fixing enforce_connectivity for maskSLIC

README.md

@@ -1,10 +1,6 @@
 # maskSLIC
 Simple linear iterative clustering (SLIC) in a region of interest
 
-## Development
-This code is still a work in progress. The following issues still need to be resolved:
-- [ ] Fix the enforce connectivity method to work with maskSLIC
-
 ## Outline
 This code demonstrates the adaption of SLIC for a defined region of interest. 
 The main contribution is in the placement of seed points within the ROI. 
@@ -23,4 +19,5 @@ Figure 2: The final superpixel regions within the ROI
 
 ![superpixels](outputs/p2.png)
 
-
+## Development
+This code is still a work in progress.

maskslic/_slic.pyx

@@ -215,7 +215,7 @@ def _slic_cython(double[:, :, :, ::1] image_zyx,
  return np.asarray(nearest_segments)
 
 
-def _enforce_label_connectivity_cython(Py_ssize_t[:, :, ::1] segments,
+def _enforce_label_connectivity_cython(int[:, :, ::1] segments,
  int[:, :, ::1] mask,
  Py_ssize_t n_segments,
  Py_ssize_t min_size,

maskslic/slic_superpixels.py

@@ -257,9 +257,9 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0,
 
  """
 
- if enforce_connectivity:
- raise NotImplementedError("Enforce connectivity has not been implemented yet for maskSLIC.\n"
- "Please set enforce connectivity to 'False' ")
+ # if enforce_connectivity:
+ # raise NotImplementedError("Enforce connectivity has not been implemented yet for maskSLIC.\n"
+ # "Please set enforce connectivity to 'False' ")
 
  if slic_zero:
  raise NotImplementedError("Slic zero has not been implemented yet for maskSLIC.")
@@ -404,14 +404,15 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=0,
  labels = _slic_cython(image, mask, segments, step, max_iter, spacing, slic_zero, only_dist=False)
 
  if enforce_connectivity:
- segment_size = depth * height * width / n_segments
+ if msk is None:
+ segment_size = depth * height * width / n_segments
+ else:
+ segment_size = msk.sum() / n_segments
+
  min_size = int(min_size_factor * segment_size)
  max_size = int(max_size_factor * segment_size)
- labels = _enforce_label_connectivity_cython(labels,
- mask,
- n_segments,
- min_size,
- max_size)
+
+ labels = _enforce_label_connectivity_cython(labels, mask, n_segments, min_size, max_size)
 
  if is_2d:
  labels = labels[0]

run_example.py

@@ -13,6 +13,8 @@
 # roi = img_as_float(chelsea_mask())
 roi = roi[:, :, 3] > 0
 
+# ~~~~~~~~~~~~ Example 1: maskSLIC ~~~~~~~~~~~~~
+
 t1 = time.time()
 # Note that compactness is defined differently because a grid is not used. Lower compactness for maskSLIC is equivalent
 segments = seg.slic(img, compactness=10, seed_type='nplace', mask=roi, n_segments=12,
@@ -25,6 +27,8 @@
 plt.contour(roi, contours=1, colors='red', linewidths=1)
 plt.axis('off')
 
+# ~~~~~~~~~~~ Example 2: SLIC ~~~~~~~~~~~~~~~~~
+
 t1 = time.time()
 segments = seg.slic(img, compactness=30, seed_type='grid', n_segments=80, plot_examples=False)
 # segments[roi==0] = -1
@@ -37,3 +41,27 @@
 plt.axis('off')
 plt.show()
 
+
+# ~~~~~~~~ Example 3: Enforcing connectivity ~~~~~~~~~~~~~
+
+# without enforcing connectivity
+# segments = seg.slic(img, compactness=4, seed_type='nplace', mask=roi, n_segments=12,
+# recompute_seeds=True, enforce_connectivity=False)
+#
+# plt.figure()
+# plt.title('maskSLIC without enforcing connectivity')
+# plt.imshow(mark_boundaries(img, segments))
+# plt.contour(roi, contours=1, colors='red', linewidths=1)
+# plt.axis('off')
+#
+# # enforcing connectivity
+# segments = seg.slic(img, compactness=4, seed_type='nplace', mask=roi, n_segments=12,
+# recompute_seeds=True, enforce_connectivity=True)
+#
+# plt.figure()
+# plt.title('maskSLIC enforcing connectivity')
+# plt.imshow(mark_boundaries(img, segments))
+# plt.contour(roi, contours=1, colors='red', linewidths=1)
+# plt.axis('off')
+
+plt.show()