color coded rois are labeled

mtor/__init__.py

@@ -20,4 +20,5 @@ def run():
 
 
 def run_data():
-    cached_data_workflow("mtor-bilder")
+    dw = cached_data_workflow("mtor-bilder")  # noqa: F841
+    # postprocessing_workflow(dw.data, dw.parameters)  # noqa: F841

mtor/postproc.py

@@ -1,6 +1,9 @@
 import pathlib
 
-from .commons import LABEL_SELECTED, LABEL_DISCARDED
+from PIL import Image, ImageDraw, ImageFont
+from tqdm import tqdm
+
+from .commons import RE_DIGITS, LABEL_SELECTED, LABEL_DISCARDED
 
 
 def stem_file_list(selected_files):
@@ -8,20 +11,38 @@ def stem_file_list(selected_files):
 
 
 def rename_color_coded_images(file_stems, parameters):
-    rename_pairs = []
+    colors = {LABEL_DISCARDED: (198, 78, 82), LABEL_SELECTED: (74, 114, 174)}
-    for path in parameters.colored_dir.iterdir():
+    top = parameters.roi_top
+    bottom = parameters.roi_bottom
+    left = parameters.roi_left
+    right = parameters.roi_right
+    try:
+        font = ImageFont.truetype("Courier New.ttf", 18)
+    except OSError:
+        font = None
+    font_y_pos = parameters.image_height - 25 - 18
+    for path in tqdm(list(parameters.colored_dir.iterdir())):
         if not path.stem.startswith("."):
             label = (
                 LABEL_SELECTED if path.stem in file_stems else LABEL_DISCARDED
             )
-            new_name = path.with_name(f"{path.stem}_{label}{path.suffix}")
+            new_path = path.with_name(f"{path.stem}_{label}{path.suffix}")
-            rename_pairs.append((path, new_name))
+            img = Image.open(path)
-    return rename_pairs
+            # draw a colored roi
+            draw = ImageDraw.Draw(img)
+            color = colors[label]
+            draw.rectangle(
+                [(left, top), (right, bottom)], outline=color, width=2
+            )
+            # add sequence number
+            sequence_nr = RE_DIGITS.search(path.name).group()
+            draw.text((25, font_y_pos), sequence_nr, font=font)
+            img.save(new_path)
+            path.unlink()
 
 
 def sort_cut_images(file_stems, parameters):
-    sort_pairs = []
+    for path in tqdm(list(parameters.cuts_dir.iterdir())):
-    for path in parameters.cuts_dir.iterdir():
         if not path.stem.startswith("."):
             label = (
                 LABEL_SELECTED if path.stem in file_stems else LABEL_DISCARDED
@@ -30,11 +51,12 @@ def sort_cut_images(file_stems, parameters):
                 parameters[f"cuts_{label}_dir"]
                 / f"{path.stem}_cut_{label}{path.suffix}"
             )
-            sort_pairs.append((path, new_path))
+        path.rename(new_path)
-    return sort_pairs
 
 
 def remove_cuts_dir(parameters):
-    for item in parameters["cuts_dir"].iterdir():
+    cuts_dir = parameters["cuts_dir"]
-        item.unlink()
+    if cuts_dir.is_dir():
-    parameters["cuts_dir"].rmdir()
+        for item in cuts_dir.iterdir():
+            item.unlink()
+        parameters["cuts_dir"].rmdir()

mtor/workflows.py

@@ -79,11 +79,8 @@ def data_workflow(stats_results, parameters):
 def postprocessing_workflow(selected_files, parameters):
     print("4/4: Post processing")
     file_stems = stem_file_list(selected_files)
-    cc_rename_pairs = rename_color_coded_images(file_stems, parameters)
+    rename_color_coded_images(file_stems, parameters)
-    cut_sort_pairs = sort_cut_images(file_stems, parameters)
+    sort_cut_images(file_stems, parameters)
-    file_pairs = cc_rename_pairs + cut_sort_pairs
-    for old_path, new_path in tqdm(file_pairs):
-        old_path.rename(new_path)
     remove_cuts_dir(parameters)
 
 

test_mtor.py

@@ -5,5 +5,5 @@ tif_dir = "original_tifs"
 #mtor.process_tifs(tif_dir, 50, 910, 300, 660, boost=5)
 
 
-#mtor.run()
+mtor.run()
-mtor.run_data()
+#mtor.run_data()