def main():
'''Parses command line arguments and config file to generate detector file'''
logging.basicConfig(filename="recon.log", level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make detector")
args = parser.special_parse_args()
det_file = os.path.join(args.main_dir,
read_config.get_filename(args.config_file,
'make_detector',
'out_detector_file'))
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(det_file)
logging.info("\n\nStarting make_detector....")
logging.info(' '.join(sys.argv))
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'], pm['dets_x'],
pm['dets_y'], pm['pixsize'],
pm['wavelength'], pm['ewald_rad'], show=args.vb)
timer.reset_and_report("Reading experiment parameters") if args.vb else timer.reset()
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
(x, y) = np.mgrid[0:pm['dets_x'], 0:pm['dets_y']]
(x, y) = (x.flatten()-pm['detc_x'], y.flatten()-pm['detc_y'])
norm = np.sqrt(x**2 + y**2 + (pm['detd']/pm['pixsize'])**2)
polar = read_config.compute_polarization(pm['polarization'], x, y, norm)
(qx, qy, qz) = (x*qscaling/norm, # pylint: disable=C0103
y*qscaling/norm,
qscaling*(pm['detd']/pm['pixsize']/norm - 1.))
logging.info('%15s:%10.4f', 'qmax', np.sqrt(qx*qx + qy*qy + qz*qz).max())
solid_angle = pm['detd'] / pm['pixsize'] / norm**3
solid_angle = polar*solid_angle
rad = np.sqrt(x*x + y*y)
if pm['mask_fname'] is None:
mask = np.zeros(solid_angle.shape, dtype='u1')
mask[rad > min(pm['detc_x'], pm['detc_y'])] = 1
mask[rad < pm['stoprad']] = 2
else:
mask = np.fromfile(pm['mask_fname'], '=u1')
mask[(rad > min(pm['detc_x'], pm['detc_y'])) & (mask == 0)] = 1
timer.reset_and_report("Creating detector") if args.vb else timer.reset()
with open(det_file, "w") as fptr:
#fptr.write(str(pm['dets_x']*pm['dets_y']) + "\n")
fptr.write("%d %.6f %.6f\n" % (pm['dets_x']*pm['dets_y'],
pm['detd']/pm['pixsize'],
pm['ewald_rad']))
for par0, par1, par2, par3, par4 in zip(qx, qy, qz, solid_angle, mask):
txt = "%21.15e %21.15e %21.15e %21.15e %d\n"%(par0, par1, par2, par3, par4)
fptr.write(txt)
timer.reset_and_report("Writing detector") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass
args = parser.special_parse_args()
logging.info('Starting cheetahtodet...')
logging.info(' '.join(sys.argv))
pm = read_config.get_detector_config(args.config_file, show=args.vb)
q_pm = read_config.compute_q_params(pm['detd'], pm['dets_x'], pm['dets_y'], pm['pixsize'], pm['wavelength'], pm['ewald_rad'], show=args.vb)
output_folder = read_config.get_filename(args.config_file, 'emc', 'output_folder')
# Cheetah geometry files have coordinates in m
with h5py.File(args.h5_name, 'r') as f:
x = f['x'][:].flatten() * 1.e3
y = f['y'][:].flatten() * 1.e3
z = f['z'][:].flatten() * 1.e3 + pm['detd']
norm = np.sqrt(x*x + y*y + z*z)
polar = read_config.compute_polarization(pm['polarization'], x, y, norm)
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
qx = x * qscaling / norm
qy = y * qscaling / norm
qz = qscaling * (z / norm - 1.)
solid_angle = pm['detd']*(pm['pixsize']*pm['pixsize']) / np.power(norm, 3.0)
solid_angle = polar*solid_angle
radius = np.sqrt(x*x + y*y)
if args.mask is None:
rmax = min(np.abs(x.max()), np.abs(x.min()), np.abs(y.max()), np.abs(y.min()))
mask = np.zeros(solid_angle.shape, dtype='u1')
mask[radius>rmax] = 1
else:
with h5py.File(args.mask, 'r') as f:
mask = f[args.mask_dset][:].astype('u1').flatten()
q_pm = read_config.compute_q_params(pm['detd'], pm['dets_x'], pm['dets_y'], pm['pixsize'], pm['wavelength'], pm['ewald_rad'], show=args.vb)
output_folder = read_config.get_filename(args.config_file, 'emc', 'output_folder')
ds = psana.DataSource(args.exp_string + ':idx')
run = ds.runs().next()
times = run.times()
evt = run.event(times[0])
det = psana.Detector(args.det_name)
cx = det.coords_x(evt).flatten() * 1.e-3
cy = det.coords_y(evt).flatten() * 1.e-3
detd = pm['detd']
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
rad = np.sqrt(cx*cx + cy*cy)
norm = np.sqrt(cx*cx + cy*cy + detd*detd)
polar = read_config.compute_polarization(pm['polarization'], cx, cy, norm)
qx = cx * qscaling / norm
qy = cy * qscaling / norm
qz = qscaling * (detd / norm - 1.)
solid_angle = pm['detd']*pm['pixsize']*pm['pixsize'] / np.power(norm, 3.0)
solid_angle = polar*solid_angle
if pm['mask_fname'] is None:
mask = det.mask(evt, status=True, calib=True, edges=True, central=True, unbondnbrs8=True).flatten()
mask = 2*(1 - mask)
rmax = min(cx.max(), np.abs(cx.min()), cy.max(), np.abs(cy.min()))
mask[(rad>rmax) & (mask==0)] = 1
else:
mask = np.fromfile(pm['mask_fname'], '=u1')
det_file = output_folder + '/det_' + args.exp_string.split(':')[0][4:] + '.dat'
def main():
"""Parse command line arguments and generate file"""
logging.basicConfig(filename='recon.log',
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description='PSANA to det')
parser.add_argument('exp_string', help='PSANA experiment string')
parser.add_argument(
'det_name', help='PSANA Detector name (either source string or alias)')
parser.add_argument(
'-C',
'--corners',
help='Set corner pixels to be irrelevant. Default = False',
action='store_true',
default=False)
args = parser.special_parse_args()
logging.info('Starting psanatodet...')
logging.info(' '.join(sys.argv))
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=invalid-name
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
output_folder = read_config.get_filename(args.config_file, 'emc',
'output_folder')
dsource = psana.DataSource(args.exp_string + ':idx')
run = dsource.runs().next()
times = run.times()
evt = run.event(times[0])
psana_det = psana.Detector(args.det_name)
cx = psana_det.coords_x(evt).flatten() * 1.e-3 # pylint: disable=invalid-name
cy = psana_det.coords_y(evt).flatten() * 1.e-3 # pylint: disable=invalid-name
detd = pm['detd'] # in mm
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
rad = np.sqrt(cx * cx + cy * cy)
norm = np.sqrt(cx * cx + cy * cy + detd * detd)
polar = read_config.compute_polarization(pm['polarization'], cx, cy, norm)
det = detector.Detector()
det.detd = detd / pm['pixsize']
det.ewald_rad = pm['ewald_rad']
det.qx = cx * qscaling / norm
det.qy = cy * qscaling / norm
det.qz = qscaling * (detd / norm - 1.)
det.corr = pm['detd'] * pm['pixsize'] * pm['pixsize'] / np.power(norm, 3.0)
det.corr *= polar
if pm['mask_fname'] is None:
det.raw_mask = psana_det.mask(evt,
status=True,
calib=True,
edges=True,
central=True,
unbondnbrs8=True).flatten()
det.raw_mask = 2 * (1 - det.raw_mask)
if args.corners:
rmax = min(cx.max(), np.abs(cx.min()), cy.max(), np.abs(cy.min()))
det.raw_mask[(rad > rmax) & (det.raw_mask == 0)] = 1
else:
det.raw_mask = np.fromfile(pm['mask_fname'], '=u1')
det_file = output_folder + '/det_' + args.exp_string.split(':')[0][4:]
try:
import h5py
det_file += '.h5'
except ImportError:
det_file += '.dat'
sys.stderr.write('Writing detector file to %s\n' % det_file)
det.write(det_file)
def main():
"""Parse command line arguments and convert file"""
logging.basicConfig(filename='recon.log',
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description='cheetahtodet')
parser.add_argument('h5_name',
help='HDF5 file to convert to detector format')
parser.add_argument(
'-M',
'--mask',
help=
'Path to detector style mask (0:good, 1:no_orient, 2:bad) in h5 file')
parser.add_argument('--mask_dset',
help='Data set in mask file. Default: /data/data',
default='data/data')
parser.add_argument(
'--dragonfly_mask',
help='Whether mask has Dragonfly style values or not. (Default: false)',
default=False,
action='store_true')
args = parser.special_parse_args()
logging.info('Starting cheetahtodet...')
logging.info(' '.join(sys.argv))
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=invalid-name
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
output_folder = read_config.get_filename(args.config_file, 'emc',
'output_folder')
# Cheetah geometry files have coordinates in m
with h5py.File(args.h5_name, 'r') as fptr:
x = fptr['x'][:].flatten() * 1.e3
y = fptr['y'][:].flatten() * 1.e3
z = fptr['z'][:].flatten() * 1.e3 + pm['detd']
det = detector.Detector()
norm = np.sqrt(x * x + y * y + z * z)
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
det.qx = x * qscaling / norm
det.qy = y * qscaling / norm
det.qz = qscaling * (z / norm - 1.)
det.corr = pm['detd'] * (pm['pixsize'] * pm['pixsize']) / np.power(
norm, 3.0)
det.corr *= read_config.compute_polarization(pm['polarization'], x, y,
norm)
if args.mask is None:
radius = np.sqrt(x * x + y * y)
rmax = min(np.abs(x.max()), np.abs(x.min()), np.abs(y.max()),
np.abs(y.min()))
det.raw_mask = np.zeros(det.corr.shape, dtype='u1')
det.raw_mask[radius > rmax] = 1
else:
with h5py.File(args.mask, 'r') as fptr:
det.raw_mask = fptr[args.mask_dset][:].astype('u1').flatten()
if not args.dragonfly_mask:
det.raw_mask = 2 - 2 * det.raw_mask
det.detd = pm['detd'] / pm['pixsize']
det.ewald_rad = pm['ewald_rad']
det_file = output_folder + '/' + os.path.splitext(
os.path.basename(args.h5_name))[0]
try:
import h5py
det_file += '.h5'
except ImportError:
det_file += '.dat'
logging.info('Writing detector file to %s', det_file)
sys.stderr.write('Writing detector file to %s\n' % det_file)
det.write(det_file)
def main():
'''Parses command line arguments and config file to generate detector file'''
logging.basicConfig(filename="recon.log",
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make detector")
args = parser.special_parse_args()
det_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_detector',
'out_detector_file'))
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(det_file)
logging.info("\n\nStarting make_detector....")
logging.info(' '.join(sys.argv))
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
timer.reset_and_report(
"Reading experiment parameters") if args.vb else timer.reset()
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
(x, y) = np.mgrid[0:pm['dets_x'], 0:pm['dets_y']]
(x, y) = (x.flatten() - pm['detc_x'], y.flatten() - pm['detc_y'])
norm = np.sqrt(x**2 + y**2 + (pm['detd'] / pm['pixsize'])**2)
polar = read_config.compute_polarization(pm['polarization'], x, y,
norm)
(qx, qy, qz) = (
x * qscaling / norm, # pylint: disable=C0103
y * qscaling / norm,
qscaling * (pm['detd'] / pm['pixsize'] / norm - 1.))
logging.info('%15s:%10.4f', 'qmax',
np.sqrt(qx * qx + qy * qy + qz * qz).max())
solid_angle = pm['detd'] / pm['pixsize'] / norm**3
solid_angle = polar * solid_angle
rad = np.sqrt(x * x + y * y)
if pm['mask_fname'] is None:
mask = np.zeros(solid_angle.shape, dtype='u1')
mask[rad > min(pm['detc_x'], pm['detc_y'])] = 1
mask[rad < pm['stoprad']] = 2
else:
mask = np.fromfile(pm['mask_fname'], '=u1')
mask[(rad > min(pm['detc_x'], pm['detc_y'])) & (mask == 0)] = 1
timer.reset_and_report(
"Creating detector") if args.vb else timer.reset()
with open(det_file, "w") as fptr:
#fptr.write(str(pm['dets_x']*pm['dets_y']) + "\n")
fptr.write("%d %.6f %.6f\n" %
(pm['dets_x'] * pm['dets_y'],
pm['detd'] / pm['pixsize'], pm['ewald_rad']))
for par0, par1, par2, par3, par4 in zip(qx, qy, qz, solid_angle,
mask):
txt = "%21.15e %21.15e %21.15e %21.15e %d\n" % (
par0, par1, par2, par3, par4)
fptr.write(txt)
timer.reset_and_report(
"Writing detector") if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass
def main():
'''Parses command line arguments and config file to generate detector file'''
logging.basicConfig(filename="recon.log",
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
parser = py_utils.MyArgparser(description="make detector")
args = parser.special_parse_args()
det_file = os.path.join(
args.main_dir,
read_config.get_filename(args.config_file, 'make_detector',
'out_detector_file'))
if args.yes:
to_write = True
else:
to_write = py_utils.check_to_overwrite(det_file)
logging.info("\n\nStarting make_detector....")
logging.info(' '.join(sys.argv))
if to_write:
timer = py_utils.MyTimer()
pm = read_config.get_detector_config(args.config_file, show=args.vb) # pylint: disable=C0103
q_pm = read_config.compute_q_params(pm['detd'],
pm['dets_x'],
pm['dets_y'],
pm['pixsize'],
pm['wavelength'],
pm['ewald_rad'],
show=args.vb)
timer.reset_and_report(
"Reading experiment parameters") if args.vb else timer.reset()
det = detector.Detector()
qscaling = 1. / pm['wavelength'] / q_pm['q_sep']
(x, y) = np.mgrid[0:pm['dets_x'], 0:pm['dets_y']]
(x, y) = (x.flatten() - pm['detc_x'], y.flatten() - pm['detc_y'])
norm = np.sqrt(x**2 + y**2 + (pm['detd'] / pm['pixsize'])**2)
(det.qx, det.qy, det.qz) = (
x * qscaling / norm, # pylint: disable=C0103
y * qscaling / norm,
qscaling * (pm['detd'] / pm['pixsize'] / norm - 1.))
logging.info('%15s:%10.4f', 'qmax',
np.sqrt(det.qx**2 + det.qy**2 + det.qz**2).max())
polar = read_config.compute_polarization(pm['polarization'], x, y,
norm)
det.corr = pm['detd'] / pm['pixsize'] / norm**3
det.corr *= polar
rad = np.sqrt(x * x + y * y)
if pm['mask_fname'] is None:
det.raw_mask = np.zeros(det.corr.shape, dtype='u1')
det.raw_mask[rad > min(pm['detc_x'], pm['detc_y'])] = 1
det.raw_mask[rad < pm['stoprad']] = 2
else:
det.raw_mask = np.fromfile(pm['mask_fname'], '=u1')
det.raw_mask[(rad > min(pm['detc_x'], pm['detc_y']))
& (mask == 0)] = 1
timer.reset_and_report(
"Creating detector") if args.vb else timer.reset()
det.detd = pm['detd'] / pm['pixsize']
det.ewald_rad = pm['ewald_rad']
det.write(det_file)
timer.reset_and_report("Writing detector to %s" %
det_file) if args.vb else timer.reset()
timer.report_time_since_beginning() if args.vb else timer.reset()
else:
pass