FAIRmat-NFDI · sanbrock · Jun 1, 2023 · May 22, 2023 · May 22, 2023 · May 22, 2023
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -1,5 +1,5 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
 #    pip-compile --extra=dev --output-file=dev-requirements.txt --resolver=backtracking pyproject.toml
@@ -124,6 +124,7 @@ h5py==3.7.0
     #   ifes-apt-tc-data-modeling
     #   jupyterlab-h5web
     #   kikuchipy
+    #   nionswift
     #   orix
     #   pyfai
     #   pynxtools (pyproject.toml)
@@ -143,17 +144,12 @@ imageio==2.22.1
     # via
     #   hyperspy
     #   kikuchipy
+    #   nionswift
+    #   nionswift-io
+    #   nionui
     #   scikit-image
 importlib-metadata==5.0.0
-    # via
-    #   hyperspy
-    #   jupyterlab-server
-    #   nbconvert
-    #   numba
-importlib-resources==5.9.0
-    # via
-    #   jsonschema
-    #   radioactivedecay
+    # via hyperspy
 iniconfig==1.1.1
     # via pytest
 ipykernel==6.16.0
@@ -312,6 +308,22 @@ networkx==2.6.3
     # via
     #   radioactivedecay
     #   scikit-image
+niondata==0.15.3
+    # via
+    #   nionswift
+    #   nionswift-io
+nionswift==0.16.8
+    # via pynxtools (pyproject.toml)
+nionswift-io==0.15.1
+    # via nionswift
+nionui==0.6.10
+    # via nionswift
+nionutils==0.4.6
+    # via
+    #   niondata
+    #   nionswift
+    #   nionswift-io
+    #   nionui
 notebook==6.5.2
     # via jupyterlab
 notebook-shim==0.2.2
@@ -344,6 +356,10 @@ numpy==1.21.6
     #   kikuchipy
     #   lmfit
     #   matplotlib
+    #   niondata
+    #   nionswift
+    #   nionswift-io
+    #   nionui
     #   numba
     #   numcodecs
     #   numexpr
@@ -407,13 +423,12 @@ pillow==9.2.0
     # via
     #   imageio
     #   matplotlib
+    #   nionswift
     #   scikit-image
 pint==0.18
     # via hyperspy
 pip-tools==6.13.0
     # via pynxtools (pyproject.toml)
-pkgutil-resolve-name==1.3.10
-    # via jsonschema
 platformdirs==2.5.2
     # via
     #   jupyter-core
@@ -487,8 +502,11 @@ python-dateutil==2.8.2
 pytz==2022.4
     # via
     #   babel
+    #   nionswift
     #   pandas
     #   pynxtools (pyproject.toml)
+pytz-deprecation-shim==0.1.0.post0
+    # via tzlocal
 pywavelets==1.3.0
     # via scikit-image
 pyxem==0.15.0
@@ -534,6 +552,8 @@ scipy==1.7.3
     #   hyperspy
     #   kikuchipy
     #   lmfit
+    #   niondata
+    #   nionswift
     #   orix
     #   pyfai
     #   pynxtools (pyproject.toml)
@@ -647,10 +667,14 @@ types-urllib3==1.26.25.5
     # via types-requests
 typing-extensions==4.3.0
     # via
-    #   astroid
     #   mypy
     #   numcodecs
-    #   pylint
+tzdata==2023.3
+    # via pytz-deprecation-shim
+tzlocal==4.3
+    # via
+    #   nionswift
+    #   pynxtools (pyproject.toml)
 uncertainties==3.1.7
     # via lmfit
 url-normalize==1.4.3
@@ -682,9 +706,7 @@ zarr==2.12.0
 zipfile37==0.1.3
     # via pynxtools (pyproject.toml)
 zipp==3.8.1
-    # via
-    #   importlib-metadata
-    #   importlib-resources
+    # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

diff --git a/examples/apm/Write.NXapm.Example.1.ipynb b/examples/apm/Write.NXapm.Example.1.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Using dataconverter/apm for mapping atom probe microscopy data to NeXus/NXapm"
+    "## Using dataconverter/apm for mapping atom probe microscopy data to NeXus/HDF5/NXapm"
    ]
   },
   {
@@ -68,7 +68,7 @@
     "tags": []
    },
    "source": [
-    "Example data can be found on Zenodo http://dx.doi.org/10.5281/zenodo.6808516."
+    "Example data can be found on Zenodo https://www.zenodo.org/record/7908429."
    ]
   },
   {
@@ -79,7 +79,7 @@
    },
    "outputs": [],
    "source": [
-    "import shutil  # unpacks in current path unless an additional path argument is provided"
+    "import zipfile as zp"
    ]
   },
   {
@@ -88,8 +88,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "! curl --output APM.LEAP.Datasets.1.zip https://zenodo.org/record/6808516/files/APM.LEAP.Datasets.1.zip\n",
-    "shutil.unpack_archive(\"APM.LEAP.Datasets.1.zip\")"
+    "! curl --output usa_denton_smith_apav_si.zip https://zenodo.org/record/7908429/files/usa_denton_smith_apav_si.zip"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "zp.ZipFile(\"usa_denton_smith_apav_si.zip\").extractall(path=\"\", members=None, pwd=None)"
    ]
   },
   {
@@ -101,7 +109,7 @@
     "  The eln_data_apm.yaml file in the example can be edited with a text editor.<br>\n",
     "* A file with **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",
-    "  POS, ePOS, or APT are allowed.<br>\n",
+    "  POS, ePOS, or APT are allowed. Inspect some of the above-mentioned examples on Zenodo.<br>\n",
     "* A file with **ranging definitions** in community, technology partner format with<br>\n",
     "  the definitions how mass-to-charge-state-ratio values map on ion species.<br>\n",
     "  RNG, RRNG and is possible. A MatLab script can be used to inject other representations<br>\n",
@@ -197,26 +205,34 @@
    "source": [
     "#parser-nexus/tests/data/tools/dataconverter/readers/em_om/\n",
     "eln_data_file_name = [\"eln_data_apm.yaml\"]\n",
-    "input_recon_file_name = [\"R31_06365-v02.pos\",\n",
+    "input_recon_file_name = [\"Si.apt\",\n",
+    "                         \"Si.epos\",\n",
+    "                         \"Si.pos\",\n",
+    "                         \"R31_06365-v02.pos\",\n",
     "                         \"R18_58152-v02.epos\",\n",
     "                         \"70_50_50.apt\"]\n",
     "#                         \"R56_01769-v01.pos\"]\n",
-    "input_range_file_name = [\"R31_06365-v02.rrng\",\n",
+    "input_range_file_name = [\"Si.RRNG\",\n",
+    "                         \"Si.RNG\",\n",
+    "                         \"Si.RNG\",\n",
+    "                         \"R31_06365-v02.rrng\",\n",
     "                         \"R31_06365-v02.rrng\",\n",
     "                         \"R31_06365-v02.rrng\"]\n",
     "#                         \"R56_01769.rng.fig.txt\"]\n",
     "output_file_name = [\"apm.case1.nxs\",\n",
     "                    \"apm.case2.nxs\",\n",
     "                    \"apm.case3.nxs\",\n",
-    "                    \"apm.case4.nxs\"]\n",
-    "for case_id in [0]:  # , 1, 2, 3]:\n",
+    "                    \"apm.case4.nxs\",\n",
+    "                    \"apm.case5.nxs\",\n",
+    "                    \"apm.case6.nxs\"]\n",
+    "for case_id in [0]:\n",
     "    ELN = eln_data_file_name[0]\n",
     "    INPUT_RECON = input_recon_file_name[case_id]\n",
     "    INPUT_RANGE = input_range_file_name[case_id]\n",
     "    OUTPUT = output_file_name[case_id]\n",
     "\n",
     "    ! dataconverter --reader apm --nxdl NXapm --input-file $ELN --input-file \\\n",
-    "    $INPUT_RECON --input-file $INPUT_RANGE --output $OUTPUT --output $OUTPUT"
+    "    $INPUT_RECON --input-file $INPUT_RANGE --output $OUTPUT"
    ]
   },
   {
@@ -242,10 +258,7 @@
    "outputs": [],
    "source": [
     "# H5Web(OUTPUT)\n",
-    "H5Web(\"apm.case1.nxs\")\n",
-    "# H5Web(\"apm.case2.nxs\")\n",
-    "# H5Web(\"apm.case3.nxs\")\n",
-    "# H5Web(\"apm.case4.nxs\")"
+    "H5Web(\"apm.case1.nxs\")"
    ]
   },
   {
@@ -258,7 +271,6 @@
   {
    "cell_type": "markdown",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
    "source": [
@@ -432,6 +444,19 @@
     "The apm reader has a functionality to generate synthetic dataset which are meant for pursuing code development."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-block alert-danger\">\n",
+    "This functionality uses recent features of ase which demands an environment that is currently not supported<br>\n",
+    "by NOMAD OASIS. As the here exemplified settings for this example are configured to represent an environment<br>\n",
+    "matching close to NOMAD users who are interested in this developer functionality should do the following:<br>\n",
+    "Run this example in a standalone environment where ase is upgraded to the latest version and then use<br>\n",
+    "the generated NeXus files either as is or upload them to NOMAD OASIS.<br>\n",
+    "</div>"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

diff --git a/examples/em_nion/README.md b/examples/em_nion/README.md
@@ -0,0 +1,24 @@
+## em_nion reader
+
+This is an example how the em_nion parser/reader/data extractor can be used as a standalone
+tool to convert data and metadata from a compressed nionswift project into an NXem-formatted
+NeXus/HDF5 file. Further details to the functionalities of the parser are documented
+in the parsers sub-directory:
+
+```
+pynxtools/pynxtools/dataconverter/readers/em_nion
+```
+
+**Write.NXem_nion.Example.1.ipynb** is the Jupyter notebook which exemplies
+how the parser can be used as a standalone version, i.e. without NOMAD.
+
+**eln_data_em_nion.yaml** is a YAML/text file which contains relevant data which are not
+contained typically in files from technology partners. These data have been collected
+either by editing the file manually or by using an electronic lab notebook (ELN),
+such as the NOMAD ELN.
+A few example files from real atom probe reconstructions and ranging definitions are
+offered as downloads to run the example with the above-mentioned Juypter notebook.
+
+Every other ELN can be used with this parser provided that this ELN writes its data
+into a YAML file with the same keywords and structure as is exemplified in the
+above-mentioned YAML file.