added the ability to read dzip files

PyNutil/coordinate_extraction.py

@@ -10,6 +10,8 @@ import cv2
 from skimage import measure
 import threading
 import re 
+from .reconstruct_dzi import reconstruct_dzi
+
 
 def number_sections(filenames, legacy=False):
     """
@@ -208,7 +210,10 @@ def segmentation_to_atlas_space(
 ):
     """Combines many functions to convert a segmentation to atlas space. It takes care
     of deformations."""
-    segmentation = cv2.imread(segmentation_path)
+    if segmentation_path.endswith(".dzip"):
+        segmentation = reconstruct_dzi(segmentation_path)
+    else:
+        segmentation = cv2.imread(segmentation_path)
     if pixel_id == "auto":
         # Remove the background from the segmentation
         segmentation_no_background = segmentation[~np.all(segmentation == 255, axis=2)]

PyNutil/main.py

@@ -8,6 +8,7 @@ from datetime import datetime
 import os
 
 
+
 class PyNutil:
     """A utility class for working with brain atlases and segmentation data.
 

PyNutil/reconstruct_dzi.py

+import cv2
+import numpy as np
+import os
+import zipfile
+import xmltodict
+
+def reconstruct_dzi(zip_file_path):
+    """
+    Reconstructs a Deep Zoom Image (DZI) from a zip file containing the tiles.
+    :param zip_file_path: Path to the zip file containing the tiles.
+    :return: The reconstructed DZI.
+    """
+    with zipfile.ZipFile(zip_file_path, "r") as zip_file:
+        # Get the highest level of the pyramid
+        highest_level = str(
+            np.max(
+                [
+                    int(os.path.split(os.path.split(i)[0])[1])
+                    for i in zip_file.namelist()
+                    if i.endswith(".png")
+                ]
+            )
+        )
+
+        # Get the filenames of the highest level tiles
+        highest_level_files = [
+            i for i in zip_file.namelist() if i.endswith(".png") and i.split("/")[-2] == highest_level
+        ]
+
+        # Read the DZI file
+        dzi_file = zip_file.open([i for i in zip_file.namelist() if i.endswith(".dzi")][0])
+        xml = dzi_file.read()
+        json_data = xmltodict.parse(xml)
+        tileSize = json_data["Image"]["@TileSize"]
+        width, height = int(json_data["Image"]["Size"]["@Width"]), int(json_data["Image"]["Size"]["@Height"])
+
+        # Create an empty image
+        image = np.zeros((height, width, 3), dtype=np.uint8)
+
+        # Fill in the image with the highest level tiles
+        for file in highest_level_files:
+            with zip_file.open(file) as f:
+                contents = f.read()
+            # Decode the binary PNG data
+            image_ = cv2.imdecode(np.frombuffer(contents, np.uint8), cv2.IMREAD_COLOR)
+            x, y = map(int, os.path.splitext(os.path.split(file)[1])[0].split("_"))
+            x, y = x * int(tileSize), y * int(tileSize)
+            image[y : y + image_.shape[0], x : x + image_.shape[1], :] = image_
+
+        # Save the image
+    return image
\ No newline at end of file