updates to register_objects to allow relabelling

jtlibrary/python/jtmodules/src/jtmodules/register_objects.handles.yaml

@@ -1,5 +1,5 @@
 ---
-version: 0.1.0
+version: 0.2.0
 
 input:
 
@@ -10,6 +10,11 @@ input:
         Binary or labeled mask image containing the objects
         (connected pixel components) that should be registered.
 
+    - name: relabel
+      type: Boolean
+      value: false
+      help: >
+        Should objects be relabeled on registration.
 output:
 
     - name: objects

jtlibrary/python/jtmodules/src/jtmodules/register_objects.py

@@ -1,4 +1,4 @@
-# Copyright (C) 2016 University of Zurich.
+# Copyright 2016 Markus D. Herrmann, University of Zurich
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,16 +17,17 @@
 '''
 import collections
 import logging
+import mahotas as mh
 from jtlib.utils import label
 
 logger = logging.getLogger(__name__)
 
-VERSION = '0.1.0'
+VERSION = '0.2.0'
 
 Output = collections.namedtuple('Output', ['objects'])
 
 
-def main(mask):
+def main(mask, relabel=False):
     '''Registers objects (connected pixel components) in an image for use by
     other (measurement) modules downstream in the pipeline. In case a binary
     mask is provided the image is automatically labeled.
@@ -46,6 +47,8 @@ def main(mask):
     '''
     if mask.dtype == 'bool':
         label_image = label(mask)
+    elif (relabel and mask.dtype == 'int32'):
+        label_image = mh.labeled.relabel(mask)[0]
     else:
         label_image = mask
     return Output(label_image)