FAIRmat-NFDI · mkuehbach · Aug 15, 2023 · Aug 15, 2023 · Aug 15, 2023 · Aug 16, 2023
diff --git a/.gitignore b/.gitignore
@@ -204,3 +204,10 @@ cython_debug/
 build/
 nexusparser.egg-info/PKG-INFO
 .python-version
+
+# em-reader-specific custom settings
+*.h5
+*.oh5
+*.edaxh5
+*.h5oina
+*.nxs
diff --git a/debug/apex.dev.ipynb b/debug/apex.dev.ipynb
@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f39f5e57-4926-4ccd-b187-9c1aba568a95",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser\n",
+    "from jupyterlab_h5web import H5Web\n",
+    "! which python"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f1617083-f6ab-4bad-ad6d-aaa6beffec89",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# fpath = f\"/home/kaiobach/Research/paper_paper_paper/scidat_nomad_ebsd/bb_analysis/\" \\\n",
+    "#         f\"data/development_spctrscpy/pdi/APEX-single-spectrum/InGaN_nanowires_spectra.edaxh5\"\n",
+    "fpath = f\"/home/kaiobach/Research/paper_paper_paper/scidat_nomad_ebsd/bb_analysis/\" \\\n",
+    "        f\"data/development_spctrscpy/ikz/GeSn_13.nxs\"\n",
+    "H5Web(fpath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a7191dce-db83-4252-bfe3-ffc36efb5e71",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hdf = HdfFiveBaseParser(file_path=fpath)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "944c0809-4ec6-406a-be61-1dd56dcf6d00",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hdf.get_content()\n",
+    "hdf.report_content()\n",
+    "hdf.store_report(store_instances=True,\n",
+    "                 store_instances_templatized=True,\n",
+    "                 store_templates=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ac77fbda-ae54-4c1d-9441-e4d771605052",
+   "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/debug/axon.batch.sh b/debug/axon.batch.sh
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+datasource="../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/development_axon/axon/"
+
+# comments is detector mode
+examples="axon/20210426T224437.049Raw0.png"  #axon
+examples="ReductionOfFeOx.zip"  # Small.zip"
+
+for example in $examples; do
+	echo $example
+	dataconverter --reader em --nxdl NXroot --input-file $datasource$example --output debug.$example.nxs 1>stdout.$example.nxs.txt 2>stderr.$example.nxs.txt
+done
diff --git a/debug/concept_mapper.ipynb b/debug/concept_mapper.ipynb
@@ -0,0 +1,74 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4f240b8f-71d4-4004-ab56-d7480b44d96e",
+   "metadata": {},
+   "source": [
+    "# Generate Python list of tuple with concept mapping to be used for the configuration of tech-partner-specific subparsers."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "869670b4-0780-4bf4-bc08-d802288fa5df",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "\n",
+    "fnm = \"image_tiff_tfs_to_nexus.ods\"\n",
+    "fnm = \"image_png_protochips_to_nexus.ods\"\n",
+    "\n",
+    "ods = pd.read_excel(fnm, engine=\"odf\")\n",
+    "ods = ods.fillna(\"\")\n",
+    "# print(ods)\n",
+    "cfg = []\n",
+    "for row_idx in np.arange(1, ods.shape[0]):\n",
+    "    nxpath = ods.iloc[row_idx, 0]\n",
+    "    functor = ods.iloc[row_idx, 1]\n",
+    "    if nxpath != \"\" and ods.iloc[row_idx, 4] != \"\":  # not in [\"IGNORE\", \"UNCLEAR\"]:\n",
+    "        if functor != \"fun\":\n",
+    "            cfg.append((f\"{nxpath}\", f\"{ods.iloc[row_idx, 4]}\"))\n",
+    "        else:\n",
+    "            cfg.append((f\"{nxpath}\", f\"{ods.iloc[row_idx, 2]}\", ods.iloc[row_idx, 4]))  # not fstring because can be a list!\n",
+    "\n",
+    "indent = \"                               \"\n",
+    "for entry in cfg:\n",
+    "    print(f\"{indent}{entry},\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f27812fa-d023-4ed6-a5ee-d417a8705828",
+   "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": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/debug/imgs.batch.sh b/debug/imgs.batch.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+datasource="../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/development_imgs/ikz_robert/"
+
+# comments is detector mode
+
+# Reetu some SEM
+# examples="kit/FeMoOx_AntiA_04_1k5x_CN.tif"  
+
+# IKZ SEM TFS Apreo for all imaging modes
+# examples="ikz_robert/0c8nA_3deg_003_AplusB_test.tif"  # T1
+# examples="ikz_martin/ALN_baoh_021.tif"  # T2
+# examples="ikz_robert/T3_image.tif"  # T3
+# examples="ikz_robert/ETD_image.tif"  # ETD
+# examples="ikz_martin/NavCam_normal_vis_light_ccd.tif"  # NavCam
+examples="0c8nA_3deg_003_AplusB_test.tif ALN_baoh_021.tif T3_image.tif ETD_image.tif NavCam_normal_vis_light_ccd.tif"
+
+for example in $examples; do
+	echo $example
+	dataconverter --reader em --nxdl NXroot --input-file $datasource$example --output debug.$example.nxs 1>stdout.$example.nxs.txt 2>stderr.$example.nxs.txt
+done