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()
if options.data is not None:
configure.data = hlr_utils.fix_filename(options.data)
if not hlr_utils.file_exists(configure.data):
parser.error("Data file [%s] does not exist" % configure.data)
else:
parser.error("Did not specify a datafile")
# create the output file name if there isn't one supplied
if options.output:
configure.output = hlr_utils.fix_filename(options.output)
print "Using %s as output file" % configure.output
else:
configure.output = None
outfile = os.path.basename(configure.data)
path = os.path.join(os.getcwd(), outfile)
if options.d_bins is not None:
configure.output_ds = hlr_utils.ext_replace(path, "nxs", "ds1")
print "Using %s as output file" % configure.output_ds
else:
configure.output_ds = None
if options.tof_bins is not None:
configure.output_tof = hlr_utils.ext_replace(path, "nxs", "gs")
print "Using %s as output file" % configure.output_tof
else:
configure.output_tof = None
if options.Q_bins is not None:
configure.output_qt = hlr_utils.ext_replace(path, "nxs", "qt1")
print "Using %s as output file" % configure.output_qt
else:
configure.output_qt = None
def BasicConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{BasicOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.BasicOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{BasicOptions}
@type options: C{Option}
@param args: The parsed arguments from C{BasicOptions}
@type args: C{list}
"""
# Set from a configuration file first
if options.config is not None:
import xml.dom.minidom
conf_doc = xml.dom.minidom.parse(options.config)
configure = hlr_utils.ConfigFromXml(conf_doc, configure)
# Now override options provided on command-line
# Set the verbosity, if present on command-line
if not configure.verbose:
configure.verbose = options.verbose
else:
# Got the verbosity from the config file, but check CLI
if hlr_utils.cli_checker("-v", "-q"):
# Override option
configure.verbose = options.verbose
else:
# No flags present, do nothing
pass
# Define instrument short name first as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "inst", "--inst"):
configure.inst = options.inst
# Define facility short name as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "facility", "--facility"):
configure.facility = options.facility
# Define proposal as stuff below depends on it.
if hlr_utils.cli_provide_override(configure, "proposal", "--proposal"):
configure.proposal = options.proposal
# Get the datafile name and check it
if options.data is not None:
configure.data = hlr_utils.determine_files(options.data,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif len(args) > 0:
configure.data = hlr_utils.determine_files(args,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif configure.data:
# We have data from the config file, so everything is OK.
pass
else:
parser.error("Did not specify a datafile")
import os
# Deal with file or directory from output option
if options.output:
filepath = hlr_utils.fix_filename(options.output)
if os.path.exists(filepath):
if os.path.isdir(filepath):
outfile = os.path.basename(configure.data[0])
path = os.path.join(filepath, outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = filepath
configure.ext_replacement = "txt"
elif os.path.isfile(filepath):
configure.output = filepath
configure.path_replacement = os.path.dirname(filepath)
configure.ext_replacement = filepath.split('.')[-1]
else:
parser.error("Cannot handle %s in output option" % filepath)
else:
# Assume that this is a file and hope that the directory exists
directory = os.path.dirname(filepath)
if directory != "":
if not os.path.exists(directory):
raise RuntimeError("The directory %s must exist!" \
% directory)
else:
pass
else:
directory = None
configure.output = filepath
configure.path_replacement = directory
configure.ext_replacement = filepath.split('.')[-1]
elif configure.output:
# We have an output file, so no need to do anything else
try:
configure.path_replacement
except AttributeError:
configure.path_replacement = None
# Create the output file name if there isn't one supplied
else:
outfile = os.path.basename(configure.data[0])
path = os.path.join(os.getcwd(), outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = None
configure.ext_replacement = "txt"
if configure.verbose and options.output:
print "Using %s as output file" % configure.output
def BasicConfiguration(parser, configure, options, args):
"""
This function sets the incoming C{Configure} object with all the options
that have been specified via the C{BasicOptions} object.
@param parser: The parser object
@type parser: L{hlr_utils.BasicOptions}
@param configure: The configuration object
@type configure: L{hlr_utils.Configure}
@param options: The parsed options from C{BasicOptions}
@type options: C{Option}
@param args: The parsed arguments from C{BasicOptions}
@type args: C{list}
"""
# Set from a configuration file first
if options.config is not None:
import xml.dom.minidom
conf_doc = xml.dom.minidom.parse(options.config)
configure = hlr_utils.ConfigFromXml(conf_doc, configure)
# Now override options provided on command-line
# Set the verbosity, if present on command-line
if not configure.verbose:
configure.verbose = options.verbose
else:
# Got the verbosity from the config file, but check CLI
if hlr_utils.cli_checker("-v", "-q"):
# Override option
configure.verbose = options.verbose
else:
# No flags present, do nothing
pass
# Define instrument short name first as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "inst", "--inst"):
configure.inst = options.inst
# Define facility short name as stuff below depends on it
if hlr_utils.cli_provide_override(configure, "facility", "--facility"):
configure.facility = options.facility
# Define proposal as stuff below depends on it.
if hlr_utils.cli_provide_override(configure, "proposal", "--proposal"):
configure.proposal = options.proposal
# Get the datafile name and check it
if options.data is not None:
configure.data = hlr_utils.determine_files(options.data,
configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif len(args) > 0:
configure.data = hlr_utils.determine_files(args, configure.inst,
configure.facility,
configure.proposal,
stop_on_none=True)
elif configure.data:
# We have data from the config file, so everything is OK.
pass
else:
parser.error("Did not specify a datafile")
import os
# Deal with file or directory from output option
if options.output:
filepath = hlr_utils.fix_filename(options.output)
if os.path.exists(filepath):
if os.path.isdir(filepath):
outfile = os.path.basename(configure.data[0])
path = os.path.join(filepath, outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = filepath
configure.ext_replacement = "txt"
elif os.path.isfile(filepath):
configure.output = filepath
configure.path_replacement = os.path.dirname(filepath)
configure.ext_replacement = filepath.split('.')[-1]
else:
parser.error("Cannot handle %s in output option" % filepath)
else:
# Assume that this is a file and hope that the directory exists
directory = os.path.dirname(filepath)
if directory != "":
if not os.path.exists(directory):
raise RuntimeError("The directory %s must exist!" \
% directory)
else:
pass
else:
directory = None
configure.output = filepath
configure.path_replacement = directory
configure.ext_replacement = filepath.split('.')[-1]
elif configure.output:
# We have an output file, so no need to do anything else
try:
configure.path_replacement
except AttributeError:
configure.path_replacement = None
# Create the output file name if there isn't one supplied
else:
outfile = os.path.basename(configure.data[0])
path = os.path.join(os.getcwd(), outfile)
configure.output = hlr_utils.ext_replace(path, "nxs", "txt")
configure.path_replacement = None
configure.ext_replacement = "txt"
if configure.verbose and options.output:
print "Using %s as output file" % configure.output
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()
if options.data is not None:
configure.data = hlr_utils.fix_filename(options.data)
if not hlr_utils.file_exists(configure.data):
parser.error("Data file [%s] does not exist" % configure.data)
else:
parser.error("Did not specify a datafile")
# create the output file name if there isn't one supplied
if options.output:
configure.output = hlr_utils.fix_filename(options.output)
print "Using %s as output file" % configure.output
else:
configure.output = None
outfile = os.path.basename(configure.data)
path = os.path.join(os.getcwd(), outfile)
if options.d_bins is not None:
configure.output_ds = hlr_utils.ext_replace(path, "nxs", "ds1")
print "Using %s as output file" % configure.output_ds
else:
configure.output_ds = None
if options.tof_bins is not None:
configure.output_tof = hlr_utils.ext_replace(path, "nxs", "gs")
print "Using %s as output file" % configure.output_tof
else:
configure.output_tof = None
if options.Q_bins is not None:
configure.output_qt = hlr_utils.ext_replace(path, "nxs", "qt1")
print "Using %s as output file" % configure.output_qt
else:
configure.output_qt = None
