Merge pull request #54 from camicroscope/develop

For 3.9.4

SlideServer.py

@@ -35,6 +35,10 @@
 # dataset storage location for the workbench tasks 
 app.config['DATASET_FOLDER'] = "/images/dataset/"
 
+#creating a uploading folder if it doesn't exist
+if not os.path.exists('/images/uploading/'):
+    os.mkdir('/images/uploading')
+
 # where to put and get slides
 app.config['UPLOAD_FOLDER'] = "/images/"
 app.config['TEMP_FOLDER'] = "/images/uploading/"

get_associated_images.py

@@ -0,0 +1,33 @@
+import openslide
+import os
+
+dir = "./PDACG/images/"
+out_dir = "./PDACG/images/associated/"
+
+for fn in os.listdir(dir):
+    if fn.endswith(".svs"):
+        try:
+            img = openslide.OpenSlide(dir + fn)
+        except:
+            print("[ERR]", fn)
+            continue
+        img_rgba  = img.associated_images;
+        if "macro" in img_rgba:
+            macro_rgb = img_rgba["macro"].convert("RGB");
+        if "label" in img_rgba:
+            label_rgb = img_rgba["label"].convert("RGB");
+        if "thumbnail" in img_rgba:
+            thumb_rgb = img_rgba["thumbnail"].convert("RGB");
+        else:
+            thumb_rgb = img.get_thumbnail((img_w,img_h)).convert("RGB");
+        fname_pre = out_dir + "/" + os.path.splitext(fn)[0];
+        if macro_rgb is not None:
+            fname_out = fname_pre + "-macro.jpg";
+            macro_rgb.save(fname_out);
+        if label_rgb is not None:
+            fname_out = fname_pre + "-label.jpg";
+            label_rgb.save(fname_out);
+        if thumb_rgb is not None:
+            fname_out = fname_pre + "-thumb.jpg";
+            thumb_rgb.save(fname_out);
+        print("[OK]", fn)