Merge pull request #139 from lguerard/fix/138-object3D-border-filtering

Add options to segment_3d_image for removing objects touching borders

Author: ehrenfeu

poetry.lock

@@ -20,7 +20,8 @@ version = "0.0.0"
 # - or: python = ">=3.10"
 
 [tool.poetry.dependencies]
-imcf-fiji-mocks = ">=0.13.0"
+# IMPORTANT: see the "poetry.lock.md" file when changing dependencies!!!
+imcf-fiji-mocks = ">=0.14.0"
 python = ">=2.7"
 python-micrometa = "^15.2.3"
 sjlogging = ">=0.5.2"
@@ -54,3 +55,9 @@ ignore = [
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
+
+[tool.coverage.report]
+exclude_also = [
+  'no-cover:jython-only',
+  'cover:jython',
+]

pyproject.toml

@@ -8,6 +8,7 @@
 from de.mpicbg.scf.imgtools.image.create.image import ImageCreationUtilities
 from de.mpicbg.scf.imgtools.image.create.labelmap import WatershedLabeling
 from ij import IJ
+from inra.ijpb.plugins import RemoveBorderLabelsPlugin
 from mcib3d.geom import Objects3DPopulation
 from mcib3d.image3d import ImageHandler, ImageLabeller
 from mcib3d.image3d.processing import MaximaFinder
@@ -71,7 +72,15 @@ def imgplus_to_population3d(imp):
     return Objects3DPopulation(img)
 
 
-def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
+def segment_3d_image(
+    imp,
+    title=None,
+    min_thresh=1,
+    min_vol=None,
+    max_vol=None,
+    remove_touching_borders=False,
+    remove_touching_borders_z=False,
+):  # cover:jython
     """Segment a 3D binary image to get a labelled stack.
 
     Parameters
@@ -90,6 +99,11 @@ def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
     max_vol : int, optional
         Maximum volume (in voxels) above which objects get filtered.
         Defaults to None.
+    remove_touching_borders : bool, optional
+        Whether to remove objects that touch the borders in X and Y. Defaults to False.
+    remove_touching_borders_z : bool, optional
+        Whether to remove objects that touch the z-axis borders. Defaults to False.
+
 
     Returns
     -------
@@ -107,14 +121,24 @@ def segment_3d_image(imp, title=None, min_thresh=1, min_vol=None, max_vol=None):
         labeler.setMinSizeCalibrated(min_vol, img)
     if max_vol:
         labeler.setMaxSizeCalibrated(max_vol, img)
-
     # Generate labelled segmentation
     seg = labeler.getLabels(img)
     seg.setScale(cal.pixelWidth, cal.pixelDepth, cal.getUnits())
+
+    seg = RemoveBorderLabelsPlugin().remove(
+        seg.getImagePlus(),
+        remove_touching_borders,
+        remove_touching_borders,
+        remove_touching_borders,
+        remove_touching_borders,
+        remove_touching_borders_z,
+        remove_touching_borders_z,
+    )
+
     if title:
         seg.setTitle(title)
 
-    return seg.getImagePlus()
+    return seg
 
 
 def maxima_finder_3d(imp, min_threshold=0, noise=100, rxy=1.5, rz=1.5):

src/imcflibs/imagej/objects3d.py

@@ -0,0 +1,12 @@
+"""Tests for the imcflibs.imagej.objects3d module."""
+
+from imcflibs.imagej.objects3d import imgplus_to_population3d
+from imcflibs.imagej.objects3d import maxima_finder_3d
+from imcflibs.imagej.objects3d import population3d_to_imgplus
+from imcflibs.imagej.objects3d import seeded_watershed
+from imcflibs.imagej.objects3d import segment_3d_image
+
+
+def test_mock_imports():
+    """Test if the mock imports work fine."""
+    assert True