Add esrf bm16 data

.github/workflows/ci.yml

@@ -37,8 +37,25 @@ jobs:
       - name: Run unit tests
         run: pytest -v .
 
+  build_docs:
+    needs: build
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
       - name: Install doc dependencies
-        run: pip install .[doc]
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          pip install .[doc]
 
       - name: Build documentation
-        run: sphinx-build ./doc ./build
+        run: sphinx-build ./doc ./build

.gitignore

@@ -9,10 +9,13 @@
 __pycache__/
 *.so
 
+# Temporary files
+/conversion_examples/*/*new*
+
 # Distribution / packaging
 /build/
 /dist/
 *.egg-info/
 .eggs/
 /doc/_generated
-/doc/_static/example_nxxas_data.h5
+/doc/_static/*.h5

CONTRIBUTING.md

@@ -1 +1,44 @@
-<a href="https://gitlab.esrf.fr/workflow/ewoksadmin/ewoksci/-/blob/main/CONTRIBUTING.md" target="_blank">CONTRIBUTING.md</a>
+## Getting started
+
+Requirements are listed in `setup.cfg` and can be installed with
+
+```bash
+pip install [--user] .[dev]
+```
+
+## Make a contribution
+
+Before making a merge request make sure the following is done on your branch
+
+1. Update HDF5 repository examples
+2. Linting
+3. Testing
+
+### Update HDF5 repository examples
+
+To be sure all HDF5 files are compliant with the latest standard
+
+```bash
+pip install -e .[dev]
+./converted/generate.sh
+```
+
+### Linting
+
+The configuration for [black](https://black.readthedocs.io/en/stable/) and [flake8](https://flake8.pycqa.org/en/latest/index.html) can be modified in `setup.cfg`.
+
+Comment lines with `# noqa: E123` to ignore certain linting errors.
+
+### Testing
+
+Tests make use [pytest](https://docs.pytest.org/en/stable/index.html) and can be run as follows
+
+```bash
+pytest .
+```
+
+Testing an installed project is done like this
+
+```bash
+pytest --pyargs <project_name>
+```

README.md

@@ -1,7 +1,7 @@
 # pynxxas
 Library for reading and writing XAS data in NeXus format.
 
-An example HDF5 file can be found [here](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fpynxxas.readthedocs.io%2Fen%2Flatest%2F_static%2Fexample_nxxas_data.h5)
+An example HDF5 file can be found [here](https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fpynxxas.readthedocs.io%2Fen%2Flatest%2F_static%2Fgeneric.h5)
 
 <p align="center">
     <a href="https://pynxxas.readthedocs.io" alt="Documentation">
@@ -12,6 +12,6 @@ An example HDF5 file can be found [here](https://myhdf5.hdfgroup.org/view?url=ht
         <img src="https://img.shields.io/badge/license-MIT-blue" /></a>
     <a href="https://github.com/psf/black" alt="Code Style">
         <img src="https://img.shields.io/badge/code%20style-black-000000.svg" /></a>
-    <a href="https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fpynxxas.readthedocs.io%2Fen%2Flatest%2F_static%2Fexample_nxxas_data.h5" alt="NeXus">
+    <a href="https://myhdf5.hdfgroup.org/view?url=https%3A%2F%2Fpynxxas.readthedocs.io%2Fen%2Flatest%2F_static%2Fgeneric.h5" alt="NeXus">
         <img src="https://raw.githubusercontent.com/nexusformat/wiki/master/public/favicon.ico" /></a>
 </p>

conversion_examples/BlissMultiModal/make_xas.py

@@ -0,0 +1,114 @@
+from pathlib import Path
+
+import h5py
+import numpy
+
+THIS_DIRECTORY = Path(__file__).parent
+
+
+def bliss2nexus(nxentry_in, expressions, metadata, nxroot_out, entry_name):
+    root = create_nxclass(nxroot_out, entry_name, "NXentry")
+    nxroot_out.attrs["default"] = entry_name
+
+    inst = create_nxclass(root, "instrument", "NXinstrument")
+
+    source = create_nxclass(inst, "source", "NXsource")
+    source["type"] = "Synchrotron X-ray Source"
+    source["probe"] = "x-ray"
+
+    monochromator = create_nxclass(inst, "monochromator", "NXmonochromator")
+    nxinstrument_input = nxentry_in["instrument"]
+    dset = nxinstrument_input[metadata["energy"]]["data"]
+    monochromator["energy"] = dset[()]
+    energy_units = dset.attrs.get("units", "keV")
+    monochromator.attrs["units"] = energy_units
+
+    for name, expression in expressions.items():
+        subroot = create_nxclass(root, name, "NXsubentry", default="plot")
+        root.attrs["default"] = name
+        subroot["definition"] = "NXxas"
+
+        mode = expression["mode"]
+        subroot["mode"] = mode
+
+        subroot["energy"] = h5py.SoftLink(monochromator["energy"].name)
+
+        if mode == "transmission":
+            I0 = nxinstrument_input[expression["I0"]]["data"][()]
+            It = nxinstrument_input[expression["It"]]["data"][()]
+            subroot["intensity"] = numpy.log(I0 / It)
+        elif mode == "fluorescence":
+            I0 = nxinstrument_input[expression["I0"]]["data"][()]
+            mca = nxinstrument_input[expression["mca"]]
+            Ifluo = mca[expression["Ifluo"]][()]
+            Lt = mca[expression["Lt"]][()]
+            subroot["intensity"] = numpy.log(Ifluo / (I0 * Lt))
+        else:
+            raise NotImplementedError(mode)
+
+        element = create_nxclass(subroot, "element", "NXelement")
+        element["symbol"] = metadata["element"]
+
+        edge = create_nxclass(subroot, "edge", "NXedge")
+        edge["name"] = metadata["edge"]
+
+        plot = create_nxclass(
+            subroot, "plot", "NXdata", signal="intensity", axes="energy"
+        )
+        plot["title"] = expression.get("title", name)
+        plot["energy"] = h5py.SoftLink(subroot["energy"].name)
+        plot["intensity"] = h5py.SoftLink(subroot["intensity"].name)
+        plot["energy"].attrs["long_name"] = f"Energy ({energy_units})"
+        plot["intensity"].attrs["long_name"] = "Normalized mu(E)"
+
+
+def create_nxclass(root, name, nx_class, **attrs):
+    """Create NeXus class instance with attributes."""
+    child = root.create_group(name, track_order=True)
+    child.attrs["NX_class"] = nx_class
+    for name, value in attrs.items():
+        child.attrs[name] = value
+    return child
+
+
+def main(output_filename):
+    with h5py.File(output_filename, "w", track_order=True) as nxroot_out:
+
+        input_filename = THIS_DIRECTORY / "test_Assolution_Mauro_0001.h5"
+
+        expressions = {
+            "itrans": {
+                "mode": "transmission",
+                "I0": "p201_1_bkg_sub",
+                "It": "p201_3_bkg_sub",
+                "title": "Transmission",
+            },
+            "iref": {
+                "mode": "transmission",
+                "I0": "p201_3_bkg_sub",
+                "It": "p201_5_bkg_sub",
+                "title": "Standard",
+            },
+        }
+        for mca_nr in range(16):
+            expressions[f"fluo{mca_nr}"] = {
+                "mode": "fluorescence",
+                "I0": "p201_1_bkg_sub",
+                "mca": f"xmapd16_det{mca_nr}",
+                "Ifluo": "roi1",
+                "Lt": "live_time",  # effective measurement time
+                "title": f"Fluorescence #{mca_nr}",
+            }
+        metadata = {"element": "As", "edge": "K", "energy": "energy_enc"}
+
+        with h5py.File(input_filename, "r") as nxroot_in:
+            for entry_name in nxroot_in:
+                if entry_name.endswith(".1"):
+                    nxentry_in = nxroot_in[entry_name]
+                    bliss2nexus(
+                        nxentry_in, expressions, metadata, nxroot_out, entry_name
+                    )
+
+
+if __name__ == "__main__":
+    main(THIS_DIRECTORY / ".." / ".." / "nxxas_examples" / f"{THIS_DIRECTORY.name}.h5")