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Small adjustments to logging

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rasmusvt 2022-06-21 18:01:53 +02:00
parent cc80a48259
commit 054311ca10
1 changed files with 11 additions and 17 deletions
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28
nafuma/xanes/io.py
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@ -16,7 +16,7 @@ def split_scan_data(data: dict, options={}) -> list:
default_options = { default_options = {
'log': False, 'log': False,
'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S.log")}_split_edges.log', 'logfile': f'{datetime.now().strftime("%Y-%m-%d-%H-%M-%S")}_split_edges.log',
'save': False, # whether to save the files or not 'save': False, # whether to save the files or not
'save_folder': '.', # root folder of where to save the files 'save_folder': '.', # root folder of where to save the files
'replace': False, # whether to replace the files if they already exist 'replace': False, # whether to replace the files if they already exist
@ -24,12 +24,6 @@ def split_scan_data(data: dict, options={}) -> list:
} }
options = aux.update_options(options=options, required_options=required_options, default_options=default_options) options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
#root is the path to the beamtime-folder
#destination should be the path to the processed data
#insert a for-loop to go through all the folders.dat-files in the folder root\xanes\raw
# FIXME Only adding this variable to pass the Linting-tests - will refactor this later
if not isinstance(data['path'], list): if not isinstance(data['path'], list):
data['path'] = [data['path']] data['path'] = [data['path']]
@ -89,12 +83,12 @@ def split_scan_data(data: dict, options={}) -> list:
edge = find_element({'xanes_data_original': xanes_df}) edge = find_element({'xanes_data_original': xanes_df})
if options['log']: if options['log']:
aux.write_log(message=f'Starting data clean-up ({edge}-edge)... ({i+1}/{len(scan_datas)})', options=options) aux.write_log(message=f'... Starting data clean-up ({edge}-edge)... ({i+1}/{len(scan_datas)})', options=options)
if not ('xmap_roi00' in headers[i]) and (not 'xmap_roi01' in headers[i]): if not ('xmap_roi00' in headers[i]) and (not 'xmap_roi01' in headers[i]):
if options['log']: if options['log']:
aux.write_log(message='... Did not find fluoresence data. Skipping...', options=options) aux.write_log(message='... ... Did not find fluoresence data. Skipping...', options=options)
continue continue
@ -106,13 +100,13 @@ def split_scan_data(data: dict, options={}) -> list:
if options['add']: if options['add']:
if options['log']: if options['log']:
aux.write_log(message=f'Addition of rois enabled. Starting addition...', options=options) aux.write_log(message=f'... Addition of rois enabled. Starting addition...', options=options)
added_edges = {'Mn': [], 'Fe': [], 'Co': [], 'Ni': []} added_edges = {'Mn': [], 'Fe': [], 'Co': [], 'Ni': []}
for edge, scans in edges.items(): for edge, scans in edges.items():
if options['log']: if options['log']:
aux.write_log(message=f'... Adding rois of the {edge}-edge...', options=options) aux.write_log(message=f'... ... Adding rois of the {edge}-edge...', options=options)
if scans: if scans:
xanes_df = scans[0] xanes_df = scans[0]
@ -121,7 +115,7 @@ def split_scan_data(data: dict, options={}) -> list:
if i > 0: if i > 0:
if options['log']: if options['log']:
aux.write_log(message=f'... ... Adding {i}/{len(scans)}', options=options) aux.write_log(message=f'... ... ... Adding {i+1}/{len(scans)}', options=options)
if 'xmap_roi00' in xanes_df.columns: if 'xmap_roi00' in xanes_df.columns:
xanes_df['xmap_roi00'] += scan['xmap_roi00'] xanes_df['xmap_roi00'] += scan['xmap_roi00']
@ -135,11 +129,11 @@ def split_scan_data(data: dict, options={}) -> list:
if options['save']: if options['save']:
if options['log']: if options['log']:
aux.write_log(message=f'Saving data to {options["save_folder"]}', options=options) aux.write_log(message=f'... Saving data to {options["save_folder"]}', options=options)
if not os.path.isdir(options['save_folder']): if not os.path.isdir(options['save_folder']):
if options['log']: if options['log']:
aux.write_log(message=f'... {options["save_folder"]} does not exist. Creating folder.', options=options) aux.write_log(message=f'... ... {options["save_folder"]} does not exist. Creating folder.', options=options)
os.makedirs(options['save_folder']) os.makedirs(options['save_folder'])
@ -154,16 +148,16 @@ def split_scan_data(data: dict, options={}) -> list:
if not os.path.isfile(path): if not os.path.isfile(path):
scan.to_csv(path) scan.to_csv(path)
if options['log']: if options['log']:
aux.write_log(message=f'... Scan saved to {path}', options=options) aux.write_log(message=f'... ... Scan saved to {path}', options=options)
elif options['replace'] and os.path.isfile(path): elif options['replace'] and os.path.isfile(path):
scan.to_csv(path) scan.to_csv(path)
if options['log']: if options['log']:
aux.write_log(message=f'... File already exists. Overwriting to {path}', options=options) aux.write_log(message=f'... ... File already exists. Overwriting to {path}', options=options)
elif not options['replace'] and os.path.isfile(path): elif not options['replace'] and os.path.isfile(path):
if options['log']: if options['log']:
aux.write_log(message=f'... File already exists. Skipping...', options=options) aux.write_log(message=f'... ... File already exists. Skipping...', options=options)
all_scans.append(edges) all_scans.append(edges)