pyvale 2025.7.1__cp311-cp311-win_amd64.whl → 2025.8.1__cp311-cp311-win_amd64.whl

pyvale/dataset.py

@@ -1,415 +0,0 @@
-#===============================================================================
-# pyvale: the python validation engine
-# License: MIT
-# Copyright (C) 2025 The Computer Aided Validation Team
-#===============================================================================
-
-"""
-Accesors for data that comes pre-packaged with pyvale for demonstrating its
-functionality. This includes moose simulation outputs as exodus files, input
-files for moose and gmsh for additional simulation cases, and images required
-for testing the image deformation and digital image correlation modules.
-"""
-
-from enum import Enum
-from pathlib import Path
-from importlib.resources import files
-
-# TODO: finish doc strings for last functions
-
-SIM_CASE_COUNT = 26
-"""Constant describing the number of simulation test case input files for moose
-and gmsh that come packaged with pyvale.
-"""
-
-class EElemTest(Enum):
-    """Enumeration used to specify different 3D element types for extracting
-    specific test simulation datasets.
-    """
-
-    TET4 = "TET4"
-    """Tetrahedral element, linear with 4 nodes.
-    """
-
-    TET10 = "TET10"
-    """Tetrahedral element, quadratic with 10 nodes.
-    """
-
-    TET14 = "TET14"
-    """Tetrahedral element, quadratic with 14 nodes.
-    """
-
-    HEX8 = "HEX8"
-    """Hexahedral element, linear with 8 nodes.
-    """
-
-    HEX20 = "HEX20"
-    """Hexahedral element, quadratic with 20 nodes.
-    """
-
-    HEX27 = "HEX27"
-    """Hexahedral element, quadratic with 27 nodes.
-    """
-
-    def __str__(self):
-        return self.value
-
-
-class DataSetError(Exception):
-    """Custom error class for file io errors associated with retrieving datasets
-    and files packaged with pyvale.
-    """
-
-
-class DataSet:
-    @staticmethod
-    def sim_case_input_file_path(case_num: int) -> Path:
-        """Gets the path to MOOSE input file (*.i) for a particular simulation
-        case.
-
-        Parameters
-        ----------
-        case_num : int
-            Integer defining the case number to be retrieved. Must be greater
-            than 0 and less than the number of simulation cases.
-
-        Returns
-        -------
-        Path
-            Path object to the MOOSE *.i file for the selected simulation case.
-
-        Raises
-        ------
-        DataSetError
-            Raised if an invalid simulation case number is specified.
-        """
-        if case_num <= 0:
-            raise DataSetError("Simulation case number must be greater than 0")
-        elif case_num > SIM_CASE_COUNT:
-            raise DataSetError("Simulation case number must be less than " \
-                                + f"{SIM_CASE_COUNT}")
-
-        case_num_str = str(case_num).zfill(2)
-        case_file = f"case{case_num_str}.i"
-        return Path(files("pyvale.simcases").joinpath(case_file))
-
-
-    @staticmethod
-    def sim_case_gmsh_file_path(case_num: int) -> Path | None:
-        """Gets the path to Gmsh input file (*.geo) for a particular simulation
-        case. Note that not all simulation cases use Gmsh for geometry and mesh
-        generation. If the specified simulation case does not have an associated
-        Gmsh *.geo file. In this case 'None' is returned
-
-        Parameters
-        ----------
-        case_num : int
-            Integer defining the case number to be retrieved. Must be greater
-            than 0 and less than the number of simulation cases.
-
-        Returns
-        -------
-        Path | None
-            Path object to the Gmsh *.geo file for the selected simulation case.
-            Returns None if there is no *.geo for this simulation case.
-
-        Raises
-        ------
-        DataSetError
-            Raised if an invalid simulation case number is specified.
-        """
-        if case_num <= 0:
-            raise DataSetError("Simulation case number must be greater than 0")
-        elif case_num > SIM_CASE_COUNT:
-            raise DataSetError("Simulation case number must be less than " \
-                                + f"{SIM_CASE_COUNT}")
-
-        case_num_str = str(case_num).zfill(2)
-        case_file = f"case{case_num_str}.geo"
-        case_path = Path(files("pyvale.simcases").joinpath(case_file))
-
-        if case_path.is_file():
-            return case_path
-
-        return None
-
-
-    @staticmethod
-    def dic_pattern_5mpx_path() -> Path:
-        """Path to a 5 mega-pixel speckle pattern image (2464 x 2056 pixels)
-        with 8 bit resolution stored as a *.tiff. Speckles are sampled by
-        5 pixels. A gaussian blur has been applied to the image to remove sharp
-        transitions from black to white.
-
-        Path
-            Path to the *.tiff file containing the speckle pattern.
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("optspeckle_2464x2056px_spec5px_8bit_gblur1px.tiff"))
-
-    @staticmethod
-    def thermal_2d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        thermal problem solving for a scalar temperature field. The geometry is
-        a 2D plate (in x,y) with a heat flux applied on one edge and a heat
-        transfer coefficient applied on the opposite edge inducing a temperature
-        gradient along the x axis of the plate.
-
-        The simulation parameters can be found in the corresponding MOOSE input
-        file: case13.i which can be retrieved using `sim_case_input_file_path`
-        in this class.
-
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case13_out.e"))
-
-    @staticmethod
-    def thermal_3d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a 3D
-        thermal problem solving for a scalar temperature field. The model is a
-        divertor armour monoblock composed of a tungsten block bonded to a
-        copper-chromium-zirconium pipe with a pure copper interlayer. A heat
-        flux is applied to the top surface of the block and a heat transfer
-        coefficient for cooling water is applied to the inner surface of the
-        pipe inducing a temperature gradient from the top of the block to the
-        pipe.
-
-        The simulation parameters can be found in the corresponding MOOSE input
-        file: case16.i which can be retrieved using `sim_case_input_file_path`
-        in this class. Note that this case uses a Gmsh *.geo file for geometry
-        and mesh creation.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case16_out.e"))
-
-    @staticmethod
-    def mechanical_2d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a 2D
-        plate with a hole in the center with the bottom edge fixed and a
-        displacement applied to the top edge. This is a mechanical problem and
-        solves for the displacement vector field and the tensorial strain field.
-
-        The simulation parameters can be found in the corresponding MOOSE input
-        file: case17.i which can be retrieved using `sim_case_input_file_path`
-        in this class. Note that this case uses a Gmsh *.geo file for geometry
-        and mesh creation.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case17_out.e"))
-
-    @staticmethod
-    def thermomechanical_2d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        thermo-mechanical analysis of a 2D plate with a heat flux applied on one
-        edge and a heat transfer coefficient applied on the opposing edge. The
-        mechanical deformation results from thermal expansion due to the imposed
-        temperature gradient. This model is solved for the scalar temperature
-        field, vector displacement and tensor strain field.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case18_1_out.e"))
-
-    @staticmethod
-    def thermomechanical_3d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        thermo-mechanical analysis of a 3D monoblock divertor armour with a heat
-        flux applied on the top surface and a heat transfer coefficient applied
-        on the inner surface of the pipe. The mechanical deformation results
-        from thermal expansion due to the imposed temperature gradient.
-        This model is solved for the scalar temperature field, vector
-        displacement and tensor strain field.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case16_out.e"))
-
-    @staticmethod
-    def thermomechanical_2d_experiment_paths() -> list[Path]:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        thermo-mechanical analysis of a 2D plate with a heat flux applied on one
-        edge and a heat transfer coefficient applied on the opposing edge. The
-        mechanical deformation results from thermal expansion due to the imposed
-        temperature gradient. This model is solved for the scalar temperature
-        field, vector temperature and tensor strain field.
-
-        Here we analyse 3 separate experiments where the thermal conductivity of
-        the material is perturbed from the nominal case by +/-10%.
-
-        The simulation parameters can be found in the corresponding MOOSE input
-        file: case18.i which can be retrieved using `sim_case_input_file_path`
-        in this class.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return [Path(files("pyvale.data").joinpath("case18_1_out.e")),
-                Path(files("pyvale.data").joinpath("case18_2_out.e")),
-                Path(files("pyvale.data").joinpath("case18_3_out.e"))]
-
-    @staticmethod
-    def render_mechanical_3d_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        purely mechanical test case in 3D meant for testing image rendering
-        algorithms for digital image correlation simulation. The simulation
-        consists of a linear elastic thin plate with a hole loaded in tension.
-        The simulation uses linear tetrahedral elements for rendering tests.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case26_out.e"))
-
-    @staticmethod
-    def render_simple_block_path() -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        a simple rectangular block in 3D loaded in tension. It uses a minimum
-        number of elements and is intended purely for testing image rendering
-        algorithms. This simulation uses linear tetrahedral elements.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data").joinpath("case25_out.e"))
-
-    @staticmethod
-    def element_case_path(elem_type: EElemTest) -> Path:
-        """Path to a MOOSE simulation output in exodus format. This case is a
-        10mm cube undergoing thermo-mechanical loading solved for the
-        temperature displacement and strain fields. This case is solved using a
-        variety of tetrahedral and hexahedral elements with linear or quadratic
-        shapes functions. These simulation cases are intended for testing
-        purposes and contain a minimal number of elements.
-
-        Parameters
-        ----------
-        elem_type : EElemTest
-            Enumeration specifying the element type for this test case.
-
-        Returns
-        -------
-        Path
-            Path to the exodus (*.e) output file for this simulation case.
-        """
-        return Path(files("pyvale.data")
-                    .joinpath(f"case00_{elem_type.value}_out.e"))
-
-    @staticmethod
-    def dic_plate_with_hole_ref() -> Path:
-        """Path to the reference image for the plate with hole example.
-        1040x1540 image in .tiff format.
-
-        Parameters
-        ----------
-        elem_type : EElemTest
-            Enumeration specifying the element type for this test case.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("plate_hole_ref0000.tiff"))
-
-    @staticmethod
-    def dic_plate_with_hole_def() -> Path:
-        """Path to the deformed images for the plate with hole example.
-        1040x1540 image in .tiff format.
-
-        Parameters
-        ----------
-        elem_type : EElemTest
-            Enumeration specifying the element type for this test case.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("plate_hole_def*.tiff"))
-
-    @staticmethod
-    def dic_plate_rigid_ref() -> Path:
-        """Path to the reference image for the plate with hole example.
-        1040x1540 image in .tiff format.
-
-        Parameters
-        ----------
-        elem_type : EElemTest
-            Enumeration specifying the element type for this test case.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("plate_rigid_ref0000.tiff"))
-
-    @staticmethod
-    def dic_plate_rigid_def() -> Path:
-        """Path to the deformed images for the plate with hole example.
-        1040x1540 image in .tiff format.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("plate_rigid_def*.tiff"))
-
-
-
-    @staticmethod
-    def dic_challenge_ref() -> Path:
-        """Path to the reference images for the 2D dic challenge.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("DIC_Challenge_Star_Noise_Ref.tif"))
-
-    @staticmethod
-    def dic_challenge_def() -> Path:
-        """Path to the reference images for the 2D dic challenge.
-
-        Returns
-        -------
-        Path
-            Path to the reference image (*.tiff).
-        """
-        return Path(files("pyvale.data")
-                    .joinpath("DIC_Challenge_Star_Noise_Def.tif"))
-
-
-

pyvale/dicdataimport.py

@@ -1,247 +0,0 @@
-# ================================================================================
-# pyvale: the python validation engine
-# License: MIT
-# Copyright (C) 2025 The Computer Aided Validation Team
-# ================================================================================
-
-
-
-import numpy as np
-import glob
-import os
-from pathlib import Path
-
-# import cython module
-from pyvale.dicresults import DICResults
-
-"""
-Module responsible for handling importing of DIC results from completed
-calculations.
-"""
-
-
-def dic_data_import(data: str | Path,
-                   binary: bool = False,
-                   layout: str = "matrix",
-                   delimiter: str = " ") -> DICResults:
-    """
-    Import DIC result data from human readable text or binary files.
-
-    Parameters
-    ----------
-
-    data : str or pathlib.Path
-        Path pattern to the data files (can include wildcards). Default is "./".
-
-    layout : str, optional
-        Format of the output data layout: "column" (flat array per frame) or "matrix" 
-        (reshaped grid per frame). Default is "column".
-
-    binary : bool, optional
-        If True, expects files in a specific binary format. If False, expects text data. 
-        Default is False.
-
-    delimiter : str, optional
-        Delimiter used in text data files. Ignored if binary=True. Default is a single space.
-
-    Returns
-    -------
-    DICResults
-        A named container with the following fields:
-            - ss_x, ss_y (grid arrays if layout=="matrix"; otherwise, 1D integer arrays)
-            - u, v, m, converged, cost, ftol, xtol, niter (arrays with shape depending on layout)
-            - filenames (python list)
-
-    Raises
-    ------
-    ValueError:
-        If `layout` is not "column" or "matrix", or text data has insufficient columns,
-        or binary rows are malformed.
-        
-    FileNotFoundError:
-        If no matching data files are found.
-    """
-
-
-    print("")
-    print("Attempting DIC Data import...")
-    print("")
-
-    # convert to str 
-    if isinstance(data, Path):
-        data = str(data)
-
-    files = sorted(glob.glob(data))
-    filenames = files
-    if not files:
-        raise FileNotFoundError(f"No results found in: {data}")
-
-    print(f"Found {len(files)} files containing DIC results:")
-    for file in files:
-        print(f"  - {file}")
-    print("")
-
-
-    # Read first file to define reference coordinates
-    read_data = read_binary if binary else read_text
-    ss_x_ref, ss_y_ref, *fields = read_data(files[0], delimiter=delimiter)
-    frames = [list(fields)]
-
-    for file in files[1:]:
-        ss_x, ss_y, *f = read_data(file, delimiter)
-        if not (np.array_equal(ss_x_ref, ss_x) and np.array_equal(ss_y_ref, ss_y)):
-            raise ValueError("Mismatch in coordinates across frames.")
-        frames.append(f)
-
-    # Stack fields into arrays
-    arrays = [np.stack([frame[i] for frame in frames]) for i in range(8)]
-
-    if layout == "matrix":
-        x_unique = np.unique(ss_x_ref)
-        y_unique = np.unique(ss_y_ref)
-        X, Y = np.meshgrid(x_unique, y_unique)
-        shape = (len(files), len(y_unique), len(x_unique))
-        arrays = [to_grid(a,shape,ss_x_ref, ss_y_ref, x_unique,y_unique) for a in arrays]
-        return DICResults(X, Y, *arrays, filenames)
-    else:
-        return DICResults(ss_x_ref, ss_y_ref, *arrays, filenames)
-
-
-
-
-
-def read_binary(file: str, delimiter: str):
-    """
-    Read a binary DIC result file and extract DIC fields.
-
-    Assumes a fixed binary structure with each row containing:
-    - 2 × int32 (subset coordinates)
-    - 6 × float64 (u, v, match quality, cost, ftol, xtol)
-    - 1 × int32 (number of iterations)
-
-    Parameters
-    ----------
-    file : str
-        Path to the binary result file.
-
-    delimiter : str
-        Ignored for binary data (included for API consistency).
-
-    Returns
-    -------
-    tuple of np.ndarray
-        Arrays corresponding to:
-        (ss_x, ss_y, u, v, m, cost, ftol, xtol, niter)
-
-    Raises
-    ------
-    ValueError
-        If the binary file size does not align with expected row size.
-    """
-
-    row_size = (3 * 4 + 6 * 8)
-    with open(file, "rb") as f:
-        raw = f.read()
-    if len(raw) % row_size != 0:
-        raise ValueError("Binary file has incomplete rows.")
-    rows = len(raw) // row_size
-    arr = np.frombuffer(raw, dtype=np.uint8).reshape(rows, row_size)
-    def extract(col, dtype, start): return np.frombuffer(arr[:, start:start+col], dtype=dtype)
-    ss_x = extract(4, np.int32, 0)
-    ss_y = extract(4, np.int32, 4)
-    u    = extract(8, np.float64, 8)
-    v    = extract(8, np.float64, 16)
-    m    = extract(8, np.float64, 24)
-    conv = extract(1, np.bool_, 25)
-    cost = extract(8, np.float64, 33)
-    ftol = extract(8, np.float64, 41)
-    xtol = extract(8, np.float64, 49)
-    niter = extract(4, np.int32, 57)
-    return ss_x, ss_y, u, v, m, conv, cost, ftol, xtol, niter
-
-
-
-
-def read_text(file: str, delimiter: str):
-    """
-    Read a human-readable text DIC result file and extract DIC fields.
-
-    Expects at least 9 columns:
-    [ss_x, ss_y, u, v, m, conv, cost, ftol, xtol, niter]
-
-    Parameters
-    ----------
-    file : str
-        Path to the text result file.
-
-    delimiter : str
-        Delimiter used in the text file (e.g., space, tab, comma).
-
-    Returns
-    -------
-    tuple of np.ndarray
-        Arrays corresponding to:
-        (ss_x, ss_y, u, v, m, conv, cost, ftol, xtol, niter)
-
-    Raises
-    ------
-    ValueError
-        If the text file has fewer than 9 columns.
-    """
-
-    data = np.loadtxt(file, delimiter=delimiter, skiprows=1)
-    if data.shape[1] < 9:
-        raise ValueError("Text data must have at least 9 columns.")
-    return (
-        data[:, 0].astype(np.int32),  # ss_x
-        data[:, 1].astype(np.int32),  # ss_y
-        data[:, 2], data[:, 3], data[:, 4], # u, v, mag
-        data[:, 5].astype(np.bool_), # convergence
-        data[:, 6], data[:, 7], data[:,8], # cost, ftol, xtol
-        data[:, 9].astype(np.int32) #niter
-    )
-
-
-
-
-
-def to_grid(data, shape, ss_x_ref, ss_y_ref, x_unique, y_unique):
-    """
-    Reshape a 2D DIC field from flat (column) format into grid (matrix) format.
-
-    This is used when output layout is specified as "matrix".
-    Maps values using reference subset coordinates (ss_x_ref, ss_y_ref).
-
-    Parameters
-    ol
-    ----------
-    data : np.ndarray
-        Array of shape (n_frames, n_points) to be reshaped into (n_frames, height, width).
-
-    shape : tuple
-        Target shape of output array: (n_frames, height, width).
-
-    ss_x_ref : np.ndarray
-        X coordinates of subset centers.
-
-    ss_y_ref : np.ndarray
-        Y coordinates of subset centers.
-
-    x_unique : np.ndarray
-        Sorted unique X coordinates in the grid.
-
-    y_unique : np.ndarray
-        Sorted unique Y coordinates in the grid.
-
-    Returns
-    -------
-    np.ndarray
-        Reshaped array with shape `shape`, filled with NaNs where no data exists.
-    """
-
-    grid = np.full(shape, np.nan)
-    for i, (x, y) in enumerate(zip(ss_x_ref, ss_y_ref)):
-        x_idx = np.where(x_unique == x)[0][0]
-        y_idx = np.where(y_unique == y)[0][0]
-        grid[:, y_idx, x_idx] = data[:, i]
-    return grid