def load_xds_special(cbfin):
h = pycbf.cbf_handle_struct()
h.read_file(cbfin, pycbf.MSG_DIGEST)
h.require_category("array_data")
h.find_column("header_contents")
header = h.get_value()
M = cbf_binary_adaptor(cbfin)
data = M.uncompress_implementation("buffer_based").uncompress_data()
#print "slow, fast=", M.dim_slow(), M.dim_fast() # can be obtained after getting data
return header, data, M.dim_slow(), M.dim_fast()
def load_xds_special(cbfin):
h = pycbf.cbf_handle_struct()
h.read_file(cbfin, pycbf.MSG_DIGEST)
h.require_category("array_data")
h.find_column("header_contents")
header = h.get_value()
M = cbf_binary_adaptor(cbfin)
data = M.uncompress_implementation("buffer_based").uncompress_data()
#print "slow, fast=", M.dim_slow(), M.dim_fast() # can be obtained after getting data
return header, data, M.dim_slow(), M.dim_fast()
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)
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)
def read(self, algorithm="buffer_based"):
self.readHeader()
if self.linearintdata != None and self.linearintdata.size() == self.size1 * self.size2:
# data has already been read
return
if self.bin == 2:
raise ImageException("2-by-2 binning not supported for miniCBF")
try:
from cbflib_adaptbx import cbf_binary_adaptor # optional package
self.adaptor = cbf_binary_adaptor(self.filename)
# assert algorithm in ["cbflib","cbflib_optimized","buffer_based"]
data = self.adaptor.uncompress_implementation(algorithm).uncompress_data(self.size1, self.size2)
self.bin_safe_set_data(data)
except Exception, e:
raise ImageException('unable to read miniCBF data; contact authors; error="%s"' % str(e).strip())
def read(self, algorithm="buffer_based"):
self.readHeader()
if self.linearintdata != None and\
self.linearintdata.size()==self.size1*self.size2:
#data has already been read
return
if self.bin == 2:
raise ImageException("2-by-2 binning not supported for miniCBF")
try:
from cbflib_adaptbx import cbf_binary_adaptor # optional package
self.adaptor = cbf_binary_adaptor(self.filename)
# assert algorithm in ["cbflib","cbflib_optimized","buffer_based"]
data = self.adaptor.uncompress_implementation(
algorithm).uncompress_data(self.size1, self.size2)
self.bin_safe_set_data(data)
except Exception:
raise ImageException(
"unable to read miniCBF data; contact authors")
def load_cbf_as_flex(filein): # This can also read XDS special cbf
M = cbf_binary_adaptor(filein)
data = M.uncompress_implementation("buffer_based").uncompress_data()
nslow, nfast = M.dim_slow(), M.dim_fast() # can be obtained after getting data
return data, nfast, nslow
def load_cbf_as_flex(filein): # This can also read XDS special cbf
M = cbf_binary_adaptor(filein)
data = M.uncompress_implementation("buffer_based").uncompress_data()
nslow, nfast = M.dim_slow(), M.dim_fast() # can be obtained after getting data
return data, nfast, nslow