Merge pull request #1 from rasmusvt/rasmus_multidiff

Integrating multiple diffractograms into master branch

beamtime/feature_list.txt

@@ -0,0 +1,2 @@
+- Must allow for automatic normalisation between different diffractograms, must only happen upon reading data
+- 

beamtime/plotting.py

@@ -313,6 +313,17 @@ def update_widgets(options):
 
         if widget['state'] != options['x_vals']:
             for arg in widget[f'{options["x_vals"]}_default']:
+                
+                # If new min value is larger than previous max, or new max value is smaller than previous min, set the opposite first
+                if arg == 'min':
+                    if widget[f'{options["x_vals"]}_default']['min'] > getattr(widget['w'], 'max'):
+                        setattr(widget['w'], 'max', widget[f'{options["x_vals"]}_default']['max'])
+                
+                elif arg == 'max':
+                    if widget[f'{options["x_vals"]}_default']['max'] < getattr(widget['w'], 'min'):
+                        setattr(widget['w'], 'min', widget[f'{options["x_vals"]}_default']['min'])
+
+            
                 setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
             
             widget['state'] = options['x_vals']
@@ -366,16 +377,20 @@ def update_rc_params(rc_params):
             plt.rcParams.update({key: rc_params[key]})
 
 
-def generate_colours(palettes):
+def generate_colours(palettes, kind=None):
 
-    # Creates a list of all the colours that is passed in the colour_cycles argument. Then makes cyclic iterables of these. 
+    if kind == 'single':
-    colour_collection = []
+        colour_cycle = itertools.cycle(palettes)
-    for palette in palettes:
-        mod = importlib.import_module("palettable.colorbrewer.%s" % palette[0])
-        colour = getattr(mod, palette[1]).mpl_colors
-        colour_collection = colour_collection + colour
 
-    colour_cycle = itertools.cycle(colour_collection)
+    else:
+        # Creates a list of all the colours that is passed in the colour_cycles argument. Then makes cyclic iterables of these. 
+        colour_collection = []
+        for palette in palettes:
+            mod = importlib.import_module("palettable.colorbrewer.%s" % palette[0])
+            colour = getattr(mod, palette[1]).mpl_colors
+            colour_collection = colour_collection + colour
+
+        colour_cycle = itertools.cycle(colour_collection)
 
 
     return colour_cycle

beamtime/xrd/io.py

@@ -27,7 +27,7 @@ def get_image_headers(path):
     return image.header
 
 
-def integrate_1d(data, options={}):
+def integrate_1d(data, options={}, index=0):
     ''' Integrates an image file to a 1D diffractogram. 
 
     Required content of data:
@@ -40,10 +40,12 @@ def integrate_1d(data, options={}):
     df: DataFrame contianing 1D diffractogram if option 'return' is True
     ''' 
 
-    required_options = ['unit', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite']
+    required_options = ['unit', 'nbins', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite']
 
     default_options = {
         'unit': '2th_deg', 
+        'nbins': 3000,
+        'extract_folder': 'tmp',
         'save': False,
         'save_filename': None,
         'save_extension': '_integrated.xy',
@@ -51,51 +53,57 @@ def integrate_1d(data, options={}):
         'overwrite': False}
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    if not isinstance(data['path'], list):
+        data['path'] = [data['path']]
     
 
     # Get image array from filename if not passed
     if 'image' not in data.keys():
-        data['image'] = get_image_array(data['path'])
+        data['image'] = get_image_array(data['path'][index])
     
     # Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file)
     ai = pyFAI.load(data['calibrant'])
 
     # Determine filename
-    filename = make_filename(data=data, options=options)
+    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'], data['nbins'], unit=options['unit'], filename=filename)
+    res = ai.integrate1d(data['image'], options['nbins'], unit=options['unit'], filename=filename)
 
-    data['path'] = filename
+    data['path'][index] = filename
-    diffractogram = read_xy(data=data, options=options)
+    diffractogram, wavelength = read_xy(data=data, options=options, index=index)
 
     if not options['save']:
         os.remove(filename)
-        shutil.rmtree('tmp')
+        shutil.rmtree(f'tmp')
+
+
+    # Reset this option
+    options['save_folder'] = None
     
-    return diffractogram
+    return diffractogram, wavelength
     
 
 
-def make_filename(data, options):
+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']:
 
         # Case 1: No filename is given. 
         if not options['save_filename']:
             # If a path is given instead of an image array, the path is taken as the trunk of the savename
-            if data['path']:
+            if path:
                 # Make filename by joining the save_folder, the filename (with extension deleted) and adding the save_extension
-                filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['save_extension'])
+                filename = os.path.join(options['save_folder'], os.path.split(path)[-1].split('.')[0] + options['save_extension'])
             else:
                 # Make filename just "integrated.dat" in the save_folder
                 filename = os.path.join(options['save_folder'], 'integrated.xy')
@@ -176,7 +184,10 @@ def view_integrator(calibrant):
 
 
 
-def read_brml(data, options={}):
+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']
@@ -194,7 +205,7 @@ def read_brml(data, options={}):
 
 
     # Extract the RawData0.xml file from the brml-file
-    with zipfile.ZipFile(data['path'], 'r') as brml:
+    with zipfile.ZipFile(data['path'][index], 'r') as brml:
         for info in brml.infolist():
             if "RawData" in info.filename:
                 brml.extract(info.filename, options['extract_folder'])
@@ -213,31 +224,66 @@ def read_brml(data, options={}):
 
     for chain in root.findall('./DataRoutes/DataRoute'):
 
-        for scantype in chain.findall('ScanInformation/ScanMode'):
-            if scantype.text == 'StillScan':
 
-                if chain.get('Description') == 'Originally measured data.':
+        # Get the scan type to be able to handle different data formats
-                    for scandata in chain.findall('Datum'):
+        scantype = chain.findall('ScanInformation')[0].get('VisibleName')
+
+        # Check if the chain is the right one to extract the data from
+        if chain.get('Description') == 'Originally measured data.':
+            
+            
+            if scantype == 'TwoTheta':
+                for scandata in chain.findall('Datum'):
+                    scandata = scandata.text.split(',')
+                    twotheta, intensity = float(scandata[2]), float(scandata[3])
+                    
+                    if twotheta > 0:
+                        diffractogram.append({'2th': twotheta, 'I': intensity})
+
+            elif scantype == 'Coupled TwoTheta/Theta':
+                for scandata in chain.findall('Datum'):
+                    scandata = scandata.text.split(',')
+                    twotheta, intensity = float(scandata[2]), float(scandata[4])
+                    
+                    if twotheta > 0:
+                        diffractogram.append({'2th': twotheta, 'I': intensity})
+
+            elif scantype == 'Still (Eiger2R_500K (1D mode))':
+
+                start = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Start')[0].text)
+                stop = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Stop')[0].text)
+                
+
+
+
+                for scandata in chain.findall('Datum'):
                         scandata = scandata.text.split(',')
-                        scandata = [float(i) for i in scandata]
+                        raw = [float(i) for i in scandata]
-                        twotheta, intensity = float(scandata[2]), float(scandata[3])
 
-        
+                        intensity = []
-            else:
+                        for r in raw:
-                if chain.get('Description') == 'Originally measured data.':
+                            if r > 601:
-                    for scandata in chain.findall('Datum'):
+                                intensity.append(r)
-                        scandata = scandata.text.split(',')
+
-                        twotheta, intensity = float(scandata[2]), float(scandata[3])
+                        intensity = np.array(intensity)
-                        
+
-                        if twotheta > 0:
+            
-                            diffractogram.append({'2th': twotheta, 'I': intensity})
+             
+
+                twotheta = np.linspace(start, stop, len(intensity))
+
+                diffractogram = {'2th': twotheta, 'I': intensity}
 
 
-    if 'wavelength' not in data.keys():
+
-        for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
+    #if 'wavelength' not in data.keys():
-            data['wavelength'] = float(chain.attrib['Value'])
+    # Find wavelength
+    for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
+        wavelength = float(chain.attrib['Value'])
+
 
     diffractogram = pd.DataFrame(diffractogram)
+    
 
 
 
@@ -249,15 +295,16 @@ def read_brml(data, options={}):
 
 
 
-    return diffractogram
+    return diffractogram, wavelength
     
 
-def read_xy(data, options={}):
+def read_xy(data, options={}, index=0):
     
-    if 'wavelength' not in data.keys():
+    #if 'wavelength' not in data.keys():
-            find_wavelength_from_xy(data=data)
+    # Get wavelength from scan
+    wavelength = find_wavelength_from_xy(path=data['path'][index])
 
-    with open(data['path'], 'r') as f:
+    with open(data['path'][index], 'r') as f:
         position = 0
 
         current_line = f.readline()
@@ -276,37 +323,70 @@ def read_xy(data, options={}):
         diffractogram.columns = ['2th', 'I', 'sigma']
 
 
-    return diffractogram
+    return diffractogram, wavelength
 
 
-def read_data(data, options={}):
+def read_data(data, options={}, index=0):
 
     beamline_extensions = ['mar3450', 'edf', 'cbf']
-    file_extension = data['path'].split('.')[-1]
+    file_extension = data['path'][index].split('.')[-1]
 
     if file_extension in beamline_extensions:
-        diffractogram = integrate_1d(data=data, options=options)
+        diffractogram, wavelength = integrate_1d(data=data, options=options, index=index)
         
     elif file_extension == 'brml':
-        diffractogram = read_brml(data=data, options=options)
+        diffractogram, wavelength = read_brml(data=data, options=options, index=index)
 
     elif file_extension in['xy', 'xye']:
-        diffractogram = read_xy(data=data, options=options)
+        diffractogram, wavelength = read_xy(data=data, options=options, index=index)
 
 
-    diffractogram = translate_wavelengths(data=diffractogram, wavelength=data['wavelength'])
+    if options['normalise']:
+        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={}):
 
-    required_options = ['wavelength', 'to_wavelength']
+    required_options = ['ref_wavelength', 'to_wavelength']
 
     default_options = {
-        'wavelength': 1.54059,
+        'ref_wavelength': 1.54059,
         'to_wavelength': None
     }
 
@@ -333,7 +413,7 @@ def load_reflection_table(data, options={}):
     # Set the new modified headers as the headers of 
     reflections.columns = headers
 
-    reflections = translate_wavelengths(data=reflections, wavelength=options['wavelength'], to_wavelength=options['to_wavelength'])
+    reflections = translate_wavelengths(data=reflections, wavelength=options['ref_wavelength'], to_wavelength=options['to_wavelength'])
 
     #print(reflections)
 
@@ -342,6 +422,8 @@ def load_reflection_table(data, options={}):
 
 
 def translate_wavelengths(data, wavelength, to_wavelength=None):
+    # FIXME Somewhere here there is an invalid arcsin-argument. Not sure where.
+
     pd.options.mode.chained_assignment = None
 
     # Translate to CuKalpha
@@ -378,8 +460,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 
     if to_wavelength:
-        
+        if to_wavelength >= cuka:
-        if to_wavelength > cuka:
             max_2th = 2*np.arcsin(cuka/to_wavelength) * 180/np.pi
         else:
             max_2th = data['2th_cuka'].max()
@@ -395,19 +476,24 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 
 
-def find_wavelength_from_xy(data):
+def find_wavelength_from_xy(path):
+
 
- 
     wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
 
-    with open(data['path'], 'r') as f:
+    with open(path, 'r') as f:
         lines = f.readlines()
 
         for line in lines:
+            # For .xy-files output from EVA
             if 'Anode' in line:
                 anode = line.split()[8].strip('"')
-                data['wavelength'] = wavelength_dict[anode]
+                wavelength = wavelength_dict[anode]
 
+            # For .xy-files output from pyFAI integration
             elif 'Wavelength' in line:
-                data['wavelength'] = float(line.split()[2])*10**10
+                wavelength = float(line.split()[2])*10**10
 
+
+
+    return wavelength

beamtime/xrd/plot.py

@@ -19,8 +19,8 @@ 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',
+    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']
+    'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
 
     default_options = {
         'x_vals': '2th', 
@@ -28,6 +28,10 @@ def plot_diffractogram(data, options={}):
         'ylabel': 'Intensity', 'xlabel': '2theta', 
         '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
@@ -41,21 +45,43 @@ def plot_diffractogram(data, options={}):
         'format_params': {},
         }
 
+    if 'offset_y' not in options.keys():
+        if len(data['path']) > 10:
+            default_options['offset_y'] = 0.05
+
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
+    # Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
+    if not isinstance(data['path'], list):
+        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():
-        diffractogram = xrd.io.read_data(data=data, options=options)
+        # Initialise empty list for diffractograms and wavelengths
-        data['diffractogram'] = diffractogram
+        data['diffractogram'] = [None for _ in range(len(data['path']))]
+        data['wavelength'] = [None for _ in range(len(data['path']))]
+
+        for index in range(len(data['path'])):
+            diffractogram, wavelength = xrd.io.read_data(data=data, options=options, index=index)
+            
+            data['diffractogram'][index] = diffractogram
+            data['wavelength'][index] = wavelength
+
+            
 
     else:
-        diffractogram = data['diffractogram']
+        if not isinstance(data['diffractogram'], list):
+            data['diffractogram'] = [data['diffractogram']]
+            data['wavelength'] = [data['wavelength']]
 
     # Sets the xlim if this has not bee specified
     if not options['xlim']:
         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
@@ -74,7 +100,6 @@ def plot_diffractogram(data, options={}):
 
 
     # Prepare plot, and read and process data
-
     fig, ax = btp.prepare_plot(options=options)
 
 
@@ -92,14 +117,18 @@ def plot_diffractogram(data, options={}):
 
         ax = ax[-1]
 
-    colours = btp.generate_colours(options['palettes'])
+    if len(data['path']) < 10:
+        colours = btp.generate_colours(options['palettes'])
+    else:
+        colours = btp.generate_colours(['black'], kind='single')
 
 
-    if options['line']:
+    for diffractogram in data['diffractogram']:
-        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
+        if options['line']:
+            diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
     
-    if options['scatter']:
+        if options['scatter']:
-        ax.scatter(x=diffractogram[options['x_vals']], y = diffractogram[options['y_vals']], c=[(1,1,1,0)], edgecolors=[next(colours)], linewidths=plt.rcParams['lines.markeredgewidth'], zorder=2) #, edgecolors=np.array([next(colours)]))
+            ax.scatter(x=diffractogram[options['x_vals']], y = diffractogram[options['y_vals']], c=[(1,1,1,0)], edgecolors=[next(colours)], linewidths=plt.rcParams['lines.markeredgewidth'], zorder=2) #, edgecolors=np.array([next(colours)]))
 
 
 
@@ -107,18 +136,18 @@ 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']
+        options['to_wavelength'] = data['wavelength'][0]
         
         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']
+        options['to_wavelength'] = data['wavelength'][0]
 
         for reference in options['reflections_data']:
             plot_reflection_indices(data=reference, ax=indices_ax, options=options)
@@ -127,6 +156,8 @@ def plot_diffractogram(data, options={}):
     if options['interactive_session_active']:
         btp.update_widgets(options=options)
 
+        xrd.io.up
+
 
     return diffractogram, fig, ax
 
@@ -149,18 +180,40 @@ def determine_grid_layout(options):
 
 def plot_diffractogram_interactive(data, options):
 
+
+    minmax = {'2th': [None, None], '2th_cuka': [None, None], '2th_moka': [None, None], 'd': [None, None], '1/d': [None, None], 'q': [None, None], 'q2': [None, None], 'q4': [None, None]}
+    
+    update_minmax(minmax, data)
+
+    ymin, ymax = None, None
+    for index, diffractogram in enumerate(data['diffractogram']):
+        if not ymin or (ymin > (diffractogram['I'].min())): #+index*options['offset_y'])):
+            ymin = diffractogram['I'].min()#+index*options['offset_y']
+
+        if not ymax or (ymax < (diffractogram['I'].max())):#+index*options['offset_y'])):
+            ymax = diffractogram['I'].max()#+index*options['offset_y']
+
+
+    ymin_start = ymin - 0.1*ymax
+    ymax_start = ymax+0.2*ymax
+    ymin = ymin - 5*ymax
+    ymax = ymax*5
+
+        
+
+
     options['widgets'] = {
         'xlim': {
-            'w': widgets.FloatRangeSlider(value=[data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], min=data['diffractogram']['2th'].min(), max=data['diffractogram']['2th'].max(), step=0.5, layout=widgets.Layout(width='95%')),
+            'w': widgets.FloatRangeSlider(value=[minmax['2th'][0], minmax['2th'][1]], min=minmax['2th'][0], max=minmax['2th'][1], step=0.5, layout=widgets.Layout(width='95%')),
-            '2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
+            'state': '2th',
-            '2th_cuka_default': {'min': data['diffractogram']['2th_cuka'].min(), 'max': data['diffractogram']['2th_cuka'].max(), 'value': [data['diffractogram']['2th_cuka'].min(), data['diffractogram']['2th_cuka'].max()], 'step': 0.5},
+            '2th_default':      {'min': minmax['2th'][0],       'max': minmax['2th'][1],        'value': [minmax['2th'][0],         minmax['2th'][1]],      'step': 0.5},
-            '2th_moka_default': {'min': data['diffractogram']['2th_moka'].min(), 'max': data['diffractogram']['2th_moka'].max(), 'value': [data['diffractogram']['2th_moka'].min(), data['diffractogram']['2th_moka'].max()], 'step': 0.5},
+            '2th_cuka_default': {'min': minmax['2th_cuka'][0],  'max': minmax['2th_cuka'][1],   'value': [minmax['2th_cuka'][0],    minmax['2th_cuka'][1]], 'step': 0.5},
-            'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], 'step': 0.5},
+            '2th_moka_default': {'min': minmax['2th_moka'][0],  'max': minmax['2th_moka'][1],   'value': [minmax['2th_moka'][0],    minmax['2th_moka'][1]], 'step': 0.5},
-            '1/d_default': {'min': data['diffractogram']['1/d'].min(), 'max': data['diffractogram']['1/d'].max(), 'value': [data['diffractogram']['1/d'].min(), data['diffractogram']['1/d'].max()], 'step': 0.5},
+            'd_default':        {'min': minmax['d'][0],         'max': minmax['d'][1],          'value': [minmax['d'][0],           minmax['d'][1]],        'step': 0.5},
-            'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], 'step': 0.5},
+            '1/d_default':      {'min': minmax['1/d'][0],       'max': minmax['1/d'][1],        'value': [minmax['1/d'][0],         minmax['1/d'][1]],      'step': 0.5},
-            'q2_default': {'min': data['diffractogram']['q2'].min(), 'max': data['diffractogram']['q2'].max(), 'value': [data['diffractogram']['q2'].min(), data['diffractogram']['q2'].max()], 'step': 0.5},
+            'q_default':        {'min': minmax['q'][0],         'max': minmax['q'][1],          'value': [minmax['q'][0],           minmax['q'][1]],        'step': 0.5},
-            'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
+            'q2_default':       {'min': minmax['q2'][0],        'max': minmax['q2'][1],         'value': [minmax['q2'][0],          minmax['q2'][1]],       'step': 0.5},
-            'state': '2th'
+            'q4_default':       {'min': minmax['q4'][0],        'max': minmax['q4'][1],         'value': [minmax['q4'][0],          minmax['q4'][1]],       'step': 0.5}
         }
     }
 
@@ -172,7 +225,10 @@ def plot_diffractogram_interactive(data, options):
         reflections_plot=widgets.ToggleButton(value=True),
         reflections_indices=widgets.ToggleButton(value=False),
         x_vals=widgets.Dropdown(options=['2th', 'd', '1/d', 'q', 'q2', 'q4', '2th_cuka', '2th_moka'], value='2th', description='X-values'),
-        xlim=options['widgets']['xlim']['w'])
+        xlim=options['widgets']['xlim']['w'],
+        ylim=widgets.FloatRangeSlider(value=[ymin_start, ymax_start], min=ymin, max=ymax, step=0.5, layout=widgets.Layout(width='95%')),
+        offset_y=widgets.FloatSlider(value=options['offset_y'], min=-5, max=5)
+        )
     
     else:
         w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(data), options=widgets.fixed(options), 
@@ -184,6 +240,29 @@ def plot_diffractogram_interactive(data, options):
     display(w)
 
 
+def update_minmax(minmax, data):
+    ''' Finds minimum and maximum values of each column and updates the minmax dictionary to contain the correct values.
+    
+    Input:
+    minmax (dict): contains '''
+
+    for index, diffractogram in enumerate(data['diffractogram']):
+        if not minmax['2th'][0] or diffractogram['2th'].min() < minmax['2th'][0]:
+            minmax['2th'][0] = diffractogram['2th'].min()
+            min_index = index
+
+        if not minmax['2th'][1] or diffractogram['2th'].max() > minmax['2th'][1]:
+            minmax['2th'][1] = diffractogram['2th'].max()
+            max_index = index
+
+    minmax['2th_cuka'][0], minmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(),  data['diffractogram'][max_index]['2th_cuka'].max()
+    minmax['2th_moka'][0], minmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(),  data['diffractogram'][max_index]['2th_moka'].max() 
+    minmax['d'][0], minmax['d'][1]               = data['diffractogram'][max_index]['d'].min(),         data['diffractogram'][min_index]['d'].max() # swapped, intended
+    minmax['1/d'][0], minmax['1/d'][1]           = data['diffractogram'][min_index]['1/d'].min(),       data['diffractogram'][max_index]['1/d'].max() 
+    minmax['q'][0], minmax['q'][1]               = data['diffractogram'][min_index]['q'].min(),         data['diffractogram'][max_index]['q'].max()
+    minmax['q2'][0], minmax['q2'][1]             = data['diffractogram'][min_index]['q2'].min(),        data['diffractogram'][max_index]['q2'].max() 
+    minmax['q4'][0], minmax['q4'][1]             = data['diffractogram'][min_index]['q4'].min(),        data['diffractogram'][max_index]['q4'].max() 
+
 def update_widgets(options):
 
     for widget in options['widgets'].values():