Merge pull request #13 from camicroscope/release

For 3.1.0

SlideUtil.py

@@ -50,8 +50,6 @@ def openslidedata(metadata):
     metadata['objective'] = float(slideData.get("aperio.AppMag", None))
     metadata['md5sum'] = file_md5(metadata['filename'])
     metadata['timestamp'] = time.time()
-    metadata['study'] = ""
-    metadata['specimen'] = ""
     thumbnail_size = config.get('thumbnail_size', None)
     if thumbnail_size:
         gen_thumbnail(metadata['filename'], slide, thumbnail_size)

thumbsFromUrl.py

@@ -1,30 +1,28 @@
-import requests
 import openslide
 from multiprocessing.pool import ThreadPool
+import requests
+import sys
+from PIL import Image
+
+Image.MAX_IMAGE_PIXELS = None
+
+if len(sys.argv <2):
+    sys.exit("Expects a url as second argument")
+
+url = sys.argv[1]
 
-FILE_FIELD = "file-location"
-NAME_FIELD = "case_id"
-URL = "http://172.20.11.223:9099/services/Camic_TCIA/Image/query/find"
-IM_SIZE = 200
-THREADS = 10
+data = requests.get(url=url).json()
 
-def gen_thumbnail(filename, slide, size, imgtype="png"):
-    dest = filename + "." + imgtype
-    print(dest)
-    slide.get_thumbnail([size, size]).save(dest, imgtype.upper())
 
-def process(record):
-    file = record[FILE_FIELD]
-    name = record[NAME_FIELD]
+def get_thumbnail(obj):
+    slide = obj['file-location']
+    dest = obj['case_id'] + '.png'
     try:
-        slide = openslide.OpenSlide(file)
-        gen_thumbnail(name, slide, IM_SIZE, imgtype="png")
-        return ""
+        image = openslide.open_slide(slide)
+        image.get_thumbnail([200,200]).save(dest, "PNG")
+        return dest
     except BaseException as e:
-        # return errors only
-        return name
+        return e
 
-# do it
-manifest = requests.get(URL).json()
-res = ThreadPool(THREADS).imap_unordered(process, manifest)
+res = ThreadPool(20).imap_unordered(get_thumbnail, data)
 print([r for r in res])