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

nafuma/xanes/io.py

@@ -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, but still proceeding ...', options=options)
+
+                    
 
             
             
@@ -362,7 +367,12 @@ def read_metadata(data: dict, options={}) -> dict:
         if options['get_timestamp']:
 
             with open(filename, 'r') as f:
-                time = f.readline().strip('# Time: ')
+                #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']:

nafuma/xanes/plot.py

@@ -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:
+		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:
+		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']):