Merge pull request #89 from scipp/write-cif

Add a CIF writer

Author: jl-wynen

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

@@ -20,8 +20,7 @@
    "outputs": [],
    "source": [
     "import scipp as sc\n",
-    "import scippneutron as scn\n",
-    "import scippneutron.io\n",
+    "from scippneutron.io import cif\n",
     "\n",
     "from ess import dream, powder\n",
     "import ess.dream.data  # noqa: F401\n",
@@ -87,6 +86,31 @@
    "cell_type": "markdown",
    "id": "6",
    "metadata": {},
+   "source": [
+    "We also need some parameters to configure the output file:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "workflow[CIFAuthors] = CIFAuthors([\n",
+    "    cif.Author(\n",
+    "        name=\"Jane Doe\",\n",
+    "        email=\"[email protected]\",\n",
+    "        orcid=\"0000-0000-0000-0001\",\n",
+    "        role=\"measurement\",\n",
+    "    ),\n",
+    "])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8",
+   "metadata": {},
    "source": [
     "## Use the workflow\n",
     "\n",
@@ -96,7 +120,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7",
+   "id": "9",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -105,27 +129,29 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8",
+   "id": "10",
    "metadata": {},
    "source": [
-    "We then call `compute()` to compute the result:"
+    "We then call `compute()` to compute the result:\n",
+    "(The `cif` object will later be used to write the result to disk.)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
-    "result = workflow.compute(IofDspacing)\n",
-    "result"
+    "results = workflow.compute([IofDspacing, ReducedDspacingCIF])\n",
+    "result = results[IofDspacing]\n",
+    "cif_data = results[ReducedDspacingCIF]"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "10",
+   "id": "12",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -135,28 +161,30 @@
   },
   {
    "cell_type": "markdown",
-   "id": "11",
+   "id": "13",
    "metadata": {},
    "source": [
-    "We can now save the result to disk:"
+    "We can now save the result to disk:\n",
+    "(The comment is optional but helps to identify the file later.)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12",
+   "id": "14",
    "metadata": {},
    "outputs": [],
    "source": [
-    "dspacing_histogram.coords[\"dspacing\"] = sc.midpoints(\n",
-    "    dspacing_histogram.coords[\"dspacing\"]\n",
-    ")\n",
-    "scn.io.save_xye(\"dspacing.xye\", dspacing_histogram)"
+    "cif_data.comment = \"\"\"This file was generated with the DREAM data reduction user guide\n",
+    "in the documentation of ESSdiffraction.\n",
+    "See https://scipp.github.io/essdiffraction/\n",
+    "\"\"\"\n",
+    "cif_data.save('dspacing.cif')"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "13",
+   "id": "15",
    "metadata": {},
    "source": [
     "## Compute intermediate results\n",
@@ -169,7 +197,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "14",
+   "id": "16",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +214,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "15",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -198,7 +226,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16",
+   "id": "18",
    "metadata": {},
    "source": [
     "## Grouping by scattering angle\n",
@@ -210,7 +238,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17",
+   "id": "19",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -222,7 +250,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "18",
+   "id": "20",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -233,7 +261,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "19",
+   "id": "21",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -251,7 +279,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "20",
+   "id": "22",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -275,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -37,8 +37,8 @@ dependencies = [
   "plopp",
   "pythreejs",
   "sciline>=24.06.0",
-  "scipp>=24.09.1",  # Fixed new hist/bin API
-  "scippneutron>=24.5.0",
+  "scipp>=24.09.1",
+  "scippneutron>=24.9.0",
   "scippnexus>=23.12.0",
 ]
 

requirements/base.in

@@ -10,5 +10,5 @@ plopp
 pythreejs
 sciline>=24.06.0
 scipp>=24.09.1
-scippneutron>=24.5.0
+scippneutron>=24.9.0
 scippnexus>=23.12.0

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:6ce1bbccfc85ced70dedc62a2266b339f1e7c814
+# SHA1:2cad3df672e12033fa21254667278ceafae15e09
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:

requirements/ci.txt

@@ -38,7 +38,7 @@ platformdirs==4.3.6
     #   virtualenv
 pluggy==1.5.0
     # via tox
-pyproject-api==1.7.2
+pyproject-api==1.8.0
     # via tox
 requests==2.32.3
     # via -r ci.in
@@ -48,7 +48,7 @@ tomli==2.0.1
     # via
     #   pyproject-api
     #   tox
-tox==4.19.0
+tox==4.20.0
     # via -r ci.in
 urllib3==2.2.3
     # via requests

requirements/docs.txt

@@ -160,7 +160,7 @@ sphinx==8.0.2
     #   sphinx-copybutton
     #   sphinx-design
     #   sphinxcontrib-bibtex
-sphinx-autodoc-typehints==2.4.3
+sphinx-autodoc-typehints==2.4.4
     # via -r docs.in
 sphinx-copybutton==0.5.2
     # via -r docs.in

src/ess/dream/__init__.py

@@ -12,18 +12,17 @@
 from .workflow import DreamGeant4Workflow, default_parameters
 
 try:
-    __version__ = importlib.metadata.version(__package__ or __name__)
+    __version__ = importlib.metadata.version("essdiffraction")
 except importlib.metadata.PackageNotFoundError:
     __version__ = "0.0.0"
 
 del importlib
 
 __all__ = [
+    '__version__',
     'DreamGeant4Workflow',
     'default_parameters',
-    'beamline',
     'instrument_view',
     'load_geant4_csv',
     'nexus',
-    'providers',
 ]

src/ess/dream/io/__init__.py

@@ -5,5 +5,8 @@
 
 from . import nexus
 from .geant4 import load_geant4_csv
+from .cif import prepare_reduced_dspacing_cif
 
-__all__ = ["nexus", "load_geant4_csv"]
+providers = (prepare_reduced_dspacing_cif,)
+
+__all__ = ["nexus", "load_geant4_csv", "prepare_reduced_dspacing_cif", "providers"]

src/ess/dream/io/cif.py

@@ -0,0 +1,48 @@
+# SPDX-License-Identifier: BSD-3-Clause
+# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
+
+"""CIF writer for DREAM."""
+
+import scipp as sc
+from scippneutron.io import cif
+
+from ess.powder.types import CIFAuthors, IofDspacing, ReducedDspacingCIF
+
+
+def prepare_reduced_dspacing_cif(
+    da: IofDspacing, *, authors: CIFAuthors
+) -> ReducedDspacingCIF:
+    """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 `'dspacing'` dimension and coordinate.
+    authors:
+        List of authors to write to the file.
+
+    Returns
+    -------
+    :
+        An object that contains the reduced data and metadata.
+        Us its ``save`` method to write the CIF file.
+    """
+    from .. import __version__
+
+    to_save = _prepare_data(da)
+    return ReducedDspacingCIF(
+        cif.CIF('reduced_dspacing')
+        .with_reducers(f'ess.dream v{__version__}')
+        .with_authors(*authors)
+        .with_beamline(beamline='DREAM', facility='ESS')
+        .with_reduced_powder_data(to_save)
+    )
+
+
+def _prepare_data(da: sc.DataArray) -> sc.DataArray:
+    hist = da.copy(deep=False) if da.bins is None else da.hist()
+    hist.coords[hist.dim] = sc.midpoints(hist.coords[hist.dim])
+    return hist

src/ess/dream/workflow.py

@@ -1,6 +1,8 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
 
+import itertools
+
 import sciline
 import scipp as sc
 
@@ -13,8 +15,11 @@
     VanadiumRun,
 )
 
+from .io.cif import CIFAuthors, prepare_reduced_dspacing_cif
 from .io.geant4 import LoadGeant4Workflow
 
+_dream_providers = (prepare_reduced_dspacing_cif,)
+
 
 def default_parameters() -> dict:
     # Quantities not available in the simulated data
@@ -28,6 +33,7 @@ def default_parameters() -> dict:
         NeXusSource[VanadiumRun]: source,
         AccumulatedProtonCharge[SampleRun]: charge,
         AccumulatedProtonCharge[VanadiumRun]: charge,
+        CIFAuthors: CIFAuthors([]),
     }
 
 
@@ -36,7 +42,7 @@ def DreamGeant4Workflow() -> sciline.Pipeline:
     Workflow with default parameters for the Dream Geant4 simulation.
     """
     wf = LoadGeant4Workflow()
-    for provider in powder_providers:
+    for provider in itertools.chain(powder_providers, _dream_providers):
         wf.insert(provider)
     for key, value in default_parameters().items():
         wf[key] = value

src/ess/powder/__init__.py

@@ -18,7 +18,7 @@
 from .masking import with_pixel_mask_filenames
 
 try:
-    __version__ = importlib.metadata.version(__package__ or __name__)
+    __version__ = importlib.metadata.version("essdiffraction")
 except importlib.metadata.PackageNotFoundError:
     __version__ = "0.0.0"
 
@@ -35,12 +35,12 @@
 """Sciline providers for powder diffraction."""
 
 __all__ = [
+    "__version__",
     "conversion",
     "correction",
     "filtering",
     "grouping",
     "masking",
-    "nexus",
     "transform",
     "providers",
     "smoothing",