New version of sum-peaks

This version gets the array dimensions automatically.  However, it still
assumes the data is "slabby".

1 files changed, 38 insertions, 33 deletions

diff --git a/scripts/sum-peaks b/scripts/sum-peaks
index eccb9fc6..5b528661 100755
--- a/scripts/sum-peaks
+++ b/scripts/sum-peaks
@@ -7,41 +7,46 @@
 #                  a research centre of the Helmholtz Association.
 #
 # Author:
-#    2017 Thomas White <taw@physics.org>
+#    2017 Alexandra Tolstikova <alexandra.tolstikova@desy.de>
 #
 
+import sys
 import numpy as np
 import h5py
-import sys
-import re
-
-f = open(sys.argv[1], 'r')
-powder = np.zeros((512,1024), dtype=float)
-peaks = []
-
-prog1 = re.compile("^\s*([\d\-\.]+)\s+([\d\-\.]+)\s+[\d\-\.]+\s+([\d\-\.]+)\s+\S+$")
-
-while True:
-
-    fline = f.readline()
-    if not fline:
-        break
-
-    if fline == '----- End chunk -----\n':
-        if len(peaks) > 10:
-            for p in peaks:
-                powder[p[1],p[0]] += p[2]
-        peaks = []
-
-    match = prog1.match(fline)
-    if match:
-        fs = int(float(match.group(1)))
-        ss = int(float(match.group(2)))
-        intensity = float(match.group(3))
-        peaks.append((fs,ss,intensity))
-
+from os.path import basename, splitext
+
+with open(sys.argv[1], 'r') as stream:
+    reading_geometry = False
+    reading_chunks = False
+    reading_peaks = False
+    max_fs = -100500
+    max_ss = -100500
+    for line in stream:
+        if reading_chunks:
+            if line.startswith('End of peak list'):
+                reading_peaks = False
+            elif line.startswith('  fs/px   ss/px (1/d)/nm^-1   Intensity  Panel'):
+                reading_peaks = True
+            elif reading_peaks:
+                fs, ss, dump, intensity = [float(i) for i in line.split()[:4]]
+                powder[int(ss), int(fs)] += intensity
+        elif line.startswith('----- End geometry file -----'):
+            reading_geometry = False
+            powder = np.zeros((max_ss + 1, max_fs + 1))
+        elif reading_geometry:
+            try:
+                par, val = line.split('=')
+                if par.split('/')[-1].strip() == 'max_fs' and int(val) > max_fs:
+                    max_fs = int(val)
+                elif par.split('/')[-1].strip() == 'max_ss' and int(val) > max_ss:
+                    max_ss = int(val)
+            except ValueError:
+                pass
+        elif line.startswith('----- Begin geometry file -----'):
+            reading_geometry = True
+        elif line.startswith('----- Begin chunk -----'):
+            reading_chunks = True
+
+f = h5py.File(splitext(basename(sys.argv[1]))[0]+'-powder.h5', 'w')
+f.create_dataset('/data/data', data=powder)
 f.close()
-
-fh = h5py.File("summed-peaks.h5", "w")
-fh.create_dataset("/data", (512,1024), data=powder)
-fh.close()