Add documentation of reduction interface.

Author: YooSunYoung

docs/user-guide/index.md

@@ -5,6 +5,7 @@
 maxdepth: 1
 ---
 
+workflow
 mcstas_workflow
 mcstas_workflow_chunk
 scaling_workflow

docs/user-guide/workflow.ipynb

@@ -0,0 +1,171 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# NMX Reduction Workflow\n",
+    "\n",
+    "> NMX does not expect users to use python interface directly.<br>\n",
+    "This documentation is mostly for istrument data scientists or instrument scientists.<br>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## TL;DR"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ess.nmx.executables import reduction\n",
+    "from ess.nmx.data import get_small_nmx_nexus\n",
+    "from ess.nmx.configurations import (\n",
+    "    ReductionConfig,\n",
+    "    OutputConfig,\n",
+    "    InputConfig,\n",
+    "    WorkflowConfig,\n",
+    "    TimeBinCoordinate,\n",
+    ")\n",
+    "\n",
+    "# Build Configuration\n",
+    "config = ReductionConfig(\n",
+    "    inputs=InputConfig(\n",
+    "        input_file=[get_small_nmx_nexus().as_posix()],\n",
+    "        detector_ids=[0, 1, 2],  # Detector index to be reduced in alphabetical order.\n",
+    "    ),\n",
+    "    output=OutputConfig(\n",
+    "        output_file=\"scipp_output.hdf\", skip_file_output=False, overwrite=True\n",
+    "    ),\n",
+    "    workflow=WorkflowConfig(\n",
+    "        time_bin_coordinate=TimeBinCoordinate.time_of_flight,\n",
+    "        nbins=10,\n",
+    "        tof_simulation_num_neutrons=1_000_000,\n",
+    "        tof_simulation_min_wavelength=1.8,\n",
+    "        tof_simulation_max_wavelength=3.6,\n",
+    "        tof_simulation_seed=42,\n",
+    "    ),\n",
+    ")\n",
+    "\n",
+    "# Run Reduction\n",
+    "reduction(config=config, display=display)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Configuration\n",
+    "\n",
+    "`essnmx` provide command line data reduction tool for the reduction between `nexus` and `dials`.<br>\n",
+    "The `essnmx-reduce` interface will reduce `nexus` file <br>\n",
+    "and save the results into `NXlauetof`(not exactly but very close) format for `dials`.<br>\n",
+    "\n",
+    "Argument options could be exhaustive therefore we wrapped them into a nested pydantic model.<br>\n",
+    "Here is a python API you can use to build the configuration and turn it into a command line arguments.\n",
+    "\n",
+    "**Configuration object is pydantic model so it strictly check the type of the arguments.**"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ess.nmx.configurations import (\n",
+    "    ReductionConfig,\n",
+    "    OutputConfig,\n",
+    "    InputConfig,\n",
+    "    WorkflowConfig,\n",
+    "    TimeBinCoordinate,\n",
+    "    to_command_arguments,\n",
+    ")\n",
+    "\n",
+    "config = ReductionConfig(\n",
+    "    inputs=InputConfig(\n",
+    "        input_file=[\"PATH_TO_THE_NEXUS_FILE.hdf\"],\n",
+    "        detector_ids=[0, 1, 2],  # Detector index to be reduced in alphabetical order.\n",
+    "    ),\n",
+    "    output=OutputConfig(output_file=\"scipp_output.hdf\", skip_file_output=True),\n",
+    "    workflow=WorkflowConfig(\n",
+    "        time_bin_coordinate=TimeBinCoordinate.time_of_flight,\n",
+    "        nbins=10,\n",
+    "        tof_simulation_num_neutrons=1_000_000,\n",
+    "        tof_simulation_min_wavelength=1.8,\n",
+    "        tof_simulation_max_wavelength=3.6,\n",
+    "        tof_simulation_seed=42,\n",
+    "    ),\n",
+    ")\n",
+    "\n",
+    "display(config)\n",
+    "print(to_command_arguments(config=config, one_line=True))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Reduce Nexus File(s)\n",
+    "\n",
+    "`OutputConfig` has an option called `skip_file_output` if you want to reduce the file and use it only on the memory.<br>\n",
+    "Then you can use `save_results` function to explicitly save the results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ess.nmx.executables import reduction\n",
+    "from ess.nmx.data import get_small_nmx_nexus\n",
+    "\n",
+    "config = ReductionConfig(\n",
+    "    inputs=InputConfig(input_file=[get_small_nmx_nexus().as_posix()]),\n",
+    "    output=OutputConfig(skip_file_output=True),\n",
+    ")\n",
+    "results = reduction(config=config, display=display)\n",
+    "results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ess.nmx.executables import save_results\n",
+    "\n",
+    "output_config = OutputConfig(output_file=\"scipp_output.hdf\", overwrite=True)\n",
+    "save_results(results=results, output_config=output_config)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "nmx-dev-313",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

src/ess/nmx/_executable_helper.py

@@ -174,42 +174,6 @@ def reduction_config_from_args(args: argparse.Namespace) -> ReductionConfig:
     )
 
 
-def to_command_arguments(
-    config: ReductionConfig, one_line: bool = True
-) -> list[str] | str:
-    """Convert the config to a list of command line arguments.
-
-    Parameters
-    ----------
-    one_line:
-        If True, return a single string with all arguments joined by spaces.
-        If False, return a list of argument strings.
-
-    """
-    args = {}
-    for instance in config._children:
-        args.update(instance.model_dump(mode='python'))
-    args = {f"--{k.replace('_', '-')}": v for k, v in args.items() if v is not None}
-
-    arg_list = []
-    for k, v in args.items():
-        if not isinstance(v, bool):
-            arg_list.append(k)
-            if isinstance(v, list):
-                arg_list.extend(str(item) for item in v)
-            elif isinstance(v, enum.StrEnum):
-                arg_list.append(v.value)
-            else:
-                arg_list.append(str(v))
-        elif v is True:
-            arg_list.append(k)
-
-    if one_line:
-        return ' '.join(arg_list)
-    else:
-        return arg_list
-
-
 def build_logger(args: argparse.Namespace | OutputConfig) -> logging.Logger:
     logger = logging.getLogger(__name__)
     if args.verbose:

src/ess/nmx/configurations.py

@@ -130,11 +130,22 @@ class OutputConfig(BaseModel):
         default=False,
     )
     # File output
+    skip_file_output: bool = Field(
+        title="Skip File Output",
+        description="If True, the output file will not be written.",
+        default=False,
+    )
     output_file: str = Field(
         title="Output File",
-        description="Path to the output file.",
+        description="Path to the output file. "
+        "It will be overwritten if ``overwrite`` is True.",
         default="scipp_output.h5",
     )
+    overwrite: bool = Field(
+        title="Overwrite Output File",
+        description="If True, overwrite the output file if ``output_file`` exists.",
+        default=False,
+    )
     compression: Compression = Field(
         title="Compression",
         description="Compress option of reduced output file.",
@@ -152,3 +163,45 @@ class ReductionConfig(BaseModel):
     @property
     def _children(self) -> list[BaseModel]:
         return [self.inputs, self.workflow, self.output]
+
+
+def to_command_arguments(
+    *, config: ReductionConfig, one_line: bool = True, separator: str = '\\\n'
+) -> list[str] | str:
+    """Convert the config to a list of command line arguments.
+
+    Parameters
+    ----------
+    one_line:
+        If True, return a single string with all arguments joined by spaces.
+        If False, return a list of argument strings.
+
+    """
+    args = {}
+    for instance in config._children:
+        args.update(instance.model_dump(mode='python'))
+    args = {f"--{k.replace('_', '-')}": v for k, v in args.items() if v is not None}
+
+    arg_list = []
+    for k, v in args.items():
+        if not isinstance(v, bool):
+            arg_list.append(k)
+            if isinstance(v, list):
+                arg_list.extend(str(item) for item in v)
+            elif isinstance(v, enum.StrEnum):
+                arg_list.append(v.value)
+            else:
+                arg_list.append(str(v))
+        elif v is True:
+            arg_list.append(k)
+
+    if one_line:
+        # Default separator is backslash + newline for better readability
+        # Users can directly copy-paste the output in a terminal or a script.
+        return (
+            (separator + '--')
+            .join(" ".join(arg_list).split('--'))
+            .removeprefix(separator)
+        )
+    else:
+        return arg_list

src/ess/nmx/executables.py

@@ -17,7 +17,7 @@
     collect_matching_input_files,
     reduction_config_from_args,
 )
-from .configurations import ReductionConfig, WorkflowConfig
+from .configurations import OutputConfig, ReductionConfig, WorkflowConfig
 from .nexus import (
     export_detector_metadata_as_nxlauetof,
     export_monitor_metadata_as_nxlauetof,
@@ -160,27 +160,17 @@ def reduction(
         display=display,
     )
     metadatas = base_wf.compute((NMXSampleMetadata, NMXSourceMetadata))
-    export_static_metadata_as_nxlauetof(
-        sample_metadata=metadatas[NMXSampleMetadata],
-        source_metadata=metadatas[NMXSourceMetadata],
-        output_file=config.output.output_file,
-    )
     tof_das = sc.DataGroup()
     detector_metas = sc.DataGroup()
     for detector_name in detector_names:
         cur_wf = base_wf.copy()
         cur_wf[NeXusName[snx.NXdetector]] = detector_name
         results = cur_wf.compute((TofDetector[SampleRun], NMXDetectorMetadata))
-        detector_meta: NMXDetectorMetadata = results[NMXDetectorMetadata]
-        export_detector_metadata_as_nxlauetof(
-            detector_metadata=detector_meta, output_file=config.output.output_file
-        )
-        detector_metas[detector_name] = detector_meta
+        detector_metas[detector_name] = results[NMXDetectorMetadata]
         # Binning into 1 bin and getting final tof bin edges later.
         tof_das[detector_name] = results[TofDetector[SampleRun]].bin(tof=1)
 
     tof_bin_edges = _finalize_tof_bin_edges(tof_das=tof_das, config=config.workflow)
-
     monitor_metadata = NMXMonitorMetadata(
         tof_bin_coord='tof',
         # TODO: Use real monitor data
@@ -190,28 +180,54 @@ def reduction(
             data=sc.ones_like(tof_bin_edges[:-1]),
         ),
     )
-    export_monitor_metadata_as_nxlauetof(
-        monitor_metadata=monitor_metadata, output_file=config.output.output_file
-    )
 
     # Histogram detector counts
     tof_histograms = sc.DataGroup()
     for detector_name, tof_da in tof_das.items():
-        det_meta: NMXDetectorMetadata = detector_metas[detector_name]
         histogram = tof_da.hist(tof=tof_bin_edges)
         tof_histograms[detector_name] = histogram
-        export_reduced_data_as_nxlauetof(
-            detector_name=det_meta.detector_name,
-            da=histogram,
-            output_file=config.output.output_file,
-            compress_mode=config.output.compression,
-        )
 
-    return sc.DataGroup(
-        metadata=detector_metas,
+    results = sc.DataGroup(
         histogram=tof_histograms,
+        detector=detector_metas,
+        sample=metadatas[NMXSampleMetadata],
+        source=metadatas[NMXSourceMetadata],
+        monitor=monitor_metadata,
         lookup_table=base_wf.compute(TimeOfFlightLookupTable),
     )
+    if not config.output.skip_file_output:
+        save_results(results=results, output_config=config.output)
+
+    return results
+
+
+def save_results(*, results: sc.DataGroup, output_config: OutputConfig) -> None:
+    # Validate if results have expected fields
+    for mandatory_key in ['histogram', 'detector', 'sample', 'source', 'monitor']:
+        if mandatory_key not in results:
+            raise ValueError(f"Missing '{mandatory_key}' in results to save.")
+
+    export_static_metadata_as_nxlauetof(
+        sample_metadata=results['sample'],
+        source_metadata=results['source'],
+        output_file=output_config.output_file,
+        overwrite=output_config.overwrite,
+    )
+    export_monitor_metadata_as_nxlauetof(
+        monitor_metadata=results['monitor'],
+        output_file=output_config.output_file,
+    )
+    for detector_name, detector_meta in results['detector'].items():
+        export_detector_metadata_as_nxlauetof(
+            detector_metadata=detector_meta,
+            output_file=output_config.output_file,
+        )
+        export_reduced_data_as_nxlauetof(
+            detector_name=detector_name,
+            da=results['histogram'][detector_name],
+            output_file=output_config.output_file,
+            compress_mode=output_config.compression,
+        )
 
 
 def main() -> None: