Merge pull request #11 from imcf/3d-suite

3d suite

Author: ehrenfeu

src/imcflibs/imagej/_loci.py

@@ -25,6 +25,7 @@
 
 from loci.plugins import BF
 
-from loci.plugins.in import ImporterOptions  # pdoc: skip
+from loci.plugins.in import ImporterOptions # pdoc: skip
+from loci.formats.in import ZeissCZIReader, DefaultMetadataOptions, MetadataLevel, DynamicMetadataOptions, MetadataOptions # pdoc: skip
 
 from loci.formats import ImageReader, Memoizer

src/imcflibs/imagej/labelimage.py

@@ -6,6 +6,7 @@
 from ij.process import FloatProcessor, ImageProcessor
 from inra.ijpb.label import LabelImages as li
 from inra.ijpb.plugins import AnalyzeRegions
+from mcib3d.image3d import ImageHandler, ImageLabeller
 
 
 def label_image_to_roi_list(label_image, low_thresh=None):
@@ -138,3 +139,44 @@ def measure_objects_size_shape_2d(label_image):
     """
     regions = AnalyzeRegions()
     return regions.process(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.
+
+    Parameters
+    ----------
+    imp : 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.
+    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
+        Segmented labeled ImagePlus.
+    """
+    cal = imp.getCalibration()
+    img = ImageHandler.wrap(imp)
+    img = img.threshold(min_thresh, False, False)
+
+    labeler = ImageLabeller()
+    if min_vol:
+        labeler.setMinSize(min_vol)
+    if max_vol:
+        labeler.setMaxSize(max_vol)
+
+    seg = labeler.getLabels(img)
+    seg.setScale(cal.pixelWidth, cal.pixelDepth, cal.getUnits())
+    seg.setTitle(title)
+
+    return seg.getImagePlus()

src/imcflibs/imagej/objects3d.py

@@ -0,0 +1,56 @@
+from ij import IJ
+from mcib3d.geom import Objects3DPopulation
+from mcib3d.image3d import ImageHandler
+
+
+def population3d_to_imgplus(imp, population):
+    """Make an ImagePlus from an Objects3DPopulation (2D/3D).
+
+    Works on: 2D and 3D.
+
+    Parameters
+    ----------
+    imp : ij.ImagePlus
+        Original ImagePlus to derive the size of the resulting ImagePlus.
+    population : mcib3d.geom.Objects3DPopulation
+        Population to use to generate the new ImagePlus.
+
+    Returns
+    -------
+    ImagePlus
+        Newly created ImagePlus from the population.
+    """
+    dim = imp.getDimensions()
+    new_imp = IJ.createImage(
+        "Filtered labeled stack",
+        "16-bit black",
+        dim[0],
+        dim[1],
+        1,
+        dim[3],
+        dim[4],
+    )
+    new_imp.setCalibration(imp.getCalibration())
+    new_img = ImageHandler.wrap(new_imp)
+    population.drawPopulation(new_img)
+
+    return new_img.getImagePlus()
+
+
+def imgplus_to_population3d(imp):
+    """Get an Objects3DPopulation from an ImagePlus (2D/3D).
+
+    Works on: 2D and 3D.
+
+    Parameters
+    ----------
+    imp : ij.ImagePlus
+        Labeled 3D stack or 2D image to use to get population.
+
+    Returns
+    -------
+    mcib3d.geom.Objects3DPopulation
+        Population from the image.
+    """
+    img = ImageHandler.wrap(imp)
+    return Objects3DPopulation(img)

src/imcflibs/strtools.py

@@ -133,6 +133,11 @@ def sort_alphanumerically(data):
     >>> sort_alphanumerically([ "foo-1", "foo-2", "foo-10" ])
     ["foo-1", "foo-2", "foo-10"]
     """
-    convert = lambda text: int(text) if text.isdigit() else text.lower()
-    alphanum_key = lambda key: [convert(c) for c in re.split("([0-9]+)", key)]
+
+    def convert(text):
+        return int(text) if text.isdigit() else text.lower()
+
+    def alphanum_key(key):
+        return [convert(c) for c in re.split("([0-9]+)", key)]
+
     return sorted(data, key=alphanum_key)