Merge branch 'main' into watcher_skip

src/toffy/rosetta.py

@@ -677,14 +677,16 @@ def rescale_raw_imgs(img_out_dir, scale=200):
         fov_dir = os.path.join(img_out_dir, fov)
         # create subdirectory for the new images
         sub_dir = os.path.join(fov_dir, "rescaled")
-        os.makedirs(sub_dir)
+        if not os.path.exists(sub_dir):
+            os.makedirs(sub_dir)
         chans = io_utils.list_files(fov_dir)
         # rescale each channel image
         for chan in chans:
-            img = io.imread(os.path.join(fov_dir, chan))
-            img = (img / scale).astype("float32")
             fname = os.path.join(sub_dir, chan)
-            image_utils.save_image(fname, img)
+            if not os.path.exists(fname):
+                img = io.imread(os.path.join(fov_dir, chan))
+                img = (img / scale).astype("float32")
+                image_utils.save_image(fname, img)
 
 
 def generate_rosetta_test_imgs(

tests/rosetta_test.py

@@ -1,6 +1,7 @@
 import copy
 import os
 import tempfile
+import time
 from pathlib import Path
 
 import numpy as np
@@ -639,10 +640,17 @@ def test_rescale_raw_imgs():
 
         # test successful rescale of data
         rescaled_img_data = load_utils.load_imgs_from_tree(temp_dir, "rescaled")
+        create_time = Path(os.path.join(temp_dir, fovs[0], "rescaled")).stat().st_ctime
         assert rescaled_img_data.all() == (img_data / 200).all()
 
         assert rescaled_img_data.dtype == "float32"
 
+        # re-run function and check the files are not re-written
+        time.sleep(3)
+        rosetta.rescale_raw_imgs(temp_dir)
+        modify_time = Path(os.path.join(temp_dir, fovs[0], "rescaled")).stat().st_mtime
+        assert np.isclose(modify_time, create_time)
+
 
 def create_rosetta_comp_structure(
     raw_data_dir,