Ellips reader and eln_data (#120)

* Reader for NXellipsometry(NXopt) * mock function for NXellipsometry(NXopt) * eln_data.yaml for NXellipsometry(NXopt) * New reader for NXellipsometry(NXopt) * Update mock.py * indentation * indentation * Update mock.py * Update mock.py * Updated metadata file to be consistent with new NXellipsometry * corrected some pycodestyle errors in the reader * corrected some pycodestyle errors * indentation * shortened lines * Added argument to FlattenSettings used in ellips reader * correcting some pylint errors * pycodestyle problems * Update reader.py * Update reader.py * Update reader.py * label function * removing err_labels * fixing header_labels args * Update reader.py * derived prms * data array functions * Update reader.py * removing unused argument header * Update reader.py * Update reader.py * removed blocks from config keys * update eln_data file * changing ang. spread unit * Corrections in the reader * Renamed black_list to ignore_keys * moved import math * Updating reader to be consistent with new eln * new eln file * Updated writer to handle attributs in ellips reader * updating definitions * Update pynxtools/dataconverter/readers/ellips/reader.py Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de> * Updates eln_data to nomad generated one * Fixes key mapping --------- Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de>
FAIRmat-NFDI · Jun 1, 2023 · 1c5d5b8 · 1c5d5b8
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diff --git a/examples/ellipsometry/eln_data.yaml b/examples/ellipsometry/eln_data.yaml
@@ -1,71 +1,72 @@
-acquisition_program/\@url: https://www.jawoollam.com/ellipsometry-software/wvase
-acquisition_program/program: WVASE
-acquisition_program/version: '3.882'
-address: Zum Großen Windkanal 2, 12489 Berlin, Germany
-affiliation: Humboldt-Universität zu Berlin
-angle_of_incidence_unit: degrees
-angular_spread:
-  unit: rad ** 2
-  value: 0.2
-atom_types: Si, O
-blocks:
-- type
-- angle_of_incidence
-calibration_status: no calibration
+Data:
+  data_identifier: 1
+  data_software: WVASE
+  data_software/@url: https://www.jawoollam.com/ellipsometry-software/wvase
+  data_software/version: '3.882'
+  data_type: Psi/Delta
+  spectrum_type: wavelength
+  spectrum_unit: Angstroms
+Instrument:
+  Beam_path:
+    Detector:
+      count_time:
+        unit: s
+        value: 1.0
+      detector_type: CCD spectrometer
+    focussing_probes:
+      angular_spread:
+        unit: rad
+        value: 0.2
+      data_correction: false
+    light_source:
+      source_type: arc lamp
+    rotating_element:
+      revolutions: 50.0
+  Sample_stage:
+    environment_conditions:
+      medium: air
+    stage_type: manual stage
+  angle_of_incidence/@unit: degrees
+  calibration_status: no calibration
+  company: J. A. Woollam Co.
+  ellipsometer_type: dual compensator
+  model: RC2
+  model/@version: 0.0.1
+  rotating_element_type: compensator (source side)
+  software: CompleteEASE
+  software/@url: https://www.jawoollam.com/ellipsometry-software/completeease
+  software/version: '6.37'
+Sample:
+  atom_types: Si, O
+  backside_roughness: false
+  chemical_formula: SiO2
+  layer_structure: 2nm SiO2 on Si
+  sample_history: Commercially purchased sample
+  sample_name: 2nm SiO2 on Si
+  sample_type: multi layer
+  substrate: Si
+User:
+  address: Zum Großen Windkanal 2, 12489 Berlin, Germany
+  affiliation: Humboldt-Universität zu Berlin
+  email: surname.name@physik.hu-berlin.de
+  name: Name Surname
 colnames:
 - type
 - wavelength
 - angle_of_incidence
-- psi
-- delta
-- err.psi
-- err.delta
-column_names:
-- psi
-- delta
-company: J. A. Woollam Co.
-count_time:
-  unit: s
-  value: 1
-data_identifier: 1
-data_type: psi/delta
+- Psi
+- Delta
+- err.Psi
+- err.Delta
 definition: NXellipsometry
-definition/\@url: https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions/NXellipsometry.nxdl.xml
-definition/\@version: 0.0.2
-detector_type: CCD spectrometer
-ellipsometry_type: dual compensator
-email: surname.name@physik.hu-berlin.de
-err-var:
-- err.psi
-- err.delta
+definition/@url: https://github.com/FAIRmat-NFDI/nexus_definitions/blob/fairmat/contributed_definitions/NXellipsometry.nxdl.xml
+definition/@version: 0.0.2
+derived_parameter_type: depolarization
 experiment_description: RC2 scan on 2nm SiO2 on Si in air
 experiment_identifier: exp-ID
+experiment_type: NIR-Vis-UV spectroscopic ellipsometry
 filename: test-data.dat
-firmware: CompleteEASE
-firmware/\@url: https://www.jawoollam.com/ellipsometry-software/completeease
-firmware/\@version: '6.37'
-focussing_probes: false
-integration_time:
-  unit: s
-  value: 0
-layer_structure: 2nm SiO2 on Si
-light_source: arc lamp
-medium: air
-model: RC2
-model/\@version: 0.0.1
-name: Name Surname
-parameters:
-- type
-- angle
-rotating_element: compensator (source side)
-sample_history: Commercially purchased sample
-sample_name: 2nm SiO2 on Si
+plot_name: Psi and Delta
 sep: \t
 skip: 3
-stage_type: manual stage
-start_time: '2022-01-27T04:35:00+00:00'
-wavelength_unit: angstrom
-x-var: wavelength
-y-var:
-- psi
-- delta
+start_time: '2022-01-27T03:35:00+00:00'
diff --git a/pynxtools/dataconverter/readers/ellips/mock.py b/pynxtools/dataconverter/readers/ellips/mock.py
@@ -38,7 +38,7 @@ class MockEllips():
         - choose_data_type:
             Chooses random entry from data_types
         - mock_signals:
-            Mock data if data_type is psi/delta or tan(psi)/cos(delta)
+            Mock data if data_type is Psi/Delta or tan(Psi)/cos(Delta)
         - mock_mueller_matrix:
             Mock data if data_type is Mueller matrix
         - mock_template:
@@ -47,10 +47,10 @@ class MockEllips():
 
     def __init__(self, data_template) -> None:
         self.data = data_template["measured_data"]
-        self.wavelength = data_template["spectrometer/wavelength"]
+        self.wavelength = data_template["data_collection/NAME_spectrum[wavelength_spectrum]"]
         self.atom_types = data_template["atom_types"]
         self.sample_list: list = []
-        self.data_types = ["psi/delta", "tan(psi)/cos(delta)", "Mueller matrix"]
+        self.data_types = ["Psi/Delta", "tan(Psi)/cos(Delta)", "Mueller matrix"]
         self.angles: list = []
         self.number_of_signals = 0
 
@@ -73,7 +73,7 @@ def choose_data_type(self, data_template) -> None:
         data_template["data_type"] = data_type
         if data_type == "Mueller matrix":
             self.number_of_signals = 16
-        elif data_type in ("psi/delta", "tan(psi)/cos(delta)"):
+        elif data_type in ("Psi/Delta", "tan(Psi)/cos(Delta)"):
             self.number_of_signals = 2
 
     def mock_chemical_formula(self) -> None:
@@ -105,45 +105,44 @@ def mock_angles(self, data_template) -> None:
             self.mock_mueller_matrix(data_template)
 
     def mock_signals(self, data_template) -> None:
-        """ Mock data if data_type is psi/delta or tan(psi)/cos(delta)
+        """ Mock data if data_type is Psi/Delta or tan(Psi)/cos(Delta)
             considering the (new) number of incident angles
         """
-        my_numpy_array = np.empty([1,
-                                   1,
-                                   len(self.angles),
-                                   self.number_of_signals,
-                                   len(self.wavelength)
-                                   ])
+        my_numpy_array = np.empty([
+            len(self.angles),
+            self.number_of_signals,
+            len(self.wavelength)
+        ])
         for index in range(0, len(self.angles)):
-            noise = np.random.normal(0, 0.5, self.data[0, 0, 0, 0, :].size)
-            my_numpy_array[0][0][index] = self.data[0][0][0] * random.uniform(0.5, 1.5) + noise
+            noise = np.random.normal(0, 0.5, self.data[0, 0, :].size)
+            my_numpy_array[index] = self.data[0] * random.uniform(0.5, 1.5) + noise
         self.data = my_numpy_array
         data_template["measured_data"] = my_numpy_array
 
     def mock_mueller_matrix(self, data_template) -> None:
         """ Mock data if data_type is Mueller matrix (i.e. 16 elements/signals)
             considering the (new) number of incident angles
         """
-        my_numpy_array = np.empty([1,
-                                   1,
-                                   len(self.angles),
-                                   self.number_of_signals,
-                                   len(self.wavelength)
-                                   ])
+        my_numpy_array = np.empty([
+            len(self.angles),
+            self.number_of_signals,
+            len(self.wavelength)
+        ])
         for idx in range(0, len(self.angles)):
-            noise = np.random.normal(0, 0.1, self .data[0, 0, 0, 0, :].size)
+            noise = np.random.normal(0, 0.1, self .data[0, 0, :].size)
             for m_idx in range(1, self.number_of_signals):
-                my_numpy_array[0][0][idx][m_idx] = self.data[0][0][0][0] * random.uniform(.5, 1.)
-                my_numpy_array[0][0][idx][m_idx] += noise
-            my_numpy_array[0][0][idx][0] = my_numpy_array[0][0][0][0] / my_numpy_array[0][0][0][0]
+                my_numpy_array[idx][m_idx] = self.data[0][0] * random.uniform(.5, 1.)
+                my_numpy_array[idx][m_idx] += noise
+            my_numpy_array[idx][0] = my_numpy_array[0][0] / my_numpy_array[0][0]
         data_template["measured_data"] = my_numpy_array
 
     def modify_spectral_range(self, data_template) -> None:
         """ Change spectral range (i.e. wavlength array) and step size,
             while length of the wavelength array remains the same.
         """
         temp = random.uniform(0.25, 23)
-        data_template["spectrometer/wavelength"] = temp * data_template["spectrometer/wavelength"]
+        data_template["data_collection/NAME_spectrum[wavelength_spectrum]"] = \
+            temp * data_template["data_collection/NAME_spectrum[wavelength_spectrum]"]
 
     def mock_template(self, data_template) -> None:
         """ Creates a mock ellipsometry template """