Apm sprint20 fixes spotted when connecting to Nomad (#10)

* Adding fixes discussed on nomad-FAIR 05b34e6916b3429630289bf8f1fecd46f859037c * ORCID is persistent * jupyter deps --------- Co-authored-by: mkuehbach <[email protected]>
FAIRmat-NFDI · May 10, 2024 · 3387238 · 3387238
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diff --git a/README.md b/README.md
@@ -32,9 +32,8 @@ A detailed summary is available in the [reference section of the documentation](
 
 # Getting started
 [A getting started tutorial](https://github.com/FAIRmat-NFDI/pynxtools-apm/tree/main/examples) is offered that guides you
-how to use the apm reader for converting your data to NeXus from a Jupyter notebook. Note that not every combination of
-supported file formats and input for the parser allows to fill required and recommended fields and attributes of the NXapm
-application definition. Therefore, you may need to provide an ELN file that contains the missing values in order for the
+how to use the apm reader for converting your data to NeXus using a Jupyter notebook. That notebook details also the commands how to convert data via command line calls. Note that not every combination of input from a supported file format and other, typically electronic lab notebook, input for the parser allows filling the required and recommended fields and attributes of the NXapm application definition.
+Therefore, you may need to provide an ELN file that contains the missing values in order for the
 validation step of the APM reader to pass.
 
 # Contributing
@@ -49,7 +48,7 @@ git clone https://github.com/FAIRmat-NFDI/pynxtools-apm.git --branch main --recu
 cd pynxtools_apm
 python -m pip install --upgrade pip
 python -m pip install -e .
-python -m pip install -e ".[dev]"
+python -m pip install -e ".[dev,docs]"
 ```
 
 <!---There is also a [pre-commit hook](https://pre-commit.com/#intro) available
@@ -71,4 +70,4 @@ python -m pytest -sv tests
 ```
 
 ## Contact person in FAIRmat for this reader
-Markus Kühbach
+[Markus Kühbach](https://www.fairmat-nfdi.eu/fairmat/about-fairmat/team-fairmat)
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -147,7 +147,9 @@ jsonschema[format-nongpl]==4.21.1
 jsonschema-specifications==2023.12.1
     # via jsonschema
 jupyter==1.0.0
-    # via ifes-apt-tc-data-modeling
+    # via
+    #   ifes-apt-tc-data-modeling
+    #   pynxtools-apm (pyproject.toml)
 jupyter-client==8.6.1
     # via
     #   ipykernel
@@ -186,8 +188,11 @@ jupyterlab==4.1.7
     # via
     #   ifes-apt-tc-data-modeling
     #   notebook
+    #   pynxtools-apm (pyproject.toml)
 jupyterlab-h5web==12.1.0
-    # via ifes-apt-tc-data-modeling
+    # via
+    #   ifes-apt-tc-data-modeling
+    #   pynxtools-apm (pyproject.toml)
 jupyterlab-pygments==0.3.0
     # via nbconvert
 jupyterlab-server==2.27.1

diff --git a/examples/HowToUseTutorial.ipynb b/examples/HowToUseTutorial.ipynb
@@ -127,7 +127,7 @@
     "* **apm.oasis.specific.yaml** frequently used metadata that are often the same for many datasets to avoid having to<br>\n",
     "  type it every time in ELN templates. This file can be considered a configuration file whereby e.g. coordinate system<br>\n",
     "  conventions can be injected or details about the atom probe instrument communicated if that is part of frequently used<br>\n",
-    "  lab equipment. The benefit of such an approach is that eventual all relevant metadata to an instrument can be read from\n",
+    "  lab equipment. The benefit of such an approach is that eventual all relevant metadata to an instrument can be read from<br>\n",
     "  this configuration file via guiding the user e.g. through the ELN with an option to select the instrument.<br>\n",
     "* **reconstructed ion positions** in community, technology partner format with<br>\n",
     "  the ion positions and mass-to-charge state ratio values for the tomographic reconstruction.<br>\n",
@@ -238,7 +238,7 @@
    "metadata": {},
    "source": [
     "### Contact person for pynxtools-apm and related examples in FAIRmat:\n",
-    "Dr.-Ing. Markus Kühbach, 2024/04/18<br>\n",
+    "Dr.-Ing. Markus Kühbach, 2024/05/10<br>\n",
     "\n",
     "### Funding\n",
     "<a href=\"https://www.fairmat-nfdi.eu/fairmat\">FAIRmat</a> is a consortium on research data management which is part of the German NFDI.<br>\n",

diff --git a/pynxtools_apm/config/eln_cfg.py b/pynxtools_apm/config/eln_cfg.py
@@ -86,7 +86,7 @@
 
 APM_INSTRUMENT_STATIC_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/measurement/instrument",
-    "prefix_src": "atom_probe/",
+    "prefix_src": "instrument/",
     "map": [("analysis_chamber/flight_path", "nominal_flight_path/value")],
     "map_to_str": [
         "status",
@@ -105,7 +105,7 @@
 
 APM_INSTRUMENT_DYNAMIC_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/measurement/event_data_apm_set/EVENT_DATA_APM[event_data_apm]/instrument",
-    "prefix_src": "atom_probe/",
+    "prefix_src": "instrument/",
     "use": [("control/target_detection_rate/@units", "ions/pulse")],
     "map": [
         ("control/target_detection_rate", "target_detection_rate"),
@@ -180,7 +180,7 @@
 APM_IDENTIFIER_TO_NEXUS = {
     "prefix_trg": "/ENTRY[entry*]/USER[user*]",
     "use": [
-        ("IDENTIFIER[identifier]/is_persistent", False),
+        ("IDENTIFIER[identifier]/is_persistent", True),
         ("IDENTIFIER[identifier]/service", "orcid"),
     ],
     "map_to_str": [

diff --git a/pynxtools_apm/utils/create_nx_default_plots.py b/pynxtools_apm/utils/create_nx_default_plots.py
@@ -105,7 +105,7 @@ def create_default_plot_reconstruction(template: dict, entry_id: int) -> dict:
     axes = []
     for dim in dims:
         axes.append(f"axis_{dim}")
-        template[f"{trg}@AXISNAME_indices[axis_{dim}]"] = np.uint32(col)
+        template[f"{trg}@AXISNAME_indices[axis_{dim}_indices]"] = np.uint32(col)
         col += 1
     template[f"{trg}@axes"] = axes
 
@@ -169,7 +169,7 @@ def create_default_plot_mass_spectrum(template: dict, entry_id: int) -> dict:
     )
     template[f"{trg}@signal"] = "intensity"
     template[f"{trg}@axes"] = "axis_mass_to_charge"
-    template[f"{trg}@AXISNAME_indices[axis_mass_to_charge]"] = np.uint32(0)
+    template[f"{trg}@AXISNAME_indices[axis_mass_to_charge_indices]"] = np.uint32(0)
     template[f"{trg}DATA[intensity]"] = {
         "compress": np.asarray(hist1d[0], np.uint32),
         "strength": 1,

diff --git a/pynxtools_apm/utils/oasis_eln_reader.py b/pynxtools_apm/utils/oasis_eln_reader.py
@@ -148,11 +148,11 @@ def parse_instrument_dynamic(self, template: dict) -> dict:
     def parse_pulser_source(self, template: dict) -> dict:
         """Copy data into the (laser)/source section of the pulser."""
         # additional laser-specific details only relevant when the laser was used
-        if "atom_probe/pulser/pulse_mode" in self.yml:
-            if self.yml["atom_probe/pulser/pulse_mode"] == "voltage":
+        if "instrument/pulser/pulse_mode" in self.yml:
+            if self.yml["instrument/pulser/pulse_mode"] == "voltage":
                 return template
 
-        src = "atom_probe/pulser/laser_source"
+        src = "instrument/pulser/laser_source"
         if src in self.yml.keys():
             if isinstance(self.yml[src], list):
                 if all(isinstance(entry, dict) for entry in self.yml[src]) is True:

diff --git a/pyproject.toml b/pyproject.toml
@@ -43,6 +43,9 @@ dev = [
     "pytest",
     "types-pyyaml",
     "pip-tools",
+    "jupyter",
+    "jupyterlab",
+    "jupyterlab-h5web"
 ]
 
 [project.entry-points."pynxtools.reader"]