merging to master

docker/wsi-worker/extract_metadata.py

@@ -1,14 +1,81 @@
 import openslide
 import sys
 import json
+import math
+
+def getCurrentLetter(n):
+    string = ""
+    while n > 0:
+        n, remainder = divmod(n - 1, 26)
+        string = chr(65 + remainder) + string
+    return string
+
+def calculateGrids(metadata):
+    verticalSize = 500
+    horizontalSize = 500
+    lineThickness = 13
+    vertical = verticalSize / float(metadata['openslide']['mpp_y']);
+    horizontal = horizontalSize / float(metadata['openslide']['mpp_y']);
+    overlay = []
+    overlayLabel = []
+    # Make sure we have the necessary information for the slide before we calculate
+    if ((metadata != None) and metadata['aperio'] and metadata['aperio']['OriginalHeight'] != None and metadata['aperio']['OriginalWidth'] != None):
+        width = int(metadata['aperio']['OriginalWidth'])
+        height = int(metadata['aperio']['OriginalHeight'])
+        gridLineLengthForHeight = (math.ceil(((height + horizontal) / horizontal)) - 1) * horizontal;
+        gridLineLengthForWidth = (math.ceil(((width + horizontal) / horizontal)) - 1) * horizontal;
+
+        # determine where to put the vertical gridlines
+        i = 0.0
+        while (i <= (width + vertical)):
+            overlay.append({
+                'px': i,
+                'py': 0,
+                'width': lineThickness,
+                'height': gridLineLengthForHeight,
+                'className': 'gridline'
+            })
+            i += vertical
+
+        # determine where to put the horizontal gridlines
+        j = 0.0
+        while (j <= (height + horizontal)):
+            overlay.append({
+                'px': 0,
+                'py': j,
+                'width': gridLineLengthForWidth,
+                'height': lineThickness,
+                'className': 'gridline'
+            })
+            j += horizontal
+
+    currentNumber = 0
+    yy = 0
+    while (yy < (height)): # loop through the rows
+        currentLetterCount = 1
+        currentLetter = getCurrentLetter(currentLetterCount)
+        i=0
+        while (i < (width)): # loop through the columns
+            overlayLabel.append(currentLetter + str(currentNumber))
+            overlay.append({
+                'id': 'labelOverlay-' + currentLetter + str(currentNumber),
+                'px': 0 + (i/vertical * vertical + lineThickness),
+                'py': 0 + (yy/horizontal * horizontal + lineThickness),
+            })
+            i+= vertical
+            currentLetterCount += 1
+            currentLetter = getCurrentLetter(currentLetterCount)
+        yy += vertical
+        currentNumber += 1
+    metadata['overlay'] = overlay
+    metadata['overlayLabel'] = overlayLabel
+
 
-print("\n ".join(sys.argv))
 
 svsfile = sys.argv[1]
 metadata_out = sys.argv[2]
 slide = openslide.OpenSlide(svsfile)
 
-
 metadata = {}
 for properties in slide.properties:
     if '.' in properties:
@@ -20,9 +87,11 @@
             metadata[mainKey][subkey] = slide.properties[properties]
         else:
             metadata[mainKey] = {subkey: slide.properties[properties]}
-
-print('metadata_out', metadata_out)
+            
+calculateGrids(metadata)
 with open(metadata_out, 'w') as metadata_file:
     metadata_file.write(json.dumps(metadata))
 
-slide.close()
+slide.close();
+
+