Synch with remote repo
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@ -1,79 +1,79 @@
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import os
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from igor2.binarywave import load as loadibw
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def read_xps_ibw_file_as_dict(filename):
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"""
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Reads IBW files from the Multiphase Chemistry Group, which contain XPS spectra and acquisition settings,
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and formats the data into a dictionary with the structure {datasets: list of datasets}. Each dataset in the
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list has the following structure:
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{
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'name': 'name',
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'data': data_array,
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'data_units': 'units',
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'shape': data_shape,
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'dtype': data_type
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}
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Parameters
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----------
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filename : str
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The IBW filename from the Multiphase Chemistry Group beamline.
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Returns
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-------
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file_dict : dict
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A dictionary containing the datasets from the IBW file.
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Raises
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------
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ValueError
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If the input IBW file is not a valid IBW file.
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"""
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file_obj = loadibw(filename)
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required_keys = ['wData','data_units','dimension_units','note']
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if sum([item in required_keys for item in file_obj['wave'].keys()]) < len(required_keys):
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raise ValueError('This is not a valid xps ibw file. It does not satisfy minimum adimissibility criteria.')
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file_dict = {}
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path_tail, path_head = os.path.split(filename)
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# Group name and attributes
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file_dict['name'] = path_head
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file_dict['attributes_dict'] = {}
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# Convert notes of bytes class to string class and split string into a list of elements separated by '\r'.
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notes_list = file_obj['wave']['note'].decode("utf-8").split('\r')
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exclude_list = ['Excitation Energy']
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for item in notes_list:
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if '=' in item:
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key, value = tuple(item.split('='))
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# TODO: check if value can be converted into a numeric type. Now all values are string type
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if not key in exclude_list:
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file_dict['attributes_dict'][key] = value
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# TODO: talk to Thorsten to see if there is an easier way to access the below attributes
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dimension_labels = file_obj['wave']['dimension_units'].decode("utf-8").split(']')
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file_dict['attributes_dict']['dimension_units'] = [item+']' for item in dimension_labels[0:len(dimension_labels)-1]]
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# Datasets and their attributes
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file_dict['datasets'] = []
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dataset = {}
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dataset['name'] = 'spectrum'
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dataset['data'] = file_obj['wave']['wData']
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dataset['data_units'] = file_obj['wave']['data_units']
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dataset['shape'] = dataset['data'].shape
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dataset['dtype'] = type(dataset['data'])
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# TODO: include energy axis dataset
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file_dict['datasets'].append(dataset)
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import os
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from igor2.binarywave import load as loadibw
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def read_xps_ibw_file_as_dict(filename):
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"""
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Reads IBW files from the Multiphase Chemistry Group, which contain XPS spectra and acquisition settings,
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and formats the data into a dictionary with the structure {datasets: list of datasets}. Each dataset in the
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list has the following structure:
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{
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'name': 'name',
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'data': data_array,
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'data_units': 'units',
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'shape': data_shape,
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'dtype': data_type
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}
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Parameters
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----------
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filename : str
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The IBW filename from the Multiphase Chemistry Group beamline.
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Returns
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-------
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file_dict : dict
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A dictionary containing the datasets from the IBW file.
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Raises
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------
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ValueError
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If the input IBW file is not a valid IBW file.
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"""
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file_obj = loadibw(filename)
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required_keys = ['wData','data_units','dimension_units','note']
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if sum([item in required_keys for item in file_obj['wave'].keys()]) < len(required_keys):
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raise ValueError('This is not a valid xps ibw file. It does not satisfy minimum adimissibility criteria.')
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file_dict = {}
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path_tail, path_head = os.path.split(filename)
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# Group name and attributes
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file_dict['name'] = path_head
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file_dict['attributes_dict'] = {}
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# Convert notes of bytes class to string class and split string into a list of elements separated by '\r'.
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notes_list = file_obj['wave']['note'].decode("utf-8").split('\r')
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exclude_list = ['Excitation Energy']
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for item in notes_list:
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if '=' in item:
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key, value = tuple(item.split('='))
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# TODO: check if value can be converted into a numeric type. Now all values are string type
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if not key in exclude_list:
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file_dict['attributes_dict'][key] = value
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# TODO: talk to Thorsten to see if there is an easier way to access the below attributes
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dimension_labels = file_obj['wave']['dimension_units'].decode("utf-8").split(']')
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file_dict['attributes_dict']['dimension_units'] = [item+']' for item in dimension_labels[0:len(dimension_labels)-1]]
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# Datasets and their attributes
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file_dict['datasets'] = []
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dataset = {}
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dataset['name'] = 'spectrum'
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dataset['data'] = file_obj['wave']['wData']
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dataset['data_units'] = file_obj['wave']['data_units']
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dataset['shape'] = dataset['data'].shape
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dataset['dtype'] = type(dataset['data'])
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# TODO: include energy axis dataset
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file_dict['datasets'].append(dataset)
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return file_dict
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