Merge branch '41-sample-data-for-xps' into 'develop'

Resolve "Sample data for XPS"

Closes #41

See merge request !31

docker/examples/xps/VisualizeXPSSpectra.01.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Exemplar visualization of XPS spectra"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import os, sys\n",
+    "import json\n",
+    "import shutil"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Get a dataset"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "shutil.unpack_archive('XPSDataExample.zip')\n",
+    "! ls"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Link to Mark Greiner's parser for reading metadata and numerical data from SPECS Prodigy *.xy files."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os, sys\n",
+    "sys.path.append('nomad_xps_parser_specsxy')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from prodigy_parser_xy import ProdigyParserXY"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Use the parser to extract (meta)data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "MYDATASET = 'XPS data example'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "parser = ProdigyParserXY( author='Mark Greiner' )\n",
+    "#parser.convertToJson(MYDATASET+'.xy')\n",
+    "parser.parseFile(MYDATASET+'.xy')\n",
+    "#the next two methods are some cleaning steps that we typically do in XPS\n",
+    "parser.removeAlign()\n",
+    "parser.extractAllTags()\n",
+    "#the dataset is a list of dictionaries, where each spectrum is one item in the list\n",
+    "data_set = parser.dataset"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Display selected spectra."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Starting with Mark Greiner's example code that comes with the parser how to visualize data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#fig, xy = plt.figure(figsize=[20, 10])\n",
+    "spectrum_types = list(set([d['metadata']['spectrum_region'] for d in data_set]))\n",
+    "print('Number of spectra_types:')\n",
+    "print(np.shape(spectrum_types))\n",
+    "#dataset contains 5 spectra, the zeroth one is an overview, the rest specific ones\n",
+    "for selection in spectrum_types:\n",
+    "    #selection = spectrum_types[4]\n",
+    "    channel_nr = 1\n",
+    "    for data in data_set:\n",
+    "        if data['metadata']['spectrum_region'] == selection:\n",
+    "            axis_id = data['metadata']['axis_id']\n",
+    "            plt.plot(data['data'][axis_id], data['data'][channel_nr])\n",
+    "            plt.xlabel(data['metadata']['data_labels'][axis_id]['label'] \n",
+    "                       + ' [' + data['metadata']['data_labels'][axis_id]['unit'] \n",
+    "                       + ']', fontsize=14)\n",
+    "            plt.ylabel(data['metadata']['data_labels'][channel_nr]['label'] + \n",
+    "                       ' [' + data['metadata']['data_labels'][channel_nr]['unit'] \n",
+    "                       + ']', fontsize=14)\n",
+    "#plt.yscale('log')\n",
+    "plt.legend(range(5))\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Next steps"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "* Reorganize/rewrite plotting functions\n",
+    "* Interface with nomad xpsparser\n",
+    "* Parse from XPS NeXus application definition\n",
+    "* Have a parser from xy/sle/vms to this NeXus application definition\n",
+    "* Thus, split the expertise which is needed for parser development<br>\n",
+    "between domain-format specialists and nomad development specialists\n",
+    "* Let nomad maintain a NeXus for XPS app def parser\n",
+    "\n",
+    "* Use widgets (e.g. bokeh or ipywidgets) to make figure interactive\n",
+    "* Use widgets to make spectra selectable\n",
+    "* Make spectrum ranges clickable/selectable to define\n",
+    "* Interface with auto-indexing tool"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

docker/examples/xps/nomad_xps_parser_specsxy/measurement_data_class.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Feb  1 08:25:00 2021
+
+@author: Mark
+"""
+
+class MetaData:
+    def __init__(self):
+        self.timestamp = ''
+        self.dwell_time = ''
+        self.n_scans = ''
+        self.excitation_energy = ''
+        self.method_type = ''
+        self.data_labels = []
+        self.device_settings = []
+        self.spectrum_region = ''
+        self.source_label = ''
+        self.primary_channel_id = 1
+        self.axis_id = 0
+        self.group_name = ''
+
+class DeviceSettings():
+    def __init__(self):
+        self.device_name = ''
+        self.channel_id = ''
+            
+class AnalyzerSettings(DeviceSettings):
+    def __init__(self):
+        super().__init__()
+        self.pass_energy = ''
+        self.lens_modes = ''
+        self.detector_voltage = ''
+    
+class DataChannel:
+    def __init__(self):   
+        pass
+        
+class MeasurementData:
+    def __init__(self):
+        self.metadata = MetaData()
+        self.data = []
+        
+    def addDataChannel(self, data_channel):
+        self.data += [data_channel]
+        
+    def appendDataChannel(self, data_channel):
+        channel_id = len(self.data)
+        self.metadata.data_labels += [{'channel_id':channel_id,
+                                       'label':data_channel['label'],
+                                       'unit':data_channel['unit']}
+                                      ]
+        if 'device_settings' in data_channel.keys():
+            device_settings = data_channel['device_settings']
+            if not isinstance(device_settings, DeviceSettings):
+                print('The device settings should be an instance of DeviceSettings')
+        else:
+            device_settings = DeviceSettings()
+            device_settings.device_name = 'unknown device'
+        device_settings.channel_id = channel_id
+        self.metadata.device_settings += [device_settings]
+        self.data += [data_channel['data']]
+        
+            
+
+        
+        
+       
\ No newline at end of file

docker/examples/xps/nomad_xps_parser_specsxy/spectrum.py

+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jan 13 14:15:11 2021
+
+@author: Mark
+"""
+class Spectrum():
+    
+    def __init__(self):
+        self.settings = Settings()
+        self.meta = Meta()
+        self.measurement_data = [MeasurementData()]
+        
+class MeasurementData():
+    
+    def __init__(self):
+        self.name = ''
+        self.units = ''
+        self.shape = []
+        self.values = []
+        
+class RegularMeasurementData(MeasurementData):
+    
+    def __init__(self):
+        super().__init__()
+        self.start = ''
+        self.stop = ''
+        self.step = []
+        
+    def generate_values(self):
+        self.values = [self.start, self.stop, self.step]
+        
+class IrregularMeasurementData(MeasurementData):
+    
+    def __init__(self):
+        super().__init__()
+     
+class MeasurementDataArray():
+    
+    def __init__(self):
+        self.name = []
+        self.units = []
+        self.shape = []
+        self.values = []
+
+class Settings():
+    
+    def __init__(self):
+        self.dwell_time = ''
+        self.emission_current = ''
+        self.excitation_energy = ''
+        self.entrance_slit = ''
+        self.exit_slit = ''
+        self.pass_energy = ''
+        self.source_voltage = ''
+        self.voltage_range = ''
+        self.workfunction = ''
+        self.iris_diameter = ''
+        self.lens_mode = ''
+        self.calibration_file = ''
+        self.scans = ''
+        self.transmission_function
+    
+class Meta():
+    
+    def __init__(self):
+        self.method = ''
+        self.users = ''
+        self.sample = ''
+        self.group_name = ''
+        self.group_id = ''
+        self.spectrum_id = ''
+        self.time_stamp = ''
+        self.devices = ''
+        self.spectrum_type = ''
+        
+reg = RegularMeasurementData()    
+        
+        
\ No newline at end of file