Merge remote-tracking branch 'imcf/devel' into save-script-params

Author: ehrenfeu

.github/workflows/pytest-poetry.yml

@@ -7,6 +7,7 @@ on:
   push:
     branches:
       - master
+      - devel
     tags:
       - "*-[0-9]+.*"
   pull_request:

.github/workflows/pytest-python2.yml

@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - master
+      - devel
     tags:
       - "*-[0-9]+.*"
   pull_request:

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

src/imcflibs/imagej/bdv.py

@@ -807,7 +807,7 @@ def define_dataset_auto(
     file_path,
     bf_series_type,
     dataset_save_path=None,
-    timepoints_per_partition=1,
+    timepoints_per_partition=0,
     resave="Re-save as multiresolution HDF5",
     subsampling_factors=None,
     hdf5_chunk_sizes=None,
@@ -830,8 +830,9 @@ def define_dataset_auto(
         Defines how Bio-Formats interprets the series.
     timepoints_per_partition : int, optional
         Split the output dataset by timepoints. Use `0` for no split, resulting
-        in a single HDF5 file containing all timepoints. By default `1`,
-        resulting in a HDF5 per timepoints.
+        in a single HDF5 file containing all timepoints. Otherwise, choose the
+        number of timepoints per file. By default `0`.
+    
     resave : str, optional
         Allow the function to either re-save the images or simply create a
         merged xml. Use `Load raw data` to avoid re-saving, by default `Re-save
@@ -864,6 +865,12 @@ def define_dataset_auto(
         hdf5_chunk_sizes = "hdf5_chunk_sizes=" + hdf5_chunk_sizes + " "
     else:
         hdf5_chunk_sizes = ""
+    if timepoints_per_partition > 0:
+        split_timepoints = "split_hdf5 timepoints_per_partition=" + str(
+            timepoints_per_partition
+        ) + " "
+    else:
+        split_timepoints = ""
 
     if bf_series_type == "Angles":
         angle_rotation = "apply_angle_rotation "
@@ -901,10 +908,7 @@ def define_dataset_auto(
         + angle_rotation
         + subsampling_factors
         + hdf5_chunk_sizes
-        + "split_hdf5 "
-        + "timepoints_per_partition="
-        + str(timepoints_per_partition)
-        + " "
+        + split_timepoints
         + "setups_per_partition=0 "
         + "use_deflate_compression "
     )

src/imcflibs/imagej/misc.py

@@ -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.
@@ -740,6 +738,36 @@ def run_imarisconvert(file_path, pixel_calibration=None, output_folder=""):
         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")
+
+
 def save_script_parameters(
     destination, save_file_name="script_parameters.txt", script_globals=None
 ):

tests/bdv/test_define_dataset_auto.py

@@ -81,6 +81,68 @@ def test_define_dataset_auto_tile(tmp_path, caplog):
     # Set the default values for dataset definitions
     options = set_default_values(project_filename, file_info["path"])
 
+    # Construct the options for dataset definitions
+    options = (
+        options
+        + "how_to_store_input_images=["
+        + "Re-save as multiresolution HDF5"
+        + "] "
+        + "load_raw_data_virtually "
+        + "metadata_save_path=["
+        + result_folder
+        + "] "
+        + "image_data_save_path=["
+        + result_folder
+        + "] "
+        + "check_stack_sizes "
+        + "setups_per_partition=0 "
+        + "use_deflate_compression "
+    )
+
+    # Construct the final call to ImageJ
+    final_call = "IJ.run(cmd=[%s], params=[%s])" % (cmd, options)
+
+    # Define the dataset using the "Auto-Loader" option
+    bdv.define_dataset_auto(project_filename, file_info["path"], bf_series_type)
+    # Check if the final call is in the log
+    assert final_call == caplog.messages[0]
+
+
+def test_define_dataset_auto_tile_split_timepoints(tmp_path, caplog):
+    """Test automatic dataset definition method for tile series.
+
+    Parameters
+    ----------
+    tmp_path : pytest.fixture
+        Temporary path for the test.
+    caplog : pytest.fixture
+        Log capturing fixture.
+    """
+
+    # Set the logging level to capture warnings
+    caplog.set_level(logging.WARNING)
+    # Clear the log
+    caplog.clear()
+
+    # Define the project and file names
+    project_filename = "proj_name"
+    file_path = tmp_path
+    file_info = pathtools.parse_path(file_path)
+
+    # Define the result and dataset save paths
+    result_folder = pathtools.join2(file_info["path"], project_filename)
+
+    # Default settings
+
+    # Define the type of Bio-Formats series
+    bf_series_type = "Tiles"
+
+    # Define the ImageJ command
+    cmd = "Define Multi-View Dataset"
+
+    # Set the default values for dataset definitions
+    options = set_default_values(project_filename, file_info["path"])
+
     # Construct the options for dataset definitions
     options = (
         options
@@ -105,7 +167,7 @@ def test_define_dataset_auto_tile(tmp_path, caplog):
     final_call = "IJ.run(cmd=[%s], params=[%s])" % (cmd, options)
 
     # Define the dataset using the "Auto-Loader" option
-    bdv.define_dataset_auto(project_filename, file_info["path"], bf_series_type)
+    bdv.define_dataset_auto(project_filename, file_info["path"], bf_series_type, timepoints_per_partition=1)
     # Check if the final call is in the log
     assert final_call == caplog.messages[0]
 
@@ -160,8 +222,6 @@ def test_define_dataset_auto_angle(tmp_path, caplog):
         + "] "
         + "check_stack_sizes "
         + "apply_angle_rotation "
-        + "split_hdf5 "
-        + "timepoints_per_partition=1 "
         + "setups_per_partition=0 "
         + "use_deflate_compression "
     )

tests/test_misc.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"