"""
CanSAS data reader - new recursive cansas_version.
"""
############################################################################
#This software was developed by the University of Tennessee as part of the
#Distributed Data Analysis of Neutron Scattering Experiments (DANSE)
#project funded by the US National Science Foundation.
#If you use DANSE applications to do scientific research that leads to
#publication, we ask that you acknowledge the use of the software with the
#following sentence:
#This work benefited from DANSE software developed under NSF award DMR-0520547.
#copyright 2008,2009 University of Tennessee
#############################################################################
import logging
import numpy
import os
import sys
import datetime
import inspect
# For saving individual sections of data
from sas.dataloader.data_info import Data1D
from sas.dataloader.data_info import Collimation
from sas.dataloader.data_info import TransmissionSpectrum
from sas.dataloader.data_info import Detector
from sas.dataloader.data_info import Process
from sas.dataloader.data_info import Aperture
# Both imports used. Do not remove either.
from xml.dom.minidom import parseString
import sas.dataloader.readers.xml_reader as xml_reader
from sas.dataloader.readers.xml_reader import XMLreader
from sas.dataloader.readers.cansas_constants import CansasConstants
_ZERO = 1e-16
PREPROCESS = "xmlpreprocess"
ENCODING = "encoding"
RUN_NAME_DEFAULT = "None"
HAS_CONVERTER = True
try:
from sas.data_util.nxsunit import Converter
except ImportError:
HAS_CONVERTER = False
CONSTANTS = CansasConstants()
CANSAS_FORMAT = CONSTANTS.format
CANSAS_NS = CONSTANTS.names
ALLOW_ALL = True
# minidom used in functions called by outside classes
import xml.dom.minidom
# DO NOT REMOVE
# Called by outside packages:
# sas.perspectives.invariant.invariant_state
# sas.perspectives.fitting.pagestate
[docs]def get_content(location, node):
"""
Get the first instance of the content of a xpath location.
:param location: xpath location
:param node: node to start at
:return: Element, or None
"""
nodes = node.xpath(location,
namespaces={'ns': CANSAS_NS.get("1.0").get("ns")})
if len(nodes) > 0:
return nodes[0]
else:
return None
# DO NOT REMOVE
# Called by outside packages:
# sas.perspectives.fitting.pagestate
[docs]def write_node(doc, parent, name, value, attr=None):
"""
:param doc: document DOM
:param parent: parent node
:param name: tag of the element
:param value: value of the child text node
:param attr: attribute dictionary
:return: True if something was appended, otherwise False
"""
if attr is None:
attr = {}
if value is not None:
node = doc.createElement(name)
node.appendChild(doc.createTextNode(str(value)))
for item in attr:
node.setAttribute(item, attr[item])
parent.appendChild(node)
return True
return False
[docs]class Reader(XMLreader):
"""
Class to load cansas 1D XML files
:Dependencies:
The CanSAS reader requires PyXML 0.8.4 or later.
"""
##CanSAS version - defaults to version 1.0
cansas_version = "1.0"
base_ns = "{cansas1d/1.0}"
logging = []
errors = []
type_name = "canSAS"
## Wildcards
type = ["XML files (*.xml)|*.xml", "SasView Save Files (*.svs)|*.svs"]
## List of allowed extensions
ext = ['.xml', '.XML', '.svs', '.SVS']
## Flag to bypass extension check
allow_all = True
def __init__(self):
## List of errors
self.errors = []
self.encoding = None
[docs] def is_cansas(self, ext="xml"):
"""
Checks to see if the xml file is a CanSAS file
:param ext: The file extension of the data file
"""
if self.validate_xml():
name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
value = self.xmlroot.get(name)
if CANSAS_NS.get(self.cansas_version).get("ns") == \
value.rsplit(" ")[0]:
return True
if ext == "svs":
return True
return False
[docs] def load_file_and_schema(self, xml_file):
"""
Loads the file and associates a schema, if a known schema exists
:param xml_file: The xml file path sent to Reader.read
"""
base_name = xml_reader.__file__
base_name = base_name.replace("\\","/")
base = base_name.split("/sas/")[0]
# Load in xml file and get the cansas version from the header
self.set_xml_file(xml_file)
self.cansas_version = self.xmlroot.get("version", "1.0")
# Generic values for the cansas file based on the version
cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
schema_path = "{0}/sas/dataloader/readers/schema/{1}".format\
(base, cansas_defaults.get("schema")).replace("\\", "/")
# Link a schema to the XML file.
self.set_schema(schema_path)
return cansas_defaults
[docs] def read(self, xml_file):
"""
Validate and read in an xml_file file in the canSAS format.
:param xml_file: A canSAS file path in proper XML format
"""
# output - Final list of Data1D objects
output = []
# ns - Namespace hierarchy for current xml_file object
ns_list = []
# Check that the file exists
if os.path.isfile(xml_file):
basename = os.path.basename(xml_file)
_, extension = os.path.splitext(basename)
# If the file type is not allowed, return nothing
if extension in self.ext or self.allow_all:
# Get the file location of
cansas_defaults = self.load_file_and_schema(xml_file)
# Try to load the file, but raise an error if unable to.
# Check the file matches the XML schema
try:
if self.is_cansas(extension):
# Get each SASentry from XML file and add it to a list.
entry_list = self.xmlroot.xpath(
'/ns:SASroot/ns:SASentry',
namespaces = {'ns': cansas_defaults.get("ns")})
ns_list.append("SASentry")
# If multiple files, modify the name for each is unique
increment = 0
# Parse each SASentry item
for entry in entry_list:
# Define a new Data1D object with zeroes for
# x_vals and y_vals
data1d = Data1D(numpy.empty(0), numpy.empty(0), \
numpy.empty(0), numpy.empty(0))
data1d.dxl = numpy.empty(0)
data1d.dxw = numpy.empty(0)
# If more than one SASentry, increment each in order
name = basename
if len(entry_list) - 1 > 0:
name += "_{0}".format(increment)
increment += 1
# Set the Data1D name and then parse the entry.
# The entry is appended to a list of entry values
data1d.filename = name
data1d.meta_data["loader"] = "CanSAS 1D"
# Get all preprocessing events and encoding
self.set_processing_instructions()
data1d.meta_data[PREPROCESS] = \
self.processing_instructions
# Parse the XML file
return_value, extras = \
self._parse_entry(entry, ns_list, data1d)
del extras[:]
return_value = self._final_cleanup(return_value)
output.append(return_value)
else:
output.append("Invalid XML at: {0}".format(\
self.find_invalid_xml()))
except:
# If the file does not match the schema, raise this error
raise RuntimeError, "%s cannot be read" % xml_file
return output
# Return a list of parsed entries that dataloader can manage
return None
def _final_cleanup(self, data1d):
"""
Final cleanup of the Data1D object to be sure it has all the
appropriate information needed for perspectives
:param data1d: Data1D object that has been populated
"""
# Final cleanup
# Remove empty nodes, verify array sizes are correct
for error in self.errors:
data1d.errors.append(error)
del self.errors[:]
numpy.trim_zeros(data1d.x)
numpy.trim_zeros(data1d.y)
numpy.trim_zeros(data1d.dy)
size_dx = data1d.dx.size
size_dxl = data1d.dxl.size
size_dxw = data1d.dxw.size
if size_dxl == 0 and size_dxw == 0:
data1d.dxl = None
data1d.dxw = None
numpy.trim_zeros(data1d.dx)
elif size_dx == 0:
data1d.dx = None
size_dx = size_dxl
numpy.trim_zeros(data1d.dxl)
numpy.trim_zeros(data1d.dxw)
return data1d
def _create_unique_key(self, dictionary, name, numb = 0):
"""
Create a unique key value for any dictionary to prevent overwriting
Recurses until a unique key value is found.
:param dictionary: A dictionary with any number of entries
:param name: The index of the item to be added to dictionary
:param numb: The number to be appended to the name, starts at 0
"""
if dictionary.get(name) is not None:
numb += 1
name = name.split("_")[0]
name += "_{0}".format(numb)
name = self._create_unique_key(dictionary, name, numb)
return name
def _unit_conversion(self, node, new_current_level, data1d, \
tagname, node_value):
"""
A unit converter method used to convert the data included in the file
to the default units listed in data_info
:param new_current_level: cansas_constants level as returned by
iterate_namespace
:param attr: The attributes of the node
:param data1d: Where the values will be saved
:param node_value: The value of the current dom node
"""
attr = node.attrib
value_unit = ''
if 'unit' in attr and new_current_level.get('unit') is not None:
try:
if isinstance(node_value, float) is False:
exec("node_value = float({0})".format(node_value))
default_unit = None
unitname = new_current_level.get("unit")
exec "default_unit = data1d.{0}".format(unitname)
local_unit = attr['unit']
if local_unit.lower() != default_unit.lower() and \
local_unit is not None and local_unit.lower() != "none" \
and default_unit is not None:
if HAS_CONVERTER == True:
try:
## Check local units - bad units raise KeyError
Converter(local_unit)
data_conv_q = Converter(attr['unit'])
value_unit = default_unit
i_string = "node_value = data_conv_q"
i_string += "(node_value, units=data1d.{0})"
exec i_string.format(unitname)
except KeyError:
err_msg = "CanSAS reader: could not convert "
err_msg += "{0} unit {1}; "
err_msg = err_msg.format(tagname, local_unit)
intermediate = "err_msg += " + \
"\"expecting [{1}] {2}\"" + \
".format(data1d.{0}, " + \
"sys.exc_info()[1])"
exec intermediate.format(unitname, "{0}", "{1}")
self.errors.append(err_msg)
raise ValueError(err_msg)
except:
err_msg = \
"CanSAS reader: could not convert the units"
self.errors.append(err_msg)
return
else:
value_unit = local_unit
err_msg = "CanSAS reader: unrecognized %s unit [%s];"\
% (node_value, default_unit)
err_msg += " expecting [%s]" % local_unit
self.errors.append(err_msg)
raise ValueError, err_msg
else:
value_unit = local_unit
except:
err_msg = "CanSAS reader: could not convert "
err_msg += "Q unit [%s]; " % attr['unit']
intermediate = "err_msg += \"expecting [%s]\n %s\" % " + \
"(data1d.{0}, sys.exc_info()[1])"
exec intermediate.format(unitname)
self.errors.append(err_msg)
raise ValueError, err_msg
elif 'unit' in attr:
value_unit = attr['unit']
node_value = "float({0})".format(node_value)
return node_value, value_unit
def _check_for_empty_data(self, data1d):
"""
Creates an empty data set if no data is passed to the reader
:param data1d: presumably a Data1D object
"""
if data1d == None:
self.errors = []
x_vals = numpy.empty(0)
y_vals = numpy.empty(0)
dx_vals = numpy.empty(0)
dy_vals = numpy.empty(0)
dxl = numpy.empty(0)
dxw = numpy.empty(0)
data1d = Data1D(x_vals, y_vals, dx_vals, dy_vals)
data1d.dxl = dxl
data1d.dxw = dxw
return data1d
def _handle_special_cases(self, tagname, data1d, children):
"""
Handle cases where the data type in Data1D is a dictionary or list
:param tagname: XML tagname in use
:param data1d: The original Data1D object
:param children: Child nodes of node
:param node: existing node with tag name 'tagname'
"""
if tagname == "SASdetector":
data1d = Detector()
elif tagname == "SAScollimation":
data1d = Collimation()
elif tagname == "SAStransmission_spectrum":
data1d = TransmissionSpectrum()
elif tagname == "SASprocess":
data1d = Process()
for child in children:
if child.tag.replace(self.base_ns, "") == "term":
term_attr = {}
for attr in child.keys():
term_attr[attr] = \
' '.join(child.get(attr).split())
if child.text is not None:
term_attr['value'] = \
' '.join(child.text.split())
data1d.term.append(term_attr)
elif tagname == "aperture":
data1d = Aperture()
if tagname == "Idata" and children is not None:
data1d = self._check_for_empty_resolution(data1d, children)
return data1d
def _check_for_empty_resolution(self, data1d, children):
"""
A method to check all resolution data sets are the same size as I and Q
"""
dql_exists = False
dqw_exists = False
dq_exists = False
di_exists = False
for child in children:
tag = child.tag.replace(self.base_ns, "")
if tag == "dQl":
dql_exists = True
if tag == "dQw":
dqw_exists = True
if tag == "Qdev":
dq_exists = True
if tag == "Idev":
di_exists = True
if dqw_exists and dql_exists == False:
data1d.dxl = numpy.append(data1d.dxl, 0.0)
elif dql_exists and dqw_exists == False:
data1d.dxw = numpy.append(data1d.dxw, 0.0)
elif dql_exists == False and dqw_exists == False \
and dq_exists == False:
data1d.dx = numpy.append(data1d.dx, 0.0)
if di_exists == False:
data1d.dy = numpy.append(data1d.dy, 0.0)
return data1d
def _restore_original_case(self,
tagname_original,
tagname,
save_data1d,
data1d):
"""
Save the special case data to the appropriate location and restore
the original Data1D object
:param tagname_original: Unmodified tagname for the node
:param tagname: modified tagname for the node
:param save_data1d: The original Data1D object
:param data1d: If a special case was handled, an object of that type
"""
if tagname_original == "SASdetector":
save_data1d.detector.append(data1d)
elif tagname_original == "SAScollimation":
save_data1d.collimation.append(data1d)
elif tagname == "SAStransmission_spectrum":
save_data1d.trans_spectrum.append(data1d)
elif tagname_original == "SASprocess":
save_data1d.process.append(data1d)
elif tagname_original == "aperture":
save_data1d.aperture.append(data1d)
else:
save_data1d = data1d
return save_data1d
def _handle_attributes(self, node, data1d, cs_values, tagname):
"""
Process all of the attributes for a node
"""
attr = node.attrib
if attr is not None:
for key in node.keys():
try:
node_value, unit = self._get_node_value(node, cs_values, \
data1d, tagname)
cansas_attrib = \
cs_values.current_level.get("attributes").get(key)
attrib_variable = cansas_attrib.get("variable")
if key == 'unit' and unit != '':
attrib_value = unit
else:
attrib_value = node.attrib[key]
store_attr = attrib_variable.format("data1d", \
attrib_value, key)
exec store_attr
except AttributeError:
pass
return data1d
def _get_node_value(self, node, cs_values, data1d, tagname):
"""
Get the value of a node and any applicable units
:param node: The XML node to get the value of
:param cs_values: A CansasConstants.CurrentLevel object
:param attr: The node attributes
:param dataid: The working object to be modified
:param tagname: The tagname of the node
"""
#Get the text from the node and convert all whitespace to spaces
units = ''
node_value = node.text
if node_value == "":
node_value = None
if node_value is not None:
node_value = ' '.join(node_value.split())
# If the value is a float, compile with units.
if cs_values.ns_datatype == "float":
# If an empty value is given, set as zero.
if node_value is None or node_value.isspace() \
or node_value.lower() == "nan":
node_value = "0.0"
#Convert the value to the base units
node_value, units = self._unit_conversion(node, \
cs_values.current_level, data1d, tagname, node_value)
# If the value is a timestamp, convert to a datetime object
elif cs_values.ns_datatype == "timestamp":
if node_value is None or node_value.isspace():
pass
else:
try:
node_value = \
datetime.datetime.fromtimestamp(node_value)
except ValueError:
node_value = None
return node_value, units
def _parse_entry(self, dom, names=None, data1d=None, extras=None):
"""
Parse a SASEntry - new recursive method for parsing the dom of
the CanSAS data format. This will allow multiple data files
and extra nodes to be read in simultaneously.
:param dom: dom object with a namespace base of names
:param names: A list of element names that lead up to the dom object
:param data1d: The data1d object that will be modified
:param extras: Any values that should go into meta_data when data1d
is not a Data1D object
"""
if extras is None:
extras = []
if names is None or names == []:
names = ["SASentry"]
data1d = self._check_for_empty_data(data1d)
self.base_ns = "{0}{1}{2}".format("{", \
CANSAS_NS.get(self.cansas_version).get("ns"), "}")
tagname = ''
tagname_original = ''
# Go through each child in the parent element
for node in dom:
try:
# Get the element name and set the current names level
tagname = node.tag.replace(self.base_ns, "")
tagname_original = tagname
if tagname == "fitting_plug_in" or tagname == "pr_inversion" or\
tagname == "invariant":
continue
names.append(tagname)
children = node.getchildren()
if len(children) == 0:
children = None
save_data1d = data1d
# Look for special cases
data1d = self._handle_special_cases(tagname, data1d, children)
# Get where to store content
cs_values = CONSTANTS.iterate_namespace(names)
# If the element is a child element, recurse
if children is not None:
# Returned value is new Data1D object with all previous and
# new values in it.
data1d, extras = self._parse_entry(node,
names, data1d, extras)
#Get the information from the node
node_value, _ = self._get_node_value(node, cs_values, \
data1d, tagname)
# If appending to a dictionary (meta_data | run_name)
# make sure the key is unique
if cs_values.ns_variable == "{0}.meta_data[\"{2}\"] = \"{1}\"":
# If we are within a Process, Detector, Collimation or
# Aperture instance, pull out old data1d
tagname = self._create_unique_key(data1d.meta_data, \
tagname, 0)
if isinstance(data1d, Data1D) == False:
store_me = cs_values.ns_variable.format("data1d", \
node_value, tagname)
extras.append(store_me)
cs_values.ns_variable = None
if cs_values.ns_variable == "{0}.run_name[\"{2}\"] = \"{1}\"":
tagname = self._create_unique_key(data1d.run_name, \
tagname, 0)
# Check for Data1D object and any extra commands to save
if isinstance(data1d, Data1D):
for item in extras:
exec item
# Don't bother saving empty information unless it is a float
if cs_values.ns_variable is not None and \
node_value is not None and \
node_value.isspace() == False:
# Format a string and then execute it.
store_me = cs_values.ns_variable.format("data1d", \
node_value, tagname)
exec store_me
# Get attributes and process them
data1d = self._handle_attributes(node, data1d, cs_values, \
tagname)
except TypeError:
pass
except Exception as excep:
exc_type, exc_obj, exc_tb = sys.exc_info()
fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]
print(excep, exc_type, fname, exc_tb.tb_lineno, \
tagname, exc_obj)
finally:
# Save special cases in original data1d object
# then restore the data1d
save_data1d = self._restore_original_case(tagname_original, \
tagname, save_data1d, data1d)
if tagname_original == "fitting_plug_in" or \
tagname_original == "invariant" or \
tagname_original == "pr_inversion":
pass
else:
data1d = save_data1d
# Remove tagname from names to restore original base
names.remove(tagname_original)
return data1d, extras
def _get_pi_string(self):
"""
Creates the processing instructions header for writing to file
"""
pis = self.return_processing_instructions()
if len(pis) > 0:
pi_tree = self.create_tree(pis[0])
i = 1
for i in range(1, len(pis) - 1):
pi_tree = self.append(pis[i], pi_tree)
pi_string = self.to_string(pi_tree)
else:
pi_string = ""
return pi_string
def _create_main_node(self):
"""
Creates the primary xml header used when writing to file
"""
xsi = "http://www.w3.org/2001/XMLSchema-instance"
version = self.cansas_version
n_s = CANSAS_NS.get(version).get("ns")
if version == "1.1":
url = "http://www.cansas.org/formats/1.1/"
else:
url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/"
schema_location = "{0} {1}cansas1d.xsd".format(n_s, url)
attrib = {"{" + xsi + "}schemaLocation" : schema_location,
"version" : version}
nsmap = {'xsi' : xsi, None: n_s}
main_node = self.create_element("{" + n_s + "}SASroot", \
attrib = attrib, \
nsmap = nsmap)
return main_node
def _write_run_names(self, datainfo, entry_node):
"""
Writes the run names to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
if datainfo.run == None or datainfo.run == []:
datainfo.run.append(RUN_NAME_DEFAULT)
datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT
for item in datainfo.run:
runname = {}
if item in datainfo.run_name and \
len(str(datainfo.run_name[item])) > 1:
runname = {'name': datainfo.run_name[item]}
self.write_node(entry_node, "Run", item, runname)
def _write_data(self, datainfo, entry_node):
"""
Writes the I and Q data to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
node = self.create_element("SASdata")
self.append(node, entry_node)
for i in range(len(datainfo.x)):
point = self.create_element("Idata")
node.append(point)
self.write_node(point, "Q", datainfo.x[i], \
{'unit': datainfo.x_unit})
if len(datainfo.y) >= i:
self.write_node(point, "I", datainfo.y[i],
{'unit': datainfo.y_unit})
if datainfo.dy != None and len(datainfo.dy) > i:
self.write_node(point, "Idev", datainfo.dy[i],
{'unit': datainfo.y_unit})
if datainfo.dx != None and len(datainfo.dx) > i:
self.write_node(point, "Qdev", datainfo.dx[i],
{'unit': datainfo.x_unit})
if datainfo.dxw != None and len(datainfo.dxw) > i:
self.write_node(point, "dQw", datainfo.dxw[i],
{'unit': datainfo.x_unit})
if datainfo.dxl != None and len(datainfo.dxl) > i:
self.write_node(point, "dQl", datainfo.dxl[i],
{'unit': datainfo.x_unit})
def _write_trans_spectrum(self, datainfo, entry_node):
"""
Writes the transmission spectrum data to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
for i in range(len(datainfo.trans_spectrum)):
spectrum = datainfo.trans_spectrum[i]
node = self.create_element("SAStransmission_spectrum",
{"name" : spectrum.name})
self.append(node, entry_node)
if isinstance(spectrum.timestamp, datetime.datetime):
node.setAttribute("timestamp", spectrum.timestamp)
for i in range(len(spectrum.wavelength)):
point = self.create_element("Tdata")
node.append(point)
self.write_node(point, "Lambda", spectrum.wavelength[i],
{'unit': spectrum.wavelength_unit})
self.write_node(point, "T", spectrum.transmission[i],
{'unit': spectrum.transmission_unit})
if spectrum.transmission_deviation != None \
and len(spectrum.transmission_deviation) >= i:
self.write_node(point, "Tdev", \
spectrum.transmission_deviation[i], \
{'unit': spectrum.transmission_deviation_unit})
def _write_sample_info(self, datainfo, entry_node):
"""
Writes the sample information to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
sample = self.create_element("SASsample")
if datainfo.sample.name is not None:
self.write_attribute(sample,
"name",
str(datainfo.sample.name))
self.append(sample, entry_node)
self.write_node(sample, "ID", str(datainfo.sample.ID))
self.write_node(sample, "thickness", datainfo.sample.thickness,
{"unit": datainfo.sample.thickness_unit})
self.write_node(sample, "transmission", datainfo.sample.transmission)
self.write_node(sample, "temperature", datainfo.sample.temperature,
{"unit": datainfo.sample.temperature_unit})
pos = self.create_element("position")
written = self.write_node(pos,
"x",
datainfo.sample.position.x,
{"unit": datainfo.sample.position_unit})
written = written | self.write_node(pos,
"y",
datainfo.sample.position.y,
{"unit": datainfo.sample.position_unit})
written = written | self.write_node(pos,
"z",
datainfo.sample.position.z,
{"unit": datainfo.sample.position_unit})
if written == True:
self.append(pos, sample)
ori = self.create_element("orientation")
written = self.write_node(ori, "roll",
datainfo.sample.orientation.x,
{"unit": datainfo.sample.orientation_unit})
written = written | self.write_node(ori, "pitch",
datainfo.sample.orientation.y,
{"unit": datainfo.sample.orientation_unit})
written = written | self.write_node(ori, "yaw",
datainfo.sample.orientation.z,
{"unit": datainfo.sample.orientation_unit})
if written == True:
self.append(ori, sample)
for item in datainfo.sample.details:
self.write_node(sample, "details", item)
def _write_instrument(self, datainfo, entry_node):
"""
Writes the instrumental information to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
instr = self.create_element("SASinstrument")
self.append(instr, entry_node)
self.write_node(instr, "name", datainfo.instrument)
return instr
def _write_source(self, datainfo, instr):
"""
Writes the source information to the XML file
:param datainfo: The Data1D object the information is coming from
:param instr: instrument node to be appended to
"""
source = self.create_element("SASsource")
if datainfo.source.name is not None:
self.write_attribute(source,
"name",
str(datainfo.source.name))
self.append(source, instr)
if datainfo.source.radiation == None or datainfo.source.radiation == '':
datainfo.source.radiation = "neutron"
self.write_node(source, "radiation", datainfo.source.radiation)
size = self.create_element("beam_size")
if datainfo.source.beam_size_name is not None:
self.write_attribute(size,
"name",
str(datainfo.source.beam_size_name))
written = self.write_node(size, "x", datainfo.source.beam_size.x,
{"unit": datainfo.source.beam_size_unit})
written = written | self.write_node(size, "y",
datainfo.source.beam_size.y,
{"unit": datainfo.source.beam_size_unit})
written = written | self.write_node(size, "z",
datainfo.source.beam_size.z,
{"unit": datainfo.source.beam_size_unit})
if written == True:
self.append(size, source)
self.write_node(source, "beam_shape", datainfo.source.beam_shape)
self.write_node(source, "wavelength",
datainfo.source.wavelength,
{"unit": datainfo.source.wavelength_unit})
self.write_node(source, "wavelength_min",
datainfo.source.wavelength_min,
{"unit": datainfo.source.wavelength_min_unit})
self.write_node(source, "wavelength_max",
datainfo.source.wavelength_max,
{"unit": datainfo.source.wavelength_max_unit})
self.write_node(source, "wavelength_spread",
datainfo.source.wavelength_spread,
{"unit": datainfo.source.wavelength_spread_unit})
def _write_collimation(self, datainfo, instr):
"""
Writes the collimation information to the XML file
:param datainfo: The Data1D object the information is coming from
:param instr: lxml node ElementTree object to be appended to
"""
if datainfo.collimation == [] or datainfo.collimation == None:
coll = Collimation()
datainfo.collimation.append(coll)
for item in datainfo.collimation:
coll = self.create_element("SAScollimation")
if item.name is not None:
self.write_attribute(coll, "name", str(item.name))
self.append(coll, instr)
self.write_node(coll, "length", item.length,
{"unit": item.length_unit})
for aperture in item.aperture:
apert = self.create_element("aperture")
if aperture.name is not None:
self.write_attribute(apert, "name", str(aperture.name))
if aperture.type is not None:
self.write_attribute(apert, "type", str(aperture.type))
self.append(apert, coll)
size = self.create_element("size")
if aperture.size_name is not None:
self.write_attribute(size,
"name",
str(aperture.size_name))
written = self.write_node(size, "x", aperture.size.x,
{"unit": aperture.size_unit})
written = written | self.write_node(size, "y", aperture.size.y,
{"unit": aperture.size_unit})
written = written | self.write_node(size, "z", aperture.size.z,
{"unit": aperture.size_unit})
if written == True:
self.append(size, apert)
self.write_node(apert, "distance", aperture.distance,
{"unit": aperture.distance_unit})
def _write_detectors(self, datainfo, instr):
"""
Writes the detector information to the XML file
:param datainfo: The Data1D object the information is coming from
:param inst: lxml instrument node to be appended to
"""
if datainfo.detector == None or datainfo.detector == []:
det = Detector()
det.name = ""
datainfo.detector.append(det)
for item in datainfo.detector:
det = self.create_element("SASdetector")
written = self.write_node(det, "name", item.name)
written = written | self.write_node(det, "SDD", item.distance,
{"unit": item.distance_unit})
if written == True:
self.append(det, instr)
off = self.create_element("offset")
written = self.write_node(off, "x", item.offset.x,
{"unit": item.offset_unit})
written = written | self.write_node(off, "y", item.offset.y,
{"unit": item.offset_unit})
written = written | self.write_node(off, "z", item.offset.z,
{"unit": item.offset_unit})
if written == True:
self.append(off, det)
ori = self.create_element("orientation")
written = self.write_node(ori, "roll", item.orientation.x,
{"unit": item.orientation_unit})
written = written | self.write_node(ori, "pitch",
item.orientation.y,
{"unit": item.orientation_unit})
written = written | self.write_node(ori, "yaw",
item.orientation.z,
{"unit": item.orientation_unit})
if written == True:
self.append(ori, det)
center = self.create_element("beam_center")
written = self.write_node(center, "x", item.beam_center.x,
{"unit": item.beam_center_unit})
written = written | self.write_node(center, "y",
item.beam_center.y,
{"unit": item.beam_center_unit})
written = written | self.write_node(center, "z",
item.beam_center.z,
{"unit": item.beam_center_unit})
if written == True:
self.append(center, det)
pix = self.create_element("pixel_size")
written = self.write_node(pix, "x", item.pixel_size.x,
{"unit": item.pixel_size_unit})
written = written | self.write_node(pix, "y", item.pixel_size.y,
{"unit": item.pixel_size_unit})
written = written | self.write_node(pix, "z", item.pixel_size.z,
{"unit": item.pixel_size_unit})
written = written | self.write_node(det, "slit_length",
item.slit_length,
{"unit": item.slit_length_unit})
if written == True:
self.append(pix, det)
def _write_process_notes(self, datainfo, entry_node):
"""
Writes the process notes to the XML file
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
for item in datainfo.process:
node = self.create_element("SASprocess")
self.append(node, entry_node)
self.write_node(node, "name", item.name)
self.write_node(node, "date", item.date)
self.write_node(node, "description", item.description)
for term in item.term:
value = term['value']
del term['value']
self.write_node(node, "term", value, term)
for note in item.notes:
self.write_node(node, "SASprocessnote", note)
if len(item.notes) == 0:
self.write_node(node, "SASprocessnote", "")
def _write_notes(self, datainfo, entry_node):
"""
Writes the notes to the XML file and creates an empty note if none
exist
:param datainfo: The Data1D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
if len(datainfo.notes) == 0:
node = self.create_element("SASnote")
self.append(node, entry_node)
else:
for item in datainfo.notes:
node = self.create_element("SASnote")
self.write_text(node, item)
self.append(node, entry_node)
def _check_origin(self, entry_node, doc):
"""
Return the document, and the SASentry node associated with
the data we just wrote.
If the calling function was not the cansas reader, return a minidom
object rather than an lxml object.
:param entry_node: lxml node ElementTree object to be appended to
:param doc: entire xml tree
"""
frm = inspect.stack()[1]
mod_name = frm[1].replace("\\", "/").replace(".pyc", "")
mod_name = mod_name.replace(".py", "")
mod = mod_name.split("sas/")
mod_name = mod[1]
if mod_name != "dataloader/readers/cansas_reader":
string = self.to_string(doc, pretty_print=False)
doc = parseString(string)
node_name = entry_node.tag
node_list = doc.getElementsByTagName(node_name)
entry_node = node_list.item(0)
return entry_node
def _to_xml_doc(self, datainfo):
"""
Create an XML document to contain the content of a Data1D
:param datainfo: Data1D object
"""
if not issubclass(datainfo.__class__, Data1D):
raise RuntimeError, "The cansas writer expects a Data1D instance"
# Get PIs and create root element
pi_string = self._get_pi_string()
# Define namespaces and create SASroot object
main_node = self._create_main_node()
# Create ElementTree, append SASroot and apply processing instructions
base_string = pi_string + self.to_string(main_node)
base_element = self.create_element_from_string(base_string)
doc = self.create_tree(base_element)
# Create SASentry Element
entry_node = self.create_element("SASentry")
root = doc.getroot()
root.append(entry_node)
# Add Title to SASentry
self.write_node(entry_node, "Title", datainfo.title)
# Add Run to SASentry
self._write_run_names(datainfo, entry_node)
# Add Data info to SASEntry
self._write_data(datainfo, entry_node)
# Transmission Spectrum Info
self._write_trans_spectrum(datainfo, entry_node)
# Sample info
self._write_sample_info(datainfo, entry_node)
# Instrument info
instr = self._write_instrument(datainfo, entry_node)
# Source
self._write_source(datainfo, instr)
# Collimation
self._write_collimation(datainfo, instr)
# Detectors
self._write_detectors(datainfo, instr)
# Processes info
self._write_process_notes(datainfo, entry_node)
# Note info
self._write_notes(datainfo, entry_node)
# Return the document, and the SASentry node associated with
# the data we just wrote
# If the calling function was not the cansas reader, return a minidom
# object rather than an lxml object.
entry_node = self._check_origin(entry_node, doc)
return doc, entry_node
[docs] def write_node(self, parent, name, value, attr=None):
"""
:param doc: document DOM
:param parent: parent node
:param name: tag of the element
:param value: value of the child text node
:param attr: attribute dictionary
:return: True if something was appended, otherwise False
"""
if value is not None:
parent = self.ebuilder(parent, name, value, attr)
return True
return False
[docs] def write(self, filename, datainfo):
"""
Write the content of a Data1D as a CanSAS XML file
:param filename: name of the file to write
:param datainfo: Data1D object
"""
# Create XML document
doc, _ = self._to_xml_doc(datainfo)
# Write the file
file_ref = open(filename, 'w')
if self.encoding == None:
self.encoding = "UTF-8"
doc.write(file_ref, encoding=self.encoding,
pretty_print=True, xml_declaration=True)
file_ref.close()
# DO NOT REMOVE - used in saving and loading panel states.
def _store_float(self, location, node, variable, storage, optional=True):
"""
Get the content of a xpath location and store
the result. Check that the units are compatible
with the destination. The value is expected to
be a float.
The xpath location might or might not exist.
If it does not exist, nothing is done
:param location: xpath location to fetch
:param node: node to read the data from
:param variable: name of the data member to store it in [string]
:param storage: data object that has the 'variable' data member
:param optional: if True, no exception will be raised
if unit conversion can't be done
:raise ValueError: raised when the units are not recognized
"""
entry = get_content(location, node)
try:
value = float(entry.text)
except:
value = None
if value is not None:
# If the entry has units, check to see that they are
# compatible with what we currently have in the data object
units = entry.get('unit')
if units is not None:
toks = variable.split('.')
local_unit = None
exec "local_unit = storage.%s_unit" % toks[0]
if local_unit != None and units.lower() != local_unit.lower():
if HAS_CONVERTER == True:
try:
conv = Converter(units)
exec "storage.%s = %g" % (variable,
conv(value, units=local_unit))
except:
_, exc_value, _ = sys.exc_info()
err_mess = "CanSAS reader: could not convert"
err_mess += " %s unit [%s]; expecting [%s]\n %s" \
% (variable, units, local_unit, exc_value)
self.errors.append(err_mess)
if optional:
logging.info(err_mess)
else:
raise ValueError, err_mess
else:
err_mess = "CanSAS reader: unrecognized %s unit [%s];"\
% (variable, units)
err_mess += " expecting [%s]" % local_unit
self.errors.append(err_mess)
if optional:
logging.info(err_mess)
else:
raise ValueError, err_mess
else:
exec "storage.%s = value" % variable
else:
exec "storage.%s = value" % variable
# DO NOT REMOVE - used in saving and loading panel states.
def _store_content(self, location, node, variable, storage):
"""
Get the content of a xpath location and store
the result. The value is treated as a string.
The xpath location might or might not exist.
If it does not exist, nothing is done
:param location: xpath location to fetch
:param node: node to read the data from
:param variable: name of the data member to store it in [string]
:param storage: data object that has the 'variable' data member
:return: return a list of errors
"""
entry = get_content(location, node)
if entry is not None and entry.text is not None:
exec "storage.%s = entry.text.strip()" % variable