Add offset of x- and y-values for stacked diffractograms

beamtime/xrd/io.py

@@ -45,6 +45,7 @@ def integrate_1d(data, options={}, index=0):
     default_options = {
         'unit': '2th_deg', 
         'nbins': 3000,
+        'extract_folder': 'tmp',
         'save': False,
         'save_filename': None,
         'save_extension': '_integrated.xy',
@@ -68,8 +69,8 @@ def integrate_1d(data, options={}, index=0):
     filename = make_filename(options=options, path=data['path'][index])
     
     # Make save_folder if this does not exist already
-    if not os.path.isdir(options['save_folder']):
+    if not os.path.isdir(options['extract_folder']):
-        os.makedirs(options['save_folder'])
+        os.makedirs(options['extract_folder'])
 
 
     res = ai.integrate1d(data['image'], options['nbins'], unit=options['unit'], filename=filename)
@@ -79,7 +80,11 @@ def integrate_1d(data, options={}, index=0):
 
     if not options['save']:
         os.remove(filename)
-        shutil.rmtree('tmp')
+        shutil.rmtree(f'tmp')
+
+
+    # Reset this option
+    options['save_folder'] = None
     
     return diffractogram, wavelength
     
@@ -89,8 +94,7 @@ def make_filename(options, path=None):
 
     # Define save location for integrated diffractogram data
     if not options['save']:
-            options['save_folder'] = 'tmp'
+            filename = os.path.join(options['extract_folder'], 'tmp_diff.dat')
-            filename = os.path.join(options['save_folder'], 'tmp_diff.dat')
 
     elif options['save']:
 
@@ -183,9 +187,12 @@ def view_integrator(calibrant):
 def read_brml(data, options={}, index=0):
 
 
+    # FIXME: Can't read RECX1-data, apparently must be formatted differently from RECX2. Check the RawData-files and compare between the two files.
+
+
     required_options = ['extract_folder', 'save_folder']
     default_options = {
-        'extract_folder': 'tmp/',
+        'extract_folder': 'tmp',
         'save_folder': None
     }
 
@@ -304,12 +311,41 @@ def read_data(data, options={}, index=0):
         diffractogram['I'] = diffractogram['I'] / diffractogram['I'].max()
 
 
+    if options['offset']:
+        diffractogram = apply_offset(diffractogram, wavelength, index, options)
+
+
     diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
 
     return diffractogram, wavelength
 
 
+def apply_offset(diffractogram, wavelength, index, options):
+    #Apply offset along y-axis
+    diffractogram['I_org'] = diffractogram['I'] # make copy of original intensities
+    diffractogram['I'] = diffractogram['I'] + index*options['offset_y']
 
+    # Apply offset along x-axis
+    relative_shift = (wavelength / 1.54059)*options['offset_x'] # Adjusts the offset-factor to account for wavelength, so that offset_x given is given in 2th_cuka-units
+    diffractogram['2th_org'] = diffractogram['2th']
+    diffractogram['2th'] = diffractogram['2th'] + index*relative_shift
+
+
+    return diffractogram
+
+def revert_offset(diffractogram,which=None):
+
+    if which == 'both':
+        diffractogram['2th'] = diffractogram['2th_org']
+        diffractogram['I'] = diffractogram['I_org']
+        
+    if which == 'y':
+        diffractogram['I'] = diffractogram['I_org']
+    
+    if which == 'x':
+        diffractogram['2th'] = diffractogram['2th_org']
+
+    return diffractogram
 
 def load_reflection_table(data, options={}):
 

beamtime/xrd/plot.py

@@ -19,7 +19,7 @@ def plot_diffractogram(data, options={}):
     data (dict): Must include path = string to diffractogram data, and plot_kind = (recx, beamline, image)'''
 
     # Update options
-    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise',
+    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y',
     'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
 
     default_options = {
@@ -29,6 +29,9 @@ def plot_diffractogram(data, options={}):
         'xunit': 'deg', 'yunit': 'a.u.',
         'xlim': None, 'ylim': None, 
         'normalise': True,
+        'offset': True,
+        'offset_x': 0,
+        'offset_y': 1,
         'line': True, # whether or not to plot diffractogram as a line plot
         'scatter': False, # whether or not to plot individual data points
         'reflections_plot': False, # whether to plot reflections as a plot
@@ -49,6 +52,8 @@ def plot_diffractogram(data, options={}):
         data['path'] = [data['path']]
 
    
+
+    # Check if there is some data stored already, load in data if not. This speeds up replotting in interactive mode.
     if not 'diffractogram' in data.keys():
         # Initialise empty list for diffractograms and wavelengths
         data['diffractogram'] = [None for _ in range(len(data['path']))]
@@ -72,7 +77,7 @@ def plot_diffractogram(data, options={}):
         options['xlim'] = [diffractogram[options['x_vals']].min(), diffractogram[options['x_vals']].max()]
 
 
-    # Start inteactive session with ipywidgets
+    # Start inteactive session with ipywidgets. Disables options['interactive'] in order for the interactive loop to not start another interactive session
     if options['interactive']:
         options['interactive'] = False
         options['interactive_session_active'] = True
@@ -91,7 +96,6 @@ def plot_diffractogram(data, options={}):
 
 
     # Prepare plot, and read and process data
-
     fig, ax = btp.prepare_plot(options=options)
 
 
@@ -125,7 +129,7 @@ def plot_diffractogram(data, options={}):
 
     
 
-    # Make the reflection plots
+    # Make the reflection plots. By default, the wavelength of the first diffractogram will be used for these.
     if options['reflections_plot'] and options['reflections_data']:
         options['xlim'] = ax.get_xlim()
         options['to_wavelength'] = data['wavelength'][0]
@@ -133,7 +137,7 @@ def plot_diffractogram(data, options={}):
         for reference, axis in zip(options['reflections_data'], ref_axes):
             plot_reflection_table(data=reference, ax=axis, options=options)
 
-    # Print the reflection indices
+    # Print the reflection indices. By default, the wavelength of the first diffractogram will be used for this.
     if options['reflections_indices'] and options['reflections_data']:
         options['xlim'] = ax.get_xlim()
         options['to_wavelength'] = data['wavelength'][0]