Merge pull request #38 from camicroscope/develop

3.8.0

SlideServer.py

@@ -9,7 +9,7 @@
 from os import listdir
 from os.path import isfile, join
 from spritemaker import createSpritesheet
-
+from PIL import Image
 import urllib
 import flask
 import flask_cors
@@ -38,6 +38,7 @@
 app.config['TEMP_FOLDER'] = "/images/uploading/"
 app.config['TOKEN_SIZE'] = 10
 app.config['SECRET_KEY'] = os.urandom(24)
+app.config['ROI_FOLDER'] = "/images/roiDownload"
 
 ALLOWED_EXTENSIONS = set(['svs', 'tif', 'tiff', 'vms', 'vmu', 'ndpi', 'scn', 'mrxs', 'bif', 'svslide'])    
 
@@ -280,38 +281,44 @@ def getLabelsZips():
 @app.route('/workbench/getCustomData', methods=['POST'])
 def getCustomData():
     data = flask.request.get_json()
-    fileName = data['fileNames'][0]
-    userFolder = ''.join(random.choice(
-    string.ascii_uppercase + string.digits) for _ in range(20))
+    fileName = data['fileName']
+    userFolder = data['userFolder']
     if not os.path.isdir(app.config['DATASET_FOLDER']+userFolder):
         os.makedirs(app.config['DATASET_FOLDER']+userFolder)
     path = os.path.join(app.config['DATASET_FOLDER']+userFolder+'/', fileName)
-    fileData = base64.b64decode(data['files'][0])
+    fileData = base64.b64decode(data['file'])
+    offset = data['offset']
     file = open(path, "ab")
-    file.seek(0)
+    file.seek(int(offset))
     file.write(fileData)
     file.close()
-    if(zipfile.is_zipfile(path) == False):
-        deleteDataset(userFolder)
-        return flask.Response(json.dumps({'error': 'Not a valid zip file/files'}), status=400)
-    file = zipfile.ZipFile(path, 'r')
-    # app.logger.info(file.namelist())
-    contents = file.namelist()
-    labelsData = {'labels': [], 'counts': [], 'userFolder': userFolder}
-    for item in contents:
-        if '/' not in item:
-            return flask.Response(json.dumps({'error': 'zip should contain only folders!'}), status=400)
-        if item.endswith('/') == False and item.endswith('.jpg') == False and item.endswith('.png') == False:
-            return flask.Response(json.dumps({'error': 'Dataset should have only png/jpg files!'}), status=400)
-        if item.split('/')[0] not in labelsData['labels']:
-            labelsData['labels'].append(item.split('/')[0])
-    for label in labelsData['labels']:
-        count = -1
+    final = data['final']
+    if(final == 'true'):
+        if(zipfile.is_zipfile(path) == False):
+            deleteDataset(userFolder)
+            return flask.Response(json.dumps({'error': 'Not a valid zip file/files'}), status=400)
+        file = zipfile.ZipFile(path, 'r')
+        # app.logger.info(file.namelist())
+        contents = file.namelist()
+        labelsData = {'labels': [], 'counts': [], 'userFolder': userFolder}
         for item in contents:
-            if item.startswith(label+'/'):
-                count+=1
-        labelsData['counts'].append(count)
-    return flask.Response(json.dumps(labelsData), status=200)
+            if '/' not in item:
+                deleteDataset(userFolder)
+                return flask.Response(json.dumps({'error': 'zip should contain only folders!'}), status=400)
+            if item.endswith('/') == False and item.endswith('.jpg') == False and item.endswith('.jpeg') == False and item.endswith('.png') == False and item.endswith('.tif') == False and item.endswith('.tiff') == False:
+                deleteDataset(userFolder)
+                return flask.Response(json.dumps({'error': 'Dataset zip should have only png/jpg/tif files!'}), status=400)
+            if item.split('/')[0] not in labelsData['labels']:
+                labelsData['labels'].append(item.split('/')[0])
+        for label in labelsData['labels']:
+            count = -1
+            for item in contents:
+                if item.startswith(label+'/'):
+                    count+=1
+            labelsData['counts'].append(count)
+        return flask.Response(json.dumps(labelsData), status=200)
+    else:
+        return flask.Response(json.dumps({'status' : 'pending'}), status=200)
 
 
 # Route to organise the extracted zip file data according to user sent customized labels and create a spritesheet
@@ -429,3 +436,95 @@ def deleteDataset(userFolder):
         return flask.Response(json.dumps({"deleted": "false", 'message': 'Traversal detected or invalid foldername'}), status=403)
     shutil.rmtree(app.config['DATASET_FOLDER']+userFolder)
     return flask.Response(json.dumps({"deleted": "true"}), status=200)
+
+
+# Helper function for converting slides into jpg 
+def _get_concat_h(img_lst):
+    width, height, h = sum([img.width for img in img_lst]), img_lst[0].height, 0
+    dst = Image.new('RGB', (width, height))
+    for img in img_lst:
+        dst.paste(img, (h, 0))
+        h += img.width
+    return dst
+
+# Helper function for converting slides into jpg 
+def _get_concat_v(img_lst):
+    width, height, v = img_lst[0].width, sum([img.height for img in img_lst]), 0
+    dst = Image.new('RGB', (width, height))
+    for img in img_lst:
+        dst.paste(img, (0, v))
+        v += img.height
+    return dst
+
+# FUnction to convert slides into jpg images
+def convert(fname, input_dir , output_dir):
+    UNIT_X, UNIT_Y = 5000, 5000
+    try:
+
+        save_name = fname.split(".")[0] + ".jpg"
+        os_obj = openslide.OpenSlide(input_dir+"/"+fname)
+        w, h = os_obj.dimensions
+        w_rep, h_rep = int(w/UNIT_X)+1, int(h/UNIT_Y)+1
+        w_end, h_end = w%UNIT_X, h%UNIT_Y
+        w_size, h_size = UNIT_X, UNIT_Y
+        w_start, h_start = 0, 0
+        v_lst = []
+        for i in range(h_rep):
+            if i == h_rep-1:
+                h_size = h_end 
+            h_lst = []
+            for j in range(w_rep):
+                if j == w_rep-1:
+                    w_size = w_end
+                img = os_obj.read_region((w_start,h_start), 0, (w_size,h_size))
+                img = img.convert("RGB")
+                h_lst.append(img)
+                w_start += UNIT_X
+            v_lst.append(h_lst)
+            w_size = UNIT_X
+            h_start += UNIT_Y
+            w_start = 0
+        concat_h = [_get_concat_h(v) for v in v_lst]
+        concat_hv = _get_concat_v(concat_h)
+        concat_hv.save(output_dir+"/"+save_name)
+    except:
+        print("Can't open image file : %s"%fname)
+        traceback.print_exc()
+    return    
+
+# Route to extract the patches using the predictions recieved 
+@app.route('/roiExtract', methods = ['POST'])
+def roiExtract():
+    data = flask.request.get_json()
+    pred = data['predictions']
+    filename = data['filename']
+    step = data['patchsize']
+    fn =filename.split(".")[0] + ".jpg"
+    if  os.path.isdir("/images/roiDownload"):
+        shutil.rmtree(app.config['ROI_FOLDER'])
+    os.makedirs("/images/roiDownload")
+    filepath = "/images/roiDownload/roi_Download" + filename + ".zip"
+    convert(filename, "/images","/images/roiDownload")
+    download_patches = zipfile.ZipFile(filepath, 'w')
+    img = Image.open("/images/roiDownload/"+fn)
+    for i in range(len(data['predictions'])):
+        img1 = img.crop((int(data['predictions'][i]['X']),int(data['predictions'][i]['Y']) , int(data['predictions'][i]['X'])+int(step),int(data['predictions'][i]['Y'])+int(step)))
+        img1.save("/images/roiDownload/"+str(data['predictions'][i]['cls'])+'_'+str(i)+'_'+ str(data['predictions'][i]['acc']*100)+".jpg")
+        download_patches.write("/images/roiDownload/"+str(data['predictions'][i]['cls'])+'_'+str(i)+'_'+ str(data['predictions'][i]['acc']*100)+".jpg" , "/patches/"+
+        str(data['predictions'][i]['cls'])+"/"+str(data['predictions'][i]['cls'])+'_'+str(i)+'_'+ str(data['predictions'][i]['acc']*100)+".jpg")
+
+    download_patches.close()
+
+    # img = openslide.OpenSlide.read_region((0,0),0,(100,100))
+    # img = slide.open_image(img_path)
+    # res= { "data" :"" }
+    # res['data']= pred
+    return flask.Response(json.dumps({"extracted": "true"}), status=200)
+
+# Route to send back the extracted
+@app.route('/roiextract/<file_name>')
+def roiextract(file_name):
+
+    return flask.send_from_directory(app.config["ROI_FOLDER"],filename=file_name, as_attachment=True, cache_timeout=0 )
+
+

SlideUtil.py

@@ -47,7 +47,7 @@ def openslidedata(metadata):
     metadata['width'] = slideData.get(openslide.PROPERTY_NAME_BOUNDS_WIDTH, None)
     metadata['vendor'] = slideData.get(openslide.PROPERTY_NAME_VENDOR, None)
     metadata['level_count'] = int(slideData.get('level_count', 1))
-    metadata['objective'] = float(slideData.get("aperio.AppMag", None))
+    metadata['objective'] = float(slideData.get("aperio.AppMag", 0.0))
     metadata['md5sum'] = file_md5(metadata['location'])
     metadata['timestamp'] = time.time()
     thumbnail_size = config.get('thumbnail_size', None)

requirements.txt

@@ -3,4 +3,5 @@ flask
 Werkzeug
 flask-cors
 requests
-numpy
+numpy
+Pillow

spritemaker.py

@@ -19,15 +19,12 @@ def createSpritesheet(datasetPath, labelsNames, width, height):
     y_offset = 0
     imageCount = 0
     imageFiles = []
-    for image_file in Path(TRAINING_PATH).glob("**/*.jpg"):
-        imageCount += 1
-        imageFiles.append(image_file)
-    for image_file in Path(TRAINING_PATH).glob("**/*.png"):
-        imageCount += 1
-        imageFiles.append(image_file)
-    for image_file in Path(TRAINING_PATH).glob("**/*.jpeg"):
-        imageCount += 1
-        imageFiles.append(image_file)
+
+    allowed_extentions = ['jpg', 'png', 'jpeg', 'tif', 'tiff']
+    for ext in allowed_extentions:
+        for image_file in Path(TRAINING_PATH).glob("**/*." + ext):
+            imageCount += 1
+            imageFiles.append(image_file)
 
     print(imageCount, file=sys.stderr)
     new_im = Image.new('RGB', (width*height, imageCount))