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Changing Reader name from STMReader to XRDReader.
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@RubelMozumder
RubelMozumder committed Sep 15, 2023
1 parent e53eb34 commit f860c80
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Showing 2 changed files with 82 additions and 2 deletions.
80 changes: 80 additions & 0 deletions pynxtools/dataconverter/readers/xrd/Untitled.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"id": "bc15a0fb-c139-4f5f-8602-a6644e1e92f0",
"metadata": {},
"outputs": [
{
"ename": "RuntimeError",
"evalue": "module compiled against API version 0x10 but this version of numpy is 0xe",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mRuntimeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;31mRuntimeError\u001b[0m: module compiled against API version 0x10 but this version of numpy is 0xe"
]
},
{
"ename": "ImportError",
"evalue": "numpy.core.multiarray failed to import",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/tmp/ipykernel_29230/4118053084.py\u001b[0m in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpynxtools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdataconverter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreaders\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxrd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mxrd_parser\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mparse_and_convert_file\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/NOMAD-FAIRmat/GH/pynxtools/pynxtools/dataconverter/readers/xrd/xrd_parser.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 22\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mos\u001b[0m \u001b[0;31m# for file path operations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mxml\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0metree\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mElementTree\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mET\u001b[0m \u001b[0;31m# for XML parsing\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 24\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mxrayutilities\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mio\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpanalytical_xml\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mXRDMLFile\u001b[0m \u001b[0;31m# for reading XRDML files\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 25\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mFileReader\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/NOMAD-FAIRmat/GH/pynxtools/.pyenv_3_10/lib/python3.10/site-packages/xrayutilities/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 30\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 31\u001b[0m \u001b[0;31m# load configuration\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 32\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0m__path__\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0manalysis\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mio\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmaterials\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmath\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msimpack\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 33\u001b[0m from .experiment import (GID, GISAXS, HXRD, Experiment, FourC, NonCOP,\n\u001b[1;32m 34\u001b[0m PowderExperiment, QConversion)\n",
"\u001b[0;32m~/NOMAD-FAIRmat/GH/pynxtools/.pyenv_3_10/lib/python3.10/site-packages/xrayutilities/analysis/__init__.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 25\u001b[0m \"\"\"\n\u001b[1;32m 26\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 27\u001b[0;31m from .line_cuts import (get_arbitrary_line, get_omega_scan, get_qx_scan,\n\u001b[0m\u001b[1;32m 28\u001b[0m \u001b[0mget_qy_scan\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mget_qz_scan\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mget_radial_scan\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 29\u001b[0m get_ttheta_scan)\n",
"\u001b[0;32m~/NOMAD-FAIRmat/GH/pynxtools/.pyenv_3_10/lib/python3.10/site-packages/xrayutilities/analysis/line_cuts.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmath\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 21\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexperiment\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mHXRD\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 22\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgridder\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mFuzzyGridder1D\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/NOMAD-FAIRmat/GH/pynxtools/.pyenv_3_10/lib/python3.10/site-packages/xrayutilities/experiment.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 37\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 38\u001b[0m \u001b[0;31m# package internal imports\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 39\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcxrayutilities\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmath\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mutilities\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 40\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m\u001b[0mexception\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mInputError\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 41\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mImportError\u001b[0m: numpy.core.multiarray failed to import"
]
}
],
"source": [
"from pynxtools.dataconverter.readers.xrd.xrd_parser import parse_and_convert_file"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "945d80f2-9fdd-4e61-8ff2-d721e50000b0",
"metadata": {},
"outputs": [],
"source": [
"import numpy.core.multiarray"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "98f6e21d-6c50-4efa-bdce-3ac1ef4c4df0",
"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": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
4 changes: 2 additions & 2 deletions pynxtools/dataconverter/readers/xrd/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@
XRD_FILE_EXTENSIONS = [".xrdml", ".udf", ".raw", ".xye"]


class STMReader(BaseReader):
class XRDReader(BaseReader):
""" Reader for XPS.
"""

Expand Down Expand Up @@ -118,4 +118,4 @@ def read(self,
return filled_template


READER = STMReader
READER = XRDReader

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