compgen 0.1.0__py3-none-any.whl

compgen/__init__.py

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+# Copyright 2026, UChicago Argonne, LLC
+# All Rights Reserved
+# Software Name: compgen
+# By: Argonne National Laboratory
+# OPEN SOURCE LICENSE (MIT)
+#
+# 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.
+
+"""Top-level package for composite structure generation and simulation workflows."""
+
+from importlib.metadata import version
+
+__version__ = version("compgen")

compgen/exoutil.py

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+# Copyright 2026, UChicago Argonne, LLC
+# All Rights Reserved
+# Software Name: compgen
+# By: Argonne National Laboratory
+# OPEN SOURCE LICENSE (MIT)
+#
+# 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.
+
+"""Various helpers for reading Exodus II files."""
+
+import numpy as np
+
+
+def get_element_field(exo, field):
+    """Retrieve an element field from an Exodus mesh.
+
+    Args:
+        exo (exodusii.File): Open Exodus file object.
+        field (str): Name of the element field to retrieve.
+    """
+    var_names = list(exo.get_element_variable_names())
+    if field not in var_names:
+        raise ValueError(f"Field '{field}' not found in output Exodus file.")
+
+    return np.concatenate(
+        [exo.get_element_variable_values(blk, field) for blk in [1, 2]], axis=-1
+    )

compgen/filters.py

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+# Copyright 2026, UChicago Argonne, LLC
+# All Rights Reserved
+# Software Name: compgen
+# By: Argonne National Laboratory
+# OPEN SOURCE LICENSE (MIT)
+#
+# 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.
+
+"""Image filtering utilities for preprocessing generated microstructures."""
+
+import numpy as np
+import skimage
+from compgen import utils
+
+
+def mean_filter(img, radius=3, periodic=True):
+    """Apply a mean filter to an image.
+
+    Args:
+        img (np.ndarray): 2D or 3D image.
+        radius (int): Radius of disk/ball footprint.
+        periodic (bool): If True, use periodic wrapping at the boundaries.
+
+    Returns:
+        np.ndarray: Smoothed binary image.
+    """
+    ndim = img.ndim
+
+    if ndim == 3:
+        footprint = skimage.morphology.ball(radius)
+    elif ndim == 2:
+        footprint = skimage.morphology.disk(radius)
+    else:
+        raise ValueError("mean_filter only supports 2D and 3D images")
+
+    def smooth(i):
+        i_u8 = skimage.util.img_as_ubyte(i.astype(float))
+
+        if periodic:
+            pad_width = [(radius, radius)] * ndim
+            i_u8 = np.pad(i_u8, pad_width=pad_width, mode="wrap")
+
+        out = skimage.filters.rank.mean(i_u8, footprint=footprint)
+        out = skimage.util.img_as_float(out)
+
+        if periodic:
+            slices = tuple(slice(radius, -radius) for _ in range(ndim))
+            out = out[slices]
+
+        return out
+
+    return utils.binary_smoother(img, smooth)
+
+
+def make_orthogonal(img):
+    """Mirror and tile the input array to give it orthogonal periodicity.
+
+    This works for arrays of arbitrary dimensionality by concatenating the
+    array with its flipped version along each axis (processing axes from
+    last to first).
+    """
+    arr = np.asarray(img)
+    for axis in reversed(range(arr.ndim)):
+        arr = np.concatenate([arr, np.flip(arr, axis=axis)], axis=axis)
+    return arr
+
+
+def make_periodic(img: np.ndarray, margin: int = 2) -> np.ndarray:
+    """
+    Make periodic for Sculpt/MOOSE workflow.
+
+    Overwrite the first and last `margin` layers of each axis with the layer at
+    index `margin`, for 2D or 3D arrays.
+
+    A value `margin` = 2 seems to work consistently with Sculpt/MOOSE.
+    """
+    arr = np.array(img, copy=True)
+
+    if arr.ndim not in (2, 3):
+        raise RuntimeError(f"Expected 2D or 3D array, got {arr.ndim}D")
+
+    if not isinstance(margin, int) or margin < 1:
+        raise ValueError(f"margin must be a positive integer, got {margin}")
+
+    if any(2 * margin >= s for s in arr.shape):
+        raise ValueError(f"margin={margin} is too large for shape {arr.shape}")
+
+    # Loop over each axis
+    for ax in range(arr.ndim):
+        # Slice selecting the master layer at index = margin
+        master = [slice(None)] * arr.ndim
+        master[ax] = slice(margin, margin + 1)
+
+        # Slice for lower and upper boundary block
+        lo = [slice(None)] * arr.ndim
+        lo[ax] = slice(0, margin)
+        hi = [slice(None)] * arr.ndim
+        hi[ax] = slice(-margin, None)
+
+        # Overwrite both boundary blocks using the master layer
+        arr[tuple(lo)] = arr[tuple(master)]
+        arr[tuple(hi)] = arr[tuple(master)]
+
+    return arr