def filter_normalization(obj, lothreshold, hithreshold, config=None):
"""
This function takes an object with normalization integration information
and a threshold and creates a mask file containing the pixel IDs that do
not make it above the threshold.
@param obj: The object containing the normalization information
@type obj: C{SOM.SOM}
@param lothreshold: The value below which a pixel will be masked.
@type lothreshold: C{float}
@param hithreshold: The value above which a pixel will be masked.
@type hithreshold: C{float}
@param config: The object holding the DR configuration
@type config: L{hlr_utils.Configure}
@raise TypeError: The incoming object is not a C{SOM}.
"""
import hlr_utils
o_descr = hlr_utils.get_descr(obj)
if o_descr != "SOM":
raise TypeError("Only SOMs are allowed in this function!")
if config is None:
# Make mask file name from object information
instname = obj.attr_list.inst.get_name()
runnum = obj.attr_list["run_number"]
outfile = "%s_%s_mask.dat" % (instname, str(runnum))
else:
# Make mask file name from configuration information
outfile = hlr_utils.ext_replace(config.output, config.ext_replacement,
"dat")
outfile = hlr_utils.add_tag(outfile, "mask")
ofile = open(outfile, "w")
import SOM
import utils
len_obj = hlr_utils.get_length(obj)
for i in xrange(len_obj):
norm = hlr_utils.get_value(obj, i, o_descr)
if utils.compare(norm, lothreshold) <= 0 or \
utils.compare(norm, hithreshold) >= 0:
map_so = hlr_utils.get_map_so(obj, None, i)
pix_id = SOM.NeXusId.fromString(str(map_so.id)).toJoinedStr()
print >> ofile, pix_id
ofile.close()
def filter_normalization(obj, lothreshold, hithreshold, config=None):
"""
This function takes an object with normalization integration information
and a threshold and creates a mask file containing the pixel IDs that do
not make it above the threshold.
@param obj: The object containing the normalization information
@type obj: C{SOM.SOM}
@param lothreshold: The value below which a pixel will be masked.
@type lothreshold: C{float}
@param hithreshold: The value above which a pixel will be masked.
@type hithreshold: C{float}
@param config: The object holding the DR configuration
@type config: L{hlr_utils.Configure}
@raise TypeError: The incoming object is not a C{SOM}.
"""
import hlr_utils
o_descr = hlr_utils.get_descr(obj)
if o_descr != "SOM":
raise TypeError("Only SOMs are allowed in this function!")
if config is None:
# Make mask file name from object information
instname = obj.attr_list.inst.get_name()
runnum = obj.attr_list["run_number"]
outfile = "%s_%s_mask.dat" % (instname, str(runnum))
else:
# Make mask file name from configuration information
outfile = hlr_utils.ext_replace(config.output, config.ext_replacement, "dat")
outfile = hlr_utils.add_tag(outfile, "mask")
ofile = open(outfile, "w")
import SOM
import utils
len_obj = hlr_utils.get_length(obj)
for i in xrange(len_obj):
norm = hlr_utils.get_value(obj, i, o_descr)
if utils.compare(norm, lothreshold) <= 0 or utils.compare(norm, hithreshold) >= 0:
map_so = hlr_utils.get_map_so(obj, None, i)
pix_id = SOM.NeXusId.fromString(str(map_so.id)).toJoinedStr()
print >> ofile, pix_id
ofile.close()
def merge_roi_files(filelist, conf):
"""
This function takes a set of ROI files and combines them into a new ROI
file.
@param filelist: The set of ROI file names.
@type filelist: C{list}
@param conf: The object containing the current configuration.
@type conf: L{hlr_utils.Configure}
@return: The filename of the combined ROI
@rtype: C{string}
"""
import hlr_utils
# Get first set of pixel IDs
rfile = open(filelist[0], 'r')
roi_set = set([rid.strip() for rid in rfile])
rfile.close()
# Merge each of the other sets of pixel IDs
for filename in filelist[1:]:
rfile = open(filename, 'r')
for rid in rfile:
roi_set.add(rid.strip())
rfile.close()
# Create output filename
import os
if conf.path_replacement is None:
path_replacement = os.getcwd()
else:
path_replacement = conf.path_replacement
ofilename = os.path.join(path_replacement, os.path.basename(filelist[0]))
ofilename = hlr_utils.add_tag(ofilename, "comb")
# Create new ROI file from combined information
ofile = open(ofilename, 'w')
for rid in roi_set:
print >> ofile, rid
ofile.close()
return ofilename
def merge_roi_files(filelist, conf):
"""
This function takes a set of ROI files and combines them into a new ROI
file.
@param filelist: The set of ROI file names.
@type filelist: C{list}
@param conf: The object containing the current configuration.
@type conf: L{hlr_utils.Configure}
@return: The filename of the combined ROI
@rtype: C{string}
"""
import hlr_utils
# Get first set of pixel IDs
rfile = open(filelist[0], 'r')
roi_set = set([rid.strip() for rid in rfile])
rfile.close()
# Merge each of the other sets of pixel IDs
for filename in filelist[1:]:
rfile = open(filename, 'r')
for rid in rfile:
roi_set.add(rid.strip())
rfile.close()
# Create output filename
import os
if conf.path_replacement is None:
path_replacement = os.getcwd()
else:
path_replacement = conf.path_replacement
ofilename = os.path.join(path_replacement, os.path.basename(filelist[0]))
ofilename = hlr_utils.add_tag(ofilename, "comb")
# Create new ROI file from combined information
ofile = open(ofilename, 'w')
for rid in roi_set:
print >> ofile, rid
ofile.close()
return ofilename
def write_file(filename, dst_type, data, **kwargs):
"""
This function performs the steps necessary to write an output file. One
can pass a data filename or an output filename. If a data filename is
passed, the data file extension, output file extension and the replace
keyword must be passed. The expected data object to write to the file is
a C{SOM}. B{NOTE}: Extra keyword arguments can be passed onto the C{DST}
instance via calling them in the kwargs list. Those arguments will not be
processed by this function, but just pass them on.
@param filename: The name of the data file from which the output is
generated or the name of an output file
@type filename: C{string}
@param dst_type: The MIME type of the output formatter
@type dst_type: C{string}
@param data: Object that contains the output to be written to file
@type data: C{SOM.SOM}
@param kwargs: A list of keyword arguments that the function accepts:
@keyword message: This is part of the message that will be printed to
STDOUT if verbose keyword is set to True. The default
message is \"output file\"
@type message: C{string}
@keyword data_ext: This is the extension on the data file. This is used in
conjunction with output_ext and replace to convert the
data filename into an output filename. The default
value is \"nxs\".
@type data_ext: C{string}
@keyword output_ext: This is the extension to be used for the output file.
The default value is \"txt\".
@type output_ext: C{string}
@keyword verbose: This determines whether or not the print statement is
executed. The default value is I{False}.
@type verbose: C{boolean}
@keyword replace_ext: This determines whether or not the extension on the
incoming filename is replaced with output_ext. The
default behavior is I{True} (replace extension)
@type replace_ext: C{boolean}
@keyword replace_path: This determines whether or not the directory path on
the incoming filename is replaced with the
directory where the driver is running. The default
behavior is I{True} (replace path)
@type replace_path: C{boolean}
@keyword path_replacement: This is a directory path that will be prepended
to the output filename. The default value is
C{None} and will cause the working directory to
be the prepended path.
@type path_replacement: C{string}
@keyword extra_tag: This is a tag that will be inserted into the file name
just before the file extension.
@type extra_tag: C{string}
@keyword getsom_kwargs: This is a collection of keyword arguments that
are to be passed to the writeSOM function call.
@type getsom_kwargs: C{dict}
"""
import os
import DST
import hlr_utils
try:
message = kwargs["message"]
except KeyError:
message = "output file"
try:
data_ext = kwargs["data_ext"]
except KeyError:
data_ext = "nxs"
try:
output_ext = kwargs["output_ext"]
except KeyError:
output_ext = "txt"
try:
verbose = kwargs["verbose"]
except KeyError:
verbose = False
try:
replace_path = kwargs["replace_path"]
except KeyError:
replace_path = True
try:
path_replacement = kwargs["path_replacement"]
except KeyError:
path_replacement = None
try:
replace_ext = kwargs["replace_ext"]
except KeyError:
replace_ext = True
try:
extra_tag = kwargs["extra_tag"]
except KeyError:
extra_tag = None
try:
arguments = kwargs["arguments"]
except KeyError:
arguments = None
getsom_kwargs = kwargs.get("getsom_kwargs", {})
if replace_path:
if path_replacement is None:
path_replacement = os.getcwd()
fixed_filename = os.path.join(path_replacement,
os.path.basename(filename))
else:
fixed_filename = filename
if replace_ext:
fixed_filename = hlr_utils.ext_replace(fixed_filename, data_ext,
output_ext)
else:
pass
if extra_tag is not None:
fixed_filename = hlr_utils.add_tag(fixed_filename, extra_tag)
# Handle difference between NeXus and other files
if dst_type != "application/x-RedNxs":
resource = open(fixed_filename, "w")
else:
resource = fixed_filename
output_dst = DST.getInstance(dst_type, resource, arguments, **kwargs)
if verbose:
print "Writing %s" % message
output_dst.writeSOM(data, **getsom_kwargs)
output_dst.release_resource()