def interpolate_run(
img_gen,
tags,
mask,
x_center,
y_center,
pixsize,
detdist,
wavelen,
prefix,
how='fetch',
interp_method='floor',
ring_locations=None,
q_resolution=0,
phi_resolution=0,
radius_unit='inv_ang',
nphi=None,
qmin=None,
qmax=None,
qmin_pix=None,
qmax_pix=None,
detector_gain=None,
index_query_fname=None):
"""
Description
===========
Interpolates polar rings from detector images using loki.RingData
and saves the output to a file specified by prefix.
Parameters
==========
img_gen, generator of 2d np.array float images,
this should generate each image in a run
tags, list, string, the tags associated w each image
generated by img_gen, (should be in order
with generation)
mask, 2d np.array bool, a masked image, True is unmasked,
False is masked, should have same dimensions of
images generated by img_gen
x_center, float, pixel unit where beam hits detector,
x dimension( fast dimension), measured from
0,0 pixel corner
y_center, float, pixel unit where beam hits detector,
y dimension( slow dimension), measured from
0,0 pixel corner
detdist, float, sample to detector distance in meter
wavelen, float, wavelength of photons in angstroms
pixsize, float pixel size in meter
prefix str, file prefix, include directory path if necessary
how, str, either ('fetch' or 'polar') method of interpolating the ring.
'fetch' is the new version, which requires q_resolution
and phi_resolution parameters. Uses RingData.RingFetch.
'polar' is the old method which makes a polar image
using RingData.InterpSimple
Required Parmeters if using 'fetch' method
==========================================
interp_method, str, should be either ['floor', 'nearest', 'nearest4', 'weighted4' ]
ring_locations, list, range of ring radii or ring momentum transfer magnitudes
q_resolution, float , resolution of rings in inverse angstroms
phi_resolution float, resolution of rings in degrees
Required Parameters if using 'polar' method
===========================================
nphi, int, azimuthal dimension of polar image, (try to keep at least
single pixel resolution at qmax, you can average over polar
pixels later)
qmin, qmax, float, min q and max q bounds of each polar image
being created (in inverse angstroms)
qmin_pix, qmax_pix, float, min q and max q bounds of each polar image
being created (in pixel units)
Optional Parameters
===================
index_query_fname, str, filename created by loki.queryRingIndices
detector_gain, float, absolute gain of detector
Returns
=======
the output filename
"""
assert( how in [ 'fetch', 'polar' , 'polar_n'] )
assert(radius_unit in ['inv_ang', 'pixels'])
num_imgs = len(tags)
if isinstance(
wavelen, (int, float, long, complex)) and isinstance(
detdist, (int, float, long, complex)):
wavelen, detdist = [wavelen] * num_imgs, [detdist] * num_imgs
else:
assert(isinstance(wavelen, (list, np.ndarray)))
assert(isinstance(detdist, (list, np.ndarray)))
assert(len(wavelen) == len(detdist) == num_imgs)
if detector_gain is None:
detector_gain, photon_conversion_factor = -1, [1] * num_imgs
else:
photon_conversion_factor = [
detector_gain * 3.65 * w / 12398.42 for w in wavelen]
with h5py.File(prefix + '.hdf5', 'w') as output_hdf:
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#======================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if how=='polar' or how == 'polar_n':
assert( nphi is not None)
for i_tag, tag in enumerate(tags):
pix2invang = lambda qpix: np.sin(np.arctan(
qpix * pixsize / detdist[i_tag]) / 2) * 4 * np.pi / wavelen[i_tag]
invang2pix = lambda qia: np.tan(
2 * np.arcsin(qia * wavelen[i_tag] / 4 / np.pi)) * detdist[i_tag] / pixsize
if qmin_pix is None or qmax_pix is None:
assert(qmin is not None)
assert (qmax is not None)
qmin_pix = invang2pix(qmin)
qmax_pix = invang2pix(qmax)
# Initialize the interpolater
interpolater = InterpSimple( x_center, y_center, qmax_pix, qmin_pix, nphi,
raw_img_shape=mask.shape )
if how == 'polar_n':
interpolater.set_polar_tree(index_query_fname, weighted=False)
pmeth = interpolater.nearest_query
else:
pmeth = interpolater.nearest
# make a polar image mask
pmask = pmeth( mask.astype(float) ) #.round()
pmask = pmask.astype(int).astype(bool)
# Make the polar images
polar_img = pmask * pmeth( img_gen.next()) \
* photon_conversion_factor[i_tag]
output_hdf.create_dataset('ring_intensities/%s'%tag, data=polar_img, dtype=np.float32)
output_hdf.create_dataset('ring_mask/%s'%tag, data=pmask.astype(np.int8), dtype=np.int8)
ring_radii = np.arange(qmin_pix, qmax_pix)
ring_mag = np.array( [pix2invang(q_pix)for q_pix in ring_radii])
output_hdf.create_dataset( 'ring_radii/%s'%tag, data = ring_radii)
output_hdf.create_dataset( 'ring_momentum_transfer/%s'%tag, data = ring_mag)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#============================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
else: # using default 'fetch' method
assert(phi_resolution is not None)
assert(q_resolution is not None)
assert(ring_locations is not None)
fetcher = RingFetch(
a=x_center,
b=y_center,
img_shape=mask.shape,
mask=mask,
q_resolution=q_resolution,
phi_resolution=phi_resolution,
pixsize=pixsize,
interp_method=interp_method,
index_query_fname=index_query_fname)
ring_radii = np.zeros((num_imgs, len(ring_locations)))
ring_mag = np.zeros_like(ring_radii)
for i_tag, tag in enumerate(tags):
fetcher.set_params(wavelen[i_tag], detdist[i_tag])
fetcher.set_photon_factor(photon_conversion_factor[i_tag])
fetcher.set_working_image(img_gen.next())
intensities = np.zeros(
(len(ring_locations), fetcher.num_phi_nodes))
if radius_unit == 'inv_ang':
for ring_index, ring_q in enumerate(ring_locations):
intensities[ring_index] = \
fetcher.fetch_a_ring(q=ring_q)
ring_radii[i_tag, ring_index] = int(
round(fetcher.q2r(ring_q)))
ring_mag[i_tag, ring_index] = ring_q
else:
for ring_index, ring_radius in enumerate(ring_locations):
intensities[ring_index] = \
fetcher.fetch_a_ring(radius=ring_radius)
ring_radii[i_tag, ring_index] = ring_radius
ring_mag[i_tag, ring_index] = fetcher.r2q(ring_radius)
output_hdf.create_dataset('ring_intensities/%s' % tag,
data=intensities, dtype=np.float32)
# define meta parameters not specified
nphi = intensities.shape[1]
pmask = np.ones((len(ring_locations), nphi))
output_hdf.create_dataset(
'ring_radii', data=ring_radii, dtype=np.float32)
output_hdf.create_dataset(
'ring_moementum_transfer',
data=ring_mag,
dtype=np.float32)
output_hdf.create_dataset('ring_mask', data=pmask.astype(np.int8))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#============================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phi_values = np.arange(nphi) * 2 * np.pi / nphi
# save meta data
output_hdf.create_dataset('how', data=how)
output_hdf.create_dataset('interp_method', data=interp_method)
output_hdf.create_dataset('x_center', data=x_center, dtype=np.float32)
output_hdf.create_dataset('y_center', data=y_center, dtype=np.float32)
output_hdf.create_dataset('wavelen', data=wavelen, dtype=np.float32)
output_hdf.create_dataset('pixsize', data=pixsize, dtype=np.float32)
output_hdf.create_dataset('detdist', data=detdist, dtype=np.float32)
output_hdf.create_dataset(
'detgain',
data=detector_gain,
dtype=np.float32)
output_hdf.create_dataset(
'photon_factor',
data=photon_conversion_factor,
dtype=np.float32)
output_hdf.create_dataset(
'q_resolution',
data=q_resolution,
dtype=np.float32)
output_hdf.create_dataset(
'phi_resolution',
data=phi_resolution,
dtype=np.float32)
output_hdf.create_dataset('num_phi', data=nphi, dtype=np.float32)
output_hdf.create_dataset(
'ring_phis',
data=phi_values,
dtype=np.float32)
# save
print ("saving data to file %s!" % (prefix + '.hdf5'))
# output_hdf.close()
return prefix + '.hdf5'
# adjust so our edge is a multiple of rbin factor
interp_rmax = int( interp_rmin + np.ceil( (interp_rmax - interp_rmin) / rbin_fct)*rbin_fct )
nphi = int( 2 * np.pi * interp_rmax )
if phibins>0:
phibin_fct = np.ceil( nphi / float( phibins ) )
else:
phibin_fct=1
nphi = int( np.ceil( 2 * np.pi * interp_rmax/phibin_fct)*phibin_fct) # number of azimuthal samples per bin
rbin_new = (interp_rmax- interp_rmin ) / rbin_fct
phibin_new = nphi / phibin_fct
binned_pol_img_sh = ( int(rbin_new), int(phibin_new) )
print("polar image dimensions: %d x %d"%(rbin_new, phibin_new))
Interp = InterpSimple( cent[0], cent[1] , interp_rmax, interp_rmin, nphi, img_sh)
pmask = Interp.nearest(mask).astype(int).astype(float)
pmask_bn = bin_ndarray( pmask, binned_pol_img_sh)
# print pmask.shape,pmask_bn.shape
# if (rbin_fct==1 and phibin_fct==1):
# print('not binning polar img')
# sys.exit()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~ data get parameters
#load the data events for the given run
ds_str = 'exp=cxilp6715:run=%d:smd' % run
ds = psana.MPIDataSource(ds_str)
np.ceil((interp_rmax - interp_rmin) / rbin_fct) * rbin_fct)
nphi = int(2 * np.pi * interp_rmax)
if phibins > 0:
phibin_fct = np.ceil(nphi / float(phibins))
else:
phibin_fct = 1
nphi = int(np.ceil(2 * np.pi * interp_rmax / phibin_fct) *
phibin_fct) # number of azimuthal samples per bin
rbin_new = (interp_rmax - interp_rmin) / rbin_fct
phibin_new = nphi / phibin_fct
binned_pol_img_sh = (int(rbin_new), int(phibin_new))
print("polar image dimensions: %d x %d" % (rbin_new, phibin_new))
Interp = InterpSimple(cent[0], cent[1], interp_rmax, interp_rmin, nphi, img_sh)
pmask = Interp.nearest(mask).astype(int).astype(float)
pmask_bn = bin_ndarray(pmask, binned_pol_img_sh)
# print pmask.shape,pmask_bn.shape
# if (rbin_fct==1 and phibin_fct==1):
# print('not binning polar img')
# sys.exit()
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~ data get parameters
#load the data events for the given run
ds_str = 'exp=cxilr6716:run=%d:smd' % run
ds = psana.MPIDataSource(ds_str)
events = ds.events()
def interpolate_run(img_gen,
tags,
mask,
x_center,
y_center,
pixsize,
detdist,
wavelen,
prefix,
how='fetch',
interp_method='floor',
ring_locations=None,
q_resolution=0,
phi_resolution=0,
radius_unit='inv_ang',
nphi=None,
qmin=None,
qmax=None,
qmin_pix=None,
qmax_pix=None,
detector_gain=None,
index_query_fname=None):
"""
Description
===========
Interpolates polar rings from detector images using loki.RingData
and saves the output to a file specified by prefix.
Parameters
==========
img_gen, generator of 2d np.array float images,
this should generate each image in a run
tags, list, string, the tags associated w each image
generated by img_gen, (should be in order
with generation)
mask, 2d np.array bool, a masked image, True is unmasked,
False is masked, should have same dimensions of
images generated by img_gen
x_center, float, pixel unit where beam hits detector,
x dimension( fast dimension), measured from
0,0 pixel corner
y_center, float, pixel unit where beam hits detector,
y dimension( slow dimension), measured from
0,0 pixel corner
detdist, float, sample to detector distance in meter
wavelen, float, wavelength of photons in angstroms
pixsize, float pixel size in meter
prefix str, file prefix, include directory path if necessary
how, str, either ('fetch' or 'polar') method of interpolating the ring.
'fetch' is the new version, which requires q_resolution
and phi_resolution parameters. Uses RingData.RingFetch.
'polar' is the old method which makes a polar image
using RingData.InterpSimple
Required Parmeters if using 'fetch' method
==========================================
interp_method, str, should be either ['floor', 'nearest', 'nearest4', 'weighted4' ]
ring_locations, list, range of ring radii or ring momentum transfer magnitudes
q_resolution, float , resolution of rings in inverse angstroms
phi_resolution float, resolution of rings in degrees
Required Parameters if using 'polar' method
===========================================
nphi, int, azimuthal dimension of polar image, (try to keep at least
single pixel resolution at qmax, you can average over polar
pixels later)
qmin, qmax, float, min q and max q bounds of each polar image
being created (in inverse angstroms)
qmin_pix, qmax_pix, float, min q and max q bounds of each polar image
being created (in pixel units)
Optional Parameters
===================
index_query_fname, str, filename created by loki.queryRingIndices
detector_gain, float, absolute gain of detector
Returns
=======
the output filename
"""
assert (how in ['fetch', 'polar', 'polar_n'])
assert (radius_unit in ['inv_ang', 'pixels'])
num_imgs = len(tags)
if isinstance(wavelen, (int, float, long, complex)) and isinstance(
detdist, (int, float, long, complex)):
wavelen, detdist = [wavelen] * num_imgs, [detdist] * num_imgs
else:
assert (isinstance(wavelen, (list, np.ndarray)))
assert (isinstance(detdist, (list, np.ndarray)))
assert (len(wavelen) == len(detdist) == num_imgs)
if detector_gain is None:
detector_gain, photon_conversion_factor = -1, [1] * num_imgs
else:
photon_conversion_factor = [
detector_gain * 3.65 * w / 12398.42 for w in wavelen
]
with h5py.File(prefix + '.hdf5', 'w') as output_hdf:
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#======================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
if how == 'polar' or how == 'polar_n':
assert (nphi is not None)
for i_tag, tag in enumerate(tags):
pix2invang = lambda qpix: np.sin(
np.arctan(qpix * pixsize / detdist[i_tag]) / 2
) * 4 * np.pi / wavelen[i_tag]
invang2pix = lambda qia: np.tan(2 * np.arcsin(qia * wavelen[
i_tag] / 4 / np.pi)) * detdist[i_tag] / pixsize
if qmin_pix is None or qmax_pix is None:
assert (qmin is not None)
assert (qmax is not None)
qmin_pix = invang2pix(qmin)
qmax_pix = invang2pix(qmax)
# Initialize the interpolater
interpolater = InterpSimple(x_center,
y_center,
qmax_pix,
qmin_pix,
nphi,
raw_img_shape=mask.shape)
if how == 'polar_n':
interpolater.set_polar_tree(index_query_fname,
weighted=False)
pmeth = interpolater.nearest_query
else:
pmeth = interpolater.nearest
# make a polar image mask
pmask = pmeth(mask.astype(float)) #.round()
pmask = pmask.astype(int).astype(bool)
# Make the polar images
polar_img = pmask * pmeth( img_gen.next()) \
* photon_conversion_factor[i_tag]
output_hdf.create_dataset('ring_intensities/%s' % tag,
data=polar_img,
dtype=np.float32)
output_hdf.create_dataset('ring_mask/%s' % tag,
data=pmask.astype(np.int8),
dtype=np.int8)
ring_radii = np.arange(qmin_pix, qmax_pix)
ring_mag = np.array(
[pix2invang(q_pix) for q_pix in ring_radii])
output_hdf.create_dataset('ring_radii/%s' % tag,
data=ring_radii)
output_hdf.create_dataset('ring_momentum_transfer/%s' % tag,
data=ring_mag)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#============================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
else: # using default 'fetch' method
assert (phi_resolution is not None)
assert (q_resolution is not None)
assert (ring_locations is not None)
fetcher = RingFetch(a=x_center,
b=y_center,
img_shape=mask.shape,
mask=mask,
q_resolution=q_resolution,
phi_resolution=phi_resolution,
pixsize=pixsize,
interp_method=interp_method,
index_query_fname=index_query_fname)
ring_radii = np.zeros((num_imgs, len(ring_locations)))
ring_mag = np.zeros_like(ring_radii)
for i_tag, tag in enumerate(tags):
fetcher.set_params(wavelen[i_tag], detdist[i_tag])
fetcher.set_photon_factor(photon_conversion_factor[i_tag])
fetcher.set_working_image(img_gen.next())
intensities = np.zeros(
(len(ring_locations), fetcher.num_phi_nodes))
if radius_unit == 'inv_ang':
for ring_index, ring_q in enumerate(ring_locations):
intensities[ring_index] = \
fetcher.fetch_a_ring(q=ring_q)
ring_radii[i_tag, ring_index] = int(
round(fetcher.q2r(ring_q)))
ring_mag[i_tag, ring_index] = ring_q
else:
for ring_index, ring_radius in enumerate(ring_locations):
intensities[ring_index] = \
fetcher.fetch_a_ring(radius=ring_radius)
ring_radii[i_tag, ring_index] = ring_radius
ring_mag[i_tag, ring_index] = fetcher.r2q(ring_radius)
output_hdf.create_dataset('ring_intensities/%s' % tag,
data=intensities,
dtype=np.float32)
# define meta parameters not specified
nphi = intensities.shape[1]
pmask = np.ones((len(ring_locations), nphi))
output_hdf.create_dataset('ring_radii',
data=ring_radii,
dtype=np.float32)
output_hdf.create_dataset('ring_moementum_transfer',
data=ring_mag,
dtype=np.float32)
output_hdf.create_dataset('ring_mask', data=pmask.astype(np.int8))
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#============================================================================
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phi_values = np.arange(nphi) * 2 * np.pi / nphi
# save meta data
output_hdf.create_dataset('how', data=how)
output_hdf.create_dataset('interp_method', data=interp_method)
output_hdf.create_dataset('x_center', data=x_center, dtype=np.float32)
output_hdf.create_dataset('y_center', data=y_center, dtype=np.float32)
output_hdf.create_dataset('wavelen', data=wavelen, dtype=np.float32)
output_hdf.create_dataset('pixsize', data=pixsize, dtype=np.float32)
output_hdf.create_dataset('detdist', data=detdist, dtype=np.float32)
output_hdf.create_dataset('detgain',
data=detector_gain,
dtype=np.float32)
output_hdf.create_dataset('photon_factor',
data=photon_conversion_factor,
dtype=np.float32)
output_hdf.create_dataset('q_resolution',
data=q_resolution,
dtype=np.float32)
output_hdf.create_dataset('phi_resolution',
data=phi_resolution,
dtype=np.float32)
output_hdf.create_dataset('num_phi', data=nphi, dtype=np.float32)
output_hdf.create_dataset('ring_phis',
data=phi_values,
dtype=np.float32)
# save
print("saving data to file %s!" % (prefix + '.hdf5'))
# output_hdf.close()
return prefix + '.hdf5'
# sum all the images in this run
if image_sum is None:
image_sum = img
else:
image_sum += img
# interpolation begins here
if shot_counter == 0:
# create SimpleInterp object if it's the first shot
img_shape = img.shape
interpolator = InterpSimple.InterpSimple(ring_center[0],
ring_center[1],
qRmax,
qRmin,
num_phi,
img_shape,
bin_fac=bin_fac,
use_zoom=False)
# threshold mask
threshold_mask = img < bright_threshold
# apply threshold to img directly
img *= threshold_mask
polar_interp = interpolator.nearest_naive_bin(img)
d = {'cspad': {'polar_intensity': polar_interp}}
# save per-event data
smldata.event(d)
shot_counter += 1
if img is None: continue
# sum all the images in this run
if image_sum is None:
image_sum = img
else:
image_sum += img
# interpolation begins here
if shot_counter == 0:
# create SimpleInterp object if it's the first shot
img_shape = img.shape
interpolator = InterpSimple (ring_center[0], ring_center[1],
qRmax, qRmin,
num_phi, img_shape,
bin_fac = bin_fac,
use_zoom = False)
# threshold mask
threshold_mask = img<bright_threshold
# apply threshold to img directly
img *= threshold_mask
polar_interp = interpolator.nearest_naive_bin( img )
d = {'cspad':{'polar_intensity': polar_interp}}
# save per-event data
smldata.event(d)
shot_counter += 1
total_shots +=1
# min ring radii
# desired dimension of image, these will be approximate
rbins =35
phibins = 360
interp_rmin = 100
interp_rmax = 450
rbin_fct = np.floor( (interp_rmax - interp_rmin) / rbins)
# adjust so our edge is a multiple of rbin factor
interp_rmax = int( interp_rmin + np.ceil( (interp_rmax - interp_rmin) / rbin_fct)*rbin_fct )
nphi = int( 2 * np.pi * interp_rmax )
phibin_fct = np.ceil( nphi / float( phibins ) )
nphi = int( np.ceil( 2 * np.pi * interp_rmax/phibin_fct)*phibin_fct) # number of azimuthal samples per bin
rbin_new = (interp_rmax- interp_rmin ) / rbin_fct
phibin_new = nphi / phibin_fct
binned_pol_img_sh = ( int(rbin_new), int(phibin_new) )
print("polar image dimensions: %d x %d"%(rbin_new, phibin_new))
Interp = InterpSimple( cent[0], cent[1] , interp_rmax, interp_rmin, nphi, img_sh)
pmask = Interp.nearest(mask).astype(int).astype(float)
pmask_bn = bin_ndarray( pmask, binned_pol_img_sh)
pmask_bn = pmask_bn.astype(int)
pmask_bn = np.array(pmask_bn==pmask_bn.max(), dtype = int)
#np.save('/reg/d/psdm/cxi/cxilp6715/scratch/water_data/binned_pmask_basic.npy', pmask_bn)
np.save('/reg/d/psdm/cxi/cxilp6715/results/shared_files/binned_pmask_basic3.npy', pmask_bn)