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_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_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_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_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_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_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_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_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_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_img_default():
""" Test default image
"""
axim = gg.plotImageLarge(img_default())
gg.move(500, 10)
gg.show()
def test_img_default() :
""" Test default image
"""
axim = gg.plotImageLarge( img_default() )
gg.move(500,10)
gg.show()