Remove configuration file and use slice options instead.

documentation/docs/guide/backproject.md

@@ -35,7 +35,7 @@ The offset of the minimum bounding box is stored in the output tiff's descriptio
 📁 - Drag and drop files from File Explorer panel into this option.
 
 - 📁 `Straightened Volume File` - Path to the volume of slices to backproject (e.g. the output tif of the slicing step).
-- 📁 `Slice Configuration File` - Path to the `-configuration.json` file which includes information generated during slicing needed for backprojection.
+- 📁 `Slice Options File` - Path to the `-slice-options.json` file which includes the information needed for backprojection.
 - 📁 `Output File Folder` - The folder to save all the resulting files into.
 - `Output File Name` - Base name for all output files.
 - `Output MIP Level` - The MIP level to output the backprojection in (essentially an upsample option). Use this if you downsampled in the slicing step.

python/ouroboros/common/file_system.py

@@ -10,7 +10,6 @@
     combine_unknown_folder,
     format_backproject_output_file,
     format_backproject_output_multiple,
-    format_slice_output_config_file,
     format_slice_output_file,
     format_slice_output_multiple,
 )
@@ -43,7 +42,7 @@ def load_options_for_backproject(options_path: str) -> BackprojectOptions | str:
 
 def load_options_for_backproject_docker(
     options_path: str, target_path: str = "./"
-) -> tuple[BackprojectOptions, str, str, str | None] | str:
+) -> tuple[BackprojectOptions, SliceOptions, str, str | None, str] | str:
     """
     Loads the options for backprojecting a volume and copies the necessary files to the docker volume.
 
@@ -56,21 +55,22 @@ def load_options_for_backproject_docker(
 
     Returns
     -------
-    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,
+    tuple[BackprojectOptions, SliceOptions, str, str | None, str] | str
+        The options for backprojecting the volume, the options for slicing the volume, the host path to the output 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
-    files = [{"sourcePath": options_path, "targetPath": target_path}]
+    files = [
+        {"sourcePath": options_path, "targetPath": target_path},
+    ]
     success, error = copy_to_volume(files)
 
     if not success:
         return error
 
     # Define the path to the copied file in the docker volume
     options_path = get_volume_path() + get_path_name(options_path)
-
     options = load_options_for_backproject(options_path)
 
     if isinstance(options, str):
@@ -79,7 +79,6 @@ def load_options_for_backproject_docker(
     # Copy the straightened volume and config files to the docker volume
     files = [
         {"sourcePath": options.straightened_volume_path, "targetPath": target_path},
-        {"sourcePath": options.config_path, "targetPath": target_path},
     ]
 
     success, error = copy_to_volume(files)
@@ -100,29 +99,37 @@ def load_options_for_backproject_docker(
         if options.make_single_file is False
         else None
     )
-    host_output_config_file = options.config_path
 
     # Define the path to the copied straightened volume and config files in the docker volume
     options.straightened_volume_path = get_volume_path() + get_path_name(
         options.straightened_volume_path
     )
-    options.config_path = get_volume_path() + get_path_name(options.config_path)
 
     # Modify the output file folder to be in the docker volume
     options.output_file_folder = get_volume_path()
 
+    # Load the options for slicing the volume,
+    # which contains necessary information for backprojecting the volume
+    slice_load_result = load_options_for_slice_docker(
+        options.slice_options_path, target_path
+    )
+
+    if isinstance(slice_load_result, str):
+        return slice_load_result
+
+    slice_options = slice_load_result[0]
+
     return (
         options,
+        slice_options,
         host_output_file,
-        host_output_config_file,
         host_output_slices,
         host_output_folder,
     )
 
 
 def save_output_for_backproject_docker(
     host_output_file: str,
-    host_output_config_file: str,
     host_output_slices=None,
     target_path: str = "./",
 ) -> None | str:
@@ -133,8 +140,6 @@ def save_output_for_backproject_docker(
     ----------
     host_output_file : str
         The path to the output file on the host.
-    host_output_config_file : str
-        The path to the config file on the host.
     host_output_slices : str, optional
         The path to the slices folder on the host, by default None
     target_path : str, optional
@@ -155,8 +160,7 @@ def save_output_for_backproject_docker(
                 else host_output_file
             ),
             "targetPath": target_path,
-        },
-        {"sourcePath": host_output_config_file, "targetPath": target_path},
+        }
     ]
 
     success, error = copy_to_host(files)
@@ -190,7 +194,7 @@ def load_options_for_slice(options_path: str) -> SliceOptions | str:
 
 def load_options_for_slice_docker(
     options_path: str, target_path: str = "./"
-) -> tuple[SliceOptions, str, str, str | None] | str:
+) -> tuple[SliceOptions, str, str | None] | str:
     """
     Loads the options for slicing a volume and copies the necessary files to the docker volume.
 
@@ -203,8 +207,8 @@ def load_options_for_slice_docker(
 
     Returns
     -------
-    tuple[SliceOptions, str, str, str | None] | str
-        The options for slicing the volume, the host path to the output file, and the host path to the config file.
+    tuple[SliceOptions, str, str | None] | str
+        The options for slicing the volume, the host path to the output file, and the host path to output slices.
     """
 
     # Copy the file to the docker volume
@@ -234,10 +238,6 @@ def load_options_for_slice_docker(
         if slice_options.make_single_file is False
         else None
     )
-    host_output_config_file = combine_unknown_folder(
-        host_output_folder,
-        format_slice_output_config_file(slice_options.output_file_name),
-    )
 
     # Modify the output file folder to be in the docker volume
     slice_options.output_file_folder = get_volume_path()
@@ -260,12 +260,11 @@ def load_options_for_slice_docker(
         slice_options.neuroglancer_json
     )
 
-    return slice_options, host_output_file, host_output_config_file, host_output_slices
+    return slice_options, host_output_file, host_output_slices
 
 
 def save_output_for_slice_docker(
     host_output_file: str,
-    host_output_config_file: str,
     host_output_slices=None,
     target_path: str = "./",
 ) -> None | str:
@@ -276,8 +275,6 @@ def save_output_for_slice_docker(
     ----------
     host_output_file : str
         The path to the output file on the host.
-    host_output_config_file : str
-        The path to the config file on the host.
     host_output_slices : str, optional
         The path to the slices folder on the host, by default None
     target_path : str, optional
@@ -299,7 +296,6 @@ def save_output_for_slice_docker(
             ),
             "targetPath": target_path,
         },
-        {"sourcePath": host_output_config_file, "targetPath": target_path},
     ]
     success, error = copy_to_host(files)
 

python/ouroboros/common/pipelines.py

@@ -6,8 +6,6 @@
     SlicesGeometryPipelineStep,
     VolumeCachePipelineStep,
     SliceParallelPipelineStep,
-    SaveConfigPipelineStep,
-    LoadConfigPipelineStep,
     BackprojectPipelineStep,
 )
 
@@ -39,7 +37,6 @@ def slice_pipeline(slice_options: SliceOptions, verbose: bool = False):
                 if verbose
                 else SliceParallelPipelineStep()
             ),
-            SaveConfigPipelineStep(),
         ]
     )
 
@@ -51,7 +48,9 @@ def slice_pipeline(slice_options: SliceOptions, verbose: bool = False):
 
 
 def backproject_pipeline(
-    backproject_options: BackprojectOptions, verbose: bool = False
+    backproject_options: BackprojectOptions,
+    slice_options: SliceOptions,
+    verbose: bool = False,
 ):
     """
     Creates a pipeline for backprojecting a volume, as well as the default input data for the pipeline.
@@ -60,6 +59,8 @@ def backproject_pipeline(
     ----------
     backproject_options : BackprojectOptions
         The options for backprojecting the volume.
+    slice_options : SliceOptions
+        The options for slicing the volume.
     verbose : bool, optional
         Whether to show a progress bar for the pipeline, by default False
 
@@ -71,19 +72,22 @@ def backproject_pipeline(
 
     pipeline = Pipeline(
         [
-            LoadConfigPipelineStep()
-            .with_custom_output_file_path(backproject_options.straightened_volume_path)
-            .with_custom_options(backproject_options),
+            ParseJSONPipelineStep(),
+            SlicesGeometryPipelineStep(),
+            VolumeCachePipelineStep(),
             (
                 BackprojectPipelineStep().with_progress_bar()
                 if verbose
                 else BackprojectPipelineStep()
             ),
-            SaveConfigPipelineStep(),
         ]
     )
 
-    default_input_data = PipelineInput(config_file_path=backproject_options.config_path)
+    default_input_data = PipelineInput(
+        slice_options=slice_options,
+        backproject_options=backproject_options,
+        json_path=slice_options.neuroglancer_json,
+    )
 
     return pipeline, default_input_data
 

python/ouroboros/common/server_handlers.py

@@ -52,9 +52,7 @@ def handle_slice_docker(task: SliceTask):
         task.status = "error"
         return
 
-    slice_options, host_output_file, host_output_config_file, host_output_slices = (
-        load_result
-    )
+    slice_options, host_output_file, host_output_slices = load_result
 
     slice_result = handle_slice_core(task, slice_options)
 
@@ -64,16 +62,16 @@ def handle_slice_docker(task: SliceTask):
         return
 
     save_result = save_output_for_slice_docker(
-        host_output_file, host_output_config_file, host_output_slices=host_output_slices
+        host_output_file, host_output_slices=host_output_slices
     )
 
     if save_result:
         task.error = save_result
         task.status = "error"
 
 
-def handle_backproject_core(task: BackProjectTask, options):
-    pipeline, input_data = backproject_pipeline(options)
+def handle_backproject_core(task: BackProjectTask, options, slice_options):
+    pipeline, input_data = backproject_pipeline(options, slice_options)
 
     # Store the pipeline in the task
     task.pipeline = pipeline
@@ -97,8 +95,9 @@ def handle_backproject_core(task: BackProjectTask, options):
 
 def handle_backproject(task: BackProjectTask):
     options = load_options_for_backproject(task.options)
+    slice_options = load_options_for_slice(options.slice_options_path)
 
-    backproject_result = handle_backproject_core(task, options)
+    backproject_result = handle_backproject_core(task, options, slice_options)
 
     if isinstance(backproject_result, str):
         task.error = backproject_result
@@ -116,13 +115,13 @@ def handle_backproject_docker(task: BackProjectTask):
 
     (
         options,
+        slice_options,
         host_output_file,
-        host_output_config_file,
         host_output_slices,
         host_output_folder,
     ) = load_result
 
-    backproject_result = handle_backproject_core(task, options)
+    backproject_result = handle_backproject_core(task, options, slice_options)
 
     if isinstance(backproject_result, str):
         task.error = backproject_result
@@ -139,7 +138,8 @@ def handle_backproject_docker(task: BackProjectTask):
             )
 
     save_result = save_output_for_backproject_docker(
-        host_output_file, host_output_config_file, host_output_slices=host_output_slices
+        host_output_file,
+        host_output_slices=host_output_slices,
     )
 
     if save_result:

python/ouroboros/helpers/options.py

@@ -56,7 +56,7 @@ def validate_bounding_box_params(cls, value: any):
 @model_with_json
 class BackprojectOptions(CommonOptions):
     straightened_volume_path: str  # Path to the straightened volume
-    config_path: str  # Path to the config file
+    slice_options_path: str  # Path to the slice options file
     backproject_min_bounding_box: bool = (
         True  # Whether to backproject to a minimum bounding box or the entire volume
     )
@@ -82,6 +82,6 @@ class BackprojectOptions(CommonOptions):
     output_file_folder="./output/",
     output_file_name="sample",
     straightened_volume_path="./sample.tif",
-    config_path="./sample-configuration.json",
+    slice_options_path="./sample-slice-options.json",
     make_single_file=False,
 )

python/ouroboros/pipeline/backproject_pipeline.py

@@ -43,7 +43,6 @@ def __init__(self, processes=multiprocessing.cpu_count()) -> None:
         super().__init__(
             inputs=(
                 "backproject_options",
-                "output_file_path",
                 "volume_cache",
                 "slice_rects",
             )
@@ -52,14 +51,14 @@ def __init__(self, processes=multiprocessing.cpu_count()) -> None:
         self.num_processes = processes
 
     def _process(self, input_data: any) -> tuple[any, None] | tuple[None, any]:
-        config, input_tiff_path, volume_cache, slice_rects, pipeline_input = input_data
+        config, volume_cache, slice_rects, pipeline_input = input_data
 
         # Verify that a config object is provided
         if not isinstance(config, BackprojectOptions):
             return "Input data must contain a BackprojectOptions object."
 
         # Verify that input_data is a string containing a path to a tif file
-        if not isinstance(input_tiff_path, str):
+        if not isinstance(config.straightened_volume_path, str):
             return "Input data must contain a string containing a path to a tif file."
 
         # Verify that a volume cache is given

python/ouroboros/pipeline/save_config_pipeline.py

@@ -1,4 +1,4 @@
-from ouroboros.helpers.files import join_path
+from ouroboros.helpers.files import format_slice_output_config_file, join_path
 from .pipeline import PipelineStep
 
 
@@ -18,7 +18,8 @@ def _process(self, input_data: tuple[any]) -> None | str:
 
         # Determine the name of the file to save to
         json_path = join_path(
-            config.output_file_folder, config.output_file_name + "-configuration.json"
+            config.output_file_folder,
+            format_slice_output_config_file(config.output_file_name),
         )
 
         currrent_pipeline_input.config_file_path = json_path

python/test/helpers/test_options.py

@@ -74,7 +74,7 @@ def test_backproject_options_to_json(tmp_path):
         output_file_folder="./output/",
         output_file_name="output",
         straightened_volume_path="./volume.tif",
-        config_path="./config.json",
+        slice_options_path="./slice-options.json",
     )
     json_path = tmp_path / "backproject_options.json"
     options.save_to_json(json_path)

src/renderer/src/interfaces/options.tsx

@@ -275,9 +275,9 @@ export class BackprojectOptionsFile extends CompoundEntry {
 			).withDescription(
 				'Path to the volume of slices to backproject (e.g. the output tif of the slicing step).'
 			),
-			new Entry('config_path', 'Slice Configuration File', '', 'filePath')
+			new Entry('slice_options_path', 'Slice Options File', '', 'filePath')
 				.withDescription(
-					'Path to the `-configuration.json` file which includes information generated during slicing needed for backprojection.'
+					'Path to the `-slice-options.json` file which includes the information needed for backprojection.'
 				)
 				.withSeparator(),
 			new Entry('output_file_folder', 'Output File Folder', './', 'filePath').withDescription(