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 01/57] 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 02/57] 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 03/57] 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 04/57] 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 05/57] 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 06/57] 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 07/57] 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 08/57] 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 09/57] 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 10/57] 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 11/57] 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 12/57] 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), 

From f504c7dd691fa7fa360680e7dbad58e218ec866f Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 31 Mar 2022 13:52:59 +0200
Subject: [PATCH 13/57] Add interactive offset_y

---
 beamtime/xrd/io.py   | 20 +++++++++++++++-----
 beamtime/xrd/plot.py | 11 ++++++++++-
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 14c0f98..dc53b29 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -341,11 +341,13 @@ 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()
 
 
-    if options['offset']:
+    if options['offset'] or options['normalise']:
+        # Make copy of the original intensities before any changes are made through normalisation or offset, to easily revert back if need to update.
+        diffractogram['I_org'] = diffractogram['I']
+        diffractogram['2th_org'] = diffractogram['2th']
+        
         diffractogram = apply_offset(diffractogram, wavelength, index, options)
 
 
@@ -355,13 +357,21 @@ def read_data(data, options={}, index=0):
 
 
 def apply_offset(diffractogram, wavelength, index, options):
+
+    options['current_offset_y'] = options['offset_y']
+    options['current_offset_x'] = options['offset_x']
+
     #Apply offset along y-axis
-    diffractogram['I_org'] = diffractogram['I'] # make copy of original intensities
+    diffractogram['I'] = diffractogram['I_org'] # Reset intensities
+
+    if options['normalise']:
+        diffractogram['I'] = diffractogram['I'] / diffractogram['I'].max()
+
     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_org']
     diffractogram['2th'] = diffractogram['2th'] + index*relative_shift
 
 
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 78c3906..d7a9a5c 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -81,6 +81,13 @@ def plot_diffractogram(data, options={}):
         options['xlim'] = [diffractogram[options['x_vals']].min(), diffractogram[options['x_vals']].max()]
 
 
+    if options['interactive_session_active']:
+        if options['offset']:
+            if (options['offset_x'] != options['current_offset_x']) or (options['offset_y'] != options['current_offset_y']):
+                for i, (diff, wl) in enumerate(zip(data['diffractogram'], data['wavelength'])):
+                    xrd.io.apply_offset(diff, wl, i, options)
+
+
     # 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
@@ -156,7 +163,9 @@ def plot_diffractogram(data, options={}):
     if options['interactive_session_active']:
         btp.update_widgets(options=options)
 
-        xrd.io.up
+        
+
+
 
 
     return diffractogram, fig, ax

From 6f9fefae086b6729e7b68379eb969ee10542e493 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 31 Mar 2022 14:02:04 +0200
Subject: [PATCH 14/57] Add interactive offset_x

---
 beamtime/xrd/plot.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index d7a9a5c..012e9b8 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -236,7 +236,8 @@ def plot_diffractogram_interactive(data, options):
         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%')),
-        offset_y=widgets.FloatSlider(value=options['offset_y'], min=-5, max=5)
+        offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01),
+        offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01)
         )
     
     else:

From 6e851b494b39f93b87dfde610542a942fc4bd327 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 31 Mar 2022 17:29:10 +0200
Subject: [PATCH 15/57] Add heatmap, lacks mapping between x-value and 2th

---
 beamtime/xrd/plot.py | 33 ++++++++++++++++++++++++---------
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 012e9b8..a073dd6 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -1,3 +1,4 @@
+import seaborn as sns
 import matplotlib.pyplot as plt
 from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
 
@@ -20,7 +21,7 @@ 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', 'interactive_session_active']
+    'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
 
     default_options = {
         'x_vals': '2th', 
@@ -37,6 +38,8 @@ def plot_diffractogram(data, options={}):
         'reflections_plot': False, # whether to plot reflections as a plot
         'reflections_indices': False, # whether to plot the reflection indices
         'reflections_data': None, # Should be passed as a list of dictionaries on the form {path: rel_path, reflection_indices: number of indices, colour: [r,g,b], min_alpha: 0-1]
+        'heatmap': False,
+        'cmap': 'viridis',
         'plot_kind': None,
         'palettes': [('qualitative', 'Dark2_8')],
         'interactive': False,
@@ -69,13 +72,20 @@ def plot_diffractogram(data, options={}):
             data['diffractogram'][index] = diffractogram
             data['wavelength'][index] = wavelength
 
-            
 
     else:
         if not isinstance(data['diffractogram'], list):
             data['diffractogram'] = [data['diffractogram']]
             data['wavelength'] = [data['wavelength']]
 
+    if options['heatmap']:
+        data['heatmap'] = []
+        for diff in data['diffractogram']:
+            data['heatmap'].append(np.array(diff['I']))
+
+        data['heatmap'] = np.array(data['heatmap'])
+        data['heatmap'] = np.flipud(data['heatmap'])
+
     # 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()]
@@ -130,12 +140,17 @@ def plot_diffractogram(data, options={}):
         colours = btp.generate_colours(['black'], kind='single')
 
 
-    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)]))
+    # FIXME Must be changed to map the x-value to the 2th-value somehow
+    if options['heatmap']:
+        sns.heatmap(data['heatmap'], cmap=options['cmap'])
+
+    else:
+        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)]))
 
 
 
@@ -168,7 +183,7 @@ def plot_diffractogram(data, options={}):
 
 
 
-    return diffractogram, fig, ax
+    return data['diffractogram'], fig, ax
 
 
 def determine_grid_layout(options):

From 567282b80b79d86892e62f144e465f20a5d6f528 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Mon, 4 Apr 2022 14:48:29 +0200
Subject: [PATCH 16/57] Fix bug where extract_folder had no default value

---
 beamtime/xrd/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index dc53b29..729b674 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -40,7 +40,7 @@ def integrate_1d(data, options={}, index=0):
     df: DataFrame contianing 1D diffractogram if option 'return' is True
     ''' 
 
-    required_options = ['unit', 'nbins', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite']
+    required_options = ['unit', 'nbins', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite', 'extract_folder']
 
     default_options = {
         'unit': '2th_deg', 

From b0629de9a3dd5e32e49ad59639d1f4ef21c35bf2 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Mon, 4 Apr 2022 14:48:59 +0200
Subject: [PATCH 17/57] Add functions to round up and down to nearest dec

---
 beamtime/auxillary.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/beamtime/auxillary.py b/beamtime/auxillary.py
index 76ec551..68785f7 100644
--- a/beamtime/auxillary.py
+++ b/beamtime/auxillary.py
@@ -1,4 +1,5 @@
 import json
+import numpy as np
 
 def update_options(options, required_options, default_options):
     ''' Takes a dictionary of options along with a list of required options and dictionary of default options, and sets all keyval-pairs of options that is not already defined to the default values'''
@@ -37,6 +38,18 @@ def swap_values(dict, key1, key2):
 
 
 
-def hello_world2(a=1, b=2):
+def ceil(a, roundto=1):
 
-    print(f'Halla, MAFAKKAS! a = {a} og b = {b}')
\ No newline at end of file
+    fac = 1/roundto
+
+    a = np.ceil(a*fac) / fac
+
+    return a
+
+def floor(a, roundto=1):
+
+    fac = 1/roundto
+
+    a = np.floor(a*fac) / fac
+
+    return a
\ No newline at end of file

From 59629fcb615a798a2ef13ad47d83394dfe859d95 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Mon, 4 Apr 2022 14:50:20 +0200
Subject: [PATCH 18/57] Add plotting of heatmaps with true xlim

---
 beamtime/plotting.py |  2 +-
 beamtime/xrd/plot.py | 88 ++++++++++++++++++++++++++++++++++++++------
 2 files changed, 77 insertions(+), 13 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index 4e058ac..500f532 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -182,7 +182,7 @@ def adjust_plot(fig, ax, options):
         ax.xaxis.set_minor_locator(MultipleLocator(options['x_tick_locators'][1]))
 
     
-    # THIS NEEDS REWORK FOR IT TO FUNCTION PROPERLY!
+    # FIXME THIS NEEDS REWORK FOR IT TO FUNCTION PROPERLY!
     if options['xticks']:
         ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
         ax.set_xticklabels(options['xticks'])
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index a073dd6..d2b7b51 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -72,23 +72,20 @@ def plot_diffractogram(data, options={}):
             data['diffractogram'][index] = diffractogram
             data['wavelength'][index] = wavelength
 
+        # Sets the xlim if this has not bee specified
+        if not options['xlim']:
+            options['xlim'] = [data['diffractogram'][0][options['x_vals']].min(), data['diffractogram'][0][options['x_vals']].max()]
+
+
+        if options['heatmap']:   
+            data['heatmap'], data['heatmap_xticks'], data['heatmap_xticklabels'] = generate_heatmap(data=data, options=options)
+            options['xlim'] = options['heatmap_xlim']
 
     else:
         if not isinstance(data['diffractogram'], list):
             data['diffractogram'] = [data['diffractogram']]
             data['wavelength'] = [data['wavelength']]
 
-    if options['heatmap']:
-        data['heatmap'] = []
-        for diff in data['diffractogram']:
-            data['heatmap'].append(np.array(diff['I']))
-
-        data['heatmap'] = np.array(data['heatmap'])
-        data['heatmap'] = np.flipud(data['heatmap'])
-
-    # 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()]
 
 
     if options['interactive_session_active']:
@@ -142,7 +139,10 @@ def plot_diffractogram(data, options={}):
 
     # FIXME Must be changed to map the x-value to the 2th-value somehow
     if options['heatmap']:
-        sns.heatmap(data['heatmap'], cmap=options['cmap'])
+        sns.heatmap(data['heatmap'], cmap=options['cmap'], cbar=False, ax=ax)
+        ax.set_xticks(data['heatmap_xticks'])
+        ax.set_xticklabels(data['heatmap_xticklabels'])
+        ax.tick_params(axis='x', which='minor', bottom=False, top=False)
 
     else:
         for diffractogram in data['diffractogram']:
@@ -186,6 +186,68 @@ def plot_diffractogram(data, options={}):
     return data['diffractogram'], fig, ax
 
 
+
+def generate_heatmap(data, options={}):
+
+    required_options = ['x_tick_locators']
+
+    default_options = {
+        'x_tick_locators': [0.5, 0.1]
+    }
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    twotheta = []
+    intensities = []
+    scans = []
+
+    for i, d in enumerate(data['diffractogram']):
+        twotheta = np.append(twotheta, d['2th'].to_numpy())
+        intensities = np.append(intensities, d['I'].to_numpy())
+        scans = np.append(scans, np.full(len(d['2th'].to_numpy()), int(i)))
+
+
+    # Generate ticks and xtick-labels
+    twotheta_max = data['diffractogram'][0]['2th'].max()
+    twotheta_min = data['diffractogram'][0]['2th'].min()
+    twotheta_span = twotheta_max - twotheta_min
+    ndatapoints = len(data['diffractogram'][0]['2th'])
+    steps = twotheta_span / ndatapoints
+
+    twotheta_label_max = aux.floor(twotheta_max, roundto=options['x_tick_locators'][0])
+    twotheta_label_min = aux.ceil(twotheta_min, roundto=options['x_tick_locators'][0])
+    label_steps = (twotheta_label_max - twotheta_label_min)/options['x_tick_locators'][0]
+
+    
+
+    xtick_labels = np.linspace(twotheta_label_min, twotheta_label_max, num=int(label_steps)+1)
+
+    options['x_tick_locators'] = None
+
+    xticks = []
+    for tick in xtick_labels:
+        xticks.append((tick - twotheta_min)/steps)
+
+    heatmap = pd.DataFrame({'2th': twotheta, 'scan': scans, 'I': intensities})
+    heatmap = heatmap.reset_index().pivot_table(index='scan', columns='2th', values='I')
+
+    options['heatmap_xlim'] = [(options['xlim'][0] - twotheta_min)/steps, (options['xlim'][1] - twotheta_min)/steps]
+
+
+    print(xticks, xtick_labels)
+
+
+    return heatmap, xticks, xtick_labels
+
+
+
+
+
+
+
+# #results = np.transpose(np.vstack([twotheta, scans, intensities]))
+
+
 def determine_grid_layout(options):
 
 
@@ -202,6 +264,8 @@ def determine_grid_layout(options):
 
 
 
+
+
 def plot_diffractogram_interactive(data, options):
 
 

From 5541f44a58b4cbc96ba2c55f3ce1b16fcc255bb4 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Mon, 4 Apr 2022 16:47:01 +0200
Subject: [PATCH 19/57] Add automatic change of xlim range with heatmaps

---
 beamtime/xrd/plot.py | 107 ++++++++++++++++++++++++++++---------------
 1 file changed, 71 insertions(+), 36 deletions(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index d2b7b51..df17e8d 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -76,9 +76,9 @@ def plot_diffractogram(data, options={}):
         if not options['xlim']:
             options['xlim'] = [data['diffractogram'][0][options['x_vals']].min(), data['diffractogram'][0][options['x_vals']].max()]
 
-
-        if options['heatmap']:   
-            data['heatmap'], data['heatmap_xticks'], data['heatmap_xticklabels'] = generate_heatmap(data=data, options=options)
+        # Generate heatmap data
+        data['heatmap'], data['heatmap_xticks'], data['heatmap_xticklabels'] = generate_heatmap(data=data, options=options)
+        if options['heatmap']:
             options['xlim'] = options['heatmap_xlim']
 
     else:
@@ -136,12 +136,10 @@ def plot_diffractogram(data, options={}):
     else:
         colours = btp.generate_colours(['black'], kind='single')
 
-
-    # FIXME Must be changed to map the x-value to the 2th-value somehow
     if options['heatmap']:
         sns.heatmap(data['heatmap'], cmap=options['cmap'], cbar=False, ax=ax)
-        ax.set_xticks(data['heatmap_xticks'])
-        ax.set_xticklabels(data['heatmap_xticklabels'])
+        ax.set_xticks(data['heatmap_xticks'][options['x_vals']])
+        ax.set_xticklabels(data['heatmap_xticklabels'][options['x_vals']])
         ax.tick_params(axis='x', which='minor', bottom=False, top=False)
 
     else:
@@ -176,7 +174,7 @@ def plot_diffractogram(data, options={}):
 
 
     if options['interactive_session_active']:
-        btp.update_widgets(options=options)
+        update_widgets(options=options)
 
         
 
@@ -207,37 +205,52 @@ def generate_heatmap(data, options={}):
         scans = np.append(scans, np.full(len(d['2th'].to_numpy()), int(i)))
 
 
-    # Generate ticks and xtick-labels
-    twotheta_max = data['diffractogram'][0]['2th'].max()
-    twotheta_min = data['diffractogram'][0]['2th'].min()
-    twotheta_span = twotheta_max - twotheta_min
+    heatmap = pd.DataFrame({'2th': twotheta, 'scan': scans, 'I': intensities})
+    xrd.io.translate_wavelengths(data=heatmap, wavelength=data['wavelength'][0])
+    min_dict = {'2th': heatmap['2th'].min(), '2th_cuka': heatmap['2th_cuka'].min(), '2th_moka': heatmap['2th_moka'].min(),
+                        'q': heatmap['q'].min(), 'q2': heatmap['q2'].min(), 'q4': heatmap['q4'].min(), '1/d': heatmap['1/d'].min()}
+
+    max_dict = {'2th': heatmap['2th'].max(), '2th_cuka': heatmap['2th_cuka'].max(), '2th_moka': heatmap['2th_moka'].max(),
+                        'q': heatmap['q'].max(), 'q2': heatmap['q2'].max(), 'q4': heatmap['q4'].max(), '1/d': heatmap['1/d'].max()}
+
+
     ndatapoints = len(data['diffractogram'][0]['2th'])
-    steps = twotheta_span / ndatapoints
 
-    twotheta_label_max = aux.floor(twotheta_max, roundto=options['x_tick_locators'][0])
-    twotheta_label_min = aux.ceil(twotheta_min, roundto=options['x_tick_locators'][0])
-    label_steps = (twotheta_label_max - twotheta_label_min)/options['x_tick_locators'][0]
+    xlims = [0, ndatapoints]
+    xticks = {}
+    xticklabels = {}
 
-    
+    for xval in min_dict.keys():
+       
+       # Add xticks labels
+        
+        label_max = aux.floor(max_dict[xval], roundto=options['x_tick_locators'][0])
+        label_min = aux.ceil(min_dict[xval], roundto=options['x_tick_locators'][0])
+        label_steps = (label_max - label_min)/options['x_tick_locators'][0]
+
+        xticklabels[xval] = np.linspace(label_min, label_max, num=int(label_steps)+1)
+
+        # Add xticks
+        xval_span = max_dict[xval] - min_dict[xval]
+        steps = xval_span / ndatapoints
+        
+        
+        xticks_xval = []
+
+        for tick in xticklabels[xval]:
+            xticks_xval.append((tick-min_dict[xval])/steps)
+
+        xticks[xval] = xticks_xval
 
-    xtick_labels = np.linspace(twotheta_label_min, twotheta_label_max, num=int(label_steps)+1)
 
     options['x_tick_locators'] = None
 
-    xticks = []
-    for tick in xtick_labels:
-        xticks.append((tick - twotheta_min)/steps)
-
-    heatmap = pd.DataFrame({'2th': twotheta, 'scan': scans, 'I': intensities})
     heatmap = heatmap.reset_index().pivot_table(index='scan', columns='2th', values='I')
 
-    options['heatmap_xlim'] = [(options['xlim'][0] - twotheta_min)/steps, (options['xlim'][1] - twotheta_min)/steps]
+    options['heatmap_xlim'] = xlims
 
 
-    print(xticks, xtick_labels)
-
-
-    return heatmap, xticks, xtick_labels
+    return heatmap, xticks, xticklabels
 
 
 
@@ -269,9 +282,9 @@ 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]}
+    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], 'heatmap': [None, None]}
     
-    update_minmax(minmax, data)
+    update_minmax(minmax=minmax, data=data, options=options)
 
     ymin, ymax = None, None
     for index, diffractogram in enumerate(data['diffractogram']):
@@ -288,8 +301,6 @@ def plot_diffractogram_interactive(data, options):
     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%')),
@@ -301,17 +312,18 @@ 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}
+            'q4_default':       {'min': minmax['q4'][0],        'max': minmax['q4'][1],         'value': [minmax['q4'][0],          minmax['q4'][1]],       'step': 0.5},
+            'heatmap_default':  {'min': minmax['heatmap'][0],   'max': minmax['heatmap'][1],    'value': [minmax['heatmap'][0],     minmax['heatmap'][1]],  'step': 10}
         }
     }
 
-
     if options['reflections_data']:
         w = widgets.interactive(btp.ipywidgets_update, func=widgets.fixed(plot_diffractogram), data=widgets.fixed(data), options=widgets.fixed(options), 
         scatter=widgets.ToggleButton(value=False), 
         line=widgets.ToggleButton(value=True), 
         reflections_plot=widgets.ToggleButton(value=True),
         reflections_indices=widgets.ToggleButton(value=False),
+        heatmap=widgets.ToggleButton(value=options['heatmap']),
         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%')),
@@ -329,7 +341,7 @@ def plot_diffractogram_interactive(data, options):
     display(w)
 
 
-def update_minmax(minmax, data):
+def update_minmax(minmax, data, options={}):
     ''' Finds minimum and maximum values of each column and updates the minmax dictionary to contain the correct values.
     
     Input:
@@ -351,15 +363,38 @@ def update_minmax(minmax, data):
     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() 
+    minmax['heatmap'] = options['heatmap_xlim']
+
+
 
 def update_widgets(options):
 
     for widget in options['widgets'].values():
 
-        if widget['state'] != options['x_vals']:
+        if options['heatmap'] and (widget['state'] != 'heatmap'):
+            setattr(widget['w'], 'min', widget['heatmap_default']['min'])
+            setattr(widget['w'], 'max', widget['heatmap_default']['max'])
+            setattr(widget['w'], 'value', widget['heatmap_default']['value'])
+            setattr(widget['w'], 'step', widget['heatmap_default']['step'])
+
+            widget['state'] = 'heatmap'
+        
+        elif not options['heatmap'] and (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']
 
 

From c0449f2e183d17f684d0906791e9a2b9e82d52f7 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 5 Apr 2022 13:52:27 +0200
Subject: [PATCH 20/57] Correct switch of ylim between diff and heatmap

---
 beamtime/xrd/plot.py | 199 +++++++++++++++++++++++++++++--------------
 1 file changed, 135 insertions(+), 64 deletions(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index df17e8d..c97dabe 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -176,9 +176,6 @@ def plot_diffractogram(data, options={}):
     if options['interactive_session_active']:
         update_widgets(options=options)
 
-        
-
-
 
 
     return data['diffractogram'], fig, ax
@@ -282,38 +279,51 @@ 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], 'heatmap': [None, None]}
+    xminmax = {'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], 'heatmap': [None, None], 'start': [None, None, None, None]}
+    yminmax = {'diff': [None, None, None, None], 'heatmap': [None, None], 'start': [None, None, None, None]}
     
-    update_minmax(minmax=minmax, data=data, options=options)
-
-    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']
+    update_xminmax(xminmax=xminmax, data=data, options=options)
+    update_yminmax(yminmax=yminmax, data=data, options=options)
 
 
-    ymin_start = ymin - 0.1*ymax
-    ymax_start = ymax+0.2*ymax
-    ymin = ymin - 5*ymax
-    ymax = ymax*5
+
+    # Get start values for ylim slider based on choice (FIXME This can be impleneted into update_yminmax). Can also make a 'start' item that stores the start values, instead of having 4 items in 'diff' as it is now.
+    if options['heatmap']:
+        ymin = yminmax['heatmap'][0]
+        ymax = yminmax['heatmap'][1]
+        ymin_start = yminmax['heatmap'][0]
+        ymax_start = yminmax['heatmap'][1]
+
+    elif not options['heatmap']:
+        ymin = yminmax['diff'][0]
+        ymax = yminmax['diff'][1]
+        ymin_start = yminmax['diff'][2]
+        ymax_start = yminmax['diff'][3]
+
+    
+    # FIXME The start values for xlim should probably also be decided by initial value of x_vals, and can likewise be implemented in update_xminmax() 
+
 
         
     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},
-            '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},
-            'heatmap_default':  {'min': minmax['heatmap'][0],   'max': minmax['heatmap'][1],    'value': [minmax['heatmap'][0],     minmax['heatmap'][1]],  'step': 10}
+            'w': widgets.FloatRangeSlider(value=[xminmax['start'][2], xminmax['start'][3]], min=xminmax['start'][0], max=xminmax['start'][1], step=0.5, layout=widgets.Layout(width='95%')),
+            'state': options['x_vals'],
+            '2th_default':      {'min': xminmax['2th'][0],          'max': xminmax['2th'][1],           'value': [xminmax['2th'][0],            xminmax['2th'][1]],             'step': 0.5},
+            '2th_cuka_default': {'min': xminmax['2th_cuka'][0],     'max': xminmax['2th_cuka'][1],      'value': [xminmax['2th_cuka'][0],       xminmax['2th_cuka'][1]],        'step': 0.5},
+            '2th_moka_default': {'min': xminmax['2th_moka'][0],     'max': xminmax['2th_moka'][1],      'value': [xminmax['2th_moka'][0],       xminmax['2th_moka'][1]],        'step': 0.5},
+            'd_default':        {'min': xminmax['d'][0],            'max': xminmax['d'][1],             'value': [xminmax['d'][0],              xminmax['d'][1]],               'step': 0.5},
+            '1/d_default':      {'min': xminmax['1/d'][0],          'max': xminmax['1/d'][1],           'value': [xminmax['1/d'][0],            xminmax['1/d'][1]],             'step': 0.5},
+            'q_default':        {'min': xminmax['q'][0],            'max': xminmax['q'][1],             'value': [xminmax['q'][0],              xminmax['q'][1]],               'step': 0.5},
+            'q2_default':       {'min': xminmax['q2'][0],           'max': xminmax['q2'][1],            'value': [xminmax['q2'][0],             xminmax['q2'][1]],              'step': 0.5},
+            'q4_default':       {'min': xminmax['q4'][0],           'max': xminmax['q4'][1],            'value': [xminmax['q4'][0],             xminmax['q4'][1]],              'step': 0.5},
+            'heatmap_default':  {'min': xminmax['heatmap'][0],      'max': xminmax['heatmap'][1],       'value': [xminmax['heatmap'][0],        xminmax['heatmap'][1]],         'step': 10}
+        },
+        'ylim': { 
+            'w': widgets.FloatRangeSlider(value=[yminmax['start'][2], yminmax['start'][3]], min=yminmax['start'][0], max=yminmax['start'][1], step=0.5, layout=widgets.Layout(width='95%')),
+            'state': 'heatmap' if options['heatmap'] else 'diff',
+            'diff_default':     {'min': yminmax['diff'][0],         'max': yminmax['diff'][1],          'value': [yminmax['diff'][2],           yminmax['diff'][3]],            'step': 0.1},
+            'heatmap_default':  {'min': yminmax['heatmap'][0],      'max': yminmax['heatmap'][1],       'value': [yminmax['heatmap'][0],        yminmax['heatmap'][1]],         'step': 0.1}
         }
     }
 
@@ -326,7 +336,7 @@ def plot_diffractogram_interactive(data, options):
         heatmap=widgets.ToggleButton(value=options['heatmap']),
         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=options['widgets']['ylim']['w'],
         offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01),
         offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01)
         )
@@ -341,61 +351,122 @@ def plot_diffractogram_interactive(data, options):
     display(w)
 
 
-def update_minmax(minmax, data, options={}):
+def update_xminmax(xminmax, data, options={}):
     ''' 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()
+        if not xminmax['2th'][0] or diffractogram['2th'].min() < xminmax['2th'][0]:
+            xminmax['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()
+        if not xminmax['2th'][1] or diffractogram['2th'].max() > xminmax['2th'][1]:
+            xminmax['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() 
-    minmax['heatmap'] = options['heatmap_xlim']
+    xminmax['2th_cuka'][0], xminmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(),  data['diffractogram'][max_index]['2th_cuka'].max()
+    xminmax['2th_moka'][0], xminmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(),  data['diffractogram'][max_index]['2th_moka'].max() 
+    xminmax['d'][0], xminmax['d'][1]               = data['diffractogram'][max_index]['d'].min(),         data['diffractogram'][min_index]['d'].max() # swapped, intended
+    xminmax['1/d'][0], xminmax['1/d'][1]           = data['diffractogram'][min_index]['1/d'].min(),       data['diffractogram'][max_index]['1/d'].max() 
+    xminmax['q'][0], xminmax['q'][1]               = data['diffractogram'][min_index]['q'].min(),         data['diffractogram'][max_index]['q'].max()
+    xminmax['q2'][0], xminmax['q2'][1]             = data['diffractogram'][min_index]['q2'].min(),        data['diffractogram'][max_index]['q2'].max() 
+    xminmax['q4'][0], xminmax['q4'][1]             = data['diffractogram'][min_index]['q4'].min(),        data['diffractogram'][max_index]['q4'].max() 
+    xminmax['heatmap'] = options['heatmap_xlim']
+
+
+    xminmax['start'][0], xminmax['start'][1] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1]
+    xminmax['start'][2], xminmax['start'][3] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1]
+
+
+def update_yminmax(yminmax: dict, data, options={}):
+    
+    for index, diffractogram in enumerate(data['diffractogram']):
+        if not yminmax['diff'][0] or (yminmax['diff'][0] > (diffractogram['I'].min())): 
+            yminmax['diff'][0] = diffractogram['I'].min()
+
+        if not yminmax['diff'][1] or (yminmax['diff'][1] < (diffractogram['I'].max())):
+            yminmax['diff'][1] = diffractogram['I'].max()
+
+
+    # Set start values of ymin and ymax to be slightly below lowest data points and slightly above highest data points to give some whitespace around the plot
+    yminmax['diff'][2] = yminmax['diff'][0] - 0.1*yminmax['diff'][1]
+    yminmax['diff'][3] = yminmax['diff'][1] + 0.2*yminmax['diff'][1]
+    
+    # Allow for adjustment up to five times ymax above and below data
+    yminmax['diff'][0] = yminmax['diff'][0] - 5*yminmax['diff'][1]
+    yminmax['diff'][1] = yminmax['diff'][1]*5
+
+
+    yminmax['heatmap'][0] = 0
+    yminmax['heatmap'][1] = data['heatmap'].shape[0]
+
+
+    if options['heatmap']:
+        yminmax['start'][0], yminmax['start'][1] = yminmax['heatmap'][0], yminmax['heatmap'][1]
+        yminmax['start'][2], yminmax['start'][3] = yminmax['heatmap'][0], yminmax['heatmap'][1]
+
+    else:
+        # The third and fourth index are different here to not be zoomed completely out to begin with.
+        yminmax['start'][0], yminmax['start'][1] = yminmax['diff'][0], yminmax['diff'][1]
+        yminmax['start'][2], yminmax['start'][3] = yminmax['diff'][2], yminmax['diff'][3]
+    
 
 
 
 def update_widgets(options):
 
-    for widget in options['widgets'].values():
+    for widget, attr in options['widgets'].items():
 
-        if options['heatmap'] and (widget['state'] != 'heatmap'):
-            setattr(widget['w'], 'min', widget['heatmap_default']['min'])
-            setattr(widget['w'], 'max', widget['heatmap_default']['max'])
-            setattr(widget['w'], 'value', widget['heatmap_default']['value'])
-            setattr(widget['w'], 'step', widget['heatmap_default']['step'])
+        if widget == 'xlim':
+
+            if options['heatmap'] and (attr['state'] != 'heatmap'):
+                setattr(attr['w'], 'min', attr['heatmap_default']['min'])
+                setattr(attr['w'], 'max', attr['heatmap_default']['max'])
+                setattr(attr['w'], 'value', attr['heatmap_default']['value'])
+                setattr(attr['w'], 'step', attr['heatmap_default']['step'])
+
+                attr['state'] = 'heatmap'
+            
+            elif not options['heatmap'] and (attr['state'] != options['x_vals']):
+                for arg in attr[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 attr[f'{options["x_vals"]}_default']['min'] > getattr(attr['w'], 'max'):
+                            setattr(attr['w'], 'max', attr[f'{options["x_vals"]}_default']['max'])
+                    
+                    elif arg == 'max':
+                        if attr[f'{options["x_vals"]}_default']['max'] < getattr(attr['w'], 'min'):
+                            setattr(attr['w'], 'min', attr[f'{options["x_vals"]}_default']['min'])
 
-            widget['state'] = 'heatmap'
-        
-        elif not options['heatmap'] and (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'])
+                    setattr(attr['w'], arg, attr[f'{options["x_vals"]}_default'][arg])
                 
-                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'])
+                
+                attr['state'] = options['x_vals']
+
+        elif widget == 'ylim':
+            state = 'heatmap' if options['heatmap'] else 'diff'
+    
+            if attr['state'] != state:
+
+                for arg in attr[f'{state}_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 attr[f'{state}_default']['min'] > getattr(attr['w'], 'max'):
+                            setattr(attr['w'], 'max', attr[f'{state}_default']['max'])
+                    
+                    elif arg == 'max':
+                        if attr[f'{state}_default']['max'] < getattr(attr['w'], 'min'):
+                            setattr(attr['w'], 'min', attr[f'{state}_default']['min'])
+
+                
+                    setattr(attr['w'], arg, attr[f'{state}_default'][arg])
+
+                attr['state'] = state
 
-            
-                setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
-            
-            
-            widget['state'] = options['x_vals']
 
 
 

From 876e0f8d3d2759a762dbaf58c317e41fbf50c4bc Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Tue, 5 Apr 2022 16:12:19 +0200
Subject: [PATCH 21/57] Allow rescaling ylim with interactive diff plot

---
 beamtime/xrd/io.py   |  11 ++-
 beamtime/xrd/plot.py | 161 ++++++++++++++++++++++++++++++-------------
 2 files changed, 122 insertions(+), 50 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 729b674..910811b 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -358,9 +358,18 @@ def read_data(data, options={}, index=0):
 
 def apply_offset(diffractogram, wavelength, index, options):
 
-    options['current_offset_y'] = options['offset_y']
+    if 'current_offset_y' not in options.keys():
+        options['current_offset_y'] = options['offset_y']
+    else:
+        if options['current_offset_y'] != options['offset_y']:
+            options['offset_change'] = True
+        
+        options['current_offset_y'] = options['offset_y']
+
     options['current_offset_x'] = options['offset_x']
 
+    
+
     #Apply offset along y-axis
     diffractogram['I'] = diffractogram['I_org'] # Reset intensities
 
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index c97dabe..9012b4a 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -20,7 +20,7 @@ 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', 'offset', 'offset_x', 'offset_y',
+    required_options = ['x_vals', 'y_vals', 'ylabel', 'xlabel', 'xunit', 'yunit', 'line', 'scatter', 'xlim', 'ylim', 'normalise', 'offset', 'offset_x', 'offset_y', 'offset_change',
     'reflections_plot', 'reflections_indices', 'reflections_data', 'heatmap', 'cmap', 'plot_kind', 'palettes', 'interactive', 'rc_params', 'format_params', 'interactive_session_active']
 
     default_options = {
@@ -33,6 +33,7 @@ def plot_diffractogram(data, options={}):
         'offset': True,
         'offset_x': 0,
         'offset_y': 1,
+        'offset_change': False,
         '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
@@ -53,6 +54,7 @@ def plot_diffractogram(data, options={}):
             default_options['offset_y'] = 0.05
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+    options['current_offset_y'] = options['offset_y']
 
     # Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
     if not isinstance(data['path'], list):
@@ -174,7 +176,8 @@ def plot_diffractogram(data, options={}):
 
 
     if options['interactive_session_active']:
-        update_widgets(options=options)
+        options['current_y_offset'] = options['widget'].kwargs['offset_y']
+        update_widgets(data=data, options=options)
 
 
 
@@ -213,7 +216,7 @@ def generate_heatmap(data, options={}):
 
     ndatapoints = len(data['diffractogram'][0]['2th'])
 
-    xlims = [0, ndatapoints]
+    xlims = [0, ndatapoints, 0, ndatapoints] # 0: xmin, 1: xmax, 2: xmin_start, 3: xmax_start
     xticks = {}
     xticklabels = {}
 
@@ -279,13 +282,18 @@ def determine_grid_layout(options):
 def plot_diffractogram_interactive(data, options):
 
 
-    xminmax = {'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], 'heatmap': [None, None], 'start': [None, None, None, None]}
-    yminmax = {'diff': [None, None, None, None], 'heatmap': [None, None], 'start': [None, None, None, None]}
+    # Format here is xminmax[0]: xmin, xminmax[1]: xmax, xminmax[2]: xmin_start, xminmax[3]: xmax_start, where "_start" denotes starting value of the slider
+    xminmax = { '2th':      [None, None, None, None], '2th_cuka':   [None, None, None, None],   '2th_moka':     [None, None, None, None], 
+                'd':        [None, None, None, None], '1/d':        [None, None, None, None], 
+                'q':        [None, None, None, None], 'q2':         [None, None, None, None],   'q4':           [None, None, None, None], 
+                'heatmap':  [None, None, None, None], 'start':      [None, None, None, None]}
+
+    yminmax = { 'diff':     [None, None, None, None], 'heatmap':    [None, None, None, None],   'start':        [None, None, None, None]}
     
     update_xminmax(xminmax=xminmax, data=data, options=options)
     update_yminmax(yminmax=yminmax, data=data, options=options)
 
-
+    options['xminmax'], options['yminmax'] = xminmax, yminmax
 
     # Get start values for ylim slider based on choice (FIXME This can be impleneted into update_yminmax). Can also make a 'start' item that stores the start values, instead of having 4 items in 'diff' as it is now.
     if options['heatmap']:
@@ -337,8 +345,8 @@ def plot_diffractogram_interactive(data, options):
         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=options['widgets']['ylim']['w'],
-        offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01),
-        offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01)
+        offset_y=widgets.BoundedFloatText(value=options['offset_y'], min=-5, max=5, step=0.01, description='offset_y'),
+        offset_x=widgets.BoundedFloatText(value=options['offset_x'], min=-1, max=1, step=0.01, description='offset_x')
         )
     
     else:
@@ -348,6 +356,8 @@ def plot_diffractogram_interactive(data, options):
         xlim=options['widgets']['xlim']['w'])
     
     
+    options['widget'] = w
+
     display(w)
 
 
@@ -357,7 +367,9 @@ def update_xminmax(xminmax, data, options={}):
     Input:
     minmax (dict): contains '''
 
+    xminmax['2th'] = [None, None, None, None]
     for index, diffractogram in enumerate(data['diffractogram']):
+        
         if not xminmax['2th'][0] or diffractogram['2th'].min() < xminmax['2th'][0]:
             xminmax['2th'][0] = diffractogram['2th'].min()
             min_index = index
@@ -366,23 +378,43 @@ def update_xminmax(xminmax, data, options={}):
             xminmax['2th'][1] = diffractogram['2th'].max()
             max_index = index
 
-    xminmax['2th_cuka'][0], xminmax['2th_cuka'][1] = data['diffractogram'][min_index]['2th_cuka'].min(),  data['diffractogram'][max_index]['2th_cuka'].max()
-    xminmax['2th_moka'][0], xminmax['2th_moka'][1] = data['diffractogram'][min_index]['2th_moka'].min(),  data['diffractogram'][max_index]['2th_moka'].max() 
-    xminmax['d'][0], xminmax['d'][1]               = data['diffractogram'][max_index]['d'].min(),         data['diffractogram'][min_index]['d'].max() # swapped, intended
-    xminmax['1/d'][0], xminmax['1/d'][1]           = data['diffractogram'][min_index]['1/d'].min(),       data['diffractogram'][max_index]['1/d'].max() 
-    xminmax['q'][0], xminmax['q'][1]               = data['diffractogram'][min_index]['q'].min(),         data['diffractogram'][max_index]['q'].max()
-    xminmax['q2'][0], xminmax['q2'][1]             = data['diffractogram'][min_index]['q2'].min(),        data['diffractogram'][max_index]['q2'].max() 
-    xminmax['q4'][0], xminmax['q4'][1]             = data['diffractogram'][min_index]['q4'].min(),        data['diffractogram'][max_index]['q4'].max() 
-    xminmax['heatmap'] = options['heatmap_xlim']
+
+    xminmax['2th'][2], xminmax['2th'][3] = xminmax['2th'][0], xminmax['2th'][1]
+
+    xminmax['2th_cuka'][0], xminmax['2th_cuka'][1]  = data['diffractogram'][min_index]['2th_cuka'].min(),  data['diffractogram'][max_index]['2th_cuka'].max()
+    xminmax['2th_cuka'][2], xminmax['2th_cuka'][3]  = xminmax['2th_cuka'][0], xminmax['2th_cuka'][1]
+
+    xminmax['2th_moka'][0], xminmax['2th_moka'][1]  = data['diffractogram'][min_index]['2th_moka'].min(),  data['diffractogram'][max_index]['2th_moka'].max()
+    xminmax['2th_moka'][2], xminmax['2th_moka'][3]  = xminmax['2th_moka'][0], xminmax['2th_moka'][1]
+
+    xminmax['d'][0], xminmax['d'][1]                = data['diffractogram'][max_index]['d'].min(),         data['diffractogram'][min_index]['d'].max() # swapped, intended
+    xminmax['d'][2], xminmax['d'][3]                = xminmax['d'][0], xminmax['d'][1]
+
+    xminmax['1/d'][0], xminmax['1/d'][1]            = data['diffractogram'][min_index]['1/d'].min(),       data['diffractogram'][max_index]['1/d'].max()
+    xminmax['1/d'][2], xminmax['1/d'][3]            = xminmax['1/d'][0], xminmax['1/d'][1]
+
+    xminmax['q'][0], xminmax['q'][1]                = data['diffractogram'][min_index]['q'].min(),         data['diffractogram'][max_index]['q'].max()
+    xminmax['q'][2], xminmax['q'][3]                = xminmax['q'][0], xminmax['q'][1]
+
+    xminmax['q2'][0], xminmax['q2'][1]              = data['diffractogram'][min_index]['q2'].min(),        data['diffractogram'][max_index]['q2'].max()
+    xminmax['q2'][2], xminmax['q2'][3]              = xminmax['q2'][0], xminmax['q2'][1]
+
+    xminmax['q4'][0], xminmax['q4'][1]              = data['diffractogram'][min_index]['q4'].min(),        data['diffractogram'][max_index]['q4'].max()
+    xminmax['q4'][2], xminmax['q4'][3]              = xminmax['q4'][0], xminmax['q4'][1]
+
+
+    xminmax['heatmap'] = options['heatmap_xlim'] # This value is set in the generate_heatmap()-function
 
 
     xminmax['start'][0], xminmax['start'][1] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1]
-    xminmax['start'][2], xminmax['start'][3] = xminmax[options['x_vals']][0], xminmax[options['x_vals']][1]
+    xminmax['start'][2], xminmax['start'][3] = xminmax[options['x_vals']][2], xminmax[options['x_vals']][3]
 
 
-def update_yminmax(yminmax: dict, data, options={}):
+def update_yminmax(yminmax: dict, data: dict, options={}) -> None:
     
-    for index, diffractogram in enumerate(data['diffractogram']):
+    yminmax['diff'] = [None, None, None, None]
+    # Go through diffractograms and find the minimum and maximum intensity values
+    for diffractogram in data['diffractogram']:
         if not yminmax['diff'][0] or (yminmax['diff'][0] > (diffractogram['I'].min())): 
             yminmax['diff'][0] = diffractogram['I'].min()
 
@@ -399,8 +431,9 @@ def update_yminmax(yminmax: dict, data, options={}):
     yminmax['diff'][1] = yminmax['diff'][1]*5
 
 
-    yminmax['heatmap'][0] = 0
-    yminmax['heatmap'][1] = data['heatmap'].shape[0]
+    # Set start values to the edges of the dataset
+    yminmax['heatmap'][0], yminmax['heatmap'][1] = 0, data['heatmap'].shape[0]
+    yminmax['heatmap'][2], yminmax['heatmap'][3] = yminmax['heatmap'][0], yminmax['heatmap'][1]
 
 
     if options['heatmap']:
@@ -413,59 +446,89 @@ def update_yminmax(yminmax: dict, data, options={}):
         yminmax['start'][2], yminmax['start'][3] = yminmax['diff'][2], yminmax['diff'][3]
     
 
+def update_defaults(widget: dict, minmax: dict) -> None:
+    ''' Updates the default x- or y-limits of a given widget. Refer to plot_diffractogram_interactive() to see the form of the widget that is passed in. An update of the min/max-values is done just prior to calling this function.
+    Changes dictionaries in place.
+    
+    Input:
+    widget (dict): A dictionary containing the widget itself (widget['w']) and all its default-values (e.g. widget['2th_default'])
+    minmax (dict): A dictionary containing min and max values, as well as min_start and max_start values. (e.g. minmax['2th'] is a list with four elements: [xmin, xmax, xmin_start, xmax_start])
+    
+    Output:
+    None.'''
+
+    for name, attr in widget.items():
+        if name.endswith('default'):
+            attr['min'] = minmax[name.replace('_default', '')][0]
+            attr['max'] = minmax[name.replace('_default', '')][1]           
+            attr['value'] = [minmax[name.replace('_default', '')][2], minmax[name.replace('_default', '')][3]]
 
 
-def update_widgets(options):
+def update_widgets(data, options):
 
-    for widget, attr in options['widgets'].items():
 
-        if widget == 'xlim':
+    for widget_name, widget in options['widgets'].items():
 
-            if options['heatmap'] and (attr['state'] != 'heatmap'):
-                setattr(attr['w'], 'min', attr['heatmap_default']['min'])
-                setattr(attr['w'], 'max', attr['heatmap_default']['max'])
-                setattr(attr['w'], 'value', attr['heatmap_default']['value'])
-                setattr(attr['w'], 'step', attr['heatmap_default']['step'])
+        # Make changes to xlim-widget
+        if widget_name == 'xlim':
+            # First update the min and max values
+            update_xminmax(xminmax=options['xminmax'], data=data, options=options)
+            update_defaults(widget=widget, minmax=options['xminmax'])
+           
 
-                attr['state'] = 'heatmap'
+            if options['heatmap'] and (widget['state'] != 'heatmap'):
+
+
+                setattr(widget['w'], 'min', widget['heatmap_default']['min'])
+                setattr(widget['w'], 'max', widget['heatmap_default']['max'])
+                setattr(widget['w'], 'value', widget['heatmap_default']['value'])
+                setattr(widget['w'], 'step', widget['heatmap_default']['step'])
+
+                widget['state'] = 'heatmap'
             
-            elif not options['heatmap'] and (attr['state'] != options['x_vals']):
-                for arg in attr[f'{options["x_vals"]}_default']:
+            elif not options['heatmap'] and (widget['state'] != options['x_vals']):              
+                # Then loop through all attributes in the widget and change to current mode.
+                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 attr[f'{options["x_vals"]}_default']['min'] > getattr(attr['w'], 'max'):
-                            setattr(attr['w'], 'max', attr[f'{options["x_vals"]}_default']['max'])
+                        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 attr[f'{options["x_vals"]}_default']['max'] < getattr(attr['w'], 'min'):
-                            setattr(attr['w'], 'min', attr[f'{options["x_vals"]}_default']['min'])
+                        if widget[f'{options["x_vals"]}_default']['max'] < getattr(widget['w'], 'min'):
+                            setattr(widget['w'], 'min', widget[f'{options["x_vals"]}_default']['min'])
 
                 
-                    setattr(attr['w'], arg, attr[f'{options["x_vals"]}_default'][arg])
+                    setattr(widget['w'], arg, widget[f'{options["x_vals"]}_default'][arg])
                 
                 
-                attr['state'] = options['x_vals']
+                widget['state'] = options['x_vals']
 
-        elif widget == 'ylim':
-            state = 'heatmap' if options['heatmap'] else 'diff'
+        # Make changes to ylim-widget
+        elif widget_name == 'ylim':
+            update_yminmax(yminmax=options['yminmax'], data=data, options=options)
+            update_defaults(widget=widget, minmax=options['yminmax'])
+            
+            state = 'heatmap' if options['heatmap'] else 'diff' 
     
-            if attr['state'] != state:
+            if widget['state'] != state or options['offset_change']:
 
-                for arg in attr[f'{state}_default']:
+                for arg in widget[f'{state}_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 attr[f'{state}_default']['min'] > getattr(attr['w'], 'max'):
-                            setattr(attr['w'], 'max', attr[f'{state}_default']['max'])
+                        if widget[f'{state}_default']['min'] > getattr(widget['w'], 'max'):
+                            setattr(widget['w'], 'max', widget[f'{state}_default']['max'])
                     
                     elif arg == 'max':
-                        if attr[f'{state}_default']['max'] < getattr(attr['w'], 'min'):
-                            setattr(attr['w'], 'min', attr[f'{state}_default']['min'])
+                        if widget[f'{state}_default']['max'] < getattr(widget['w'], 'min'):
+                            setattr(widget['w'], 'min', widget[f'{state}_default']['min'])
 
                 
-                    setattr(attr['w'], arg, attr[f'{state}_default'][arg])
-
-                attr['state'] = state
+                    setattr(widget['w'], arg, widget[f'{state}_default'][arg])
+                
+                options['offset_change'] = False
+                widget['state'] = state
 
 
 

From dd7f2d9dea4f91ea3758ab776d0ef5c01037fce3 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 12:44:33 +0200
Subject: [PATCH 22/57] Fix bug making last commit not work as intended

---
 beamtime/xrd/plot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index 9012b4a..db60b1a 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -54,7 +54,7 @@ def plot_diffractogram(data, options={}):
             default_options['offset_y'] = 0.05
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
-    options['current_offset_y'] = options['offset_y']
+    #options['current_offset_y'] = options['offset_y']
 
     # Convert data['path'] to list to allow iteration over this to accommodate both single and multiple diffractograms
     if not isinstance(data['path'], list):

From 63726033249475c45a897d45fb311f08feb7ce99 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 13:42:34 +0200
Subject: [PATCH 23/57] Translate relfections to heatmap x-coords

---
 beamtime/xrd/io.py   | 25 ++++++++++++++++----
 beamtime/xrd/plot.py | 54 ++++++++++++++++++++++++--------------------
 2 files changed, 49 insertions(+), 30 deletions(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index 910811b..c2447d8 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -400,7 +400,7 @@ def revert_offset(diffractogram,which=None):
 
     return diffractogram
 
-def load_reflection_table(data, options={}):
+def load_reflection_table(data: dict, reflections_params: dict, options={}):
 
     required_options = ['ref_wavelength', 'to_wavelength']
 
@@ -413,12 +413,12 @@ def load_reflection_table(data, options={}):
 
     # VESTA outputs the file with a header that has a space between the parameter and units - so there is some extra code to rectify the issue
     # that ensues from this formatting
-    reflections = pd.read_csv(data['path'], delim_whitespace=True)
+    reflections = pd.read_csv(reflections_params['path'], delim_whitespace=True)
 
     # Remove the extra column that appears from the headers issue
     reflections.drop(reflections.columns[-1], axis=1, inplace=True)
 
-    with open(data['path'], 'r') as f:
+    with open(reflections_params['path'], 'r') as f:
         line = f.readline()
 
         headers = line.split()
@@ -434,13 +434,28 @@ def load_reflection_table(data, options={}):
 
     reflections = translate_wavelengths(data=reflections, wavelength=options['ref_wavelength'], to_wavelength=options['to_wavelength'])
 
-    #print(reflections)
+    if 'heatmap' in data.keys():
+        
+        start_2th, stop_2th = data['diffractogram'][0]['2th'].min(), data['diffractogram'][0]['2th'].max()
+        len_2th = stop_2th - start_2th 
+        #print(start_2th, stop_2th, len_2th)
+        
+        start_heatmap, stop_heatmap = 0, data['heatmap'].shape[1]
+        len_heatmap = stop_heatmap - start_heatmap
+        #print(start_heatmap, stop_heatmap, len_heatmap)
+
+        scale = len_heatmap/len_2th
+
+        #print(scale)
+        #print(stop_2th * scale)
+
+        reflections['heatmap'] = (reflections['2th']-start_2th) * scale
 
     return reflections
 
 
 
-def translate_wavelengths(data, wavelength, to_wavelength=None):
+def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=None) -> pd.DataFrame:
     # FIXME Somewhere here there is an invalid arcsin-argument. Not sure where.
 
     pd.options.mode.chained_assignment = None
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index db60b1a..cc6baa3 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -80,6 +80,8 @@ def plot_diffractogram(data, options={}):
 
         # Generate heatmap data
         data['heatmap'], data['heatmap_xticks'], data['heatmap_xticklabels'] = generate_heatmap(data=data, options=options)
+        options['heatmap_loaded'] = True
+
         if options['heatmap']:
             options['xlim'] = options['heatmap_xlim']
 
@@ -163,16 +165,16 @@ def plot_diffractogram(data, options={}):
         options['xlim'] = ax.get_xlim()
         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)
+        for reflections_params, axis in zip(options['reflections_data'], ref_axes):
+            plot_reflection_table(data=data, reflections_params=reflections_params, ax=axis, options=options)
 
     # 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]
 
-        for reference in options['reflections_data']:
-            plot_reflection_indices(data=reference, ax=indices_ax, options=options)
+        for reflections_params in options['reflections_data']:
+            plot_reflection_indices(data=data, reflections_params=reflections_params, ax=indices_ax, options=options)
 
 
     if options['interactive_session_active']:
@@ -533,7 +535,7 @@ def update_widgets(data, options):
 
 
 
-def plot_reflection_indices(data, ax, options={}):
+def plot_reflection_indices(data, reflections_params, ax, options={}):
     ''' Print reflection indices from output generated by VESTA.
     
     Required contents of data:
@@ -547,20 +549,21 @@ def plot_reflection_indices(data, ax, options={}):
         'hide_indices': False
     }
 
-    data = aux.update_options(options=data, required_options=required_options, default_options=default_options)
+    reflections_params = aux.update_options(options=reflections_params, required_options=required_options, default_options=default_options)
 
-    if not data['hide_indices']:
-        reflection_table = xrd.io.load_reflection_table(data=data, options=options)
+    if not reflections_params['hide_indices']:
+        reflection_table = xrd.io.load_reflection_table(data=data, reflections_params=reflections_params, options=options)
         
-        if data['reflection_indices'] > 0:
+        if reflections_params['reflection_indices'] > 0:
 
             # Get the data['reflection_indices'] number of highest reflections within the subrange options['xlim']
-            reflection_indices = reflection_table.loc[(reflection_table[options['x_vals']] > options['xlim'][0]) & (reflection_table[options['x_vals']] < options['xlim'][1])].nlargest(options['reflection_indices'], 'I')
+            x_vals = 'heatmap' if options['heatmap'] else options['x_vals']
+            reflection_indices = reflection_table.loc[(reflection_table[x_vals] > options['xlim'][0]) & (reflection_table[x_vals] < options['xlim'][1])].nlargest(options['reflection_indices'], 'I')
 
             # Plot the indices
-            for i in range(data['reflection_indices']):
+            for i in range(reflections_params['reflection_indices']):
                 if reflection_indices.shape[0] > i:
-                    ax.text(s=f'({reflection_indices["h"].iloc[i]} {reflection_indices["k"].iloc[i]} {reflection_indices["l"].iloc[i]})', x=reflection_indices[options['x_vals']].iloc[i], y=0, fontsize=2.5, rotation=90, va='bottom', ha='center', c=data['text_colour'])    
+                    ax.text(s=f'({reflection_indices["h"].iloc[i]} {reflection_indices["k"].iloc[i]} {reflection_indices["l"].iloc[i]})', x=reflection_indices[x_vals].iloc[i], y=0, fontsize=2.5, rotation=90, va='bottom', ha='center', c=reflections_params['text_colour'])    
 
         
         if options['xlim']:
@@ -571,7 +574,7 @@ def plot_reflection_indices(data, ax, options={}):
 
     return
     
-def plot_reflection_table(data, ax=None, options={}):
+def plot_reflection_table(data, reflections_params, ax=None, options={}):
     ''' Plots a reflection table from output generated by VESTA.
     
     Required contents of data:
@@ -590,15 +593,15 @@ def plot_reflection_table(data, ax=None, options={}):
     }
 
     if 'colour' in data.keys():
-        options['reflections_colour'] = data['colour']
-    if 'min_alpha' in data.keys():
-        options['min_alpha'] = data['min_alpha']
-    if 'reflection_indices' in data.keys():
-        options['reflection_indices'] = data['reflection_indices']
-    if 'label' in data.keys():
-        options['label'] = data['label']
-    if 'wavelength' in data.keys():
-        options['wavelength'] = data['wavelength']
+        options['reflections_colour'] = reflections_params['colour']
+    if 'min_alpha' in reflections_params.keys():
+        options['min_alpha'] = reflections_params['min_alpha']
+    if 'reflection_indices' in reflections_params.keys():
+        options['reflection_indices'] = reflections_params['reflection_indices']
+    if 'label' in reflections_params.keys():
+        options['label'] = reflections_params['label']
+    if 'wavelength' in reflections_params.keys():
+        options['wavelength'] = reflections_params['wavelength']
 
     options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
 
@@ -606,9 +609,10 @@ def plot_reflection_table(data, ax=None, options={}):
     if not ax:
         _, ax = btp.prepare_plot(options)
 
-    reflection_table = xrd.io.load_reflection_table(data=data, options=options)
+    x_vals = 'heatmap' if options['heatmap'] else options['x_vals']
 
-    reflections, intensities  = reflection_table[options['x_vals']], reflection_table['I']
+    reflection_table = xrd.io.load_reflection_table(data=data, reflections_params=reflections_params, options=options)
+    reflections, intensities  = reflection_table[x_vals], reflection_table['I']
 
 
     
@@ -638,7 +642,7 @@ def plot_reflection_table(data, ax=None, options={}):
         xlim_range = ax.get_xlim()[1] - ax.get_xlim()[0]
         ylim_avg = (ax.get_ylim()[0]+ax.get_ylim()[1])/2
 
-        ax.text(s=data['label'], x=(ax.get_xlim()[0]-0.01*xlim_range), y=ylim_avg, ha = 'right', va = 'center')
+        ax.text(s=reflections_params['label'], x=(ax.get_xlim()[0]-0.01*xlim_range), y=ylim_avg, ha = 'right', va = 'center')
 
 
 

From bdfc31901341309a725e5450615fc2823a2554ba Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 14:43:07 +0200
Subject: [PATCH 24/57] Initial commit of test

---
 beamtime/test/__init__.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 beamtime/test/__init__.py

diff --git a/beamtime/test/__init__.py b/beamtime/test/__init__.py
new file mode 100644
index 0000000..e69de29

From 1146c04a383086fd41f4362c36de0e9a08a34298 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 15:02:38 +0200
Subject: [PATCH 25/57] Add first tests

---
 beamtime/test/pytest.ini        |  6 ++++++
 beamtime/test/test_auxillary.py | 29 +++++++++++++++++++++++++++++
 beamtime/test/test_plotting.py  |  8 ++++++++
 beamtime/test/xrd/test_io.py    |  0
 beamtime/test/xrd/test_plot.py  |  0
 5 files changed, 43 insertions(+)
 create mode 100644 beamtime/test/pytest.ini
 create mode 100644 beamtime/test/test_auxillary.py
 create mode 100644 beamtime/test/test_plotting.py
 create mode 100644 beamtime/test/xrd/test_io.py
 create mode 100644 beamtime/test/xrd/test_plot.py

diff --git a/beamtime/test/pytest.ini b/beamtime/test/pytest.ini
new file mode 100644
index 0000000..8108e29
--- /dev/null
+++ b/beamtime/test/pytest.ini
@@ -0,0 +1,6 @@
+# pytest.ini
+
+[pytest]
+minversion = 6.0
+testpaths = 
+	.
diff --git a/beamtime/test/test_auxillary.py b/beamtime/test/test_auxillary.py
new file mode 100644
index 0000000..5a9e85e
--- /dev/null
+++ b/beamtime/test/test_auxillary.py
@@ -0,0 +1,29 @@
+import beamtime.auxillary as aux
+
+def test_swap_values():
+
+
+    dict = {'test1': 1, 'test2': 2}
+    key1 = 'test1'
+    key2 = 'test2'
+
+    oldval1 = dict[key1]
+    oldval2 = dict[key2]
+
+    new_dict = aux.swap_values(dict=dict, key1=key1, key2=key2) 
+
+    assert (dict[key1] == oldval2) and (dict[key2] == oldval1)
+
+
+def test_ceil() -> None:
+
+    assert aux.ceil(1.05, 0.5) == 1.5
+    assert aux.ceil(1.05, 1) == 2.0
+    assert aux.ceil(1.1, 0.2) == 1.2
+
+
+def test_floor() -> None:
+
+    assert aux.floor(2.02, 1) == 2.0
+    assert aux.floor(2.02, 0.01) == 2.02
+    assert aux.floor(2.013, 0.01) == 2.01
\ No newline at end of file
diff --git a/beamtime/test/test_plotting.py b/beamtime/test/test_plotting.py
new file mode 100644
index 0000000..1374778
--- /dev/null
+++ b/beamtime/test/test_plotting.py
@@ -0,0 +1,8 @@
+import beamtime.plotting as btp
+from cycler import cycler
+import itertools
+
+
+def test_generate_colours() -> None:
+
+    assert type(btp.generate_colours('black', kind='single')) == itertools.cycle
\ No newline at end of file
diff --git a/beamtime/test/xrd/test_io.py b/beamtime/test/xrd/test_io.py
new file mode 100644
index 0000000..e69de29
diff --git a/beamtime/test/xrd/test_plot.py b/beamtime/test/xrd/test_plot.py
new file mode 100644
index 0000000..e69de29

From e07acdb4bb839580b541777ebc8937a624aecec6 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 15:06:03 +0200
Subject: [PATCH 26/57] Remove packages not used

---
 beamtime/plotting.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index 500f532..946a4e4 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -1,13 +1,11 @@
 import beamtime.auxillary as aux
 
 import matplotlib.pyplot as plt
-from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,AutoMinorLocator)
-from mpl_toolkits.axes_grid.inset_locator import (inset_axes, InsetPosition, mark_inset)
+from matplotlib.ticker import (MultipleLocator)
 import importlib
 import matplotlib.patches as mpatches
 from matplotlib.lines import Line2D
 import matplotlib.lines as mlines
-from cycler import cycler
 import itertools
 
 

From 657276eb9177669dc4e4bda468759ea64c93ee20 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 15:57:30 +0200
Subject: [PATCH 27/57] Add tests for auxillary.py

---
 beamtime/test/test_auxillary.py | 51 ++++++++++++++++++++++++++++++++-
 1 file changed, 50 insertions(+), 1 deletion(-)

diff --git a/beamtime/test/test_auxillary.py b/beamtime/test/test_auxillary.py
index 5a9e85e..668b792 100644
--- a/beamtime/test/test_auxillary.py
+++ b/beamtime/test/test_auxillary.py
@@ -1,4 +1,5 @@
 import beamtime.auxillary as aux
+import os
 
 def test_swap_values():
 
@@ -26,4 +27,52 @@ def test_floor() -> None:
 
     assert aux.floor(2.02, 1) == 2.0
     assert aux.floor(2.02, 0.01) == 2.02
-    assert aux.floor(2.013, 0.01) == 2.01
\ No newline at end of file
+    assert aux.floor(2.013, 0.01) == 2.01
+
+
+
+def test_options() -> None:
+
+
+    options = {}
+    required_options = ['test1', 'test2', 'test3', 'test4']
+    default_options = {
+        'test1': 1,
+        'test2': 2, 
+        'test3': 3,
+        'test4': 4,
+        'test5': 5,
+    }
+
+
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
+
+    assert options['test1'] == default_options['test1']
+    assert len(options.items()) == len(required_options)
+    assert 'test5' not in options.keys()
+
+
+def test_save_options() -> None:
+    
+    options = {'test1': 1, 'test2': 2}
+    path = 'tmp.dat'
+
+    aux.save_options(options, path)
+
+    assert os.path.isfile(path)
+
+    os.remove(path)
+
+
+def test_load_options() -> None:
+    
+    options = {'test1': 1, 'test2': 2}
+    path = 'tmp.dat'
+
+    aux.save_options(options, path)
+
+    loaded_options = aux.load_options(path)
+
+    assert (loaded_options['test1'] == 1) and (loaded_options['test2'] == 2)
+
+    os.remove(path)
\ No newline at end of file

From 4587322a9b199016f443e03b459e5fa1a447ac4b Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 17:25:46 +0200
Subject: [PATCH 28/57] Add tests for plotting.py

---
 beamtime/test/test_plotting.py | 126 ++++++++++++++++++++++++++++++++-
 1 file changed, 125 insertions(+), 1 deletion(-)

diff --git a/beamtime/test/test_plotting.py b/beamtime/test/test_plotting.py
index 1374778..3b9ccda 100644
--- a/beamtime/test/test_plotting.py
+++ b/beamtime/test/test_plotting.py
@@ -1,8 +1,132 @@
 import beamtime.plotting as btp
 from cycler import cycler
 import itertools
+import numpy as np
+
+import matplotlib.pyplot as plt
 
 
 def test_generate_colours() -> None:
 
-    assert type(btp.generate_colours('black', kind='single')) == itertools.cycle
\ No newline at end of file
+    assert type(btp.generate_colours('black', kind='single')) == itertools.cycle
+
+    palettes = [('qualitative', 'Dark2_8')]
+    colour_cycle = btp.generate_colours(palettes)
+
+    assert type(colour_cycle) == itertools.cycle
+
+
+    # Test that it actually loaded 8 colours when given a set of 8 colours to 
+
+    same_colour = None
+    for i in range(10):
+        colour = next(colour_cycle)
+        if i == 0:
+            first_colour = colour
+        
+        if colour == first_colour:
+            repeat_colour_index = i
+
+        
+    assert repeat_colour_index == 8
+
+
+
+
+def test_update_rc_params() -> None:
+
+    rc_params = {
+        'lines.linewidth': 100
+    }
+
+    prev_params = plt.rcParams['lines.linewidth']
+    
+    # Update run commands if any is passed (will pass an empty dictionary if not passed)
+    btp.update_rc_params(rc_params)
+
+    new_params = plt.rcParams['lines.linewidth']
+    
+    assert new_params == 100
+    assert prev_params != new_params
+
+
+    # Reset run commands
+    plt.rcdefaults()
+
+
+
+def test_scale_figure() -> None:
+
+    width, height = 1, 1
+
+    format_params = {
+        'upscaling_factor': 2,
+        'compress_width': 1,
+        'compress_height': 1
+    }
+
+    width1, height1 = btp.scale_figure(format_params=format_params, width=width, height=height)
+
+    assert width1 == 2 and height1 == 2
+
+    format_params = {
+        'upscaling_factor': 1,
+        'compress_width': 0.5,
+        'compress_height': 1
+    }
+
+    width2, height2 = btp.scale_figure(format_params=format_params, width=width, height=height)
+
+    assert width2 == 0.5 and height2 == 1
+
+    format_params = {
+        'upscaling_factor': 2,
+        'compress_width': 0.5,
+        'compress_height': 0.2
+    }
+
+    width2, height2 = btp.scale_figure(format_params=format_params, width=width, height=height)
+
+    assert width2 == 1 and height2 == 0.4
+
+    
+def test_determine_width() -> None:
+
+    conversion_cm_inch = 0.3937008 # cm to inch
+
+    format_params = {
+        'column_type': 'single',
+        'single_column_width': 5,
+        'double_column_width': 10,
+        'width_ratio': '1:1'
+    }
+
+    assert np.round(btp.determine_width(format_params),6) == np.round(5*conversion_cm_inch,6)
+    
+    format_params['column_type'] = 'double'
+
+    assert np.round(btp.determine_width(format_params), 6) == np.round(10*conversion_cm_inch, 6)
+    
+
+    format_params['column_type'] = 'single'
+    format_params['width_ratio'] = '1:2'
+
+    assert np.round(btp.determine_width(format_params), 6) == np.round(2.5*conversion_cm_inch, 6)
+
+def test_determine_height() -> None:
+
+
+    width = 1
+
+    format_params = {
+        'aspect_ratio': '1:1'
+    }
+
+    assert btp.determine_height(format_params=format_params, width=width) == 1
+
+    format_params['aspect_ratio'] = '3:1'
+
+    assert (btp.determine_height(format_params=format_params, width=width) - 0.333333333333333) < 10e-7
+
+    assert True
+

From d702875ab6ff31aed76a2c4e5c75a3e32894ed8c Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 17:28:04 +0200
Subject: [PATCH 29/57] Ignore DeprecationWarning

---
 beamtime/test/pytest.ini | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/beamtime/test/pytest.ini b/beamtime/test/pytest.ini
index 8108e29..c317621 100644
--- a/beamtime/test/pytest.ini
+++ b/beamtime/test/pytest.ini
@@ -4,3 +4,6 @@
 minversion = 6.0
 testpaths = 
 	.
+
+filterwarnings =
+	ignore::DeprecationWarning

From e3b0e2bc14fee5733f87803254aa4fe2e614b9f6 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Wed, 6 Apr 2022 17:29:45 +0200
Subject: [PATCH 30/57] Move some files to root folder

---
 beamtime/README.md => README.md               | 0
 beamtime/feature_list.txt => feature_list.txt | 0
 beamtime/reqirements2.txt => reqirements2.txt | 0
 beamtime/requirements.txt => requirements.txt | 0
 4 files changed, 0 insertions(+), 0 deletions(-)
 rename beamtime/README.md => README.md (100%)
 rename beamtime/feature_list.txt => feature_list.txt (100%)
 rename beamtime/reqirements2.txt => reqirements2.txt (100%)
 rename beamtime/requirements.txt => requirements.txt (100%)

diff --git a/beamtime/README.md b/README.md
similarity index 100%
rename from beamtime/README.md
rename to README.md
diff --git a/beamtime/feature_list.txt b/feature_list.txt
similarity index 100%
rename from beamtime/feature_list.txt
rename to feature_list.txt
diff --git a/beamtime/reqirements2.txt b/reqirements2.txt
similarity index 100%
rename from beamtime/reqirements2.txt
rename to reqirements2.txt
diff --git a/beamtime/requirements.txt b/requirements.txt
similarity index 100%
rename from beamtime/requirements.txt
rename to requirements.txt

From 1db489c21ddd0926b95ae617f56bb4f167201dbe Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 12:02:13 +0200
Subject: [PATCH 31/57] First commit on new repo

---
 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..2bf4342
--- /dev/null
+++ b/beamtime/test.txt
@@ -0,0 +1 @@
+Testing new repository
\ No newline at end of file

From a84bd065b2bc1b6bd62277af160088982bc398fa Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 12:20:08 +0200
Subject: [PATCH 32/57] Testing push on new repo

---
 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 2bf4342..0000000
--- a/beamtime/test.txt
+++ /dev/null
@@ -1 +0,0 @@
-Testing new repository
\ No newline at end of file

From e8ae6ba1224450ef587eac25ea5289a53c36a768 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 12:21:43 +0200
Subject: [PATCH 33/57] Testing push on new repo again

---
 beamtime/test.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 beamtime/test.txt

diff --git a/beamtime/test.txt b/beamtime/test.txt
new file mode 100644
index 0000000..e69de29

From aafcc5a1ed5b432e1ab6e4b8ed7f0eeda71cb90d Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 12:25:31 +0200
Subject: [PATCH 34/57] Test of push in VS Code

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

diff --git a/beamtime/test.txt b/beamtime/test.txt
index e69de29..85476a8 100644
--- a/beamtime/test.txt
+++ b/beamtime/test.txt
@@ -0,0 +1 @@
+sdfsdfsdfsdf
\ No newline at end of file

From ab6bf231001a82deb1e29048d43eedf6033d9443 Mon Sep 17 00:00:00 2001
From: halvorhv <h.h.hval@kjemi.uio.no>
Date: Thu, 7 Apr 2022 12:30:32 +0200
Subject: [PATCH 35/57] testing from terminal

---
 beamtime/test2.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 beamtime/test2.txt

diff --git a/beamtime/test2.txt b/beamtime/test2.txt
new file mode 100644
index 0000000..e69de29

From bf689886659bb64be611d1d6441269a8db96222b Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 14:05:40 +0200
Subject: [PATCH 36/57] Add more tests for plotting.py and made more general

---
 beamtime/plotting.py           | 78 ++++++----------------------------
 beamtime/test/test_plotting.py | 49 +++++++++++++++++++++
 2 files changed, 62 insertions(+), 65 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index 946a4e4..780a022 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -20,8 +20,15 @@ def prepare_plot(options={}):
     
     format_params will determine the size, aspect ratio, resolution etc. of the figure. Should be modified to conform with any requirements from a journal.'''
 
-    rc_params = options['rc_params']
-    format_params = options['format_params']
+    if 'rc_params' in options.keys():
+        rc_params = options['rc_params']
+    else:
+        rc_params = {}
+
+    if 'format_params' in options.keys():
+        format_params = options['format_params']
+    else:
+        format_params = {}
     
     required_format_params = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 
     'width', 'height', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi',
@@ -80,53 +87,14 @@ def prepare_plot(options={}):
 
         return fig, axes
 
-def prepare_plots(options={}):
-
-    rc_params = options['rc_params']
-    format_params = options['format_params']
-    
-    required_options = ['single_column_width', 'double_column_width', 'column_type', 'width_ratio', 'aspect_ratio', 'compress_width', 'compress_height', 'upscaling_factor', 'dpi']
-
-    default_options = {
-    'single_column_width': 8.3,
-    'double_column_width': 17.1,
-    'column_type': 'single',
-    'width_ratio': '1:1',
-    'aspect_ratio': '1:1',
-    'compress_width': 1,
-    'compress_height': 1,
-    'upscaling_factor': 1.0,
-    'dpi': 600, 
-    }
-    
-    format_params = aux.update_options(format_params, required_options, default_options)
-
-
-    # Reset run commands
-    plt.rcdefaults()
-    
-    # Update run commands if any is passed (will pass an empty dictionary if not passed)
-    update_rc_params(rc_params)
-    
-    width = determine_width(format_params)
-    height = determine_height(format_params, width)
-    width, height = scale_figure(options=format_params, width=width, height=height)
-
-
-    if options['plot_kind'] == 'relative':
-        fig, axes = plt.subplots(nrows=1, ncols=options['number_of_frames'], figsize=(width,height), facecolor='w', dpi=format_params['dpi'])
-
-    elif options['plot_kind'] == 'absolute':
-        fig, axes = plt.subplots(nrows=2, ncols=options['number_of_frames'], figsize=(width,height), gridspec_kw={'height_ratios': [1,5]}, facecolor='w', dpi=format_params['dpi'])
-    
-    return fig, axes
-
 
 def adjust_plot(fig, ax, options):
     ''' A general function to adjust plot according to contents of the options-dictionary '''
     
     required_options = [
     'plot_kind', 
+    'xlabel', 'ylabel',
+    'xunit', 'yunit',
     'hide_x_labels', 'hide_y_labels',
     'hide_x_ticklabels', 'hide_y_ticklabels',
     'hide_x_ticks', 'hide_y_ticks',
@@ -141,6 +109,8 @@ def adjust_plot(fig, ax, options):
 
     default_options = {
         'plot_kind': None, # defaults to None, but should be utilised when requiring special formatting for a particular plot 
+        'xlabel': None, 'ylabel': None,
+        'xunit': None, 'yunit': None,
         'hide_x_labels': False, 'hide_y_labels': False, # Whether the main labels on the x- and/or y-axes should be hidden
         'hide_x_ticklabels': False, 'hide_y_ticklabels': False, # Whether ticklabels on the x- and/or y-axes should be hidden
         'hide_x_ticks': False, 'hide_y_ticks': False, # Whether the ticks on the x- and/or y-axes should be hidden
@@ -305,28 +275,6 @@ def ipywidgets_update(func, data, options={}, **kwargs):
     func(data=data, options=options)
 
 
-def update_widgets(options):
-
-    for widget in options['widgets'].values():
-
-        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']
-
-
 
 def determine_width(format_params):
     ''' '''
diff --git a/beamtime/test/test_plotting.py b/beamtime/test/test_plotting.py
index 3b9ccda..8979bc1 100644
--- a/beamtime/test/test_plotting.py
+++ b/beamtime/test/test_plotting.py
@@ -4,6 +4,7 @@ import itertools
 import numpy as np
 
 import matplotlib.pyplot as plt
+import matplotlib as mpl
 
 
 def test_generate_colours() -> None:
@@ -130,3 +131,51 @@ def test_determine_height() -> None:
 
     assert True
 
+
+
+def test_prepare_plot() -> None:
+
+    fig, ax = btp.prepare_plot()
+
+    assert type(fig) == plt.Figure
+    assert fig.get_dpi() == 600
+    assert ax.get_xlim() == (0.0, 1.0)
+
+
+
+def test_adjust_plot() -> None:
+
+    fig, ax = btp.prepare_plot()
+
+    options = {
+        'xlim': (0.0, 2.0),
+        'title': 'Test'
+    }
+
+    fig, ax = btp.adjust_plot(fig, ax, options)
+
+
+    assert ax.get_xlim() == (0.0, 2.0)
+    assert ax.get_title() == 'Test'
+
+
+    
+def test_ipywidgets_update() -> None:
+
+
+
+    def test_func(data, options):
+        test1 = options['test1']
+        test2 = options['test2']
+
+        assert type(data) == dict
+        assert test1 == 1
+        assert test2 == 2
+
+
+
+    data = {}
+    options = {}
+
+    btp.ipywidgets_update(func=test_func, data=data, options=options, test1=1, test2=2)
+

From 239ea9f61e5fd8d1db1e8fc2e8a4f15429bddd23 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:10:25 +0200
Subject: [PATCH 37/57] Create automated testing

---
 .github/workflows/python-app.yml | 39 ++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 .github/workflows/python-app.yml

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
new file mode 100644
index 0000000..2e8690d
--- /dev/null
+++ b/.github/workflows/python-app.yml
@@ -0,0 +1,39 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest

From 5c9c93fbb60b6a6b28ba155d34206215d95dbb1c Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 14:14:38 +0200
Subject: [PATCH 38/57] Exporting new requirements and environment

---
 environment.yml  | 154 +++++++++++++++++++++++++++++
 reqirements2.txt | 141 --------------------------
 requirements.txt | 253 +++++++++++++++++++++++++++--------------------
 3 files changed, 302 insertions(+), 246 deletions(-)
 create mode 100644 environment.yml
 delete mode 100644 reqirements2.txt

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..b80378b
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,154 @@
+name: beamtime
+channels:
+  - conda-forge
+  - diffpy
+  - defaults
+dependencies:
+  - argon2-cffi=21.3.0=pyhd3eb1b0_0
+  - argon2-cffi-bindings=21.2.0=py39h2bbff1b_0
+  - atomicwrites=1.4.0=py_0
+  - attrs=21.4.0=pyhd3eb1b0_0
+  - backcall=0.2.0=pyhd3eb1b0_0
+  - blas=1.0=mkl
+  - bleach=4.1.0=pyhd3eb1b0_0
+  - bottleneck=1.3.2=py39h7cc1a96_1
+  - ca-certificates=2022.3.29=haa95532_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - certifi=2021.10.8=py39haa95532_2
+  - cffi=1.15.0=py39h2bbff1b_1
+  - colorama=0.4.4=pyhd3eb1b0_0
+  - cycler=0.10.0=py_2
+  - debugpy=1.4.1=py39hd77b12b_0
+  - decorator=5.1.0=pyhd3eb1b0_0
+  - defusedxml=0.7.1=pyhd3eb1b0_0
+  - entrypoints=0.3=py39haa95532_0
+  - fabio=0.12.0=py39h5d4886f_0
+  - freetype=2.10.4=h546665d_1
+  - glymur=0.9.4=pyhd8ed1ab_0
+  - h5py=3.2.1=nompi_py39hf27771d_100
+  - hdf5=1.10.6=nompi_h5268f04_1114
+  - hdf5plugin=3.1.1=py39h71586dd_0
+  - icc_rt=2019.0.0=h0cc432a_1
+  - icu=68.1=h6c2663c_0
+  - importlib-metadata=4.8.2=py39haa95532_0
+  - importlib_metadata=4.8.2=hd3eb1b0_0
+  - iniconfig=1.1.1=pyhd3eb1b0_0
+  - intel-openmp=2021.3.0=haa95532_3372
+  - ipykernel=6.4.1=py39haa95532_1
+  - ipython=7.27.0=py39hd4e2768_0
+  - ipython_genutils=0.2.0=pyhd3eb1b0_1
+  - ipywidgets=7.6.5=pyhd3eb1b0_1
+  - jbig=2.1=h8d14728_2003
+  - jedi=0.18.0=py39haa95532_1
+  - jinja2=3.0.2=pyhd3eb1b0_0
+  - jpeg=9d=h2bbff1b_0
+  - jsonschema=3.2.0=pyhd3eb1b0_2
+  - jupyter_client=7.0.1=pyhd3eb1b0_0
+  - jupyter_core=4.8.1=py39haa95532_0
+  - jupyterlab_pygments=0.1.2=py_0
+  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
+  - kiwisolver=1.3.2=py39h2e07f2f_0
+  - krb5=1.19.2=hbae68bd_2
+  - lerc=3.0=h0e60522_0
+  - libclang=11.1.0=default_h5c34c98_1
+  - libcurl=7.79.1=h789b8ee_1
+  - libdeflate=1.8=h2bbff1b_5
+  - libiconv=1.16=he774522_0
+  - libpng=1.6.37=h1d00b33_2
+  - libssh2=1.10.0=h680486a_2
+  - libtiff=4.3.0=hd413186_2
+  - libwebp=1.2.0=h2bbff1b_0
+  - libxml2=2.9.12=h0ad7f3c_0
+  - libxslt=1.1.34=he774522_0
+  - libzlib=1.2.11=h8ffe710_1013
+  - lxml=4.6.3=py39h4fd7cdf_0
+  - lz4-c=1.9.3=h8ffe710_1
+  - mako=1.1.5=pyhd8ed1ab_0
+  - markupsafe=2.0.1=py39h2bbff1b_0
+  - matplotlib=3.4.3=py39hcbf5309_1
+  - matplotlib-base=3.4.3=py39h581301d_1
+  - matplotlib-inline=0.1.2=pyhd3eb1b0_2
+  - mistune=0.8.4=py39h2bbff1b_1000
+  - mkl=2021.3.0=haa95532_524
+  - mkl-service=2.4.0=py39h2bbff1b_0
+  - mkl_fft=1.3.1=py39h277e83a_0
+  - mkl_random=1.2.2=py39hf11a4ad_0
+  - mpmath=1.2.1=py39haa95532_0
+  - nbclient=0.5.11=pyhd3eb1b0_0
+  - nbconvert=6.1.0=py39haa95532_0
+  - nbformat=5.1.3=pyhd3eb1b0_0
+  - nest-asyncio=1.5.1=pyhd3eb1b0_0
+  - notebook=6.4.8=py39haa95532_0
+  - numexpr=2.7.3=py39hb80d3ca_1
+  - numpy=1.21.2=py39hfca59bb_0
+  - numpy-base=1.21.2=py39h0829f74_0
+  - olefile=0.46=pyh9f0ad1d_1
+  - openjpeg=2.4.0=hb211442_1
+  - openssl=1.1.1n=h2bbff1b_0
+  - packaging=21.3=pyhd3eb1b0_0
+  - palettable=3.3.0=pyhd3eb1b0_0
+  - pandas=1.3.3=py39h6214cd6_0
+  - pandocfilters=1.5.0=pyhd3eb1b0_0
+  - parso=0.8.2=pyhd3eb1b0_0
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
+  - pillow=8.4.0=py39hd45dc43_0
+  - pip=21.2.4=py39haa95532_0
+  - pluggy=1.0.0=py39haa95532_1
+  - prometheus_client=0.13.1=pyhd3eb1b0_0
+  - prompt-toolkit=3.0.20=pyhd3eb1b0_0
+  - py=1.11.0=pyhd3eb1b0_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pyfai=0.20.0=hd8ed1ab_0
+  - pyfai-base=0.20.0=py39h2e25243_0
+  - pygments=2.10.0=pyhd3eb1b0_0
+  - pyparsing=2.4.7=pyhd3eb1b0_0
+  - pyqt=5.12.3=py39hcbf5309_7
+  - pyqt-impl=5.12.3=py39h415ef7b_7
+  - pyqt5-sip=4.19.18=py39h415ef7b_7
+  - pyqtchart=5.12=py39h415ef7b_7
+  - pyqtwebengine=5.12.1=py39h415ef7b_7
+  - pyreadline=2.1=py39hcbf5309_1004
+  - pyrsistent=0.18.0=py39h196d8e1_0
+  - pytest=7.1.1=py39haa95532_0
+  - python=3.9.7=h6244533_1
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python_abi=3.9=2_cp39
+  - pytz=2021.3=pyhd3eb1b0_0
+  - pywin32=228=py39hbaba5e8_1
+  - pywinpty=2.0.2=py39h5da7b33_0
+  - pyzmq=22.2.1=py39hd77b12b_1
+  - qt=5.12.9=h5909a2a_4
+  - qtconsole=5.1.1=pyhd3eb1b0_0
+  - qtpy=1.11.2=pyhd8ed1ab_0
+  - scipy=1.7.1=py39hbe87c03_2
+  - seaborn=0.11.2=pyhd3eb1b0_0
+  - send2trash=1.8.0=pyhd3eb1b0_1
+  - setuptools=58.0.4=py39haa95532_0
+  - silx=0.15.2=hd8ed1ab_0
+  - silx-base=0.15.2=py39h2e25243_0
+  - six=1.16.0=pyhd3eb1b0_0
+  - sqlite=3.36.0=h2bbff1b_0
+  - sympy=1.9=py39haa95532_0
+  - terminado=0.13.1=py39haa95532_0
+  - testpath=0.5.0=pyhd3eb1b0_0
+  - tk=8.6.11=h8ffe710_1
+  - tomli=1.2.2=pyhd3eb1b0_0
+  - tornado=6.1=py39h2bbff1b_0
+  - traitlets=5.1.0=pyhd3eb1b0_0
+  - typing-extensions=3.10.0.2=hd3eb1b0_0
+  - typing_extensions=3.10.0.2=pyh06a4308_0
+  - tzdata=2021a=h5d7bf9c_0
+  - vc=14.2=h21ff451_1
+  - vs2015_runtime=14.27.29016=h5e58377_2
+  - wcwidth=0.2.5=pyhd3eb1b0_0
+  - webencodings=0.5.1=py39haa95532_1
+  - wheel=0.37.0=pyhd3eb1b0_1
+  - widgetsnbextension=3.5.2=py39haa95532_0
+  - wincertstore=0.2=py39haa95532_2
+  - winpty=0.4.3=4
+  - xz=5.2.5=h62dcd97_1
+  - zipp=3.7.0=pyhd3eb1b0_0
+  - zlib=1.2.11=h8ffe710_1013
+  - zstd=1.5.0=h6255e5f_0
+prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime
diff --git a/reqirements2.txt b/reqirements2.txt
deleted file mode 100644
index 5cef354..0000000
--- a/reqirements2.txt
+++ /dev/null
@@ -1,141 +0,0 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: win-64
-argon2-cffi=21.3.0=pyhd3eb1b0_0
-argon2-cffi-bindings=21.2.0=py39h2bbff1b_0
-attrs=21.4.0=pyhd3eb1b0_0
-backcall=0.2.0=pyhd3eb1b0_0
-beamtime=0.1=pypi_0
-blas=1.0=mkl
-bleach=4.1.0=pyhd3eb1b0_0
-bottleneck=1.3.2=py39h7cc1a96_1
-ca-certificates=2022.2.1=haa95532_0
-cached-property=1.5.2=hd8ed1ab_1
-cached_property=1.5.2=pyha770c72_1
-certifi=2021.10.8=py39haa95532_2
-cffi=1.15.0=py39h2bbff1b_1
-colorama=0.4.4=pyhd3eb1b0_0
-cycler=0.10.0=py_2
-debugpy=1.4.1=py39hd77b12b_0
-decorator=5.1.0=pyhd3eb1b0_0
-defusedxml=0.7.1=pyhd3eb1b0_0
-entrypoints=0.3=py39haa95532_0
-fabio=0.12.0=py39h5d4886f_0
-freetype=2.10.4=h546665d_1
-glymur=0.9.4=pyhd8ed1ab_0
-h5py=3.2.1=nompi_py39hf27771d_100
-hdf5=1.10.6=nompi_h5268f04_1114
-hdf5plugin=3.1.1=py39h71586dd_0
-icc_rt=2019.0.0=h0cc432a_1
-icu=68.1=h6c2663c_0
-importlib-metadata=4.8.2=py39haa95532_0
-importlib_metadata=4.8.2=hd3eb1b0_0
-intel-openmp=2021.3.0=haa95532_3372
-ipykernel=6.4.1=py39haa95532_1
-ipython=7.27.0=py39hd4e2768_0
-ipython_genutils=0.2.0=pyhd3eb1b0_1
-ipywidgets=7.6.5=pyhd3eb1b0_1
-jbig=2.1=h8d14728_2003
-jedi=0.18.0=py39haa95532_1
-jinja2=3.0.2=pyhd3eb1b0_0
-jpeg=9d=h2bbff1b_0
-jsonschema=3.2.0=pyhd3eb1b0_2
-jupyter_client=7.0.1=pyhd3eb1b0_0
-jupyter_core=4.8.1=py39haa95532_0
-jupyterlab_pygments=0.1.2=py_0
-jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
-kiwisolver=1.3.2=py39h2e07f2f_0
-krb5=1.19.2=hbae68bd_2
-lerc=3.0=h0e60522_0
-libclang=11.1.0=default_h5c34c98_1
-libcurl=7.79.1=h789b8ee_1
-libdeflate=1.8=h2bbff1b_5
-libiconv=1.16=he774522_0
-libpng=1.6.37=h1d00b33_2
-libssh2=1.10.0=h680486a_2
-libtiff=4.3.0=hd413186_2
-libwebp=1.2.0=h2bbff1b_0
-libxml2=2.9.12=h0ad7f3c_0
-libxslt=1.1.34=he774522_0
-libzlib=1.2.11=h8ffe710_1013
-lxml=4.6.3=py39h4fd7cdf_0
-lz4-c=1.9.3=h8ffe710_1
-mako=1.1.5=pyhd8ed1ab_0
-markupsafe=2.0.1=py39h2bbff1b_0
-matplotlib=3.4.3=py39hcbf5309_1
-matplotlib-base=3.4.3=py39h581301d_1
-matplotlib-inline=0.1.2=pyhd3eb1b0_2
-mistune=0.8.4=py39h2bbff1b_1000
-mkl=2021.3.0=haa95532_524
-mkl-service=2.4.0=py39h2bbff1b_0
-mkl_fft=1.3.1=py39h277e83a_0
-mkl_random=1.2.2=py39hf11a4ad_0
-nbclient=0.5.11=pyhd3eb1b0_0
-nbconvert=6.1.0=py39haa95532_0
-nbformat=5.1.3=pyhd3eb1b0_0
-nest-asyncio=1.5.1=pyhd3eb1b0_0
-notebook=6.4.8=py39haa95532_0
-numexpr=2.7.3=py39hb80d3ca_1
-numpy=1.21.2=py39hfca59bb_0
-numpy-base=1.21.2=py39h0829f74_0
-olefile=0.46=pyh9f0ad1d_1
-openjpeg=2.4.0=hb211442_1
-openssl=1.1.1m=h2bbff1b_0
-packaging=21.3=pyhd3eb1b0_0
-pandas=1.3.3=py39h6214cd6_0
-pandocfilters=1.5.0=pyhd3eb1b0_0
-parso=0.8.2=pyhd3eb1b0_0
-pickleshare=0.7.5=pyhd3eb1b0_1003
-pillow=8.4.0=py39hd45dc43_0
-pip=21.2.4=py39haa95532_0
-prometheus_client=0.13.1=pyhd3eb1b0_0
-prompt-toolkit=3.0.20=pyhd3eb1b0_0
-pycparser=2.21=pyhd3eb1b0_0
-pyfai=0.20.0=hd8ed1ab_0
-pyfai-base=0.20.0=py39h2e25243_0
-pygments=2.10.0=pyhd3eb1b0_0
-pyparsing=2.4.7=pyhd3eb1b0_0
-pyqt=5.12.3=py39hcbf5309_7
-pyqt-impl=5.12.3=py39h415ef7b_7
-pyqt5-sip=4.19.18=py39h415ef7b_7
-pyqtchart=5.12=py39h415ef7b_7
-pyqtwebengine=5.12.1=py39h415ef7b_7
-pyreadline=2.1=py39hcbf5309_1004
-pyrsistent=0.18.0=py39h196d8e1_0
-python=3.9.7=h6244533_1
-python-dateutil=2.8.2=pyhd3eb1b0_0
-python_abi=3.9=2_cp39
-pytz=2021.3=pyhd3eb1b0_0
-pywin32=228=py39hbaba5e8_1
-pywinpty=2.0.2=py39h5da7b33_0
-pyzmq=22.2.1=py39hd77b12b_1
-qt=5.12.9=h5909a2a_4
-qtconsole=5.1.1=pyhd3eb1b0_0
-qtpy=1.11.2=pyhd8ed1ab_0
-scipy=1.7.1=py39hbe87c03_2
-send2trash=1.8.0=pyhd3eb1b0_1
-setuptools=58.0.4=py39haa95532_0
-silx=0.15.2=hd8ed1ab_0
-silx-base=0.15.2=py39h2e25243_0
-six=1.16.0=pyhd3eb1b0_0
-sqlite=3.36.0=h2bbff1b_0
-terminado=0.13.1=py39haa95532_0
-testpath=0.5.0=pyhd3eb1b0_0
-tk=8.6.11=h8ffe710_1
-tornado=6.1=py39h2bbff1b_0
-traitlets=5.1.0=pyhd3eb1b0_0
-typing-extensions=3.10.0.2=hd3eb1b0_0
-typing_extensions=3.10.0.2=pyh06a4308_0
-tzdata=2021a=h5d7bf9c_0
-vc=14.2=h21ff451_1
-vs2015_runtime=14.27.29016=h5e58377_2
-wcwidth=0.2.5=pyhd3eb1b0_0
-webencodings=0.5.1=py39haa95532_1
-wheel=0.37.0=pyhd3eb1b0_1
-widgetsnbextension=3.5.2=py39haa95532_0
-wincertstore=0.2=py39haa95532_2
-winpty=0.4.3=4
-xz=5.2.5=h62dcd97_1
-zipp=3.7.0=pyhd3eb1b0_0
-zlib=1.2.11=h8ffe710_1013
-zstd=1.5.0=h6255e5f_0
diff --git a/requirements.txt b/requirements.txt
index d8eeb75..8b428c5 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,108 +1,151 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: win-64
-@EXPLICIT
-https://repo.anaconda.com/pkgs/main/win-64/blas-1.0-mkl.conda
-https://conda.anaconda.org/conda-forge/win-64/ca-certificates-2021.10.8-h5b45459_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/icc_rt-2019.0.0-h0cc432a_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/intel-openmp-2021.3.0-haa95532_3372.conda
-https://repo.anaconda.com/pkgs/main/noarch/tzdata-2021a-h5d7bf9c_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/vs2015_runtime-14.27.29016-h5e58377_2.conda
-https://repo.anaconda.com/pkgs/main/win-64/mkl-2021.3.0-haa95532_524.conda
-https://repo.anaconda.com/pkgs/main/win-64/vc-14.2-h21ff451_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/icu-68.1-h6c2663c_0.conda
-https://conda.anaconda.org/conda-forge/win-64/jbig-2.1-h8d14728_2003.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/jpeg-9d-h2bbff1b_0.conda
-https://conda.anaconda.org/conda-forge/win-64/lerc-3.0-h0e60522_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/libclang-11.1.0-default_h5c34c98_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/libdeflate-1.8-h2bbff1b_5.conda
-https://conda.anaconda.org/conda-forge/win-64/libiconv-1.16-he774522_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/libwebp-1.2.0-h2bbff1b_0.conda
-https://conda.anaconda.org/conda-forge/win-64/libzlib-1.2.11-h8ffe710_1013.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/lz4-c-1.9.3-h8ffe710_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/openssl-1.1.1l-h8ffe710_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/sqlite-3.36.0-h2bbff1b_0.conda
-https://conda.anaconda.org/conda-forge/win-64/tk-8.6.11-h8ffe710_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/xz-5.2.5-h62dcd97_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/krb5-1.19.2-hbae68bd_2.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/python-3.9.7-h6244533_1.conda
-https://conda.anaconda.org/conda-forge/win-64/zlib-1.2.11-h8ffe710_1013.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/backcall-0.2.0-pyhd3eb1b0_0.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/cached_property-1.5.2-pyha770c72_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/certifi-2021.10.8-py39haa95532_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/colorama-0.4.4-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/debugpy-1.4.1-py39hd77b12b_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/decorator-5.1.0-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/entrypoints-0.3-py39haa95532_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/ipython_genutils-0.2.0-pyhd3eb1b0_1.conda
-https://conda.anaconda.org/conda-forge/win-64/libpng-1.6.37-h1d00b33_2.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/libssh2-1.10.0-h680486a_2.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/libxml2-2.9.12-h0ad7f3c_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/markupsafe-2.0.1-py39h2bbff1b_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/nest-asyncio-1.5.1-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/noarch/olefile-0.46-pyh9f0ad1d_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/parso-0.8.2-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/pickleshare-0.7.5-pyhd3eb1b0_1003.conda
-https://repo.anaconda.com/pkgs/main/noarch/pyparsing-2.4.7-pyhd3eb1b0_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/python_abi-3.9-2_cp39.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/pytz-2021.3-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/pywin32-228-py39hbaba5e8_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/pyzmq-22.2.1-py39hd77b12b_1.conda
-https://conda.anaconda.org/conda-forge/noarch/qtpy-1.11.2-pyhd8ed1ab_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/six-1.16.0-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/tornado-6.1-py39h2bbff1b_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/traitlets-5.1.0-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/wcwidth-0.2.5-pyhd3eb1b0_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/wheel-0.37.0-pyhd3eb1b0_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/wincertstore-0.2-py39haa95532_2.conda
-https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.0-h6255e5f_0.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/cycler-0.10.0-py_2.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/freetype-2.10.4-h546665d_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/jedi-0.18.0-py39haa95532_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/jupyter_core-4.8.1-py39haa95532_0.conda
-https://conda.anaconda.org/conda-forge/win-64/kiwisolver-1.3.2-py39h2e07f2f_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/libcurl-7.79.1-h789b8ee_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/libtiff-4.3.0-hd413186_2.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/libxslt-1.1.34-he774522_0.conda
-https://conda.anaconda.org/conda-forge/noarch/mako-1.1.5-pyhd8ed1ab_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/matplotlib-inline-0.1.2-pyhd3eb1b0_2.conda
-https://repo.anaconda.com/pkgs/main/win-64/mkl-service-2.4.0-py39h2bbff1b_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/prompt-toolkit-3.0.20-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/win-64/pyqt5-sip-4.19.18-py39h415ef7b_7.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/pyreadline-2.1-py39hcbf5309_1004.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/python-dateutil-2.8.2-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/win-64/qt-5.12.9-h5909a2a_4.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/setuptools-58.0.4-py39haa95532_0.conda
-https://conda.anaconda.org/conda-forge/win-64/hdf5-1.10.6-nompi_h5268f04_1114.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/jupyter_client-7.0.1-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/win-64/lxml-4.6.3-py39h4fd7cdf_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/numpy-base-1.21.2-py39h0829f74_0.conda
-https://conda.anaconda.org/conda-forge/win-64/openjpeg-2.4.0-hb211442_1.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/pillow-8.4.0-py39hd45dc43_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/pip-21.2.4-py39haa95532_0.conda
-https://repo.anaconda.com/pkgs/main/noarch/pygments-2.10.0-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/win-64/pyqt-impl-5.12.3-py39h415ef7b_7.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/ipython-7.27.0-py39hd4e2768_0.conda
-https://conda.anaconda.org/conda-forge/win-64/pyqtchart-5.12-py39h415ef7b_7.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/pyqtwebengine-5.12.1-py39h415ef7b_7.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/ipykernel-6.4.1-py39haa95532_1.conda
-https://conda.anaconda.org/conda-forge/win-64/pyqt-5.12.3-py39hcbf5309_7.tar.bz2
-https://repo.anaconda.com/pkgs/main/noarch/qtconsole-5.1.1-pyhd3eb1b0_0.conda
-https://conda.anaconda.org/conda-forge/noarch/glymur-0.9.4-pyhd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/fabio-0.12.0-py39h5d4886f_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/h5py-3.2.1-nompi_py39hf27771d_100.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/hdf5plugin-3.1.1-py39h71586dd_0.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/matplotlib-3.4.3-py39hcbf5309_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/matplotlib-base-3.4.3-py39h581301d_1.tar.bz2
-https://conda.anaconda.org/conda-forge/win-64/silx-base-0.15.2-py39h2e25243_0.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/silx-0.15.2-hd8ed1ab_0.tar.bz2
-https://conda.anaconda.org/conda-forge/noarch/pyfai-0.20.0-hd8ed1ab_0.tar.bz2
-https://repo.anaconda.com/pkgs/main/win-64/bottleneck-1.3.2-py39h7cc1a96_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/mkl_fft-1.3.1-py39h277e83a_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/mkl_random-1.2.2-py39hf11a4ad_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/numpy-1.21.2-py39hfca59bb_0.conda
-https://repo.anaconda.com/pkgs/main/win-64/numexpr-2.7.3-py39hb80d3ca_1.conda
-https://repo.anaconda.com/pkgs/main/win-64/scipy-1.7.1-py39hbe87c03_2.conda
-https://repo.anaconda.com/pkgs/main/win-64/pandas-1.3.3-py39h6214cd6_0.conda
-https://conda.anaconda.org/conda-forge/win-64/pyfai-base-0.20.0-py39h2e25243_0.tar.bz2
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+kiwisolver=1.3.2=py39h2e07f2f_0
+krb5=1.19.2=hbae68bd_2
+lerc=3.0=h0e60522_0
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+libcurl=7.79.1=h789b8ee_1
+libdeflate=1.8=h2bbff1b_5
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+libzlib=1.2.11=h8ffe710_1013
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+lz4-c=1.9.3=h8ffe710_1
+mako=1.1.5=pyhd8ed1ab_0
+markupsafe=2.0.1=py39h2bbff1b_0
+matplotlib=3.4.3=py39hcbf5309_1
+matplotlib-base=3.4.3=py39h581301d_1
+matplotlib-inline=0.1.2=pyhd3eb1b0_2
+mistune=0.8.4=py39h2bbff1b_1000
+mkl=2021.3.0=haa95532_524
+mkl-service=2.4.0=py39h2bbff1b_0
+mkl_fft=1.3.1=py39h277e83a_0
+mkl_random=1.2.2=py39hf11a4ad_0
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+pickleshare=0.7.5=pyhd3eb1b0_1003
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+pip=21.2.4=py39haa95532_0
+pluggy=1.0.0=py39haa95532_1
+prometheus_client=0.13.1=pyhd3eb1b0_0
+prompt-toolkit=3.0.20=pyhd3eb1b0_0
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+pyfai=0.20.0=hd8ed1ab_0
+pyfai-base=0.20.0=py39h2e25243_0
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+pyqtchart=5.12=py39h415ef7b_7
+pyqtwebengine=5.12.1=py39h415ef7b_7
+pyreadline=2.1=py39hcbf5309_1004
+pyrsistent=0.18.0=py39h196d8e1_0
+pytest=7.1.1=py39haa95532_0
+python=3.9.7=h6244533_1
+python-dateutil=2.8.2=pyhd3eb1b0_0
+python_abi=3.9=2_cp39
+pytz=2021.3=pyhd3eb1b0_0
+pywin32=228=py39hbaba5e8_1
+pywinpty=2.0.2=py39h5da7b33_0
+pyzmq=22.2.1=py39hd77b12b_1
+qt=5.12.9=h5909a2a_4
+qtconsole=5.1.1=pyhd3eb1b0_0
+qtpy=1.11.2=pyhd8ed1ab_0
+scipy=1.7.1=py39hbe87c03_2
+seaborn=0.11.2=pyhd3eb1b0_0
+send2trash=1.8.0=pyhd3eb1b0_1
+setuptools=58.0.4=py39haa95532_0
+silx=0.15.2=hd8ed1ab_0
+silx-base=0.15.2=py39h2e25243_0
+six=1.16.0=pyhd3eb1b0_0
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+sympy=1.9=py39haa95532_0
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+tornado=6.1=py39h2bbff1b_0
+traitlets=5.1.0=pyhd3eb1b0_0
+typing-extensions=3.10.0.2=hd3eb1b0_0
+typing_extensions=3.10.0.2=pyh06a4308_0
+tzdata=2021a=h5d7bf9c_0
+vc=14.2=h21ff451_1
+vs2015_runtime=14.27.29016=h5e58377_2
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+wheel=0.37.0=pyhd3eb1b0_1
+widgetsnbextension=3.5.2=py39haa95532_0
+wincertstore=0.2=py39haa95532_2
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+zipp=3.7.0=pyhd3eb1b0_0
+zlib=1.2.11=h8ffe710_1013
+zstd=1.5.0=h6255e5f_0

From b5f4f98070dd30292f98b06f056d34a76526454d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:22:28 +0200
Subject: [PATCH 39/57] Delete first attempt at automated testing

---
 .github/workflows/python-app.yml | 39 --------------------------------
 1 file changed, 39 deletions(-)
 delete mode 100644 .github/workflows/python-app.yml

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
deleted file mode 100644
index 2e8690d..0000000
--- a/.github/workflows/python-app.yml
+++ /dev/null
@@ -1,39 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python application
-
-on:
-  push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
-
-permissions:
-  contents: read
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest

From 739b197e9aca699af70dd5cb984417d155b1071f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:23:03 +0200
Subject: [PATCH 40/57] Set up automated testing with conda

---
 .github/workflows/python-package-conda.yml | 34 ++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 0000000..57940bd
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,34 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.10
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

From c9885976f6d9a71b8ca6ae79e7142e0197a0ac01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:24:57 +0200
Subject: [PATCH 41/57] Change python version in automated testing

---
 .github/workflows/python-package-conda.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 57940bd..6261945 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -10,10 +10,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.10
+    - name: Set up Python 3.9
       uses: actions/setup-python@v3
       with:
-        python-version: 3.10
+        python-version: 3.9.7
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory

From c10317c1d32df92724ffd802b6cdc7e50f9e3143 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 14:35:41 +0200
Subject: [PATCH 42/57] Update requirements with --no-build tag

---
 requirements.txt | 305 ++++++++++++++++++++++++-----------------------
 1 file changed, 154 insertions(+), 151 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 8b428c5..e7bc821 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,151 +1,154 @@
-# This file may be used to create an environment using:
-# $ conda create --name <env> --file <this file>
-# platform: win-64
-argon2-cffi=21.3.0=pyhd3eb1b0_0
-argon2-cffi-bindings=21.2.0=py39h2bbff1b_0
-atomicwrites=1.4.0=py_0
-attrs=21.4.0=pyhd3eb1b0_0
-backcall=0.2.0=pyhd3eb1b0_0
-beamtime=0.1=dev_0
-blas=1.0=mkl
-bleach=4.1.0=pyhd3eb1b0_0
-bottleneck=1.3.2=py39h7cc1a96_1
-ca-certificates=2022.3.29=haa95532_0
-cached-property=1.5.2=hd8ed1ab_1
-cached_property=1.5.2=pyha770c72_1
-certifi=2021.10.8=py39haa95532_2
-cffi=1.15.0=py39h2bbff1b_1
-colorama=0.4.4=pyhd3eb1b0_0
-cycler=0.10.0=py_2
-debugpy=1.4.1=py39hd77b12b_0
-decorator=5.1.0=pyhd3eb1b0_0
-defusedxml=0.7.1=pyhd3eb1b0_0
-entrypoints=0.3=py39haa95532_0
-fabio=0.12.0=py39h5d4886f_0
-freetype=2.10.4=h546665d_1
-glymur=0.9.4=pyhd8ed1ab_0
-h5py=3.2.1=nompi_py39hf27771d_100
-hdf5=1.10.6=nompi_h5268f04_1114
-hdf5plugin=3.1.1=py39h71586dd_0
-icc_rt=2019.0.0=h0cc432a_1
-icu=68.1=h6c2663c_0
-importlib-metadata=4.8.2=py39haa95532_0
-importlib_metadata=4.8.2=hd3eb1b0_0
-iniconfig=1.1.1=pyhd3eb1b0_0
-intel-openmp=2021.3.0=haa95532_3372
-ipykernel=6.4.1=py39haa95532_1
-ipython=7.27.0=py39hd4e2768_0
-ipython_genutils=0.2.0=pyhd3eb1b0_1
-ipywidgets=7.6.5=pyhd3eb1b0_1
-jbig=2.1=h8d14728_2003
-jedi=0.18.0=py39haa95532_1
-jinja2=3.0.2=pyhd3eb1b0_0
-jpeg=9d=h2bbff1b_0
-jsonschema=3.2.0=pyhd3eb1b0_2
-jupyter_client=7.0.1=pyhd3eb1b0_0
-jupyter_core=4.8.1=py39haa95532_0
-jupyterlab_pygments=0.1.2=py_0
-jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
-kiwisolver=1.3.2=py39h2e07f2f_0
-krb5=1.19.2=hbae68bd_2
-lerc=3.0=h0e60522_0
-libclang=11.1.0=default_h5c34c98_1
-libcurl=7.79.1=h789b8ee_1
-libdeflate=1.8=h2bbff1b_5
-libiconv=1.16=he774522_0
-libpng=1.6.37=h1d00b33_2
-libssh2=1.10.0=h680486a_2
-libtiff=4.3.0=hd413186_2
-libwebp=1.2.0=h2bbff1b_0
-libxml2=2.9.12=h0ad7f3c_0
-libxslt=1.1.34=he774522_0
-libzlib=1.2.11=h8ffe710_1013
-lxml=4.6.3=py39h4fd7cdf_0
-lz4-c=1.9.3=h8ffe710_1
-mako=1.1.5=pyhd8ed1ab_0
-markupsafe=2.0.1=py39h2bbff1b_0
-matplotlib=3.4.3=py39hcbf5309_1
-matplotlib-base=3.4.3=py39h581301d_1
-matplotlib-inline=0.1.2=pyhd3eb1b0_2
-mistune=0.8.4=py39h2bbff1b_1000
-mkl=2021.3.0=haa95532_524
-mkl-service=2.4.0=py39h2bbff1b_0
-mkl_fft=1.3.1=py39h277e83a_0
-mkl_random=1.2.2=py39hf11a4ad_0
-mpmath=1.2.1=py39haa95532_0
-nbclient=0.5.11=pyhd3eb1b0_0
-nbconvert=6.1.0=py39haa95532_0
-nbformat=5.1.3=pyhd3eb1b0_0
-nest-asyncio=1.5.1=pyhd3eb1b0_0
-notebook=6.4.8=py39haa95532_0
-numexpr=2.7.3=py39hb80d3ca_1
-numpy=1.21.2=py39hfca59bb_0
-numpy-base=1.21.2=py39h0829f74_0
-olefile=0.46=pyh9f0ad1d_1
-openjpeg=2.4.0=hb211442_1
-openssl=1.1.1n=h2bbff1b_0
-packaging=21.3=pyhd3eb1b0_0
-palettable=3.3.0=pyhd3eb1b0_0
-pandas=1.3.3=py39h6214cd6_0
-pandocfilters=1.5.0=pyhd3eb1b0_0
-parso=0.8.2=pyhd3eb1b0_0
-pickleshare=0.7.5=pyhd3eb1b0_1003
-pillow=8.4.0=py39hd45dc43_0
-pip=21.2.4=py39haa95532_0
-pluggy=1.0.0=py39haa95532_1
-prometheus_client=0.13.1=pyhd3eb1b0_0
-prompt-toolkit=3.0.20=pyhd3eb1b0_0
-py=1.11.0=pyhd3eb1b0_0
-pycparser=2.21=pyhd3eb1b0_0
-pyfai=0.20.0=hd8ed1ab_0
-pyfai-base=0.20.0=py39h2e25243_0
-pygments=2.10.0=pyhd3eb1b0_0
-pyparsing=2.4.7=pyhd3eb1b0_0
-pyqt=5.12.3=py39hcbf5309_7
-pyqt-impl=5.12.3=py39h415ef7b_7
-pyqt5-sip=4.19.18=py39h415ef7b_7
-pyqtchart=5.12=py39h415ef7b_7
-pyqtwebengine=5.12.1=py39h415ef7b_7
-pyreadline=2.1=py39hcbf5309_1004
-pyrsistent=0.18.0=py39h196d8e1_0
-pytest=7.1.1=py39haa95532_0
-python=3.9.7=h6244533_1
-python-dateutil=2.8.2=pyhd3eb1b0_0
-python_abi=3.9=2_cp39
-pytz=2021.3=pyhd3eb1b0_0
-pywin32=228=py39hbaba5e8_1
-pywinpty=2.0.2=py39h5da7b33_0
-pyzmq=22.2.1=py39hd77b12b_1
-qt=5.12.9=h5909a2a_4
-qtconsole=5.1.1=pyhd3eb1b0_0
-qtpy=1.11.2=pyhd8ed1ab_0
-scipy=1.7.1=py39hbe87c03_2
-seaborn=0.11.2=pyhd3eb1b0_0
-send2trash=1.8.0=pyhd3eb1b0_1
-setuptools=58.0.4=py39haa95532_0
-silx=0.15.2=hd8ed1ab_0
-silx-base=0.15.2=py39h2e25243_0
-six=1.16.0=pyhd3eb1b0_0
-sqlite=3.36.0=h2bbff1b_0
-sympy=1.9=py39haa95532_0
-terminado=0.13.1=py39haa95532_0
-testpath=0.5.0=pyhd3eb1b0_0
-tk=8.6.11=h8ffe710_1
-tomli=1.2.2=pyhd3eb1b0_0
-tornado=6.1=py39h2bbff1b_0
-traitlets=5.1.0=pyhd3eb1b0_0
-typing-extensions=3.10.0.2=hd3eb1b0_0
-typing_extensions=3.10.0.2=pyh06a4308_0
-tzdata=2021a=h5d7bf9c_0
-vc=14.2=h21ff451_1
-vs2015_runtime=14.27.29016=h5e58377_2
-wcwidth=0.2.5=pyhd3eb1b0_0
-webencodings=0.5.1=py39haa95532_1
-wheel=0.37.0=pyhd3eb1b0_1
-widgetsnbextension=3.5.2=py39haa95532_0
-wincertstore=0.2=py39haa95532_2
-winpty=0.4.3=4
-xz=5.2.5=h62dcd97_1
-zipp=3.7.0=pyhd3eb1b0_0
-zlib=1.2.11=h8ffe710_1013
-zstd=1.5.0=h6255e5f_0
+name: beamtime
+channels:
+  - conda-forge
+  - diffpy
+  - defaults
+dependencies:
+  - argon2-cffi=21.3.0
+  - argon2-cffi-bindings=21.2.0
+  - atomicwrites=1.4.0
+  - attrs=21.4.0
+  - backcall=0.2.0
+  - blas=1.0
+  - bleach=4.1.0
+  - bottleneck=1.3.2
+  - ca-certificates=2022.3.29
+  - cached-property=1.5.2
+  - cached_property=1.5.2
+  - certifi=2021.10.8
+  - cffi=1.15.0
+  - colorama=0.4.4
+  - cycler=0.10.0
+  - debugpy=1.4.1
+  - decorator=5.1.0
+  - defusedxml=0.7.1
+  - entrypoints=0.3
+  - fabio=0.12.0
+  - freetype=2.10.4
+  - glymur=0.9.4
+  - h5py=3.2.1
+  - hdf5=1.10.6
+  - hdf5plugin=3.1.1
+  - icc_rt=2019.0.0
+  - icu=68.1
+  - importlib-metadata=4.8.2
+  - importlib_metadata=4.8.2
+  - iniconfig=1.1.1
+  - intel-openmp=2021.3.0
+  - ipykernel=6.4.1
+  - ipython=7.27.0
+  - ipython_genutils=0.2.0
+  - ipywidgets=7.6.5
+  - jbig=2.1
+  - jedi=0.18.0
+  - jinja2=3.0.2
+  - jpeg=9d
+  - jsonschema=3.2.0
+  - jupyter_client=7.0.1
+  - jupyter_core=4.8.1
+  - jupyterlab_pygments=0.1.2
+  - jupyterlab_widgets=1.0.0
+  - kiwisolver=1.3.2
+  - krb5=1.19.2
+  - lerc=3.0
+  - libclang=11.1.0
+  - libcurl=7.79.1
+  - libdeflate=1.8
+  - libiconv=1.16
+  - libpng=1.6.37
+  - libssh2=1.10.0
+  - libtiff=4.3.0
+  - libwebp=1.2.0
+  - libxml2=2.9.12
+  - libxslt=1.1.34
+  - libzlib=1.2.11
+  - lxml=4.6.3
+  - lz4-c=1.9.3
+  - mako=1.1.5
+  - markupsafe=2.0.1
+  - matplotlib=3.4.3
+  - matplotlib-base=3.4.3
+  - matplotlib-inline=0.1.2
+  - mistune=0.8.4
+  - mkl=2021.3.0
+  - mkl-service=2.4.0
+  - mkl_fft=1.3.1
+  - mkl_random=1.2.2
+  - mpmath=1.2.1
+  - nbclient=0.5.11
+  - nbconvert=6.1.0
+  - nbformat=5.1.3
+  - nest-asyncio=1.5.1
+  - notebook=6.4.8
+  - numexpr=2.7.3
+  - numpy=1.21.2
+  - numpy-base=1.21.2
+  - olefile=0.46
+  - openjpeg=2.4.0
+  - openssl=1.1.1n
+  - packaging=21.3
+  - palettable=3.3.0
+  - pandas=1.3.3
+  - pandocfilters=1.5.0
+  - parso=0.8.2
+  - pickleshare=0.7.5
+  - pillow=8.4.0
+  - pip=21.2.4
+  - pluggy=1.0.0
+  - prometheus_client=0.13.1
+  - prompt-toolkit=3.0.20
+  - py=1.11.0
+  - pycparser=2.21
+  - pyfai=0.20.0
+  - pyfai-base=0.20.0
+  - pygments=2.10.0
+  - pyparsing=2.4.7
+  - pyqt=5.12.3
+  - pyqt-impl=5.12.3
+  - pyqt5-sip=4.19.18
+  - pyqtchart=5.12
+  - pyqtwebengine=5.12.1
+  - pyreadline=2.1
+  - pyrsistent=0.18.0
+  - pytest=7.1.1
+  - python=3.9.7
+  - python-dateutil=2.8.2
+  - python_abi=3.9
+  - pytz=2021.3
+  - pywin32=228
+  - pywinpty=2.0.2
+  - pyzmq=22.2.1
+  - qt=5.12.9
+  - qtconsole=5.1.1
+  - qtpy=1.11.2
+  - scipy=1.7.1
+  - seaborn=0.11.2
+  - send2trash=1.8.0
+  - setuptools=58.0.4
+  - silx=0.15.2
+  - silx-base=0.15.2
+  - six=1.16.0
+  - sqlite=3.36.0
+  - sympy=1.9
+  - terminado=0.13.1
+  - testpath=0.5.0
+  - tk=8.6.11
+  - tomli=1.2.2
+  - tornado=6.1
+  - traitlets=5.1.0
+  - typing-extensions=3.10.0.2
+  - typing_extensions=3.10.0.2
+  - tzdata=2021a
+  - vc=14.2
+  - vs2015_runtime=14.27.29016
+  - wcwidth=0.2.5
+  - webencodings=0.5.1
+  - wheel=0.37.0
+  - widgetsnbextension=3.5.2
+  - wincertstore=0.2
+  - winpty=0.4.3
+  - xz=5.2.5
+  - zipp=3.7.0
+  - zlib=1.2.11
+  - zstd=1.5.0
+prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime

From e8bc4d4bc4f9615ee4f27cd7e83ee0ce41226031 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:39:03 +0200
Subject: [PATCH 43/57] Delete second attempt at setting up automated testing

---
 .github/workflows/python-package-conda.yml | 34 ----------------------
 1 file changed, 34 deletions(-)
 delete mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
deleted file mode 100644
index 6261945..0000000
--- a/.github/workflows/python-package-conda.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: Python Package using Conda
-
-on: [push]
-
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9.7
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda env update --file environment.yml --name base
-    - name: Lint with flake8
-      run: |
-        conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        conda install pytest
-        pytest

From c8f1f64af86d8c3060616b2e136921c955b562e6 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 14:40:38 +0200
Subject: [PATCH 44/57] Update environment.yml without build

---
 environment.yml  | 294 +++++++++++++++++++++++------------------------
 requirements.txt | 154 -------------------------
 2 files changed, 147 insertions(+), 301 deletions(-)
 delete mode 100644 requirements.txt

diff --git a/environment.yml b/environment.yml
index b80378b..e7bc821 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,151 +4,151 @@ channels:
   - diffpy
   - defaults
 dependencies:
-  - argon2-cffi=21.3.0=pyhd3eb1b0_0
-  - argon2-cffi-bindings=21.2.0=py39h2bbff1b_0
-  - atomicwrites=1.4.0=py_0
-  - attrs=21.4.0=pyhd3eb1b0_0
-  - backcall=0.2.0=pyhd3eb1b0_0
-  - blas=1.0=mkl
-  - bleach=4.1.0=pyhd3eb1b0_0
-  - bottleneck=1.3.2=py39h7cc1a96_1
-  - ca-certificates=2022.3.29=haa95532_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
-  - certifi=2021.10.8=py39haa95532_2
-  - cffi=1.15.0=py39h2bbff1b_1
-  - colorama=0.4.4=pyhd3eb1b0_0
-  - cycler=0.10.0=py_2
-  - debugpy=1.4.1=py39hd77b12b_0
-  - decorator=5.1.0=pyhd3eb1b0_0
-  - defusedxml=0.7.1=pyhd3eb1b0_0
-  - entrypoints=0.3=py39haa95532_0
-  - fabio=0.12.0=py39h5d4886f_0
-  - freetype=2.10.4=h546665d_1
-  - glymur=0.9.4=pyhd8ed1ab_0
-  - h5py=3.2.1=nompi_py39hf27771d_100
-  - hdf5=1.10.6=nompi_h5268f04_1114
-  - hdf5plugin=3.1.1=py39h71586dd_0
-  - icc_rt=2019.0.0=h0cc432a_1
-  - icu=68.1=h6c2663c_0
-  - importlib-metadata=4.8.2=py39haa95532_0
-  - importlib_metadata=4.8.2=hd3eb1b0_0
-  - iniconfig=1.1.1=pyhd3eb1b0_0
-  - intel-openmp=2021.3.0=haa95532_3372
-  - ipykernel=6.4.1=py39haa95532_1
-  - ipython=7.27.0=py39hd4e2768_0
-  - ipython_genutils=0.2.0=pyhd3eb1b0_1
-  - ipywidgets=7.6.5=pyhd3eb1b0_1
-  - jbig=2.1=h8d14728_2003
-  - jedi=0.18.0=py39haa95532_1
-  - jinja2=3.0.2=pyhd3eb1b0_0
-  - jpeg=9d=h2bbff1b_0
-  - jsonschema=3.2.0=pyhd3eb1b0_2
-  - jupyter_client=7.0.1=pyhd3eb1b0_0
-  - jupyter_core=4.8.1=py39haa95532_0
-  - jupyterlab_pygments=0.1.2=py_0
-  - jupyterlab_widgets=1.0.0=pyhd3eb1b0_1
-  - kiwisolver=1.3.2=py39h2e07f2f_0
-  - krb5=1.19.2=hbae68bd_2
-  - lerc=3.0=h0e60522_0
-  - libclang=11.1.0=default_h5c34c98_1
-  - libcurl=7.79.1=h789b8ee_1
-  - libdeflate=1.8=h2bbff1b_5
-  - libiconv=1.16=he774522_0
-  - libpng=1.6.37=h1d00b33_2
-  - libssh2=1.10.0=h680486a_2
-  - libtiff=4.3.0=hd413186_2
-  - libwebp=1.2.0=h2bbff1b_0
-  - libxml2=2.9.12=h0ad7f3c_0
-  - libxslt=1.1.34=he774522_0
-  - libzlib=1.2.11=h8ffe710_1013
-  - lxml=4.6.3=py39h4fd7cdf_0
-  - lz4-c=1.9.3=h8ffe710_1
-  - mako=1.1.5=pyhd8ed1ab_0
-  - markupsafe=2.0.1=py39h2bbff1b_0
-  - matplotlib=3.4.3=py39hcbf5309_1
-  - matplotlib-base=3.4.3=py39h581301d_1
-  - matplotlib-inline=0.1.2=pyhd3eb1b0_2
-  - mistune=0.8.4=py39h2bbff1b_1000
-  - mkl=2021.3.0=haa95532_524
-  - mkl-service=2.4.0=py39h2bbff1b_0
-  - mkl_fft=1.3.1=py39h277e83a_0
-  - mkl_random=1.2.2=py39hf11a4ad_0
-  - mpmath=1.2.1=py39haa95532_0
-  - nbclient=0.5.11=pyhd3eb1b0_0
-  - nbconvert=6.1.0=py39haa95532_0
-  - nbformat=5.1.3=pyhd3eb1b0_0
-  - nest-asyncio=1.5.1=pyhd3eb1b0_0
-  - notebook=6.4.8=py39haa95532_0
-  - numexpr=2.7.3=py39hb80d3ca_1
-  - numpy=1.21.2=py39hfca59bb_0
-  - numpy-base=1.21.2=py39h0829f74_0
-  - olefile=0.46=pyh9f0ad1d_1
-  - openjpeg=2.4.0=hb211442_1
-  - openssl=1.1.1n=h2bbff1b_0
-  - packaging=21.3=pyhd3eb1b0_0
-  - palettable=3.3.0=pyhd3eb1b0_0
-  - pandas=1.3.3=py39h6214cd6_0
-  - pandocfilters=1.5.0=pyhd3eb1b0_0
-  - parso=0.8.2=pyhd3eb1b0_0
-  - pickleshare=0.7.5=pyhd3eb1b0_1003
-  - pillow=8.4.0=py39hd45dc43_0
-  - pip=21.2.4=py39haa95532_0
-  - pluggy=1.0.0=py39haa95532_1
-  - prometheus_client=0.13.1=pyhd3eb1b0_0
-  - prompt-toolkit=3.0.20=pyhd3eb1b0_0
-  - py=1.11.0=pyhd3eb1b0_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pyfai=0.20.0=hd8ed1ab_0
-  - pyfai-base=0.20.0=py39h2e25243_0
-  - pygments=2.10.0=pyhd3eb1b0_0
-  - pyparsing=2.4.7=pyhd3eb1b0_0
-  - pyqt=5.12.3=py39hcbf5309_7
-  - pyqt-impl=5.12.3=py39h415ef7b_7
-  - pyqt5-sip=4.19.18=py39h415ef7b_7
-  - pyqtchart=5.12=py39h415ef7b_7
-  - pyqtwebengine=5.12.1=py39h415ef7b_7
-  - pyreadline=2.1=py39hcbf5309_1004
-  - pyrsistent=0.18.0=py39h196d8e1_0
-  - pytest=7.1.1=py39haa95532_0
-  - python=3.9.7=h6244533_1
-  - python-dateutil=2.8.2=pyhd3eb1b0_0
-  - python_abi=3.9=2_cp39
-  - pytz=2021.3=pyhd3eb1b0_0
-  - pywin32=228=py39hbaba5e8_1
-  - pywinpty=2.0.2=py39h5da7b33_0
-  - pyzmq=22.2.1=py39hd77b12b_1
-  - qt=5.12.9=h5909a2a_4
-  - qtconsole=5.1.1=pyhd3eb1b0_0
-  - qtpy=1.11.2=pyhd8ed1ab_0
-  - scipy=1.7.1=py39hbe87c03_2
-  - seaborn=0.11.2=pyhd3eb1b0_0
-  - send2trash=1.8.0=pyhd3eb1b0_1
-  - setuptools=58.0.4=py39haa95532_0
-  - silx=0.15.2=hd8ed1ab_0
-  - silx-base=0.15.2=py39h2e25243_0
-  - six=1.16.0=pyhd3eb1b0_0
-  - sqlite=3.36.0=h2bbff1b_0
-  - sympy=1.9=py39haa95532_0
-  - terminado=0.13.1=py39haa95532_0
-  - testpath=0.5.0=pyhd3eb1b0_0
-  - tk=8.6.11=h8ffe710_1
-  - tomli=1.2.2=pyhd3eb1b0_0
-  - tornado=6.1=py39h2bbff1b_0
-  - traitlets=5.1.0=pyhd3eb1b0_0
-  - typing-extensions=3.10.0.2=hd3eb1b0_0
-  - typing_extensions=3.10.0.2=pyh06a4308_0
-  - tzdata=2021a=h5d7bf9c_0
-  - vc=14.2=h21ff451_1
-  - vs2015_runtime=14.27.29016=h5e58377_2
-  - wcwidth=0.2.5=pyhd3eb1b0_0
-  - webencodings=0.5.1=py39haa95532_1
-  - wheel=0.37.0=pyhd3eb1b0_1
-  - widgetsnbextension=3.5.2=py39haa95532_0
-  - wincertstore=0.2=py39haa95532_2
-  - winpty=0.4.3=4
-  - xz=5.2.5=h62dcd97_1
-  - zipp=3.7.0=pyhd3eb1b0_0
-  - zlib=1.2.11=h8ffe710_1013
-  - zstd=1.5.0=h6255e5f_0
+  - argon2-cffi=21.3.0
+  - argon2-cffi-bindings=21.2.0
+  - atomicwrites=1.4.0
+  - attrs=21.4.0
+  - backcall=0.2.0
+  - blas=1.0
+  - bleach=4.1.0
+  - bottleneck=1.3.2
+  - ca-certificates=2022.3.29
+  - cached-property=1.5.2
+  - cached_property=1.5.2
+  - certifi=2021.10.8
+  - cffi=1.15.0
+  - colorama=0.4.4
+  - cycler=0.10.0
+  - debugpy=1.4.1
+  - decorator=5.1.0
+  - defusedxml=0.7.1
+  - entrypoints=0.3
+  - fabio=0.12.0
+  - freetype=2.10.4
+  - glymur=0.9.4
+  - h5py=3.2.1
+  - hdf5=1.10.6
+  - hdf5plugin=3.1.1
+  - icc_rt=2019.0.0
+  - icu=68.1
+  - importlib-metadata=4.8.2
+  - importlib_metadata=4.8.2
+  - iniconfig=1.1.1
+  - intel-openmp=2021.3.0
+  - ipykernel=6.4.1
+  - ipython=7.27.0
+  - ipython_genutils=0.2.0
+  - ipywidgets=7.6.5
+  - jbig=2.1
+  - jedi=0.18.0
+  - jinja2=3.0.2
+  - jpeg=9d
+  - jsonschema=3.2.0
+  - jupyter_client=7.0.1
+  - jupyter_core=4.8.1
+  - jupyterlab_pygments=0.1.2
+  - jupyterlab_widgets=1.0.0
+  - kiwisolver=1.3.2
+  - krb5=1.19.2
+  - lerc=3.0
+  - libclang=11.1.0
+  - libcurl=7.79.1
+  - libdeflate=1.8
+  - libiconv=1.16
+  - libpng=1.6.37
+  - libssh2=1.10.0
+  - libtiff=4.3.0
+  - libwebp=1.2.0
+  - libxml2=2.9.12
+  - libxslt=1.1.34
+  - libzlib=1.2.11
+  - lxml=4.6.3
+  - lz4-c=1.9.3
+  - mako=1.1.5
+  - markupsafe=2.0.1
+  - matplotlib=3.4.3
+  - matplotlib-base=3.4.3
+  - matplotlib-inline=0.1.2
+  - mistune=0.8.4
+  - mkl=2021.3.0
+  - mkl-service=2.4.0
+  - mkl_fft=1.3.1
+  - mkl_random=1.2.2
+  - mpmath=1.2.1
+  - nbclient=0.5.11
+  - nbconvert=6.1.0
+  - nbformat=5.1.3
+  - nest-asyncio=1.5.1
+  - notebook=6.4.8
+  - numexpr=2.7.3
+  - numpy=1.21.2
+  - numpy-base=1.21.2
+  - olefile=0.46
+  - openjpeg=2.4.0
+  - openssl=1.1.1n
+  - packaging=21.3
+  - palettable=3.3.0
+  - pandas=1.3.3
+  - pandocfilters=1.5.0
+  - parso=0.8.2
+  - pickleshare=0.7.5
+  - pillow=8.4.0
+  - pip=21.2.4
+  - pluggy=1.0.0
+  - prometheus_client=0.13.1
+  - prompt-toolkit=3.0.20
+  - py=1.11.0
+  - pycparser=2.21
+  - pyfai=0.20.0
+  - pyfai-base=0.20.0
+  - pygments=2.10.0
+  - pyparsing=2.4.7
+  - pyqt=5.12.3
+  - pyqt-impl=5.12.3
+  - pyqt5-sip=4.19.18
+  - pyqtchart=5.12
+  - pyqtwebengine=5.12.1
+  - pyreadline=2.1
+  - pyrsistent=0.18.0
+  - pytest=7.1.1
+  - python=3.9.7
+  - python-dateutil=2.8.2
+  - python_abi=3.9
+  - pytz=2021.3
+  - pywin32=228
+  - pywinpty=2.0.2
+  - pyzmq=22.2.1
+  - qt=5.12.9
+  - qtconsole=5.1.1
+  - qtpy=1.11.2
+  - scipy=1.7.1
+  - seaborn=0.11.2
+  - send2trash=1.8.0
+  - setuptools=58.0.4
+  - silx=0.15.2
+  - silx-base=0.15.2
+  - six=1.16.0
+  - sqlite=3.36.0
+  - sympy=1.9
+  - terminado=0.13.1
+  - testpath=0.5.0
+  - tk=8.6.11
+  - tomli=1.2.2
+  - tornado=6.1
+  - traitlets=5.1.0
+  - typing-extensions=3.10.0.2
+  - typing_extensions=3.10.0.2
+  - tzdata=2021a
+  - vc=14.2
+  - vs2015_runtime=14.27.29016
+  - wcwidth=0.2.5
+  - webencodings=0.5.1
+  - wheel=0.37.0
+  - widgetsnbextension=3.5.2
+  - wincertstore=0.2
+  - winpty=0.4.3
+  - xz=5.2.5
+  - zipp=3.7.0
+  - zlib=1.2.11
+  - zstd=1.5.0
 prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index e7bc821..0000000
--- a/requirements.txt
+++ /dev/null
@@ -1,154 +0,0 @@
-name: beamtime
-channels:
-  - conda-forge
-  - diffpy
-  - defaults
-dependencies:
-  - argon2-cffi=21.3.0
-  - argon2-cffi-bindings=21.2.0
-  - atomicwrites=1.4.0
-  - attrs=21.4.0
-  - backcall=0.2.0
-  - blas=1.0
-  - bleach=4.1.0
-  - bottleneck=1.3.2
-  - ca-certificates=2022.3.29
-  - cached-property=1.5.2
-  - cached_property=1.5.2
-  - certifi=2021.10.8
-  - cffi=1.15.0
-  - colorama=0.4.4
-  - cycler=0.10.0
-  - debugpy=1.4.1
-  - decorator=5.1.0
-  - defusedxml=0.7.1
-  - entrypoints=0.3
-  - fabio=0.12.0
-  - freetype=2.10.4
-  - glymur=0.9.4
-  - h5py=3.2.1
-  - hdf5=1.10.6
-  - hdf5plugin=3.1.1
-  - icc_rt=2019.0.0
-  - icu=68.1
-  - importlib-metadata=4.8.2
-  - importlib_metadata=4.8.2
-  - iniconfig=1.1.1
-  - intel-openmp=2021.3.0
-  - ipykernel=6.4.1
-  - ipython=7.27.0
-  - ipython_genutils=0.2.0
-  - ipywidgets=7.6.5
-  - jbig=2.1
-  - jedi=0.18.0
-  - jinja2=3.0.2
-  - jpeg=9d
-  - jsonschema=3.2.0
-  - jupyter_client=7.0.1
-  - jupyter_core=4.8.1
-  - jupyterlab_pygments=0.1.2
-  - jupyterlab_widgets=1.0.0
-  - kiwisolver=1.3.2
-  - krb5=1.19.2
-  - lerc=3.0
-  - libclang=11.1.0
-  - libcurl=7.79.1
-  - libdeflate=1.8
-  - libiconv=1.16
-  - libpng=1.6.37
-  - libssh2=1.10.0
-  - libtiff=4.3.0
-  - libwebp=1.2.0
-  - libxml2=2.9.12
-  - libxslt=1.1.34
-  - libzlib=1.2.11
-  - lxml=4.6.3
-  - lz4-c=1.9.3
-  - mako=1.1.5
-  - markupsafe=2.0.1
-  - matplotlib=3.4.3
-  - matplotlib-base=3.4.3
-  - matplotlib-inline=0.1.2
-  - mistune=0.8.4
-  - mkl=2021.3.0
-  - mkl-service=2.4.0
-  - mkl_fft=1.3.1
-  - mkl_random=1.2.2
-  - mpmath=1.2.1
-  - nbclient=0.5.11
-  - nbconvert=6.1.0
-  - nbformat=5.1.3
-  - nest-asyncio=1.5.1
-  - notebook=6.4.8
-  - numexpr=2.7.3
-  - numpy=1.21.2
-  - numpy-base=1.21.2
-  - olefile=0.46
-  - openjpeg=2.4.0
-  - openssl=1.1.1n
-  - packaging=21.3
-  - palettable=3.3.0
-  - pandas=1.3.3
-  - pandocfilters=1.5.0
-  - parso=0.8.2
-  - pickleshare=0.7.5
-  - pillow=8.4.0
-  - pip=21.2.4
-  - pluggy=1.0.0
-  - prometheus_client=0.13.1
-  - prompt-toolkit=3.0.20
-  - py=1.11.0
-  - pycparser=2.21
-  - pyfai=0.20.0
-  - pyfai-base=0.20.0
-  - pygments=2.10.0
-  - pyparsing=2.4.7
-  - pyqt=5.12.3
-  - pyqt-impl=5.12.3
-  - pyqt5-sip=4.19.18
-  - pyqtchart=5.12
-  - pyqtwebengine=5.12.1
-  - pyreadline=2.1
-  - pyrsistent=0.18.0
-  - pytest=7.1.1
-  - python=3.9.7
-  - python-dateutil=2.8.2
-  - python_abi=3.9
-  - pytz=2021.3
-  - pywin32=228
-  - pywinpty=2.0.2
-  - pyzmq=22.2.1
-  - qt=5.12.9
-  - qtconsole=5.1.1
-  - qtpy=1.11.2
-  - scipy=1.7.1
-  - seaborn=0.11.2
-  - send2trash=1.8.0
-  - setuptools=58.0.4
-  - silx=0.15.2
-  - silx-base=0.15.2
-  - six=1.16.0
-  - sqlite=3.36.0
-  - sympy=1.9
-  - terminado=0.13.1
-  - testpath=0.5.0
-  - tk=8.6.11
-  - tomli=1.2.2
-  - tornado=6.1
-  - traitlets=5.1.0
-  - typing-extensions=3.10.0.2
-  - typing_extensions=3.10.0.2
-  - tzdata=2021a
-  - vc=14.2
-  - vs2015_runtime=14.27.29016
-  - wcwidth=0.2.5
-  - webencodings=0.5.1
-  - wheel=0.37.0
-  - widgetsnbextension=3.5.2
-  - wincertstore=0.2
-  - winpty=0.4.3
-  - xz=5.2.5
-  - zipp=3.7.0
-  - zlib=1.2.11
-  - zstd=1.5.0
-prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime

From bae40fcabdf6acae4f9a9c2a9550082e74479518 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 14:41:29 +0200
Subject: [PATCH 45/57] Set up third attempt at autotesting

---
 .github/workflows/python-package-conda.yml | 34 ++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 0000000..6261945
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,34 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.9.7
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

From 89ea45a9bf3aa5f8d7f137764df0ee3e34cef966 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 14:50:09 +0200
Subject: [PATCH 46/57] Make manual environment file

---
 environment.yml | 155 +++---------------------------------------------
 1 file changed, 8 insertions(+), 147 deletions(-)

diff --git a/environment.yml b/environment.yml
index e7bc821..9500050 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,151 +4,12 @@ channels:
   - diffpy
   - defaults
 dependencies:
-  - argon2-cffi=21.3.0
-  - argon2-cffi-bindings=21.2.0
-  - atomicwrites=1.4.0
-  - attrs=21.4.0
-  - backcall=0.2.0
-  - blas=1.0
-  - bleach=4.1.0
-  - bottleneck=1.3.2
-  - ca-certificates=2022.3.29
-  - cached-property=1.5.2
-  - cached_property=1.5.2
-  - certifi=2021.10.8
-  - cffi=1.15.0
-  - colorama=0.4.4
-  - cycler=0.10.0
-  - debugpy=1.4.1
-  - decorator=5.1.0
-  - defusedxml=0.7.1
-  - entrypoints=0.3
-  - fabio=0.12.0
-  - freetype=2.10.4
-  - glymur=0.9.4
-  - h5py=3.2.1
-  - hdf5=1.10.6
-  - hdf5plugin=3.1.1
-  - icc_rt=2019.0.0
-  - icu=68.1
-  - importlib-metadata=4.8.2
-  - importlib_metadata=4.8.2
-  - iniconfig=1.1.1
-  - intel-openmp=2021.3.0
-  - ipykernel=6.4.1
-  - ipython=7.27.0
-  - ipython_genutils=0.2.0
-  - ipywidgets=7.6.5
-  - jbig=2.1
-  - jedi=0.18.0
-  - jinja2=3.0.2
-  - jpeg=9d
-  - jsonschema=3.2.0
-  - jupyter_client=7.0.1
-  - jupyter_core=4.8.1
-  - jupyterlab_pygments=0.1.2
-  - jupyterlab_widgets=1.0.0
-  - kiwisolver=1.3.2
-  - krb5=1.19.2
-  - lerc=3.0
-  - libclang=11.1.0
-  - libcurl=7.79.1
-  - libdeflate=1.8
-  - libiconv=1.16
-  - libpng=1.6.37
-  - libssh2=1.10.0
-  - libtiff=4.3.0
-  - libwebp=1.2.0
-  - libxml2=2.9.12
-  - libxslt=1.1.34
-  - libzlib=1.2.11
-  - lxml=4.6.3
-  - lz4-c=1.9.3
-  - mako=1.1.5
-  - markupsafe=2.0.1
-  - matplotlib=3.4.3
-  - matplotlib-base=3.4.3
-  - matplotlib-inline=0.1.2
-  - mistune=0.8.4
-  - mkl=2021.3.0
-  - mkl-service=2.4.0
-  - mkl_fft=1.3.1
-  - mkl_random=1.2.2
-  - mpmath=1.2.1
-  - nbclient=0.5.11
-  - nbconvert=6.1.0
-  - nbformat=5.1.3
-  - nest-asyncio=1.5.1
-  - notebook=6.4.8
-  - numexpr=2.7.3
-  - numpy=1.21.2
-  - numpy-base=1.21.2
-  - olefile=0.46
-  - openjpeg=2.4.0
-  - openssl=1.1.1n
-  - packaging=21.3
-  - palettable=3.3.0
-  - pandas=1.3.3
-  - pandocfilters=1.5.0
-  - parso=0.8.2
-  - pickleshare=0.7.5
-  - pillow=8.4.0
-  - pip=21.2.4
-  - pluggy=1.0.0
-  - prometheus_client=0.13.1
-  - prompt-toolkit=3.0.20
-  - py=1.11.0
-  - pycparser=2.21
-  - pyfai=0.20.0
-  - pyfai-base=0.20.0
-  - pygments=2.10.0
-  - pyparsing=2.4.7
-  - pyqt=5.12.3
-  - pyqt-impl=5.12.3
-  - pyqt5-sip=4.19.18
-  - pyqtchart=5.12
-  - pyqtwebengine=5.12.1
-  - pyreadline=2.1
-  - pyrsistent=0.18.0
-  - pytest=7.1.1
-  - python=3.9.7
-  - python-dateutil=2.8.2
-  - python_abi=3.9
-  - pytz=2021.3
-  - pywin32=228
-  - pywinpty=2.0.2
-  - pyzmq=22.2.1
-  - qt=5.12.9
-  - qtconsole=5.1.1
-  - qtpy=1.11.2
-  - scipy=1.7.1
-  - seaborn=0.11.2
-  - send2trash=1.8.0
-  - setuptools=58.0.4
-  - silx=0.15.2
-  - silx-base=0.15.2
-  - six=1.16.0
-  - sqlite=3.36.0
-  - sympy=1.9
-  - terminado=0.13.1
-  - testpath=0.5.0
-  - tk=8.6.11
-  - tomli=1.2.2
-  - tornado=6.1
-  - traitlets=5.1.0
-  - typing-extensions=3.10.0.2
-  - typing_extensions=3.10.0.2
-  - tzdata=2021a
-  - vc=14.2
-  - vs2015_runtime=14.27.29016
-  - wcwidth=0.2.5
-  - webencodings=0.5.1
-  - wheel=0.37.0
-  - widgetsnbextension=3.5.2
-  - wincertstore=0.2
-  - winpty=0.4.3
-  - xz=5.2.5
-  - zipp=3.7.0
-  - zlib=1.2.11
-  - zstd=1.5.0
+  - pandas
+  - numpy
+  - matplotlib
+  - ipywidgets
+  - palettable
+  - sympy
+  - seaborn
+  - pytest
 prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime

From ceb9d1ab462ecc4574cb2cde55fe7df1478fb344 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:15:12 +0200
Subject: [PATCH 47/57] Upload new environment

---
 environment.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/environment.yml b/environment.yml
index 9500050..24ccf4d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,15 +1,15 @@
-name: beamtime
+name: nafuma
 channels:
-  - conda-forge
   - diffpy
   - defaults
 dependencies:
-  - pandas
-  - numpy
-  - matplotlib
   - ipywidgets
-  - palettable
-  - sympy
   - seaborn
+  - sympy
+  - matplotlib
   - pytest
-prefix: C:\Users\rasmusvt\Anaconda3\envs\beamtime
+  - numpy
+  - pandas
+  - palettable
+  - pyfai
+prefix: C:\Users\rasmusvt\Anaconda3\envs\nafuma

From 19918b3207f791563814fff54600e0b68390b8da Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:17:39 +0200
Subject: [PATCH 48/57] Remove old workflow

---
 .github/workflows/python-package-conda.yml | 34 ----------------------
 1 file changed, 34 deletions(-)
 delete mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
deleted file mode 100644
index 6261945..0000000
--- a/.github/workflows/python-package-conda.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-name: Python Package using Conda
-
-on: [push]
-
-jobs:
-  build-linux:
-    runs-on: ubuntu-latest
-    strategy:
-      max-parallel: 5
-
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9.7
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        conda env update --file environment.yml --name base
-    - name: Lint with flake8
-      run: |
-        conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        conda install pytest
-        pytest

From 2c697be9da6abd969b2846618eacaa246b864796 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rasmus=20Vester=20Th=C3=B8gersen?=
 <34004462+rasmusthog@users.noreply.github.com>
Date: Thu, 7 Apr 2022 15:18:17 +0200
Subject: [PATCH 49/57] New attempt at setting up workflow

---
 .github/workflows/python-package-conda.yml | 34 ++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 .github/workflows/python-package-conda.yml

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
new file mode 100644
index 0000000..2c3dce4
--- /dev/null
+++ b/.github/workflows/python-package-conda.yml
@@ -0,0 +1,34 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: 3.10.4
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name base
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

From 601a5b061911c6be8effcbe0f70dbf769bcda490 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:19:57 +0200
Subject: [PATCH 50/57] Add conda-forge to channels

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 24ccf4d..04c88d5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,6 +2,7 @@ name: nafuma
 channels:
   - diffpy
   - defaults
+  - conda-forge
 dependencies:
   - ipywidgets
   - seaborn

From de8c0ab8d5baada16e01adef6b08f21c864ff109 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:28:49 +0200
Subject: [PATCH 51/57] Add install of package to workflow

---
 .github/workflows/python-package-conda.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 2c3dce4..ebf95a8 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -21,6 +21,7 @@ jobs:
     - name: Install dependencies
       run: |
         conda env update --file environment.yml --name base
+        pip install .
     - name: Lint with flake8
       run: |
         conda install flake8

From 3d99af9a7a8e7d64721ba63026cb4bfb08b5c34c Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:39:07 +0200
Subject: [PATCH 52/57] Fix linting issues

---
 beamtime/plotting.py    |  6 ++---
 beamtime/xanes/calib.py |  2 +-
 beamtime/xrd/plot.py    | 49 +----------------------------------------
 3 files changed, 5 insertions(+), 52 deletions(-)

diff --git a/beamtime/plotting.py b/beamtime/plotting.py
index 780a022..e8c5457 100644
--- a/beamtime/plotting.py
+++ b/beamtime/plotting.py
@@ -151,9 +151,9 @@ def adjust_plot(fig, ax, options):
 
     
     # FIXME THIS NEEDS REWORK FOR IT TO FUNCTION PROPERLY!
-    if options['xticks']:
-        ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
-        ax.set_xticklabels(options['xticks'])
+    #if options['xticks']:
+    #    ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
+    #    ax.set_xticklabels(options['xticks'])
     # else:
     #     ax.set_xticks(np.arange(plot_data['start'], plot_data['end']+1))
     #     ax.set_xticklabels([x/2 for x in np.arange(plot_data['start'], plot_data['end']+1)])
diff --git a/beamtime/xanes/calib.py b/beamtime/xanes/calib.py
index 2ef6c4d..6a4c8f6 100644
--- a/beamtime/xanes/calib.py
+++ b/beamtime/xanes/calib.py
@@ -13,7 +13,7 @@ def rbkerbest():
 ##Better to make a new function that loops through the files, and performing the split_xanes_scan on
 
 
-def split_xanes_scan(root, destination=None, replace=False):
+def split_xanes_scan(filename, destination=None, replace=False):
     #root is the path to the beamtime-folder
     #destination should be the path to the processed data
     
diff --git a/beamtime/xrd/plot.py b/beamtime/xrd/plot.py
index cc6baa3..950a27f 100644
--- a/beamtime/xrd/plot.py
+++ b/beamtime/xrd/plot.py
@@ -7,6 +7,7 @@ import numpy as np
 import math
 
 import ipywidgets as widgets
+from IPython.display import display
 
 import beamtime.xrd as xrd
 import beamtime.auxillary as aux
@@ -657,54 +658,6 @@ def prettify_labels(label):
 
 	return labels_dict[label]
 
-def plot_diffractograms(paths, kind, options=None):
-
-
-    fig, ax = prepare_diffractogram_plot(options=options)
-
-    diffractograms = []
-
-    for path in paths:
-        diffractogram = xrd.io.read_data(path=path, kind=kind, options=options)
-        diffractograms.append(diffractogram)
-
-
-    required_options = ['type', 'xvals', 'yvals', 'x_offset', 'y_offset', 'normalise', 'normalise_around', 'reverse_order']
-    default_options = {
-        'type': 'stacked',
-        'xvals': '2th',
-        'yvals': 'I',
-        'x_offset': 0,
-        'y_offset': 0.2,
-        'normalise': True,
-        'normalise_around': None,
-        'reverse_order': False
-    }
-
-
-    # If reverse_order is enabled, reverse the order
-    if options['reverse_order']:
-        diffractograms = reverse_diffractograms(diffractograms)
-
-
-    # If normalise is enbaled, normalise all the diffractograms
-    if options['normalise']:
-        if not options['normalise_around']:
-            for diffractogram in diffractograms:
-                diffractogram["I"] = diffractogram["I"]/diffractogram["I"].max()
-            else:
-                diffractogram["I"] = diffractogram["I"]/diffractogram["I"].loc[(diffractogram['2th'] > options['normalise_around'][0]) & (diffractogram['2th'] < options['normalise_around'][1])].max()
-
-    
-    if options['type'] == 'stacked':
-        for diffractogram in diffractograms:
-            diffractogram.plot(x=options['xvals'], y=options['yvals'], ax=ax)
-
-
-    fig, ax = prettify_diffractogram_plot(fig=fig, ax=ax, options=options)
-
-
-    return diffractogram, fig, ax
 
 
 def reverse_diffractograms(diffractograms):

From 049f30d96b492573a5e64e8e091b9b5d7c16fa16 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 15:47:26 +0200
Subject: [PATCH 53/57] Fix last remaining liniting issue

---
 beamtime/xrd/io.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/beamtime/xrd/io.py b/beamtime/xrd/io.py
index c2447d8..fc5c292 100644
--- a/beamtime/xrd/io.py
+++ b/beamtime/xrd/io.py
@@ -149,7 +149,7 @@ def average_images(images):
     image_arrays = []
 
     for image in images:
-        image_array = xrd.io.get_image_array(image)
+        image_array = get_image_array(image)
         image_arrays.append(image_array)
     
     

From 27c911cf5454ed48aab8cb90f8ca3691bb7d68a4 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 17:05:52 +0200
Subject: [PATCH 54/57] Rename package to nafuma from beamtime

---
 feature_list.txt                                     |  2 --
 {beamtime => nafuma}/__init__.py                     |  0
 {beamtime => nafuma}/auxillary.py                    |  0
 {beamtime => nafuma}/electrochemistry/__init__.py    |  0
 {beamtime => nafuma}/electrochemistry/io.py          |  0
 {beamtime => nafuma}/electrochemistry/plot.py        |  0
 {beamtime => nafuma}/electrochemistry/unit_tables.py |  0
 {beamtime => nafuma}/pdf/__init__.py                 |  0
 {beamtime => nafuma}/plotting.py                     |  0
 {beamtime => nafuma}/test.txt                        |  0
 {beamtime => nafuma}/test/__init__.py                |  0
 {beamtime => nafuma}/test/pytest.ini                 |  0
 {beamtime => nafuma}/test/test_auxillary.py          |  0
 {beamtime => nafuma}/test/test_plotting.py           |  0
 {beamtime => nafuma}/test/xrd/test_io.py             |  0
 {beamtime => nafuma}/test/xrd/test_plot.py           |  0
 {beamtime => nafuma}/test2.txt                       |  0
 {beamtime => nafuma}/xanes/__init__.py               |  0
 {beamtime => nafuma}/xanes/calib.py                  |  0
 {beamtime => nafuma}/xanes/io.py                     |  0
 {beamtime => nafuma}/xrd/__init__.py                 |  0
 {beamtime => nafuma}/xrd/io.py                       |  0
 {beamtime => nafuma}/xrd/plot.py                     |  0
 {beamtime => nafuma}/xrd/test.txt                    |  0
 setup.py                                             | 10 +++++-----
 25 files changed, 5 insertions(+), 7 deletions(-)
 delete mode 100644 feature_list.txt
 rename {beamtime => nafuma}/__init__.py (100%)
 rename {beamtime => nafuma}/auxillary.py (100%)
 rename {beamtime => nafuma}/electrochemistry/__init__.py (100%)
 rename {beamtime => nafuma}/electrochemistry/io.py (100%)
 rename {beamtime => nafuma}/electrochemistry/plot.py (100%)
 rename {beamtime => nafuma}/electrochemistry/unit_tables.py (100%)
 rename {beamtime => nafuma}/pdf/__init__.py (100%)
 rename {beamtime => nafuma}/plotting.py (100%)
 rename {beamtime => nafuma}/test.txt (100%)
 rename {beamtime => nafuma}/test/__init__.py (100%)
 rename {beamtime => nafuma}/test/pytest.ini (100%)
 rename {beamtime => nafuma}/test/test_auxillary.py (100%)
 rename {beamtime => nafuma}/test/test_plotting.py (100%)
 rename {beamtime => nafuma}/test/xrd/test_io.py (100%)
 rename {beamtime => nafuma}/test/xrd/test_plot.py (100%)
 rename {beamtime => nafuma}/test2.txt (100%)
 rename {beamtime => nafuma}/xanes/__init__.py (100%)
 rename {beamtime => nafuma}/xanes/calib.py (100%)
 rename {beamtime => nafuma}/xanes/io.py (100%)
 rename {beamtime => nafuma}/xrd/__init__.py (100%)
 rename {beamtime => nafuma}/xrd/io.py (100%)
 rename {beamtime => nafuma}/xrd/plot.py (100%)
 rename {beamtime => nafuma}/xrd/test.txt (100%)

diff --git a/feature_list.txt b/feature_list.txt
deleted file mode 100644
index f4a0efd..0000000
--- a/feature_list.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-- Must allow for automatic normalisation between different diffractograms, must only happen upon reading data
-- 
diff --git a/beamtime/__init__.py b/nafuma/__init__.py
similarity index 100%
rename from beamtime/__init__.py
rename to nafuma/__init__.py
diff --git a/beamtime/auxillary.py b/nafuma/auxillary.py
similarity index 100%
rename from beamtime/auxillary.py
rename to nafuma/auxillary.py
diff --git a/beamtime/electrochemistry/__init__.py b/nafuma/electrochemistry/__init__.py
similarity index 100%
rename from beamtime/electrochemistry/__init__.py
rename to nafuma/electrochemistry/__init__.py
diff --git a/beamtime/electrochemistry/io.py b/nafuma/electrochemistry/io.py
similarity index 100%
rename from beamtime/electrochemistry/io.py
rename to nafuma/electrochemistry/io.py
diff --git a/beamtime/electrochemistry/plot.py b/nafuma/electrochemistry/plot.py
similarity index 100%
rename from beamtime/electrochemistry/plot.py
rename to nafuma/electrochemistry/plot.py
diff --git a/beamtime/electrochemistry/unit_tables.py b/nafuma/electrochemistry/unit_tables.py
similarity index 100%
rename from beamtime/electrochemistry/unit_tables.py
rename to nafuma/electrochemistry/unit_tables.py
diff --git a/beamtime/pdf/__init__.py b/nafuma/pdf/__init__.py
similarity index 100%
rename from beamtime/pdf/__init__.py
rename to nafuma/pdf/__init__.py
diff --git a/beamtime/plotting.py b/nafuma/plotting.py
similarity index 100%
rename from beamtime/plotting.py
rename to nafuma/plotting.py
diff --git a/beamtime/test.txt b/nafuma/test.txt
similarity index 100%
rename from beamtime/test.txt
rename to nafuma/test.txt
diff --git a/beamtime/test/__init__.py b/nafuma/test/__init__.py
similarity index 100%
rename from beamtime/test/__init__.py
rename to nafuma/test/__init__.py
diff --git a/beamtime/test/pytest.ini b/nafuma/test/pytest.ini
similarity index 100%
rename from beamtime/test/pytest.ini
rename to nafuma/test/pytest.ini
diff --git a/beamtime/test/test_auxillary.py b/nafuma/test/test_auxillary.py
similarity index 100%
rename from beamtime/test/test_auxillary.py
rename to nafuma/test/test_auxillary.py
diff --git a/beamtime/test/test_plotting.py b/nafuma/test/test_plotting.py
similarity index 100%
rename from beamtime/test/test_plotting.py
rename to nafuma/test/test_plotting.py
diff --git a/beamtime/test/xrd/test_io.py b/nafuma/test/xrd/test_io.py
similarity index 100%
rename from beamtime/test/xrd/test_io.py
rename to nafuma/test/xrd/test_io.py
diff --git a/beamtime/test/xrd/test_plot.py b/nafuma/test/xrd/test_plot.py
similarity index 100%
rename from beamtime/test/xrd/test_plot.py
rename to nafuma/test/xrd/test_plot.py
diff --git a/beamtime/test2.txt b/nafuma/test2.txt
similarity index 100%
rename from beamtime/test2.txt
rename to nafuma/test2.txt
diff --git a/beamtime/xanes/__init__.py b/nafuma/xanes/__init__.py
similarity index 100%
rename from beamtime/xanes/__init__.py
rename to nafuma/xanes/__init__.py
diff --git a/beamtime/xanes/calib.py b/nafuma/xanes/calib.py
similarity index 100%
rename from beamtime/xanes/calib.py
rename to nafuma/xanes/calib.py
diff --git a/beamtime/xanes/io.py b/nafuma/xanes/io.py
similarity index 100%
rename from beamtime/xanes/io.py
rename to nafuma/xanes/io.py
diff --git a/beamtime/xrd/__init__.py b/nafuma/xrd/__init__.py
similarity index 100%
rename from beamtime/xrd/__init__.py
rename to nafuma/xrd/__init__.py
diff --git a/beamtime/xrd/io.py b/nafuma/xrd/io.py
similarity index 100%
rename from beamtime/xrd/io.py
rename to nafuma/xrd/io.py
diff --git a/beamtime/xrd/plot.py b/nafuma/xrd/plot.py
similarity index 100%
rename from beamtime/xrd/plot.py
rename to nafuma/xrd/plot.py
diff --git a/beamtime/xrd/test.txt b/nafuma/xrd/test.txt
similarity index 100%
rename from beamtime/xrd/test.txt
rename to nafuma/xrd/test.txt
diff --git a/setup.py b/setup.py
index 4c93b78..b3f9f34 100644
--- a/setup.py
+++ b/setup.py
@@ -1,11 +1,11 @@
 from setuptools import setup, find_packages
 
-setup(name='beamtime',
-      version='0.1',
-      description='Package for process and analysis of beamtime data from SNBL',
-      url='http://github.uio.no/rasmusvt/beamtime',
+setup(name='nafuma',
+      version='0.2',
+      description='Analysis tools for inorganic materials chemistry at the NAFUMA-group at the University of Oslo',
+      url='https://github.com/rasmusthog/nafuma',
       author='Rasmus Vester Thøgersen, Halvor Høen Hval',
-      author_email='rasmusvt@smn.uio.no',
+      author_email='code@rasmusthog.me',
       license='MIT',
       packages=find_packages(),
       zip_safe=False)

From 08276301f251e25eb66cce51c46edee6f19f9955 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 17:11:14 +0200
Subject: [PATCH 55/57] Update imports to match new package name

---
 nafuma/electrochemistry/plot.py | 2 +-
 nafuma/plotting.py              | 2 +-
 nafuma/test/test_auxillary.py   | 2 +-
 nafuma/test/test_plotting.py    | 2 +-
 nafuma/xrd/io.py                | 2 +-
 nafuma/xrd/plot.py              | 6 +++---
 6 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/nafuma/electrochemistry/plot.py b/nafuma/electrochemistry/plot.py
index 64b7115..df977a5 100644
--- a/nafuma/electrochemistry/plot.py
+++ b/nafuma/electrochemistry/plot.py
@@ -5,7 +5,7 @@ import pandas as pd
 import numpy as np
 import math
 
-import beamtime.electrochemistry as ec
+import nafuma.electrochemistry as ec
 
 
 def plot_gc(path, kind, options=None):
diff --git a/nafuma/plotting.py b/nafuma/plotting.py
index e8c5457..2233ab7 100644
--- a/nafuma/plotting.py
+++ b/nafuma/plotting.py
@@ -1,4 +1,4 @@
-import beamtime.auxillary as aux
+import nafuma.auxillary as aux
 
 import matplotlib.pyplot as plt
 from matplotlib.ticker import (MultipleLocator)
diff --git a/nafuma/test/test_auxillary.py b/nafuma/test/test_auxillary.py
index 668b792..4cb9cd1 100644
--- a/nafuma/test/test_auxillary.py
+++ b/nafuma/test/test_auxillary.py
@@ -1,4 +1,4 @@
-import beamtime.auxillary as aux
+import nafuma.auxillary as aux
 import os
 
 def test_swap_values():
diff --git a/nafuma/test/test_plotting.py b/nafuma/test/test_plotting.py
index 8979bc1..e1af0b8 100644
--- a/nafuma/test/test_plotting.py
+++ b/nafuma/test/test_plotting.py
@@ -1,4 +1,4 @@
-import beamtime.plotting as btp
+import nafuma.plotting as btp
 from cycler import cycler
 import itertools
 import numpy as np
diff --git a/nafuma/xrd/io.py b/nafuma/xrd/io.py
index fc5c292..b3f3951 100644
--- a/nafuma/xrd/io.py
+++ b/nafuma/xrd/io.py
@@ -9,7 +9,7 @@ import zipfile
 import xml.etree.ElementTree as ET
 
 
-import beamtime.auxillary as aux
+import nafuma.auxillary as aux
 
 
 def get_image_array(path):
diff --git a/nafuma/xrd/plot.py b/nafuma/xrd/plot.py
index 950a27f..8dd6a27 100644
--- a/nafuma/xrd/plot.py
+++ b/nafuma/xrd/plot.py
@@ -9,9 +9,9 @@ import math
 import ipywidgets as widgets
 from IPython.display import display
 
-import beamtime.xrd as xrd
-import beamtime.auxillary as aux
-import beamtime.plotting as btp
+import nafuma.xrd as xrd
+import nafuma.auxillary as aux
+import nafuma.plotting as btp
 
 
 def plot_diffractogram(data, options={}):

From f53527fe0b2f8bbc350d850154e1c9a6d811c3b3 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 17:17:28 +0200
Subject: [PATCH 56/57] Clean up test files

---
 nafuma/test.txt     | 1 -
 nafuma/test2.txt    | 0
 nafuma/xrd/test.txt | 0
 3 files changed, 1 deletion(-)
 delete mode 100644 nafuma/test.txt
 delete mode 100644 nafuma/test2.txt
 delete mode 100644 nafuma/xrd/test.txt

diff --git a/nafuma/test.txt b/nafuma/test.txt
deleted file mode 100644
index 85476a8..0000000
--- a/nafuma/test.txt
+++ /dev/null
@@ -1 +0,0 @@
-sdfsdfsdfsdf
\ No newline at end of file
diff --git a/nafuma/test2.txt b/nafuma/test2.txt
deleted file mode 100644
index e69de29..0000000
diff --git a/nafuma/xrd/test.txt b/nafuma/xrd/test.txt
deleted file mode 100644
index e69de29..0000000

From de2616067daf2ebc333a592f2729a2425b9b1e25 Mon Sep 17 00:00:00 2001
From: rasmusvt <r.v.thogersen@kjemi.uio.no>
Date: Thu, 7 Apr 2022 17:19:26 +0200
Subject: [PATCH 57/57] Rename automated test workflow

---
 .../{python-package-conda.yml => automated-testing.yml}         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename .github/workflows/{python-package-conda.yml => automated-testing.yml} (96%)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/automated-testing.yml
similarity index 96%
rename from .github/workflows/python-package-conda.yml
rename to .github/workflows/automated-testing.yml
index ebf95a8..5b553a3 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/automated-testing.yml
@@ -1,4 +1,4 @@
-name: Python Package using Conda
+name: Automated testing
 
 on: [push]