""" 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.sascalc.dataloader.data_info import Data1D from sas.sascalc.dataloader.data_info import Collimation from sas.sascalc.dataloader.data_info import TransmissionSpectrum from sas.sascalc.dataloader.data_info import Detector from sas.sascalc.dataloader.data_info import Process from sas.sascalc.dataloader.data_info import Aperture import sas.sascalc.dataloader.readers.xml_reader as xml_reader from sas.sascalc.dataloader.readers.xml_reader import XMLreader from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants # The following 2 imports *ARE* used. Do not remove either. import xml.dom.minidom from xml.dom.minidom import parseString ## TODO: Refactor to load multiple as separate Data1D objects ## TODO: Refactor to allow invalid XML, but give a useful warning when loaded _ZERO = 1e-16 PREPROCESS = "xmlpreprocess" ENCODING = "encoding" RUN_NAME_DEFAULT = "None" HAS_CONVERTER = True try: from sas.sascalc.data_util.nxsunit import Converter except ImportError: HAS_CONVERTER = False CONSTANTS = CansasConstants() CANSAS_FORMAT = CONSTANTS.format CANSAS_NS = CONSTANTS.names ALLOW_ALL = True # DO NOT REMOVE Called by outside packages: # sas.sasgui.perspectives.invariant.invariant_state # sas.sasgui.perspectives.fitting.pagestate 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 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 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 = None errors = None 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 = set() self.logging = [] self.encoding = None 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 def load_file_and_schema(self, xml_file, schema_path=""): """ 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") if schema_path == "": schema_path = "{0}/sas/sascalc/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 ## TODO: Test loading invalid CanSAS XML files and see if this works ## TODO: Once works, try adding a warning that the data is invalid def read(self, xml_file, schema_path=""): """ 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, schema_path) # 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: raise RuntimeError, "Invalid XML at: {0}".format(\ self.find_invalid_xml()) except: # If the file does not match the schema, raise this error schema_path = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid.xsd" invalid_xml = self.find_invalid_xml() invalid_xml = "\n\nThe loaded xml file does not fully meet the CanSAS v1.x specification. SasView " + \ "loaded as much of the data as possible.\n\n" + invalid_xml self.errors.add(invalid_xml) self.set_schema(schema_path) if self.is_cansas(): output = self.read(xml_file, schema_path) else: 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) self.errors.clear() 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 data1d._xunit != data1d.x_unit: data1d.x_unit = data1d._xunit if data1d._yunit != data1d.y_unit: data1d.y_unit = data1d._yunit 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 = '' err_msg = None default_unit = None if 'unit' in attr and new_current_level.get('unit') is not None: try: local_unit = attr['unit'] if isinstance(node_value, float) is False: exec("node_value = float({0})".format(node_value)) unitname = new_current_level.get("unit") exec "default_unit = data1d.{0}".format(unitname) if local_unit is not None and default_unit is not None and \ local_unit.lower() != default_unit.lower() \ and local_unit.lower() != "none": if HAS_CONVERTER == True: ## Check local units - bad units raise KeyError 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 err_msg = "Unit converter is not available.\n" else: value_unit = local_unit except KeyError: 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: 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) 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 = set() 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, node_value) 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, frm): """ 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 frm: 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 != "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 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. frm = inspect.stack()[1] doc, entry_node = self._check_origin(entry_node, doc, frm) return doc, entry_node 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 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.add(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.add(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