Merge branch 'devel' into pr/122

Author: ehrenfeu

README.md

@@ -56,13 +56,22 @@ following necessary update sites for this package.
 - TrackMate-MorpholibJ
 
 The **`IMCF Uni Basel`** update-site will always provide the latest compatible
-combination of *official*`.jar` file to use this package.
+combination of *official* `.jar` files to use this package.
+
+### Manual Downloads for OMERO
+
+In addition to the update sites, two manual downloads concerning OMERO are
+necessary:
+
+- [simple-omero-client]
+- [omero-insight]
 
 ### 🏗 Alternative: SciJava Maven Package 👷
 
 💡 **IMPORTANT:** 💡 same as for the *default* installation previously
-described, you will need to enable **all Update Sites listed above** in your
-Fiji as well when using the method described here!
+described, you will need to enable **all Update Sites listed above** (and
+obviously the respective OMERO downloads) in your Fiji as well when using the
+method described here!
 
 The most up-to-date `.jar` (or any other published version, including
 pre-releases) for this package can be always found on the [Scijava Maven
@@ -122,3 +131,5 @@ correct_and_project(raw_image, out_path, model, "Maximum", ".ics")
 [apidocs]: https://imcf.one/apidocs/imcflibs/imcflibs.html
 [pdoc]: https://pdoc.dev/
 [pypi]: https://pypi.org/project/imcflibs/
+[simple-omero-client]: https://github.com/GReD-Clermont/simple-omero-client
+[omero-insight]: https://github.com/ome/omero-insight

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

@@ -10,15 +10,13 @@
 
 from ij import IJ  # pylint: disable-msg=import-error
 from ij.plugin import Duplicator, ImageCalculator, StackWriter
+from org.scijava.widget import TextWidget, WidgetStyle
 
 from .. import pathtools
 from ..log import LOG as log
 from . import bioformats as bf
 from . import prefs
 
-from org.scijava.widget import WidgetStyle
-from org.scijava.widget import TextWidget
-
 
 def show_status(msg):
     """Update the ImageJ status bar and issue a log message.
@@ -533,7 +531,9 @@ def write_ordereddict_to_csv(out_file, content):
             dict_writer.writerows(content)
 
 
-def save_image_in_format(imp, format, out_dir, series, pad_number, split_channels, suffix=""):
+def save_image_in_format(
+    imp, format, out_dir, series, pad_number, split_channels, suffix=""
+):
     """Save an ImagePlus object in the specified format.
 
     This function provides flexible options for saving ImageJ images in various
@@ -737,3 +737,32 @@ def run_imarisconvert(file_path, pixel_calibration=None, output_folder=""):
     else:
         timed_log("Error converting [%s]: %d" % (file_path, result))
 
+
+def bytes_to_human_readable(size):
+    """Convert a byte count to a human-readable string using binary units.
+
+    Parameters
+    ----------
+    size : int
+        Byte size (number of bytes).
+
+    Returns
+    -------
+    str
+        Human-friendly size string, e.g. `"512.0 bytes"`, `"2.0 KB"`,
+        `"1.0 MB"`.
+
+    Notes
+    -----
+    - Uses powers of 1024 (KB = 1024 bytes).
+    - Always returns a string with one decimal place and the unit.
+    """
+
+    for unit in ["bytes", "KB", "MB", "GB", "TB"]:
+        if size < 1024.0:
+            return "%3.1f %s" % (size, unit)
+        size /= 1024.0
+
+    # If the value is larger than the largest unit, fall back to TB with
+    # the current value (already divided accordingly).
+    return "%3.1f %s" % (size, "TB")

src/imcflibs/imagej/misc.py

@@ -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 +1,18 @@
+"""Tests for `imcflibs.imagej.misc` utility functions."""
+
+from imcflibs.imagej.misc import bytes_to_human_readable
+
+
+def test_bytes_to_human_readable_simple():
+    """Ensure common sizes are formatted into human-readable strings."""
+    assert bytes_to_human_readable(500) == "500.0 bytes"
+    assert bytes_to_human_readable(2048) == "2.0 KB"
+    assert bytes_to_human_readable(1024 * 1024) == "1.0 MB"
+    assert bytes_to_human_readable(5 * 1024**3) == "5.0 GB"
+
+
+def test_bytes_to_human_readable_large():
+    """Verify formatting for large sizes such as terabytes."""
+    # 1.5 TB in bytes should format as 1.5 TB
+    size = int(1.5 * (1024**4))
+    assert bytes_to_human_readable(size) == "1.5 TB"

tests/test_misc.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