Bugfixes, mainly type conversions for apm_app

FAIRmat-NFDI · Jan 28, 2025 · f72395c · f72395c
1 parent f088889
commit f72395c
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Showing 4 changed files with 16 additions and 7 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -11,14 +11,14 @@
             "cwd": "${workspaceFolder}",
             "program": "../../.py3.11.11/bin/dataconverter",
             "args": [//workflow files str.str, hits.hits, root.root should be created via touch str.str ...
-                     //"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/001.0.c4b1b412f46833ef7b72164858f3fa2daea60de212b2a62cd7121c07a92d5837.rhit.CRunHeader.dat.Parsed.cameca",
-                     "../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/019.0.8d12016f3d152ce8a02194b126bd6c896f517928dada673864e93e4dfc418738.root.CAnalysis.dat.Parsed.cameca",
+                     "../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/001.0.c4b1b412f46833ef7b72164858f3fa2daea60de212b2a62cd7121c07a92d5837.rhit.CRunHeader.dat.Parsed.cameca",
+                     //"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/019.0.8d12016f3d152ce8a02194b126bd6c896f517928dada673864e93e4dfc418738.root.CAnalysis.dat.Parsed.cameca",
                      "--reader",
                      "apm",
                      "--nxdl",
                      "NXapm",
-                     //"--output=tests/prod/out_recon.nxs"]
-                     "--output=tests/prod/out_range.nxs"]
+                     "--output=tests/prod/out_recon.nxs"]
+                     //"--output=tests/prod/out_range.nxs"]
         }
     ]
 }
diff --git a/src/pynxtools_apm/concepts/mapping_functors_pint.py b/src/pynxtools_apm/concepts/mapping_functors_pint.py
@@ -43,6 +43,7 @@
     "i8": np.int64,
     "f8": np.float64,
     "bool": bool,
+    "str": str,
 }
 
 # general conversion workflow
@@ -201,7 +202,9 @@ def set_value(template: dict, trg: str, src_val: Any, trg_dtype: str = "") -> di
             )
     else:  # do an explicit type conversion
         # e.g. in cases when tech partner writes float32 but e.g. NeXus assumes float64
-        if isinstance(src_val, (str, bool)):
+        if isinstance(src_val, str):
+            template[f"{trg}"] = f"{src_val}"
+        if isinstance(src_val, bool):
             template[f"{trg}"] = try_interpret_as_boolean(src_val)
         elif isinstance(src_val, ureg.Quantity):
             if isinstance(src_val.magnitude, (np.ndarray, np.generic)):

diff --git a/src/pynxtools_apm/configurations/cameca_cfg.py b/src/pynxtools_apm/configurations/cameca_cfg.py
@@ -95,7 +95,11 @@
             ureg.millimeter,
             "fMaximumFlightPathMm",
         ),
-        ("measurement/stage/specimen_temperature", ureg.kelvin, "fSpecimenTemperature"),
+        (
+            "measurement/instrument/stage/specimen_temperature",
+            ureg.kelvin,
+            "fSpecimenTemperature",
+        ),
         (
             "atom_probe/voltage_and_bowl/tof_zero_estimate",
             ureg.nanosecond,

diff --git a/src/pynxtools_apm/utils/oasis_apsuite_reader.py b/src/pynxtools_apm/utils/oasis_apsuite_reader.py
@@ -186,6 +186,7 @@ def parse_ranging_definitions(self, template: dict) -> dict:
                     template[f"{trg}nuclide_list"] = ion.nuclide_list.values
                     template[f"{trg}name"] = ion.name.values
 
+                    """
                     if ion.charge_state_model["n_cand"] > 0:
                         path = f"{trg}charge_state_analysis/"
                         template[f"{path}nuclides"] = np.asarray(
@@ -263,8 +264,9 @@ def parse_ranging_definitions(self, template: dict) -> dict:
                                 "strength": 1,
                             }
                             template[f"{path}shortest_half_life/@units"] = "s"
+                    """
 
-                trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/ranging/"
+                trg = f"/ENTRY[entry{self.entry_id}]/atom_probe/ranging/peak_identification/"
                 template[f"{trg}number_of_ion_types"] = np.uint32(ion_id)
                 template[f"{trg}maximum_number_of_atoms_per_molecular_ion"] = np.uint32(
                     MAX_NUMBER_OF_ATOMS_PER_ION