def get_array(file_name=None,labels=None):
print("Reading from %s" %(file_name))
from iotbx import reflection_file_reader
reflection_file = reflection_file_reader.any_reflection_file(
file_name=file_name)
array_to_use=None
if labels:
for array in reflection_file.as_miller_arrays():
if ",".join(array.info().labels)==labels:
array_to_use=array
break
else:
for array in reflection_file.as_miller_arrays():
if array.is_complex_array() or array.is_xray_amplitude_array() or\
array.is_xray_intensity_array():
array_to_use=array
break
if not array_to_use:
text=""
for array in reflection_file.as_miller_arrays():
text+=" %s " %(",".join(array.info().labels))
raise Sorry("Cannot identify array to use...possibilities: %s" %(text))
print("Using the array %s" %(",".join(array_to_use.info().labels)))
return array_to_use
def get_array(file_name=None,labels=None):
print "Reading from %s" %(file_name)
from iotbx import reflection_file_reader
reflection_file = reflection_file_reader.any_reflection_file(
file_name=file_name)
array_to_use=None
if labels:
for array in reflection_file.as_miller_arrays():
if ",".join(array.info().labels)==labels:
array_to_use=array
break
else:
for array in reflection_file.as_miller_arrays():
if array.is_complex_array() or array.is_xray_amplitude_array() or\
array.is_xray_intensity_array():
array_to_use=array
break
if not array_to_use:
text=""
for array in reflection_file.as_miller_arrays():
text+=" %s " %(",".join(array.info().labels))
raise Sorry("Cannot identify array to use...possibilities: %s" %(text))
print "Using the array %s" %(",".join(array_to_use.info().labels))
return array_to_use
def get_amplitudes(args):
if not args or 'help' in args or '--help' in args:
print("\nsharpen.py")
print("Read in map coefficients or amplitudes and sharpen")
return
new_args=[]
file_name=None
for arg in args:
if os.path.isfile(arg) and arg.endswith(".mtz"):
file_name=arg
else:
new_args.append(arg)
args=new_args
labels=None
array_list=[]
array_list.append(get_array(file_name=file_name,labels=labels))
array=array_list[-1]
phases=None
assert array.is_complex_array()
return array
def get_amplitudes(args):
if not args or 'help' in args or '--help' in args:
print "\nsharpen.py"
print "Read in map coefficients or amplitudes and sharpen"
return
new_args=[]
file_name=None
for arg in args:
if os.path.isfile(arg) and arg.endswith(".mtz"):
file_name=arg
else:
new_args.append(arg)
args=new_args
labels=None
array_list=[]
array_list.append(get_array(file_name=file_name,labels=labels))
array=array_list[-1]
phases=None
assert array.is_complex_array()
return array