Using refactored NXapm, possibly BREAKING CHANGE, next through testin…

…g with run-throughs

src/pynxtools_apm/configurations/cameca_cfg.py

@@ -32,11 +32,11 @@
         ("measurement/instrument/fabrication/model", "fLeapModel"),
         ("measurement/instrument/fabrication/serial_number", "fSerialNumber"),
         (
-            "measurement/instrument/pulser/SOURCE[source*]/fabrication/model",
+            "measurement/instrument/pulser/sourceID[source*]/fabrication/model",
             "fLaserModelString",
         ),
         (
-            "measurement/instrument/pulser/SOURCE[source*]/fabrication/serial_number",
+            "measurement/instrument/pulser/sourceID[source*]/fabrication/serial_number",
             "fLaserSerialNumber",
         ),
         (
@@ -73,18 +73,18 @@
         ("atom_probe/reconstruction/tip_radius_zero", ureg.nanometer, "fTipRadius0"),
         ("atom_probe/reconstruction/voltage_zero", ureg.volt, "fVoltage0"),
         (
-            "measurement/instrument/analysis_chamber/pressure",
+            "measurement/events/eventID[event*]/instrument/analysis_chamber/pressure",
             ureg.torr,
             "fAnalysisPressure",
         ),
         (
-            "measurement/instrument/local_electrode/voltage",
+            "measurement/events/eventID[event*]/instrument/local_electrode/voltage",
             ureg.volt,
             "fAnodeAccelVoltage",
         ),
         ("elapsed_time", ureg.second, "fElapsedTime"),
         (
-            "measurement/instrument/pulser/pulse_frequency",
+            "measurement/events/eventID[event*]/instrument/pulser/pulse_frequency",
             ureg.kilohertz,
             "fInitialPulserFreq",
         ),
@@ -96,7 +96,7 @@
             "fMaximumFlightPathMm",
         ),
         (
-            "measurement/instrument/stage/specimen_temperature",
+            "measurement/events/eventID[event*]/instrument/stage/specimen_temperature",
             ureg.kelvin,
             "fSpecimenTemperature",
         ),

src/pynxtools_apm/configurations/eln_cfg.py

@@ -22,21 +22,21 @@
 APM_ENTRY_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]",
     "prefix_src": "entry/",
-    "map": [
-        "run_number",
+    "map_to_str": [
         "operation_mode",
         "start_time",
         "end_time",
         "experiment_description",
         ("experiment_alias", "run_number"),
     ],
+    "map_to_u4": ["run_number"],
 }
 
 
 APM_SAMPLE_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/sample",
     "prefix_src": "sample/",
-    "map": [
+    "map_to_str": [
         "alias",
         "description",
         ("type", "method"),
@@ -88,7 +88,7 @@
 APM_SPECIMEN_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/specimen",
     "prefix_src": "specimen/",
-    "map": [
+    "map_to_str": [
         "alias",
         "preparation_date",
         "description",
@@ -116,16 +116,15 @@
 APM_INSTRUMENT_STATIC_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/measurement/instrument",
     "prefix_src": "instrument/",
-    "map": [
-        "status",
-        ("name", "instrument_name"),
+    "map_to_str": [
+        # "status",
         "location",
+        ("name", "instrument_name"),
         ("fabrication/vendor", "fabrication_vendor"),
         ("fabrication/model", "fabrication_model"),
         ("fabrication/identifier/identifier", "fabrication_identifier"),
         ("reflectron/status", "reflectron_status"),
         ("local_electrode/name", "local_electrode_name"),
-        ("pulser/pulse_mode", "pulser/pulse_mode"),
     ],
     "map_to_f8": [
         (
@@ -139,11 +138,11 @@
 
 
 APM_INSTRUMENT_DYNAMIC_TO_NEXUS = {
-    "prefix_trg": "/ENTRY[entry*]/measurement/event_data_apm_set/event_data_apm/instrument",
+    "prefix_trg": "/ENTRY[entry*]/measurement/events/eventID[event*]/instrument",
     "prefix_src": "instrument/",
     "use": [("control/target_detection_rate/@units", "ions/pulse")],
-    "map": [
-        "pulser_pulse_mode",
+    "map_to_str": [
+        ("pulser/pulse_mode", "pulser/pulse_mode"),
         ("control/evaporation_control", "evaporation_control"),
     ],
     "map_to_f8": [
@@ -156,7 +155,7 @@
         ),
         ("pulser/pulse_fraction", "pulser/pulse_fraction"),
         (
-            "analysis_chamber/chamber_pressure",
+            "analysis_chamber/pressure",
             ureg.bar,
             "chamber_pressure/value",
             "chamber_pressure/unit",
@@ -174,7 +173,7 @@
 APM_RANGE_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/atom_probe/ranging",
     "prefix_src": "ranging/",
-    "map": [
+    "map_to_str": [
         ("programID[program1]/program", "program"),
         ("programID[program1]/program/@version", "program_version"),
     ],
@@ -184,7 +183,7 @@
 APM_RECON_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/atom_probe/reconstruction",
     "prefix_src": "reconstruction/",
-    "map": [
+    "map_to_str": [
         "protocol_name",
         "crystallographic_calibration",
         "parameter",

src/pynxtools_apm/configurations/oasis_cfg.py

@@ -49,7 +49,7 @@
             f"{dt.datetime.now(dt.timezone.utc).isoformat().replace('+00:00', 'Z')}",
         ),
     ],
-    "map": ["operation_mode"],
+    "map_to_str": ["operation_mode"],
 }
 
 
@@ -89,5 +89,5 @@
 APM_EXAMPLE_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/CITE[cite*]",
     "prefix_src": "",
-    "map": ["authors", "doi", "description", "url"],
+    "map_to_str": ["authors", "doi", "description", "url"],
 }

src/pynxtools_apm/utils/generate_synthetic_data.py

@@ -68,6 +68,8 @@ class ApmCreateExampleData:
     """A synthesized dataset meant to be used for development purposes only!."""
 
     def __init__(self, synthesis_id):
+        """Construct class."""
+        raise NotImplementedError()
         # assure deterministic behaviour of the PRNG
         np.random.seed(seed=synthesis_id)
 
@@ -106,6 +108,7 @@ def create_reconstructed_positions(self):
 
         # assumptions:
         # identity orientation, no periodic boundary conditions
+        raise NotImplementedError()
         print(f"Using the following version of ase {ase.__version__}")
         xyz = np.asarray(
             FaceCenteredCubic(
@@ -159,6 +162,7 @@ def place_atoms_from_periodic_table(self):
         create (hypothetical) charged molecular ions from them
         and evaluate their mass-to-charge-state ratio to be used
         as values in the example dataset."""
+        raise NotImplementedError()
 
         # uniform random model for how many different ions
         # !! warning: for real world datasets this depends on real specimen composition
@@ -268,6 +272,7 @@ def place_atoms_from_periodic_table(self):
 
     def composition_to_ranging_definitions(self, template: dict) -> dict:
         """Create ranging definitions based on composition."""
+        raise NotImplementedError()
         assert len(self.nrm_composition) > 0, "Composition is not defined!"
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/ranging/"
         template[f"{trg}programID[program1]/program"] = NX_APM_EXEC_NAME
@@ -303,6 +308,7 @@ def composition_to_ranging_definitions(self, template: dict) -> dict:
 
     def emulate_entry(self, template: dict) -> dict:
         """Copy data in entry section."""
+        raise NotImplementedError()
         # check if required fields exists and are valid
         # print("Parsing entry...")
         trg = f"/ENTRY[entry{self.entry_id}]/"
@@ -328,6 +334,7 @@ def emulate_entry(self, template: dict) -> dict:
 
     def emulate_user(self, template: dict) -> dict:
         """Copy data in user section."""
+        raise NotImplementedError()
         # check if required fields exists and are valid
         # print("Parsing user...")
         prefix = f"/ENTRY[entry{self.entry_id}]/"
@@ -367,6 +374,7 @@ def emulate_user(self, template: dict) -> dict:
 
     def emulate_specimen(self, template: dict) -> dict:
         """Copy data in specimen section."""
+        raise NotImplementedError()
         # check if required fields exists and are valid
         # print("Parsing specimen...")
         trg = f"/ENTRY[entry{self.entry_id}]/specimen/"
@@ -397,6 +405,7 @@ def emulate_specimen(self, template: dict) -> dict:
 
     def emulate_control_software(self, template: dict) -> dict:
         """Copy data in control software section."""
+        raise NotImplementedError()
         # print("Parsing control software...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/control_software/"
         template[f"{trg}programID[program1]/program"] = "IVAS"
@@ -407,6 +416,7 @@ def emulate_control_software(self, template: dict) -> dict:
 
     def emulate_instrument_header(self, template: dict) -> dict:
         """Copy data in instrument_header section."""
+        raise NotImplementedError()
         # check if required fields exists and are valid
         # print("Parsing instrument header...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/"
@@ -419,6 +429,7 @@ def emulate_instrument_header(self, template: dict) -> dict:
 
     def emulate_fabrication(self, template: dict) -> dict:
         """Copy data in fabrication section."""
+        raise NotImplementedError()
         # print("Parsing fabrication...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/FABRICATION[fabrication]/"
         template[f"{trg}vendor"] = str(
@@ -446,6 +457,7 @@ def emulate_fabrication(self, template: dict) -> dict:
 
     def emulate_analysis_chamber(self, template: dict) -> dict:
         """Copy data in analysis_chamber section."""
+        raise NotImplementedError()
         # print("Parsing analysis chamber...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/analysis_chamber/"
         template[f"{trg}pressure"] = np.float64(
@@ -456,20 +468,23 @@ def emulate_analysis_chamber(self, template: dict) -> dict:
 
     def emulate_reflectron(self, template: dict) -> dict:
         """Copy data in reflectron section."""
+        raise NotImplementedError()
         # print("Parsing reflectron...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/REFLECTRON[reflectron]/"
         template[f"{trg}applied"] = bool(np.random.choice([0, 1], 1)[0])
         return template
 
     def emulate_local_electrode(self, template: dict) -> dict:
         """Copy data in local_electrode section."""
+        raise NotImplementedError()
         # print("Parsing local electrode...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/local_electrode/"
         template[f"{trg}name"] = str(f"electrode {np.random.choice(1000, 1)[0]}")
         return template
 
     def emulate_detector(self, template: dict) -> dict:
         """Copy data in ion_detector section."""
+        raise NotImplementedError()
         # print("Parsing detector...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/ion_detector/"
         detector_model_type = str(np.random.choice(["cameca", "mcp", "custom"], 1)[0])
@@ -483,6 +498,7 @@ def emulate_detector(self, template: dict) -> dict:
 
     def emulate_stage_lab(self, template: dict) -> dict:
         """Copy data in stage lab section."""
+        raise NotImplementedError()
         # print("Parsing stage lab...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/stage_lab/"
         template[f"{trg}base_temperature"] = np.float64(10 + np.random.choice(50, 1)[0])
@@ -491,6 +507,7 @@ def emulate_stage_lab(self, template: dict) -> dict:
 
     def emulate_specimen_monitoring(self, template: dict) -> dict:
         """Copy data in specimen_monitoring section."""
+        raise NotImplementedError()
         # print("Parsing specimen monitoring...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/specimen_monitoring/"
         eta = np.min((np.random.normal(loc=0.6, scale=0.1), 1.0))
@@ -503,6 +520,7 @@ def emulate_specimen_monitoring(self, template: dict) -> dict:
 
     def emulate_pulser(self, template: dict) -> dict:
         """Copy data in pulser section."""
+        raise NotImplementedError()
         # print("Parsing pulser...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/pulser/"
         pulse_mode = str(
@@ -537,6 +555,7 @@ def emulate_pulser(self, template: dict) -> dict:
 
     def emulate_reconstruction(self, template: dict) -> dict:
         """Copy data in reconstruction section."""
+        raise NotImplementedError()
         # print("Parsing reconstruction...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/reconstruction/"
         src = f"/ENTRY[entry{self.entry_id}]/atom_probe/control_software/"
@@ -555,6 +574,7 @@ def emulate_reconstruction(self, template: dict) -> dict:
 
     def emulate_ranging(self, template: dict) -> dict:
         """Copy data in ranging section."""
+        raise NotImplementedError()
         # print("Parsing ranging...")
         trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/ranging/"
         src = f"/ENTRY[entry{self.entry_id}]/atom_probe/control_software/"
@@ -568,6 +588,7 @@ def emulate_ranging(self, template: dict) -> dict:
 
     def emulate_random_input_from_eln(self, template: dict) -> dict:
         """Emulate random input as could come from an ELN."""
+        raise NotImplementedError()
         self.emulate_entry(template)
         self.emulate_user(template)
         self.emulate_specimen(template)
@@ -594,6 +615,7 @@ def emulate_random_input_from_eln(self, template: dict) -> dict:
 
     def synthesize(self, template: dict) -> dict:
         """Hand-over instantiated dataset to dataconverter template."""
+        raise NotImplementedError()
         # heavy data, synthetic/mocked dataset
         for entry_id in np.arange(1, self.n_entries + 1):
             self.entry_id = entry_id

src/pynxtools_apm/utils/oasis_apsuite_reader.py

@@ -132,7 +132,7 @@ def assume_pulse_mode(self, template: dict) -> dict:
             else:
                 pulse_mode = "unknown"
             template[
-                f"/ENTRY[entry{self.entry_id}]/measurement/instrument/pulser/pulse_mode"
+                f"/ENTRY[entry{self.entry_id}]/measurement/events/eventID[event1]/instrument/pulser/pulse_mode"
             ] = pulse_mode
         return template
 

src/pynxtools_apm/utils/oasis_eln_reader.py

@@ -162,7 +162,8 @@ def parse_pulser_source(self, template: dict) -> dict:
                     for ldct in self.yml[src]:
                         trg_sta = (
                             f"/ENTRY[entry{self.entry_id}]/measurement/"
-                            f"instrument/pulser/sourceID[source{laser_id}]"
+                            f"events/eventID[event1]/instrument/"
+                            f"pulser/sourceID[source{laser_id}]"
                         )
                         if "name" in ldct:
                             template[f"{trg_sta}/name"] = ldct["name"]
@@ -174,7 +175,7 @@ def parse_pulser_source(self, template: dict) -> dict:
 
                         trg_dyn = (
                             f"/ENTRY[entry{self.entry_id}]/measurement/"
-                            f"event_data_apm_set/event_data_apm/instrument/"
+                            f"events/eventID[event1]/instrument/"
                             f"pulser/sourceID[source{laser_id}]"
                         )
                         quantities = ["power", "pulse_energy"]