if args.list:
logging.info('Reading file names in list %s' % args.condor_fname)
with open(args.condor_fname, 'r') as f:
flist = [fname.rstrip() for fname in f.readlines()]
logging.info
else:
flist = [args.condor_fname]
# Read meta information from condor CXI file
with h5py.File(flist[0], 'r') as f:
wavelength = f['source/wavelength'][...]
nx = f['detector/nx'][0]
ny = f['detector/ny'][0]
emcwriter = writeemc.EMC_writer('%s/%s.emc' % (output_folder, os.path.splitext(os.path.basename(args.condor_fname))[0]), nx*ny)
for fname in flist:
f = h5py.File(fname, 'r')
dset = f['entry_1/data_1/data']
mask = f['entry_1/data_1/mask']
num_frames = dset.shape[0]
if not args.list:
logging.info('Converting %d frames in %s' % (num_frames, args.condor_fname))
for i in range(num_frames):
photons = dset[i] * (~(mask[i]==512))
photons[photons<0] = 0
emcwriter.write_frame(photons.flatten())
if not args.list:
sys.stderr.write('\rFinished %d/%d' % (i+1, num_frames))
logging.error('Data file %s not found. Exiting.' % args.h5_name)
sys.exit()
if args.list:
logging.info('Reading file names in list %s' % args.h5_name)
with open(args.h5_name, 'r') as f:
flist = [
os.path.realpath(fname.rstrip()) for fname in f.readlines()
]
logging.info
else:
flist = [args.h5_name]
if args.out_fname is None:
emcwriter = writeemc.EMC_writer(
'%s/%s.emc' %
(output_folder, os.path.splitext(os.path.basename(
args.h5_name))[0]), pm['dets_x'] * pm['dets_y'])
else:
emcwriter = writeemc.EMC_writer(args.out_fname,
pm['dets_x'] * pm['dets_y'])
for fnum, fname in enumerate(flist):
f = h5py.File(fname, 'r')
dset = get_dset(f, args)
if dset is None:
continue
ind, num_frames = get_indices(f, dset, args)
curr_num_data += num_frames
if not args.list:
out = array.reshape(s[0] / bs, bs, s[1] / bs, bs).sum(axis=(1, 3))
return out
tag = ''
if len(sys.argv) > 2:
binsize = int(sys.argv[2])
tag = '_%d' % binsize
num_pix = (1700 / binsize)**2
print num_pix, 'pixels in detector'
flist = np.loadtxt(sys.argv[1], dtype='S')
print len(flist), 'files in list'
emcwriter = writeemc.EMC_writer(
['temp.po', 'temp.pm', 'temp.cm'], 'data/%s%s.emc' %
(os.path.splitext(os.path.basename(sys.argv[1]))[0], tag), num_pix)
i = 1
for fname in flist:
f = h5py.File(fname, 'r')
pattern = (f['data/data'][:] * 1.e-8).astype('i4')
#pattern = f['data/data'][:].astype('i4')
pattern = binimg(pattern, binsize)
#pattern[pattern > 1] = 1
f.close()
emcwriter.write_frame(pattern.flatten())
sys.stderr.write('\rFinished %d/%d' % (i, len(flist)))
i += 1
sys.exit()
f = h5py.File(args.h5_name, 'r')
if args.dset_name is None:
for name, obj in f['photonConverter'].items():
try:
temp = obj.keys()
dset = obj['photonCount']
break
except AttributeError:
pass
logging.info('Converting data in '+ dset.name)
else:
dset = f[args.dset_name]
logging.info('Converting data in '+ args.dset_name)
frames = dset[:]
ind = range(len(frames))
num_frames = len(ind)
logging.info('%d frames in %s' % (num_frames, args.h5_name))
emcwriter = writeemc.EMC_writer('data/%s.emc' % os.path.splitext(os.path.basename(sys.argv[1]))[0],
pm['dets_x']*pm['dets_y'])
for i in range(num_frames):
emcwriter.write_frame(frames[i].flatten().astype('i4'))
sys.stderr.write('\rFinished %d/%d' % (i+1, num_frames))
f.close()
sys.stderr.write('\n')
emcwriter.finish_write()
print ind.shape, 'single hits'
if len(sys.argv) > 3:
binsize = int(sys.argv[3])
tag += '_%d' % binsize
f = h5py.File(sys.argv[1], 'r')
num_frames = f['dataPhotons/back/index'].shape[0]
print num_frames, "frames in h5 file"
index = f['dataPhotons/back/index']
count = f['dataPhotons/back/photonCount']
ix = f['dataPhotons/back/iX'][:].flatten()
iy = f['dataPhotons/back/iY'][:].flatten()
emcwriter = writeemc.EMC_writer(
'data/%s_%s.emc' %
(os.path.splitext(os.path.basename(sys.argv[1]))[0], tag),
1028 * 1040 / binsize / binsize)
j = 0
for i in ind:
pattern = np.zeros((1028, 1040), dtype='i4')
place = index[i]
pattern[iy[place], ix[place]] = count[i]
if binsize > 1:
pattern = binimg(pattern, binsize)
emcwriter.write_frame(pattern.flatten())
sys.stderr.write('\rFinished %d/%d' % (j + 1, len(ind)))
j += 1
f.close()