Merge pull request #27 from scipp/orso-filewriter

Reimplement ORSO filewriter

conda/meta.yaml

@@ -12,6 +12,7 @@ requirements:
  - setuptools_scm
  run:
  - dask
+ - python-dateutil
  - graphviz
  - plopp
  - pythreejs

docs/api-reference/index.md

@@ -29,7 +29,8 @@
  :template: module-template.rst
  :recursive:
 
- types
  amor
+ orso
  supermirror
+ types
 ```

docs/examples/amor.ipynb

@@ -29,7 +29,7 @@
  "metadata": {},
  "outputs": [],
  "source": [
- "params={\n",
+ "params = {\n",
  " **default_parameters,\n",
  " QBins: sc.geomspace(dim='Q', start=0.008, stop=0.075, num=200, unit='1/angstrom'),\n",
  " SampleRotation[Sample]: sc.scalar(0.7989, unit='deg'),\n",
@@ -118,6 +118,150 @@
  "source": [
  "This plot can be used to check if the value of the sample rotation angle $\\omega$ is correct. The bright triangles should be pointing back to the origin $\\lambda = \\theta = 0$."
  ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Save data\n",
+ "\n",
+ "We can save the computed $I(Q)$ to an [ORSO](https://www.reflectometry.org) [.ort](https://github.com/reflectivity/file_format/blob/master/specification.md) file using the [orsopy](https://orsopy.readthedocs.io/en/latest/index.html) package.\n",
+ "\n",
+ "First, we need to collect the metadata for that file.\n",
+ "To this end, we build a pipeline with additional providers.\n",
+ "We also insert a parameter to indicate the creator of the processed data."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "from essreflectometry import orso\n",
+ "from essreflectometry.amor import orso as amor_orso\n",
+ "from orsopy import fileio"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "providers_with_metadata = (\n",
+ " *providers,\n",
+ " *orso.providers,\n",
+ " *amor_orso.providers,\n",
+ ")\n",
+ "\n",
+ "params[orso.OrsoCreator] = orso.OrsoCreator(fileio.base.Person(\n",
+ " name='Max Mustermann',\n",
+ " affiliation='European Spallation Source ERIC',\n",
+ " contact='max.mustermann@ess.eu',\n",
+ "))\n",
+ "\n",
+ "metadata_pipeline = sciline.Pipeline(\n",
+ " providers_with_metadata,\n",
+ " params=params\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Then, we recompute $I(Q)$ and and combine it with the ORSO metadata:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "iofq_dataset = metadata_pipeline.compute(orso.OrsoIofQDataset)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Unfortunately, some metadata could not be determined autoamtically.\n",
+ "In particular, we need to specify the sample manually:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "iofq_dataset.info.data_source.sample"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "iofq_dataset.info.data_source.sample = fileio.data_source.Sample(\n",
+ " name='Ni / Ti Multilayer',\n",
+ " model=fileio.data_source.SampleModel(\n",
+ " stack='air | (Ni | Ti) * 5 | Si',\n",
+ " ),\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "And we also add the URL of this notebook to make it easier to reproduce the data:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "iofq_dataset.info.reduction.script = 'https://scipp.github.io/essreflectometry/examples/amor.html'"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Finally, we can save the data to a file.\n",
+ "Note that `iofq_dataset` is an [orsopy.fileio.orso.OrsoDataset](https://orsopy.readthedocs.io/en/latest/orsopy.fileio.orso.html#orsopy.fileio.orso.OrsoDataset)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "iofq_dataset.save('amor_reduced_iofq.ort')"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Look at the first 50 lines of the file to inspect the metadata:"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "!head amor_reduced_iofq.ort -n50"
+ ]
  }
  ],
  "metadata": {
@@ -136,7 +280,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.10.12"
+ "version": "3.10.13"
  }
  },
  "nbformat": 4,

pyproject.toml

@@ -31,6 +31,7 @@ requires-python = ">=3.10"
 # Make sure to list one dependency per line.
 dependencies = [
  "dask",
+ "python-dateutil",
  "graphviz",
  "plopp",
  "pythreejs",

requirements/base.in

@@ -6,6 +6,7 @@ ipython==8.9.0
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
+python-dateutil
 graphviz
 plopp
 pythreejs

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:301651c34ea6fe2705e74c10ff13dedb897c14ff
+# SHA1:df5a1bd38eaeab3b3099d7d737171e2192615a39
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -9,7 +9,7 @@ asttokens==2.4.1
  # via stack-data
 backcall==0.2.0
  # via ipython
-certifi==2023.11.17
+certifi==2024.2.2
  # via requests
 charset-normalizer==3.3.2
  # via requests
@@ -23,13 +23,13 @@ contourpy==1.2.0
  # via matplotlib
 cycler==0.12.1
  # via matplotlib
-dask==2023.12.1
+dask==2024.1.1
  # via -r base.in
 decorator==5.1.1
  # via ipython
 executing==2.0.1
  # via stack-data
-fonttools==4.47.0
+fonttools==4.47.2
  # via matplotlib
 fsspec==2023.12.2
  # via dask
@@ -92,9 +92,9 @@ pickleshare==0.7.5
  # via ipython
 pillow==10.2.0
  # via matplotlib
-platformdirs==4.1.0
+platformdirs==4.2.0
  # via pooch
-plopp==23.11.0
+plopp==24.1.1
  # via -r base.in
 pooch==1.8.0
  # via scippneutron
@@ -112,6 +112,7 @@ pyparsing==3.1.1
  # via matplotlib
 python-dateutil==2.8.2
  # via
+ # -r base.in
  # matplotlib
  # scippnexus
 pythreejs==2.4.2
@@ -122,18 +123,18 @@ pyyaml==6.0.1
  # orsopy
 requests==2.31.0
  # via pooch
-sciline==24.1.0
+sciline==24.1.1
  # via -r base.in
 scipp==23.12.0
  # via
  # -r base.in
  # scippneutron
  # scippnexus
-scippneutron==23.11.0
+scippneutron==24.1.0
  # via -r base.in
-scippnexus==23.12.0
+scippnexus==23.12.1
  # via scippneutron
-scipy==1.11.4
+scipy==1.12.0
  # via
  # scippneutron
  # scippnexus
@@ -143,7 +144,7 @@ six==1.16.0
  # python-dateutil
 stack-data==0.6.3
  # via ipython
-toolz==0.12.0
+toolz==0.12.1
  # via
  # dask
  # partd
@@ -157,9 +158,9 @@ traitlets==5.14.1
  # traittypes
 traittypes==0.2.1
  # via ipydatawidgets
-urllib3==2.1.0
+urllib3==2.2.0
  # via requests
-wcwidth==0.2.12
+wcwidth==0.2.13
  # via prompt-toolkit
 widgetsnbextension==4.0.9
  # via ipywidgets

requirements/basetest.txt

@@ -11,9 +11,9 @@ iniconfig==2.0.0
  # via pytest
 packaging==23.2
  # via pytest
-pluggy==1.3.0
+pluggy==1.4.0
  # via pytest
-pytest==7.4.4
+pytest==8.0.0
  # via -r basetest.in
 tomli==2.0.1
  # via pytest

requirements/ci.txt

@@ -7,7 +7,7 @@
 #
 cachetools==5.3.2
  # via tox
-certifi==2023.11.17
+certifi==2024.2.2
  # via requests
 chardet==5.2.0
  # via tox
@@ -23,7 +23,7 @@ filelock==3.13.1
  # virtualenv
 gitdb==4.0.11
  # via gitpython
-gitpython==3.1.40
+gitpython==3.1.41
  # via -r ci.in
 idna==3.6
  # via requests
@@ -32,11 +32,11 @@ packaging==23.2
  # -r ci.in
  # pyproject-api
  # tox
-platformdirs==4.1.0
+platformdirs==4.2.0
  # via
  # tox
  # virtualenv
-pluggy==1.3.0
+pluggy==1.4.0
  # via tox
 pyproject-api==1.6.1
  # via tox
@@ -48,9 +48,9 @@ tomli==2.0.1
  # via
  # pyproject-api
  # tox
-tox==4.11.4
+tox==4.12.1
  # via -r ci.in
-urllib3==2.1.0
+urllib3==2.2.0
  # via requests
 virtualenv==20.25.0
  # via tox