Composite parser

ijroi/ijroi.py

@@ -62,19 +62,17 @@ def getfloat():
         v = np.int32(get32())
         return v.view(np.float32)
 
+    #===========================================================================
+    #Read Header data
+
     magic = fileobj.read(4)
-    if magic != b'Iout':
-        raise ValueError('Magic number not found')
     version = get16()
 
     # It seems that the roi type field occupies 2 Bytes, but only one is used
     roi_type = get8()
     # Discard second Byte:
     get8()
-
-    if roi_type not in [RoiType.FREEHAND, RoiType.POLYGON, RoiType.RECT, RoiType.POINT]:
-        raise NotImplementedError('roireader: ROI type %s not supported' % roi_type)
-
+
     top = get16()
     left = get16()
     bottom = get16()
@@ -89,17 +87,65 @@ def getfloat():
     stroke_color = get32()
     fill_color = get32()
     subtype = get16()
-    if subtype != 0:
-        raise NotImplementedError('roireader: ROI subtype %s not supported (!= 0)' % subtype)
+
     options = get16()
     arrow_style = get8()
     arrow_head_size = get8()
     rect_arc_size = get16()
     position = get32()
     header2offset = get32()
 
+    # End Header data
+    #===========================================================================
+
+    #RoiDecoder.java#L177
+    subPixelResolution = ((options&SUB_PIXEL_RESOLUTION)!=0) and (version>=222)
+
+    # Check exceptions
+    if magic != b'Iout':
+        raise ValueError('Magic number not found')
+
+    if roi_type not in [RoiType.FREEHAND, RoiType.TRACED, RoiType.POLYGON, RoiType.RECT, RoiType.POINT]:
+        raise NotImplementedError('roireader: ROI type %s not supported' % roi_type)
+
+    if subtype != 0:
+        raise NotImplementedError('roireader: ROI subtype %s not supported (!= 0)' % subtype)
+
+    #Composite ROI
+    if shape_roi_size > 0:
+        coords_bytes = fileobj.read()
+        buffer = np.frombuffer(coords_bytes, dtype='>f4', count=shape_roi_size)
+
+        segments = []
+
+        # the number of units to read depens on the type of segement...
+        # this only works with basic line segemnts (ie type 1, type 2 is quadratic
+        # and type 3 is cubic
+
+        rc = {4:1, 0:3, 1:3, 2:5, 3:7}
+
+        # scrolls through the buffer one line segment at a time,
+        # line segments are stored as x,y tuples, I reverse the
+        # segment, in order to remain consitant with the other return types
+        i = 0
+        these_points = []
+        while i < buffer.size:
+            _type = buffer[i]
+            read_len = rc[_type]
+            seg = buffer[i+1:i+read_len]
+            if seg.size == 0:
+                segments.append(np.r_[these_points])
+                these_points = []
+
+            else:
+                these_points.append(seg[::-1])
+
+            i = i+read_len
+
+        return segments
+
     if roi_type == RoiType.RECT:
-        if options & SUB_PIXEL_RESOLUTION:
+        if subPixelResolution:
             return np.array(
                 [[y1, x1], [y1, x1+x2], [y1+y2, x1+x2], [y1+y2, x1]],
                 dtype=np.float32)
@@ -108,7 +154,7 @@ def getfloat():
                 [[top, left], [top, right], [bottom, right], [bottom, left]],
                 dtype=np.int16)
 
-    if options & SUB_PIXEL_RESOLUTION:
+    if subPixelResolution:
         getc = getfloat
         points = np.empty((n_coordinates, 2), dtype=np.float32)
         fileobj.seek(4*n_coordinates, 1)
@@ -119,7 +165,7 @@ def getfloat():
     points[:, 1] = [getc() for i in range(n_coordinates)]
     points[:, 0] = [getc() for i in range(n_coordinates)]
 
-    if options & SUB_PIXEL_RESOLUTION == 0:
+    if not subPixelResolution:
         points[:, 1] += left
         points[:, 0] += top