stream2sol.py: Strip trailing whitespace

1 files changed, 43 insertions, 44 deletions

diff --git a/scripts/stream2sol.py b/scripts/stream2sol.py
index d12ea2ba..1b081119 100755
--- a/scripts/stream2sol.py
+++ b/scripts/stream2sol.py
@@ -21,13 +21,13 @@ GENERATOR = 'Generated by diffractem StreamParser'
 PEAK_COLUMNS = ['fs/px', 'ss/px', '(1/d)/nm^-1', 'Intensity', 'Panel']
 REFLECTION_COLUMNS = ['h', 'k', 'l', 'I', 'Sigma(I)', 'Peak', 'Background', 'fs/px', 'ss/px', 'Panel']
 ID_FIELDS = ['file', 'Event', 'serial']
-CRYSTAL_DATA_FIELS = ['astar', 'bstar', 'cstar', 'predict_refine/det_shift', 
+CRYSTAL_DATA_FIELS = ['astar', 'bstar', 'cstar', 'predict_refine/det_shift',
                       'profile_radius', 'diffraction_resolution_limit']
 
 args = None
 
 class Crystal:
-    
+
     def __init__(self, line):
         self.astar = (None, None, None)
         self.bstar = (None, None, None)
@@ -39,17 +39,17 @@ class Crystal:
 
     @property
     def initialized(self):
-        return all([x is not None 
+        return all([x is not None
                     for x in [*self.astar, *self.bstar, *self.cstar,
-                              *self.det_shift, self.profile_radius, 
+                              *self.det_shift, self.profile_radius,
                               self.resolution]])
     
     def __str__(self):
         if not self.initialized:
             warn('Trying to get string from non-initialized crystal from line {}.'.format(self.start_line))
-            return None        
+            return None
         else:
-            cs = ' '.join(['{0[0]} {0[1]} {0[2]}'.format(vec) 
+            cs = ' '.join(['{0[0]} {0[1]} {0[2]}'.format(vec)
                             for vec in [self.astar, self.bstar, self.cstar]])
             cs += ' {0[0]} {0[1]}'.format(self.det_shift)
             if args.include_pars: # this is a bit dirty but will become obsolete one day
@@ -65,21 +65,21 @@ class Chunk:
         self.start_line = line
         self.x_shift = 0
         self.y_shift = 0
-        
+
     @property
     def n_cryst(self):
         return len(self.crystals)
-    
-    @property 
+
+    @property
     def initialized(self):
         return (self.file is not None) and (self.Event is not None)
-        
+
     def add_crystal(self, crystal):
         if (not crystal.initialized) or (crystal is None):
             raise RuntimeError('Trying to add non-initialied crystal to chunk from line {}.'.format(self.start_line))
         self.crystals.append(deepcopy(crystal))
         # print(crystal)
-        
+
     def __str__(self):
         if not self.initialized:
             warn('Trying to get string from non-initialized chunk from line {}.'.format(self.start_line))
@@ -92,7 +92,7 @@ class Chunk:
                         for ii, cryst in enumerate(self.crystals)])
 
 
-def parse_stream(stream, sol=None, return_meta=True, 
+def parse_stream(stream, sol=None, return_meta=True,
                  file_label='Image filename', event_label='Event',
                  x_shift_label=None, y_shift_label=None, shift_factor=1):
 
@@ -109,18 +109,18 @@ def parse_stream(stream, sol=None, return_meta=True,
     have_command = False
     parsing_reflections = False
     parse_vec = lambda l: tuple(float(k) for k in re.findall(r'[+-]?\d*\.\d*', l))
-    
+
     with open(stream, 'r') as fh_in, (StringIO() if sol is None else open(sol,'w')) as fh_out:
 
         for ln, l in enumerate(fh_in):
-            
+
             if parsing_reflections:
                 if l.startswith(END_REFLECTIONS):
                     parsing_reflections = False
                 else:
                     # here, any reflection parsing would go
                     pass
-                    
+
             elif parsing_peaks:
                 if l.startswith(END_PEAKS):
                     parsing_peaks = False
@@ -130,10 +130,10 @@ def parse_stream(stream, sol=None, return_meta=True,
 
             elif l.startswith(BEGIN_CHUNK):
                 curr_chunk = Chunk(ln)
-                
+
             elif (curr_chunk is not None) and (curr_cryst is None):
                 # parsing chunks (= events = shots) _outside_ crystals
-                
+
                 if l.startswith(END_CHUNK):
                     if not curr_chunk.initialized:
                         raise RuntimeError('Incomplete chunk found before line ' + str(ln))
@@ -141,10 +141,10 @@ def parse_stream(stream, sol=None, return_meta=True,
                         fh_out.write(str(curr_chunk) + '\n')
                         # print(str(curr_chunk))
                     curr_chunk = None
-                    
+
                 elif l.startswith(file_label):
                     curr_chunk.file = l.split(' ')[-1].strip()
-                    
+
                 elif l.startswith(event_label):
                     curr_chunk.Event = l.split(' ')[-1].strip()
 
@@ -156,49 +156,49 @@ def parse_stream(stream, sol=None, return_meta=True,
 
                 elif l.startswith(BEGIN_CRYSTAL):
                     if not curr_chunk.initialized:
-                        raise RuntimeError('Crystal for incomplete chunk in ' + str(ln))                
+                        raise RuntimeError('Crystal for incomplete chunk in ' + str(ln))
                     curr_cryst = Crystal(ln)
-                
+
             elif curr_cryst is not None:
                 # parsing a (single) crystal
-                
+
                 if l.startswith(END_CRYSTAL):
                     curr_chunk.add_crystal(curr_cryst)
                     curr_cryst = None
-                        
+
                 elif l.startswith('astar'):
                     curr_cryst.astar = parse_vec(l)
-                    
+
                 elif l.startswith('bstar'):
                     curr_cryst.bstar = parse_vec(l)
-                    
+
                 elif l.startswith('cstar'):
                     curr_cryst.cstar = parse_vec(l)
                     
                 elif l.startswith('profile_radius'):
                     curr_cryst.profile_radius = parse_vec(l)[0]
-                    
+
                 elif l.startswith('predict_refine/det_shift'):
                     curr_cryst.det_shift = parse_vec(l)
                     curr_cryst.det_shift = (curr_cryst.det_shift[0] + curr_chunk.x_shift,
                                             curr_cryst.det_shift[1] + curr_chunk.y_shift)
-                    
+
                 elif l.startswith('diffraction_resolution_limit'):
                     curr_cryst.resolution = parse_vec(l)[0]
-                    
+
             elif  l.startswith(BEGIN_GEOM) and not have_geom:
                 parsing_geom = True
-                
+
             elif parsing_geom:
                 if not l.startswith(END_GEOM):
                     geom += l
                 else:
                     parsing_geom = False
                     have_geom = True
-                
+
             elif l.startswith(BEGIN_CELL) and not have_cell:
                 parsing_cell = True
-                
+
             elif parsing_cell:
                 if not l.startswith(END_CELL):
                     cell += l
@@ -209,30 +209,30 @@ def parse_stream(stream, sol=None, return_meta=True,
             elif ('indexamajig' in l) and not have_command:
                 command = l
                 have_command = True
-                                    
+
             elif l.startswith(BEGIN_PEAKS):
                 parsing_peaks = True
-                
+
             elif l.startswith(BEGIN_REFLECTIONS):
-                parsing_reflections = True                    
-                
+                parsing_reflections = True
+
         if sol is None:
             out = fh_out.getvalue()
             if return_meta:
                 return out, (command, geom, cell)
             else:
                 return out
-        
+
         else:
             if return_meta:
                 return command, geom, cell
 
 def main():
     global args
-    
+
     from argparse import ArgumentParser
     parser = ArgumentParser(description='Conversion tool from stream to solution file(s) for re-integration/-refinement.')
-    
+
     parser.add_argument('-i', '--input', type=str, help='Input stream file', required=True)
     parser.add_argument('-o', '--output', type=str, help='Output solution file', required=True)
     parser.add_argument('-g', '--geometry-out', type=str, help='Output geometry file (optional)')
@@ -241,27 +241,26 @@ def main():
     parser.add_argument('--event-field', type=str, help='Field in chunk for event identifier', default='Event')
     parser.add_argument('--x-shift-field', type=str, help='Field in chunk for x-shift identifier', default='')
     parser.add_argument('--y-shift-field', type=str, help='Field in chunk for y-shift identifier', default='')
-    parser.add_argument('--shift-factor', type=float, 
+    parser.add_argument('--shift-factor', type=float,
                         help='Pre-factor for shifts, typically the pixel size in mm if the shifts are in pixel', default=1)
     parser.add_argument('--include-pars', help='Include profile radius and resolution estimate into sol file', action='store_true')
 
     args = parser.parse_args()
-    
-    meta = parse_stream(args.input, args.output, return_meta=True, 
+
+    meta = parse_stream(args.input, args.output, return_meta=True,
                         file_label=args.file_field, event_label=args.event_field,
                         x_shift_label=args.x_shift_field, y_shift_label=args.y_shift_field)
     # print('Original indexamajig call was: \n' + meta[0])
     if args.geometry_out:
         with open(args.geometry_out, 'w') as fh:
             fh.write(meta[1])
-    
+
     if args.cell_out:
         if not meta[1]:
             print('No cell found in stream file. Not writing cell file.')
         else:
             with open(args.cell_out, 'w') as fh:
                 fh.write(meta[2])
-     
+
 if __name__ == '__main__':
     main()
-    
\ No newline at end of file