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Merge branch 'master' of github.com:rasmusthog/nafuma

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This commit is contained in:
rasmusvt 2022-09-18 15:50:59 +02:00
commit 39f59e472c
2 changed files with 26 additions and 8 deletions
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22
nafuma/xanes/io.py
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@ -10,7 +10,7 @@ def split_scan_data(data: dict, options={}) -> list:
''' Splits a XANES-file from BM31 into different files depending on the edge. Has the option to add intensities of all scans of same edge into the same file.
As of now only picks out xmap_rois (fluoresence mode) and for Mn, Fe, Co and Ni K-edges.'''
required_options = ['log', 'logfile', 'save', 'save_folder', 'replace', 'active_roi', 'add_rois', 'return']
required_options = ['log', 'logfile', 'save', 'save_folder', 'replace', 'active_roi', 'add_rois', 'return', 'skip_if_no_roi']
default_options = {
'log': False,
@ -20,7 +20,8 @@ def split_scan_data(data: dict, options={}) -> list:
'replace': False, # whether to replace the files if they already exist
'active_roi': None,
'add_rois': False, # Whether to add the rois of individual scans of the same edge together
'return': True
'return': True,
'skip_if_no_roi': True
}
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
@ -100,10 +101,14 @@ def split_scan_data(data: dict, options={}) -> list:
if not ('xmap_roi00' in headers[i]) and (not 'xmap_roi01' in headers[i]):
if options['skip_if_no_roi']:
if options['log']:
aux.write_log(message='... ... Did not find fluoresence data. Skipping...', options=options)
continue
if options['log']:
aux.write_log(message='... ... Did not find fluoresence data. Skipping...', options=options)
aux.write_log(message='... ... Did not find fluoresence data, but still proceeding ...', options=options)
continue
@ -362,8 +367,13 @@ def read_metadata(data: dict, options={}) -> dict:
if options['get_timestamp']:
with open(filename, 'r') as f:
time = f.readline().strip('# Time: ')
time = datetime.datetime.strptime(time, "%a %b %d %H:%M:%S %Y ")
#time = f.readline().strip('# Time: ') #<-- Previous code
time = f.readline().split('# Time: ')[-1] #Hope this does not fuck you up, Rasmus - but I needed another space here
split_operator=time[-9] #This should be the operator that splits hours, minutes and seconds
if split_operator == ".":
time = datetime.datetime.strptime(time, "%a %b %d %H.%M.%S %Y ")
if split_operator == ":":
time = datetime.datetime.strptime(time, "%a %b %d %H:%M:%S %Y ")
if options['adjust_time']:
time_elapsed = scan_data['Htime'].iloc[-1] - scan_data['Htime'].iloc[0]

12
nafuma/xanes/plot.py
View file

@ -64,14 +64,22 @@ def plot_xanes(data, options={}):
def pick_out_scans(metadata: dict, timestamp: list):
# If either start or end are None, set to way back when or way into the future
split_operator=timestamp[0][-3] #Adding this to enable reading of both "." and ":" as operators to split hour:minute:second
if not timestamp[0]:
timestamp[0] = datetime.datetime.strptime('1970 01 01 00:00:00', '%Y %m %d %H:%M:%S')
else:
timestamp[0] = datetime.datetime.strptime(timestamp[0], "%d.%b %y %H.%M.%S")
if split_operator == ".":
timestamp[0] = datetime.datetime.strptime(timestamp[0], "%d.%b %y %H.%M.%S")
if split_operator == ":":
timestamp[0] = datetime.datetime.strptime(timestamp[0], "%d.%b %y %H:%M:%S")
if not timestamp[1]:
timestamp[1] = datetime.datetime.strptime('3000 01 01 00:00:00', '%Y %m %d %H:%M:%S')
else:
timestamp[1] = datetime.datetime.strptime(timestamp[1], "%d.%b %y %H.%M.%S")
if split_operator == ".":
timestamp[1] = datetime.datetime.strptime(timestamp[1], "%d.%b %y %H.%M.%S")
if split_operator == ":":
timestamp[1] = datetime.datetime.strptime(timestamp[1], "%d.%b %y %H:%M:%S")
scans = []
for i, time in enumerate(metadata['time']):