Fix arcsin issue and allow plotting w/o reflection data

nafuma/xrd/io.py

@@ -80,7 +80,8 @@ def integrate_1d(data, options={}, index=0):
     res = ai.integrate1d(data['image'], options['nbins'], unit=options['unit'], filename=filename)
 
     data['path'][index] = filename
-    diffractogram, wavelength = read_xy(data=data, options=options, index=index)
+    diffractogram, _ = read_xy(data=data, options=options, index=index)
+    wavelength = find_wavelength_from_poni(path=data['calibrant'])
 
     if not options['save']:
         os.remove(filename)
@@ -282,8 +283,12 @@ def read_brml(data, options={}, index=0):
 
     #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'])
+    if not data['wavelength'][index]:
+        for chain in root.findall('./FixedInformation/Instrument/PrimaryTracks/TrackInfoData/MountedOptics/InfoData/Tube/WaveLengthAlpha1'):
+            wavelength = float(chain.attrib['Value'])
+    else:
+        wavelength = data['wavelength'][index]
 
 
     diffractogram = pd.DataFrame(diffractogram)
@@ -306,7 +311,11 @@ def read_xy(data, options={}, index=0):
     
     #if 'wavelength' not in data.keys():
     # Get wavelength from scan
-    wavelength = find_wavelength_from_xy(path=data['path'][index])
+
+    if not data['wavelength'][index]:
+        wavelength = find_wavelength_from_xy(path=data['path'][index])
+    else:
+        wavelength = data['wavelength'][index]
 
     with open(data['path'][index], 'r') as f:
         position = 0
@@ -387,6 +396,7 @@ def read_data(data, options={}, index=0):
         diffractogram = apply_offset(diffractogram, wavelength, index, options)
 
 
+    
     diffractogram = translate_wavelengths(data=diffractogram, wavelength=wavelength)
 
     return diffractogram, wavelength
@@ -506,7 +516,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
 
     data['2th_cuka'] = np.NAN
 
-    data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
+    data['2th_cuka'].loc[data['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_cuka]/2) * np.pi/180)) * 180/np.pi
 
     # Translate to MoKalpha
     moka = 0.71073 # Å
@@ -518,7 +528,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
 
     data['2th_moka'] = np.NAN
 
-    data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th']/2) * np.pi/180)) * 180/np.pi
+    data['2th_moka'].loc[data['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((data['2th'].loc[data['2th'] <= max_2th_moka]/2) * np.pi/180)) * 180/np.pi
     
     
     # Convert to other parameters
@@ -537,7 +547,7 @@ def translate_wavelengths(data: pd.DataFrame, wavelength: float, to_wavelength=N
 
         
         data['2th'] = np.NAN
-        data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka']/2) * np.pi/180)) * 180/np.pi 
+        data['2th'].loc[data['2th_cuka'] <= max_2th] = 2*np.arcsin(to_wavelength/cuka * np.sin((data['2th_cuka'].loc[data['2th_cuka'] <= max_2th]/2) * np.pi/180)) * 180/np.pi 
 
 
 
@@ -564,6 +574,22 @@ def find_wavelength_from_xy(path):
             elif 'Wavelength' in line:
                 wavelength = float(line.split()[2])*10**10
 
+            else:
+                wavelength = None
+
+
+
+    return wavelength
+
+
+def find_wavelength_from_poni(path):
+
+    with open(path, 'r') as f:
+        lines = f.readlines()
+
+        for line in lines:
+            if 'Wavelength' in line:
+                wavelength = float(line.split()[-1])*10**10
 
 
     return wavelength

nafuma/xrd/plot.py

@@ -13,7 +13,6 @@ import nafuma.xrd as xrd
 import nafuma.auxillary as aux
 import nafuma.plotting as btp
 
-
 def plot_diffractogram(data, options={}):
     ''' Plots a diffractogram.
     
@@ -67,7 +66,14 @@ def plot_diffractogram(data, options={}):
     if not 'diffractogram' in data.keys():
         # 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']))]
+        
+        # If wavelength is not manually passed it should be automatically gathered from the .xy-file
+        if 'wavelength' not in data.keys():
+            data['wavelength'] = [None for _ in range(len(data['path']))]
+        else:
+            # If only a single value is passed it should be set to be the same for all diffractograms passed
+            if not isinstance(data['wavelength'], list):
+                data['wavelength'] = [data['wavelength'] 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)
@@ -117,7 +123,7 @@ def plot_diffractogram(data, options={}):
             options['reflections_data'] = [options['reflections_data']]
 
     # Determine number of subplots and height ratios between them
-    if len(options['reflections_data']) >= 1:
+    if options['reflections_data'] and len(options['reflections_data']) >= 1:
         options = determine_grid_layout(options=options)
 
 
@@ -334,10 +340,10 @@ def plot_diffractogram_interactive(data, options):
             '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%')),
+            'w': widgets.FloatRangeSlider(value=[yminmax['start'][2], yminmax['start'][3]], min=yminmax['start'][0], max=yminmax['start'][1], step=0.01, 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},
+            'diff_default':     {'min': yminmax['diff'][0],         'max': yminmax['diff'][1],          'value': [yminmax['diff'][2],           yminmax['diff'][3]],            'step': 0.01},
-            'heatmap_default':  {'min': yminmax['heatmap'][0],      'max': yminmax['heatmap'][1],       'value': [yminmax['heatmap'][0],        yminmax['heatmap'][1]],         'step': 0.1}
+            'heatmap_default':  {'min': yminmax['heatmap'][0],      'max': yminmax['heatmap'][1],       'value': [yminmax['heatmap'][0],        yminmax['heatmap'][1]],         'step': 0.01}
         }
     }
 
@@ -359,7 +365,12 @@ def plot_diffractogram_interactive(data, options):
         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),
-        xlim=options['widgets']['xlim']['w'])
+        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=options['widgets']['ylim']['w'],
+        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'))
     
     
     options['widget'] = w