From da2b2f855b2002358b94e6533fdf19f5d2dad6dc Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 22 Mar 2022 19:57:21 +0100
Subject: [PATCH 01/12] Change plotting method to allow for multiple
 diffractograms

---
 beamtime/plotting.py | 11 ++++++
 beamtime/xrd/io.py   | 77 ++++++++++++++++++++++-----------------
 beamtime/xrd/plot.py | 87 +++++++++++++++++++++++++++++++++++---------
 3 files changed, 124 insertions(+), 51 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index 3430a2a..dd9a481 100644
--- a/beamtime/plotting.py
+++ b/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']
diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 6b0bb7a..3e29b80 100644
--- a/beamtime/xrd/io.py
+++ b/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:
@@ -51,11 +51,14 @@ 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'])
@@ -70,18 +73,18 @@ def integrate_1d(data, options={}):
 
     res = ai.integrate1d(data['image'], data['nbins'], unit=options['unit'], filename=filename)
 
-    data['path'] = filename
-    diffractogram = read_xy(data=data, options=options)
+    data['path'][index] = filename
+    diffractogram, wavelength = read_xy(data=data, options=options)
 
     if not options['save']:
         os.remove(filename)
         shutil.rmtree('tmp')
     
-    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']:
@@ -93,7 +96,7 @@ def make_filename(data, options):
         # 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'])
             else:
@@ -176,12 +179,12 @@ def view_integrator(calibrant):
 
 
 
-def read_brml(data, options={}):
+def read_brml(data, options={}, index=0):
 
 
     required_options = ['extract_folder', 'save_folder']
     default_options = {
-        'extract_folder': 'tmp',
+        'extract_folder': 'tmp/',
         'save_folder': None
     }
 
@@ -194,7 +197,7 @@ 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'])
@@ -233,9 +236,10 @@ def read_brml(data, options={}):
                             diffractogram.append({'2th': twotheta, 'I': intensity})
 
 
-    if 'wavelength' not in data.keys():
-        for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
-            data['wavelength'] = float(chain.attrib['Value'])
+    #if 'wavelength' not in data.keys():
+    # 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 +253,16 @@ 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():
-            find_wavelength_from_xy(data=data)
+    #if 'wavelength' not in data.keys():
+    # 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 +281,37 @@ 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'])
+    diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
 
-    return diffractogram
+    return diffractogram, wavelength
                 
 
 
 
 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 +338,7 @@ 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)
 
@@ -378,6 +383,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 
     if to_wavelength:
+
         
         if to_wavelength > cuka:
             max_2th = 2*np.arcsin(cuka/to_wavelength) * 180/np.pi
@@ -395,19 +401,24 @@ 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
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index daa7eaf..cec2d1e 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -43,12 +43,25 @@ def plot_diffractogram(data, options={}):
 
     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']]
+
+   
     if not 'diffractogram' in data.keys():
-        diffractogram = xrd.io.read_data(data=data, options=options)
-        data['diffractogram'] = diffractogram
+        # Initialise empty list for diffractograms and wavelengths
+        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']:
@@ -95,11 +108,12 @@ def plot_diffractogram(data, options={}):
     colours = btp.generate_colours(options['palettes'])
 
 
-    if options['line']:
-        diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
+    for diffractogram in data['diffractogram']:
+        if options['line']:
+            diffractogram.plot(x=options['x_vals'], y=options['y_vals'], ax=ax, c=next(colours), zorder=1)
     
-    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)]))
+        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)]))
 
 
 
@@ -110,7 +124,7 @@ def plot_diffractogram(data, options={}):
     # Make the reflection plots
     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)
@@ -118,7 +132,7 @@ def plot_diffractogram(data, options={}):
     # Print the reflection indices
     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)
@@ -149,17 +163,54 @@ 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]}
+    
+    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() 
+    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() 
+
+
+
+    # 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%')),
+    #         '2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
+    #         '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_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},
+    #         'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], '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},
+    #         'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], '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},
+    #         'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
+    #         'state': '2th'
+    #     }
+    # }
+
     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%')),
-            '2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
-            '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_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},
-            'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], '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},
-            'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], '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},
-            'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
+            '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': minmax['2th'][0],       'max': minmax['2th'][1],        'value': [minmax['2th'][0],         minmax['2th'][1]],      '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},
+            '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},
+            'd_default':        {'min': minmax['d'][0],         'max': minmax['d'][1],          'value': [minmax['d'][0],           minmax['d'][1]],        '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},
+            'q_default':        {'min': minmax['q'][0],         'max': minmax['q'][1],          'value': [minmax['q'][0],           minmax['q'][1]],        'step': 0.5},
+            'q2_default':       {'min': minmax['q2'][0],        'max': minmax['q2'][1],         'value': [minmax['q2'][0],          minmax['q2'][1]],       'step': 0.5},
+            'q4_default':       {'min': minmax['q4'][0],        'max': minmax['q4'][1],         'value': [minmax['q4'][0],          minmax['q4'][1]],       'step': 0.5},
             'state': '2th'
         }
     }

From f26153757a9527449d6e082d72bcd25141328af4 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 22 Mar 2022 20:03:23 +0100
Subject: [PATCH 02/12] testing this branching stuff

---
 beamtime/test.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 beamtime/test.txt

diff --git a/beamtime/test.txt b/beamtime/test.txt
new file mode 100644
index 0000000..30a1328
--- /dev/null
+++ b/beamtime/test.txt
@@ -0,0 +1 @@
+something something test

From b2ee68859a93b41a3d0b85f1bc203896ccadaeb2 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 22 Mar 2022 20:08:11 +0100
Subject: [PATCH 03/12] removing test-file

---
 beamtime/test.txt | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 beamtime/test.txt

diff --git a/beamtime/test.txt b/beamtime/test.txt
deleted file mode 100644
index 30a1328..0000000
--- a/beamtime/test.txt
+++ /dev/null
@@ -1 +0,0 @@
-something something test

From 86a2ae2379dfcc71e5761a215b4ba2179a7b96e6 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 22 Mar 2022 20:25:53 +0100
Subject: [PATCH 04/12] Fix bug to iterate correctly through filenames

---
 beamtime/xrd/io.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 3e29b80..16991a2 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -40,10 +40,11 @@ def integrate_1d(data, options={}, index=0):
     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,
         'save': False,
         'save_filename': None,
         'save_extension': '_integrated.xy',
@@ -64,17 +65,17 @@ def integrate_1d(data, options={}, index=0):
     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']):
         os.makedirs(options['save_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'][index] = filename
-    diffractogram, wavelength = read_xy(data=data, options=options)
+    diffractogram, wavelength = read_xy(data=data, options=options, index=index)
 
     if not options['save']:
         os.remove(filename)
@@ -98,7 +99,7 @@ def make_filename(options, path=None):
             # If a path is given instead of an image array, the path is taken as the trunk of the savename
             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')
@@ -403,6 +404,8 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 def find_wavelength_from_xy(path):
 
+    print(path)
+
  
     wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
 

From d31adb9585e95400191d79ca0b2fa5ef441fe969 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 22 Mar 2022 20:26:38 +0100
Subject: [PATCH 05/12] Add feature list

---
 beamtime/feature_list.txt | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 beamtime/feature_list.txt

diff --git a/beamtime/feature_list.txt b/beamtime/feature_list.txt
new file mode 100644
index 0000000..f4a0efd
--- /dev/null
+++ b/beamtime/feature_list.txt
@@ -0,0 +1,2 @@
+- Must allow for automatic normalisation between different diffractograms, must only happen upon reading data
+- 

From 06753ab6b2d0f685e21929f63dbb762b2008690a Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 23 Mar 2022 14:20:19 +0100
Subject: [PATCH 06/12] Move minmax-determiniation to own function

---
 beamtime/xrd/plot.py | 61 +++++++++++++++++++-------------------------
 1 file changed, 26 insertions(+), 35 deletions(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index cec2d1e..173da03 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -166,43 +166,12 @@ 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]}
     
-    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() 
-    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() 
-
-
-
-    # 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%')),
-    #         '2th_default': {'min': data['diffractogram']['2th'].min(), 'max': data['diffractogram']['2th'].max(), 'value': [data['diffractogram']['2th'].min(), data['diffractogram']['2th'].max()], 'step': 0.5},
-    #         '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_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},
-    #         'd_default': {'min': data['diffractogram']['d'].min(), 'max': data['diffractogram']['d'].max(), 'value': [data['diffractogram']['d'].min(), data['diffractogram']['d'].max()], '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},
-    #         'q_default': {'min': data['diffractogram']['q'].min(), 'max': data['diffractogram']['q'].max(), 'value': [data['diffractogram']['q'].min(), data['diffractogram']['q'].max()], '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},
-    #         'q4_default': {'min': data['diffractogram']['q4'].min(), 'max': data['diffractogram']['q4'].max(), 'value': [data['diffractogram']['q4'].min(), data['diffractogram']['q4'].max()], 'step': 0.5},
-    #         'state': '2th'
-    #     }
-    # }
+    update_minmax(minmax, data)
 
     options['widgets'] = {
         'xlim': {
             '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%')),
+            'state': '2th',
             '2th_default':      {'min': minmax['2th'][0],       'max': minmax['2th'][1],        'value': [minmax['2th'][0],         minmax['2th'][1]],      '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},
             '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},
@@ -210,8 +179,7 @@ def plot_diffractogram_interactive(data, options):
             '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},
             'q_default':        {'min': minmax['q'][0],         'max': minmax['q'][1],          'value': [minmax['q'][0],           minmax['q'][1]],        'step': 0.5},
             'q2_default':       {'min': minmax['q2'][0],        'max': minmax['q2'][1],         'value': [minmax['q2'][0],          minmax['q2'][1]],       'step': 0.5},
-            'q4_default':       {'min': minmax['q4'][0],        'max': minmax['q4'][1],         'value': [minmax['q4'][0],          minmax['q4'][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}
         }
     }
 
@@ -235,6 +203,29 @@ 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():

From 0fb8883d198ac6d57ac9a6dde3f2a6ed32084731 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 23 Mar 2022 14:26:43 +0100
Subject: [PATCH 07/12] Add normalisation of diffractograms (default: True=

---
 beamtime/xrd/io.py   | 4 ++++
 beamtime/xrd/plot.py | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 16991a2..fc05654 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -300,6 +300,10 @@ def read_data(data, options={}, index=0):
         diffractogram, wavelength = read_xy(data=data, options=options, index=index)
 
 
+    if options['normalise']:
+        diffractogram['I'] = diffractogram['I'] / diffractogram['I'].max()
+
+
     diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
 
     return diffractogram, wavelength
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 173da03..d196f2c 100644
--- a/beamtime/xrd/plot.py
+++ b/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',
+    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise',
     'reflections_plot', 'reflections_indices', 'reflections_data', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params']
 
     default_options = {
@@ -28,6 +28,7 @@ def plot_diffractogram(data, options={}):
         'ylabel': 'Intensity', 'xlabel': '2theta', 
         'xunit': 'deg', 'yunit': 'a.u.',
         'xlim': None, 'ylim': None, 
+        'normalise': True,
         '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
@@ -55,9 +56,12 @@ def plot_diffractogram(data, options={}):
 
         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:
         if not isinstance(data['diffractogram'], list):
             data['diffractogram'] = [data['diffractogram']]

From 2424d89156adc085a4fb5c2a82ee632469ccbedf Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 23 Mar 2022 15:31:47 +0100
Subject: [PATCH 08/12] Add offset of x- and y-values for stacked
 diffractograms

---
 beamtime/xrd/io.py   | 50 +++++++++++++++++++++++++++++++++++++-------
 beamtime/xrd/plot.py | 14 ++++++++-----
 2 files changed, 52 insertions(+), 12 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index fc05654..263eaae 100644
--- a/beamtime/xrd/io.py
+++ b/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']):
-        os.makedirs(options['save_folder'])
+    if not os.path.isdir(options['extract_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['save_folder'], 'tmp_diff.dat')
+            filename = os.path.join(options['extract_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={}):
 
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index d196f2c..17ad70b 100644
--- a/beamtime/xrd/plot.py
+++ b/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]

From 606bfc180d13e5a5df3436b3dc08c5368ac6b286 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 23 Mar 2022 16:03:34 +0100
Subject: [PATCH 09/12] Add first stab at ylim widget, should be improved

---
 beamtime/xrd/io.py   |  6 +++---
 beamtime/xrd/plot.py | 21 ++++++++++++++++++++-
 2 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 263eaae..612cc16 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -388,6 +388,8 @@ 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
@@ -424,9 +426,7 @@ 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()
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 17ad70b..770b5a8 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -176,6 +176,24 @@ def plot_diffractogram_interactive(data, options):
     
     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']
+            print(ymax)
+
+
+    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=[minmax['2th'][0], minmax['2th'][1]], min=minmax['2th'][0], max=minmax['2th'][1], step=0.5, layout=widgets.Layout(width='95%')),
@@ -199,7 +217,8 @@ 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%')))
     
     else:
         w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(data), options=widgets.fixed(options), 

From 0fbfd20a74cebea5d14daaf207ff7ba51edae2b0 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 30 Mar 2022 16:11:34 +0200
Subject: [PATCH 10/12] Enable reading of CoupledTwoTheta-scans

---
 beamtime/xrd/io.py | 64 +++++++++++++++++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 15 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 612cc16..5aa2fb1 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -224,24 +224,56 @@ def read_brml(data, options={}, index=0):
 
     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.':
-                    for scandata in chain.findall('Datum'):
-                        scandata = scandata.text.split(',')
-                        scandata = [float(i) for i in scandata]
-                        twotheta, intensity = float(scandata[2]), float(scandata[3])
+        # Get the scan type to be able to handle different data formats
+        scantype = chain.findall('ScanInformation')[0].get('VisibleName')
 
-        
-            else:
-                if chain.get('Description') == 'Originally measured data.':
-                    for scandata in chain.findall('Datum'):
+        # 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)
+                increment = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Increment')[0].text)
+
+
+
+                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})
+                        raw = [float(i) for i in scandata]
+
+                        intensity = []
+                        for r in raw:
+                            if r > 600:
+                                intensity.append(r)
+
+                        intensity = np.array(intensity)
+
+            
+             
+
+                twotheta = np.linspace(start, stop, len(intensity))
+
+                diffractogram = {'2th': twotheta, 'I': intensity}
+
 
 
     #if 'wavelength' not in data.keys():
@@ -249,7 +281,9 @@ def read_brml(data, options={}, index=0):
     for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
         wavelength = float(chain.attrib['Value'])
 
+
     diffractogram = pd.DataFrame(diffractogram)
+    
 
 
 

From 223be18c3e451b8be2a962bba126f44c9eab41db Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 30 Mar 2022 17:40:06 +0200
Subject: [PATCH 11/12] Change default behaviour with 10+ plots

---
 beamtime/plotting.py | 20 ++++++++++++--------
 beamtime/xrd/io.py   |  6 ++----
 beamtime/xrd/plot.py | 13 ++++++++++---
 3 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index dd9a481..4e058ac 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -377,16 +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. 
-    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
+    if kind == 'single':
+        colour_cycle = itertools.cycle(palettes)
 
-    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
\ No newline at end of file
diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 5aa2fb1..14c0f98 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -252,7 +252,7 @@ def read_brml(data, options={}, index=0):
 
                 start = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Start')[0].text)
                 stop = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Stop')[0].text)
-                increment = float(chain.findall('ScanInformation/ScaleAxes/ScaleAxisInfo/Increment')[0].text)
+                
 
 
 
@@ -262,7 +262,7 @@ def read_brml(data, options={}, index=0):
 
                         intensity = []
                         for r in raw:
-                            if r > 600:
+                            if r > 601:
                                 intensity.append(r)
 
                         intensity = np.array(intensity)
@@ -478,9 +478,7 @@ def translate_wavelengths(data, wavelength, to_wavelength=None):
 
 def find_wavelength_from_xy(path):
 
-    print(path)
 
- 
     wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
 
     with open(path, 'r') as f:
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 770b5a8..1a9429c 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -20,7 +20,7 @@ def plot_diffractogram(data, options={}):
 
     # Update options
     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', 
@@ -45,6 +45,10 @@ 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
@@ -62,6 +66,7 @@ def plot_diffractogram(data, options={}):
         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
 
@@ -113,7 +118,10 @@ 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')
 
 
     for diffractogram in data['diffractogram']:
@@ -183,7 +191,6 @@ def plot_diffractogram_interactive(data, options):
 
         if not ymax or (ymax < (diffractogram['I'].max())):#+index*options['offset_y'])):
             ymax = diffractogram['I'].max()#+index*options['offset_y']
-            print(ymax)
 
 
     ymin_start = ymin - 0.1*ymax

From 3e4c0a9fc2bbc95b8b6525902727dd30863c30b7 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 30 Mar 2022 17:50:41 +0200
Subject: [PATCH 12/12] Add slider for offset_y (not working yet)

---
 beamtime/xrd/plot.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 1a9429c..78c3906 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -66,7 +66,6 @@ def plot_diffractogram(data, options={}):
         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
 
@@ -157,6 +156,8 @@ def plot_diffractogram(data, options={}):
     if options['interactive_session_active']:
         btp.update_widgets(options=options)
 
+        xrd.io.up
+
 
     return diffractogram, fig, ax
 
@@ -225,7 +226,9 @@ def plot_diffractogram_interactive(data, options):
         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'],
-        ylim=widgets.FloatRangeSlider(value=[ymin_start, ymax_start], min=ymin, max=ymax, step=0.5, layout=widgets.Layout(width='95%')))
+        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),