pyvcell 0.0.1__tar.gz

pyvcell-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024, Jim Schaff
+
+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.

pyvcell-0.0.1/PKG-INFO

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+Metadata-Version: 2.1
+Name: pyvcell
+Version: 0.0.1
+Summary: This is the python wrapper for vcell modeling and simulation
+Home-page: https://github.com/virtualcell/pyvcell
+Author: Jim Schaff
+Author-email: fschaff@uchc.edu
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: h5py (>=3.11.0,<4.0.0)
+Requires-Dist: numexpr (>=2.10.0,<3.0.0)
+Requires-Dist: numpy (>=1.26.4,<2.0.0)
+Requires-Dist: orjson (>=3.10.3,<4.0.0)
+Requires-Dist: pyvcell-fvsolver (>=0.0.4,<0.0.5)
+Requires-Dist: typer (>=0.12.3,<0.13.0)
+Requires-Dist: vtk (>=9.3.1,<10.0.0)
+Requires-Dist: zarr (>=2.17.2,<3.0.0)
+Project-URL: Documentation, https://virtualcell.github.io/pyvcell/
+Project-URL: Repository, https://github.com/virtualcell/pyvcell
+Description-Content-Type: text/markdown
+
+# pyvcell
+
+[![Release](https://img.shields.io/github/v/release/virtualcell/pyvcell)](https://img.shields.io/github/v/release/virtualcell/pyvcell)
+[![Build status](https://img.shields.io/github/actions/workflow/status/virtualcell/pyvcell/main.yml?branch=main)](https://github.com/virtualcell/pyvcell/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/virtualcell/pyvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/pyvcell)
+[![Commit activity](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)
+[![License](https://img.shields.io/github/license/virtualcell/pyvcell)](https://img.shields.io/github/license/virtualcell/pyvcell)
+
+This is the python wrapper for vcell modeling and simulation
+
+- **Github repository**: <https://github.com/virtualcell/pyvcell/>
+- **Documentation** <https://virtualcell.github.io/pyvcell/>
+
+## Getting started with your project
+
+First, create a repository on GitHub with the same name as this project, and then run the following commands:
+
+```bash
+git init -b main
+git add .
+git commit -m "init commit"
+git remote add origin git@github.com:virtualcell/pyvcell.git
+git push -u origin main
+```
+
+Finally, install the environment and the pre-commit hooks with
+
+```bash
+make install
+```
+
+You are now ready to start development on your project!
+The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+
+To finalize the set-up for publishing to PyPi or Artifactory, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/publishing/#set-up-for-pypi).
+For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/mkdocs/#enabling-the-documentation-on-github).
+To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/codecov/).
+
+## Releasing a new version
+
+- Create an API Token on [Pypi](https://pypi.org/).
+- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/virtualcell/pyvcell/settings/secrets/actions/new).
+- Create a [new release](https://github.com/virtualcell/pyvcell/releases/new) on Github.
+- Create a new tag in the form `*.*.*`.
+
+For more details, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/cicd/#how-to-trigger-a-release).
+
+---
+
+Repository initiated with [fpgmaas/cookiecutter-poetry](https://github.com/fpgmaas/cookiecutter-poetry).
+

pyvcell-0.0.1/README.md

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+# pyvcell
+
+[![Release](https://img.shields.io/github/v/release/virtualcell/pyvcell)](https://img.shields.io/github/v/release/virtualcell/pyvcell)
+[![Build status](https://img.shields.io/github/actions/workflow/status/virtualcell/pyvcell/main.yml?branch=main)](https://github.com/virtualcell/pyvcell/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/virtualcell/pyvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/pyvcell)
+[![Commit activity](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)
+[![License](https://img.shields.io/github/license/virtualcell/pyvcell)](https://img.shields.io/github/license/virtualcell/pyvcell)
+
+This is the python wrapper for vcell modeling and simulation
+
+- **Github repository**: <https://github.com/virtualcell/pyvcell/>
+- **Documentation** <https://virtualcell.github.io/pyvcell/>
+
+## Getting started with your project
+
+First, create a repository on GitHub with the same name as this project, and then run the following commands:
+
+```bash
+git init -b main
+git add .
+git commit -m "init commit"
+git remote add origin git@github.com:virtualcell/pyvcell.git
+git push -u origin main
+```
+
+Finally, install the environment and the pre-commit hooks with
+
+```bash
+make install
+```
+
+You are now ready to start development on your project!
+The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+
+To finalize the set-up for publishing to PyPi or Artifactory, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/publishing/#set-up-for-pypi).
+For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/mkdocs/#enabling-the-documentation-on-github).
+To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/codecov/).
+
+## Releasing a new version
+
+- Create an API Token on [Pypi](https://pypi.org/).
+- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/virtualcell/pyvcell/settings/secrets/actions/new).
+- Create a [new release](https://github.com/virtualcell/pyvcell/releases/new) on Github.
+- Create a new tag in the form `*.*.*`.
+
+For more details, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/cicd/#how-to-trigger-a-release).
+
+---
+
+Repository initiated with [fpgmaas/cookiecutter-poetry](https://github.com/fpgmaas/cookiecutter-poetry).

pyvcell-0.0.1/pyproject.toml

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+[tool.poetry]
+name = "pyvcell"
+version = "0.0.1"
+description = "This is the python wrapper for vcell modeling and simulation"
+authors = ["Jim Schaff <fschaff@uchc.edu>"]
+repository = "https://github.com/virtualcell/pyvcell"
+documentation = "https://virtualcell.github.io/pyvcell/"
+readme = "README.md"
+packages = [
+  {include = "pyvcell"}
+]
+
+[tool.poetry.dependencies]
+python = ">=3.10,<4.0"
+numexpr = "^2.10.0"
+zarr = "^2.17.2"
+h5py = "^3.11.0"
+numpy = "^1.26.4"
+orjson = "^3.10.3"
+vtk = "^9.3.1"
+pyvcell-fvsolver = "^0.0.4"
+typer = "^0.12.3"
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.2.0"
+pytest-cov = "^4.0.0"
+deptry = "^0.16.2"
+mypy = "^1.5.1"
+pre-commit = "^3.8.0"
+tox = "^4.11.1"
+h5py-stubs = "^0.1.1"
+
+[tool.poetry.group.docs.dependencies]
+mkdocs = "^1.4.2"
+mkdocs-material = "^9.2.7"
+mkdocstrings = {extras = ["python"], version = "^0.23.0"}
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.mypy]
+files = ["pyvcell"]
+disallow_untyped_defs = "True"
+disallow_any_unimported = "True"
+no_implicit_optional = "True"
+check_untyped_defs = "True"
+warn_return_any = "True"
+warn_unused_ignores = "True"
+show_error_codes = "True"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+target-version = "py39"
+line-length = 120
+fix = true
+select = [
+    # flake8-2020
+    "YTT",
+    # flake8-bandit
+    "S",
+    # flake8-bugbear
+    "B",
+    # flake8-builtins
+    "A",
+    # flake8-comprehensions
+    "C4",
+    # flake8-debugger
+    "T10",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # mccabe
+    "C90",
+    # pycodestyle
+    "E", "W",
+    # pyflakes
+    "F",
+    # pygrep-hooks
+    "PGH",
+    # pyupgrade
+    "UP",
+    # ruff
+    "RUF",
+    # tryceratops
+    "TRY",
+]
+ignore = [
+    # LineTooLong
+    "E501",
+    # DoNotAssignLambda
+    "E731",
+    # avoid specifiying long messages outside the exception class
+    "TRY003",
+    # avoid functions which are too complex
+    "C901",
+    # avoid uses of Uses of `tarfile.extractall()
+    "S202",
+    #  B008 Do not perform function call `typer.Argument` in argument defaults
+    "B008",
+]
+
+[tool.ruff.format]
+preview = true
+
+[tool.coverage.report]
+skip_empty = true
+
+[tool.coverage.run]
+branch = true
+source = ["pyvcell"]
+
+
+[tool.ruff.per-file-ignores]
+"tests/*" = ["S101"]

pyvcell-0.0.1/pyvcell/foo.py

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+def foo(bar: str) -> str:
+    """Summary line.
+
+    Extended description of function.
+
+    Args:
+        bar: Description of input argument.
+
+    Returns:
+        Description of return value
+    """
+
+    return bar
+
+
+if __name__ == "__main__":  # pragma: no cover
+    pass

pyvcell-0.0.1/pyvcell/simdata/main.py

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+from pathlib import Path
+
+import typer
+
+from pyvcell.simdata.mesh import CartesianMesh
+from pyvcell.simdata.simdata_models import DataFunctions, PdeDataSet
+from pyvcell.simdata.zarr_writer import write_zarr
+
+app = typer.Typer()
+
+
+@app.command(name="vc_to_zarr", help="Convert a VCell FiniteVolume simulation dataset to Zarr")
+def n5_to_zarr(
+    sim_data_dir: Path = typer.Argument(..., help="path to vcell dataset directory"),
+    sim_id: int = typer.Argument(..., help="simulation id (e.g. 946368938)"),
+    job_id: int = typer.Argument(..., help="job id (e.g. 0"),
+    zarr_path: Path = typer.Argument(..., help="path to zarr dataset to write to"),
+) -> None:
+    pde_dataset = PdeDataSet(base_dir=sim_data_dir, log_filename=f"SimID_{sim_id}_{job_id}_.log")
+    pde_dataset.read()
+    data_functions = DataFunctions(function_file=sim_data_dir / f"SimID_{sim_id}_{job_id}_.functions")
+    data_functions.read()
+    mesh = CartesianMesh(mesh_file=sim_data_dir / f"SimID_{sim_id}_{job_id}_.mesh")
+    mesh.read()
+
+    write_zarr(pde_dataset=pde_dataset, data_functions=data_functions, mesh=mesh, zarr_dir=zarr_path)
+
+
+def main() -> None:
+    app()
+
+
+if __name__ == "__main__":
+    main()

pyvcell-0.0.1/pyvcell/simdata/mesh.py

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+import zlib
+from pathlib import Path
+
+import numpy as np
+
+from pyvcell.simdata.vtk.vismesh import Box3D
+
+
+class CartesianMesh:
+    """
+    reads the .mesh file and extracts the mesh information
+
+    Example .mesh file:
+    Version 1.2
+    CartesianMesh {
+        //              X          Y          Z
+        Size           71         71         25
+        Extent 74.239999999999995 74.239999999999995         26
+        Origin          0          0          0
+
+        VolumeRegionsMapSubvolume {
+        6
+        //VolRegID   SubvolID     Volume
+                 0          0 124767.54117864356 //ec
+                 1          1 14855.904388351477 //cytosol
+                 2          1 1.2185460680272107 //cytosol
+                 3          1 1.2185460680272107 //cytosol
+                 4          1 1.2185460680272107 //cytosol
+                 5          2 3673.9163951019395 //Nucleus
+        }
+
+        MembraneRegionsMapVolumeRegion {
+        5
+        //MemRegID    VolReg1    VolReg2    Surface
+                 0          1          0 4512.8782874369472
+                 1          2          0 1.7113582585034091
+                 2          3          0 1.7113582585033937
+                 3          4          0 1.711358258503394
+                 4          5          1 1306.5985272332098
+        }
+
+        VolumeElementsMapVolumeRegion {
+        126025 Compressed
+        789CEDDD8D72DBC81100612389DFFF9573572A5912B9BF2066A66176B32A57B12CE22B8022E5DD11
+        F5EB9799999999999999999999999999999999999999999999999999999999999999999999999999
+        ...
+        3333338B8F3625C09A5BE069281EE2BC0BC543D530FA907034666666666666666666666666666666
+        6666666666666666666666667F67FF07ABF56A9C
+        }
+
+        MembraneElements {
+        7817
+        //Indx Vol1 Vol2 Conn0 Conn1 Conn2 Conn3 MemRegID
+             0 6710 11751     5   507   493     1        0
+             1 6711 11752     6     0   494   510        0
+             2 6771 11812    10   524   503     3        0
+             3 6772 11813    11     2   505   527        0
+             4 6780 11821    16   533   508     5        0
+             ....
+            7808 109155 104114  7807  7805  7792  7806        4
+            7809 104179 104180  7810  7551  7798  7811        4
+            7810 104251 104180  7812  7551  7809    -1        4
+            7811 109221 104180    -1  7809  7799  7813        4
+            7812 104252 104181  7815  7553  7810    -1        4
+            7813 109222 104181    -1  7811  7800  7816        4
+            7814 104183 104182  7815  7556  7802  7816        4
+            7815 104253 104182  7814  7554  7812    -1        4
+            7816 109223 104182    -1  7813  7801  7814        4
+        }
+    }
+    """
+
+    mesh_file: Path
+    size: list[int]  # [x, y, z]
+    extent: list[float]  # [x, y, z]
+    origin: list[float]  # [x, y, z]
+    volume_regions: list[tuple[int, int, float, str]]  # list of tuples (vol_reg_id, subvol_id, volume, domain_name)
+    membrane_regions: list[tuple[int, int, int, float]]  # list of tuples (mem_reg_id, vol_reg1, vol_reg2, surface)
+
+    # membrane_element[m,:] = [idx, vol1, vol2, conn0, conn1, conn2, conn3, mem_reg_id]
+    membrane_elements: np.ndarray  # shape (num_membrane_elements, 8)
+
+    # volume_region_map[m] = vol_reg_id
+    volume_region_map: np.ndarray  # shape (size[0] * size[1] * size[2],)
+
+    def __init__(self, mesh_file: Path) -> None:
+        self.mesh_file = mesh_file
+        self.size = []
+        self.extent = []
+        self.origin = []
+        self.volume_regions = []
+        self.membrane_regions = []
+        # self.membrane_elements
+        self.volume_region_map = np.array([], dtype=np.uint8)
+
+    @property
+    def dimension(self) -> int:
+        if self.size[1] == 1 and self.size[2] == 1:
+            return 1
+        elif self.size[2] == 1:
+            return 2
+        else:
+            return 3
+
+    def read(self) -> None:
+        # read file as lines and parse
+        with self.mesh_file.open("r") as f:
+            # get line enumerator from f
+
+            iter_lines = iter(f.readlines())
+
+            if next(iter_lines) != "Version 1.2\n":
+                raise RuntimeError("Expected 'Version 1.2' at the beginning of the file")
+            if next(iter_lines) != "CartesianMesh {\n":
+                raise RuntimeError("Expected 'CartesianMesh {' after version")
+            if next(iter_lines) != "\t//              X          Y          Z\n":
+                raise RuntimeError("Expected coordinate comment line")
+
+            size_line = next(iter_lines).split()
+            if size_line[0] == "Size":
+                self.size = [int(size_line[1]), int(size_line[2]), int(size_line[3])]
+
+            extent_line = next(iter_lines).split()
+            if extent_line[0] == "Extent":
+                self.extent = [float(extent_line[1]), float(extent_line[2]), float(extent_line[3])]
+
+            origin_line = next(iter_lines).split()
+            if origin_line[0] == "Origin":
+                self.origin = [float(origin_line[1]), float(origin_line[2]), float(origin_line[3])]
+
+            while next(iter_lines) != "\tVolumeRegionsMapSubvolume {\n":
+                pass
+            num_volume_regions = int(next(iter_lines))
+            _header_line = next(iter_lines)
+            self.volume_regions = []
+            for _i in range(num_volume_regions):
+                parts = next(iter_lines).split()
+                self.volume_regions.append((int(parts[0]), int(parts[1]), float(parts[2]), parts[3].strip("/")))
+
+            while next(iter_lines) != "\tMembraneRegionsMapVolumeRegion {\n":
+                pass
+            num_membrane_regions = int(next(iter_lines))
+            _header_line = next(iter_lines)
+            self.membrane_regions = []
+            for _i in range(num_membrane_regions):
+                parts = next(iter_lines).split()
+                self.membrane_regions.append((int(parts[0]), int(parts[1]), int(parts[2]), float(parts[3])))
+
+            while next(iter_lines) != "\tVolumeElementsMapVolumeRegion {\n":
+                pass
+            compressed_line = next(iter_lines).split()
+            num_volume_elements = int(compressed_line[0])
+            if compressed_line[1] != "Compressed":
+                raise ValueError("Expected 'Compressed' in VolumeElementsMapVolumeRegion")
+            # read HEX lines until "}" line, and concatenate into one string, then convert to bytes and decompress
+            hex_lines = []
+            while True:
+                line = next(iter_lines)
+                if line.strip() == "}":
+                    break
+                hex_lines.append(line.strip())
+            hex_string: str = "".join(hex_lines).strip()
+            compressed_bytes = bytes.fromhex(hex_string)
+            uncompressed_bytes: bytes = zlib.decompress(compressed_bytes)
+            self.volume_region_map = np.frombuffer(uncompressed_bytes, dtype="<u2")  # unsigned 2-byte integers
+            if self.volume_region_map.shape[0] != self.size[0] * self.size[1] * self.size[2]:
+                raise ValueError("Expected number of volume elements to match the size of volume region map")
+            if num_volume_elements != self.volume_region_map.shape[0]:
+                raise ValueError("Expected number of volume elements to match the size of volume region map")
+            if set(np.unique(self.volume_region_map)) != {v[0] for v in self.volume_regions}:
+                raise ValueError("Expected volume region map to have the same unique values as volume regions")
+
+            while next(iter_lines).strip() != "MembraneElements {":
+                pass
+            num_membrane_elements = int(next(iter_lines))
+            self.membrane_elements = np.zeros((num_membrane_elements, 8), dtype=np.int32)
+            _header_line = next(iter_lines)
+            mem_index = 0
+            while True:
+                line = next(iter_lines)
+                if line.strip() == "}":
+                    break
+                parts = line.split()
+                idx = int(parts[0])
+                vol1 = int(parts[1])
+                vol2 = int(parts[2])
+                conn0 = int(parts[3])
+                conn1 = int(parts[4])
+                conn2 = int(parts[5])
+                conn3 = int(parts[6])
+                mem_reg_id = int(parts[7])
+                self.membrane_elements[mem_index, :] = [idx, vol1, vol2, conn0, conn1, conn2, conn3, mem_reg_id]
+                mem_index += 1
+            if self.membrane_elements.shape != (num_membrane_elements, 8):
+                raise RuntimeError("Expected membrane elements to have the correct shape")
+            if set(np.unique(self.membrane_elements[:, 7])) != {v[0] for v in self.membrane_regions}:
+                raise RuntimeError("Expected volume region ids in membrane elements to match volume regions")
+
+    def get_volume_element_box(self, i: int, j: int, k: int) -> Box3D:
+        x_lo = self.origin[0] + i * self.extent[0] / self.size[0]
+        y_lo = self.origin[1] + j * self.extent[1] / self.size[1]
+        z_lo = self.origin[2] + k * self.extent[2] / self.size[2]
+        x_hi = self.origin[0] + (i + 1) * self.extent[0] / self.size[0]
+        y_hi = self.origin[1] + (j + 1) * self.extent[1] / self.size[1]
+        z_hi = self.origin[2] + (k + 1) * self.extent[2] / self.size[2]
+        return Box3D(x_lo, y_lo, z_lo, x_hi, y_hi, z_hi)
+
+    def get_membrane_region_index(self, mem_element_index: int) -> int:
+        return int(self.membrane_elements[mem_element_index, 7])
+
+    def get_membrane_region_ids(self, volume_domain_name: str) -> set[int]:
+        return {
+            mem_reg_id
+            for mem_reg_id, vol_reg1, vol_reg2, surface in self.membrane_regions
+            if self.volume_regions[vol_reg1][3] == volume_domain_name
+            or self.volume_regions[vol_reg2][3] == volume_domain_name
+        }
+
+    def get_volume_region_ids(self, volume_domain_name: str) -> set[int]:
+        return {
+            vol_reg_id
+            for vol_reg_id, subvol_id, volume, domain_name in self.volume_regions
+            if domain_name == volume_domain_name
+        }