Implementated module to read file of common types arising in multiphase chemistry group experiments. Status: in progres.

g5505_file_reader.py

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+import numpy as np
+import pandas as np
+import matplotlib.pyplot as plt
+import plotly.express as px
+import plotly.graph_objects as go
+from plotly.subplots import make_subplots
+from igor2.binarywave import load as loadibw
+
+
+def read_xps_ibw_file_as_dict(filename):
+
+    """ Reads ibw files from multiphase chemistry group, which contain xps spectra and acquisition settings."""
+
+    file_obj = loadibw(filename)
+
+    required_keys = ['wData','data_units','dimension_units','note'] 
+    if sum([item in required_keys for item in file_obj['wave'].keys()]) < len(required_keys):
+        raise ValueError('This is not a valid xps ibw file. It does not satisfy minimum adimissibility criteria.')
+    
+    file_dict = {}
+    file_dict['name'] = filename
+    file_dict['data'] = file_obj['wave']['wData']
+    file_dict['data_units'] = file_obj['wave']['data_units']
+    file_dict['shape'] = file_dict['data'].shape
+    file_dict['dtype'] = type(file_dict['data'])   
+ 
+    # Convert notes of bytes class to string class and split string into a list of elements separated by '\r'. 
+    notes_list = file_obj['wave']['note'].decode("utf-8").split('\r')
+    exclude_list = ['Excitation Energy']
+    for item in notes_list:
+        if '=' in item:
+            key, value = tuple(item.split('='))
+            # TODO: check if value can be converted into a numeric type. Now all values are string type
+            if not key in exclude_list:
+                file_dict[key] = value
+
+    # TODO: talk to thorsten to see if there is an easier way to access the below attributes
+    dimension_labels = file_obj['wave']['dimension_units'].decode("utf-8").split(']')
+    file_dict['dimension_units'] = [item+']' for item in dimension_labels[0:len(dimension_labels)-1]]
+    
+
+    return file_dict
+
+def main():
+
+    inputfile_dir = '\\\\fs101\\5505\\People\\Juan\\TypicalBeamTime'
+
+    file_dict = read_xps_ibw_file_as_dict(inputfile_dir+'\\SES\\0069069_N1s_495eV.ibw')
+
+    for key in file_dict.keys():
+        print(key,file_dict[key])
+
+
+if __name__ == '__main__':
+
+    main()
+
+    print(':)')