Add option to include backproject offset in file name.

documentation/docs/guide/backproject.md

@@ -44,6 +44,7 @@ The offset of the minimum bounding box is stored in the output tiff's descriptio
 - `Output Single File` - Whether to output one tiff stack file or a folder of files.
 - `Output Min Bounding Box` - Save only the minimum volume needed to contain the backprojected slices. The offset will be stored in the `-configuration.json` file under `backprojection_offset`. This value is the (x_min, y_min, z_min).
 - `Binary Backprojection` - Whether or not to binarize all the values of the backprojection. Enable this to backproject a segmentation.
+- `Offset in Filename` - Whether or not to include the (x_min, y_min, z_min) offset for min bounding box in the output file name. Only applies if `Output Min Bounding Box` is true.
 - `Max RAM (GB)` - 0 indicates no RAM limit. Setting a RAM limit allows Ouroboros to optimize performance and avoid overusing RAM.
 
 ### How Does Backprojection Work?

python/ouroboros/common/file_system.py

@@ -56,9 +56,9 @@ def load_options_for_backproject_docker(
 
     Returns
     -------
-    tuple[BackprojectOptions, str, str, str | None] | str
+    tuple[BackprojectOptions, str, str, str | None, str] | str
         The options for backprojecting the volume, the host path to the output file, the host path to the config file,
-        and the host path to the slices folder if the output is not a single file.
+        the host path to the slices folder if the output is not a single file, and the host output folder.
     """
 
     # Copy the file to the docker volume
@@ -111,7 +111,13 @@ def load_options_for_backproject_docker(
     # Modify the output file folder to be in the docker volume
     options.output_file_folder = get_volume_path()
 
-    return options, host_output_file, host_output_config_file, host_output_slices
+    return (
+        options,
+        host_output_file,
+        host_output_config_file,
+        host_output_slices,
+        host_output_folder,
+    )
 
 
 def save_output_for_backproject_docker(

python/ouroboros/common/server_handlers.py

@@ -9,6 +9,7 @@
 from ouroboros.common.logging import logger
 from ouroboros.common.pipelines import backproject_pipeline, slice_pipeline
 from ouroboros.common.server_types import BackProjectTask, SliceTask, Task
+from ouroboros.helpers.files import combine_unknown_folder
 
 
 def handle_slice_core(task: SliceTask, slice_options):
@@ -82,7 +83,7 @@ def handle_backproject_core(task: BackProjectTask, options):
 
     task.status = "started"
 
-    _, error = pipeline.process(input_data)
+    output, error = pipeline.process(input_data)
 
     if error:
         return error
@@ -91,6 +92,8 @@ def handle_backproject_core(task: BackProjectTask, options):
     logger.info("Backproject Pipeline Statistics:")
     logger.info(pipeline.get_step_statistics())
 
+    return output
+
 
 def handle_backproject(task: BackProjectTask):
     options = load_options_for_backproject(task.options)
@@ -111,14 +114,29 @@ def handle_backproject_docker(task: BackProjectTask):
         task.status = "error"
         return
 
-    options, host_output_file, host_output_config_file, host_output_slices = load_result
+    (
+        options,
+        host_output_file,
+        host_output_config_file,
+        host_output_slices,
+        host_output_folder,
+    ) = load_result
 
     backproject_result = handle_backproject_core(task, options)
 
     if isinstance(backproject_result, str):
         task.error = backproject_result
         task.status = "error"
         return
+    else:
+        if options.make_single_file:
+            host_output_file = combine_unknown_folder(
+                host_output_folder, backproject_result.output_file_path
+            )
+        else:
+            host_output_slices = combine_unknown_folder(
+                host_output_folder, backproject_result.output_file_path
+            )
 
     save_result = save_output_for_backproject_docker(
         host_output_file, host_output_config_file, host_output_slices=host_output_slices

python/ouroboros/helpers/files.py

@@ -144,11 +144,21 @@ def format_slice_output_config_file(output_name: str):
     return output_name + "-configuration.json"
 
 
-def format_backproject_output_file(output_name: str):
+def format_backproject_output_file(output_name: str, offset: tuple[int] | None = None):
+    if offset is not None:
+        offset_str = "-".join(map(str, offset))
+        return output_name + f"-backprojected-{offset_str}.tif"
+
     return output_name + "-backprojected.tif"
 
 
-def format_backproject_output_multiple(output_name: str):
+def format_backproject_output_multiple(
+    output_name: str, offset: tuple[int] | None = None
+):
+    if offset is not None:
+        offset_str = "-".join(map(str, offset))
+        return output_name + f"-backprojected-{offset_str}"
+
     return output_name + "-backprojected"
 
 

python/ouroboros/helpers/options.py

@@ -61,6 +61,7 @@ class BackprojectOptions(CommonOptions):
         "zlib"  # Compression type for the backprojected file
     )
     upsample_order: int = 2  # Order of the interpolation for upsampling
+    offset_in_name: bool = True  # Whether to include the offset in the output file name
 
 
 DEFAULT_SLICE_OPTIONS = SliceOptions(

python/ouroboros/pipeline/backproject_pipeline.py

@@ -72,7 +72,7 @@ def _process(self, input_data: any) -> tuple[any, None] | tuple[None, any]:
         if not isinstance(slice_rects, np.ndarray):
             return "Input data must contain an array of slice rects."
 
-        straightened_volume_path = input_tiff_path
+        straightened_volume_path = config.straightened_volume_path
 
         # Make sure the straightened volume exists
         if not os.path.exists(straightened_volume_path):
@@ -193,15 +193,29 @@ def _process(self, input_data: any) -> tuple[any, None] | tuple[None, any]:
             pipeline_input.backprojection_offset = f"{min_bounding_box.x_min},{min_bounding_box.y_min},{min_bounding_box.z_min}"
 
         # Save the backprojected volume to a series of tif files
+        offset = (
+            None
+            if not config.backproject_min_bounding_box or not config.offset_in_name
+            else (
+                min_bounding_box.x_min,
+                min_bounding_box.y_min,
+                min_bounding_box.z_min,
+            )
+        )
         folder_path = join_path(
             config.output_file_folder,
-            format_backproject_output_multiple(config.output_file_name),
+            format_backproject_output_multiple(config.output_file_name, offset=offset),
         )
         if os.path.exists(folder_path):
             shutil.rmtree(folder_path)
 
         os.makedirs(folder_path, exist_ok=True)
 
+        # Set the output file name to match the folder path
+        pipeline_input.output_file_path = format_backproject_output_multiple(
+            config.output_file_name, offset=offset
+        ) + (".tif" if config.make_single_file else "")
+
         dtype = volume_cache.get_volume_dtype()
         volume_shape = volume_cache.get_volume_shape()
 

python/test/helpers/test_files.py

@@ -130,11 +130,21 @@ def test_format_slice_output_config_file():
 def test_format_backproject_output_file():
     result = format_backproject_output_file("test")
     assert isinstance(result, str)
+    assert result == "test-backprojected.tif"
+
+    result = format_backproject_output_file("test", offset=(1, 2, 3))
+    assert isinstance(result, str)
+    assert result == "test-backprojected-1-2-3.tif"
 
 
 def test_format_backproject_output_multiple():
     result = format_backproject_output_multiple("test")
     assert isinstance(result, str)
+    assert result == "test-backprojected"
+
+    result = format_backproject_output_multiple("test", offset=(1, 2, 3))
+    assert isinstance(result, str)
+    assert result == "test-backprojected-1-2-3"
 
 
 def test_format_backproject_tempvolumes():

src/renderer/src/interfaces/options.tsx

@@ -202,6 +202,7 @@ export class BackprojectOptionsFile extends CompoundEntry {
 			new Entry('make_single_file', 'Output Single File', false, 'boolean'),
 			new Entry('backproject_min_bounding_box', 'Output Min Bounding Box', true, 'boolean'),
 			new Entry('make_backprojection_binary', 'Binary Backprojection', false, 'boolean'),
+			new Entry('offset_in_name', 'Offset in Filename', true, 'boolean'),
 			new Entry('flush_cache', 'Flush CloudVolume Cache', false, 'boolean').withHidden(),
 			new Entry('max_ram_gb', 'Max RAM (GB) (0 = no limit)', 0, 'number')
 		])