Add CLI flag to set continuous scan subset start and stop indices

docs/source/howto/run_httomo.rst

@@ -235,7 +235,7 @@ directory created by HTTomo would be
 Options/flags
 #############
 
-The :code:`run` command has 17 options/flags:
+The :code:`run` command has 18 options/flags:
 
 - :code:`--output-folder-name`
 - :code:`--save-all`
@@ -254,6 +254,7 @@ The :code:`run` command has 17 options/flags:
 - :code:`--recon-filename-stem`
 - :code:`--pipeline-format`
 - :code:`--mpi-abort-hook`
+- :code:`--continuous-scan-subset`
 
 :code:`--output-folder-name`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -542,6 +543,28 @@ before the MPI abort mechanism begins to terminate the python processes. Thus, t
 terminal when MPI abort is invoked may only contain partial information about the exception
 that triggered the MPI abort.
 
+:code:`--continuous-scan-subset`
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This is an alternative to the :code:`continuous_scan_subset` loader parameter, see
+:ref:`continuous_scan_subset_selection` for more details.
+
+This flag takes two values, the first one being the start index and the second one being the
+stop index. For example, an equivalent of the following config:
+
+.. literalinclude:: ../../../tests/samples/pipeline_template_examples/testing/loader_with_offset_param.yaml
+   :language: yaml
+   :emphasize-lines: 7-9
+
+can be achieved with the flag via :code:`--continuous-scan-subset 90 180`
+
+.. note:: This flag overrides the :code:`continuous_scan_subset` parameter in the YAML
+   config. Meaning, if the :code:`continuous_scan_subset` parameter is present in the loader's
+   config in the YAML pipeline but the :code:`--continuous-scan-subset` flag is used, then the
+   values given in the YAML config are ignored and the values given to the flag take
+   precedence. If this occurs, it will be logged to the :code:`debug.log` file that HTTomo
+   produces.
+
 Developer options
 +++++++++++++++++
 

docs/source/reference/loaders.rst

@@ -260,6 +260,8 @@ passed along to the first method. The loader has the :code:`preview` parameter
 for configuring the cropping/previewing. Please see :ref:`previewing` for more
 details on previewing.
 
+.. _continuous_scan_subset_selection:
+
 Continuous Scan Subset Selection
 ================================
 

httomo/cli.py

@@ -206,6 +206,13 @@ def check(pipeline: Union[Path, str], in_data_file: Optional[Path] = None):
     is_flag=True,
     help="Enable hook that invokes MPI abort if an unhandled exception is encountered",
 )
+@click.option(
+    "--continuous-scan-subset",
+    nargs=2,
+    type=click.INT,
+    default=None,
+    help="Start and stop indices for selecting subset of projections along angular dimension",
+)
 def run(
     in_data_file: Path,
     pipeline: Union[Path, str],
@@ -227,6 +234,7 @@ def run(
     frames_per_chunk: int,
     recon_filename_stem: Optional[str],
     mpi_abort_hook: bool,
+    continuous_scan_subset: Optional[tuple[int, int]],
 ):
     """Run a pipeline on input data."""
     if mpi_abort_hook:
@@ -242,6 +250,7 @@ def run(
         syslog_port,
         output_folder_name,
         recon_filename_stem,
+        continuous_scan_subset,
     )
 
     does_contain_sweep = is_sweep_pipeline(pipeline)
@@ -329,6 +338,7 @@ def set_global_constants(
     syslog_port: int,
     output_folder_name: Optional[Path],
     recon_filename_stem: Optional[str],
+    continuous_scan_subset: Optional[tuple[int, int]],
 ) -> None:
     if compress_intermediate and frames_per_chunk == 0:
         # 0 means write contiguously but compression must have chunk
@@ -340,6 +350,7 @@ def set_global_constants(
     httomo.globals.SYSLOG_SERVER = syslog_host
     httomo.globals.SYSLOG_PORT = syslog_port
     httomo.globals.RECON_FILENAME_STEM = recon_filename_stem
+    httomo.globals.CONTINUOUS_SCAN_SUBSET = continuous_scan_subset
 
     if output_folder_name is None:
         httomo.globals.run_out_dir = out_dir.joinpath(

httomo/globals.py

@@ -16,3 +16,4 @@
 SYSLOG_SERVER = "localhost"
 SYSLOG_PORT = 514
 RECON_FILENAME_STEM: Optional[str] = None
+CONTINUOUS_SCAN_SUBSET: Optional[tuple[int, int]] = None

httomo/ui_layer.py

@@ -1,3 +1,4 @@
+import logging
 import yaml
 from enum import Enum, auto
 from typing import Any, Dict, List, Optional, TypeAlias, Union
@@ -13,17 +14,20 @@
 from httomo.runner.method_wrapper import MethodWrapper
 from httomo.runner.pipeline import Pipeline
 
+import httomo.globals
 from httomo.method_wrappers import make_method_wrapper
 from httomo.loaders import make_loader
 from httomo.runner.loader import LoaderInterface
 from httomo.runner.output_ref import OutputRef
 from httomo.sweep_runner.param_sweep_json_loader import ParamSweepJsonLoader
 from httomo.sweep_runner.param_sweep_yaml_loader import get_param_sweep_yaml_loader
 from httomo.transform_loader_params import (
+    ContinuousScanSubsetParam,
     select_continuous_scan_subset,
     parse_config,
     parse_preview,
 )
+from httomo.utils import log_once
 from httomo_backends.methods_database.query import MethodDatabaseRepository
 
 MethodConfig: TypeAlias = Dict[str, Any]
@@ -144,7 +148,28 @@ def _setup_loader(self) -> LoaderInterface:
         with h5py.File(data_config.in_file, "r") as f:
             data_shape = f[data_config.data_path].shape
         preview = parse_preview(parameters.get("preview", None), data_shape)
-        continuous_scan_subset_config = parameters.get("continuous_scan_subset", None)
+        continuous_scan_subset_param = parameters.get("continuous_scan_subset", None)
+        if (
+            continuous_scan_subset_param is not None
+            and httomo.globals.CONTINUOUS_SCAN_SUBSET is not None
+        ):
+            warn_str = (
+                "continuous_scan_subset parameter exists in loader config with "
+                f"start={continuous_scan_subset_param["start"]} and "
+                f"stop={continuous_scan_subset_param["stop"]}, but is overidden by "
+                "values given to --continuous-scan-subset flag "
+                f"start={httomo.globals.CONTINUOUS_SCAN_SUBSET[0]} and "
+                f"stop={httomo.globals.CONTINUOUS_SCAN_SUBSET[1]}"
+            )
+            log_once(warn_str, level=logging.DEBUG)
+        continuous_scan_subset_config = (
+            ContinuousScanSubsetParam(
+                start=httomo.globals.CONTINUOUS_SCAN_SUBSET[0],
+                stop=httomo.globals.CONTINUOUS_SCAN_SUBSET[1],
+            )
+            if httomo.globals.CONTINUOUS_SCAN_SUBSET is not None
+            else continuous_scan_subset_param
+        )
         if continuous_scan_subset_config is not None:
             preview = select_continuous_scan_subset(
                 preview, continuous_scan_subset_config