.Intracomm, path: str | Path) -> "Geometry":
         path = Path(path)
+
         mesh = adios4dolfinx.read_mesh(comm=comm, filename=path)
         markers = adios4dolfinx.read_attributes(comm=comm, filename=path, name="markers")
-        ffun = adios4dolfinx.read_meshtags(mesh=mesh, meshtag_name="Facet tags", filename=path)
+        tags = {}
+        for name, meshtag_name in (
+            ("cfun", "Cell tags"),
+            ("ffun", "Facet tags"),
+            ("efun", "Edge tags"),
+            ("vfun", "Vertex tags"),
+        ):
+            try:
+                tags[name] = adios4dolfinx.read_meshtags(
+                    mesh=mesh, meshtag_name=meshtag_name, filename=path
+                )
+            except KeyError:
+                tags[name] = None
+
+        functions = {}
         function_space = adios4dolfinx.read_attributes(
             comm=comm, filename=path, name="function_space"
         )
-        element = utils.array2element(function_space["f0"])
-        # Assume same function space for all functions
-        V = dolfinx.fem.functionspace(mesh, element)
-        f0 = dolfinx.fem.Function(V, name="f0")
-        s0 = dolfinx.fem.Function(V, name="s0")
-        n0 = dolfinx.fem.Function(V, name="n0")
-
-        adios4dolfinx.read_function(u=f0, filename=path, name="f0")
-        adios4dolfinx.read_function(u=s0, filename=path, name="s0")
-        adios4dolfinx.read_function(u=n0, filename=path, name="n0")
-        return cls(mesh=mesh, markers=markers, ffun=ffun, f0=f0, s0=s0, n0=n0)
+        for name, el in function_space.items():
+            element = utils.array2element(el)
+            V = dolfinx.fem.functionspace(mesh, element)
+            f = dolfinx.fem.Function(V, name=name)
+            try:
+                adios4dolfinx.read_function(u=f, filename=path, name=name)
+            except KeyError:
+                continue
+            else:
+                functions[name] = f
+
+        return cls(
+            mesh=mesh,
+            markers=markers,
+            **functions,
+            **tags,
+        )
 
     @classmethod
     def from_folder(cls, comm: MPI.Intracomm, folder: str | Path) -> "Geometry":
@@ -87,7 +133,7 @@ class Geometry:
 
         # Read mesh
         if (folder / "mesh.xdmf").exists():
-            mesh, cfun, ffun = utils.read_mesh(comm=comm, filename=folder / "mesh.xdmf")
+            mesh, tags = utils.read_mesh(comm=comm, filename=folder / "mesh.xdmf")
         else:
             raise ValueError("No mesh file found")
 
@@ -101,22 +147,26 @@ class Geometry:
         else:
             markers = {}
 
+        functions = {}
         microstructure_path = folder / "microstructure.bp"
         if microstructure_path.exists():
             function_space = adios4dolfinx.read_attributes(
                 comm=MPI.COMM_WORLD, filename=microstructure_path, name="function_space"
             )
-            # Assume same function space for all functions
-            element = utils.array2element(function_space["f0"])
-            V = dolfinx.fem.functionspace(mesh, element)
-            f0 = dolfinx.fem.Function(V, name="f0")
-            s0 = dolfinx.fem.Function(V, name="s0")
-            n0 = dolfinx.fem.Function(V, name="n0")
-
-            adios4dolfinx.read_function(u=f0, filename=microstructure_path, name="f0")
-            adios4dolfinx.read_function(u=s0, filename=microstructure_path, name="s0")
-            adios4dolfinx.read_function(u=n0, filename=microstructure_path, name="n0")
-        else:
-            f0 = s0 = n0 = None
-
-        return cls(mesh=mesh, ffun=ffun, cfun=cfun, markers=markers, f0=f0, s0=s0, n0=n0)
+            for name, el in function_space.items():
+                element = utils.array2element(el)
+                V = dolfinx.fem.functionspace(mesh, element)
+                f = dolfinx.fem.Function(V, name=name)
+                try:
+                    adios4dolfinx.read_function(u=f, filename=microstructure_path, name=name)
+                except KeyError:
+                    continue
+                else:
+                    functions[name] = f
+
+        return cls(
+            mesh=mesh,
+            markers=markers,
+            **functions,
+            **tags,
+        )