Return position

ijroi/ijroi.py

@@ -3,14 +3,16 @@
 # License: MIT
 
 import numpy as np
+from collections import namedtuple
 
 
 def read_roi(fileobj):
     '''
-    points = read_roi(fileobj)
+    points, position = read_roi(fileobj)
 
     Read ImageJ's ROI format. Points are returned in a nx2 array. Each row
-    is in [row, column] -- that is, (y,x) -- order.
+    is in [row, column] -- that is, (y,x) -- order. Position is the slice 
+    number.
     '''
     # This is based on:
     # http://rsbweb.nih.gov/ij/developer/source/ij/io/RoiDecoder.java.html
@@ -119,8 +121,11 @@ def getfloat():
     if options & SUB_PIXEL_RESOLUTION == 0:
         points[:, 1] += left
         points[:, 0] += top
-
-    return points
+
+    Roi = namedtuple('Roi', 'points position')
+    roi = Roi(points=points, position=position)
+
+    return roi
 
 
 def read_roi_zip(fname):

ijroi/tests/test_ijroi.py

@@ -29,46 +29,52 @@ def test_rectangle():
 def test_freehand_circle():
     fixture = get_fixture("freehand_circle.roi")
     with fixture.open("rb") as f:
-        circle = ijroi.read_roi(f)
+        circle, position = ijroi.read_roi(f)
     assert len(circle) == 100
     assert abs(circle[:, 1].mean()-10) < 0.01
     assert abs(circle[:, 0].mean()-15) < 0.01
+    assert position == 0
 
 def test_integer_freehand():
     fixture = get_fixture("freehand_integer.roi")
     with fixture.open("rb") as f:
-        freehand = ijroi.read_roi(f)
+        freehand, position = ijroi.read_roi(f)
     assert len(freehand) == 3
     assert all(freehand[2, :] == [1, 10])
     assert freehand.dtype == np.int16
+    assert position == 0
 
 def test_polygon():
     fixture = get_fixture("polygon_circle.roi")
     with fixture.open("rb") as f:
-        circle = ijroi.read_roi(f)
+        circle, position = ijroi.read_roi(f)
     assert len(circle) == 100
     assert abs(circle[:, 1].mean()-10) < 0.01
     assert abs(circle[:, 0].mean()-15) < 0.01
+    assert position == 0
 
     fixture = get_fixture("polygon_integer.roi")
     with fixture.open("rb") as f:
-        polyint = ijroi.read_roi(f)
+        polyint, position = ijroi.read_roi(f)
     assert len(polyint) == 3
     assert all(polyint[2, :] == [1, 10])
     assert polyint.dtype == np.int16
+    assert position == 0
 
 def test_point():
     fixture = get_fixture("int_point.roi")
     with fixture.open("rb") as f:
-        point = ijroi.read_roi(f)
+        point, position = ijroi.read_roi(f)
     assert point.ndim == 2
     assert point[0,0] == 256
     assert point[0,1] == 128
+    assert position == 0
 
 def test_float_point():
     fixture = get_fixture("float_point.roi")
     with fixture.open("rb") as f:
-        point = ijroi.read_roi(f)
+        point, position = ijroi.read_roi(f)
     assert point.ndim == 2
     assert abs(point[0,0] - 567.8) < 0.01
     assert abs(point[0,1] - 123.4) < 0.01
+    assert position == 0