def do_main():
""" Main method to do work
"""
from pyimgalgos.FiberIndexing import BinPars
from pyimgalgos.GlobalUtils import create_directory
# h-k space image parameters
hmax = 4
kmax = 6
# recipical space image parameters, bins for 2-d image
bpq = BinPars((-0.25, 0.25), 1200, vtype=np.float32, endpoint=True)
#fname = '/reg/neh/home1/dubrovin/LCLS/rel-mengning/work/peak-idx-cxif5315-r0169-2015-11-13T17:04:37.txt'
#fname = '/reg/neh/home1/dubrovin/LCLS/rel-mengning/work/peak-idx-cxif5315-r0169-2015-12-01T15:44:49.txt'
fname = '/reg/neh/home1/dubrovin/LCLS/rel-mengning/work/peak-idx-cxif5315-r0169-2016-05-12T18:17:57.txt'
rdir = './results-idx'
create_directory(rdir)
sp.prefix = '%s/2016-05-13-v01-idx-res-matched' % rdir # file name prefix for histograms
#sp.prefix = '%s/2016-05-13-v01-idx-res-peak-nm' % rdir # file name prefix for histograms
img_space, img_recip = proc_file(fname, hmax, kmax, bpq)
print_crystal_in_hk_space(img_space, hmax, kmax)
print 'img_recip.shape=', img_recip.shape
if sp.DO_HIST: plot_histograms()
if sp.DO_PLOT:
import pyimgalgos.GlobalGraphics as gg
img = img_space
img_range = (-kmax - 0.5, kmax + 0.5, -hmax - 0.5, hmax + 0.5)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=(0,1), figsize=(8,6),\
title='Crystal structure in h-k space', origin='upper', window=(0.1, 0.1, 0.9, 0.86))
axim.set_xlabel('k index', fontsize=18)
axim.set_ylabel('h index', fontsize=18)
gg.savefig('%s-%s-crystal-in-hk-space.png' %
(sp.prefix, sp.exp_run)) # sp.tstamp
img = img_recip
ave, rms = img.mean(), img.std()
amin, amax = 0, ave + 5 * rms
img_range = (bpq.vmin, bpq.vmax, bpq.vmin, bpq.vmax)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=(amin, amax), figsize=(10,8),\
title='Crystal structure in reciprocal space', origin='upper', window=(0.1, 0.1, 0.86, 0.86))
axim.set_xlabel('$q_x$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$q_y$ ($1/\AA$)', fontsize=18)
gg.savefig('%s-%s-crystal-in-recip-space.png' %
(sp.prefix, sp.exp_run))
gg.show()
def test_plot_beta_l0() :
print """Test plot for beta angle"""
import pyimgalgos.GlobalGraphics as gg
xarr = np.linspace(-2,2,50)
phi = 0
cmt = 'l0'
y_000 = [funcy_l0(x, phi, 0) for x in xarr]
y_p10 = [funcy_l0(x, phi, 10) for x in xarr]
y_p20 = [funcy_l0(x, phi, 20) for x in xarr]
y_p30 = [funcy_l0(x, phi, 30) for x in xarr]
y_p40 = [funcy_l0(x, phi, 40) for x in xarr]
y_p50 = [funcy_l0(x, phi, 50) for x in xarr] # 48
y_m10 = [funcy_l0(x, phi, -10) for x in xarr]
y_m20 = [funcy_l0(x, phi, -20) for x in xarr]
y_m30 = [funcy_l0(x, phi, -30) for x in xarr]
y_m40 = [funcy_l0(x, phi, -40) for x in xarr]
y_m50 = [funcy_l0(x, phi, -50) for x in xarr] # -48
#fig2, ax2 = gg.plotGraph(xarr, y_m01, pfmt='k.', figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80))
fig2, ax2 = gg.plotGraph(xarr, y_000, pfmt='k-', figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80), lw=2)
#b: blue
#g: green
#r: red
#c: cyan
#m: magenta
#y: yellow
#k: black
#w: white
ax2.plot(xarr, y_p50,'g-x', label=' 50')
ax2.plot(xarr, y_p40,'m-', label=' 40')
ax2.plot(xarr, y_p30,'b-', label=' 30')
ax2.plot(xarr, y_p20,'y-', label=' 20')
ax2.plot(xarr, y_p10,'r-', label=' 10')
ax2.plot(xarr, y_000,'k-', label=' 0')
ax2.plot(xarr, y_m10,'r.', label='-10')
ax2.plot(xarr, y_m20,'y.', label='-20')
ax2.plot(xarr, y_m30,'b.', label='-30')
ax2.plot(xarr, y_m40,'m.', label='-40')
ax2.plot(xarr, y_m50,'g+', label='-50')
ax2.legend(loc='upper right')
ax2.set_xlabel('x', fontsize=14)
ax2.set_ylabel('y', fontsize=14)
ax2.set_title('%s: phi=%.1f, beta=[-50,50]' % (cmt,phi), color='k', fontsize=20)
gg.savefig('test-plot-beta-l0.png')
gg.show()
def test_plot_beta_l1(DoR=0.4292, sgnrt=1.) :
print """Test plot for beta angle"""
import pyimgalgos.GlobalGraphics as gg
xarr = np.linspace(-2,2,50)
phi = 0
fancy_plt = funcy_l1_v1
#fancy_plt = funcy_l1_v0
cmt = 'POS' if sgnrt > 0 else 'NEG' #'-B -/+ sqrt(B*B-C)'
cmt = '%s-DoR-%.3f' % (cmt, DoR)
y_p10 = [fancy_plt(x, phi, 10, DoR, sgnrt) for x in xarr]
y_000 = [fancy_plt(x, phi, 0, DoR, sgnrt) for x in xarr]
y_m10 = [fancy_plt(x, phi, -10, DoR, sgnrt) for x in xarr]
y_m13 = [fancy_plt(x, phi, -13, DoR, sgnrt) for x in xarr]
y_m15 = [fancy_plt(x, phi, -15, DoR, sgnrt) for x in xarr]
y_m20 = [fancy_plt(x, phi, -20, DoR, sgnrt) for x in xarr]
y_m30 = [fancy_plt(x, phi, -30, DoR, sgnrt) for x in xarr]
y_m35 = [fancy_plt(x, phi, -35, DoR, sgnrt) for x in xarr]
y_m40 = [fancy_plt(x, phi, -40, DoR, sgnrt) for x in xarr]
fig2, ax2 = gg.plotGraph(xarr, y_000, pfmt='k-', figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80), lw=2)
ax2.plot(xarr, y_p10,'g-', label=' 10')
ax2.plot(xarr, y_000,'k-', label=' 0')
ax2.plot(xarr, y_m10,'g.', label='-10')
ax2.plot(xarr, y_m13,'r-.', label='-13')
ax2.plot(xarr, y_m15,'y.', label='-14')
ax2.plot(xarr, y_m20,'r.', label='-20')
ax2.plot(xarr, y_m30,'c.', label='-30')
ax2.plot(xarr, y_m35,'m.', label='-35')
ax2.plot(xarr, y_m40,'b+', label='-40')
ax2.legend(loc='upper right')
ax2.set_title('%s: phi=%.1f, beta=[-40,10]' % (cmt,phi), color='k', fontsize=20)
ax2.set_xlabel('x', fontsize=14)
ax2.set_ylabel('y', fontsize=14)
gg.savefig('test-plot-beta-l1-%s.png' % cmt)
gg.show()
def test_plot_beta_l1_zoom(DoR=0.4292, sgnrt=1.) :
print """Test plot for beta angle"""
import pyimgalgos.GlobalGraphics as gg
phi = 0
fancy_plt = funcy_l1_v1
#fancy_plt = funcy_l1_v0
if sgnrt > 0 :
cmt = 'POS' #'-B -/+ sqrt(B*B-C)'
cmt = '%s-DoR-%.3f' % (cmt, DoR)
xarr = np.linspace(-0.29,0.29,60)
y_000 = [fancy_plt(x, phi, 0, DoR, sgnrt) for x in xarr]
y_m05 = [fancy_plt(x, phi, -5, DoR, sgnrt) for x in xarr]
y_m09 = [fancy_plt(x, phi, -9, DoR, sgnrt) for x in xarr]
y_m13 = [fancy_plt(x, phi, -13.3, DoR, sgnrt) for x in xarr]
y_m18 = [fancy_plt(x, phi, -18, DoR, sgnrt) for x in xarr]
y_m20 = [fancy_plt(x, phi, -20, DoR, sgnrt) for x in xarr]
fig2, ax2 = gg.plotGraph(xarr, y_000, pfmt='k-', figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80), lw=2)
ax2.plot(xarr, y_000,'k-', label=' 0')
ax2.plot(xarr, y_m05,'g.', label=' -5')
ax2.plot(xarr, y_m09,'y.', label=' -9')
ax2.plot(xarr, y_m13,'r-.', label='-13')
ax2.plot(xarr, y_m18,'c.', label='-18')
ax2.plot(xarr, y_m20,'b.', label='-20')
ax2.set_title('%s: phi=%.1f, beta=[-20,0]' % (cmt,phi), color='k', fontsize=20)
ax2.legend(loc='upper center')
if sgnrt < 0 :
cmt = 'NEG' #'-B -/+ sqrt(B*B-C)'
cmt = '%s-DoR-%.3f' % (cmt, DoR)
xarr = np.linspace(-1,1,50)
y_m20 = [fancy_plt(x, phi, -20, DoR, sgnrt) for x in xarr]
y_m23 = [fancy_plt(x, phi, -23, DoR, sgnrt) for x in xarr]
y_m25 = [fancy_plt(x, phi, -25, DoR, sgnrt) for x in xarr]
y_m27 = [fancy_plt(x, phi, -27, DoR, sgnrt) for x in xarr]
y_m30 = [fancy_plt(x, phi, -30, DoR, sgnrt) for x in xarr]
y_m35 = [fancy_plt(x, phi, -35, DoR, sgnrt) for x in xarr]
y_m40 = [fancy_plt(x, phi, -40, DoR, sgnrt) for x in xarr]
y_m60 = [fancy_plt(x, phi, -60, DoR, sgnrt) for x in xarr]
fig2, ax2 = gg.plotGraph(xarr, y_m25, pfmt='k-', figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80), lw=2)
ax2.plot(xarr, y_m20,'g+-', label='-20')
ax2.plot(xarr, y_m23,'m-', label='-23')
ax2.plot(xarr, y_m25,'k-', label='-25')
ax2.plot(xarr, y_m27,'b.', label='-27')
ax2.plot(xarr, y_m30,'y.', label='-30')
ax2.plot(xarr, y_m35,'r.', label='-35')
ax2.plot(xarr, y_m40,'c.', label='-40')
ax2.plot(xarr, y_m60,'+', label='-60')
ax2.set_title('%s: phi=%.1f, beta=[-60,-20]' % (cmt,phi), color='k', fontsize=20)
ax2.legend(loc='lower right')
ax2.set_xlabel('x', fontsize=14)
ax2.set_ylabel('y', fontsize=14)
gg.savefig('test-plot-beta-l1-%s-zoomed.png' % cmt)
gg.show()
