Update for latest version BigStitcher, add fusion (BDV-playground)

src/imcflibs/imagej/bdv.py

@@ -13,6 +13,9 @@
 import shutil
 import sys
 
+from ch.epfl.biop.scijava.command.spimdata import (
+    FuseBigStitcherDatasetIntoOMETiffCommand,
+)
 from ij import IJ
 
 from .. import pathtools
@@ -198,8 +201,8 @@
         range_end : int, optional
             Contains the end of the range, by default None.
 
         Notes:
         ------
         Previous function name : angle_select().
         """
 
@@ -224,8 +227,8 @@
         range_end : int, optional
             Contains the end of the range, by default None.
 
         Notes:
         ------
         Previous function name : channel_select().
         """
 
@@ -250,8 +253,8 @@
         range_end : int, optional
             Contains the end of the range, by default None.
 
         Notes:
         ------
         Previous function name : illumination_select().
         """
 
@@ -276,8 +279,8 @@
         range_end : int, optional
             Contains the end of the range, by default None.
 
         Notes:
         ------
         Previous function name : tile_select().
         """
 
@@ -302,8 +305,8 @@
         range_end : int, optional
             Contains the end of the range, by default None.
 
         Notes:
         ------
         Previous function name : timepoint_select().
         """
 
@@ -506,7 +509,7 @@
     >>> opts.fmt_acitt_options()
     ... multiple_angles=[NO (one angle)]
     ... multiple_channels=[YES (all channels in one file)]
-    ... multiple_illuminations=[NO (one illumination direction)]
+    ... multiple_illuminations_directions=[NO (one illumination direction)]
     ... multiple_tiles=[YES (all tiles in one file)]
     ... multiple_timepoints=[NO (one time-point)]
     """
@@ -543,15 +546,43 @@
             "multi_multi": MULTI_MULTI_FILE,
         }
 
+    def check_definition_option_ang_ill(self, value):
+        """Check if the value is a valid definition option.
+
+        This is needed for angles and illuminations because support is not
+        available for multiple angles and illuminations in a single file.
+
+        Parameters
+        ----------
+        value : str
+            Entered value by the user.
+
+        Returns
+        -------
+        dict(str, str): dictionary containing the correct string definition.
+        """
+        if value not in [
+            "single",
+            "multi_multi",
+        ]:
+            raise ValueError(
+                "Value must be one of single, multi_multi. Support for multi_single is not available for angles and illuminations"
+            )
+
+        return {
+            "single": SINGLE_FILE,
+            "multi_multi": MULTI_MULTI_FILE,
+        }
+
     def set_angle_definition(self, value):
         """Set the value for the angle definition
 
         Parameters
         ----------
         value : str
-            One of `single`, `multi_single` or `multi_multi`.
+            One of `single` or `multi_multi`.
         """
-        choices = self.check_definition_option(value)
+        choices = self.check_definition_option_ang_ill(value)
         self._angle_definition = choices[value] % "angle"
         log.debug("New 'angle_definition' setting: %s", self._angle_definition)
 
@@ -575,7 +606,7 @@
         value : str
             One of `single`, `multi_single` or `multi_multi`.
         """
-        choices = self.check_definition_option(value)
+        choices = self.check_definition_option_ang_ill(value)
         self._illumination_definition = choices[value] % "illumination direction"
         log.debug(
             "New 'illumination_definition' setting: %s", self._illumination_definition
@@ -609,7 +640,7 @@
         """Format Angle / Channel / Illumination / Tile / Timepoint options.
 
         Build a string providing the `multiple_angles`, `multiple_channels`,
-        `multiple_illuminations`, `multiple_tiles` and `multiple_timepoints` options
+        `multiple_illuminations_directions`, `multiple_tiles` and `multiple_timepoints` options
         that can be used in a BDV-related `IJ.run` call.
 
         Returns
@@ -619,7 +650,7 @@
         parameters = [
             "multiple_angles=" + self._angle_definition,
             "multiple_channels=" + self._channel_definition,
-            "multiple_illuminations=" + self._illumination_definition,
+            "multiple_illuminations_directions=" + self._illumination_definition,
             "multiple_tiles=" + self._tile_definition,
             "multiple_timepoints=" + self._timepoint_definition,
         ]
@@ -807,23 +838,29 @@
         angle_rotation = ""
 
     options = (
-        "define_dataset=[Automatic Loader (Bioformats based)] "
+        "define_dataset=[Automatic Loader (Bioformats based)]"
+        + " "
         + "project_filename=["
         + project_filename
         + ".xml"
         + "] "
         + "path=["
-        + file_info["path"]
+        + file_info["full"]
         + "] "
         + "exclude=10 "
-        # + "bioformats_series_are?="
-        # + bf_series_type
-        # + " "
+        + "bioformats_series_are?="
+        + bf_series_type
+        + " "
         + "move_tiles_to_grid_(per_angle)?=[Do not move Tiles to Grid (use Metadata if available)] "
-        + "how_to_load_images=["
+        + "how_to_store_input_images=["
         + resave
         + "] "
-        + "dataset_save_path=["
+        + "load_raw_data_virtually"
+        + " "
+        + "metadata_save_path=["
+        + dataset_save_path
+        + "] "
+        + "image_data_save_path=["
         + dataset_save_path
         + "] "
         + "check_stack_sizes "
@@ -836,21 +873,11 @@
         + " "
         + "setups_per_partition=0 "
         + "use_deflate_compression "
-        # + "export_path=["
-        # + dataset_save_path
-        # + "]",
     )
 
     log.debug(options)
 
-    if bf_series_type == "Tiles":
-        log.debug("Doing tiled dataset definition")
-        IJ.run("Define dataset ...", str(options))
-    elif bf_series_type == "Angles":
-        log.debug("Doing multi-view dataset definition")
-        IJ.run("Define Multi-View Dataset", str(options))
-    else:
-        raise ValueError("Wrong answer for series type")
+    IJ.run("Define Multi-View Dataset", str(options))
 
 
 def define_dataset_manual(
@@ -892,6 +919,7 @@
         + "project_filename=["
         + xml_filename
         + "] "
+        + "_____"
         + definition_opts.fmt_acitt_options()
         + " "
         + "image_file_directory="
@@ -903,11 +931,11 @@
         + " "
         + "calibration_type=[Same voxel-size for all views] "
         + "calibration_definition=[Load voxel-size(s) from file(s)] "
-        + "imglib2_data_container=[ArrayImg (faster)]"
+        # + "imglib2_data_container=[ArrayImg (faster)]"
     )
 
-    log.debug("Manual dataset defintion options: <%s>", options)
-    IJ.run("Define dataset ...", str(options))
+    log.debug("Manual dataset definition options: <%s>", options)
+    IJ.run("Define Multi-View Dataset", str(options))
 
 
 def resave_as_h5(
@@ -1424,7 +1452,9 @@
     downsampling=1,
     interpolation="[Linear Interpolation]",
     pixel_type="[16-bit unsigned integer]",
+    fusion_type="Avg, Blending",
     export="HDF5",
+    compression="Zstandard",
 ):
     """Call BigStitcher's "Fuse Dataset" command.
 
@@ -1475,11 +1505,13 @@
         + "interpolation="
         + interpolation
         + " "
+        + "fusion_type=["
+        + fusion_type
+        + "] "
         + "pixel_type="
         + pixel_type
         + " "
         + "interest_points_for_non_rigid=[-= Disable Non-Rigid =-] "
-        + "blend "
         + "preserve_original "
         + "produce=[Each timepoint & channel] "
     )
@@ -1506,9 +1538,12 @@
 
         options = (
             options
-            + "fused_image=[ZARR/N5/HDF5 export using N5-API] "
+            + "fused_image=[OME-ZARR/N5/HDF5 export using N5-API] "
             + "define_input=[Auto-load from input data (values shown below)] "
             + "export=HDF5 "
+            + "compression="
+            + compression
+            + " "
             + "create "
             + "create_0 "
             + "hdf5_file=["
@@ -1527,4 +1562,64 @@
         )
 
     log.debug("Dataset fusion options: <%s>", options)
-    IJ.run("Fuse dataset ...", str(options))
+    IJ.run("Image Fusion", str(options))
+
+
+def fuse_dataset_bdvp(
+    project_path,
+    command,
+    processing_opts=None,
+    result_path=None,
+    compression="LZW",
+):
+    """Export a BigDataViewer project using the BIOP Kheops exporter.
+
+    This function uses the BIOP Kheops exporter to convert a BigDataViewer project into a
+    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.
+    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.
+    """
+    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,
+        "image",
+        project_path,
+        "output_dir",
+        result_path,
+        "compression",
+        compression,
+        "subset_channels",
+        "",
+        "subset_slices",
+        "",
+        "subset_frames",
+        "",
+        "compress_temp_files",
+        False,
+    )

src/imcflibs/imagej/misc.py

@@ -1,5 +1,6 @@
 """Miscellaneous ImageJ related functions, mostly convenience wrappers."""
 
+import csv
 import sys
 import time
 import smtplib
@@ -417,3 +418,33 @@
     threshold_value = int(round(threshold_value.get()))
 
     return threshold_value
+
+
+def write_results(out_file, content):
+    """Write the results to a csv file.
+
+    Parameters
+    ----------
+    out_file : str
+        Path to the output file.
+    content : list of OrderedDict
+        List of dictionaries representing the results.
+
+    """
+
+    # Check if the output file exists
+    if not os.path.exists(out_file):
+        # If the file does not exist, create it and write the header
+        with open(out_file, "wb") as f:
+            dict_writer = csv.DictWriter(
+                f, content[0].keys(), delimiter=";"
+            )
+            dict_writer.writeheader()
+            dict_writer.writerows(content)
+    else:
+        # If the file exists, append the results
+        with open(out_file, "ab") as f:
+            dict_writer = csv.DictWriter(
+                f, content[0].keys(), delimiter=";"
+            )
+            dict_writer.writerows(content)