Remove mappings

pynxtools_mpes/reader.py

@@ -27,8 +27,6 @@
 from pynxtools.dataconverter.readers.multi.reader import MultiFormatReader
 from pynxtools.dataconverter.readers.utils import parse_yml
 
-from pynxtools_mpes.mappings import CONVERT_DICT, DEFAULT_UNITS, REPLACE_NESTED
-
 logger = logging.getLogger("pynxtools")
 
 
@@ -121,15 +119,15 @@ def h5_to_xarray(faddr: str, mode: str = "r") -> xr.DataArray:
                     f"ax{axis}"
                 ].attrs["unit"]
             except (KeyError, TypeError):
-                xarray[bin_names[axis]].attrs["unit"] = DEFAULT_UNITS[bin_names[axis]]
+                xarray[bin_names[axis]].attrs["unit"] = ""
         try:
             xarray.attrs["units"] = h5_file["binned"]["BinnedData"].attrs["units"]
             xarray.attrs["long_name"] = h5_file["binned"]["BinnedData"].attrs[
                 "long_name"
             ]
         except (KeyError, TypeError):
-            xarray.attrs["units"] = "counts"
-            xarray.attrs["long_name"] = "photoelectron counts"
+            xarray.attrs["units"] = ""
+            xarray.attrs["long_name"] = ""
 
         if metadata is not None:
             xarray.attrs["metadata"] = metadata
@@ -146,8 +144,7 @@ def iterate_dictionary(dic, key_string):
         if not len(keys) == 1:
             return iterate_dictionary(dic[keys[0]], keys[1])
     else:
-        raise KeyError
-    return None
+        return None
 
 
 def rgetattr(obj, attr):
@@ -196,8 +193,6 @@ def set_config_file(self, file_path: str) -> Dict[str, Any]:
     def handle_eln_file(self, file_path: str) -> Dict[str, Any]:
         self.eln_data = parse_yml(
             file_path,
-            convert_dict=CONVERT_DICT,
-            replace_nested=REPLACE_NESTED,
             parent_key="/ENTRY",
         )
 
@@ -208,9 +203,7 @@ def get_eln_data(self, key: str, path: str) -> Any:
         if self.eln_data is None:
             return None
 
-        return self.eln_data.get(
-            key.replace(f"/ENTRY[{self.callbacks.entry_name}]", "/ENTRY")
-        )
+        return self.eln_data.get(path)
 
     def handle_objects(self, objects: Tuple[Any]) -> Dict[str, Any]:
         if isinstance(objects, xr.DataArray):
@@ -253,10 +246,7 @@ def get_data_dims(self, key: str, path: str) -> List[str]:
         return list(map(str, self.data_xarray.dims))
 
     def get_attr(self, key: str, path: str) -> Any:
-        try:
-            return iterate_dictionary(self.data_xarray.attrs, path)
-        except KeyError:
-            logger.info(f"Path {path} not found. Skipping the entry.")
+        return iterate_dictionary(self.data_xarray.attrs, path)
 
 
 READER = MPESReader

scripts/regenerate_examples.sh

@@ -7,7 +7,13 @@ function update_mpes_example {
   dataconverter xarray_saved_small_calibration.h5 config_file.json --reader $READER --nxdl $NXDL --output example.nxs
 }
 
+function update_mpes_eln_example {
+  echo "Update mpes example with eln file"
+  dataconverter xarray_saved_small_calibration.h5 config_file.json eln_data.yaml --reader $READER --nxdl $NXDL --output example_eln.nxs
+}
+
 project_dir=$(dirname $(dirname $(realpath $0)))
 cd $project_dir/tests/data
 
-update_mpes_example
+update_mpes_example
+update_mpes_eln_example

tests/data/config_file.json

@@ -2,7 +2,7 @@
   "/@default": "entry",
   "/ENTRY/@default": "data",
   "/ENTRY/definition": "NXmpes",
-  "/ENTRY/title": "@attrs:metadata/entry_title",
+  "/ENTRY/title": "['@eln:/ENTRY/title', '@attrs:metadata/entry_title']",
   "/ENTRY/start_time": "@attrs:metadata/timing/acquisition_start",
   "/ENTRY/experiment_institution": "Fritz Haber Institute - Max Planck Society",
   "/ENTRY/experiment_facility": "Time Resolved ARPES",
@@ -24,8 +24,8 @@
     "name": "Time-of-flight momentum microscope equipped delay line detector, at the endstation of the high rep-rate HHG source at FHI",
     "name/@short_name": "TR-ARPES @ FHI",
     "energy_resolution": {
-      "resolution": 140.0,
-      "resolution/@units": "meV",
+      "resolution": "['@eln:/ENTRY/Instrument/energy_resolution', '140.0']",
+      "resolution/@units": "['@eln:/ENTRY/Instrument/energy_resolution/@units', 'meV']",
       "physical_quantity": "energy",
       "type": "estimated"
     },

tests/data/eln_data.yaml

@@ -1,109 +1,8 @@
-title: Valence Band Dynamics - 1030 nm linear p-polarized pump, 0.6 mJ/cm2 absorbed fluence
+title: Title from ELN file
 Instrument:
   energy_resolution:
-    unit: meV
-    value: 140.0
-  momentum_resolution:
-    unit: 1/angstrom
-    value: 0.08
-  temporal_resolution:
-    unit: fs
-    value: 35.0
-  Analyzer:
-    energy_resolution:
-      unit: eV
-      value: 110.0
-    momentum_resolution:
-      unit: 1/angstrom
-      value: 0.08
-    slow_axes: delay
-    spatial_resolution:
-      unit: µm
-      value: 10.0
-  Manipulator:
-    sample_temperature:
-      unit: K
-      value: 300.0
-  Source:
-    Probe:
-      frequency:
-        unit: KHz
-        value: 500.0
-      photon_energy:
-        unit: eV
-        value: 21.7
-    Pump:
-      frequency:
-        unit: KHz
-        value: 500.0
-      photon_energy:
-        unit: eV
-        value: 1.55
-  Beam:
-    Probe:
-      extent:
-        unit: µm
-        value:
-        - 80.0
-        - 80.0
-      incident_energy:
-        unit: eV
-        value: 21.7
-      incident_energy_spread:
-        unit: eV
-        value: 0.11
-      incident_polarization:
-        - 1
-        - 1
-        - 0
-        - 0
-      pulse_duration:
-        unit: fs
-        value: 20.0
-    Pump:
-      extent:
-        unit: µm
-        value:
-        - 230.0
-        - 265.0
-      incident_energy:
-        unit: eV
-        value: 1.55
-      incident_energy_spread:
-        unit: eV
-        value: 0.08
-      incident_polarization:
-        - 1
-        - -1
-        - 0
-        - 0
-      incident_wavelength:
-        unit: nm
-        value: 800.0
-      average_power:
-        unit: mW
-        value: 300.0
-      pulse_energy:
-        unit: µJ
-        value: 0.6
-      fluence:
-        unit: mJ / cm ** 2
-        value: 0.15
-      pulse_duration:
-        unit: fs
-        value: 35.0
+    unit: eV
+    value: 0.14
 Sample:
-  chemical_formula: WSe2
-  description: Sample
-  name: WSe2 Single Crystal
-  preparation_date: "2019-01-13T09:00:00+00:00"
-  pressure:
-    unit: bar
-    value: 5.0e-14
-  sample_history: Cleaved
-User:
-  address: Faradayweg 4-6, 14915 Berlin
-  affiliation: Fritz Haber Institute of the Max Planck Society
-  email: [email protected]
-  name: Julian Maklar
-  role: Principal Investigator
+  name: My ELN sample name
+  preparation_date: "2019-01-13T09:00:00+00:00"

tests/test_reader.py

@@ -2,10 +2,8 @@
 Basic example based test for the stm reader
 """
 
-import os
 from pathlib import Path
 
-import pynxtools.dataconverter.convert as dataconverter
 from pynxtools.testing.nexus_conversion import ReaderTest
 
 
@@ -30,18 +28,23 @@ def test_nexus_conversion(caplog, tmp_path):
     test.check_reproducibility_of_nexus()
 
 
-def test_eln_data(tmp_path):
-    """Check if the subsections in the eln_data.yml file work."""
+def test_conversion_w_eln_data(caplog, tmp_path):
+    """
+    Tests the conversion with additional ELN data
+    """
+    caplog.clear()
     dir_path = Path(__file__).parent / "data"
-    dataconverter.convert(
-        input_file=(
+    test = ReaderTest(
+        nxdl="NXmpes",
+        reader_name="mpes",
+        files_or_dir=[
             str(dir_path / "xarray_saved_small_calibration.h5"),
             str(dir_path / "config_file.json"),
             str(dir_path / "eln_data.yaml"),
-        ),
-        reader="mpes",
-        nxdl="NXmpes",
-        output=os.path.join(tmp_path, "mpes.small_test.nxs"),
-        skip_verify=False,
-        ignore_undocumented=False,
+            str(dir_path / "example_eln.nxs"),
+        ],
+        tmp_path=tmp_path,
+        caplog=caplog,
     )
+    test.convert_to_nexus(caplog_level="WARNING", ignore_undocumented=False)
+    test.check_reproducibility_of_nexus()