dpm-srm 0.1.0__cp310-cp310-macosx_14_0_arm64.whl

dpm_srm/__init__.py

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+from .py_srm import segment
+from ._dpm_srm import SRM2D_u8, SRM2D_u16, SRM2D_u32, SRM3D_u8, SRM3D_u16, SRM3D_u32
+
+__all__ = [
+    # C++ wrapped functions
+    "SRM2D_u8", "SRM2D_u16", "SRM2D_u32", 
+    "SRM3D_u8", "SRM3D_u16", "SRM3D_u32",
+    
+    # Python getter function
+    "segment",
+]

dpm_srm/py_srm.py

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+from ._dpm_srm import SRM2D_u8, SRM2D_u16, SRM2D_u32, SRM3D_u8, SRM3D_u16, SRM3D_u32
+import numpy as np
+
+
+def segment(image: np.ndarray, Q: float = 25., rescale: bool = True) -> np.ndarray:
+    """
+    Statistical Region Merging Segmentation as implemented in <NAME> et al.
+
+    Parameters:
+    ---
+    image: A 2D or 3D Numpy array of the image to be segmented
+    Q: Used as part of the merging criterion. Larger Q -> more regions. Default: 25.
+    rescale: Rescale the image to fit [0-dtype::max()]. This will provide better segmentation results. Default: True
+
+    Returns:
+    ---
+    segmented_image: A 2D or 3D Numpy array of the image with each region labelled.
+    
+    """
+    srm_dtypes = ["uint8", "uint16", "uint32", "uint64"]
+    assert image.ndim == 2 or image.ndim == 3, f"Image must be 2D or 3D, not {image.ndim}D."
+    assert str(image.dtype) in srm_dtypes, f"Image must be of type {srm_dtypes}."
+
+    if rescale:
+        original_dtype = image.dtype
+        original_bytes = image.itemsize
+        try:
+            dtype_min = np.iinfo(original_dtype).min
+            bytes_max = 2**(original_bytes * 8) - 1
+        
+        except ValueError:
+            dtype_min = np.finfo(original_dtype).min
+            bytes_max = 2**(original_bytes * 8) - 1
+            
+        min_val = np.percentile(image, 1)
+        max_val = np.percentile(image, 99)
+        image[image < min_val] = min_val
+        image[image > max_val] = max_val   
+        image = (image - min_val) / (max_val - min_val) * bytes_max + dtype_min
+        image = image.astype(original_dtype)
+
+    srm_funcs = {"2": {"uint8": SRM2D_u8,
+                       "uint16": SRM2D_u16,
+                       "uint32": SRM2D_u32},
+                "3": {"uint8": SRM3D_u8,
+                      "uint16": SRM3D_u16,
+                      "uint32": SRM3D_u32}}
+    srm_func = srm_funcs[str(image.ndim)][str(image.dtype)]
+    srm_obj = srm_func(image, Q)
+    srm_obj.segment()
+    segmentation = srm_obj.get_result()
+
+    return segmentation
+
+# if __name__ == "__main__":
+#     import tifffile
+#     import matplotlib.pyplot as plt
+#     image = tifffile.imread("/mnt/d/Petrobras_Data/uCT/Depth_1/F4635H_CLEAN_P_13000nm_small.tif")
+#     image = image[:50, :50, :50]
+#     image = image.astype(np.uint32)
+
+#     # image = image.astype(np.float32)
+#     # min_val = np.percentile(image, 1)
+#     # max_val = np.percentile(image, 99)
+#     # image[image < min_val] = min_val
+#     # image[image > max_val] = max_val   
+#     # image = (image - min_val) / (max_val - min_val) * 255 - 128
+#     # image = image.astype(np.uint8)
+#     # rescale = False
+
+#     # if rescale:
+#     #     original_dtype = image.dtype
+#     #     original_bytes = image.itemsize
+#     #     try:
+#     #         dtype_min = np.iinfo(original_dtype).min
+#     #         bytes_max = 2**(original_bytes * 8) - 1
+        
+#     #     except ValueError:
+#     #         dtype_min = np.finfo(original_dtype).min
+#     #         bytes_max = 2**(original_bytes * 8) - 1
+        
+#     #     print(dtype_min, bytes_max)
+#     #     min_val = np.percentile(image, 1)
+#     #     max_val = np.percentile(image, 99)
+#     #     image[image < min_val] = min_val
+#     #     image[image > max_val] = max_val   
+#     #     image = (image - min_val) / (max_val - min_val) * bytes_max + dtype_min
+#     #     image = image.astype(original_dtype)
+
+    
+
+#     # print(np.amin(image), np.amax(image), image.dtype)
+
+#     segmentation = srm(image, Q=25, rescale=True)
+
+#     plt.figure()
+#     plt.imshow(image[20], cmap="Greys_r")
+#     plt.colorbar()
+
+
+#     plt.figure()
+#     plt.imshow(segmentation[20], cmap="Greys_r")
+#     plt.colorbar()
+
+#     plt.figure()
+#     plt.hist(image.flatten(), bins=50, range=(np.amin(image), np.amax(image)), density=True)
+#     plt.hist(segmentation.flatten(), bins=50, range=(np.amin(image), np.amax(image)), density=True)
+#     # plt.colorbar()
+#     plt.show()
+

dpm_srm-0.1.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: dpm_srm
+Version: 0.1.0
+Summary: Statistical Region Merging Segmentation
+Author-Email: Digital Porous Media <bcchang@utexas.edu>
+License: MIT
+Requires-Python: >=3.8
+Requires-Dist: numpy

dpm_srm-0.1.0.dist-info/RECORD

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+dpm_srm/__init__.py,sha256=3PRYCBbGnevQdRoWk6Lwp4INySbtKBuxn_fW4BCb0pE,289
+dpm_srm/py_srm.py,sha256=QYU7bQ_w5dYb9mdz6zEF-dA-75UcJyyvgW8k5KNViOU,4044
+dpm_srm-0.1.0.dist-info/METADATA,sha256=KnoqOaSaLuqy-1RAcVt4OELDkC-mWKQ6Dq-4dMl1Jhs,213
+dpm_srm-0.1.0.dist-info/WHEEL,sha256=VXk61i1nf3sOvr06rM-yjYh1D_tpHM2qhkUOd9d9DEg,114
+dpm_srm-0.1.0.dist-info/licenses/LICENSE,sha256=DPkH2YUOqq6GA9joNyrjSii3kGn-7Wn2CMYV5rY-Gok,3073
+dpm_srm-0.1.0.dist-info/RECORD,,

dpm_srm-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: scikit-build-core 0.10.7
+Root-Is-Purelib: false
+Tag: cp310-cp310-macosx_14_0_arm64
+

dpm_srm-0.1.0.dist-info/licenses/LICENSE

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+BSD 2-Clause License
+
+# Attribution
+This project includes code adapted from Statistical Region Merging by Johannes Schindelin, licensed under the BSD 2-Clause License.
+
+# Original License
+Copyright (C) 2009 - 2013, Johannes Schindelin
+
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * 
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+
+
+# Our Contributions
+Copyright (c) 2024, Digital Porous Media
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.