feat: supports zipped tiffs (#142)

Co-authored-by: anna-grim <[email protected]>

Author: anna-grim

demo/demo.py

@@ -28,7 +28,7 @@ def evaluate():
 
     """
     # Initializations
-    pred_labels = TiffReader(pred_labels_path)
+    pred_labels = TiffReader(pred_labels_path, swap_axes=False)
     skeleton_metric = SkeletonMetric(
         groundtruth_pointer,
         pred_labels,

demo/results-overview.txt

@@ -13,3 +13,18 @@ Average Results...
 Total Results...
   # Splits: 31
   # Merges: 0
+Average Results...
+  # Splits: 7.9680
+  # Merges: 0.0000
+  Split Rate: 114.6940
+  Merge Rate: 0.0000
+  % Split Edges: 1.1996
+  % Omit Edges: 4.5086
+  % Merged Edges: 0.0000
+  Edge Accuracy: 95.4914
+  ERL: 180.8849
+  Normalized ERL: 0.3949
+
+Total Results...
+  # Splits: 31
+  # Merges: 0

demo/results.csv

@@ -1,12 +1,12 @@
 ,# Splits,# Merges,Split Rate,Merge Rate,% Split Edges,% Omit Edges,% Merged Edges,Edge Accuracy,ERL,Normalized ERL,GT Run Length
-SNT_Data-002,0,,84.0837616185713,,0.0,0.0,0.0,100.0,84.08,1.0,84.08
+SNT_Data-002,0,,84.08376161857129,,0.0,0.0,0.0,100.0,84.08,1.0,84.08
 SNT_Data-035,0,,163.37074041968347,,0.0,0.0,0.0,100.0,163.37,1.0,163.37
-SNT_Data-037,1,,211.98055903143307,,0.98,1.96,0.0,98.04,184.57,0.8585,214.98
-SNT_Data-038,1,,251.78664303157586,,0.83,1.65,0.0,98.35,144.38,0.5667,254.79
-SNT_Data-041,4,,55.46881994891756,,2.83,7.55,0.0,92.45,52.62,0.2286,230.17
+SNT_Data-037,1,,211.9805590314331,,0.98,1.96,0.0,98.04,184.57,0.8585,214.98
+SNT_Data-038,1,,251.78664303157595,,0.83,1.65,0.0,98.35,144.38,0.5667,254.79
+SNT_Data-041,4,,55.46881994891758,,2.83,7.55,0.0,92.45,52.62,0.2286,230.17
 SNT_Data-043,2,,46.354813254114404,,1.92,9.62,0.0,90.38,35.32,0.3334,105.96
 SNT_Data-051,0,,106.56843799568803,,0.0,0.0,0.0,100.0,106.57,1.0,106.57
-SNT_Data-052,6,,99.17738848187408,,1.37,6.48,0.0,93.52,265.1,0.4184,633.57
-SNT_Data-053,15,,98.71530688808681,,1.31,4.46,0.0,95.54,207.79,0.1343,1547.45
-SNT_Data-062,2,,105.18979564964228,,0.9,8.11,0.0,91.89,116.9,0.5144,227.24
-SNT_Data-074,0,,80.17991450259144,,0.0,0.0,0.0,100.0,80.18,1.0,80.18
+SNT_Data-052,6,,99.17738848187402,,1.37,6.48,0.0,93.52,265.1,0.4184,633.57
+SNT_Data-053,15,,98.7153068880868,,1.31,4.46,0.0,95.54,207.79,0.1343,1547.45
+SNT_Data-062,2,,105.1897956496423,,0.9,8.11,0.0,91.89,116.9,0.5144,227.24
+SNT_Data-074,0,,80.17991450259146,,0.0,0.0,0.0,100.0,80.18,1.0,80.18

src/segmentation_skeleton_metrics/utils/img_util.py

@@ -12,8 +12,10 @@
 from abc import ABC, abstractmethod
 from tifffile import imread
 
+import io
 import numpy as np
 import tensorstore as ts
+import zipfile
 
 
 class ImageReader(ABC):
@@ -168,18 +170,22 @@ class TiffReader(ImageReader):
     Class that reads an image with the Tifffile library.
     """
 
-    def __init__(self, img_path, swap_axes=True):
+    def __init__(self, img_path, inner_tiff_filename=None, swap_axes=True):
         """
         Instantiates a TiffReader image reader.
 
         Parameters
         ----------
         img_path : str
-            Path to a TIFF image.
+            Path to a TIFF image or ZIP archive containing a TIFF image.
+        inner_tiff_filename : str or None, optional
+            If img_path is a ZIP file, specifies the TIFF filename inside the
+            ZIP. Default is None.
         swap_axes : bool, optional
             Indication of whether to swap axes 0 and 2. Default is True.
         """
         # Instance attributes
+        self.inner_tiff_filename = inner_tiff_filename
         self.swap_axes = swap_axes
 
         # Call parent class
@@ -189,7 +195,15 @@ def _load_image(self):
         """
         Loads image using the Tifffile library.
         """
-        self.img = imread(self.img_path)
+        #  Read image
+        if self.img_path.lower().endswith(".zip"):
+            with zipfile.ZipFile(self.img_path, "r") as z:
+                with z.open(self.inner_tiff_filename) as f:
+                    self.img = imread(io.BytesIO(f.read()))
+        else:
+            self.img = imread(self.img_path)
+
+        # Swap axes (if applicable)
         if self.swap_axes:
             self.img = np.swapaxes(self.img, 0, 2)
 

src/segmentation_skeleton_metrics/utils/util.py

@@ -267,7 +267,7 @@ def read_txt_from_gcs(bucket_name, path):
     """
     client = storage.Client()
     bucket = client.bucket(bucket_name)
-    blob = bucket.blob(filename)
+    blob = bucket.blob(path)
     return blob.download_as_text()