Fix (x, y) vs. (y, x) confusion.

README.rst

@@ -13,6 +13,9 @@ it like:
  >>> isinstance(roi, np.ndarray)
  True
 
+read\_roi returns a Nx2 array, where each row is a (row, column) or (y,
+x) pair.
+
 Based on `Luis Pedro Coelho <https://github.com/luispedro>`__'s
 `readroi.py gist <https://gist.github.com/luispedro/3437255>`__.
 

ijroi/ijroi.py

@@ -9,7 +9,8 @@ def read_roi(fileobj):
  '''
  points = read_roi(fileobj)
 
- Read ImageJ's ROI format
+ Read ImageJ's ROI format. Points are returned in a nx2 array. Each row
+ is in [row, column] -- that is, (y,x) -- order.
  '''
  # This is based on:
  # http://rsbweb.nih.gov/ij/developer/source/ij/io/RoiDecoder.java.html
@@ -97,11 +98,11 @@ def getfloat():
  if roi_type == RoiType.RECT:
  if options & SUB_PIXEL_RESOLUTION:
  return np.array(
- [[x1, y1], [x1+x2, y1], [x1+x2, y1+y2], [x1, y1+y2]],
+ [[y1, x1], [y1, x1+x2], [y1+y2, x1+x2], [y1+y2, x1]],
  dtype=np.float32)
  else:
  return np.array(
- [[left, top], [right, top], [right, bottom], [left, bottom]],
+ [[top, left], [top, right], [bottom, right], [bottom, left]],
  dtype=np.int16)
 
  if options & SUB_PIXEL_RESOLUTION:

ijroi/tests/fixtures/generate_fixtures.js

@@ -18,7 +18,7 @@ var y = new java.lang.reflect.Array.newInstance(java.lang.Float.TYPE, 100);
 
 for(var i = 0; i < 100; ++i) {
  x[i] = 10 + Math.cos(i/100.0 * 2*Math.PI);
- y[i] = 10 + Math.sin(i/100.0 * 2*Math.PI);
+ y[i] = 15 + Math.sin(i/100.0 * 2*Math.PI);
 }
 
 freehand_circle = PolygonRoi(x, y, 100, Roi.FREEROI);

ijroi/tests/test_ijroi.py

@@ -17,20 +17,21 @@ def test_rectangle():
  fixture = get_fixture("subpixel_rectangle.roi")
  with fixture.open("rb") as f:
  rect = ijroi.read_roi(f)
- assert (rect == np.array([[4, 5], [8, 5], [8, 10], [4, 10]])).all()
+ assert (rect == np.array([[5, 4], [5, 8], [10, 8], [10, 4]])).all()
  assert rect.dtype == np.float32
 
  fixture = get_fixture("integer_rectangle.roi")
  with fixture.open("rb") as f:
  rect = ijroi.read_roi(f)
- assert (rect == np.array([[4, 5], [8, 5], [8, 10], [4, 10]])).all()
+ assert (rect == np.array([[5, 4], [5, 8], [10, 8], [10, 4]])).all()
  assert rect.dtype == np.int16
 
 def test_freehand_circle():
  fixture = get_fixture("freehand_circle.roi")
  with fixture.open("rb") as f:
  circle = ijroi.read_roi(f)
- assert abs(circle[:,1].mean()-10) < 0.01
+ assert abs(circle[:, 1].mean()-10) < 0.01
+ assert abs(circle[:, 0].mean()-15) < 0.01
 
 def test_integer_freehand():
  fixture = get_fixture("freehand_integer.roi")