axon parser using v3 and tested

FAIRmat-NFDI · Aug 19, 2024 · e083309 · e083309
1 parent 4334a53
commit e083309
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Showing 5 changed files with 127 additions and 84 deletions.
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -13,8 +13,9 @@
             "args": ["convert",
                      // eln_data/oasis_specific
                      //"examples/em.conventions.yaml",
-                     "examples/eln_data.yaml",
-                     "examples/em.oasis.specific.yaml",
+                     //"examples/eln_data.yaml",
+                     //"examples/em.oasis.specific.yaml",
+                     "../axon/ReductionOfFeOxSmall.zip",
                      //"../nion-parsing/2022-02-18_Metadata_Kuehbach.zip",
                      //"/media/kaiobach/production/paper_paper_paper/scidat_nomad_em/digitalmicrograph/241.a2c338fd458e6b7023ec946a5e3ce8c85bd2befcb5d17dae7ae5f44b2dede81b.dm4",
                      //"/media/kaiobach/production/paper_paper_paper/scidat_nomad_em/digitalmicrograph/218.ebdf722abcf63000e2fa71fc6a72cd4b4747991c702a2dc65e400196f990cbad.dm3",
@@ -28,8 +29,9 @@
                      "em",
                      "--nxdl",
                      "NXem",
-                     //"--output=dbg/conv.nxs"
-                     "--output=dbg/eln.nxs"],
+                     //"--output=dbg/conv.nxs",
+                     //"--output=dbg/eln.nxs",
+                     "--output=dbg/axon.nxs"],
         }
     ]
 }
diff --git a/src/pynxtools_em/configurations/image_png_protochips_cfg.py b/src/pynxtools_em/configurations/image_png_protochips_cfg.py
@@ -18,7 +18,8 @@
 """Configuration of the image_png_protochips parser."""
 
 import re
-from typing import Dict
+
+from pynxtools_em.utils.pint_custom_unit_registry import ureg
 
 
 def specific_to_variadic(token):
@@ -46,7 +47,8 @@ def specific_to_variadic(token):
 
 
 AXON_DETECTOR_STATIC_TO_NX_EM = {
-    "prefix": "/ENTRY[entry*]/measurement/em_lab/DETECTOR[detector*]",
+    "prefix_trg": "/ENTRY[entry*]/measurement/em_lab/detectorID[detector*]",
+    "prefix_src": "",
     "use": [
         (
             "local_name",
@@ -59,34 +61,33 @@ def specific_to_variadic(token):
 AXON_STAGE_DYNAMIC_TO_NX_EM = {
     "prefix_trg": "/ENTRY[entry*]/measurement/event_data_em_set/EVENT_DATA_EM[event_data_em*]/em_lab/STAGE_LAB[stage_lab]",
     "prefix_src": "MicroscopeControlImageMetadata.ActivePositionerSettings.PositionerSettings.[*].Stage.",
-    "map_to_real_and_join": [("position", ["X", "Y", "Z"])],
-}  # "use": [("position/@units", "m")], values are much to large to be m
+    "map_to_f8": [
+        ("position", ureg.meter, ["X", "Y", "Z"], ureg.meter)
+    ],  # values are much to large to be in m!
+}
 
 
 AXON_CHIP_DYNAMIC_TO_NX_EM = {
     "prefix_trg": "/ENTRY[entry*]/measurement/event_data_em_set/EVENT_DATA_EM[event_data_em*]/em_lab/heater",
     "prefix_src": "MicroscopeControlImageMetadata.AuxiliaryData.AuxiliaryDataCategory.[*].DataValues.AuxiliaryDataValue.[*].",
-    "use": [("current/@units", "A"), ("power/@units", "W"), ("voltage/@units", "V")],
-    "map_to_real": [
-        ("current", "HeatingCurrent"),
-        ("power", "HeatingPower"),
-        ("voltage", "HeatingVoltage"),
+    "map_to_f8": [
+        ("current", ureg.ampere, "HeatingCurrent", ureg.ampere),
+        ("power", ureg.watt, "HeatingPower", ureg.watt),
+        ("voltage", ureg.volt, "HeatingVoltage", ureg.volt),
     ],
 }
 
 
 AXON_AUX_DYNAMIC_TO_NX_EM = {
-    "prefix_trg": "/ENTRY[entry*]/measurement/event_data_em_set/EVENT_DATA_EM[event_data_em*]/em_lab/STAGE_LAB[stage_lab]",
+    "prefix_trg": "/ENTRY[entry*]/measurement/event_data_em_set/EVENT_DATA_EM[event_data_em*]/em_lab/ebeam_column",
     "prefix_src": "MicroscopeControlImageMetadata.AuxiliaryData.AuxiliaryDataCategory.[*].DataValues.AuxiliaryDataValue.[*].",
     "use": [
-        ("SENSOR[sensor2]/value/@units", "torr"),
-        ("SENSOR[sensor2]/measurement", "pressure"),
-        ("SENSOR[sensor1]/value/@units", "°C"),
-        ("SENSOR[sensor1]/measurement", "temperature"),
+        ("sensorID[sensor1]/measurement", "temperature"),
+        ("sensorID[sensor2]/measurement", "pressure"),
     ],
-    "map_to_real": [
-        ("SENSOR[sensor2]/value", "HolderPressure"),
-        ("SENSOR[sensor1]/value", "HolderTemperature"),
+    "map_to_f8": [
+        ("sensorID[sensor1]/value", ureg.degC, "HolderTemperature", ureg.degC),
+        ("sensorID[sensor2]/value", ureg.bar, "HolderPressure", ureg.torr),
     ],
 }
 
@@ -95,7 +96,6 @@ def specific_to_variadic(token):
     "prefix_trg": "/ENTRY[entry*]/measurement/event_data_em_set/EVENT_DATA_EM[event_data_em*]",
     "prefix_src": "MicroscopeControlImageMetadata.MicroscopeSettings.",
     "use": [
-        ("em_lab/EBEAM_COLUMN[ebeam_column]/electron_source/voltage/@units", "V"),
         (
             "event_type",
             "As tested with AXON 10.4.4.21, 2021-04-26T22:51:28.4539893-05:00 not included in Protochips PNG metadata",
@@ -104,22 +104,25 @@ def specific_to_variadic(token):
             "em_lab/DETECTOR[detector*]/mode",
             "As tested with AXON 10.4.4.21, 2021-04-26T22:51:28.4539893-05:00 not included in Protochips PNG metadata",
         ),
-        ("em_lab/OPTICAL_SYSTEM_EM[optical_system_em]/camera_length", "m"),
     ],
     "map": [
         (
             "em_lab/EBEAM_COLUMN[ebeam_column]/DEFLECTOR[beam_blanker1]/state",
             "BeamBlankerState",
         ),
     ],
-    "map_to_real": [
+    "map_to_f8": [
         (
             "em_lab/EBEAM_COLUMN[ebeam_column]/electron_source/voltage",
+            ureg.volt,
             "AcceleratingVoltage",
+            ureg.volt,
         ),
         (
             "em_lab/OPTICAL_SYSTEM_EM[optical_system_em]/camera_length",
+            ureg.meter,
             "CameraLengthValue",
+            ureg.meter,
         ),
         (
             "em_lab/OPTICAL_SYSTEM_EM[optical_system_em]/magnification",