Merge pull request #170 from scipp/subtract-empty-can

Move empty can subtraction to end

Author: jl-wynen

docs/user-guide/dream/dream-advanced-powder-reduction.ipynb

@@ -111,7 +111,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacingTwoTheta, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(IofDspacingTwoTheta[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -129,7 +129,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "grouped_dspacing = workflow.compute(IofDspacingTwoTheta)\n",
+    "grouped_dspacing = workflow.compute(IofDspacingTwoTheta[SampleRun])\n",
     "grouped_dspacing"
    ]
   },
@@ -209,7 +209,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(IofDspacing[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -227,7 +227,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = workflow.compute(IofDspacing)\n",
+    "result = workflow.compute(IofDspacing[SampleRun])\n",
     "result.hist().plot(title=result.coords['detector'].value.capitalize())"
    ]
   },
@@ -285,7 +285,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(IofDspacing[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -303,7 +303,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = workflow.compute(IofDspacing)\n",
+    "result = workflow.compute(IofDspacing[SampleRun])\n",
     "result.hist().plot(title=result.coords['detector'].value.capitalize())"
    ]
   },
@@ -424,8 +424,10 @@
     ").rename_axis(index='detector')\n",
     "\n",
     "all_detector_workflow = workflow.copy()\n",
-    "mapped = all_detector_workflow[IofDspacing].map(parameter_table)\n",
-    "all_detector_workflow[IofDspacing] = mapped.reduce(func=powder.grouping.collect_detectors)"
+    "mapped = all_detector_workflow[EmptyCanSubtractedIofDspacing[SampleRun]].map(parameter_table)\n",
+    "all_detector_workflow[EmptyCanSubtractedIofDspacing[SampleRun]] = mapped.reduce(\n",
+    "    func=powder.grouping.collect_detectors\n",
+    ")"
    ]
   },
   {
@@ -443,7 +445,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "all_detector_workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"}, compact=True)"
+    "all_detector_workflow.visualize(\n",
+    "    EmptyCanSubtractedIofDspacing[SampleRun],\n",
+    "    graph_attr={\"rankdir\": \"LR\"},\n",
+    "    compact=True\n",
+    ")"
    ]
   },
   {
@@ -461,7 +467,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = all_detector_workflow.compute(IofDspacing)"
+    "result = all_detector_workflow.compute(EmptyCanSubtractedIofDspacing[SampleRun])"
    ]
   },
   {
@@ -534,8 +540,10 @@
     ").rename_axis(index='detector')\n",
     "\n",
     "all_detector_workflow = workflow.copy()\n",
-    "mapped = all_detector_workflow[IofDspacingTwoTheta].map(parameter_table)\n",
-    "all_detector_workflow[IofDspacingTwoTheta] = mapped.reduce(func=powder.grouping.collect_detectors)"
+    "mapped = all_detector_workflow[EmptyCanSubtractedIofDspacingTwoTheta[SampleRun]].map(parameter_table)\n",
+    "all_detector_workflow[EmptyCanSubtractedIofDspacingTwoTheta[SampleRun]] = mapped.reduce(\n",
+    "    func=powder.grouping.collect_detectors\n",
+    ")"
    ]
   },
   {
@@ -545,7 +553,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "all_detector_workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"}, compact=True)"
+    "all_detector_workflow.visualize(\n",
+    "    EmptyCanSubtractedIofDspacingTwoTheta[SampleRun],\n",
+    "    graph_attr={\"rankdir\": \"LR\"},\n",
+    "    compact=True\n",
+    ")"
    ]
   },
   {
@@ -555,7 +567,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = all_detector_workflow.compute(IofDspacingTwoTheta)"
+    "result = all_detector_workflow.compute(EmptyCanSubtractedIofDspacingTwoTheta[SampleRun])"
    ]
   },
   {
@@ -592,7 +604,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "pp.imagefigure(*(pp.Node(da.hist()) for da in result.values()), norm='log', cbar=True)"
+    "pp.imagefigure(\n",
+    "    *(pp.Node(da.hist()) for da in result.values()),\n",
+    "    norm='log',\n",
+    "    cbar=True,\n",
+    "    vmin=1e-3,\n",
+    ")"
    ]
   }
  ],

docs/user-guide/dream/dream-powder-reduction.ipynb

@@ -58,7 +58,6 @@
    "source": [
     "workflow = dream.DreamGeant4Workflow(\n",
     "    run_norm=powder.RunNormalization.monitor_histogram,\n",
-    "    subtract_empty_can=True,\n",
     ")"
    ]
   },
@@ -108,8 +107,11 @@
     "## Use the reduction workflow\n",
     "\n",
     "We then call [workflow.compute(target)](https://scipp.github.io/sciline/generated/classes/sciline.Pipeline.html#sciline.Pipeline.compute) to compute the result.\n",
-    "`IofDspacing` is the normalized intensity as a function of $d$-spacing.\n",
-    "`ReducedTofCIF` encode the same data but converted back to time-of-flight and ready to be written to a CIF file."
+    "\n",
+    "- `EmptyCanSubtractedIofDspacing` is the normalized intensity as a function of $d$-spacing.\n",
+    "- `ReducedEmptyCanSubtractedTofCIF` encode the same data but converted back to time-of-flight and ready to be written to a CIF file.\n",
+    "\n",
+    "If we didn't want to subtract an empty can measurement from the sample measurement, we would instead request `IofDspacing[SampleRun]` and `ReducedTofCIF`."
    ]
   },
   {
@@ -119,9 +121,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = workflow.compute([IofDspacing, ReducedTofCIF])\n",
-    "intensity = results[IofDspacing]\n",
-    "cif_data = results[ReducedTofCIF]"
+    "results = workflow.compute([\n",
+    "    EmptyCanSubtractedIofDspacing[SampleRun],\n",
+    "    ReducedEmptyCanSubtractedTofCIF\n",
+    "])\n",
+    "intensity = results[EmptyCanSubtractedIofDspacing[SampleRun]]\n",
+    "cif_data = results[ReducedEmptyCanSubtractedTofCIF]"
    ]
   },
   {
@@ -185,7 +190,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(ReducedTofCIF, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(ReducedEmptyCanSubtractedTofCIF, graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {

docs/user-guide/dream/workflow-widget-dream.ipynb

@@ -59,7 +59,7 @@
     "wfw = widget.children[1].children[0]\n",
     "outputs = wfw.output_selection_box.typical_outputs_widget\n",
     "keys, values = zip(*outputs.options, strict=True)\n",
-    "ind = keys.index(\"IofTof\")\n",
+    "ind = keys.index(\"IofDspacing[SampleRun]\")\n",
     "outputs.value = (values[ind],)\n",
     "# Refresh parameters\n",
     "pbox = wfw.parameter_box\n",
@@ -116,7 +116,7 @@
    "outputs": [],
    "source": [
     "(da,) = results.values()\n",
-    "da.hist(tof=200).plot()"
+    "da.hist(dspacing=200).plot()"
    ]
   }
  ],

docs/user-guide/sns-instruments/POWGEN_data_reduction.ipynb

@@ -106,7 +106,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "IofDspacing in workflow.get(IofDspacing).keys()"
+    "IofDspacing[SampleRun] in workflow.get(IofDspacing[SampleRun]).keys()"
    ]
   },
   {
@@ -116,7 +116,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacing, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(IofDspacing[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -134,7 +134,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = workflow.compute(IofDspacing)\n",
+    "result = workflow.compute(IofDspacing[SampleRun])\n",
     "result"
    ]
   },
@@ -172,7 +172,7 @@
    "outputs": [],
    "source": [
     "def save_xye(\n",
-    "    reduced_data: IofDspacing,\n",
+    "    reduced_data: IofDspacing[SampleRun],\n",
     "    out_filename: OutFilename,\n",
     ") -> None:\n",
     "    data = reduced_data.hist()\n",
@@ -319,7 +319,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "workflow.visualize(IofDspacingTwoTheta, graph_attr={\"rankdir\": \"LR\"})"
+    "workflow.visualize(IofDspacingTwoTheta[SampleRun], graph_attr={\"rankdir\": \"LR\"})"
    ]
   },
   {
@@ -337,7 +337,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "grouped_dspacing = workflow.compute(IofDspacingTwoTheta)\n",
+    "grouped_dspacing = workflow.compute(IofDspacingTwoTheta[SampleRun])\n",
     "grouped_dspacing"
    ]
   },

src/ess/dream/io/cif.py

@@ -10,7 +10,9 @@
 from ess.powder.types import (
     Beamline,
     CIFAuthors,
+    EmptyCanSubtractedIofTof,
     IofTof,
+    ReducedEmptyCanSubtractedTofCIF,
     ReducedTofCIF,
     ReducerSoftwares,
     Source,
@@ -53,6 +55,71 @@ def prepare_reduced_tof_cif(
         An object that contains the reduced data and metadata.
         Us its ``save`` method to write the CIF file.
     """
+    return _prepare_reduced_tof_cif_impl(
+        da,
+        authors=authors,
+        beamline=beamline,
+        source=source,
+        reducers=reducers,
+        calibration=calibration,
+    )
+
+
+def prepare_reduced_empty_can_subtracted_tof_cif(
+    da: EmptyCanSubtractedIofTof,
+    *,
+    authors: CIFAuthors,
+    beamline: Beamline,
+    source: Source,
+    reducers: ReducerSoftwares,
+    calibration: OutputCalibrationData,
+) -> ReducedEmptyCanSubtractedTofCIF:
+    """Construct a CIF builder with reduced data in d-spacing.
+
+    The object contains the d-spacing coordinate, intensities,
+    and some metadata.
+
+    Parameters
+    ----------
+    da:
+        Reduced 1d data with a ``'tof'`` dimension and coordinate.
+    authors:
+        List of authors to write to the file.
+    beamline:
+        Information about the beamline that the data was produced at.
+    source:
+        Information about the neutron source.
+    reducers:
+        List of software pieces used to reduce the data.
+    calibration:
+        Coefficients for conversion between d-spacing and final ToF.
+        See :meth:`scippneutron.io.cif.CIF.with_powder_calibration`.
+
+    Returns
+    -------
+    :
+        An object that contains the reduced data and metadata.
+        Us its ``save`` method to write the CIF file.
+    """
+    return _prepare_reduced_tof_cif_impl(
+        da,
+        authors=authors,
+        beamline=beamline,
+        source=source,
+        reducers=reducers,
+        calibration=calibration,
+    )
+
+
+def _prepare_reduced_tof_cif_impl(
+    da: IofTof,
+    *,
+    authors: CIFAuthors,
+    beamline: Beamline,
+    source: Source,
+    reducers: ReducerSoftwares,
+    calibration: OutputCalibrationData,
+) -> ReducedTofCIF:
     to_save = _prepare_data(da)
     return ReducedTofCIF(
         cif.CIF('reduced_tof')

src/ess/dream/parameters.py

@@ -9,8 +9,8 @@
     CalibrationFilename,
     DspacingBins,
     Filename,
+    IofDspacing,
     IofDspacingTwoTheta,
-    IofTof,
     MonitorFilename,
     NeXusDetectorName,
     PixelMaskFilename,
@@ -68,4 +68,8 @@
 # that allows to define a python function in the notebook and pass it to the workflow.
 # We defer this to later; the masks are set to None by default in the workflow for now.
 
-typical_outputs = (IofTof, IofDspacingTwoTheta, ReducedTofCIF)
+typical_outputs = (
+    IofDspacing[SampleRun],
+    IofDspacingTwoTheta[SampleRun],
+    ReducedTofCIF,
+)