Perform prediction refinement straight after indexing

This allows indexing to be attempted again (either a new method or with
"retry") if the prediction refinement fails, increasing overall indexing
rate.

Side-effect: there are some hoops which would need to be jumped through
to store the profile radius before refinement and hence enable
scripts/plot-predict-refine to work.  For now, we'll ignore this as it's
clear that the prediction refinement is working.

1 files changed, 0 insertions, 64 deletions

diff --git a/scripts/plot-predict-refine b/scripts/plot-predict-refine
deleted file mode 100755
index 04f6ffa8..00000000
--- a/scripts/plot-predict-refine
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-
-#
-# Visualise behaviour of prediction refinement
-#
-# Copyright (c) 2015 Deutsches Elektronen-Synchrotron DESY,
-#                    a research centre of the Helmholtz Association.
-#
-# Author:
-#    2015 Thomas White <taw@physics.org>
-#
-
-import sys
-import os
-import re
-import matplotlib.pyplot as plt
-
-
-def show_frac(ratios, v):
-    n = len([x for x in ratios if x < v])
-    print "%4i (%.2f%%) new/old ratios are below %.2f" % (n, 100*float(n)/len(ratios), v)
-
-
-f = open(sys.argv[1], 'r')
-
-oldR = []
-newR = []
-
-prog1 = re.compile("^predict_refine/R\sold\s=\s([0-9\.\-]+)\snew\s=\s([0-9\.\-]+)\s")
-
-while True:
-
-    fline = f.readline()
-    if not fline:
-        break
-
-    match = prog1.match(fline)
-    if match:
-        old = float(match.group(1))
-        new = float(match.group(2))
-        oldR.append(old)
-        newR.append(new)
-
-f.close()
-
-mean_oldR = sum(oldR) / len(oldR)
-mean_newR = sum(newR) / len(newR)
-ratios = [new/old for new,old in zip(newR, oldR)];
-print 'Mean profile radius before: %.2e, after: %.2e nm^-1' % (mean_oldR,mean_newR)
-show_frac(ratios, 1.2)
-show_frac(ratios, 1.1)
-show_frac(ratios, 1.0)
-show_frac(ratios, 0.9)
-show_frac(ratios, 0.8)
-
-#plt.plot(oldR, newR, 'rx')
-plt.hist(ratios, 50)
-#plt.axis([-2,2,-2,2])
-plt.title('Profile radius before and after refinement')
-plt.xlabel('x shift / mm')
-plt.ylabel('y shift / mm')
-plt.grid(True)
-plt.show()
-