Merge branch 'main' of https://gitlab.ub.uni-bielefeld.de/thuxohl/mu-map

mu_map/data/datasets.py

 import os
 from typing import Optional
 
+import cv2 as cv
 import pandas as pd
 import pydicom
 import numpy as np
@@ -129,8 +130,6 @@ __all__ = [MuMapDataset.__name__]
 if __name__ == "__main__":
     import argparse
 
-    import cv2 as cv
-
     from mu_map.util import to_grayscale, COLOR_WHITE
 
     parser = argparse.ArgumentParser(

mu_map/data/patch_dataset.py

+import math
+import random
+
+from mu_map.data.datasets import MuMapDataset
+
+
+class MuMapPatchDataset(MuMapDataset):
+    def __init__(self, dataset_dir, patches_per_image=100, patch_size=32, shuffle=True):
+        super().__init__(dataset_dir)
+
+        self.patches_per_image = patches_per_image
+        self.patch_size = patch_size
+        self.shuffle = shuffle
+
+        self.patches = []
+        self.generate_patches()
+
+    def generate_patches(self):
+        for i, (recon, mu_map) in enumerate(zip(self.reconstructions, self.mu_maps)):
+            assert (
+                recon.shape[0] == mu_map.shape[0]
+            ), f"Reconstruction and MuMap were not aligned for patch dataset"
+
+            _id = self.table.iloc[i]["id"]
+
+            z_range = (0, max(recon.shape[0] - self.patch_size, 0))
+            # sometimes the mu_maps have fewer than 32 slices
+            # in this case the z-axis will be padded to the patch size, but this means we only have a single option for z
+            y_range = (0, recon.shape[1] - self.patch_size)
+            x_range = (0, recon.shape[2] - self.patch_size)
+
+            padding = [(0, 0), (0, 0), (0, 0)]
+            if recon.shape[0] < self.patch_size:
+                diff = self.patch_size - recon.shape[0]
+                padding_bef = math.ceil(diff / 2)
+                padding_aft = math.floor(diff / 2)
+                padding[0] = (padding_bef, padding_aft)
+
+            for j in range(self.patches_per_image):
+                z = random.randint(*z_range)
+                y = random.randint(*y_range)
+                x = random.randint(*x_range)
+                self.patches.append(_id, z, y, x)
+
+    def __getitem___(self, index: int):
+        _id, z, y, x, padding = self.patches[index]
+        s = self.patches
+
+        recon = self.reconstructions[_id]
+        mu_map = self.mu_maps[_id]
+
+        recon = np.pad(recon, padding, mode="constant", constant_values=0)
+        mu_map = np.pad(mu_map, padding, mode="constant", constant_values=0)
+
+        recon = recon[z : z + s, y : y + s, x : x + s]
+        mu_map = mu_map[z : z + s, y : y + s, x : x + s]
+
+        return recon, mu_map
+
+    def __len__(self):
+        return len(self.patches)
+
+
+if __name__ == "__main__":
+    import cv2 as cv
+
+    from mu_map.util import to_grayscale, grayscale_to_rgb
+
+    wname = "Dataset"
+    cv.namedWindow(wname, cv.WINDOW_NORMAL)
+    cv.resizeWindow(wname, 1600, 900)
+
+    dataset = MuMapPatchDataset("data/initial/", patches_per_image=5)
+
+    print(f"Images (Patches) in the dataset {len(dataset)}")
+
+    def create_image(recon, mu_map, recon_orig, patch, _slice):
+        s = recon.shape[0]
+        _id, _, y, x, padding = patch
+
+        _recon_orig = np.pad(recon_orig, patch, mode="constant", constant_values=0)
+        _recon_orig = recon_orig[_slice]
+        _recon_orig = to_grayscale(_recon_orig)
+        _recon_orig = grayscale_to_rgb(_recon_orig)
+        _recon_orig = cv.rectangle(_recon_orig, (x, y), (x + s, y + s), thickness=1)
+        _recon_orig = cv.resize(_recon_orig, (512, 512), cv.INTER_AREA)
+
+        _recon = recon[_slice]
+        _recon = to_grayscale(_recon)
+        _recon = cv.resize(_recon, (512, 512), cv.INTER_AREA)
+        _recon = grayscale_to_rgb(_recon)
+
+        _mu_map = mu_map[_slice]
+        _mu_map = to_grayscale(_mu_map)
+        _mu_map = cv.resize(_mu_map, (512, 512), cv.INTER_AREA)
+        _mu_map = grayscale_to_rgb(_mu_map)
+
+        space = np.full((3, 512, 10), 239, np.uint8)
+        return np.hstack((_recon, space, _mu_map, space, _recon_orig))
+
+    for i in range(len(dataset)):
+        _i = 0
+
+        patch = dataset.patches[i]
+        _id, z, y, x, padding = patch
+        print(
+            "Patch {str(i+1):>len(str(len(dataset)))}/{len(dataset)} - Location [{z:02d}, {y:02d}, {x:02d}] - Padding [{padding[0][0], padding[0][0]}]"
+        )
+        recon, mu_map = dataset[i]
+        recon_orig = dataset.reconstructions[_id]
+
+        cv.imshow(combine_images(recon, mu_map, recon_orig, patch, _i))
+        key = cv.waitKey(100)
+
+        while True:
+            _i = (_i + 1) % recon.shape[0]
+
+            cv.imshow(combine_images(recon, mu_map, recon_orig, patch, _i))
+
+            if key == ord("n"):
+                break
+            elif key == ord("q"):
+                exit(0)