Add HTXRD-reading with saving in individual files

nafuma/xrd/io.py

@@ -5,6 +5,7 @@ import numpy as np
 import os
 import shutil
 import sys
+import datetime
 
 import zipfile
 import xml.etree.ElementTree as ET
@@ -320,13 +321,20 @@ def read_brml(data, options={}, index=0):
 
 def read_htxrd(data, options={}, index=0):
 
-    required_options = ['extract_folder', 'save_folder', 'save_filename']
+    required_options = ['extract_folder', 'save_folder', 'save_filename', 'adjust_time']
     default_options = {
         'extract_folder': 'tmp',
         'save_folder': None,
-        'save_filename': None
+        'save_filename': None,
+        'adjust_time': True
     }
 
+    if not isinstance(data['path'], list):
+        data['path'] = [data['path']]
+
+    if 'wavelength' not in data.keys():
+        data['wavelength'] = [None for i in range(len(data['path']))]
+
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
     
@@ -344,6 +352,9 @@ def read_htxrd(data, options={}, index=0):
     diffractograms = []
     wavelengths = []
     
+    active_scan = False
+    timestamps = []
+
     # Loop through all RawData-files and extract all data and temperatures
     for i, file in enumerate(files):
 
@@ -357,7 +368,6 @@ def read_htxrd(data, options={}, index=0):
         # initalise empty list to store data from this particular scan
         diffractogram = []
 
-
         for chain in root.findall('./DataRoutes/DataRoute'):
             
             scantypes = chain.findall('ScanInformation')
@@ -367,6 +377,7 @@ def read_htxrd(data, options={}, index=0):
                     continue
 
                 else:
+                    active_scan = True
                     if chain.get('RouteFlag') == 'Final':
                         for scandata in chain.findall('Datum'):
                             scandata = scandata.text.split(',')
@@ -387,8 +398,22 @@ def read_htxrd(data, options={}, index=0):
                         wavelengths.append(wavelength)
 
 
+        if active_scan:
+            for chain in root.findall('./TimeStampStarted'):
+                time_start = datetime.datetime.strptime(chain.text[:-7], "%Y-%m-%dT%H:%M:%S.%f")
+            for chain in root.findall('./TimeStampFinished'):
+                time_end = datetime.datetime.strptime(chain.text[:-7], "%Y-%m-%dT%H:%M:%S.%f")
+
+
+            time_diff = time_end - time_start
+
+            if options['adjust_time']:
+                timestamps.append(time_start + time_diff/2)
+
+
     if options['save_folder']:
-        for i, (diffractogram, wavelength) in enumerate(zip(diffractograms, wavelengths)):
+        print(options['save_folder'])
+        for i, (diffractogram, wavelength, timestamp) in enumerate(zip(diffractograms, wavelengths, timestamps)):
             if not options['save_filename']:
                 filename = os.path.basename(data['path'][index]).split('.')[0] + '_' + str(i).zfill(4) +'.xy'
             else:
@@ -398,7 +423,7 @@ def read_htxrd(data, options={}, index=0):
             if not os.path.isdir(options['save_folder']):
                 os.makedirs(options['save_folder'])
 
-            save_htxrd_as_xy(diffractogram, wavelength, filename, options['save_folder'])
+            save_htxrd_as_xy(diffractogram, wavelength, timestamp, filename, options['save_folder'])
 
 
 
@@ -408,19 +433,20 @@ def read_htxrd(data, options={}, index=0):
 
     return diffractograms, wavelengths
 
-def save_htxrd_as_xy(diffractogram, wavelength, filename, save_path):
+def save_htxrd_as_xy(diffractogram, wavelength, timestamp, filename, save_path):
 
     headers = '\n'.join(
         [line for line in 
             [f'# Temperature {np.round(diffractogram["T"].mean())}',
             f'# Wavelength {wavelength}',
+            f'# Time {timestamp}'
             ]
         ]
     )
 
     diffractogram = diffractogram.drop('T', axis=1)
 
-    with open(os.path.join(save_path, filename), 'w') as f:
+    with open(os.path.join(save_path, filename), 'w', newline='\n') as f:
         for line in headers:
             f.write(line)