Add translation functions

beamtime/xrd/io.py

@@ -8,6 +8,9 @@ import zipfile
 import xml.etree.ElementTree as ET
 
 
+import beamtime.auxillary as aux
+
+
 def get_image_array(path):
 
     image = fabio.open(path)
@@ -29,66 +32,95 @@ def integrate_1d(data, options={}):
     Required content of data:
     calibrant (str): path to .poni-file
     nbins (int): Number of bins to divide image into
-    path (str) (optional): path to image file - either this or image must be specified. If both is passed, image is prioritsed
+    path (str) (optional, dependent on image): path to image file - either this or image must be specified. If both is passed, image is prioritsed
-    image (str) (optional): image array (Numpy) as extracted from get_image_array
+    image (NumPy 2D Array) (optional, dependent on path): image array as extracted from get_image_array
 
     Output:
     df: DataFrame contianing 1D diffractogram if option 'return' is True
     ''' 
 
-    required_options = ['unit', 'extension', 'filename', 'save_folder', 'overwrite', 'return']
+    required_options = ['unit', 'save', 'save_filename', 'save_extension', 'save_folder', 'overwrite']
 
     default_options = {
         'unit': '2th_deg', 
-        'extension': '_integrated.dat',
+        'save': False,
-        'filename': None,
+        'save_filename': None,
+        'save_extension': '_integrated.xy',
         'save_folder': '.',
-        'overwrite': False,
+        'overwrite': False}
-        'return': False}
 
-    if not options:
+    options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
-        options = default_options
-    
-    else:
-        for option in required_options:
-            if option not in options.keys():
-                options[option] = default_options[option]
-    
     
+
+    # Get image array from filename if not passed
     if 'image' not in data.keys():
         data['image'] = get_image_array(data['path'])
     
+    # Instanciate the azimuthal integrator from pyFAI from the calibrant (.poni-file)
     ai = pyFAI.load(data['calibrant'])
 
-
+    # Determine filename
-    if not options['filename']:
+    filename = make_filename(data=data, options=options)
-        if data['path']:
+    
-            filename = os.path.join(options['save_folder'], os.path.split(data['path'])[-1].split('.')[0] + options['extension'])
+    # Make save_folder if this does not exist already
-        else:
-            filename = os.path.join(options['save_folder'], 'integrated.dat')
-
-
-    if not options['overwrite']:
-        trunk = os.path.join(options['save_folder'], filename.split('\\')[-1].split('.')[0])
-        extension = filename.split('.')[-1]
-        counter = 0
-
-        while os.path.isfile(filename):
-            counter_string = str(counter)
-            filename = trunk + '_' + counter_string.zfill(4) + '.' + extension
-            counter += 1
-
-
     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)
 
-    return read_diffractogram(filename)
+    diffractogram = read_xy(filename)
+
+    if not options['save']:
+        os.remove(filename)
+        shutil.rmtree('tmp')
+    
+    return diffractogram
     
 
 
+def make_filename(data, options):
+
+    # 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')
+
+    elif options['save']:
+
+        # Case 1: No filename is given. 
+        if not options['save_filename']:
+            # If a path is given instead of an image array, the path is taken as the trunk of the savename
+            if data['path']:
+                # 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:
+                # Make filename just "integrated.dat" in the save_folder
+                filename = os.path.join(options['save_folder'], 'integrated.xy')
+
+
+        else:
+            filename = os.path.join(options['save_folder'], options['save_filename'])
+
+
+        if not options['overwrite']:
+            trunk = filename.split('.')[0]
+            extension = filename.split('.')[-1]
+            counter = 0
+
+            while os.path.isfile(filename):
+                
+                # Rename first file to match naming scheme if already exists
+                if counter == 0:
+                    os.rename(filename, trunk + '_' + str(counter).zfill(4) + '.' + extension)
+                
+                # Increment counter and make new filename
+                counter += 1
+                counter_string = str(counter)
+                filename = trunk + '_' + counter_string.zfill(4) + '.' + extension
+
+
+    return filename
     
 
 
@@ -220,16 +252,15 @@ def read_brml(path, options=None):
     return diffractogram
     
 
-def read_diffractogram(path):
+def read_xy(data):
 
-    
+    with open(data['path'], 'r') as f:
-
-    with open(path, 'r') as f:
         position = 0
     
         current_line = f.readline()
         
-        while current_line[0] == '#':
+        while current_line[0] == '#' or "\'":
+            find_wavelength(line=current_line, data=data)
             position = f.tell()
             current_line = f.readline()
             
@@ -237,7 +268,10 @@ def read_diffractogram(path):
 
         diffractogram = pd.read_csv(f, header=None, delim_whitespace=True)
 
-    diffractogram.columns = ['2th', 'I']
+    if diffractogram.shape[1] == 2:
+        diffractogram.columns = ['2th', 'I']
+    elif diffractogram.shape[1] == 3:
+        diffractogram.columns = ['2th', 'I', 'sigma']
 
 
     return diffractogram
@@ -245,22 +279,17 @@ def read_diffractogram(path):
 
 def read_data(data, options={}):
 
-    if data['plot_kind'] == 'beamline':
+    beamline_extensions = ['mar3450', 'edf', 'cbf']
+    file_extension = data['path'].split('.')[-1]
 
-        beamline = ['mar3450', 'edf', 'cbf']
+    if file_extension in beamline_extensions:
-
+        diffractogram = integrate_1d(data=data, options=options)
-        if data['path'].split('.')[-1] in beamline:
-            diffractogram = integrate_1d(data=data, options=options)
         
-        else:
+    elif file_extension == 'brml':
-            diffractogram = read_diffractogram(data['path'])
+        diffractogram = read_brml(path=data['path'], options=options)
-
-    elif data['plot_kind'] == 'recx':
-        diffractogram = read_brml(data['path'], options=options)
-
-    elif data['plot_kind'] == 'image':
-        diffractogram = get_image_array(data['path'])
 
+    elif file_extension in['xy', 'xye']:
+        diffractogram = read_xy(data['path'])
 
     return diffractogram
                 
@@ -290,4 +319,50 @@ def load_reflection_table(path):
     # Set the new modified headers as the headers of 
     reflections.columns = headers
 
-    return reflections
+    return reflections
+
+
+
+def translate_wavelengths(diffractogram, wavelength):
+
+    # Translate to CuKalpha
+    cuka = 1.54059 # Å
+
+    if cuka > wavelength:
+        max_2th_cuka = 2*np.arcsin(wavelength/cuka) * 180/np.pi
+    else:
+        max_2th_cuka = diffractogram['2th'].max()
+
+    diffractogram['2th_cuka'] = np.NAN
+
+    diffractogram['2th_cuka'].loc[diffractogram['2th'] <= max_2th_cuka] = 2*np.arcsin(cuka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
+
+    # Translate to MoKalpha
+    moka = 0.71073 # Å
+
+    if moka > wavelength:
+        max_2th_moka = 2*np.arcsin(wavelength/moka) * 180/np.pi
+    else:
+        max_2th_moka = diffractogram['2th'].max()
+
+    diffractogram['2th_moka'] = np.NAN
+
+    diffractogram['2th_moka'].loc[diffractogram['2th'] <= max_2th_moka] = 2*np.arcsin(moka/wavelength * np.sin((diffractogram['2th']/2) * np.pi/180)) * 180/np.pi
+    
+    
+    # Convert to other parameters
+    diffractogram['d'] = wavelength  / (2*np.sin(2*diffractogram['2th']) * 180/np.pi)
+    diffractogram['1/d'] = 1/diffractogram['d']
+    diffractogram['q'] = np.abs((4*np.pi/wavelength)*np.sin(diffractogram['2th']/2 * np.pi/180))
+    diffractogram['q2'] = diffractogram['q']**2
+    diffractogram['q4'] = diffractogram['q']**4
+
+
+
+def find_wavelength(line, data):
+
+    # Find from EVA-exports
+    wavelength_dict = {'Cu': 1.54059, 'Mo': 0.71073}
+
+    if 'Anode' in line:
+        

beamtime/xrd/plot.py

@@ -183,11 +183,14 @@ def plot_reflection_indices(data, ax, options={}):
         reflection_table = xrd.io.load_reflection_table(data['path'])
         
         if data['reflection_indices'] > 0:
-            reflection_indices = reflection_table.nlargest(options['reflection_indices'], 'I')
 
-        
+            # Get the data['reflection_indices'] number of highest reflections within the subrange options['xlim']
-        for i in range(data['reflection_indices']):
+            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')
-            ax.text(s=f'({reflection_indices["h"].iloc[i]} {reflection_indices["k"].iloc[i]} {reflection_indices["l"].iloc[i]})', x=reflection_indices['2th'].iloc[i], y=0, fontsize=2.5, rotation=90, va='bottom', ha='center', c=data['text_colour'])    
+
+            # Plot the indices
+            for i in range(data['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'])    
 
         
         if options['xlim']: