Merge branch 'devel' into bdv_update_library

Author: ehrenfeu

.vscode/settings.json

@@ -11,6 +11,35 @@
         }
     },
     "cSpell.words": [
-        "Prefs"
+        "acitt",
+        "bdvp",
+        "biop",
+        "imageplus",
+        "imglib",
+        "interestpoint",
+        "intermodes",
+        "Kheops",
+        "micrometa",
+        "multiresolution",
+        "otsu",
+        "pathtools",
+        "Prefs",
+        "PTBIOP",
+        "PYENV",
+        "pylint",
+        "ransac",
+        "renyi",
+        "repartitions",
+        "RETVAL",
+        "scijava",
+        "shanbhag",
+        "sjlogging",
+        "spimdata",
+        "strtools",
+        "subfolders",
+        "subsampling",
+        "trackmate",
+        "virtualenv",
+        "virtualfish"
     ],
 }

poetry.lock

@@ -20,7 +20,7 @@ version = "0.0.0"
 # - or: python = ">=3.10"
 
 [tool.poetry.dependencies]
-imcf-fiji-mocks = ">=0.10.0"
+imcf-fiji-mocks = ">=0.13.0"
 python = ">=2.7"
 python-micrometa = "^15.2.2"
 sjlogging = ">=0.5.2"
@@ -53,4 +53,4 @@ ignore = [
 ]
 
 [tool.ruff.lint.pydocstyle]
-convention = "numpy"
+convention = "numpy"

poetry.lock.md

@@ -17,6 +17,9 @@
     FuseBigStitcherDatasetIntoOMETiffCommand,
 )
 from ij import IJ
+from java.io import File, FileInputStream, InputStreamReader
+from javax.xml.parsers import DocumentBuilderFactory
+from org.xml.sax import InputSource
 
 from .. import pathtools
 from ..log import LOG as log
@@ -731,6 +734,22 @@ def get_processing_settings(dimension, selection, value, range_end):
     tuple of str
         processing_option, dimension_select
     """
+    processing_option = dimension_select = ""
+
+    # Validate inputs according to the function docstring
+    valid_dimensions = ("angle", "channel", "illumination", "tile", "timepoint")
+    if dimension not in valid_dimensions:
+        raise ValueError(
+            "Invalid dimension '%s', expected one of: %s"
+            % (dimension, ", ".join(valid_dimensions))
+        )
+
+    valid_selections = ("single", "multiple", "range")
+    if selection not in valid_selections:
+        raise ValueError(
+            "Invalid selection '%s', expected one of: %s"
+            % (selection, ", ".join(valid_selections))
+        )
 
     if selection == "single":
         processing_option = SINGLE % dimension
@@ -1085,7 +1104,7 @@ def phase_correlation_pairwise_shifts_calculation(
     project_path : str
         Full path to the `.xml` file.
     processing_opts : imcflibs.imagej.bdv.ProcessingOptions, optional
-        The `ProcessingOptinos` object defining parameters for the run. Will
+        The `ProcessingOptions` object defining parameters for the run. Will
         fall back to the defaults defined in the corresponding class if the
         parameter is `None` or skipped.
     downsampling_xyz : list of int, optional
@@ -1204,7 +1223,7 @@ def optimize_and_apply_shifts(
     project_path : str
         Path to the `.xml` on which to optimize and apply the shifts.
     processing_opts : imcflibs.imagej.bdv.ProcessingOptions, optional
-        The `ProcessingOptinos` object defining parameters for the run. Will
+        The `ProcessingOptions` object defining parameters for the run. Will
         fall back to the defaults defined in the corresponding class if the
         parameter is `None` or skipped.
     relative_error : float, optional
@@ -1355,11 +1374,13 @@ def interest_points_registration(
         + "transformation=Affine "
         + "regularize_model "
         + "model_to_regularize_with=Affine "
-        + "lamba=0.10 "
+        + "lambda=0.10 "
         + "number_of_neighbors=3 "
         + "redundancy=1 "
         + "significance=3 "
+        + "search_radius=100 "
         + "allowed_error_for_ransac=5 "
+        + "inlier_factor=3 "
         + "ransac_iterations=Normal "
         + "global_optimization_strategy=["
         + "Two-Round: Handle unconnected tiles, "
@@ -1377,7 +1398,7 @@ def interest_points_registration(
 def duplicate_transformations(
     project_path,
     transformation_type="channel",
-    channel_source=None,
+    channel_source=0,
     tile_source=None,
     transformation_to_use="[Replace all transformations]",
 ):
@@ -1394,7 +1415,7 @@ def duplicate_transformations(
         Transformation mode, one of `channel` (to propagate from one channel to
         all others) and `tiles` (to propagate from one tile to all others).
     channel_source : int, optional
-        Reference channel nummber (starting at 1), by default None.
+        Reference channel number (starting at 1), by default None.
     tile_source : int, optional
         Reference tile, by default None.
     transformation_to_use : str, optional
@@ -1410,13 +1431,16 @@ def duplicate_transformations(
     tile_apply = ""
     tile_process = ""
 
-    chnl_apply = ""
-    chnl_process = ""
+    ch_apply = ""
+    ch_process = ""
 
     if transformation_type == "channel":
         apply = "[One channel to other channels]"
         target = "[All Channels]"
-        source = str(channel_source - 1)
+        if channel_source > 0:
+            source = str(channel_source - 1)
+        else:
+            source = "0"
         if tile_source:
             tile_apply = "apply_to_tile=[Single tile (Select from List)] "
             tile_process = "processing_tile=[tile " + str(tile_source) + "] "
@@ -1426,15 +1450,13 @@ def duplicate_transformations(
         apply = "[One tile to other tiles]"
         target = "[All Tiles]"
         source = str(tile_source)
-        if channel_source:
-            chnl_apply = "apply_to_channel=[Single channel (Select from List)] "
-            chnl_process = (
-                "processing_channel=[channel " + str(channel_source - 1) + "] "
-            )
+        if channel_source > 0:
+            ch_apply = "apply_to_channel=[Single channel (Select from List)] "
+            ch_process = "processing_channel=[channel " + str(channel_source - 1) + "] "
         else:
-            chnl_apply = "apply_to_channel=[All channels] "
+            ch_apply = "apply_to_channel=[All channels] "
     else:
-        sys.exit("Issue with transformation duplication")
+        raise ValueError("Invalid transformation type: %s" % transformation_type)
 
     options = (
         "apply="
@@ -1447,8 +1469,8 @@ def duplicate_transformations(
         + "apply_to_illumination=[All illuminations] "
         + tile_apply
         + tile_process
-        + chnl_apply
-        + chnl_process
+        + ch_apply
+        + ch_process
         + "apply_to_timepoint=[All Timepoints] "
         + "source="
         + source
@@ -1493,7 +1515,7 @@ def fuse_dataset(
     project_path : str
         Path to the `.xml` on which to run the fusion.
     processing_opts : imcflibs.imagej.bdv.ProcessingOptions, optional
-        The `ProcessingOptinos` object defining parameters for the run. Will
+        The `ProcessingOptions` object defining parameters for the run. Will
         fall back to the defaults defined in the corresponding class if the
         parameter is `None` or skipped.
     result_path : str, optional

pyproject.toml

@@ -352,6 +352,31 @@ def export_using_orig_name(imp, path, orig_name, tag, suffix, overwrite=False):
     return out_file
 
 
+def get_reader(path_to_file, setFlattenedResolutions=False):
+    """Get a Bio-Formats ImageReader for the specified file.
+
+    Parameters
+    ----------
+    path_to_file : str
+        The full path to the image file.
+    setFlattenedResolutions : bool, optional
+        Whether to flatten resolutions in the ImageReader (default: False).
+
+    Returns
+    -------
+    ImageReader
+        A configured ImageReader instance for the specified file.
+    """
+    reader = ImageReader()
+    ome_meta = MetadataTools.createOMEXMLMetadata()
+    reader.setMetadataStore(ome_meta)
+    m = DynamicMetadataOptions()
+    m.setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, False)
+    reader.setMetadataOptions(m)
+    reader.setId(str(path_to_file))
+    return reader, ome_meta
+
+
 def get_series_info_from_ome_metadata(path_to_file, skip_labels=False):
     """Get the Bio-Formats series information from a file on disk.
 
@@ -378,44 +403,31 @@ def get_series_info_from_ome_metadata(path_to_file, skip_labels=False):
     >>> count, indices = get_series_info_from_ome_metadata("image.nd2", skip_labels=True)
     """
 
+    reader, ome_meta = get_reader(path_to_file, skip_labels)
+    series_count = reader.getSeriesCount()
     if not skip_labels:
-        reader = ImageReader()
-        reader.setFlattenedResolutions(False)
-        ome_meta = MetadataTools.createOMEXMLMetadata()
-        reader.setMetadataStore(ome_meta)
-        reader.setId(path_to_file)
-        series_count = reader.getSeriesCount()
-
-        reader.close()
+        # If we are not skipping labels, return the full range
         return series_count, range(series_count)
 
-    else:
-        reader = ImageReader()
-        # reader.setFlattenedResolutions(True)
-        ome_meta = MetadataTools.createOMEXMLMetadata()
-        reader.setMetadataStore(ome_meta)
-        reader.setId(path_to_file)
-        series_count = reader.getSeriesCount()
-
-        series_ids = []
-        series_names = []
-        x = 0
-        y = 0
-        for i in range(series_count):
-            reader.setSeries(i)
+    series_ids = []
+    series_names = []
+    x = 0
+    y = 0
+    for i in range(series_count):
+        reader.setSeries(i)
 
-            if reader.getSizeX() > x and reader.getSizeY() > y:
-                name = ome_meta.getImageName(i)
+        if reader.getSizeX() > x and reader.getSizeY() > y:
+            name = ome_meta.getImageName(i)
 
-                if name not in ["label image", "macro image"]:
-                    series_ids.append(i)
-                    series_names.append(name)
+            if name not in ["label image", "macro image"]:
+                series_ids.append(i)
+                series_names.append(name)
 
-            x = reader.getSizeX()
-            y = reader.getSizeY()
+        x = reader.getSizeX()
+        y = reader.getSizeY()
 
-        print(series_names)
-        return len(series_ids), series_ids
+    print(series_names)
+    return len(series_ids), series_ids
 
 
 def write_bf_memoryfile(path_to_file):
@@ -452,10 +464,7 @@ def get_metadata_from_file(path_to_image):
         An instance of `imcflibs.imagej.bioformats.ImageMetadata` containing the extracted metadata.
     """
 
-    reader = ImageReader()
-    ome_meta = MetadataTools.createOMEXMLMetadata()
-    reader.setMetadataStore(ome_meta)
-    reader.setId(str(path_to_image))
+    reader, ome_meta = get_reader(path_to_image)
 
     metadata = ImageMetadata(
         unit_width=ome_meta.getPixelsPhysicalSizeX(0).value(),
@@ -507,11 +516,7 @@ def get_stage_coords(filenames):
     max_phys_size_z = 0.0
 
     for counter, image in enumerate(filenames):
-        reader = ImageReader()
-        reader.setFlattenedResolutions(False)
-        ome_meta = MetadataTools.createOMEXMLMetadata()
-        reader.setMetadataStore(ome_meta)
-        reader.setId(str(image))
+        reader, ome_meta = get_reader(image)
         series_count = reader.getSeriesCount()
 
         # Process only the first image to get values not dependent on series
@@ -569,8 +574,7 @@ def get_stage_coords(filenames):
             if series_count > 1 and not str(image).endswith(".vsi"):
                 series_names.append(ome_meta.getImageName(series))
             else:
-                series_names.append(str(image))
-
+                series_names.append(os.path.basename(str(image)))
             current_position_x = getattr(
                 ome_meta.getPlanePositionX(series, 0), "value", lambda: 0
             )()