def test_plot_beta() :
print """Test plot for beta angle"""
import algos.graph.GlobalGraphics as gg
xarr = np.linspace(-2,2,50)
phi = 0
y0 = [funcy(x, phi, 0) for x in xarr]
y1 = [funcy(x, phi, -2) for x in xarr]
y2 = [funcy(x, phi, -5) for x in xarr]
y3 = [funcy(x, phi, -6) for x in xarr]
y4 = [funcy(x, phi, -7) for x in xarr]
y5 = [funcy(x, phi, -10) for x in xarr]
y6 = [funcy(x, phi, 2) for x in xarr]
y7 = [funcy(x, phi, 5) for x in xarr]
y8 = [funcy(x, phi, 10) for x in xarr]
fig2, ax2 = gg.plotGraph(xarr, y0, figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80))
ax2.plot(xarr, y1,'r-')
ax2.plot(xarr, y2,'y-')
ax2.plot(xarr, y3,'b-')
ax2.plot(xarr, y4,'m-')
ax2.plot(xarr, y5,'g-')
ax2.plot(xarr, y6,'r.')
ax2.plot(xarr, y7,'g.')
ax2.plot(xarr, y8,'b.')
ax2.set_xlabel('x', fontsize=14)
ax2.set_ylabel('y', fontsize=14)
ax2.set_title('phi=0, theta=10, 5, 2, 0,-2,-5,-6,-7,-10', color='k', fontsize=20)
#gg.savefig('variation-theta.png')
gg.show()
def test_epix100a() :
""" Test test_epix100a geometry table
"""
basedir = '/reg/g/psdm/detector/alignment/cspad/calib-cxi-ds1-2014-05-15/'
fname_geometry = basedir + 'calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/geometry/2-end.data'
fname_data = basedir + 'cspad-arr-cxid2714-r0023-lysozyme-rings.txt'
#basedir = '/reg/neh/home1/dubrovin/LCLS/GeometryCalib/calib-xpp-Epix100a-2014-11-05/'
#fname_geometry = basedir + 'calib/Epix100a::CalibV1/NoDetector.0:Epix100a.0/geometry/0-end.data'
#fname_data = basedir + 'epix100a-ndarr-ave-clb-xppi0614-r0073.dat'
geometry = GeometryAccess(fname_geometry, 0177777)
amp_range = (-4,10)
iX, iY = geometry.get_pixel_coord_indexes()
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data, dtype=np.float)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX,iY,W=arr)
axim = gg.plotImageLarge(img,amp_range=amp_range)
gg.move(500,10)
gg.show()
def test_cspad2x2() :
""" Test cspad2x2 geometry table
"""
## MecTargetChamber.0:Cspad2x2.1
basedir = '/reg/neh/home1/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/'
fname_geometry = basedir + 'calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.1/geometry/0-end.data'
fname_data = basedir + 'cspad2x2.1-ndarr-ave-meca6113-r0028.dat'
## MecTargetChamber.0:Cspad2x2.2
#basedir = '/reg/neh/home1/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-02-2013-02-13/'
#fname_geometry = basedir + 'calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.2/geometry/0-end.data'
#fname_data = basedir + 'cspad2x2.2-ndarr-ave-meca6113-r0028.dat'
geometry = GeometryAccess(fname_geometry, 0377)
amp_range = (0,15000)
# get pixel coordinate index arrays:
#xyc = xc, yc = 1000, 1000
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc)
iX, iY = geometry.get_pixel_coord_indexes(do_tilt=True)
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= (185,388,2)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX,iY,W=arr)
axim = gg.plotImageLarge(img,amp_range=amp_range)
gg.move(500,10)
gg.show()
def example_varsize() :
print """Test HSpectrum for variable size bins"""
from time import time
edges = (0, 30, 40, 50, 60, 70, 100) # array of bin edges
mu, sigma = 50, 10 # parameters of random Gaussian distribution of intensities
nevts = 10 # number of events in this test
ashape = (32,185,388) # data array shape
spec = HSpectrum(edges, pbits=0377)
for ev in range(nevts) :
arr = random_standard_array(ashape, mu, sigma)
t0_sec = time()
spec.fill(arr)
print 'Event:%3d, t = %10.6f sec' % (ev, time()-t0_sec)
if True :
import algos.graph.GlobalGraphics as gg
histarr, edges, nbins = spec.spectrum()
#gg.plotImageLarge(arr, amp_range=(vmin,vmax), title='random')
gg.plotImageLarge(histarr[0:500,:], amp_range=(0,nevts/3), title='indexes')
gg.show()
def test_cspad_xy_at_z() :
""" Test cspad geometry table
"""
## 'CxiDs1.0:Cspad.0)' or 'DscCsPad'
basedir = '/reg/g/psdm/detector/alignment/cspad/calib-cxi-camera1-2014-09-24/'
fname_geometry = basedir + '2016-06-03-geometry-cxi06216-r25-camera1-z175mm.txt'
fname_data = basedir + '2016-06-03-chun-cxi06216-0025-DscCsPad-max.txt'
geometry = GeometryAccess(fname_geometry, 0377)
# get pixel coordinate index arrays:
xyc = xc, yc = 1000, 1000
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc)
#iX, iY = geometry.get_pixel_coord_indexes(do_tilt=True)
#iX, iY = geometry.get_pixel_xy_inds_at_z(zplane=None, xy0_off_pix=xyc)
iX, iY = geometry.get_pixel_xy_inds_at_z(zplane=150000)
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data, dtype=np.float)
#print 'arr.shape=', arr.shape
arr.shape= (32,185,388)
#ave, rms = arr.mean(), arr.std()
#amp_range = (ave-rms, ave+3*rms)
amp_range = (0, 1000)
print 'amp_range', amp_range
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX,iY,W=arr)
axim = gg.plotImageLarge(img,amp_range=amp_range)
gg.move(500,10)
gg.show()
def test_2x2_img_easy() :
pc2x2 = SegGeometryEpix100V1(use_wide_pix_center=False)
X,Y = pc2x2.get_seg_xy_maps_pix_with_offset()
iX, iY = (X+0.25).astype(int), (Y+0.25).astype(int)
img = gg.getImageFromIndexArrays(iX,iY,iX+iY)
gg.plotImageLarge(img, amp_range=(0, 1500), figsize=(8,10))
gg.show()
def test_cspad2x2():
""" Test cspad2x2 geometry table
"""
## MecTargetChamber.0:Cspad2x2.1
basedir = '/reg/neh/home1/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-01-2013-02-13/'
fname_geometry = basedir + 'calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.1/geometry/0-end.data'
fname_data = basedir + 'cspad2x2.1-ndarr-ave-meca6113-r0028.dat'
## MecTargetChamber.0:Cspad2x2.2
#basedir = '/reg/neh/home1/dubrovin/LCLS/CSPad2x2Alignment/calib-cspad2x2-02-2013-02-13/'
#fname_geometry = basedir + 'calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.2/geometry/0-end.data'
#fname_data = basedir + 'cspad2x2.2-ndarr-ave-meca6113-r0028.dat'
geometry = GeometryAccess(fname_geometry, 0377)
amp_range = (0, 15000)
# get pixel coordinate index arrays:
#xyc = xc, yc = 1000, 1000
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc)
iX, iY = geometry.get_pixel_coord_indexes(do_tilt=True)
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 = (185, 388, 2)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
axim = gg.plotImageLarge(img, amp_range=amp_range)
gg.move(500, 10)
gg.show()
def test_cspad_xy_at_z():
""" Test cspad geometry table
"""
## 'CxiDs1.0:Cspad.0)' or 'DscCsPad'
basedir = '/reg/g/psdm/detector/alignment/cspad/calib-cxi-camera1-2014-09-24/'
fname_geometry = basedir + '2016-06-03-geometry-cxi06216-r25-camera1-z175mm.txt'
fname_data = basedir + '2016-06-03-chun-cxi06216-0025-DscCsPad-max.txt'
geometry = GeometryAccess(fname_geometry, 0377)
# get pixel coordinate index arrays:
xyc = xc, yc = 1000, 1000
#iX, iY = geometry.get_pixel_coord_indexes(xy0_off_pix=xyc)
#iX, iY = geometry.get_pixel_coord_indexes(do_tilt=True)
#iX, iY = geometry.get_pixel_xy_inds_at_z(zplane=None, xy0_off_pix=xyc)
iX, iY = geometry.get_pixel_xy_inds_at_z(zplane=150000)
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data,
dtype=np.float)
#print 'arr.shape=', arr.shape
arr.shape = (32, 185, 388)
#ave, rms = arr.mean(), arr.std()
#amp_range = (ave-rms, ave+3*rms)
amp_range = (0, 1000)
print 'amp_range', amp_range
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
axim = gg.plotImageLarge(img, amp_range=amp_range)
gg.move(500, 10)
gg.show()
def test_epix100a():
""" Test test_epix100a geometry table
"""
basedir = '/reg/g/psdm/detector/alignment/cspad/calib-cxi-ds1-2014-05-15/'
fname_geometry = basedir + 'calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/geometry/2-end.data'
fname_data = basedir + 'cspad-arr-cxid2714-r0023-lysozyme-rings.txt'
#basedir = '/reg/neh/home1/dubrovin/LCLS/GeometryCalib/calib-xpp-Epix100a-2014-11-05/'
#fname_geometry = basedir + 'calib/Epix100a::CalibV1/NoDetector.0:Epix100a.0/geometry/0-end.data'
#fname_data = basedir + 'epix100a-ndarr-ave-clb-xppi0614-r0073.dat'
geometry = GeometryAccess(fname_geometry, 0177777)
amp_range = (-4, 10)
iX, iY = geometry.get_pixel_coord_indexes()
root, ext = os.path.splitext(fname_data)
arr = np.load(fname_data) if ext == '.npy' else np.loadtxt(fname_data,
dtype=np.float)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
axim = gg.plotImageLarge(img, amp_range=amp_range)
gg.move(500, 10)
gg.show()
def test_plot_beta_l0():
print """Test plot for beta angle"""
import algos.graph.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_img() :
t0_sec = time()
w = SegGeometryMatrixV1()
print 'Consumed time for coordinate arrays (sec) =', time()-t0_sec
X,Y = w.get_seg_xy_maps_pix()
w.print_seg_info(0377)
#print 'X(pix) :\n', X
print 'X.shape =', X.shape
xmin, ymin, zmin = w.get_xyz_min_um()
xmax, ymax, zmax = w.get_xyz_max_um()
xmin /= w.pixel_scale_size()
xmax /= w.pixel_scale_size()
ymin /= w.pixel_scale_size()
ymax /= w.pixel_scale_size()
xsize = xmax - xmin + 1
ysize = ymax - ymin + 1
print 'xsize =', xsize # 391.0
print 'ysize =', ysize # 185.0
H, Xedges, Yedges = np.histogram2d(X.flatten(), Y.flatten(), bins=[xsize,ysize], range=[[xmin, xmax], [ymin, ymax]], normed=False, weights=X.flatten()+Y.flatten())
print 'Xedges:', Xedges
print 'Yedges:', Yedges
print 'H.shape:', H.shape
gg.plotImageLarge(H, amp_range=(0, 1100), figsize=(8,10)) # range=(-1, 2),
gg.show()
def test_plot_phi():
print """Test plot for phi angle"""
import algos.graph.GlobalGraphics as gg
xarr = np.linspace(-2, 2, 50)
tet = -12
y0 = [funcy(x, 0, tet) for x in xarr]
y1 = [funcy(x, -5, tet) for x in xarr]
y2 = [funcy(x, -6, tet) for x in xarr]
y3 = [funcy(x, -7, tet) for x in xarr]
y4 = [funcy(x, -10, tet) for x in xarr]
y5 = [funcy(x, 10, tet) for x in xarr]
fig1, ax1 = gg.plotGraph(xarr,
y0,
figsize=(10, 5),
window=(0.15, 0.10, 0.78, 0.80))
ax1.plot(xarr, y1, 'r-')
ax1.plot(xarr, y2, 'y-')
ax1.plot(xarr, y3, 'k-')
ax1.plot(xarr, y4, 'm-')
ax1.plot(xarr, y5, 'g.')
ax1.set_xlabel('x', fontsize=14)
ax1.set_ylabel('y', fontsize=14)
ax1.set_title('tet=-12, phi=10,0,-5,-6,-7,-10', color='k', fontsize=20)
#gg.savefig('variation-phi.png')
gg.show()
def test_plot_phi() :
print """Test plot for phi angle"""
import algos.graph.GlobalGraphics as gg
xarr = np.linspace(-2,2,50)
tet = -12
y0 = [funcy(x, 0, tet) for x in xarr]
y1 = [funcy(x, -5, tet) for x in xarr]
y2 = [funcy(x, -6, tet) for x in xarr]
y3 = [funcy(x, -7, tet) for x in xarr]
y4 = [funcy(x, -10, tet) for x in xarr]
y5 = [funcy(x, 10, tet) for x in xarr]
fig1, ax1 = gg.plotGraph(xarr, y0, figsize=(10,5), window=(0.15, 0.10, 0.78, 0.80))
ax1.plot(xarr, y1,'r-')
ax1.plot(xarr, y2,'y-')
ax1.plot(xarr, y3,'k-')
ax1.plot(xarr, y4,'m-')
ax1.plot(xarr, y5,'g.')
ax1.set_xlabel('x', fontsize=14)
ax1.set_ylabel('y', fontsize=14)
ax1.set_title('tet=-12, phi=10,0,-5,-6,-7,-10', color='k', fontsize=20)
#gg.savefig('variation-phi.png')
gg.show()
def test_2x2_img_easy():
pc2x2 = SegGeometryEpix100V1(use_wide_pix_center=False)
X, Y = pc2x2.get_seg_xy_maps_pix_with_offset()
iX, iY = (X + 0.25).astype(int), (Y + 0.25).astype(int)
img = gg.getImageFromIndexArrays(iX, iY, iX + iY)
gg.plotImageLarge(img, amp_range=(0, 1500), figsize=(8, 10))
gg.show()
def test_mask(mbits=0377) :
pc2x1 = SegGeometryMatrixV1()
X, Y = pc2x1.get_seg_xy_maps_pix_with_offset()
mask = pc2x1.pixel_mask_array(mbits)
iX, iY = (X+0.25).astype(int), (Y+0.25).astype(int)
img = gg.getImageFromIndexArrays(iX,iY,mask)
gg.plotImageLarge(img, amp_range=(-1, 2), figsize=(8,10))
gg.show()
def test_img_easy():
pc2x1 = SegGeometryMatrixV1()
#X,Y = pc2x1.get_seg_xy_maps_pix()
X, Y = pc2x1.get_seg_xy_maps_pix_with_offset()
iX, iY = (X + 0.25).astype(int), (Y + 0.25).astype(int)
img = gg.getImageFromIndexArrays(iX, iY, iX + iY)
gg.plotImageLarge(img, amp_range=(0, 1100), figsize=(8, 10))
gg.show()
def test_img_easy() :
pc2x1 = SegGeometryMatrixV1()
#X,Y = pc2x1.get_seg_xy_maps_pix()
X,Y = pc2x1.get_seg_xy_maps_pix_with_offset()
iX, iY = (X+0.25).astype(int), (Y+0.25).astype(int)
img = gg.getImageFromIndexArrays(iX,iY,iX+iY)
gg.plotImageLarge(img, amp_range=(0, 1100), figsize=(8,10))
gg.show()
def test_mask(mbits=0377):
pc2x1 = SegGeometryMatrixV1()
X, Y = pc2x1.get_seg_xy_maps_pix_with_offset()
mask = pc2x1.pixel_mask_array(mbits)
iX, iY = (X + 0.25).astype(int), (Y + 0.25).astype(int)
img = gg.getImageFromIndexArrays(iX, iY, mask)
gg.plotImageLarge(img, amp_range=(-1, 2), figsize=(8, 10))
gg.show()
def test01(ntest, prefix='fig-v01') :
"""Test for radial 1-d binning of entire image.
"""
from time import time
import algos.graph.GlobalGraphics as gg
from PSCalib.GeometryAccess import img_from_pixel_arrays
arr, geo = data_geo(ntest)
t0_sec = time()
iX, iY = geo.get_pixel_coord_indexes()
X, Y, Z = geo.get_pixel_coords()
mask = geo.get_pixel_mask(mbits=0377).flatten()
print 'Time to retrieve geometry %.3f sec' % (time()-t0_sec)
t0_sec = time()
hp = HPolar(X, Y, mask, nradbins=500, nphibins=1) # v1
print 'HPolar initialization time %.3f sec' % (time()-t0_sec)
t0_sec = time()
nda, title = arr, None
if ntest == 1 : nda, title = arr, 'averaged data'
elif ntest == 2 : nda, title = hp.pixel_rad(), 'pixel radius value'
elif ntest == 3 : nda, title = hp.pixel_phi(), 'pixel phi value'
elif ntest == 4 : nda, title = hp.pixel_irad() + 2, 'pixel radial bin index'
elif ntest == 5 : nda, title = hp.pixel_iphi() + 2, 'pixel phi bin index'
elif ntest == 6 : nda, title = hp.pixel_iseq() + 2, 'pixel sequential (rad and phi) bin index'
elif ntest == 7 : nda, title = mask, 'mask'
elif ntest == 8 : nda, title = hp.pixel_avrg(nda), 'averaged radial intensity'
elif ntest == 9 : nda, title = hp.pixel_avrg_interpol(arr) * mask , 'interpolated radial intensity'
else :
print 'Test %d is not implemented' % ntest
return
print 'Get %s n-d array time %.3f sec' % (title, time()-t0_sec)
img = img_from_pixel_arrays(iX, iY, nda) if not ntest in (21,) else nda[100:300,:]
da, ds = None, None
colmap = 'jet' # 'cubehelix' 'cool' 'summer' 'jet' 'winter'
if ntest in (2,3,4,5,6,7) :
da = ds = (nda.min()-1., nda.max()+1.)
else :
ave, rms = nda.mean(), nda.std()
da = ds = (ave-2*rms, ave+3*rms)
gg.plotImageLarge(img, amp_range=da, figsize=(14,12), title=title, cmap=colmap)
gg.save('%s-%02d-img.png' % (prefix, ntest))
gg.hist1d(nda, bins=None, amp_range=ds, weights=None, color=None, show_stat=True, log=False, \
figsize=(6,5), axwin=(0.18, 0.12, 0.78, 0.80), \
title=None, xlabel='Pixel value', ylabel='Number of pixels', titwin=title)
gg.save('%s-%02d-his.png' % (prefix, ntest))
gg.show()
print 'End of test for %s' % title
def test_2x2_mask(mbits=0377):
pc2x2 = SegGeometryEpix100V1(use_wide_pix_center=False)
X, Y = pc2x2.get_seg_xy_maps_pix_with_offset()
mask = pc2x2.pixel_mask_array(mbits)
mask[mask == 0] = 3
iX, iY = (X + 0.25).astype(int), (Y + 0.25).astype(int)
img = gg.getImageFromIndexArrays(iX, iY, mask)
gg.plotImageLarge(img, amp_range=(-1, 2), figsize=(8, 10))
gg.show()
def test_2x2_mask(mbits=0377) :
pc2x2 = SegGeometryEpix100V1(use_wide_pix_center=False)
X, Y = pc2x2.get_seg_xy_maps_pix_with_offset()
mask = pc2x2.pixel_mask_array(mbits)
mask[mask==0]=3
iX, iY = (X+0.25).astype(int), (Y+0.25).astype(int)
img = gg.getImageFromIndexArrays(iX,iY,mask)
gg.plotImageLarge(img, amp_range=(-1, 2), figsize=(8,10))
gg.show()
def test_plot_beta_l0() :
print """Test plot for beta angle"""
import algos.graph.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_2x1_mask(mbits=0377) :
pc2x1 = SegGeometryCspad2x1V1(use_wide_pix_center=False)
X, Y = pc2x1.get_seg_xy_maps_pix_with_offset()
mask = pc2x1.pixel_mask_array(mbits)
print 'mask:\n%s' % mask
print 'mask.shape: ', mask.shape
iX, iY = (X+0.25).astype(int), (Y+0.25).astype(int)
img = gg.getImageFromIndexArrays(iX,iY,mask)
gg.plotImageLarge(img, amp_range=(-1, 2), figsize=(8,10))
gg.show()
def test_plot_beta_l1(DoR=0.4292, sgnrt=1.):
print """Test plot for beta angle"""
import algos.graph.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(DoR=0.4292, sgnrt=1.) :
print """Test plot for beta angle"""
import algos.graph.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_img():
t0_sec = time()
w = SegGeometryMatrixV1()
print 'Consumed time for coordinate arrays (sec) =', time() - t0_sec
X, Y = w.get_seg_xy_maps_pix()
w.print_seg_info(0377)
#print 'X(pix) :\n', X
print 'X.shape =', X.shape
xmin, ymin, zmin = w.get_xyz_min_um()
xmax, ymax, zmax = w.get_xyz_max_um()
xmin /= w.pixel_scale_size()
xmax /= w.pixel_scale_size()
ymin /= w.pixel_scale_size()
ymax /= w.pixel_scale_size()
xsize = xmax - xmin + 1
ysize = ymax - ymin + 1
print 'xsize =', xsize # 391.0
print 'ysize =', ysize # 185.0
H, Xedges, Yedges = np.histogram2d(X.flatten(),
Y.flatten(),
bins=[xsize, ysize],
range=[[xmin, xmax], [ymin, ymax]],
normed=False,
weights=X.flatten() + Y.flatten())
print 'Xedges:', Xedges
print 'Yedges:', Yedges
print 'H.shape:', H.shape
gg.plotImageLarge(H, amp_range=(0, 1100),
figsize=(8, 10)) # range=(-1, 2),
gg.show()
def test_plot_beta():
print """Test plot for beta angle"""
import algos.graph.GlobalGraphics as gg
xarr = np.linspace(-2, 2, 50)
phi = 0
y0 = [funcy(x, phi, 0) for x in xarr]
y1 = [funcy(x, phi, -2) for x in xarr]
y2 = [funcy(x, phi, -5) for x in xarr]
y3 = [funcy(x, phi, -6) for x in xarr]
y4 = [funcy(x, phi, -7) for x in xarr]
y5 = [funcy(x, phi, -10) for x in xarr]
y6 = [funcy(x, phi, 2) for x in xarr]
y7 = [funcy(x, phi, 5) for x in xarr]
y8 = [funcy(x, phi, 10) for x in xarr]
fig2, ax2 = gg.plotGraph(xarr,
y0,
figsize=(10, 5),
window=(0.15, 0.10, 0.78, 0.80))
ax2.plot(xarr, y1, 'r-')
ax2.plot(xarr, y2, 'y-')
ax2.plot(xarr, y3, 'b-')
ax2.plot(xarr, y4, 'm-')
ax2.plot(xarr, y5, 'g-')
ax2.plot(xarr, y6, 'r.')
ax2.plot(xarr, y7, 'g.')
ax2.plot(xarr, y8, 'b.')
ax2.set_xlabel('x', fontsize=14)
ax2.set_ylabel('y', fontsize=14)
ax2.set_title('phi=0, theta=10, 5, 2, 0,-2,-5,-6,-7,-10',
color='k',
fontsize=20)
#gg.savefig('variation-theta.png')
gg.show()
def test_xyz_maps() :
w = SegGeometryMatrixV1()
w.print_maps_seg_um()
titles = ['X map','Y map']
#for i,arr2d in enumerate([w.x_pix_arr,w.y_pix_arr]) :
for i,arr2d in enumerate( w.get_seg_xy_maps_pix() ) :
amp_range = (arr2d.min(), arr2d.max())
gg.plotImageLarge(arr2d, amp_range=amp_range, figsize=(10,5), title=titles[i])
gg.move(200*i,100*i)
gg.show()
def test_xyz_maps():
w = SegGeometryMatrixV1()
w.print_maps_seg_um()
titles = ['X map', 'Y map']
#for i,arr2d in enumerate([w.x_pix_arr,w.y_pix_arr]) :
for i, arr2d in enumerate(w.get_seg_xy_maps_pix()):
amp_range = (arr2d.min(), arr2d.max())
gg.plotImageLarge(arr2d,
amp_range=amp_range,
figsize=(10, 5),
title=titles[i])
gg.move(200 * i, 100 * i)
gg.show()
def test_plot_quad(geometry) :
""" Tests geometry acess methods of the class GeometryAccess object for CSPAD quad
"""
## get index arrays
iX, iY = geometry.get_pixel_coord_indexes('QUAD:V1', 1, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)
# get intensity array
arr = tig.cspad_nparr(n2x1=iX.shape[0])
arr.shape = (8,185,388)
amp_range = (0,185+388)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX,iY,W=arr)
gg.plotImageLarge(img,amp_range=amp_range)
gg.move(500,10)
gg.show()
def test_mask_quad(geometry, mbits) :
""" Tests geometry acess methods of the class GeometryAccess object for CSPAD quad
"""
## get index arrays
iX, iY = geometry.get_pixel_coord_indexes('QUAD:V1', 1, pix_scale_size_um=None, xy0_off_pix=None, do_tilt=True)
# get intensity array
arr = geometry.get_pixel_mask('QUAD:V1', 1, mbits)
arr.shape = (8,185,388)
amp_range = (-1,2)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr, vbase=0.5)
gg.plotImageLarge(img,amp_range=amp_range)
gg.move(500,10)
gg.show()
def test_mask_quad(geometry, mbits):
""" Tests geometry acess methods of the class GeometryAccess object for CSPAD quad
"""
## get index arrays
iX, iY = geometry.get_pixel_coord_indexes('QUAD:V1',
1,
pix_scale_size_um=None,
xy0_off_pix=None,
do_tilt=True)
# get intensity array
arr = geometry.get_pixel_mask('QUAD:V1', 1, mbits)
arr.shape = (8, 185, 388)
amp_range = (-1, 2)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr, vbase=0.5)
gg.plotImageLarge(img, amp_range=amp_range)
gg.move(500, 10)
gg.show()
def test_plot_quad(geometry):
""" Tests geometry acess methods of the class GeometryAccess object for CSPAD quad
"""
## get index arrays
iX, iY = geometry.get_pixel_coord_indexes('QUAD:V1',
1,
pix_scale_size_um=None,
xy0_off_pix=None,
do_tilt=True)
# get intensity array
arr = tig.cspad_nparr(n2x1=iX.shape[0])
arr.shape = (8, 185, 388)
amp_range = (0, 185 + 388)
print 'iX, iY, W shape:', iX.shape, iY.shape, arr.shape
img = img_from_pixel_arrays(iX, iY, W=arr)
gg.plotImageLarge(img, amp_range=amp_range)
gg.move(500, 10)
gg.show()
def test_08() :
from time import time
import algos.graph.GlobalGraphics as gg
from algos.core.NDArrGenerators import random_standard
print '%s\n%s\n' % (80*'_','Test method locxymax(nda, order, mode):')
#data = random_standard(shape=(32,185,388), mu=0, sigma=10)
data = random_standard(shape=(2,185,388), mu=0, sigma=10)
t0_sec = time()
mask = locxymax(data, order=1, mode='clip')
print 'Consumed t = %10.6f sec' % (time()-t0_sec)
if True :
img = data if len(data.shape)==2 else reshape_to_2d(data)
msk = mask if len(mask.shape)==2 else reshape_to_2d(mask)
ave, rms = img.mean(), img.std()
amin, amax = ave-2*rms, ave+2*rms
gg.plotImageLarge(img, amp_range=(amin, amax), title='random')
gg.plotImageLarge(msk, amp_range=(0, 1), title='mask loc max')
gg.show()
def test02(ntest, prefix='fig-v01') :
"""Test for 2-d (default) binning of the rad-phi range of entire image
"""
#from Detector.GlobalUtils import print_ndarr
from time import time
import algos.graph.GlobalGraphics as gg
from PSCalib.GeometryAccess import img_from_pixel_arrays
arr, geo = data_geo(ntest)
iX, iY = geo.get_pixel_coord_indexes()
X, Y, Z = geo.get_pixel_coords()
mask = geo.get_pixel_mask(mbits=0377).flatten()
t0_sec = time()
rb = RadialBkgd(X, Y, mask) # v0
#rb = RadialBkgd(X, Y, mask, nradbins=500) # , nphibins=8, phiedges=(-20, 240), radedges=(10000,80000))
print 'RadialBkgd initialization time %.3f sec' % (time()-t0_sec)
#print 'npixels_per_bin:', rb.npixels_per_bin()
#print 'intensity_per_bin:', rb.intensity_per_bin(arr)
#print 'average_per_bin:', rb.average_per_bin(arr)
t0_sec = time()
nda, title = arr, None
if ntest == 21 : nda, title = arr, 'averaged data'
elif ntest == 22 : nda, title = rb.pixel_rad(), 'pixel radius value'
elif ntest == 23 : nda, title = rb.pixel_phi(), 'pixel phi value'
elif ntest == 24 : nda, title = rb.pixel_irad() + 2, 'pixel radial bin index'
elif ntest == 25 : nda, title = rb.pixel_iphi() + 2, 'pixel phi bin index'
elif ntest == 26 : nda, title = rb.pixel_iseq() + 2, 'pixel sequential (rad and phi) bin index'
elif ntest == 27 : nda, title = mask, 'mask'
elif ntest == 28 : nda, title = rb.pixel_avrg(nda), 'averaged radial background'
elif ntest == 29 : nda, title = rb.subtract_bkgd(nda) * mask, 'background-subtracted data'
elif ntest == 30 : nda, title = rb.bin_avrg_rad_phi(nda),'r-phi'
elif ntest == 31 : nda, title = rb.pixel_avrg_interpol(nda), 'averaged radial interpolated background'
elif ntest == 32 : nda, title = rb.subtract_bkgd_interpol(nda, method='linear', verb=True) * mask, 'interpol-background-subtracted data'
else :
print 'Test %d is not implemented' % ntest
return
print 'Get %s n-d array time %.3f sec' % (title, time()-t0_sec)
img = img_from_pixel_arrays(iX, iY, nda) if not ntest in (30,) else nda # [100:300,:]
colmap = 'jet' # 'cubehelix' 'cool' 'summer' 'jet' 'winter' 'gray'
da = (nda.min()-1, nda.max()+1)
ds = da
if ntest in (21,28,29,30,31) :
ave, rms = nda.mean(), nda.std()
da = ds = (ave-2*rms, ave+3*rms)
elif ntest in (32,) :
colmap = 'gray'
ds = da = (-20, 20)
gg.plotImageLarge(img, amp_range=da, figsize=(14,12), title=title, cmap=colmap)
gg.save('%s-%02d-img.png' % (prefix, ntest))
gg.hist1d(nda, bins=None, amp_range=ds, weights=None, color=None, show_stat=True, log=False, \
figsize=(6,5), axwin=(0.18, 0.12, 0.78, 0.80), \
title=None, xlabel='Pixel value', ylabel='Number of pixels', titwin=title)
gg.save('%s-%02d-his.png' % (prefix, ntest))
gg.show()
print 'End of test for %s' % title
def test_img_default():
""" Test default image
"""
axim = gg.plotImageLarge(img_default())
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 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 test_img_default() :
""" Test default image
"""
axim = gg.plotImageLarge( img_default() )
gg.move(500,10)
gg.show()
def test_plot_beta_l1_zoom(DoR=0.4292, sgnrt=1.):
print """Test plot for beta angle"""
import algos.graph.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()
def test_plot_beta_l1_zoom(DoR=0.4292, sgnrt=1.) :
print """Test plot for beta angle"""
import algos.graph.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()
def test03(ntest, prefix='fig-v01'):
"""Test for 2-d binning of the restricted rad-phi range of entire image
"""
from time import time
import algos.graph.GlobalGraphics as gg
from PSCalib.GeometryAccess import img_from_pixel_arrays
arr, geo = data_geo(ntest)
iX, iY = geo.get_pixel_coord_indexes()
X, Y, Z = geo.get_pixel_coords()
mask = geo.get_pixel_mask(mbits=0377).flatten()
t0_sec = time()
#hp = HPolar(X, Y, mask, nradbins=5, nphibins=8, phiedges=(-20, 240), radedges=(10000,80000))
hp = HPolar(X,
Y,
mask,
nradbins=3,
nphibins=8,
phiedges=(240, -20),
radedges=(80000, 10000)) # v3
print 'HPolar initialization time %.3f sec' % (time() - t0_sec)
#print 'bin_number_of_pixels:', hp.bin_number_of_pixels()
#print 'bin_intensity:', hp.bin_intensity(arr)
#print 'bin_avrg:', hp.bin_avrg(arr)
t0_sec = time()
nda, title = arr, None
if ntest == 41: nda, title = arr, 'averaged data'
elif ntest == 44:
nda, title = hp.pixel_irad() + 2, 'pixel radial bin index'
elif ntest == 45:
nda, title = hp.pixel_iphi() + 2, 'pixel phi bin index'
elif ntest == 46:
nda, title = hp.pixel_iseq(
) + 2, 'pixel sequential (rad and phi) bin index'
#elif ntest == 47 : nda, title = mask, 'mask'
elif ntest == 48:
nda, title = hp.pixel_avrg(nda), 'averaged radial intensity'
elif ntest == 49:
nda, title = hp.pixel_avrg_interpol(
nda), 'averaged radial interpolated intensity'
elif ntest == 50:
nda, title = hp.bin_avrg_rad_phi(nda), 'r-phi'
else:
print 'Test %d is not implemented' % ntest
return
print 'Get %s n-d array time %.3f sec' % (title, time() - t0_sec)
img = img_from_pixel_arrays(
iX, iY, nda) if not ntest in (50, ) else nda # [100:300,:]
colmap = 'jet' # 'cubehelix' 'cool' 'summer' 'jet' 'winter' 'gray'
da = (nda.min() - 1, nda.max() + 1)
ds = da
if ntest in (41, 48, 49, 50):
ave, rms = nda.mean(), nda.std()
da = ds = (ave - 2 * rms, ave + 3 * rms)
gg.plotImageLarge(img,
amp_range=da,
figsize=(14, 12),
title=title,
cmap=colmap)
gg.save('%s-%02d-img.png' % (prefix, ntest))
gg.hist1d(nda, bins=None, amp_range=ds, weights=None, color=None, show_stat=True, log=False, \
figsize=(6,5), axwin=(0.18, 0.12, 0.78, 0.80), \
title=None, xlabel='Pixel value', ylabel='Number of pixels', titwin=title)
gg.save('%s-%02d-his.png' % (prefix, ntest))
gg.show()
print 'End of test for %s' % title
def test01(ntest, prefix='fig-v01'):
"""Test for radial 1-d binning of entire image.
"""
from time import time
import algos.graph.GlobalGraphics as gg
from PSCalib.GeometryAccess import img_from_pixel_arrays
arr, geo = data_geo(ntest)
t0_sec = time()
iX, iY = geo.get_pixel_coord_indexes()
X, Y, Z = geo.get_pixel_coords()
mask = geo.get_pixel_mask(mbits=0377).flatten()
print 'Time to retrieve geometry %.3f sec' % (time() - t0_sec)
t0_sec = time()
hp = HPolar(X, Y, mask, nradbins=500, nphibins=1) # v1
print 'HPolar initialization time %.3f sec' % (time() - t0_sec)
t0_sec = time()
nda, title = arr, None
if ntest == 1: nda, title = arr, 'averaged data'
elif ntest == 2: nda, title = hp.pixel_rad(), 'pixel radius value'
elif ntest == 3: nda, title = hp.pixel_phi(), 'pixel phi value'
elif ntest == 4: nda, title = hp.pixel_irad() + 2, 'pixel radial bin index'
elif ntest == 5: nda, title = hp.pixel_iphi() + 2, 'pixel phi bin index'
elif ntest == 6:
nda, title = hp.pixel_iseq(
) + 2, 'pixel sequential (rad and phi) bin index'
elif ntest == 7:
nda, title = mask, 'mask'
elif ntest == 8:
nda, title = hp.pixel_avrg(nda), 'averaged radial intensity'
elif ntest == 9:
nda, title = hp.pixel_avrg_interpol(
arr) * mask, 'interpolated radial intensity'
else:
print 'Test %d is not implemented' % ntest
return
print 'Get %s n-d array time %.3f sec' % (title, time() - t0_sec)
img = img_from_pixel_arrays(
iX, iY, nda) if not ntest in (21, ) else nda[100:300, :]
da, ds = None, None
colmap = 'jet' # 'cubehelix' 'cool' 'summer' 'jet' 'winter'
if ntest in (2, 3, 4, 5, 6, 7):
da = ds = (nda.min() - 1., nda.max() + 1.)
else:
ave, rms = nda.mean(), nda.std()
da = ds = (ave - 2 * rms, ave + 3 * rms)
gg.plotImageLarge(img,
amp_range=da,
figsize=(14, 12),
title=title,
cmap=colmap)
gg.save('%s-%02d-img.png' % (prefix, ntest))
gg.hist1d(nda, bins=None, amp_range=ds, weights=None, color=None, show_stat=True, log=False, \
figsize=(6,5), axwin=(0.18, 0.12, 0.78, 0.80), \
title=None, xlabel='Pixel value', ylabel='Number of pixels', titwin=title)
gg.save('%s-%02d-his.png' % (prefix, ntest))
gg.show()
print 'End of test for %s' % title
def make_index_table(prefix='./v01-'):
from algos.core.GlobalUtils import str_tstamp
fname = '%s**t-cxif5315-r0169-%s.txt' % (prefix, str_tstamp())
fout = open(fname, 'w')
fout.write('# file name: %s\n' % fname)
#------------------------------
# Photon energy
Egamma_eV = 6003.1936 # eV SIOC:SYS0:ML00:AO541
wavelen_nm = wavelength_nm_from_energy_ev(Egamma_eV) # nm
evald_rad = wave_vector_value(Egamma_eV) # 1/A
#-------
sigma_ql = 0.002 * evald_rad
sigma_qt = 0.002 * evald_rad
#-------
rec = '\n# photon energy = %.4f eV' % (Egamma_eV)\
+ '\n# wavelength = %.4f A' % (wavelen_nm*10)\
+ '\n# wave number/Evald radius k = 1/lambda = %.6f 1/A' % (evald_rad)\
+ '\n# sigma_ql = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_ql)\
+ '\n# sigma_qt = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_qt)\
+ '<sample-to-detector distance> = k*100um/100mm)'\
+ '\n# 3*sigma_ql = %.6f 1/A\n' % (3*sigma_ql)\
+ '\n# 3*sigma_qt = %.6f 1/A\n' % (3*sigma_qt)
print rec
fout.write(rec)
#------------------------------
# Lattice parameters
# from previous analysis note:
#a, b, c = 18.36, 26.65, 4.81 # Angstrom
#alpha, beta, gamma = 90, 90, 77.17 # 180 - 102.83 degree
a = 18.55 # Angstrom
b, c = 1.466 * a, 0.262 * a # Angstrom
alpha, beta, gamma = 90, 90, 78.47 # 180 - 101.53 degree
hmax, kmax, lmax = 4, 6, 0 # size of lattice to consider
a1, a2, a3 = triclinic_primitive_vectors(a, b, c, alpha, beta, gamma)
b1, b2, b3 = reciprocal_from_bravias(a1, a2, a3)
msg1 = '\n# Triclinic crystal cell parameters:'\
+ '\n# a = %.2f A\n# b = %.2f A\n# c = %.2f A' % (a, b, c)\
+ '\n# alpha = %.2f deg\n# beta = %.2f deg\n# gamma = %.2f deg' % (alpha, beta, gamma)
msg2 = '\n# 3-d space primitive vectors:\n# a1 = %s\n# a2 = %s\n# a3 = %s' %\
(str(a1), str(a2), str(a3))
msg3 = '\n# reciprocal space primitive vectors:\n# b1 = %s\n# b2 = %s\n# b3 = %s' %\
(str(b1), str(b2), str(b3))
rec = '%s\n%s\n%s\n' % (msg1, msg2, msg3)
print rec
fout.write(rec)
fout.write('\n# %s\n\n' % (89 * '_'))
#for line in triclinic_primitive_vectors.__doc__.split('\n') : fout.write('\n# %s' % line)
test_lattice(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, 1, cdtype=np.float32)
#------------------------------
#return
#------------------------------
# binning for look-up table and plots
# bin parameters for q in units of k = Evald's sphere radius [1/A]
bpq = BinPars((-0.25, 0.25), 1000, vtype=np.float32, endpoint=False)
# bin parameters for omega [degree] - fiber rotation angle around axis
bpomega = BinPars((0., 180.), 360, vtype=np.float32, endpoint=False)
# bin parameters for beta [degree] - fiber axis tilt angle
#bpbeta = BinPars((15., 195.), 2, vtype=np.float32, endpoint=True)
#bpbeta = BinPars((15., 15.), 1, vtype=np.float32, endpoint=False)
#bpbeta = BinPars((5., 25.), 2, vtype=np.float32, endpoint=True)
bpbeta = BinPars((0., 50.), 11, vtype=np.float32, endpoint=True)
bpbeta2 = BinPars((180., 230.), 11, vtype=np.float32, endpoint=True)
str_beta = 'for-beta:%s' % (bpbeta.strrange)
print '\n%s\nIndexing lookup table\n' % (91 * '_')
lut = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32,
evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega,
bpbeta)
lut2 = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32,
evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega,
bpbeta2)
fout.close()
print '\nIndexing lookup table is saved in the file: %s' % fname
#------------------------------
# produce and save plots
import algos.graph.GlobalGraphics as gg
img = lut # or lut2
img = lut + lut2
img_range = (bpq.vmin, bpq.vmax, bpomega.vmax, bpomega.vmin)
axim = gg.plotImageLarge(lut, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Non-symmetrized for beta', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Symmetrized for beta (beta, beta+pi)', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-sym-%s.png' % (prefix, str_beta),
pbits=1)
arrhi = np.sum(img, 0)
fighi, axhi, hi = gg.hist1d(bpq.binedges, bins=bpq.nbins-1, amp_range=(bpq.vmin, bpq.vmax), weights=arrhi,\
color='b', show_stat=True, log=False,\
figsize=(15,5), axwin=(0.05, 0.12, 0.85, 0.80),\
title=None, xlabel='$q_{H}$ ($1/\AA$)', ylabel='Intensity', titwin=None)
gg.show()
gg.save_fig(fighi,
'%splot-his-prob-vs-qh-%s.png' % (prefix, str_beta),
pbits=1)
qh_weight = zip(bpq.bincenters, arrhi)
fname = '%sarr-qh-weight-%s.npy' % (prefix, str_beta)
print 'Save qh:weigt array in file %s' % fname
np.save(fname, qh_weight)
def test03(ntest, prefix='fig-v01') :
"""Test for 2-d binning of the restricted rad-phi range of entire image
"""
from time import time
import algos.graph.GlobalGraphics as gg
from PSCalib.GeometryAccess import img_from_pixel_arrays
arr, geo = data_geo(ntest)
iX, iY = geo.get_pixel_coord_indexes()
X, Y, Z = geo.get_pixel_coords()
mask = geo.get_pixel_mask(mbits=0377).flatten()
t0_sec = time()
#hp = HPolar(X, Y, mask, nradbins=5, nphibins=8, phiedges=(-20, 240), radedges=(10000,80000))
hp = HPolar(X, Y, mask, nradbins=3, nphibins=8, phiedges=(240, -20), radedges=(80000,10000)) # v3
print 'HPolar initialization time %.3f sec' % (time()-t0_sec)
#print 'bin_number_of_pixels:', hp.bin_number_of_pixels()
#print 'bin_intensity:', hp.bin_intensity(arr)
#print 'bin_avrg:', hp.bin_avrg(arr)
t0_sec = time()
nda, title = arr, None
if ntest == 41 : nda, title = arr, 'averaged data'
elif ntest == 44 : nda, title = hp.pixel_irad() + 2, 'pixel radial bin index'
elif ntest == 45 : nda, title = hp.pixel_iphi() + 2, 'pixel phi bin index'
elif ntest == 46 : nda, title = hp.pixel_iseq() + 2, 'pixel sequential (rad and phi) bin index'
#elif ntest == 47 : nda, title = mask, 'mask'
elif ntest == 48 : nda, title = hp.pixel_avrg(nda), 'averaged radial intensity'
elif ntest == 49 : nda, title = hp.pixel_avrg_interpol(nda), 'averaged radial interpolated intensity'
elif ntest == 50 : nda, title = hp.bin_avrg_rad_phi(nda),'r-phi'
else :
print 'Test %d is not implemented' % ntest
return
print 'Get %s n-d array time %.3f sec' % (title, time()-t0_sec)
img = img_from_pixel_arrays(iX, iY, nda) if not ntest in (50,) else nda # [100:300,:]
colmap = 'jet' # 'cubehelix' 'cool' 'summer' 'jet' 'winter' 'gray'
da = (nda.min()-1, nda.max()+1)
ds = da
if ntest in (41,48,49,50) :
ave, rms = nda.mean(), nda.std()
da = ds = (ave-2*rms, ave+3*rms)
gg.plotImageLarge(img, amp_range=da, figsize=(14,12), title=title, cmap=colmap)
gg.save('%s-%02d-img.png' % (prefix, ntest))
gg.hist1d(nda, bins=None, amp_range=ds, weights=None, color=None, show_stat=True, log=False, \
figsize=(6,5), axwin=(0.18, 0.12, 0.78, 0.80), \
title=None, xlabel='Pixel value', ylabel='Number of pixels', titwin=title)
gg.save('%s-%02d-his.png' % (prefix, ntest))
gg.show()
print 'End of test for %s' % title
def make_index_table(prefix='./v01-') :
from algos.core.GlobalUtils import str_tstamp
fname = '%s**t-cxif5315-r0169-%s.txt' % (prefix, str_tstamp())
fout = open(fname,'w')
fout.write('# file name: %s\n' % fname)
#------------------------------
# Photon energy
Egamma_eV = 6003.1936 # eV SIOC:SYS0:ML00:AO541
wavelen_nm = wavelength_nm_from_energy_ev(Egamma_eV) # nm
evald_rad = wave_vector_value(Egamma_eV) # 1/A
#-------
sigma_ql = 0.002 * evald_rad
sigma_qt = 0.002 * evald_rad
#-------
rec = '\n# photon energy = %.4f eV' % (Egamma_eV)\
+ '\n# wavelength = %.4f A' % (wavelen_nm*10)\
+ '\n# wave number/Evald radius k = 1/lambda = %.6f 1/A' % (evald_rad)\
+ '\n# sigma_ql = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_ql)\
+ '\n# sigma_qt = %.6f 1/A (approximately = k * <pixel size>/' % (sigma_qt)\
+ '<sample-to-detector distance> = k*100um/100mm)'\
+ '\n# 3*sigma_ql = %.6f 1/A\n' % (3*sigma_ql)\
+ '\n# 3*sigma_qt = %.6f 1/A\n' % (3*sigma_qt)
print rec
fout.write(rec)
#------------------------------
# Lattice parameters
# from previous analysis note:
#a, b, c = 18.36, 26.65, 4.81 # Angstrom
#alpha, beta, gamma = 90, 90, 77.17 # 180 - 102.83 degree
a= 18.55 # Angstrom
b, c = 1.466*a, 0.262*a # Angstrom
alpha, beta, gamma = 90, 90, 78.47 # 180 - 101.53 degree
hmax, kmax, lmax = 4, 6, 0 # size of lattice to consider
a1, a2, a3 = triclinic_primitive_vectors(a, b, c, alpha, beta, gamma)
b1, b2, b3 = reciprocal_from_bravias(a1, a2, a3)
msg1 = '\n# Triclinic crystal cell parameters:'\
+ '\n# a = %.2f A\n# b = %.2f A\n# c = %.2f A' % (a, b, c)\
+ '\n# alpha = %.2f deg\n# beta = %.2f deg\n# gamma = %.2f deg' % (alpha, beta, gamma)
msg2 = '\n# 3-d space primitive vectors:\n# a1 = %s\n# a2 = %s\n# a3 = %s' %\
(str(a1), str(a2), str(a3))
msg3 = '\n# reciprocal space primitive vectors:\n# b1 = %s\n# b2 = %s\n# b3 = %s' %\
(str(b1), str(b2), str(b3))
rec = '%s\n%s\n%s\n' % (msg1, msg2, msg3)
print rec
fout.write(rec)
fout.write('\n# %s\n\n' % (89*'_'))
#for line in triclinic_primitive_vectors.__doc__.split('\n') : fout.write('\n# %s' % line)
test_lattice (b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, lmax, cdtype=np.float32)
lattice_node_radius(b1, b2, b3, hmax, kmax, 1, cdtype=np.float32)
#------------------------------
#return
#------------------------------
# binning for look-up table and plots
# bin parameters for q in units of k = Evald's sphere radius [1/A]
bpq = BinPars((-0.25, 0.25), 1000, vtype=np.float32, endpoint=False)
# bin parameters for omega [degree] - fiber rotation angle around axis
bpomega = BinPars((0., 180.), 360, vtype=np.float32, endpoint=False)
# bin parameters for beta [degree] - fiber axis tilt angle
#bpbeta = BinPars((15., 195.), 2, vtype=np.float32, endpoint=True)
#bpbeta = BinPars((15., 15.), 1, vtype=np.float32, endpoint=False)
#bpbeta = BinPars((5., 25.), 2, vtype=np.float32, endpoint=True)
bpbeta = BinPars((0., 50.), 11, vtype=np.float32, endpoint=True)
bpbeta2 = BinPars((180., 230.), 11, vtype=np.float32, endpoint=True)
str_beta = 'for-beta:%s' % (bpbeta.strrange)
print '\n%s\nIndexing lookup table\n' % (91*'_')
lut = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32, evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega, bpbeta)
lut2 = make_lookup_table(b1, b2, b3, hmax, kmax, lmax, np.float32, evald_rad, sigma_ql, sigma_qt, fout, bpq, bpomega, bpbeta2)
fout.close()
print '\nIndexing lookup table is saved in the file: %s' % fname
#------------------------------
# produce and save plots
import algos.graph.GlobalGraphics as gg
img = lut # or lut2
img = lut + lut2
img_range = (bpq.vmin, bpq.vmax, bpomega.vmax, bpomega.vmin)
axim = gg.plotImageLarge(lut, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Non-symmetrized for beta', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
axim = gg.plotImageLarge(img, img_range=img_range, amp_range=None, figsize=(15,13),\
title='Symmetrized for beta (beta, beta+pi)', origin='upper', window=(0.05, 0.06, 0.94, 0.94))
axim.set_xlabel('$q_{H}$ ($1/\AA$)', fontsize=18)
axim.set_ylabel('$\omega$ (degree)', fontsize=18)
gg.save('%splot-img-prob-omega-vs-qh-sym-%s.png' % (prefix, str_beta), pbits=1)
arrhi = np.sum(img,0)
fighi, axhi, hi = gg.hist1d(bpq.binedges, bins=bpq.nbins-1, amp_range=(bpq.vmin, bpq.vmax), weights=arrhi,\
color='b', show_stat=True, log=False,\
figsize=(15,5), axwin=(0.05, 0.12, 0.85, 0.80),\
title=None, xlabel='$q_{H}$ ($1/\AA$)', ylabel='Intensity', titwin=None)
gg.show()
gg.save_fig(fighi, '%splot-his-prob-vs-qh-%s.png' % (prefix, str_beta), pbits=1)
qh_weight = zip(bpq.bincenters, arrhi)
fname = '%sarr-qh-weight-%s.npy' % (prefix, str_beta)
print 'Save qh:weigt array in file %s' % fname
np.save(fname, qh_weight)