Merge pull request #91 from camicroscope/develop

for 3.12.1

Author: birm

DicomAnnotUtils.py

@@ -134,7 +134,7 @@ def create_annotation_dicom(annot_arrays, slide_file, geojson):
 
     # add the annotation data
     ds.AnnotationGroupSequence = []
-    i = 0
+    i = 1
     idx = 1
     point_indices = []
     # make the array first?
@@ -298,7 +298,7 @@ def dicomToCamic(annot_path, image_dimensions, output_file, source_url=None, sli
                 newFeature = deepcopy(featureTemplate)
                 newFeature['geometry']['type'] = "Ellipse"
                 newFeature['geometry']['coordinates'] = [center_x, center_y]
-                newFeature['geometry']["radius"] = [major_axis_length,minor_axis_length],
+                newFeature['geometry']["radius"] = [major_axis_length,minor_axis_length]
                 newFeature['geometry']["rotation"] = rotation
                 newFeature['bound']['type'] = "Point"
                 newFeature['bound']['coordinates'] = [center_x, center_y]
@@ -378,11 +378,15 @@ def dicomToCamic(annot_path, image_dimensions, output_file, source_url=None, sli
                     #print("prev", prevIndex, "idx", idx)
                     # make a thing 
                     points = coordinates_array[prevIndex:end_idx, :]
-                    points = np.concatenate((points, [points[0]]))
+                    polygon = np.concatenate((points, [points[0]]))
                     #print('len(points)', len(points))
                     if len(points) > 0:
                         newFeature = deepcopy(featureTemplate)
-                        newFeature['geometry']['coordinates'].append(points.tolist())
+                        if x.GraphicType == "POLYLINE":
+                            newFeature['geometry']['type'] = "Polyline"
+                            newFeature['geometry']['coordinates'].append(points.tolist())
+                        else:
+                            newFeature['geometry']['coordinates'].append(polygon.tolist())
                         bounding_box = _makeBound(points)
                         # [[min_x, min_y], [min_x, max_y], [max_x, max_y], [max_x, min_y],[min_x, min_y]]
                         newFeature['bound']['coordinates'].append(bounding_box)
@@ -401,10 +405,14 @@ def dicomToCamic(annot_path, image_dimensions, output_file, source_url=None, sli
                     # and the bound
                 # then add the last one
                 points = coordinates_array[prevIndex:, :]
-                points = np.concatenate((points, [points[0]]))
+                polygon = np.concatenate((points, [points[0]]))
                 if len(points) > 0:
                     newFeature = deepcopy(featureTemplate)
-                    newFeature['geometry']['coordinates'].append(points.tolist())
+                    if x.GraphicType == "POLYLINE":
+                        newFeature['geometry']['type'] = "Polyline"
+                        newFeature['geometry']['coordinates'].append(points.tolist())
+                    else:
+                        newFeature['geometry']['coordinates'].append(polygon.tolist())
                     bounding_box = _makeBound(points)
                     # [[min_x, min_y], [min_x, max_y], [max_x, max_y], [max_x, min_y],[min_x, min_y]]
                     newFeature['bound']['coordinates'].append(bounding_box)
@@ -422,9 +430,13 @@ def dicomToCamic(annot_path, image_dimensions, output_file, source_url=None, sli
             else:
                 # whole thing at once. Only do area and circumference here.
                 points = coordinates_array
-                points = np.concatenate((points, [points[0]]))
+                polygon = np.concatenate((points, [points[0]]))
                 newFeature = deepcopy(featureTemplate)
-                newFeature['geometry']['coordinates'].append(points.tolist())
+                if x.GraphicType == "POLYLINE":
+                    newFeature['geometry']['type'] = "Polyline"
+                    newFeature['geometry']['coordinates'].append(points.tolist())
+                else:
+                    newFeature['geometry']['coordinates'].append(polygon.tolist())
                 bounding_box = _makeBound(points)
                 # [[min_x, min_y], [min_x, max_y], [max_x, max_y], [max_x, min_y],[min_x, min_y]]
                 newFeature['bound']['coordinates'].append(bounding_box)

SlideServer.py

@@ -31,6 +31,8 @@
 import hashlib
 from urllib.parse import urlparse
 from dicomweb_client.api import DICOMwebClient
+import aiohttp
+import asyncio
 
 from DicomAnnotUtils import dicomToCamic
 import pydicom
@@ -59,6 +61,12 @@
 app.config['SECRET_KEY'] = os.urandom(24)
 app.config['ROI_FOLDER'] = "/images/roiDownload"
 
+download_folder = os.getenv('DOWNLOAD_FOLDER', app.config['UPLOAD_FOLDER'])
+app.config['DOWNLOAD_FOLDER'] = download_folder
+
+if os.getenv("ALLOW_DOWNLOAD_ZIP") == "True":
+    ALLOWED_EXTENSIONS.add("zip")
+
 #creating a uploading folder if it doesn't exist
 if not os.path.exists(app.config['TEMP_FOLDER']):
     os.mkdir(app.config['TEMP_FOLDER'])
@@ -311,7 +319,7 @@ def getSlide(image_name):
     image_name = secure_relative_path(image_name)
     if not verify_extension(image_name):
         return flask.Response(json.dumps({"error": "Bad image type requested"}), status=400, mimetype='text/json')
-    folder = app.config['UPLOAD_FOLDER']
+    folder = app.config['DOWNLOAD_FOLDER']
     if os.sep in image_name:
         folder_and_file = image_name.rsplit(os.sep, 1)
         folder = os.path.join(folder, folder_and_file[0])
@@ -775,7 +783,7 @@ def find_referenced_image_by_files(source_url, study, ds):
     # If the instance is not found in the study
     return None, None
 
-def downloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn):
+def OLDdownloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn):
     instance_url = source_url + f"/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}"
     response = requests.get(instance_url, stream=True)
     if response.status_code == 200:
@@ -788,9 +796,9 @@ def downloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn)
                 if chunk:
                     if not dicom_started:
                         # Check if the chunk contains "\r\n\r\n""
-                        if b"\r\n\r\n" in chunk:
+                        start_idx = chunk.find(b"\r\n\r\n")
+                        if start_idx != -1:
                             # Find the position of "\r\n\r\n"" in the chunk
-                            start_idx = chunk.find(b"\r\n\r\n")
                             file.write(chunk[start_idx + 4:])
                             # Set dicom_started to True
                             dicom_started = True
@@ -805,6 +813,34 @@ def downloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn)
     else:
         print(f"Failed to retrieve DICOM instance. Status code: {response.status_code}")
 
+def downloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn):
+    asyncio.run(doDownloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn))
+
+async def doDownloadRawDicom(source_url, study_uid, series_uid, instance_uid, output_fn):
+    instance_url = source_url + f"/studies/{study_uid}/series/{series_uid}/instances/{instance_uid}"
+    async with aiohttp.ClientSession(trust_env=True) as session:
+        async with session.get(instance_url) as resp:
+            reader = aiohttp.MultipartReader.from_response(resp)
+            metadata = None
+            filedata = None
+            while True:
+                part = await reader.next()
+                if part is None:
+                    break
+                else:
+                    #print(dir(part))
+                    #filedata = await part.read(decode=False)
+                    app.logger.info("Working on file: " +  output_fn)
+                    with open(output_fn, 'wb') as fd:
+                        while True:
+                            part_chunk = await part.read_chunk(1024*1024)
+                            if part_chunk is None or len(part_chunk)==0:
+                                break
+                            else:
+                                fd.write(part_chunk)
+
+
+
 # dicom web based routes
 
 def doDicomSlideDownloads(source_url, study, series, instance_list, camic_slide_id):

requirements.txt

@@ -13,4 +13,5 @@ google-auth-oauthlib
 pycurl
 pydicom
 dicomweb-client
-pymongo
+pymongo
+aiohttp