Revert combined commits

Author: CellKai

DEPENDENCIES.md

@@ -1593,98 +1593,58 @@ def fuse_dataset(
 def fuse_dataset_bdvp(
     project_path,
     command,
+    processing_opts=None,
     result_path=None,
-    range_channels="",
-    range_slices="",
-    range_frames="",
-    n_resolution_levels=5,
-    use_lzw_compression=True,
-    split_slices=False,
-    split_channels=False,
-    split_frames=False,
-    override_z_ratio=False,
-    z_ratio=1.0,
-    use_interpolation=True,
+    compression="LZW",
 ):
     """Export a BigDataViewer project using the BIOP Kheops exporter.
 
-    Use BIOP Kheops exporter to fuse a BigDataViewer project and save
-    it as pyramidal OME-TIFF.
+    Use the BIOP Kheops exporter to convert a BigDataViewer project into
+    OME-TIFF files, with optional compression.
 
     Parameters
     ----------
     project_path : str
         Full path to the BigDataViewer XML project file.
     command : CommandService
         The Scijava CommandService instance to execute the export command.
+    processing_opts : ProcessingOptions, optional
+        Options defining which parts of the dataset to process. If None, default
+        processing options will be used (process all angles, channels, etc.).
     result_path : str, optional
         Path where to store the exported files. If None, files will be saved in
         the same directory as the input project.
-    range_channels : str, optional
-        Channels to include in the export. Default is all channels.
-    range_slices : str, optional
-        Slices to include in the export. Default is all slices.
-    range_frames : str, optional
-        Frames to include in the export. Default is all frames.
-    n_resolution_levels : int, optional
-        Number of pyramid resolution levels to use for the export. Default is 5.
-    use_lzw_compression : bool, optional
-        If True, compressed the output file using LZW. Default is True.
-    split_slices : bool, optional
-        If True, splits the output into separate files for each slice. Default is False.
-    split_channels : bool, optional
-        If True, splits the output into separate files for each channel. Default is False.
-    split_frames : bool, optional
-        If True, splits the output into separate files for each frame. Default is False.
-    override_z_ratio : bool, optional
-        If True, overrides the default z_ratio value. Default is False.
-    z_ratio : float, optional
-        The z ratio to use for the export. Default is 1.0.
-    use_interpolation : bool, optional
-        If True, interpolates during fusion (takes ~4x longer). Default is True.
+    compression : str, optional
+        Compression method to use for the TIFF files. Default is "LZW".
 
     Notes
     -----
     This function requires the PTBIOP update site to be enabled in Fiji/ImageJ.
-
-    Examples
-    --------
-    fuse_dataset_bdvp(xml_input, cs)
     """
+    if processing_opts is None:
+        processing_opts = ProcessingOptions()
 
     file_info = pathtools.parse_path(project_path)
     if not result_path:
         result_path = file_info["path"]
+        # if not os.path.exists(result_path):
+        #     os.makedirs(result_path)
 
     command.run(
         FuseBigStitcherDatasetIntoOMETiffCommand,
         True,
-        "xml_bigstitcher_file",
+        "image",
         project_path,
-        "output_path_directory",
+        "output_dir",
         result_path,
-        "range_channels",
-        range_channels,
-        "range_slices",
-        range_slices,
-        "range_frames",
-        range_frames,
-        "n_resolution_levels",
-        n_resolution_levels,
-        "fusion_method",
-        "SMOOTH AVERAGE",
-        "use_lzw_compression",
-        use_lzw_compression,
-        "split_slices",
-        split_slices,
-        "split_channels",
-        split_channels,
-        "split_frames",
-        split_frames,
-        "override_z_ratio",
-        override_z_ratio,
-        "z_ratio",
-        z_ratio,
-        "use_interpolation",
-        use_interpolation,
+        "compression",
+        compression,
+        "subset_channels",
+        "",
+        "subset_slices",
+        "",
+        "subset_frames",
+        "",
+        "compress_temp_files",
+        False,
     )