Initial commit

gen/fitlor.py

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+#!/usr/bin/python
+# above line tells us which program to handle this script
+#
+# M.Zolliker June 2081
+#
+usage='''
+Usage:
+
+> fitlor -fit <output-file> <input-file>
+
+   fit is called first, you should treat your peaks:
+ 
+   fit> data 5182       get data file 5182
+   fit> data [34]       get peak number 34 from above datafile
+   fit> fun 0           as an example: select one gaussian
+   fit> fit             you might play with parameters and reapeat
+   fit> k               saving the data on the intermediate <input-file>
+                        k means: keep data of this peak, might also be used
+                        in the plot window
+   fit> exit            exit and run the conversion program
+
+when starting fit from fitlor, the commands 'open' and 'k' are used to
+configure the outputfile for the needs of single crystal analysis
+
+> fitlor <output-file> <input-file>
+
+   do the conversion of already existing input files
+
+if file names are omitted, default values are used
+'''
+
+import sys
+from math import sin, cos, radians
+from subprocess import call
+from collections import Mapping
+from tempfile import NamedTemporaryFile
+
+# each entry is contained witinh curly brackets {} and
+# contains the variable name and the format separated by ':'
+# <n>d      n characters wide integer
+# <n>.<m>d  n characterws wide fixed point with m decimal digits
+
+output_format = '{n:6d}{h:4d}{k:4d}{l:4d}'\
+    '{i1:10.2f}{sigi1:10.2f}'\
+    '{th1:8.2f}{p1:8.2f}{chi:8.2f}{phi:8.2f}'
+
+# treating the arguments
+if len(sys.argv) > 1 and sys.argv[1] == '-fit':
+    call_fit = True
+    sys.argv.pop(1)
+else:
+    call_fit = False
+    
+if len(sys.argv) > 1:
+    outfile = sys.argv[1]
+    sys.argv.pop(0)
+else:
+    outfile = 'fitlor_out.txt'
+    print('output-file: %s' % outfile)
+
+if len(sys.argv) > 1:
+    datafile = sys.argv[1]
+    sys.argv.pop(1)
+else:
+    datafile = 'fitlor_data.txt'
+    print('input-file: %s' % datafile)
+
+if call_fit:
+    with NamedTemporaryFile('w') as cmdfil:
+        cmdfil.write('k h,k,l,i1,p1,intexp,two_theta,chi,phi\n')
+        cmdfil.write('open %s\n' % datafile)
+        cmdfil.flush()
+        call(('fit', '-F', cmdfil.name))
+    
+tilt_geometry = False
+lorentz_correction = True
+
+class Row(object):
+    def __init__(self, keys, values, fmt):
+        if keys is None:
+            raise ValueError('no keys')
+        for k,v in zip(keys, values):
+            v = float(v)
+            if v == int(v):
+                v = int(v)
+            setattr(self, k.lower(), v)
+	self.fmt = fmt
+
+    def write(self, fil):
+	fil.write(self.fmt.format(**self.__dict__) + '\n')
+
+keys = None
+rows = []
+try:
+  with open(datafile) as inp:
+    for line in inp:
+        values = line.split()
+        try:
+            row = Row(keys, values, output_format)
+        except ValueError:
+            keys = values
+            continue
+        rows.append(row)
+        row.n = len(rows)
+        row.th1=row.two_theta * 0.2
+        if lorentz_correction:
+            lor_cor = sin(abs(radians(row.two_theta)))
+            if tilt_geometry:
+                lor_cor *= cos(radians(row.chi))
+        row.intcor = row.i1 * lor_cor
+        row.sigcor = row.sigi1 * lor_cor
+except IOError:
+    print(usage)
+  
+with open(outfile, 'w') as out:
+    for row in rows:
+        row.write(out)
+