APM refactoring / APMv2

apm.dev.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "6da1aea0-545b-446b-a3d1-1574af72f6c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import numpy as np\n",
+    "from jupyterlab_h5web import H5Web"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "3889c47f-11c4-4bf3-97de-04fc52f0798d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "/home/kaiobach/Research/hu_hu_hu/sprint17/pynx-apm/pynxtools\n"
+     ]
+    }
+   ],
+   "source": [
+    "src = f\"{os.getcwd()}\"\n",
+    "print(src)\n",
+    "fnm = [\"debug.nor_trondheim_hatzeglou_0.nxs\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "aec5b20a-20ed-4fe3-8097-a53bcc9dded0",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/x-hdf5": "/home/kaiobach/Research/hu_hu_hu/sprint17/pynx-apm/pynxtools/debug/debug.nor_trondheim_hatzeglou_0.nxs",
+      "text/plain": [
+       "<jupyterlab_h5web.widget.H5Web object>"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "H5Web(f\"{src}/debug/{fnm[0]}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "77198c3d-7830-49a6-8e75-c8569ab84e76",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

debug/apm.oasis.specific.yaml

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+citation:
+- doi: https://doi.org/repo
+  description: DOI to the respective entry in a data repository.
+- doi: https://doi.org/paper
+  description: DOI to the respective publication.

debug/batch_queue.04.sh

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+#!/bin/bash
+
+dataconverter --reader apm --nxdl NXapm --input-file="/home/kaiobach/Research/paper_paper_paper/joss_nomad_apt/bb_analysis/analysis/harvest_examples/production/ErMnO_pole.pos" --input-file="/home/kaiobach/Research/paper_paper_paper/joss_nomad_apt/bb_analysis/analysis/harvest_examples/production/ErMnO.env" --input-file="apm.oasis.specific.yaml" --input-file="eln_data_apm.yaml" --output=debug.nor_trondheim_hatzeglou_0.nxs 1>stdout.debug.nor_trondheim_hatzeglou_0.txt 2>stderr.debug.nor_trondheim_hatzeglou_0.txt

debug/eln_data_apm.yaml

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+atom_probe:
+  fabrication_identifier: '12'
+  fabrication_model: LEAP3000
+  fabrication_vendor: Cameca
+  instrument_name: LEAP
+  local_electrode_name: L1
+  location: Denton
+  pulser:
+    laser_source:
+    - name: laser1
+      power:
+        unit: nW
+        value: 24.0
+      pulse_energy:
+        unit: pJ
+        value: 24.0
+      wavelength:
+        unit: nm
+        value: 355.0
+    - name: laser2
+      power:
+        unit: nW
+        value: 12.0
+      pulse_energy:
+        unit: pJ
+        value: 12.0
+      wavelength:
+        unit: nm
+        value: 254.0
+    pulse_fraction: 0.8
+    pulse_frequency:
+      unit: kHz
+      value: 250.0
+    pulse_mode: laser_and_voltage
+  reflectron_status: used
+  evaporation_control: detection_rate
+  target_detection_rate: 0.01
+  chamber_pressure:
+    unit: torr
+    value: 2.0e-10
+  base_temperature:
+    unit: K
+    value: 20.0
+  nominal_flight_path:
+    unit: m
+    value: 1.2
+  status: success
+entry:
+  experiment_description: '<p>Normal</p>
+
+    <p><strong>Bold</strong></p>
+
+    <p><em>Italics</em></p>'
+  start_time: '2023-06-11T11:20:00+00:00'
+  end_time: '2023-06-11T11:20:00+00:00'
+  run_number: '2121'
+  operation_mode: apt
+workflow:
+  raw_dat_file: str.str
+  hit_dat_file: hits.hits
+  recon_cfg_file: root.root
+  # recon_res_file: recon.apt
+  # range_dat_file: recon.rrng
+ranging:
+  program: IVAS
+  program_version: 3.6.8
+reconstruction:
+  program: IVAS
+  program_version: 3.6.8
+  crystallographic_calibration: n/a
+  parameter: kf = 1.8, icf = 3.3
+  protocol_name: bas
+  field_of_view:
+    unit: nm
+    value: 20.
+sample:
+  composition:
+  - Mo
+  - Al 12 +- 3
+  - B 50 ppm +- 12
+  - C 3.6
+  method: measurement
+  alias: Si
+  grain_diameter:
+    unit: µm
+    value: 200.0
+  grain_diameter_error:
+    unit: µm
+    value: 50.0
+  heat_treatment_temperature:
+    unit: K
+    value: 600.0
+  heat_treatment_temperature_error:
+    unit: K
+    value: 20.0
+  heat_treatment_quenching_rate:
+    unit: K / s
+    value: 150.0
+  heat_treatment_quenching_rate_error:
+    unit: K / s
+    value: 10.0
+  description: '<p>nothing</p>'
+specimen:
+  method: measurement
+  alias: usa_denton_smith_si
+  description: '<p>normal</p>
+
+    <p><em>bold</em></p>
+
+    <p><em>italics</em></p>'
+  is_polycrystalline: true
+  is_amorphous: false
+  preparation_date: '2023-06-11T12:51:00+00:00'
+  initial_radius:
+    unit: nm
+    value: 12.0
+  shank_angle:
+    unit: °
+    value: 5.0
+user:
+- name: MarkusK
+  orcid: '0000'
+  orcid_platform: orcid
+- name: AlexR
+- {}