def test_plot_cspad(geometry, fname_data, amp_range=(0, 0.5)):
""" The same test as previous, but use get_pixel_coord_indexes(...) method
"""
#rad1 = 93
#rad2 = 146
rad1 = 655
rad2 = 670
# get pixel coordinate index arrays:
xc, yc = 1000, 1000
xyc = xc, yc # None
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=None)
iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc, do_tilt=True)
ixo, iyo = geometry.point_coord_indexes(xy0_off_pix=xyc, do_tilt=True)
print 'Detector origin indexes ixo, iyo:', ixo, iyo
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data,
dtype=np.float)
arr.shape = (4, 8, 185, 388)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
arr.shape = iX.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
xyc_ring = (yc, xc)
axim = gg.plotImageLarge(img, amp_range=amp_range)
gg.drawCircle(axim, xyc_ring, rad1, linewidth=1, color='w', fill=False)
gg.drawCircle(axim, xyc_ring, rad2, linewidth=1, color='w', fill=False)
gg.drawCenter(axim, xyc_ring, rad1, linewidth=1, color='w')
gg.move(500, 10)
gg.show()
def test_plot_cspad(geometry, fname_data, amp_range=(0,0.5)) :
""" The same test as previous, but use get_pixel_coord_indexes(...) method
"""
#rad1 = 93
#rad2 = 146
rad1 = 655
rad2 = 670
# get pixel coordinate index arrays:
xc, yc = 1000, 1000
xyc = xc, yc # None
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=None)
iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc, do_tilt=True)
ixo, iyo = geometry.point_coord_indexes(xy0_off_pix=xyc, do_tilt=True)
print 'Detector origin indexes ixo, iyo:', ixo, iyo
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data, dtype=np.float)
arr.shape= (4,8,185,388)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
arr.shape = iX.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
xyc_ring = (yc, xc)
axim = gg.plotImageLarge(img,amp_range=amp_range)
gg.drawCircle(axim, xyc_ring, rad1, linewidth=1, color='w', fill=False)
gg.drawCircle(axim, xyc_ring, rad2, linewidth=1, color='w', fill=False)
gg.drawCenter(axim, xyc_ring, rad1, linewidth=1, color='w')
gg.move(500,10)
gg.show()
def plot_lattice(b1 = (1.,0.,0.), b2 = (0.,1.,0.), b3 = (0.,0.,1.),\
hmax=3, kmax=2, lmax=1, cdtype=np.float32,\
evald_rad=0.5, qtol=0.01, prefix='', do_movie=False, delay=400) :
"""Plots 2-d reciprocal space lattice, evald sphere,
generates series of plots for rotated lattice and movie from these plots.
- do_movie = True/False - on/off production of movie
- delay - is a time in msec between movie frames.
"""
import matplotlib.pyplot as plt
import algos.graph.GlobalGraphics as gg
print '\nIn %s' % sys._getframe().f_code.co_name
print '%s\nTest lattice with default parameters' % (80*'_')
x, y, z, r, h, k, l = lattice(b1, b2, b3, hmax, kmax, lmax, cdtype)
xlimits = ylimits = (-0.3, 0.3) # plot limits in (1/A)
#ylimits = (-0.4, 0.4) # plot limits in (1/A)
#xlimits = (-0.5, 0.3) # plot limits in (1/A)
fig, ax = gg.plotGraph(x,y, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.86), pfmt='bo')
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.save_fig(fig, '%sreciprocal-space-lattice.png' % prefix, pbits=1)
lst_omega = range(0,180,2) if do_movie else range(0,13,11)
#lst_omega = range(0,180,5) if do_movie else range(0,13,11)
#lst_omega = range(0,180,45) if do_movie else range(0,13,11)
beta_deg = 0
for omega_deg in lst_omega :
xrot1, yrot1 = rotation(x, y, omega_deg)
xrot2, zrot2 = rotation(xrot1, z, beta_deg)
dr, qv, qh = radial_distance(xrot2, yrot1, zrot2, evald_rad)
xhit = [xr for dq,xr in zip(dr.flatten(), xrot2.flatten()) if math.fabs(dq)<qtol]
yhit = [yr for dq,yr in zip(dr.flatten(), yrot1.flatten()) if math.fabs(dq)<qtol]
#fig, ax = gg.plotGraph(xrot2, yrot1, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.84), pfmt='bo')
ax.cla()
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.plot(xrot1, yrot1, 'yo')
if len(xhit)>0 and len(yhit)>0 : ax.plot(xhit, yhit, 'bo')
ax.set_title('beta=%.0f omega=%.0f' % (beta_deg, omega_deg), color='k', fontsize=20)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.drawCenter(ax, (-evald_rad,0), s=0.04, linewidth=2, color='k')
gg.drawCircle(ax, (-evald_rad,0), evald_rad, linewidth=1, color='k', fill=False)
fig.canvas.draw()
gg.show('Do not hold!')
gg.save_fig(fig, '%sreciprocal-space-lattice-rotated-beta=%03d-omega=%03d.png'%\
(prefix, int(beta_deg), int(omega_deg)), pbits=1)
if do_movie :
import os
#dir_movie = 'movie'
#os.system('mkdir %s'% dir_movie)
cmd = 'convert -delay %f %sreciprocal-space-lattice-rotated-beta=*.png movie.gif' % (delay, prefix)
print 'Wait for completion of the command: %s' % cmd
os.system(cmd)
print 'DONE!'
gg.show()
def plot_lattice(b1 = (1.,0.,0.), b2 = (0.,1.,0.), b3 = (0.,0.,1.),\
hmax=3, kmax=2, lmax=1, cdtype=np.float32,\
evald_rad=0.5, qtol=0.01, prefix='', do_movie=False, delay=400) :
"""Plots 2-d reciprocal space lattice, evald sphere,
generates series of plots for rotated lattice and movie from these plots.
- do_movie = True/False - on/off production of movie
- delay - is a time in msec between movie frames.
"""
import matplotlib.pyplot as plt
import algos.graph.GlobalGraphics as gg
print '\nIn %s' % sys._getframe().f_code.co_name
print '%s\nTest lattice with default parameters' % (80 * '_')
x, y, z, r, h, k, l = lattice(b1, b2, b3, hmax, kmax, lmax, cdtype)
xlimits = ylimits = (-0.3, 0.3) # plot limits in (1/A)
#ylimits = (-0.4, 0.4) # plot limits in (1/A)
#xlimits = (-0.5, 0.3) # plot limits in (1/A)
fig, ax = gg.plotGraph(x,
y,
figsize=(8, 7.5),
window=(0.15, 0.10, 0.78, 0.86),
pfmt='bo')
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.save_fig(fig, '%sreciprocal-space-lattice.png' % prefix, pbits=1)
lst_omega = range(0, 180, 2) if do_movie else range(0, 13, 11)
#lst_omega = range(0,180,5) if do_movie else range(0,13,11)
#lst_omega = range(0,180,45) if do_movie else range(0,13,11)
beta_deg = 0
for omega_deg in lst_omega:
xrot1, yrot1 = rotation(x, y, omega_deg)
xrot2, zrot2 = rotation(xrot1, z, beta_deg)
dr, qv, qh = radial_distance(xrot2, yrot1, zrot2, evald_rad)
xhit = [
xr for dq, xr in zip(dr.flatten(), xrot2.flatten())
if math.fabs(dq) < qtol
]
yhit = [
yr for dq, yr in zip(dr.flatten(), yrot1.flatten())
if math.fabs(dq) < qtol
]
#fig, ax = gg.plotGraph(xrot2, yrot1, figsize=(8,7.5), window=(0.15, 0.10, 0.78, 0.84), pfmt='bo')
ax.cla()
ax.set_xlim(xlimits)
ax.set_ylim(ylimits)
ax.plot(xrot1, yrot1, 'yo')
if len(xhit) > 0 and len(yhit) > 0: ax.plot(xhit, yhit, 'bo')
ax.set_title('beta=%.0f omega=%.0f' % (beta_deg, omega_deg),
color='k',
fontsize=20)
ax.set_xlabel('Reciprocal x ($1/\AA$)', fontsize=18)
ax.set_ylabel('Reciprocal y ($1/\AA$)', fontsize=18)
gg.drawCenter(ax, (-evald_rad, 0), s=0.04, linewidth=2, color='k')
gg.drawCircle(ax, (-evald_rad, 0),
evald_rad,
linewidth=1,
color='k',
fill=False)
fig.canvas.draw()
gg.show('Do not hold!')
gg.save_fig(fig, '%sreciprocal-space-lattice-rotated-beta=%03d-omega=%03d.png'%\
(prefix, int(beta_deg), int(omega_deg)), pbits=1)
if do_movie:
import os
#dir_movie = 'movie'
#os.system('mkdir %s'% dir_movie)
cmd = 'convert -delay %f %sreciprocal-space-lattice-rotated-beta=*.png movie.gif' % (
delay, prefix)
print 'Wait for completion of the command: %s' % cmd
os.system(cmd)
print 'DONE!'
gg.show()