odblab 0.1.0__py3-none-any.whl

odblab/__init__.py

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+from odblab.core import Database as Database
+from odblab.core import load as load
+from odblab.viewer import view as view

odblab/core/__init__.py

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+from odblab.core.database import Database as Database
+from odblab.core.util import computeMagnitude as computeMagnitude
+from odblab.core.util import computePrincipal as computePrincipal
+from odblab.core.util import computeEquivalentStress as computeEquivalentStress
+from odblab.core.util import autoComputeMagnitude as autoComputeMagnitude
+from odblab.core.util import autoComputeInvariants as autoComputeInvariants
+from odblab.core.load import load as load

odblab/core/database.py

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+import os
+import numpy as np
+from numpy import ndarray as Array
+from numpy.ma import MaskedArray
+from dataclasses import dataclass
+from collections.abc import Sequence, Mapping, Collection, Callable
+from typing import Literal
+
+@dataclass(frozen=True)
+class Database:
+    """
+    A data container for extracted finite element analysis mesh and results.
+    This container holds the finite element mesh, node/element sets, and temporal field output data.
+
+    Notes
+    -----
+    Do not instantiate this class directly. Use `odblab.load` instead.
+    """
+    nodes: Array
+    elements: MaskedArray
+    types: Array
+    nodeSets: dict[str, Array]
+    elementSets: dict[str, Array]
+    times: Array
+    nodeHeaders: Array
+    centroidHeaders: Array
+    nodeData: Array
+    centroidData: Array
+    path: str
+
+    def __post_init__(self) -> None:
+        """Post dataclass object initialization."""
+        for array in (
+            self.nodes, self.elements, self.types, self.times, self.nodeHeaders, self.centroidHeaders, self.nodeData,
+            self.centroidData, *self.nodeSets.values(), *self.elementSets.values()
+        ):
+            array.setflags(write=False)
+
+    def __repr__(self) -> str:
+        """Readable database summary."""
+        indent: str = " "*2
+        join: Callable[[Collection[str]], str] = lambda items: \
+            "\n".join(f"{indent*2}\"{item}\"" for item in items) if len(items) else f"{indent*2}None"
+        typeSummary: str = "; ".join(f"{t}: {c}" for t, c in zip(*np.unique(self.types, return_counts=True)))
+        timeSummary: str = "\n".join(f"{indent}{i}: {t}" for i, t in enumerate(self.times))
+        return f"""\
+{os.path.splitext(self.path)[1][1:].upper()} Database - {self.path}
+Mesh:
+{indent}Number of nodes: {self.nodes.shape[0]}
+{indent}Number of elements: {self.elements.shape[0]} ({typeSummary})
+Sets:
+{indent}Available node sets ({len(self.nodeSets)}):\n{join(self.nodeSets.keys())}
+{indent}Available element sets ({len(self.elementSets)}):\n{join(self.elementSets.keys())}
+Time steps ({self.times.size}):\n{timeSummary}
+Fields:
+{indent}Node fields ({self.nodeHeaders.size}):\n{join(self.nodeHeaders)}
+{indent}Centroid fields ({self.centroidHeaders.size}):\n{join(self.centroidHeaders)}"""
+
+    def get(
+        self,
+        position: Literal["nodes", "centroids"],
+        fields: Sequence[str],
+        subset: str | None = None,
+        frame: int | None = None
+    ) -> tuple[Array, ...]:
+        """
+        Retrieve field output data for the specified position, region, and time.
+
+        Parameters
+        ----------
+        position : {'nodes', 'centroids'}
+            The spatial location of the requested data.
+        fields : sequence of strings
+            The names/headers of the requested fields, e.g., `['U.U1', 'U.U2', 'U.U3']`, `['S.MISES', 'S.TRESCA']`.
+        subset : string, optional
+            Optional node (if `position='nodes'`) or element (if `position='centroids'`) set name defining the region
+            for which the data is to be extracted. If not specified, extracts data for all nodes or centroids.
+        frame : integer, optional
+            The time frame index for which the data is to be extracted. If not specified, extracts data for all frames.
+
+        Returns
+        -------
+        out : tuple of arrays
+            Arrays containing the requested field output data. If the data is requested at a specific frame, the
+            returned arrays are vectors of size `m`; otherwise, they are matrices of size `m`-by-`n`, where `m` is the
+            number of nodes (if `position='nodes'`) or elements (if `position='centroids'`) and `n` is the number of
+            available frames.
+        """
+
+        # get requested position
+        targetData: Array; targetSets: dict[str, Array]; targetHeaders: Array
+        match position:
+            case "nodes":
+                targetData = self.nodeData
+                targetSets = self.nodeSets
+                targetHeaders = self.nodeHeaders
+            case "centroids":
+                targetData = self.centroidData
+                targetSets = self.elementSets
+                targetHeaders = self.centroidHeaders
+            case _:
+                raise ValueError(f"invalid position '{position}'; position must be 'nodes' or 'centroids'")
+
+        # get j-indexing
+        j: slice | Array = slice(None)
+        if subset is not None:
+            if subset not in targetSets.keys():
+                raise ValueError(
+                    f"set '{subset}' not available for position '{position}'; available sets: " +
+                    ", ".join(f"'{key}'" for key in targetSets.keys())
+                )
+            j = targetSets[subset]
+
+        # get k-indexing
+        k: slice | int = slice(None) if frame is None else frame
+
+        # get fields
+        out: list[Array] = []
+        for header in (fields,) if isinstance(fields, str) else fields:
+            found: Array = np.where(targetHeaders == header)[0]
+            if found.size == 0:
+                raise ValueError(
+                    f"field '{header}' not available at position '{position}'; available fields: " +
+                    ", ".join(f"'{h}'" for h in targetHeaders)
+                )
+            i: int = int(found[0])
+            out.append(targetData[i, j, k])
+        return tuple(out)
+
+    def add(
+        self,
+        data: Mapping[str, Array],
+        position: Literal["nodes", "centroids"],
+        subset: str | None = None,
+        frame: int | None = None
+    ) -> None:
+        """
+        Add field output arrays to the database.
+
+        Parameters
+        ----------
+        data : mapping of strings to arrays
+            A dict-like object mapping names/headers to the corresponding data arrays to be inserted in the database.
+            The names/headers must be unique, and the arrays must have the correct shape for the position, region, and
+            time frame(s).
+        position : {'nodes', 'centroids'}
+            The spatial location where the new data should be added.
+        subset : string, optional
+            Optional node (if `position='nodes'`) or element (if `position='centroids'`) set name defining the region
+            for which the data is to be added. If not specified, adds data for all nodes or centroids. If specified, 
+            nodes/centroids outside this subset will be padded with NaN.
+        frame : integer, optional
+            The time frame index for which the data is to be added. If not specified, adds data for all frames. If
+            specified, frames outside this index will be padded with NaN.
+        """
+
+        # get requested position
+        dataAttribute: str; headerAttribute: str
+        targetData: Array; targetSets: dict[str, Array]; targetHeaders: Array
+        match position:
+            case "nodes":
+                targetData = self.nodeData
+                targetSets = self.nodeSets
+                targetHeaders = self.nodeHeaders
+                dataAttribute, headerAttribute = "nodeData", "nodeHeaders"
+            case "centroids":
+                targetData = self.centroidData
+                targetSets = self.elementSets
+                targetHeaders = self.centroidHeaders
+                dataAttribute, headerAttribute = "centroidData", "centroidHeaders"
+            case _:
+                raise ValueError(f"invalid position '{position}'; position must be 'nodes' or 'centroids'")
+
+        # get j-indexing
+        j: slice | Array = slice(None)
+        if subset is not None:
+            if subset not in targetSets.keys():
+                raise ValueError(
+                    f"set '{subset}' not available for position '{position}'; available sets: " +
+                    ", ".join(f"'{key}'" for key in targetSets.keys())
+                )
+            j = targetSets[subset]
+
+        # get k-indexing
+        k: slice | int = slice(None) if frame is None else frame
+
+        # get expected array shape
+        expectedEntityCount: int = int(targetData.shape[1]) if isinstance(j, slice) else j.size
+        expectedShape: tuple[int, ...] = \
+            (expectedEntityCount, int(targetData.shape[2])) if frame is None else (expectedEntityCount,)
+        newArray: Array = np.full(
+            shape=(len(data), targetData.shape[1], targetData.shape[2]),
+            fill_value=np.nan,
+            dtype=targetData.dtype
+        )
+
+        # loop provided data arrays
+        for i, (header, array) in enumerate(data.items()):
+            if np.where(targetHeaders == header)[0].size > 0:
+                raise ValueError(f"header '{header}' already exists at position '{position}'")
+            if array.shape != expectedShape:
+                raise ValueError(
+                    f"bad shape for '{header}' field output array at position '{position}'; "
+                    f"expected shape {expectedShape}, but got {array.shape}"
+                )
+            newArray[i, j, k] = array
+
+        # concatenate
+        object.__setattr__(self, dataAttribute, np.concatenate((targetData, newArray), axis=0))
+        object.__setattr__(self, headerAttribute, np.append(targetHeaders, [*data.keys()]))
+        getattr(self, dataAttribute).setflags(write=False)
+        getattr(self, headerAttribute).setflags(write=False)
+
+    def save(self) -> None:
+        """Save the database state to disk."""
+        with open(self.path, "wb") as file:
+            np.savez(file, allow_pickle=False, **{
+                "__nodes__": self.nodes,
+                "__types__": self.types,
+                "__elements__": np.ma.getdata(self.elements),
+                **{f"__node_set__.\"{name}\"": array for name, array in self.nodeSets.items()},
+                **{f"__element_set__.\"{name}\"": array for name, array in self.elementSets.items()},
+                "__times__": self.times,
+                "__node_data__": self.nodeData,
+                "__centroid_data__": self.centroidData,
+                "__node_headers__": self.nodeHeaders,
+                "__centroid_headers__": self.centroidHeaders,
+            })

odblab/core/load.py

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+import sys
+import subprocess
+import numpy as np
+from pathlib import Path
+from numpy.ma import MaskedArray
+from numpy import ndarray as Array
+from importlib import resources
+from odblab.core import Database, autoComputeMagnitude, autoComputeInvariants
+
+def _loadNpz(npzPath: str | Path, autoComputeAllInvariants: bool = False) -> Database:
+    """Loads the requested *.npz file."""
+    if not isinstance(npzPath, Path): npzPath = Path(npzPath)
+    npzPath = npzPath.resolve()
+    with np.load(npzPath) as data:
+        nodes: Array = data["__nodes__"]
+        types: Array = data["__types__"]
+        elements: MaskedArray = np.ma.array(data=data["__elements__"], mask=data["__elements__"] < 0, fill_value=-1)
+        nodeSets: dict[str, Array] = {
+            key.removeprefix("__node_set__.")[1:-1]: data[key]
+            for key in data.files if key.startswith("__node_set__")
+        }
+        elementSets: dict[str, Array] = {
+            key.removeprefix("__element_set__.")[1:-1]: data[key]
+            for key in data.files if key.startswith("__element_set__")
+        }
+        times: Array = data["__times__"]
+        nodeData: Array = data["__node_data__"]
+        centroidData: Array = data["__centroid_data__"]
+        nodeHeaders: Array = data["__node_headers__"]
+        centroidHeaders: Array = data["__centroid_headers__"]
+        database: Database = Database(
+            nodes, elements, types, nodeSets, elementSets,
+            times, nodeHeaders, centroidHeaders, nodeData, centroidData,
+            str(npzPath)
+        )
+        if autoComputeAllInvariants:
+            print("Computing invariants...")
+            autoComputeMagnitude(database)
+            autoComputeInvariants(database)
+            database.save()
+            print("Database updated with invariants.")
+        return database
+
+def _loadOdb(odbPath: str | Path) -> Database:
+    """Loads the requested *.odb file."""
+    if not isinstance(odbPath, Path): odbPath = Path(odbPath)
+    odbPath = odbPath.resolve()
+    odbzPath: Path = odbPath.with_suffix(".odbz")
+    autoComputeAllInvariants: bool = True
+    if odbPath.exists() and odbzPath.exists() and odbzPath.stat().st_mtime > odbPath.stat().st_mtime:
+        print("Using cached ODBZ database.")
+        autoComputeAllInvariants = False
+    else:
+        print("ODBZ database not found or outdated. Converting ODB to ODBZ...")
+        script: str = str(resources.files("odblab.scripts") / "odb2npz.py")
+        if subprocess.run(("abaqus", "python", script, "--odb", str(odbPath)), shell=True, check=True).returncode:
+            raise RuntimeError("abaqus command not found; abaqus must be installed on the system")
+        with open("odb2npz.log", "r") as log:
+            if log.readline().strip() != "EXIT_SUCCESS":
+                raise RuntimeError("error in 'odb2npz.py'\n  " + log.readline().strip())
+    return _loadNpz(odbzPath, autoComputeAllInvariants)
+
+def _loadRst(rstPath: str | Path) -> Database:
+    """Loads the requested *.rst file."""
+    if not isinstance(rstPath, Path): rstPath = Path(rstPath)
+    rstPath = rstPath.resolve()
+    rstzPath: Path = rstPath.with_suffix(".rstz")
+    autoComputeAllInvariants: bool = True
+    if rstPath.exists() and rstzPath.exists() and rstzPath.stat().st_mtime > rstPath.stat().st_mtime:
+        print("Using cached RSTZ database.")
+        autoComputeAllInvariants = False
+    else:
+        print("RSTZ database not found or outdated. Converting RST to RSTZ...")
+        script: str = str(resources.files("odblab.scripts") / "rst2npz.py")
+        subprocess.run((sys.executable, script, "--rst", str(rstPath)), shell=True, check=True)
+    return _loadNpz(rstzPath, autoComputeAllInvariants)
+
+def load(filePath: str | Path) -> Database:
+    """Loads the requested finite element analysis database file."""
+    if not isinstance(filePath, Path): filePath = Path(filePath)
+    filePath = filePath.resolve()
+    if not filePath.exists(): raise FileNotFoundError(filePath)
+    match filePath.suffix.lower():
+        case ".odbz" | ".rstz": return _loadNpz(filePath)
+        case ".odb": return _loadOdb(filePath)
+        case ".rst": return _loadRst(filePath)
+        case _: raise ValueError(f"unexpected file extension '{filePath.suffix}': {filePath}")

odblab/core/util.py

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+import re
+import numpy as np
+from re import Pattern
+from numpy import ndarray as Array
+from odblab.core import Database
+
+def _findVectors(database: Database) -> tuple[dict[str, dict[str, str]], dict[str, dict[str, str]]]:
+    """Scan database headers to identify and group vector components."""
+    nodeVectors: dict[str, dict[str, str]] = {}
+    centroidVectors: dict[str, dict[str, str]] = {}
+    pattern: Pattern[str] = re.compile(r"^(.*?)\.[a-zA-Z]*([123])$")
+    for vectors, headers in (nodeVectors, database.nodeHeaders), (centroidVectors, database.centroidHeaders):
+        for header in headers:
+            if match := pattern.match(header := str(header)):
+                vectors.setdefault(match.group(1), {})[match.group(2)] = header
+    return nodeVectors, centroidVectors
+
+def _findTensors(database: Database) -> tuple[dict[str, dict[str, str]], dict[str, dict[str, str]]]:
+    """Scan database headers to identify and group tensor components."""
+    nodeTensors: dict[str, dict[str, str]] = {}
+    centroidTensors: dict[str, dict[str, str]] = {}
+    pattern: Pattern[str] = re.compile(r"^(.*?)\.[a-zA-Z]*([0-9]{2})$")
+    for tensors, headers in (nodeTensors, database.nodeHeaders), (centroidTensors, database.centroidHeaders):
+        for header in headers:
+            if match := pattern.match(header := str(header)):
+                tensors.setdefault(match.group(1), {})[match.group(2)] = header
+    return nodeTensors, centroidTensors
+
+def computeMagnitude(u1: Array, u2: Array, u3: Array | None) -> Array:
+    """Compute the element-wise magnitude of a 2D or 3D vector field."""
+    if u3 is None: return np.sqrt(u1*u1 + u2*u2)
+    else: return np.sqrt(u1*u1 + u2*u2 + u3*u3)
+
+def computePrincipal(*, s11: Array, s22: Array, s33: Array | None, s12: Array, s13: Array | None, s23: Array | None) \
+    -> tuple[Array, Array, Array, Array]:
+    """Compute the element-wise max., mid., and min. principal tensor values."""
+    tensor: Array = np.zeros(shape=(*s11.shape, 3, 3), dtype=s11.dtype)
+    tensor[..., 0, 0] = s11
+    tensor[..., 1, 1] = s22
+    tensor[..., 0, 1] = tensor[..., 1, 0] = s12
+    if s33 is not None: tensor[..., 2, 2] = s33
+    if s13 is not None: tensor[..., 0, 2] = tensor[..., 2, 0] = s13
+    if s23 is not None: tensor[..., 1, 2] = tensor[..., 2, 1] = s23
+    validMask: Array = np.isfinite(tensor).all(axis=(-2, -1))
+    eigenvalues: Array = np.full(shape=(*s11.shape, 3), fill_value=np.nan, dtype=s11.dtype)
+    eigenvalues[validMask] = np.linalg.eigvalsh(tensor[validMask])
+    max: Array = eigenvalues[..., 2]
+    mid: Array = eigenvalues[..., 1]
+    min: Array = eigenvalues[..., 0]
+    major: Array = np.where(np.abs(max) > np.abs(min), max, min)
+    return max, mid, min, major
+
+def computeEquivalentStress(s1: Array, s2: Array, s3: Array) -> tuple[Array, Array, Array]:
+    """Compute the equivalent von Mises, Tresca, and pressure stress based on the provided principal stresses."""
+    mises: Array = np.sqrt(0.5*((s1 - s2)**2 + (s2 - s3)**2 + (s3 - s1)**2))
+    tresca: Array = s1 - s3
+    pressure: Array = -(s1 + s2 + s3)/3
+    return mises, tresca, pressure
+
+def autoComputeMagnitude(database: Database) -> None:
+    """
+    Auto-discover node and centroid vector fields and compute their element-wise magnitude.
+    Results are appended to the database, e.g., "U.MAGNITUDE".
+    """
+    for position, currentHeaders, vectors in zip(
+        ("nodes", "centroids"),
+        (database.nodeHeaders, database.centroidHeaders),
+        _findVectors(database)
+    ):
+        magnitudes: dict[str, Array] = {}
+        for label, components in vectors.items():
+            if f"{label}.MAGNITUDE" in currentHeaders: continue
+            if "1" not in components or "2" not in components: continue
+            u1, u2 = database.get(position, (components["1"], components["2"]))
+            u3, = database.get(position, (components["3"],)) if "3" in components else (None,)
+            magnitudes[f"{label}.MAGNITUDE"] = computeMagnitude(u1, u2, u3)
+        database.add(magnitudes, position)
+
+def autoComputeInvariants(database: Database) -> None:
+    """
+    Auto-discover node and centroid tensor fields and compute their element-wise invariants.
+    Results are appended to the database, e.g., "LE.MAX_PRINCIPAL", "S.MISES".
+    """
+    for position, currentHeaders, tensors in zip(
+        ("nodes", "centroids"),
+        (database.nodeHeaders, database.centroidHeaders),
+        _findTensors(database)
+    ):
+        invariants: dict[str, Array] = {}
+        for label, components in tensors.items():
+            if any(f"{label}.{invariant}" in currentHeaders for invariant in (
+                "MAX_PRINCIPAL", "MID_PRINCIPAL", "MIN_PRINCIPAL", "MAJOR_PRINCIPAL",
+                "MISES", "TRESCA", "PRESSURE"
+            )): continue
+            if any(ij not in components for ij in ("11", "22", "12")): continue
+            s11, s22, s12 = database.get(position, (components["11"], components["22"], components["12"]))
+            s33, = database.get(position, (components["33"],)) if "33" in components else (None,)
+            s13, = database.get(position, (components["13"],)) if "13" in components else (None,)
+            s23, = database.get(position, (components["23"],)) if "23" in components else (None,)
+            if label != "S":
+                s12 = s12/2
+                if s13 is not None: s13 = s13/2
+                if s23 is not None: s23 = s23/2
+            s1, s2, s3, major = computePrincipal(s11=s11, s22=s22, s33=s33, s12=s12, s13=s13, s23=s23)
+            invariants[f"{label}.MAX_PRINCIPAL"] = s1
+            invariants[f"{label}.MID_PRINCIPAL"] = s2
+            invariants[f"{label}.MIN_PRINCIPAL"] = s3
+            invariants[f"{label}.MAJOR_PRINCIPAL"] = major
+            if label == "S":
+                mises, tresca, pressure = computeEquivalentStress(s1, s2, s3)
+                invariants[f"{label}.MISES"] = mises
+                invariants[f"{label}.TRESCA"] = tresca
+                invariants[f"{label}.PRESSURE"] = pressure
+        database.add(invariants, position)

odblab/icons/file-exit.svg

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odblab/icons/frame-first.svg

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odblab/icons/frame-last.svg

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odblab/icons/frame-next.svg

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odblab/icons/frame-pause.svg

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odblab/icons/frame-play.svg

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odblab/icons/frame-previous.svg

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odblab/icons/utilities-print.svg

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odblab/icons/view-colormap.svg

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odblab/icons/view-deformation.svg

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odblab/icons/view-mirror.svg

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odblab/icons/view-region.svg

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odblab/icons/view-render-style.svg

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odblab/icons/views-autofit.svg

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odblab/icons/views-back.svg

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odblab/icons/views-bottom.svg

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odblab/icons/views-front.svg

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odblab/icons/views-isometric.svg

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odblab/icons/views-left.svg

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odblab/icons/views-right.svg

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odblab/icons/views-rotateccw.svg

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odblab/icons/views-rotatecw.svg

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odblab/icons/views-top.svg

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