def do_work():
prefix = './%s-figs-ti_vs_tj' % gu.str_tstamp(
fmt='%Y-%m-%d', time_sec=None) # '%Y-%m-%dT%H:%M:%S%z'
gu.create_directory(prefix, mode=0o775)
path = os.path.abspath(os.path.dirname(__file__))
print('path to npy flies dir:', path)
ti_vs_tj = np.load('%s/ti_vs_tj.npy' % path)
t_all = np.load('%s/t_all.npy' % path)
trange = (1400., 2900.)
print_ndarr(ti_vs_tj, 'ti_vs_tj:\n')
print_ndarr(t_all, 't_all:\n')
sum_bkg = t_all.sum()
sum_cor = ti_vs_tj.sum()
print('sum_bkg:', sum_bkg)
print('sum_cor:', sum_cor)
imrange = trange + trange # (1400., 2900., 1400., 2900.)
axim = gr.plotImageLarge(ti_vs_tj, img_range=imrange, amp_range=(0,500), figsize=(11,10),\
title='ti_vs_tj', origin='lower', window=(0.10, 0.08, 0.88, 0.88), cmap='inferno')
gr.save('%s/fig-ti_vs_tj.png' % prefix)
bkg = np.outer(t_all, t_all) / sum_bkg
print_ndarr(bkg, 'bkg:\n')
axim = gr.plotImageLarge(bkg, img_range=imrange, amp_range=(0,500), figsize=(11,10),\
title='bkg', origin='lower', window=(0.10, 0.08, 0.88, 0.88), cmap='inferno')
gr.save('%s/fig-ti_vs_tj-bkg.png' % prefix)
harr = t_all
nbins = harr.size
ht = HBins(trange, nbins, vtype=np.float32) # ht.binedges()
fig, axhi, hi = gr.hist1d(ht.bincenters(), bins=nbins, amp_range=ht.limits(), weights=harr, color='b', show_stat=True,\
log=True, figsize=(7,6), axwin=(0.10, 0.10, 0.88, 0.85), title='1-d bkg',\
xlabel='time of all hits (ns)', ylabel='number of hits', titwin='1-d bkg')
gr.save('%s/fig-time-hits.png' % prefix)
gr.show()
class HPolar():
def __init__(self,
xarr,
yarr,
mask=None,
radedges=None,
nradbins=100,
phiedges=(0, 360),
nphibins=32):
"""Parameters
- mask - n-d array with mask
- xarr - n-d array with pixel x coordinates in any units
- yarr - n-d array with pixel y coordinates in the same units as xarr
- radedges - radial bin edges for corrected region in the same units of xarr;
default=None - all radial range
- nradbins - number of radial bins
- phiedges - phi angle bin edges for corrected region.
default=(0,360)
Difference of the edge limits should not exceed +/-360 degree
- nphibins - number of angular bins
default=32 - bin size equal to 1 rhumb for default phiedges
"""
self.rad, self.phi0 = cart2polar(xarr, yarr)
self.shapeflat = (self.rad.size, )
self.rad.shape = self.shapeflat
self.phi0.shape = self.shapeflat
self.mask = mask
phimin = min(phiedges[0], phiedges[-1])
self.phi = np.select((self.phi0 < phimin, self.phi0 >= phimin),
(self.phi0 + 360., self.phi0))
self._set_rad_bins(radedges, nradbins)
self._set_phi_bins(phiedges, nphibins)
npbins = self.pb.nbins()
nrbins = self.rb.nbins()
self.ntbins = npbins * nrbins # total number of bins in r-phi array
self.irad = self.rb.bin_indexes(self.rad, edgemode=1)
self.iphi = self.pb.bin_indexes(self.phi, edgemode=1)
self.cond = np.logical_and(\
np.logical_and(self.irad > -1, self.irad < nrbins),
np.logical_and(self.iphi > -1, self.iphi < npbins)
)
if mask is not None:
self.cond = np.logical_and(self.cond, mask.astype(np.bool).ravel())
# index ntbins stands for overflow bin
self.iseq = np.select((self.cond, ),
(self.iphi * nrbins + self.irad, ),
self.ntbins).ravel()
#self.npix_per_bin = np.bincount(self.iseq, weights=None, minlength=None)
self.npix_per_bin = np.bincount(self.iseq,
weights=None,
minlength=self.ntbins + 1)
self.griddata = None
def _set_rad_bins(self, radedges, nradbins):
rmin = math.floor(np.amin(
self.rad)) if radedges is None else radedges[0]
rmax = math.ceil(np.amax(
self.rad)) if radedges is None else radedges[-1]
if rmin < 1: rmin = 1
self.rb = HBins((rmin, rmax), nradbins)
def _set_phi_bins(self, phiedges, nphibins):
if phiedges[-1] > phiedges[0]+360\
or phiedges[-1] < phiedges[0]-360:
raise ValueError('Difference between angular edges should not exceed 360 degree;'\
' phiedges: %.0f, %.0f' % (phiedges[0], phiedges[-1]))
self.pb = HBins(phiedges, nphibins)
phi1, phi2 = self.pb.limits()
self.is360 = math.fabs(math.fabs(phi2 - phi1) - 360) < 1e-3
def info_attrs(self):
return '%s attrbutes:' % self.__class__.__name__\
+ self.pb.strrange(fmt='\nPhi bins: min:%8.1f max:%8.1f nbins:%5d')\
+ self.rb.strrange(fmt='\nRad bins: min:%8.1f max:%8.1f nbins:%5d')
def print_attrs(self):
print(self.info_attrs())
def print_ndarrs(self):
print('%s n-d arrays:' % self.__class__.__name__)
print_ndarr(self.rad, ' rad')
print_ndarr(self.phi, ' phi')
print_ndarr(self.mask, ' mask')
#print('Phi limits: ', phiedges[0], phiedges[-1])
def obj_radbins(self):
"""Returns HBins object for radial bins."""
return self.rb
def obj_phibins(self):
"""Returns HBins object for angular bins."""
return self.pb
def pixel_rad(self):
"""Returns 1-d numpy array of pixel radial parameters."""
return self.rad
def pixel_irad(self):
"""Returns 1-d numpy array of pixel radial indexes [-1,nrbins] - extended edgemode."""
return self.irad
def pixel_phi0(self):
"""Returns 1-d numpy array of pixel angules in the range [-180,180] degree."""
return self.phi0
def pixel_phi(self):
"""Returns 1-d numpy array of pixel angules in the range [phi_min, phi_min+360] degree."""
return self.phi
def pixel_iphi(self):
"""Returns 1-d numpy array of pixel angular indexes [-1,npbins] - extended edgemode."""
return self.iphi
def pixel_iseq(self):
"""Returns 1-d numpy array of sequentially (in rad and phi) numerated pixel indexes [0,ntbins].
WARNING: pixels outside the r-phi region of interest marked by the index ntbins,
ntbins - total number of r-phi bins, which exceeds allowed range of r-phi indices...
"""
return self.iseq
def bin_number_of_pixels(self):
"""Returns 1-d numpy array of number of accounted pixels per bin."""
return self.npix_per_bin
def _ravel_(self, nda):
if len(nda.shape) > 1:
#nda.shape = self.shapeflat
return nda.ravel(
) # return ravel copy in order to preserve input array shape
return nda
def bin_intensity(self, nda):
"""Returns 1-d numpy array of total pixel intensity per bin for input array nda."""
#return np.bincount(self.iseq, weights=self._ravel_(nda), minlength=None)
return np.bincount(self.iseq,
weights=self._ravel_(nda),
minlength=self.ntbins + 1) # +1 for overflow bin
def bin_avrg(self, nda):
"""Returns 1-d numpy array of averaged in r-phi bin intensities for input image array nda.
WARNING array range [0, nrbins*npbins + 1], where +1 bin intensity is for all off ROI pixels.
"""
num = self.bin_intensity(self._ravel_(nda))
den = self.bin_number_of_pixels()
#print_ndarr(nda, name='ZZZ bin_avrg: nda', first=0, last=5)
#print_ndarr(num, name='ZZZ bin_avrg: num', first=0, last=5)
#print_ndarr(den, name='ZZZ bin_avrg: den', first=0, last=5)
return divide_protected(num, den, vsub_zero=0)
def bin_avrg_rad_phi(self, nda, do_transp=True):
"""Returns 2-d (rad,phi) numpy array of averaged in bin intensity for input array nda."""
arr_rphi = self.bin_avrg(
self._ravel_(nda))[:-1] # -1 removes off ROI bin
arr_rphi.shape = (self.pb.nbins(), self.rb.nbins())
return np.transpose(arr_rphi) if do_transp else arr_rphi
def pixel_avrg(self, nda, subs_value=0):
"""Makes r-phi histogram of intensities from input image array and
projects r-phi averaged intensities back to image.
Returns ravel 1-d numpy array of per-pixel intensities taken from r-phi histogram.
- nda - input (2-d or 1-d-ravel) pixel array.
- subs_value - value sabstituted for pixels out of ROI defined by the min/max in r-phi.
"""
bin_avrg = self.bin_avrg(self._ravel_(nda))
return np.select((self.cond, ), (bin_avrg[self.iseq], ),
subs_value).ravel()
#return np.array([bin_avrg[i] for i in self.iseq]) # iseq may be outside the bin_avrg range
def pixel_avrg_interpol(self,
nda,
method='linear',
verb=False,
subs_value=0): # 'nearest' 'cubic'
"""Makes r-phi histogram of intensities from input image and
projects r-phi averaged intensities back to image with per-pixel interpolation.
Returns 1-d numpy array of per-pixel interpolated intensities taken from r-phi histogram.
- subs_value - value sabstituted for pixels out of ROI defined by the min/max in r-phi.
"""
#if not is360: raise ValueError('Interpolation works for 360 degree coverage ONLY')
if self.griddata is None:
from scipy.interpolate import griddata
self.griddata = griddata
# 1) get values in bin centers
binv = self.bin_avrg_rad_phi(self._ravel_(nda), do_transp=False)
# 2) add values in bin edges
if verb: print('binv.shape: ', binv.shape)
vrad_a1, vrad_a2 = binv[0, :], binv[-1, :]
if self.is360:
vrad_a1 = vrad_a2 = 0.5 * (binv[0, :] + binv[-1, :]
) # [iphi, irad]
nodea = np.vstack((vrad_a1, binv, vrad_a2))
vang_rmin, vang_rmax = nodea[:, 0], nodea[:, -1]
vang_rmin.shape = vang_rmax.shape = (vang_rmin.size, 1
) # it should be 2d for hstack
val_nodes = np.hstack((vang_rmin, nodea, vang_rmax))
if verb: print('nodear.shape: ', val_nodes.shape)
# 3) extend bin-centers by limits
bcentsr = self.rb.bincenters()
bcentsp = self.pb.bincenters()
blimsr = self.rb.limits()
blimsp = self.pb.limits()
rad_nodes = np.concatenate(((blimsr[0], ), bcentsr, (blimsr[1], )))
phi_nodes = np.concatenate(((blimsp[0], ), bcentsp, (blimsp[1], )))
if verb: print('rad_nodes.shape', rad_nodes.shape)
if verb: print('phi_nodes.shape', phi_nodes.shape)
# 4) make point coordinate and value arrays
points_rad, points_phi = np.meshgrid(rad_nodes, phi_nodes)
if verb: print('points_phi.shape', points_phi.shape)
if verb: print('points_rad.shape', points_rad.shape)
points = np.vstack((points_phi.ravel(), points_rad.ravel())).T
values = val_nodes.ravel()
if verb:
#print('points:', points)
print('points.shape', points.shape)
print('values.shape', values.shape)
# 5) return interpolated data on (phi, rad) grid
grid_vals = self.griddata(points,
values, (self.phi, self.rad),
method=method)
return np.select((self.iseq < self.ntbins, ), (grid_vals, ),
default=subs_value)
class HPolar():
def __init__(self,
xarr,
yarr,
mask=None,
radedges=None,
nradbins=100,
phiedges=(0, 360),
nphibins=32):
"""Parameters
- mask - n-d array with mask
- xarr - n-d array with pixel x coordinates in any units
- yarr - n-d array with pixel y coordinates in the same units as xarr
- radedges - radial bin edges for corrected region in the same units of xarr;
default=None - all radial range
- nradbins - number of radial bins
- phiedges - phi ange bin edges for corrected region.
default=(0,360)
Difference of the edge limits should not exceed +/-360 degree
- nphibins - number of angular bins
default=32 - bin size equal to 1 rhumb for default phiedges
"""
self.rad, self.phi0 = cart2polar(xarr, yarr)
self.shapeflat = (self.rad.size, )
self.rad.shape = self.shapeflat
self.phi0.shape = self.shapeflat
self.mask = mask
phimin = min(phiedges[0], phiedges[-1])
self.phi = np.select((self.phi0 < phimin, self.phi0 >= phimin),
(self.phi0 + 360., self.phi0))
self._set_rad_bins(radedges, nradbins)
self._set_phi_bins(phiedges, nphibins)
npbins = self.pb.nbins()
nrbins = self.rb.nbins()
ntbins = npbins * nrbins
self.irad = self.rb.bin_indexes(self.rad, edgemode=1)
self.iphi = self.pb.bin_indexes(self.phi, edgemode=1)
cond = np.logical_and(\
np.logical_and(self.irad > -1, self.irad < nrbins),
np.logical_and(self.iphi > -1, self.iphi < npbins)
)
if mask is not None:
cond = np.logical_and(cond, mask.astype(np.bool).flatten())
self.iseq = np.select((cond, ), (self.iphi * nrbins + self.irad, ),
ntbins).flatten()
self.npix_per_bin = np.bincount(self.iseq,
weights=None,
minlength=None)
self.griddata = None
self.print_ndarr = None
def _set_rad_bins(self, radedges, nradbins):
rmin = math.floor(np.amin(
self.rad)) if radedges is None else radedges[0]
rmax = math.ceil(np.amax(
self.rad)) if radedges is None else radedges[-1]
if rmin < 1: rmin = 1
self.rb = HBins((rmin, rmax), nradbins)
def _set_phi_bins(self, phiedges, nphibins):
if phiedges[-1] > phiedges[0]+360\
or phiedges[-1] < phiedges[0]-360:
raise ValueError('Difference between angular edges should not exceed 360 degree;'\
' phiedges: %.0f, %.0f' % (phiedges[0], phiedges[-1]))
self.pb = HBins(phiedges, nphibins)
phi1, phi2 = self.pb.limits()
self.is360 = math.fabs(math.fabs(phi2 - phi1) - 360) < 1e-3
def print_attrs(self):
print('%s attrbutes:' % self.__class__.__name__)
print(
self.pb.strrange(fmt='Phi bins: min:%8.1f max:%8.1f nbins:%5d'))
print(
self.rb.strrange(fmt='Rad bins: min:%8.1f max:%8.1f nbins:%5d'))
def print_ndarrs(self):
print('%s n-d arrays:' % self.__class__.__name__)
if self.print_ndarr is None:
from psana.pyalgos.generic.NDArrUtils import print_ndarr
self.print_ndarr = print_ndarr
self.print_ndarr(self.rad, ' rad')
self.print_ndarr(self.phi, ' phi')
self.print_ndarr(self.mask, ' mask')
#print('Phi limits: ', phiedges[0], phiedges[-1])
def obj_radbins(self):
"""Returns HBins object for radial bins."""
return self.rb
def obj_phibins(self):
"""Returns HBins object for angular bins."""
return self.pb
def pixel_rad(self):
"""Returns 1-d numpy array of pixel radial parameters."""
return self.rad
def pixel_irad(self):
"""Returns 1-d numpy array of pixel radial indexes."""
return self.irad
def pixel_phi0(self):
"""Returns 1-d numpy array of pixel angules in the range [-180,180] degree."""
return self.phi0
def pixel_phi(self):
"""Returns 1-d numpy array of pixel angules in the range [phi_min, phi_min+360] degree."""
return self.phi
def pixel_iphi(self):
"""Returns 1-d numpy array of pixel angular indexes."""
return self.iphi
def pixel_iseq(self):
"""Returns 1-d numpy array of sequentially (in rad and phi) numerated pixel indexes."""
return self.iseq
def bin_number_of_pixels(self):
"""Returns 1-d numpy array of number of accounted pixels per bin."""
return self.npix_per_bin
def _flatten_(self, nda):
if len(nda.shape) > 1:
#nda.shape = self.shapeflat
return nda.flatten(
) # return flatten copy in order to preserve input array shape
return nda
def bin_intensity(self, nda):
"""Returns 1-d numpy array of total pixel intensity per bin for input array nda."""
return np.bincount(self.iseq,
weights=self._flatten_(nda),
minlength=None)
def bin_avrg(self, nda):
"""Returns 1-d numpy array of averaged in bin intensity for input array nda."""
num = self.bin_intensity(self._flatten_(nda))
den = self.bin_number_of_pixels()
return divide_protected(num, den, vsub_zero=0)
def bin_avrg_rad_phi(self, nda, do_transp=True):
"""Returns 2-d (rad,phi) numpy array of averaged in bin intensity for input array nda."""
arr_rphi = self.bin_avrg(self._flatten_(nda))[:-1]
arr_rphi.shape = (self.pb.nbins(), self.rb.nbins())
return np.transpose(arr_rphi) if do_transp else arr_rphi
def pixel_avrg(self, nda):
"""Returns 1-d numpy array of per-pixel background for input array nda."""
bin_avrg = self.bin_avrg(self._flatten_(nda))
return np.array([bin_avrg[i] for i in self.iseq])
def pixel_avrg_interpol(self,
nda,
method='linear',
verb=False): # 'nearest' 'cubic'
"""Returns 1-d numpy array of per-pixel interpolated background for averaged input data."""
#if not is360 : raise ValueError('Interpolation works for 360 degree coverage ONLY')
if self.griddata is None:
from scipy.interpolate import griddata
self.griddata = griddata
# 1) get values in bin centers
binv = self.bin_avrg_rad_phi(self._flatten_(nda), do_transp=False)
# 2) add values in bin edges
if verb: print('binv.shape: ', binv.shape)
vrad_a1, vrad_a2 = binv[0, :], binv[-1, :]
if self.is360:
vrad_a1 = vrad_a2 = 0.5 * (binv[0, :] + binv[-1, :]
) # [iphi, irad]
nodea = np.vstack((vrad_a1, binv, vrad_a2))
vang_rmin, vang_rmax = nodea[:, 0], nodea[:, -1]
vang_rmin.shape = vang_rmax.shape = (vang_rmin.size, 1
) # it should be 2d for hstack
val_nodes = np.hstack((vang_rmin, nodea, vang_rmax))
if verb: print('nodear.shape: ', val_nodes.shape)
# 3) extend bin-centers by limits
bcentsr = self.rb.bincenters()
bcentsp = self.pb.bincenters()
blimsr = self.rb.limits()
blimsp = self.pb.limits()
rad_nodes = np.concatenate(((blimsr[0], ), bcentsr, (blimsr[1], )))
phi_nodes = np.concatenate(((blimsp[0], ), bcentsp, (blimsp[1], )))
if verb: print('rad_nodes.shape', rad_nodes.shape)
if verb: print('phi_nodes.shape', phi_nodes.shape)
# 4) make point coordinate and value arrays
points_rad, points_phi = np.meshgrid(rad_nodes, phi_nodes)
if verb: print('points_phi.shape', points_phi.shape)
if verb: print('points_rad.shape', points_rad.shape)
points = np.array(zip(points_phi.flatten(), points_rad.flatten()))
if verb: print('points.shape', points.shape)
values = val_nodes.flatten()
if verb: print('values.shape', values.shape)
# 4) return interpolated data on (phi, rad) grid
grid_vals = self.griddata(points,
values, (self.phi, self.rad),
method=method)
return np.select((self.iseq < self.pb.nbins() * self.rb.nbins(), ),
(grid_vals, ),
default=0)