Merge pull request #29 from imcf/labelimage

Merge changes in labelimage branch

Author: ehrenfeu

src/imcflibs/imagej/labelimage.py

@@ -1,6 +1,8 @@
+# -*- coding: utf-8 -*-
+
 """Functions to work with ImageJ label images."""
 
-from ij import IJ, ImagePlus, Prefs
+from ij import IJ, ImagePlus, Prefs, ImageStack
 from ij.plugin import Duplicator, ImageCalculator
 from ij.plugin.filter import ThresholdToSelection
 from ij.process import FloatProcessor, ImageProcessor
@@ -146,39 +148,105 @@ def measure_objects_size_shape_2d(label_image):
 def binary_to_label(imp, title, min_thresh=1, min_vol=None, max_vol=None):
     """Segment a binary image to get a label image (2D/3D).
 
-    Works on: 2D and 3D binary data.
+    Works on both 2D and 3D binary data.
 
     Parameters
     ----------
-    imp : ImagePlus
+    imp : ij.ImagePlus
         Binary 3D stack or 2D image.
     title : str
         Title of the new image.
     min_thresh : int, optional
-        Threshold to do segmentation, also allows for label filtering, by
-        default 1.
+        Threshold to do segmentation, also allows for label filtering, by default 1.
     min_vol : float, optional
         Volume under which to exclude objects, by default None.
     max_vol : float, optional
         Volume above which to exclude objects, by default None.
 
     Returns
     -------
-    ImagePlus
+    ij.ImagePlus
         Segmented labeled ImagePlus.
     """
+    # Get the calibration of the input ImagePlus
     cal = imp.getCalibration()
+
+    # Wrap the ImagePlus in an ImageHandler
     img = ImageHandler.wrap(imp)
+
+    # Threshold the image using the specified threshold value
     img = img.threshold(min_thresh, False, False)
 
+    # Create an ImageLabeller instance
     labeler = ImageLabeller()
+
+    # Set the minimum size for labeling if provided
     if min_vol:
         labeler.setMinSize(min_vol)
+
+    # Set the maximum size for labeling if provided
     if max_vol:
         labeler.setMaxSize(max_vol)
 
+    # Get the labeled image
     seg = labeler.getLabels(img)
+
+    # Set the scale of the labeled image
     seg.setScale(cal.pixelWidth, cal.pixelDepth, cal.getUnits())
+
+    # Set the title of the labeled image
     seg.setTitle(title)
 
+    # Return the segmented labeled ImagePlus
     return seg.getImagePlus()
+
+
+def dilate_labels_2d(imp, dilation_radius):
+    """Dilate each label in the given ImagePlus using the specified dilation radius.
+
+    This method will use a 2D dilation to be applied to each slice of the ImagePlus
+    and return a new stack.
+
+    Parameters
+    ----------
+    imp : ij.ImagePlus
+        Input ImagePlus with the labels to dilate
+    dilation_radius : int
+        Number of pixels to dilate each label
+
+    Returns
+    -------
+    ij.ImagePlus
+        New ImagePlus with the dilated labels
+    """
+
+    # Create a list of the dilated labels
+    dilated_labels_list = []
+
+    # Iterate over each slice of the input ImagePlus
+    for i in range(1, imp.getNSlices() + 1):
+        # Duplicate the current slice
+        current_imp = Duplicator().run(imp, 1, 1, i, imp.getNSlices(), 1, 1)
+
+        # Perform a dilation of the labels in the current slice
+        IJ.run(
+            current_imp,
+            "Label Morphological Filters",
+            "operation=Dilation radius=" + str(dilation_radius) + " from_any_label",
+        )
+
+        # Get the dilated labels
+        dilated_labels_imp = IJ.getImage()
+
+        # Hide the dilated labels to avoid visual clutter
+        dilated_labels_imp.hide()
+
+        # Append the dilated labels to the list
+        dilated_labels_list.append(dilated_labels_imp)
+
+    # Create a new ImagePlus with the dilated labels
+    dilated_labels_imp = ImagePlus(
+        "Dilated labels", ImageStack().create(dilated_labels_list)
+    )
+
+    return dilated_labels_imp