scripts/detector-shift: Add placeholder message

We don't do per-crystal beam center refinement any more, so it won't
work.

1 files changed, 14 insertions, 174 deletions

diff --git a/scripts/detector-shift b/scripts/detector-shift
index b16d788b..083188f6 100755
--- a/scripts/detector-shift
+++ b/scripts/detector-shift
@@ -1,174 +1,14 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Determine mean detector shift based on prediction refinement results
-#
-# Copyright © 2015-2020 Deutsches Elektronen-Synchrotron DESY,
-#                       a research centre of the Helmholtz Association.
-#
-# Author:
-#    2015-2018 Thomas White <taw@physics.org>
-#    2016      Mamoru Suzuki <mamoru.suzuki@protein.osaka-u.ac.jp>
-#    2018      Chun Hong Yoon
-#
-
-import sys
-import os
-import re
-import numpy as np
-import matplotlib.pyplot as plt
-
-infiles = []
-
-if sys.argv[1] == "--":
-    have_geom = 0
-    infiles += sys.argv[2:]
-else:
-    if len(sys.argv) > 2:
-        infiles += [sys.argv[1]]
-        geom = sys.argv[2]
-        have_geom = 1
-    else:
-        have_geom = 0
-        infiles += sys.argv[1:]
-
-# Determine the mean shifts
-x_shifts = []
-y_shifts = []
-z_shifts = []
-
-prog1 = re.compile("^predict_refine/det_shift\sx\s=\s([0-9\.\-]+)\sy\s=\s([0-9\.\-]+)\smm$")
-prog2 = re.compile("^predict_refine/clen_shift\s=\s([0-9\.\-]+)\smm$")
-
-for file in infiles:
-
-    print("Reading "+file)
-    if file == "-":
-        f = sys.stdin
-    else:
-        f = open(file, 'r')
-
-    while True:
-
-        fline = f.readline()
-        if not fline:
-            break
-
-        match = prog1.match(fline)
-        if match:
-            xshift = float(match.group(1))
-            yshift = float(match.group(2))
-            x_shifts.append(xshift)
-            y_shifts.append(yshift)
-
-        match = prog2.match(fline)
-        if match:
-            zshift = float(match.group(1))
-            z_shifts.append(zshift)
-
-    f.close()
-
-mean_x = sum(x_shifts) / len(x_shifts)
-mean_y = sum(y_shifts) / len(y_shifts)
-print('Mean shifts: dx = {:.2} mm,  dy = {:.2} mm'.format(mean_x,mean_y))
-print('Shifts will be applied to geometry file when you close the graph window')
-print('Click anywhere on the graph to override the detector shift')
-
-def plotNewCentre(x, y):
-    circle1 = plt.Circle((x,y),.1,color='r',fill=False)
-    fig.gca().add_artist(circle1)
-    plt.plot(x, y, 'b8', color='m')
-    plt.grid(True)
-
-def onclick(event):
-    print('New shifts: dx = {:.2} mm,  dy = {:.2} mm'.format(event.xdata, event.ydata))
-    print('Shifts will be applied to geometry file when you close the graph window')
-    mean_x = event.xdata
-    mean_y = event.ydata
-    plotNewCentre(mean_x, mean_y)
-
-nbins = 200
-H, xedges, yedges = np.histogram2d(x_shifts,y_shifts,bins=nbins)
-H = np.rot90(H)
-H = np.flipud(H)
-Hmasked = np.ma.masked_where(H==0,H)
-
-# Plot 2D histogram using pcolor
-plt.ion()
-fig2 = plt.figure()
-cid = fig2.canvas.mpl_connect('button_press_event', onclick)
-plt.pcolormesh(xedges,yedges,Hmasked)
-plt.title('Detector shifts according to prediction refinement')
-plt.xlabel('x shift / mm')
-plt.ylabel('y shift / mm')
-plt.plot(0, 0, 'bH', color='c')
-fig = plt.gcf()
-cbar = plt.colorbar()
-cbar.ax.set_ylabel('Counts')
-plotNewCentre(mean_x, mean_y)
-plt.show(block=True)
-
-# Apply shifts to geometry
-if have_geom:
-
-    out = os.path.splitext(geom)[0]+'-predrefine.geom'
-    print('Applying corrections to {}, output filename {}'.format(geom,out))
-    g = open(geom, '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
-                print('Using default resolution ({} px/m) for panel {}'.format(res, panel))
-            h.write('%s/corner_x = %f\n' % (panel,panel_cnx+(mean_x*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
-                print('Using default resolution ({} px/m) for panel {}'.format(res, panel))
-            h.write('%s/corner_y = %f\n' % (panel,panel_cny+(mean_y*res*1e-3)))
-            continue
-
-        h.write(fline)
-
-    g.close()
-    h.close()
-
+#!/bin/sh
+
+echo -------------------------------------------------------------
+echo
+echo In this CrystFEL version, all detector geometry refinement is
+echo done using the new program align_detector.
+echo
+echo To update the detector center based on the indexing results,
+echo add --mille to the indexamajig arguments, then run the following:
+echo
+echo align_detector -i old.geom -o new.geom --level=0 mille-data-*.bin
+echo
+echo -------------------------------------------------------------
+exit 1