save marked preview in preview directory

TODO.md

@@ -8,10 +8,10 @@ Tasks related to the quality check algorithms.
 
 
 ## Previews
-- [ ] Put font file in resources directory
+- [X] Put font file in resources directory
 - [x] Add checkbox to mark outlier pixels in preview
     - Also save clean preview
-- [ ] Save marked preview in preview directory
+- [X] Save marked preview in preview directory
 
 
 ## GUI / UX
@@ -24,7 +24,7 @@ Tasks related to the quality check algorithms.
 ## Technical
 - [ ] validate config input
 - [ ] add requirements.txt or setup.py
-- [ ] use default config file that is used when no config is found
+- [X] use default config file that is used when no config is found
 # DONE
 - [X] introduce pixel sampling quality check
 - [X] automatically filter tiles without tissue
\ No newline at end of file

generate_preview.py

@@ -127,7 +127,7 @@ def insert_labels(preview, xdim, ydim):
     img = Image.fromarray(preview)
     draw = ImageDraw.Draw(img)
     preview_tile_x = preview.shape[0] / xdim
-    font = ImageFont.truetype(config['PREVIEWS']['font_path'], int(preview_tile_x*0.08))
+    font = ImageFont.truetype('resources/DejaVuSans.ttf', int(preview_tile_x*0.08))
     # TODO scale font with resolution
 
     # tile dimensions

quality_check_gui.py

@@ -134,9 +134,11 @@ def clicked_start(frame):
                 if frame.mark_outliers_state.get():  # generate preview with marked outliers
                     # TODO catch error when no preview was generated
                     marked_preview = mark_preview(preview, error_matrix, outlier_coords, filtered_coords)
-                    plt.imsave('marked_preview.png', marked_preview)
-                    # TODO fix path (not program dir)
-                    subprocess.Popen([config['PREVIEWS']['fiji_path'], 'marked_preview.png'])
+                    norm = os.path.normpath(path)
+                    # identify the section that is being analysed by its directory name
+                    dir_name = norm.split(os.sep)[-2] + '_marked'
+                    save_preview(marked_preview, frame, dir_name)
+
 
             frame.print(f'')
         frame.progress_text.set('Done!')
@@ -144,13 +146,10 @@ def clicked_start(frame):
     threading.Thread(target=logic_thread_task).start()
 
 
-def save_preview(preview, frame, tiff_path):
+def save_preview(preview, frame, dir_name):
     preview_root = config['PREVIEWS']['preview_path']
     # save preview to a fixed path
     time_stamp = datetime.now(tzlocal()).strftime('%Y%m%d_%H-%M')
-    norm = os.path.normpath(tiff_path)
-    # identify the section that is being analysed by its directory name
-    dir_name = norm.split(os.sep)[-2]
     preview_path = f'{preview_root}/{dir_name}_{time_stamp}.png'
 
     # TODO ensure no file overrides happen
@@ -206,7 +205,10 @@ def process_preview_gen(frame, tiff_path):
 
     time_post = time.time()
     frame.print(f'Generated preview in {time_post - time_pre:.2f}s')
-    save_preview(preview, frame, tiff_path)
+    norm = os.path.normpath(tiff_path)
+    # identify the section that is being analysed by its directory name
+    dir_name = norm.split(os.sep)[-2]
+    save_preview(preview, frame, dir_name)
 
     return preview