Add scripts/move-entire-detector and scripts/split-by-mask

3 files changed, 216 insertions, 1 deletions

diff --git a/Makefile.am b/Makefile.am
index 5a916cad..eb10db9c 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -181,7 +181,8 @@ script_DATA = scripts/alternate-stream scripts/cell-please \
               scripts/ave-resolution scripts/crystal-frame-number \
               scripts/plot-radius-resolution \
               scripts/detector-shift scripts/turbo-index \
-              scripts/gaincal-to-saturation-map
+              scripts/gaincal-to-saturation-map scripts/move-entire-detector \
+              scripts/split-by-mask
 
 EXTRA_DIST += $(script_DATA)
 
diff --git a/scripts/move-entire-detector b/scripts/move-entire-detector
new file mode 100755
index 00000000..0833845b
--- /dev/null
+++ b/scripts/move-entire-detector
@@ -0,0 +1,127 @@
+#!/usr/bin/env python
+
+#
+# Shift the detector by a given amount
+#
+# Copyright (c) 2016 Deutsches Elektronen-Synchrotron DESY,
+#                    a research centre of the Helmholtz Association.
+#
+# Author:
+#    2016 Thomas White <taw@physics.org>
+#
+
+import sys
+import optparse
+import os
+import re
+
+op = optparse.OptionParser(usage="%prog input.geom xshift yshift")
+op.add_option('', '--output', action='store', type='string', dest='ofn',
+              help="Output geometry file")
+op.add_option('', '--pixels', action='store_true', dest='px',
+              help="Specify shifts in pixel units")
+op.add_option('', '--mm', action='store_false', dest='px',
+              help="Specify shifts in millimeters (this is the default)")
+op.add_option('', '--beam', action='store_true', dest='beam',
+              help="Specify shift of X-ray beam")
+op.add_option('', '--detector', action='store_false', dest='beam',
+              help="Specify shift of detector (this is the default)")
+opt,args = op.parse_args(sys.argv)
+
+if len(args) < 3:
+    print 'Usage: %s input.geom xshift yshift' % args[0]
+    sys.exit(1)
+
+geom = args[1]
+if not opt.ofn:
+    out = os.path.splitext(geom)[0]+'-shifted.geom'
+else:
+    out = opt.ofn
+xshift = float(args[2])
+yshift = float(args[3])
+
+if opt.px:
+    units = 'px'
+else:
+    units = 'mm'
+
+if opt.beam:
+    bm = 'beam'
+else:
+    bm = 'detector'
+
+print 'Input filename %s\nOutput filename %s' % (geom,out)
+print 'Shifting %s by %f,%f %s' % (bm, xshift, yshift, units)
+
+if opt.beam:
+    xshift = -xshift
+    yshift = -yshift
+
+f = open(geom, 'r')
+g = open(args[1], 'r')
+h = open(out, 'w')
+panel_resolutions = {}
+
+prog1 = re.compile("^\s*res\s+=\s+([0-9\.]+)\s")
+prog2 = re.compile("^\s*(.*)\/res\s+=\s+([0-9\.]+)\s")
+prog3 = re.compile("^\s*(.*)\/corner_x\s+=\s+([0-9\.\-]+)\s")
+prog4 = re.compile("^\s*(.*)\/corner_y\s+=\s+([0-9\.\-]+)\s")
+default_res = 0
+while True:
+
+    fline = g.readline()
+    if not fline:
+        break
+
+    match = prog1.match(fline)
+    if match:
+        default_res = float(match.group(1))
+        h.write(fline)
+        continue
+
+    match = prog2.match(fline)
+    if match:
+        panel = match.group(1)
+        panel_res = float(match.group(2))
+        default_res =  panel_res
+        panel_resolutions[panel] = panel_res
+        h.write(fline)
+        continue
+
+    match = prog3.match(fline)
+    if match:
+        panel = match.group(1)
+        panel_cnx = float(match.group(2))
+        if panel in panel_resolutions:
+            res = panel_resolutions[panel]
+        else:
+            res = default_res
+            if not opt.px:
+                print 'Using default resolution (%f px/m) for panel %s' % (res, panel)
+        if opt.px:
+            h.write('%s/corner_x = %f\n' % (panel,panel_cnx+xshift))
+        else:
+            h.write('%s/corner_x = %f\n' % (panel,panel_cnx+(xshift*res*1e-3)))
+        continue
+
+    match = prog4.match(fline)
+    if match:
+        panel = match.group(1)
+        panel_cny = float(match.group(2))
+        if panel in panel_resolutions:
+            res = panel_resolutions[panel]
+        else:
+            res = default_res
+            if not opt.px:
+                print 'Using default resolution (%f px/m) for panel %s' % (res, panel)
+        if opt.px:
+            h.write('%s/corner_y = %f\n' % (panel,panel_cny+yshift))
+        else:
+            h.write('%s/corner_y = %f\n' % (panel,panel_cny+(yshift*res*1e-3)))
+        continue
+
+    h.write(fline)
+
+g.close()
+h.close()
+
diff --git a/scripts/split-by-mask b/scripts/split-by-mask
new file mode 100755
index 00000000..aede3f43
--- /dev/null
+++ b/scripts/split-by-mask
@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+
+#
+# Split stream according to an external mask
+#
+# Copyright (c) 2014-2016 Deutsches Elektronen-Synchrotron DESY,
+#                         a research centre of the Helmholtz Association.
+#
+# Author:
+#    2014-2016 Thomas White <taw@physics.org>
+#
+
+import sys
+import optparse
+from collections import deque
+import h5py
+import re
+
+prog = re.compile("^\s+([\d-]+)\s+([\d-]+)\s+([\d-]+)\s+[\d\.\-]+\s+[\d\.\-]+\s+[\d\.\-]+\s+[\d\.\-]+\s+([\d\.]+)\s+([\d\.]+)")
+
+def process_refln(fline, g, h, mask):
+    match = prog.match(fline)
+    if not match:
+        print 'Line not understood, WTF? %s' % fline
+	return
+    fs = int(round(float(match.group(4))))
+    ss = int(round(float(match.group(5))))
+    m = mask[ss][fs]
+    if m:
+        g.write(fline)
+    else:
+        h.write(fline)
+
+op = optparse.OptionParser()
+
+op.add_option('', '--input', action='store', type='string', dest='ifn',
+              help="Input stream")
+
+op.add_option('', '--output1', action='store', type='string', dest='ofn1',
+              help="Output stream", default='mask-split.stream1')
+
+op.add_option('', '--output2', action='store', type='string', dest='ofn2',
+              help="Output stream", default='mask-split.stream2')
+
+op.add_option('', '--mask', action='store', type='string', dest='mask_fn',
+              help="Filename of mask", default='mask.h5')
+
+opt,arg = op.parse_args(sys.argv)
+
+if not opt.ifn:
+    print "You need at least --input"
+    exit(1)
+
+f = open(opt.ifn, 'r')
+g = open(opt.ofn1, 'w')
+h = open(opt.ofn2, 'w')
+
+fh = h5py.File(opt.mask_fn, 'r')
+mask = fh['/data/data'].value
+fh.close()
+
+in_refl = 0
+while True:
+
+    fline = f.readline()
+    if not fline:
+        break
+    if fline.find("End of reflections") != -1:
+        in_refl = 0
+
+    if in_refl == 1:
+        process_refln(fline, g, h, mask)
+    else:
+        g.write(fline)
+        h.write(fline)
+	if in_refl == 2:
+	    in_refl = 1
+
+    if fline.find("Reflections measured after indexing") != -1:
+        in_refl = 2
+
+
+
+
+f.close()
+g.close()
+