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Merge pull request #89 from scipp/write-cif
Add a CIF writer
2 parents c4ee9b4 + 8380d27 commit 7772e69

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

+53-25
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@@ -20,8 +20,7 @@
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"outputs": [],
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"source": [
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"import scipp as sc\n",
23-
"import scippneutron as scn\n",
24-
"import scippneutron.io\n",
23+
"from scippneutron.io import cif\n",
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"\n",
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"from ess import dream, powder\n",
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"import ess.dream.data # noqa: F401\n",
@@ -87,6 +86,31 @@
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"cell_type": "markdown",
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"id": "6",
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"metadata": {},
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"source": [
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"We also need some parameters to configure the output file:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7",
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"metadata": {},
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"outputs": [],
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"source": [
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"workflow[CIFAuthors] = CIFAuthors([\n",
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" cif.Author(\n",
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" name=\"Jane Doe\",\n",
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" email=\"[email protected]\",\n",
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" orcid=\"0000-0000-0000-0001\",\n",
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" role=\"measurement\",\n",
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" ),\n",
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"])"
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]
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},
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{
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"cell_type": "markdown",
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"id": "8",
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"metadata": {},
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"source": [
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"## Use the workflow\n",
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"\n",
@@ -96,7 +120,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "7",
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"id": "9",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -105,27 +129,29 @@
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},
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{
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"cell_type": "markdown",
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"id": "8",
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"id": "10",
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"metadata": {},
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"source": [
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"We then call `compute()` to compute the result:"
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"We then call `compute()` to compute the result:\n",
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"(The `cif` object will later be used to write the result to disk.)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "9",
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"id": "11",
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"metadata": {},
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"outputs": [],
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"source": [
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"result = workflow.compute(IofDspacing)\n",
122-
"result"
146+
"results = workflow.compute([IofDspacing, ReducedDspacingCIF])\n",
147+
"result = results[IofDspacing]\n",
148+
"cif_data = results[ReducedDspacingCIF]"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "10",
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"id": "12",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -135,28 +161,30 @@
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},
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{
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"cell_type": "markdown",
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"id": "11",
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"id": "13",
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"metadata": {},
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"source": [
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"We can now save the result to disk:"
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"We can now save the result to disk:\n",
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"(The comment is optional but helps to identify the file later.)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "12",
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"id": "14",
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"metadata": {},
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"outputs": [],
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"source": [
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"dspacing_histogram.coords[\"dspacing\"] = sc.midpoints(\n",
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" dspacing_histogram.coords[\"dspacing\"]\n",
153-
")\n",
154-
"scn.io.save_xye(\"dspacing.xye\", dspacing_histogram)"
178+
"cif_data.comment = \"\"\"This file was generated with the DREAM data reduction user guide\n",
179+
"in the documentation of ESSdiffraction.\n",
180+
"See https://scipp.github.io/essdiffraction/\n",
181+
"\"\"\"\n",
182+
"cif_data.save('dspacing.cif')"
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]
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},
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{
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"cell_type": "markdown",
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"id": "13",
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"id": "15",
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"metadata": {},
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"source": [
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"## Compute intermediate results\n",
@@ -169,7 +197,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "14",
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"id": "16",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "15",
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"id": "17",
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"metadata": {},
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"outputs": [],
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"source": [
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},
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{
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"cell_type": "markdown",
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"id": "16",
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"id": "18",
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"metadata": {},
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"source": [
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"## Grouping by scattering angle\n",
@@ -210,7 +238,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "17",
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"id": "19",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -222,7 +250,7 @@
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "18",
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"id": "20",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "19",
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"id": "21",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "20",
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"id": "22",
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"metadata": {},
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"outputs": [],
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"source": [
@@ -275,7 +303,7 @@
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
278-
"version": "3.10.14"
306+
"version": "3.10.13"
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}
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},
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"nbformat": 4,

‎pyproject.toml

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@@ -37,8 +37,8 @@ dependencies = [
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"plopp",
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"pythreejs",
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"sciline>=24.06.0",
40-
"scipp>=24.09.1", # Fixed new hist/bin API
41-
"scippneutron>=24.5.0",
40+
"scipp>=24.09.1",
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"scippneutron>=24.9.0",
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"scippnexus>=23.12.0",
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]
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‎requirements/base.in

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@@ -10,5 +10,5 @@ plopp
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pythreejs
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sciline>=24.06.0
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scipp>=24.09.1
13-
scippneutron>=24.5.0
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scippneutron>=24.9.0
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scippnexus>=23.12.0

‎requirements/base.txt

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

‎requirements/ci.txt

+2-2
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@@ -38,7 +38,7 @@ platformdirs==4.3.6
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# virtualenv
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pluggy==1.5.0
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# via tox
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pyproject-api==1.7.2
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pyproject-api==1.8.0
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# via tox
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requests==2.32.3
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# via -r ci.in
@@ -48,7 +48,7 @@ tomli==2.0.1
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# via
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# pyproject-api
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# tox
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tox==4.19.0
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tox==4.20.0
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# via -r ci.in
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urllib3==2.2.3
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# via requests

‎requirements/docs.txt

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

‎src/ess/dream/__init__.py

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@@ -12,18 +12,17 @@
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from .workflow import DreamGeant4Workflow, default_parameters
1313

1414
try:
15-
__version__ = importlib.metadata.version(__package__ or __name__)
15+
__version__ = importlib.metadata.version("essdiffraction")
1616
except importlib.metadata.PackageNotFoundError:
1717
__version__ = "0.0.0"
1818

1919
del importlib
2020

2121
__all__ = [
22+
'__version__',
2223
'DreamGeant4Workflow',
2324
'default_parameters',
24-
'beamline',
2525
'instrument_view',
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'load_geant4_csv',
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'nexus',
28-
'providers',
2928
]

‎src/ess/dream/io/__init__.py

+4-1
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@@ -5,5 +5,8 @@
55

66
from . import nexus
77
from .geant4 import load_geant4_csv
8+
from .cif import prepare_reduced_dspacing_cif
89

9-
__all__ = ["nexus", "load_geant4_csv"]
10+
providers = (prepare_reduced_dspacing_cif,)
11+
12+
__all__ = ["nexus", "load_geant4_csv", "prepare_reduced_dspacing_cif", "providers"]

‎src/ess/dream/io/cif.py

+48
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@@ -0,0 +1,48 @@
1+
# SPDX-License-Identifier: BSD-3-Clause
2+
# Copyright (c) 2023 Scipp contributors (https://github.com/scipp)
3+
4+
"""CIF writer for DREAM."""
5+
6+
import scipp as sc
7+
from scippneutron.io import cif
8+
9+
from ess.powder.types import CIFAuthors, IofDspacing, ReducedDspacingCIF
10+
11+
12+
def prepare_reduced_dspacing_cif(
13+
da: IofDspacing, *, authors: CIFAuthors
14+
) -> ReducedDspacingCIF:
15+
"""Construct a CIF builder with reduced data in d-spacing.
16+
17+
The object contains the d-spacing coordinate, intensities,
18+
and some metadata.
19+
20+
Parameters
21+
----------
22+
da:
23+
Reduced 1d data with a `'dspacing'` dimension and coordinate.
24+
authors:
25+
List of authors to write to the file.
26+
27+
Returns
28+
-------
29+
:
30+
An object that contains the reduced data and metadata.
31+
Us its ``save`` method to write the CIF file.
32+
"""
33+
from .. import __version__
34+
35+
to_save = _prepare_data(da)
36+
return ReducedDspacingCIF(
37+
cif.CIF('reduced_dspacing')
38+
.with_reducers(f'ess.dream v{__version__}')
39+
.with_authors(*authors)
40+
.with_beamline(beamline='DREAM', facility='ESS')
41+
.with_reduced_powder_data(to_save)
42+
)
43+
44+
45+
def _prepare_data(da: sc.DataArray) -> sc.DataArray:
46+
hist = da.copy(deep=False) if da.bins is None else da.hist()
47+
hist.coords[hist.dim] = sc.midpoints(hist.coords[hist.dim])
48+
return hist

‎src/ess/dream/workflow.py

+7-1
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@@ -1,6 +1,8 @@
11
# SPDX-License-Identifier: BSD-3-Clause
22
# Copyright (c) 2024 Scipp contributors (https://github.com/scipp)
33

4+
import itertools
5+
46
import sciline
57
import scipp as sc
68

@@ -13,8 +15,11 @@
1315
VanadiumRun,
1416
)
1517

18+
from .io.cif import CIFAuthors, prepare_reduced_dspacing_cif
1619
from .io.geant4 import LoadGeant4Workflow
1720

21+
_dream_providers = (prepare_reduced_dspacing_cif,)
22+
1823

1924
def default_parameters() -> dict:
2025
# Quantities not available in the simulated data
@@ -28,6 +33,7 @@ def default_parameters() -> dict:
2833
NeXusSource[VanadiumRun]: source,
2934
AccumulatedProtonCharge[SampleRun]: charge,
3035
AccumulatedProtonCharge[VanadiumRun]: charge,
36+
CIFAuthors: CIFAuthors([]),
3137
}
3238

3339

@@ -36,7 +42,7 @@ def DreamGeant4Workflow() -> sciline.Pipeline:
3642
Workflow with default parameters for the Dream Geant4 simulation.
3743
"""
3844
wf = LoadGeant4Workflow()
39-
for provider in powder_providers:
45+
for provider in itertools.chain(powder_providers, _dream_providers):
4046
wf.insert(provider)
4147
for key, value in default_parameters().items():
4248
wf[key] = value

‎src/ess/powder/__init__.py

+2-2
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@@ -18,7 +18,7 @@
1818
from .masking import with_pixel_mask_filenames
1919

2020
try:
21-
__version__ = importlib.metadata.version(__package__ or __name__)
21+
__version__ = importlib.metadata.version("essdiffraction")
2222
except importlib.metadata.PackageNotFoundError:
2323
__version__ = "0.0.0"
2424

@@ -35,12 +35,12 @@
3535
"""Sciline providers for powder diffraction."""
3636

3737
__all__ = [
38+
"__version__",
3839
"conversion",
3940
"correction",
4041
"filtering",
4142
"grouping",
4243
"masking",
43-
"nexus",
4444
"transform",
4545
"providers",
4646
"smoothing",

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