class CBFImage(MARIPImage):
def __init__(self, filename):
DetectorImageBase.__init__(self, filename)
try:
from cbflib_adaptbx import CBFAdaptor # optional package
self.adaptor = CBFAdaptor(filename)
# for testing only:
'''
self.adaptor.read_header()
print " size1:", self.adaptor.size1()
print " size2:", self.adaptor.size2()
print " overload:", self.adaptor.overload()
print "wavelength:", self.adaptor.wavelength()
print " distance:", self.adaptor.distance()
print "pixel size:", self.adaptor.pixel_size()
print " beamx:", self.adaptor.beam_index_slow*self.adaptor.pixel_size()
print " beamy:", self.adaptor.beam_index_fast*self.adaptor.pixel_size()
print " osc_start:", self.adaptor.osc_start()
print " osc_range:", self.adaptor.osc_range()
print self.adaptor.raster_description()
flags = self.adaptor.transform_flags()
print flags.transpose, flags.reverse_slow, flags.reverse_fast
'''
except Exception:
from iotbx.detectors.marIP import NullAdaptor
self.adaptor = NullAdaptor()
self.vendortype = "CBF"
self.readHeader()
try:
self.vendor_specific_null_value = int(
self.adaptor.undefined_value())
except RuntimeError as e:
self.vendor_specific_null_value = 0
def beam_center_slow(self):
return self.adaptor.beam_index_slow * self.adaptor.pixel_size()
def beam_center_fast(self):
return self.adaptor.beam_index_fast * self.adaptor.pixel_size()
def read(self):
T = self.adaptor.transform_flags()
#future: use these tests to trigger in-place column & row swaps
assert T.reverse_fast == False
assert T.reverse_slow == False
from cbflib_adaptbx import cbf_binary_adaptor
M = cbf_binary_adaptor(self.filename)
data = M.uncompress_implementation("buffer_based").uncompress_data()
if T.transpose == True:
#very inefficient; 0.09 sec for 3K x 3K uncompression
# yet 0.54 sec for in-place transpose
# other options not tried: a) alloc & set new matrix; b) use data as is
data.matrix_transpose_in_place()
self.bin_safe_set_data(data)
class CBFImage(MARIPImage):
def __init__(self,filename):
DetectorImageBase.__init__(self,filename)
try:
from cbflib_adaptbx import CBFAdaptor # optional package
self.adaptor = CBFAdaptor(filename)
# for testing only:
'''
self.adaptor.read_header()
print " size1:", self.adaptor.size1()
print " size2:", self.adaptor.size2()
print " overload:", self.adaptor.overload()
print "wavelength:", self.adaptor.wavelength()
print " distance:", self.adaptor.distance()
print "pixel size:", self.adaptor.pixel_size()
print " beamx:", self.adaptor.beam_index_slow*self.adaptor.pixel_size()
print " beamy:", self.adaptor.beam_index_fast*self.adaptor.pixel_size()
print " osc_start:", self.adaptor.osc_start()
print " osc_range:", self.adaptor.osc_range()
print self.adaptor.raster_description()
flags = self.adaptor.transform_flags()
print flags.transpose, flags.reverse_slow, flags.reverse_fast
'''
except Exception:
from iotbx.detectors.marIP import NullAdaptor
self.adaptor = NullAdaptor()
self.vendortype = "CBF"
self.readHeader()
self.vendor_specific_null_value = int(self.adaptor.undefined_value())
def beam_center_slow(self):
return self.adaptor.beam_index_slow*self.adaptor.pixel_size()
def beam_center_fast(self):
return self.adaptor.beam_index_fast*self.adaptor.pixel_size()
def read(self):
T = self.adaptor.transform_flags()
#future: use these tests to trigger in-place column & row swaps
assert T.reverse_fast == False
assert T.reverse_slow == False
from cbflib_adaptbx import cbf_binary_adaptor
M = cbf_binary_adaptor( self.filename )
data = M.uncompress_implementation("buffer_based").uncompress_data()
if T.transpose==True:
#very inefficient; 0.09 sec for 3K x 3K uncompression
# yet 0.54 sec for in-place transpose
# other options not tried: a) alloc & set new matrix; b) use data as is
data.matrix_transpose_in_place()
self.bin_safe_set_data(data)
