fetoflow 0.1.0__tar.gz

fetoflow-0.1.0/LICENSE

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fetoflow-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: fetoflow
+Version: 0.1.0
+Summary: A Python library for fetoplacental vasculature modelling.
+Author: Jordan Blennerhassett, Jude Beullens
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/VirtualPregnancy/fetoflow
+Project-URL: Source, https://github.com/VirtualPregnancy/fetoflow
+Keywords: blood flow,placenta,network,hemodynamics,feto-placental
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: pandas>=1.3
+Requires-Dist: networkx>=2.6
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Dynamic: license-file
+
+# FetoFlow
+
+This is a Python Library developed by Jordan Blennerhassett and Jude Beullens under the guidance of Alys Clark and Sahan Jayatissa for use in computational modelling of fetoplacental vascular networks.
+
+**Documentation:** https://virtualpregnancy.github.io/fetoflow/

fetoflow-0.1.0/README.md

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+# FetoFlow
+
+This is a Python Library developed by Jordan Blennerhassett and Jude Beullens under the guidance of Alys Clark and Sahan Jayatissa for use in computational modelling of fetoplacental vascular networks.
+
+**Documentation:** https://virtualpregnancy.github.io/fetoflow/

fetoflow-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+
+[project]
+name = "fetoflow"
+version = "0.1.0"
+description = "A Python library for fetoplacental vasculature modelling."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "Apache-2.0" }
+authors = [
+  { name = "Jordan Blennerhassett" },
+  { name = "Jude Beullens" }
+]
+keywords = ["blood flow", "placenta", "network", "hemodynamics", "feto-placental"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Topic :: Scientific/Engineering",
+]
+
+dependencies = [
+  "numpy>=1.20",
+  "scipy>=1.7",
+  "pandas>=1.3",
+  "networkx>=2.6",
+]
+
+[project.urls]
+Homepage = "https://github.com/VirtualPregnancy/fetoflow"
+Source = "https://github.com/VirtualPregnancy/fetoflow"
+
+[project.optional-dependencies]
+dev = ["pytest>=6.0"]
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]

fetoflow-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

fetoflow-0.1.0/src/fetoflow/__init__.py

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+from .geometry_utils import (
+    create_geometry,
+    calcLength,
+    create_anastomosis,
+    create_venous_mesh,
+    calculate_branching_angles
+)
+from .bc_utils import generate_boundary_conditions
+from .matrix_builder import create_matrices, create_small_matrices
+from .resistance_utils import (
+    calculate_capillary_equivalent_resistance,
+    calculate_resistance,
+    calculate_convolute_resistance,
+    calculate_viscosity_factor_from_radius
+)
+from .file_parsing_utils import read_nodes, read_elements, define_fields_from_files
+from .helper_functions import (
+    getRadii,
+    getEdgeData,
+    getNode,
+    getNumVessels,
+    getRadius,
+    getVesselLength,
+)
+from .pressure_flow_utils import (
+    pressures_and_flows,
+)
+from.solve_utils import(
+    solve_small_system,
+    solve_system,
+    update_small_matrix,
+    iterative_solve_small
+    )

fetoflow-0.1.0/src/fetoflow/bc_utils.py

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+from warnings import warn
+def generate_boundary_conditions(inlet_pressure=None, inlet_flow=None, outlet_pressure=None):
+    # TODO: IF ONLY INLET FLOW, SET OUTLET PRESSURE TO 0 AND WE LOOK AT THE PRESSURE DROP. THEN NOTE THIS SOMEWHERE.
+    if inlet_pressure and inlet_flow:
+        raise TypeError(f"Cannot have both an inlet pressure and inlet flow defined. Inlet pressure: {inlet_pressure}Inlet Flow: {inlet_flow}")
+    elif inlet_pressure is None and inlet_flow is None:
+        raise TypeError("No inlet boundary condition defined. Must define one of inlet_pressure or inlet flow for a valid boundary condition.")
+    bcs = {}
+
+    if outlet_pressure is None and inlet_flow is None:
+        raise TypeError(
+            "No valid outlet pressure for boundary condition. "
+            "Currently Reprosim does not support outlet flow boundary conditions and must have a defined outlet pressure."
+        )
+    elif outlet_pressure is None and inlet_flow is not None:
+        warn("No outlet pressure defined with flow inlet. Setting outlet pressure to 0.")
+
+
+    # Outlet Pressure
+    if outlet_pressure:
+        if not (isinstance(outlet_pressure, int) or isinstance(outlet_pressure, float)):
+            raise TypeError(f"Outlet pressure type '{type(outlet_pressure)}' is not valid. Valid types include float or int.")
+        elif not outlet_pressure >= 0:
+            raise ValueError(f"Outlet pressure value of '{outlet_pressure}' is not valid. Must be greater than or equal to 0.")
+
+        bcs["outlet"] = {"pressure": outlet_pressure}
+
+    # TODO Add outlet flows potentially?
+
+    # Inlet Pressure
+    if inlet_pressure:
+        if not (isinstance(inlet_pressure, int) or isinstance(inlet_pressure, float) or isinstance(inlet_pressure, dict)):
+            raise TypeError(
+                f"Inlet pressure type '{type(inlet_pressure)}' is not valid. Valid types include float or int for single inputs and dict for multiple inputs."
+            )
+        elif isinstance(inlet_pressure, int) or isinstance(inlet_pressure, float):
+            if not inlet_pressure > 0:
+                raise ValueError(f"Invalid inlet pressure of '{inlet_pressure}' Pa. Must be greater than 0.")
+            bcs["inlet"] = {"pressure": inlet_pressure}
+        elif isinstance(inlet_pressure, dict):
+            inlet_pressures = {}
+            for key, value in inlet_pressure.items():
+                if not isinstance(key, int) or not key > 0:
+                    raise ValueError(f"Invalid Node Id {key} for multiple inlet pressures. Must be a positive integer.")
+                if not (isinstance(value, float) or isinstance(value, int)) or not value > 0:
+                    raise ValueError(f"Invalid inlet pressure for node {key} of '{inlet_pressure}' Pa. Must be greater than 0.")
+                # Fix indexing here (1-based for IPNODE and IPELEM to 0 based for NetworkX)
+                # TODO: Update this if we change input file types.
+                inlet_pressures[key - 1] = value
+            bcs["inlet"] = {"pressure": inlet_pressures}
+
+    # Inlet flow
+    if inlet_flow:
+        if not (isinstance(inlet_flow, int) or isinstance(inlet_flow, float) or isinstance(inlet_flow, dict)):
+            raise TypeError(
+                f"Inlet flow type '{type(inlet_flow)}' is not valid. Valid types include float or int for single inputs and dict for multiple inputs."
+            )
+        elif isinstance(inlet_flow, int) or isinstance(inlet_flow, float):
+            if not inlet_flow > 0:
+                raise ValueError(f"Invalid inlet flow of '{inlet_flow}' Pa. Must be greater than 0.")
+            bcs["inlet"] = {"flow": inlet_flow}
+        elif isinstance(inlet_flow, dict):
+            inlet_flows = {}
+            for key, value in inlet_flow.items():
+                if not isinstance(key, int) or not key > 0:
+                    raise ValueError(f"Invalid Element Id {key} for multiple inlet flows. Must be a positive integer.")
+                if not (isinstance(value, float) or isinstance(value, int)) or not value > 0:
+                    raise ValueError(f"Invalid inlet flow for element {key} of '{inlet_flow}'. Must be greater than 0.")
+                # Fix indexing here (1-based for IPNODE and IPELEM to 0 based for NetworkX)
+                # TODO: Update this if we change input file types.
+                inlet_flows[key - 1] = value
+            bcs["inlet"] = {"flow": inlet_flows}
+
+    return bcs
+
+
+"""
+# TODO: Some form that allows:
+- inlet type
+- inlet BC's
+
+- multiple inlet BC's either flow or pressure (for now say that can only do same type cause otherwise this is hell)
+- if multiple inlet BC's:
+    - must provide the inlet ID's they are referring to. MATCH THESE ID's with Placentagen.
+    NOTE: THIS MEANS WE HAVE TO UPDATE INDEXING SLIGHTLY TO MATCH, AS IPELEM FILES HAVE 1-BASED INDEXING AND NETWORKX HAS 0 BASED INDEXING
+
+
+
+- outlet pressure.
+- defaults to setting this outlet pressure at all outlet nodes (this makes the most sense to me, can be changed later)
+
+
+
+function inputs:
+
+inlet_pressure - value or dict[node_id, pressure]
+inlet_flow - value or dict [edge_id, flow]
+outlet_pressure - value
+
+
+
+function output:
+
+bcs: dict[inlet/outlet, dict[pressure/flow, value or dict[node/element_id, pressure/flow]]]
+(if pressure must be node in inner dict, if flow must be element.)
+
+"""

fetoflow-0.1.0/src/fetoflow/file_parsing_utils.py

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+def read_nodes(filename):
+    if not isinstance(filename,str):
+        raise(TypeError("File name should be a string!"))
+    if not filename[-7:] == ".ipnode":
+        raise(TypeError("This function expects a .ipnode file."))
+    with open(filename, "r") as f:
+        lines = f.readlines()
+        nodes = {}
+        numVars = int(lines[4].split()[-1])
+        baseStep = numVars + 2
+        i = 4 + 2 * numVars + 2
+        while i < len(lines):
+            node_id = int(lines[i].split()[-1])
+            nversions = int(lines[i + 1].split()[-1])
+            i_step = baseStep + nversions * numVars + (nversions * numVars if nversions > 1 else 0)
+            c_step = numVars * nversions - 1
+            coords = []
+            for c in range(1 + nversions, i_step, c_step):
+                coord = lines[i + c].split()[-1]
+                coords.append(float(coord))
+            nodes[node_id - 1] = coords  # 0-based indexing for the networkX geometry.
+            i += i_step
+    return nodes
+
+
+def read_elements(filename):
+    if not isinstance(filename,str):
+        raise(TypeError("File name should be a string!"))
+    if not filename[-7:] == ".ipelem":
+        raise(TypeError("This function expects a .ipelem file."))
+    
+    with open(filename, "r") as f:
+        lines = f.readlines()
+        elems = []
+        i = 5
+        while i < len(lines):
+            intraElementStep = 5
+            nodes = tuple(int(x) - 1 for x in lines[i + intraElementStep].split()[-2:])  # Translate to 0-based indexing.
+            elems.append(nodes)
+            while len(lines[i].split()) != 0:
+                i += 1
+                if i + 1 == len(lines):
+                    return elems
+            i += 1
+        return elems
+
+
+def define_fields_from_files(files: dict[str]):
+    """
+    Defines field(s) as specified in ipfield file(s).
+    """
+    if not isinstance(files, dict):
+        raise (TypeError("files must be a dictionary in the format files[field_name] = filename"))
+    fields = {}
+    for field in files.keys():
+        file_name = files[field]
+        if not file_name[-7:] == ".ipfiel":
+            ext_start = -(str.__reversed__(file_name).find(".") + 1)
+            if ext_start is not None:
+                raise(TypeError(f"This function expects a .ipfiel file, got {file_name[ext_start:]}"))
+            else:
+                raise(TypeError(f"This function expects a .ipfiel file. No file extension found."))
+        with open(file_name, "r") as f:
+            i = 7  # ignore metadata
+            lines = f.readlines()
+            max_digits = len(lines[3][lines[3].find(":") + 1 :].strip())
+            currentField = {}
+            while i < len(lines):
+                j = i + 2
+                id = (
+                    int(lines[i][-max_digits-1:].strip()) - 1
+                )  # assuming for now these correspond to element ids, -1 to 0 based
+                val = float(lines[j][lines[j].find(":")+1:].strip())
+                currentField[id] = val
+                i += 4
+        fields[field] = currentField
+    return fields