import logging
import os
import sys
import datetime
import inspect
import numpy as np
# The following 2 imports *ARE* used. Do not remove either.
import xml.dom.minidom
from xml.dom.minidom import parseString
from lxml import etree
from sas.sascalc.data_util.nxsunit import Converter
# For saving individual sections of data
from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \
Collimation, TransmissionSpectrum, Detector, Process, Aperture
from ..loader_exceptions import FileContentsException, DefaultReaderException, \
DataReaderException
from . import xml_reader
from .xml_reader import XMLreader
from .cansas_constants import CansasConstants
logger = logging.getLogger(__name__)
PREPROCESS = "xmlpreprocess"
ENCODING = "encoding"
RUN_NAME_DEFAULT = "None"
INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd"
INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd"
INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \
"as much of the data as possible.\n\n"
CONSTANTS = CansasConstants()
CANSAS_FORMAT = CONSTANTS.format
CANSAS_NS = CONSTANTS.names
ALLOW_ALL = True
[docs]class Reader(XMLreader):
cansas_version = "1.0"
base_ns = "{cansas1d/1.0}"
cansas_defaults = None
type_name = "canSAS"
invalid = True
frm = ""
# Log messages and errors
logging = None
errors = set()
# Namespace hierarchy for current xml_file object
names = None
ns_list = None
# Temporary storage location for loading multiple data sets in a single file
current_data1d = None
data = None
# Wildcards
type = ["XML files (*.xml)|*.xml", "SasView Save Files (*.svs)|*.svs"]
# List of allowed extensions
ext = ['.xml', '.svs']
# Flag to bypass extension check
allow_all = True
[docs] def reset_state(self):
"""
Resets the class state to a base case when loading a new data file so previous
data files do not appear a second time
"""
super(Reader, self).reset_state()
self.data = []
self.process = Process()
self.transspectrum = TransmissionSpectrum()
self.aperture = Aperture()
self.collimation = Collimation()
self.detector = Detector()
self.names = []
self.cansas_defaults = {}
self.ns_list = None
self.logging = []
self.encoding = None
def _read(self, xml_file, schema_path="", invalid=True):
if schema_path != "" or not invalid:
# read has been called from self.get_file_contents because xml file doens't conform to schema
_, self.extension = os.path.splitext(os.path.basename(xml_file))
return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid)
# Otherwise, read has been called by the data loader - file_reader_base_class handles this
return super(XMLreader, self).read(xml_file)
[docs] def get_file_contents(self):
return self._get_file_contents(xml_file=None, schema_path="", invalid=True)
def _get_file_contents(self, xml_file=None, schema_path="", invalid=True):
# Reset everything since we're loading a new file
self.reset_state()
self.invalid = invalid
if xml_file is None:
xml_file = self.f_open.name
# We don't sure f_open since lxml handles opnening/closing files
try:
# Raises FileContentsException
self.load_file_and_schema(xml_file, schema_path)
# Parse each SASentry
entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry',
namespaces={
'ns': self.cansas_defaults.get(
"ns")
})
self.is_cansas(self.extension)
self.set_processing_instructions()
for entry in entry_list:
self._parse_entry(entry)
self.data_cleanup()
except FileContentsException as fc_exc:
# File doesn't meet schema - try loading with a less strict schema
base_name = xml_reader.__file__
base_name = base_name.replace("\\", "/")
base = base_name.split("/sas/")[0]
if self.cansas_version == "1.1":
invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema"))
else:
invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema"))
self.set_schema(invalid_schema)
if self.invalid:
try:
# Load data with less strict schema
self._get_file_contents(xml_file, invalid_schema, False)
# File can still be read but doesn't match schema, so raise exception
self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file
invalid_xml = self.find_invalid_xml()
if invalid_xml != "":
basename, _ = os.path.splitext(
os.path.basename(self.f_open.name))
invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml
raise DataReaderException(invalid_xml) # Handled by base class
except FileContentsException as fc_exc:
msg = "CanSAS Reader could not load the file {}".format(xml_file)
if fc_exc.message is not None: # Propagate error messages from earlier
msg = fc_exc.message
if not self.extension in self.ext: # If the file has no associated loader
raise DefaultReaderException(msg)
raise FileContentsException(msg)
pass
else:
raise fc_exc
except Exception as e: # Convert all other exceptions to FileContentsExceptions
raise FileContentsException(str(e))
finally:
if not self.f_open.closed:
self.f_open.close()
[docs] def load_file_and_schema(self, xml_file, schema_path=""):
base_name = xml_reader.__file__
base_name = base_name.replace("\\", "/")
base = base_name.split("/sas/")[0]
# Try and parse the XML file
try:
self.set_xml_file(xml_file)
except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded
msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file)
raise FileContentsException(msg)
self.cansas_version = self.xmlroot.get("version", "1.0")
self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0")
if schema_path == "":
schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format(
base, self.cansas_defaults.get("schema").replace("\\", "/")
)
self.set_schema(schema_path)
[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
:raises FileContentsException: Raised if XML file isn't valid CanSAS
"""
if self.validate_xml(): # Check file is valid XML
name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation"
value = self.xmlroot.get(name)
# Check schema CanSAS version matches file CanSAS version
if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]:
return True
if ext == "svs":
return True # Why is this required?
# If we get to this point then file isn't valid CanSAS
logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.")
raise FileContentsException("The file is not valid CanSAS")
def _parse_entry(self, dom, recurse=False):
if not self._is_call_local() and not recurse:
self.reset_state()
if not recurse:
self.current_datainfo = DataInfo()
# Raises FileContentsException if file doesn't meet CanSAS schema
self.invalid = False
# Look for a SASentry
self.data = []
self.parent_class = "SASentry"
self.names.append("SASentry")
self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D"
self.current_datainfo.meta_data[
PREPROCESS] = self.processing_instructions
if self._is_call_local() and not recurse:
basename, _ = os.path.splitext(os.path.basename(self.f_open.name))
self.current_datainfo.filename = basename + self.extension
# Create an empty dataset if no data has been passed to the reader
if self.current_dataset is None:
self._initialize_new_data_set(dom)
self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}"
# Loop through each child in the parent element
for node in dom:
attr = node.attrib
name = attr.get("name", "")
type = attr.get("type", "")
# Get the element name and set the current names level
tagname = node.tag.replace(self.base_ns, "")
tagname_original = tagname
# Skip this iteration when loading in save state information
if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]:
continue
# Get where to store content
self.names.append(tagname_original)
self.ns_list = CONSTANTS.iterate_namespace(self.names)
# If the element is a child element, recurse
if len(node.getchildren()) > 0:
self.parent_class = tagname_original
if tagname == 'SASdata':
self._initialize_new_data_set(node)
if isinstance(self.current_dataset, plottable_2D):
x_bins = attr.get("x_bins", "")
y_bins = attr.get("y_bins", "")
if x_bins is not "" and y_bins is not "":
self.current_dataset.shape = (x_bins, y_bins)
else:
self.current_dataset.shape = ()
# Recurse to access data within the group
self._parse_entry(node, recurse=True)
if tagname == "SASsample":
self.current_datainfo.sample.name = name
elif tagname == "beam_size":
self.current_datainfo.source.beam_size_name = name
elif tagname == "SAScollimation":
self.collimation.name = name
elif tagname == "aperture":
self.aperture.name = name
self.aperture.type = type
self._add_intermediate()
else:
# TODO: Clean this up to make it faster (fewer if/elifs)
if isinstance(self.current_dataset, plottable_2D):
data_point = node.text
unit = attr.get('unit', '')
else:
data_point, unit = self._get_node_value(node, tagname)
# If this is a dataset, store the data appropriately
if tagname == 'Run':
self.current_datainfo.run_name[data_point] = name
self.current_datainfo.run.append(data_point)
elif tagname == 'Title':
self.current_datainfo.title = data_point
elif tagname == 'SASnote':
self.current_datainfo.notes.append(data_point)
# I and Q points
elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D):
self.current_dataset.yaxis("Intensity", unit)
self.current_dataset.y = np.append(self.current_dataset.y, data_point)
elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D):
self.current_dataset.dy = np.append(self.current_dataset.dy, data_point)
elif tagname == 'Q':
self.current_dataset.xaxis("Q", unit)
self.current_dataset.x = np.append(self.current_dataset.x, data_point)
elif tagname == 'Qdev':
self.current_dataset.dx = np.append(self.current_dataset.dx, data_point)
elif tagname == 'dQw':
self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point)
elif tagname == 'dQl':
self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point)
elif tagname == 'Qmean':
pass
elif tagname == 'Shadowfactor':
pass
elif tagname == 'Sesans':
self.current_datainfo.isSesans = bool(data_point)
self.current_dataset.xaxis(attr.get('x_axis'),
attr.get('x_unit'))
self.current_dataset.yaxis(attr.get('y_axis'),
attr.get('y_unit'))
elif tagname == 'yacceptance':
self.current_datainfo.sample.yacceptance = (data_point, unit)
elif tagname == 'zacceptance':
self.current_datainfo.sample.zacceptance = (data_point, unit)
# I and Qx, Qy - 2D data
elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D):
self.current_dataset.yaxis("Intensity", unit)
self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D):
self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Qx':
self.current_dataset.xaxis("Qx", unit)
self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Qy':
self.current_dataset.yaxis("Qy", unit)
self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Qxdev':
self.current_dataset.xaxis("Qxdev", unit)
self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Qydev':
self.current_dataset.yaxis("Qydev", unit)
self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",")
elif tagname == 'Mask':
inter = [item == "1" for item in data_point.split(",")]
self.current_dataset.mask = np.asarray(inter, dtype=bool)
# Sample Information
elif tagname == 'ID' and self.parent_class == 'SASsample':
self.current_datainfo.sample.ID = data_point
elif tagname == 'Title' and self.parent_class == 'SASsample':
self.current_datainfo.sample.name = data_point
elif tagname == 'thickness' and self.parent_class == 'SASsample':
self.current_datainfo.sample.thickness = data_point
self.current_datainfo.sample.thickness_unit = unit
elif tagname == 'transmission' and self.parent_class == 'SASsample':
self.current_datainfo.sample.transmission = data_point
elif tagname == 'temperature' and self.parent_class == 'SASsample':
self.current_datainfo.sample.temperature = data_point
self.current_datainfo.sample.temperature_unit = unit
elif tagname == 'details' and self.parent_class == 'SASsample':
self.current_datainfo.sample.details.append(data_point)
elif tagname == 'x' and self.parent_class == 'position':
self.current_datainfo.sample.position.x = data_point
self.current_datainfo.sample.position_unit = unit
elif tagname == 'y' and self.parent_class == 'position':
self.current_datainfo.sample.position.y = data_point
self.current_datainfo.sample.position_unit = unit
elif tagname == 'z' and self.parent_class == 'position':
self.current_datainfo.sample.position.z = data_point
self.current_datainfo.sample.position_unit = unit
elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names:
self.current_datainfo.sample.orientation.x = data_point
self.current_datainfo.sample.orientation_unit = unit
elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names:
self.current_datainfo.sample.orientation.y = data_point
self.current_datainfo.sample.orientation_unit = unit
elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names:
self.current_datainfo.sample.orientation.z = data_point
self.current_datainfo.sample.orientation_unit = unit
# Instrumental Information
elif tagname == 'name' and self.parent_class == 'SASinstrument':
self.current_datainfo.instrument = data_point
# Detector Information
elif tagname == 'name' and self.parent_class == 'SASdetector':
self.detector.name = data_point
elif tagname == 'SDD' and self.parent_class == 'SASdetector':
self.detector.distance = data_point
self.detector.distance_unit = unit
elif tagname == 'slit_length' and self.parent_class == 'SASdetector':
self.detector.slit_length = data_point
self.detector.slit_length_unit = unit
elif tagname == 'x' and self.parent_class == 'offset':
self.detector.offset.x = data_point
self.detector.offset_unit = unit
elif tagname == 'y' and self.parent_class == 'offset':
self.detector.offset.y = data_point
self.detector.offset_unit = unit
elif tagname == 'z' and self.parent_class == 'offset':
self.detector.offset.z = data_point
self.detector.offset_unit = unit
elif tagname == 'x' and self.parent_class == 'beam_center':
self.detector.beam_center.x = data_point
self.detector.beam_center_unit = unit
elif tagname == 'y' and self.parent_class == 'beam_center':
self.detector.beam_center.y = data_point
self.detector.beam_center_unit = unit
elif tagname == 'z' and self.parent_class == 'beam_center':
self.detector.beam_center.z = data_point
self.detector.beam_center_unit = unit
elif tagname == 'x' and self.parent_class == 'pixel_size':
self.detector.pixel_size.x = data_point
self.detector.pixel_size_unit = unit
elif tagname == 'y' and self.parent_class == 'pixel_size':
self.detector.pixel_size.y = data_point
self.detector.pixel_size_unit = unit
elif tagname == 'z' and self.parent_class == 'pixel_size':
self.detector.pixel_size.z = data_point
self.detector.pixel_size_unit = unit
elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
self.detector.orientation.x = data_point
self.detector.orientation_unit = unit
elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
self.detector.orientation.y = data_point
self.detector.orientation_unit = unit
elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names:
self.detector.orientation.z = data_point
self.detector.orientation_unit = unit
# Collimation and Aperture
elif tagname == 'length' and self.parent_class == 'SAScollimation':
self.collimation.length = data_point
self.collimation.length_unit = unit
elif tagname == 'name' and self.parent_class == 'SAScollimation':
self.collimation.name = data_point
elif tagname == 'distance' and self.parent_class == 'aperture':
self.aperture.distance = data_point
self.aperture.distance_unit = unit
elif tagname == 'x' and self.parent_class == 'size':
self.aperture.size.x = data_point
self.collimation.size_unit = unit
elif tagname == 'y' and self.parent_class == 'size':
self.aperture.size.y = data_point
self.collimation.size_unit = unit
elif tagname == 'z' and self.parent_class == 'size':
self.aperture.size.z = data_point
self.collimation.size_unit = unit
# Process Information
elif tagname == 'name' and self.parent_class == 'SASprocess':
self.process.name = data_point
elif tagname == 'description' and self.parent_class == 'SASprocess':
self.process.description = data_point
elif tagname == 'date' and self.parent_class == 'SASprocess':
try:
self.process.date = datetime.datetime.fromtimestamp(data_point)
except:
self.process.date = data_point
elif tagname == 'SASprocessnote':
self.process.notes.append(data_point)
elif tagname == 'term' and self.parent_class == 'SASprocess':
unit = attr.get("unit", "")
dic = { "name": name, "value": data_point, "unit": unit }
self.process.term.append(dic)
# Transmission Spectrum
elif tagname == 'T' and self.parent_class == 'Tdata':
self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point)
self.transspectrum.transmission_unit = unit
elif tagname == 'Tdev' and self.parent_class == 'Tdata':
self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point)
self.transspectrum.transmission_deviation_unit = unit
elif tagname == 'Lambda' and self.parent_class == 'Tdata':
self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point)
self.transspectrum.wavelength_unit = unit
# Source Information
elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'):
self.current_datainfo.source.wavelength = data_point
self.current_datainfo.source.wavelength_unit = unit
elif tagname == 'wavelength_min' and self.parent_class == 'SASsource':
self.current_datainfo.source.wavelength_min = data_point
self.current_datainfo.source.wavelength_min_unit = unit
elif tagname == 'wavelength_max' and self.parent_class == 'SASsource':
self.current_datainfo.source.wavelength_max = data_point
self.current_datainfo.source.wavelength_max_unit = unit
elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource':
self.current_datainfo.source.wavelength_spread = data_point
self.current_datainfo.source.wavelength_spread_unit = unit
elif tagname == 'x' and self.parent_class == 'beam_size':
self.current_datainfo.source.beam_size.x = data_point
self.current_datainfo.source.beam_size_unit = unit
elif tagname == 'y' and self.parent_class == 'beam_size':
self.current_datainfo.source.beam_size.y = data_point
self.current_datainfo.source.beam_size_unit = unit
elif tagname == 'z' and self.parent_class == 'pixel_size':
self.current_datainfo.source.data_point.z = data_point
self.current_datainfo.source.beam_size_unit = unit
elif tagname == 'radiation' and self.parent_class == 'SASsource':
self.current_datainfo.source.radiation = data_point
elif tagname == 'beam_shape' and self.parent_class == 'SASsource':
self.current_datainfo.source.beam_shape = data_point
# Everything else goes in meta_data
else:
new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname)
self.current_datainfo.meta_data[new_key] = data_point
self.names.remove(tagname_original)
length = 0
if len(self.names) > 1:
length = len(self.names) - 1
self.parent_class = self.names[length]
if not self._is_call_local() and not recurse:
self.frm = ""
self.current_datainfo.errors = set()
for error in self.errors:
self.current_datainfo.errors.add(error)
self.data_cleanup()
self.sort_data()
self.reset_data_list()
return self.output[0], None
def _is_call_local(self):
if self.frm == "":
inter = inspect.stack()
self.frm = inter[2]
mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
mod_name = mod_name.replace(".py", "")
mod = mod_name.split("sas/")
mod_name = mod[1]
if mod_name != "sascalc/dataloader/readers/cansas_reader":
return False
return True
def _add_intermediate(self):
"""
This method stores any intermediate objects within the final data set after fully reading the set.
"""
if self.parent_class == 'SASprocess':
self.current_datainfo.process.append(self.process)
self.process = Process()
elif self.parent_class == 'SASdetector':
self.current_datainfo.detector.append(self.detector)
self.detector = Detector()
elif self.parent_class == 'SAStransmission_spectrum':
self.current_datainfo.trans_spectrum.append(self.transspectrum)
self.transspectrum = TransmissionSpectrum()
elif self.parent_class == 'SAScollimation':
self.current_datainfo.collimation.append(self.collimation)
self.collimation = Collimation()
elif self.parent_class == 'aperture':
self.collimation.aperture.append(self.aperture)
self.aperture = Aperture()
elif self.parent_class == 'SASdata':
self.data.append(self.current_dataset)
def _get_node_value(self, node, tagname):
"""
Get the value of a node and any applicable units
:param node: The XML node to get the value of
: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 is not None:
node_value = ' '.join(node_value.split())
else:
node_value = ""
# If the value is a float, compile with units.
if self.ns_list.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, tagname, node_value)
# If the value is a timestamp, convert to a datetime object
elif self.ns_list.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 _unit_conversion(self, node, 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 node: XML node
:param tagname: name of the node
:param node_value: The value of the current dom node
"""
attr = node.attrib
value_unit = ''
err_msg = None
default_unit = None
if not isinstance(node_value, float):
node_value = float(node_value)
if 'unit' in attr and attr.get('unit') is not None:
try:
unit = attr['unit']
# Split the units to retain backwards compatibility with
# projects, analyses, and saved data from v4.1.0
unit_list = unit.split("|")
if len(unit_list) > 1:
local_unit = unit_list[1]
else:
local_unit = unit
unitname = self.ns_list.current_level.get("unit", "")
if "SASdetector" in self.names:
save_in = "detector"
elif "aperture" in self.names:
save_in = "aperture"
elif "SAScollimation" in self.names:
save_in = "collimation"
elif "SAStransmission_spectrum" in self.names:
save_in = "transspectrum"
elif "SASdata" in self.names:
x = np.zeros(1)
y = np.zeros(1)
self.current_data1d = Data1D(x, y)
save_in = "current_data1d"
elif "SASsource" in self.names:
save_in = "current_datainfo.source"
elif "SASsample" in self.names:
save_in = "current_datainfo.sample"
elif "SASprocess" in self.names:
save_in = "process"
else:
save_in = "current_datainfo"
default_unit = getattrchain(self, '.'.join((save_in, unitname)))
if (local_unit and default_unit
and local_unit.lower() != default_unit.lower()
and local_unit.lower() != "none"):
# Check local units - bad units raise KeyError
#print("loading", tagname, node_value, local_unit, default_unit)
data_conv_q = Converter(local_unit)
value_unit = default_unit
node_value = data_conv_q(node_value, units=default_unit)
else:
value_unit = local_unit
except KeyError:
# Do not throw an error for loading Sesans data in cansas xml
# This is a temporary fix.
if local_unit != "A" and local_unit != 'pol':
err_msg = "CanSAS reader: unexpected "
err_msg += "\"{0}\" unit [{1}]; "
err_msg = err_msg.format(tagname, local_unit)
err_msg += "expecting [{0}]".format(default_unit)
value_unit = local_unit
except Exception:
err_msg = "CanSAS reader: unknown error converting "
err_msg += "\"{0}\" unit [{1}]"
err_msg = err_msg.format(tagname, local_unit)
value_unit = local_unit
elif 'unit' in attr:
value_unit = attr['unit']
if err_msg:
self.errors.add(err_msg)
return node_value, value_unit
def _initialize_new_data_set(self, node=None):
if node is not None:
for child in node:
if child.tag.replace(self.base_ns, "") == "Idata":
for i_child in child:
if i_child.tag.replace(self.base_ns, "") == "Qx":
self.current_dataset = plottable_2D()
return
self.current_dataset = plottable_1D(np.array(0), np.array(0))
## Writing Methods
[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, 'wb')
if self.encoding is None:
self.encoding = "UTF-8"
doc.write(file_ref, encoding=self.encoding,
pretty_print=True, xml_declaration=True)
file_ref.close()
def _to_xml_doc(self, datainfo):
"""
Create an XML document to contain the content of a Data1D
:param datainfo: Data1D object
"""
is_2d = False
if issubclass(datainfo.__class__, Data2D):
is_2d = True
# 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
if is_2d:
self._write_data_2d(datainfo, entry_node)
else:
self._write_data(datainfo, entry_node)
# Transmission Spectrum Info
# TODO: fix the writer to linearize all data, including T_spectrum
# 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.
self.frm = inspect.stack()[1]
doc, 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
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 is 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 1D 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._xunit})
if len(datainfo.y) >= i:
self.write_node(point, "I", datainfo.y[i],
{'unit': datainfo._yunit})
if datainfo.dy is not None and len(datainfo.dy) > i:
self.write_node(point, "Idev", datainfo.dy[i],
{'unit': datainfo._yunit})
if datainfo.dx is not None and len(datainfo.dx) > i:
self.write_node(point, "Qdev", datainfo.dx[i],
{'unit': datainfo._xunit})
if datainfo.dxw is not None and len(datainfo.dxw) > i:
self.write_node(point, "dQw", datainfo.dxw[i],
{'unit': datainfo._xunit})
if datainfo.dxl is not None and len(datainfo.dxl) > i:
self.write_node(point, "dQl", datainfo.dxl[i],
{'unit': datainfo._xunit})
if datainfo.isSesans:
sesans_attrib = {'x_axis': datainfo._xaxis,
'y_axis': datainfo._yaxis,
'x_unit': datainfo.x_unit,
'y_unit': datainfo.y_unit}
sesans = self.create_element("Sesans", attrib=sesans_attrib)
sesans.text = str(datainfo.isSesans)
entry_node.append(sesans)
self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0],
{'unit': datainfo.sample.yacceptance[1]})
self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0],
{'unit': datainfo.sample.zacceptance[1]})
def _write_data_2d(self, datainfo, entry_node):
"""
Writes 2D data to the XML file
:param datainfo: The Data2D object the information is coming from
:param entry_node: lxml node ElementTree object to be appended to
"""
attr = {}
if datainfo.data.shape:
attr["x_bins"] = str(len(datainfo.x_bins))
attr["y_bins"] = str(len(datainfo.y_bins))
node = self.create_element("SASdata", attr)
self.append(node, entry_node)
point = self.create_element("Idata")
node.append(point)
qx = ','.join(str(v) for v in datainfo.qx_data)
qy = ','.join(str(v) for v in datainfo.qy_data)
intensity = ','.join(str(v) for v in datainfo.data)
self.write_node(point, "Qx", qx,
{'unit': datainfo._xunit})
self.write_node(point, "Qy", qy,
{'unit': datainfo._yunit})
self.write_node(point, "I", intensity,
{'unit': datainfo._zunit})
if datainfo.err_data is not None:
err = ','.join(str(v) for v in datainfo.err_data)
self.write_node(point, "Idev", err,
{'unit': datainfo._zunit})
if datainfo.dqy_data is not None:
dqy = ','.join(str(v) for v in datainfo.dqy_data)
self.write_node(point, "Qydev", dqy,
{'unit': datainfo._yunit})
if datainfo.dqx_data is not None:
dqx = ','.join(str(v) for v in datainfo.dqx_data)
self.write_node(point, "Qxdev", dqx,
{'unit': datainfo._xunit})
if datainfo.mask is not None:
mask = ','.join("1" if v else "0" for v in datainfo.mask)
self.write_node(point, "Mask", mask)
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 is not 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:
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:
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 is 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:
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 is 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:
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 is 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:
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:
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:
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:
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})
if written:
self.append(pix, det)
self.write_node(det, "slit_length", item.slit_length,
{"unit": item.slit_length_unit})
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:
if isinstance(term, list):
value = term['value']
del term['value']
elif isinstance(term, dict):
value = term.get("value")
del term['value']
else:
value = term
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
"""
if not self.frm:
self.frm = inspect.stack()[1]
mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "")
mod_name = mod_name.replace(".py", "")
mod = mod_name.split("sas/")
mod_name = mod[1]
if mod_name != "sascalc/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 doc, entry_node
# 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 ValueError:
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 = getattr(storage, toks[0]+"_unit")
if local_unit is not None and units.lower() != local_unit.lower():
try:
conv = Converter(units)
setattrchain(storage, variable, conv(value, units=local_unit))
except Exception as exc:
err_mess = "CanSAS reader: could not convert"
err_mess += " %s unit [%s]; expecting [%s]\n %s" \
% (variable, units, local_unit, exc)
self.errors.add(err_mess)
if optional:
logger.info(err_mess)
else:
raise ValueError(err_mess)
else:
setattrchain(storage, variable, value)
else:
setattrchain(storage, variable, value)
# 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:
setattrchain(storage, variable, entry.text.strip())
# DO NOT REMOVE Called by outside packages:
# sas.sasgui.perspectives.invariant.invariant_state
# sas.sasgui.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.sasgui.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]def getattrchain(obj, chain, default=None):
"""Like getattr, but the attr may contain multiple parts separated by '.'"""
for part in chain.split('.'):
if hasattr(obj, part):
obj = getattr(obj, part, None)
else:
return default
return obj
[docs]def setattrchain(obj, chain, value):
"""Like setattr, but the attr may contain multiple parts separated by '.'"""
parts = list(chain.split('.'))
for part in parts[-1]:
obj = getattr(obj, part, None)
if obj is None:
raise ValueError("missing parent object "+part)
setattr(obj, value)