Option to reverse the offset/size array orders when getting blobs in …

…an ROI

Allow the `offset` and `size` parameters to be given in x,y,z or z,y,x order that the function will support arrays given for either ROIs or sub-images. Continue to use x,y,z as default since the current convent for ROI parameters has been to use x,y,z ordering, but this change helps prepare for changing the order to z,y,x.

magmap/cv/detector.py

@@ -659,7 +659,7 @@ def remove_close_blobs_within_sorted_array(blobs, tol):
     #print("blobs without close duplicates:\n{}".format(blobs_all))
     return blobs_all
 
-def get_blobs_in_roi(blobs, offset, size, padding=(0, 0, 0)):
+def get_blobs_in_roi(blobs, offset, size, padding=(0, 0, 0), reverse=True):
     """Get blobs within an ROI based on offset and size.
     
     Note that dimensions are in x,y,z for natural ordering but may 
@@ -668,21 +668,28 @@ def get_blobs_in_roi(blobs, offset, size, padding=(0, 0, 0)):
     Args:
         blobs: The blobs to retrieve, given as 2D array of 
             ``[n, [z, row, column, radius, ...]]``.
-        offset: Offset coordinates in x,y,z.
+        offset: Offset coordinates in .
         size: Size of ROI in x,y,z.
         padding: Additional padding outside the ROI to include.
+        reverse (bool): True to reverse the order of ``offset`` and ``size``,
+            assuming that they are in x,y,z rather than z,y,x order.
+            Defaults to True for backward compatibility with the ROI
+            convention used here.
     
     Returns:
         Tuple of blobs within the ROI and the mask used to retrieve 
         these blobs.
     """
+    if reverse:
+        offset = offset[::-1]
+        size = size[::-1]
     mask = np.all([
-        blobs[:, 0] >= offset[2] - padding[2], 
-        blobs[:, 0] < offset[2] + size[2] + padding[2],
+        blobs[:, 0] >= offset[0] - padding[0],
+        blobs[:, 0] < offset[0] + size[0] + padding[0],
         blobs[:, 1] >= offset[1] - padding[1], 
         blobs[:, 1] < offset[1] + size[1] + padding[1],
-        blobs[:, 2] >= offset[0] - padding[0], 
-        blobs[:, 2] < offset[0] + size[0] + padding[0]], axis=0)
+        blobs[:, 2] >= offset[2] - padding[2],
+        blobs[:, 2] < offset[2] + size[2] + padding[2]], axis=0)
     segs_all = blobs[mask]
     return segs_all, mask