""" 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 as np import os import sys import datetime import inspect # For saving individual sections of data from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \ plottable_1D, plottable_2D from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \ Detector, Process, Aperture from sas.sascalc.dataloader.data_info import \ combine_data_info_with_plottable as combine_data 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, CurrentLevel # The following 2 imports *ARE* used. Do not remove either. import xml.dom.minidom from xml.dom.minidom import parseString 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" 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 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}" 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_datainfo = None current_dataset = None current_data1d = None data = None # List of data1D objects to be sent back to SasView output = None # 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 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 """ self.current_datainfo = None self.current_dataset = None self.current_data1d = None self.data = [] self.process = Process() self.transspectrum = TransmissionSpectrum() self.aperture = Aperture() self.collimation = Collimation() self.detector = Detector() self.names = [] self.cansas_defaults = {} self.output = [] self.ns_list = None self.logging = [] self.encoding = None def read(self, xml_file, schema_path="", invalid=True): """ Validate and read in an xml_file file in the canSAS format. :param xml_file: A canSAS file path in proper XML format :param schema_path: A file path to an XML schema to validate the xml_file against """ # For every file loaded, reset everything to a base state self.reset_state() self.invalid = invalid # Check that the file exists if os.path.isfile(xml_file): basename, extension = os.path.splitext(os.path.basename(xml_file)) # If the file type is not allowed, return nothing if extension in self.ext or self.allow_all: # Get the file location of self.load_file_and_schema(xml_file, schema_path) self.add_data_set() # Try to load the file, but raise an error if unable to. # Check the file matches the XML schema try: self.is_cansas(extension) self.invalid = False # Get each SASentry from XML file and add it to a list. entry_list = self.xmlroot.xpath( '/ns:SASroot/ns:SASentry', namespaces={'ns': self.cansas_defaults.get("ns")}) self.names.append("SASentry") # Get all preprocessing events and encoding self.set_processing_instructions() # Parse each item for entry in entry_list: # Create a new DataInfo object for every # Set the file name and then parse the entry. self.current_datainfo.filename = basename + extension self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D" self.current_datainfo.meta_data[PREPROCESS] = \ self.processing_instructions # Parse the XML SASentry self._parse_entry(entry) # Combine datasets with datainfo self.add_data_set() except RuntimeError: # If the file does not match the schema, raise this error invalid_xml = self.find_invalid_xml() invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml self.errors.add(invalid_xml) # Try again with an invalid CanSAS schema, that requires only a data set in each 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) try: if self.invalid: if self.is_cansas(): self.output = self.read(xml_file, invalid_schema, False) else: raise RuntimeError else: raise RuntimeError except RuntimeError: x = np.zeros(1) y = np.zeros(1) self.current_data1d = Data1D(x,y) self.current_data1d.errors = self.errors return [self.current_data1d] else: self.output.append("Not a valid file path.") # Return a list of parsed entries that dataloader can manage return self.output def _parse_entry(self, dom, recurse=False): """ 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 """ self._check_for_empty_data() self._initialize_new_data_set(dom) self.names.append("SASentry") self.parent_class = "SASentry" self.base_ns = "{0}{1}{2}".format("{", \ CANSAS_NS.get(self.cansas_version).get("ns"), "}") self.ns_list = CONSTANTS.iterate_namespace(self.names) # Go through each child in the parent element for sasNode in dom: # Get the element name and set the current name's level currentTagName = sasNode.tag.replace(self.base_ns, "") # As this is the most likely tag to examine, lets put it first! if currentTagName == "SASdata": # Are there multiple entries here? if len(sasNode) <= 1: multipleEntries = False else: multipleEntries = True for setupNode in sasNode[0]: # Iterating through the tags in the unit node, getting their tag name and respective unit setupTagName = setupNode.tag.replace(self.base_ns, "") units = setupNode.attrib.get("unit", "") # Creating our data array first, if there's only one dataNode we will handle this... startArray = np.fromstring(setupNode.text, dtype=float, sep=",") if multipleEntries == True: setupArray = np.zeros((len(sasNode), len(startArray))) setupArray[0] = startArray else: setupArray = startArray # Now put this into the relevant location if setupTagName == "I": self.current_dataset.yaxis("Intensity", units) self.current_dataset.y = setupArray elif setupTagName == "Q": self.current_dataset.xaxis("Q", units) self.current_dataset.x = setupArray elif setupTagName == "Idev": self.current_dataset.dy = setupArray elif setupTagName == "Qdev": self.current_dataset.dx = setupArray elif setupTagName == "Qx": self.current_dataset.xaxis("Qx", units) self.current_dataset.qx_data = setupArray elif setupTagName == "Qy": self.current_dataset.yaxis("Qy", units) self.current_dataset.qy_data = setupArray elif setupTagName == "Qxdev": self.current_dataset.xaxis("Qxdev", units) self.current_dataset.dqx_data = setupArray elif setupTagName == "Qydev": self.current_dataset.yaxis("Qydev", units) self.current_dataset.dqy_data = setupArray elif setupTagName == "dQw": self.current_dataset.dxw = setupArray elif setupTagName == "dQl": self.current_dataset.dxl = setupArray elif setupTagName == "Mask": self.current_dataset.mask = np.ndarray.astype(setupArray, dtype=bool) elif setupTagName == "Sesans": self.current_datainfo.isSesans = bool(setupNode.text) elif setupTagName == "yacceptance": self.current_datainfo.sample.yacceptance = (setupNode.text, units) elif setupTagName == "zacceptance": self.current_datainfo.sample.zacceptance = (setupNode.text, units) elif setupTagName == "Qmean": pass elif setupTagName == "Shadowfactor": pass # If there's more data present, let's deal with that too for loopIter in range(1, len(sasNode)): for dataNode in sasNode[loopIter]: # Iterating through the tags in the unit node, getting their tag name and respective unit dataTagName = dataNode.tag.replace(self.base_ns, "") # Creating our data array first dataArray = np.fromstring(dataNode.text, dtype=float, sep=",") if dataTagName == "I": self.current_dataset.y[loopIter] = dataArray elif dataTagName == "Q": self.current_dataset.x[loopIter] = dataArray elif dataTagName == "Idev": self.current_dataset.dy[loopIter] = dataArray elif dataTagName == "Qdev": self.current_dataset.dx[loopIter] = dataArray elif dataTagName == "Qx": self.current_dataset.qx_data[loopIter] = dataArray elif dataTagName == "Qy": self.current_dataset.qy_data[loopIter] = dataArray elif dataTagName == "Qxdev": self.current_dataset.dqx_data[loopIter] = dataArray elif dataTagName == "Qydev": self.current_dataset.dqy_data[loopIter] = dataArray elif dataTagName == "dQw": self.current_dataset.dxw[loopIter] = dataArray elif dataTagName == "dQl": self.current_dataset.dxl[loopIter] = dataArray self._check_for_empty_resolution() self.data.append(self.current_dataset) # If it's not data, let's check for other tags starting with skippable ones... elif currentTagName == "fitting_plug_in" or currentTagName == "pr_inversion" or currentTagName == "invariant": continue # If we'e dealing with a title node then extract the text of the node and put it in the right place elif currentTagName == "Title": self.current_datainfo.title = sasNode.text # If we'e dealing with a run node then extract the name and text of the node and put it in the right place elif currentTagName == "Run": self.current_datainfo.run_name[sasNode.text] = sasNode.attrib.get("name", "") self.current_datainfo.run.append(sasNode.text) # If we'e dealing with a sample node elif currentTagName == "SASsample": for sampleNode in sasNode: # Get the variables sampleTagName = sampleNode.tag.replace(self.base_ns, "") sampleUnits = sampleNode.attrib.get("unit", "") sampleData = sampleNode.text # Populate it via if switching if sampleTagName == "ID": self.current_datainfo.sample.ID = sampleData elif sampleTagName == "Title": self.current_datainfo.sample.name = sampleData elif sampleTagName == "thickness": self.current_datainfo.sample.thickness = sampleData self.current_datainfo.sample.thickness_unit = sampleUnits elif sampleTagName == "transmission": self.current_datainfo.sample.transmission = sampleData elif sampleTagName == "temperature": self.current_datainfo.sample.temperature = sampleData self.current_datainfo.sample.temperature_unit = sampleUnits elif sampleTagName == "details": self.current_datainfo.sample.details.append(sampleData) # Extract the positional data elif sampleTagName == "position": for positionNode in sampleNode: positionTagName = positionNode.tag.replace(self.base_ns, "") positionUnits = positionNode.attrib.get("unit", "") positionData = positionNode.text # Extract specific tags if positionTagName == "x": self.current_datainfo.sample.position.x = positionData self.current_datainfo.sample.position_unit = positionUnits elif positionTagName == "y": self.current_datainfo.sample.position.y = positionData self.current_datainfo.sample.position_unit = positionUnits elif positionTagName == "z": self.current_datainfo.sample.position.z = positionData self.current_datainfo.sample.position_unit = positionUnits # Extract the orientation data elif sampleTagName == "orientation": for orientationNode in sampleNode: orientationTagName = orientationNode.tag.replace(self.base_ns, "") orientationUnits = orientationNode.attrib.get("unit", "") orientationData = orientationNode.text # Extract specific tags if orientationTagName == "roll": self.current_datainfo.sample.orientation.x = orientationData self.current_datainfo.sample.orientation_unit = orientationUnits elif orientationTagName == "pitch": self.current_datainfo.sample.orientation.y = orientationData self.current_datainfo.sample.orientation_unit = orientationUnits elif orientationTagName == "yaw": self.current_datainfo.sample.orientation.z = orientationData self.current_datainfo.sample.orientation_unit = orientationUnits # If we're dealing with an instrument node elif currentTagName == "SASinstrument": for instrumentNode in sasNode: instrumentTagName = instrumentNode.tag.replace(self.base_ns, "") instrumentUnits = instrumentNode.attrib.get("unit", "") instrumentData = instrumentNode.text # Extract the source name if instrumentTagName == "SASsource": self.name = instrumentNode.attrib.get("name", "") for sourceNode in instrumentNode: sourceTagName = sourceNode.tag.replace(self.base_ns, "") sourceUnits = sourceNode.attrib.get("unit", "") sourceData = sourceNode.text ## Source Information if sourceTagName == "wavelength": self.current_datainfo.source.wavelength = sourceData self.current_datainfo.source.wavelength_unit = sourceUnits elif sourceTagName == "wavelength_min": self.current_datainfo.source.wavelength_min = sourceData self.current_datainfo.source.wavelength_min_unit = sourceUnits elif sourceTagName == "wavelength_max": self.current_datainfo.source.wavelength_max = sourceData self.current_datainfo.source.wavelength_max_unit = sourceUnits elif sourceTagName == "wavelength_spread": self.current_datainfo.source.wavelength_spread = sourceData self.current_datainfo.source.wavelength_spread_unit = sourceUnits elif sourceTagName == "radiation": self.current_datainfo.source.radiation = sourceData elif sourceTagName == "beam_shape": self.current_datainfo.source.beam_shape = sourceData elif sourceTagName == "beam_size": for beamNode in sourceNode: beamTagName = beamNode.tag.replace(self.base_ns, "") beamUnits = beamNode.attrib.get("unit", "") beamData = beamNode.text if beamTagName == "x": self.current_datainfo.source.beam_size.x = beamData self.current_datainfo.source.beam_size_unit = beamUnits elif beamTagName == "y": self.current_datainfo.source.beam_size.y = beamData self.current_datainfo.source.beam_size_unit = beamUnits elif sourceTagName == "pixel_size": for pixelNode in sourceNode: pixelTagName = pixelNode.tag.replace(self.base_ns, "") pixelUnits = pixelNode.attrib.get("unit", "") pixelData = pixelNode.text if pixelTagName == "z": self.current_datainfo.source.data_point.z = pixelData self.current_datainfo.source.beam_size_unit = pixelUnits # Extract the collimation elif instrumentTagName == "SAScollimation": self.collimation.name = instrumentNode.attrib.get("name", "") for collimationNode in instrumentNode: collimationTagName = pixelNode.tag.replace(self.base_ns, "") collimationUnits = pixelNode.attrib.get("unit", "") collimationData = pixelNode.text if collimationTagName == "length": self.collimation.length = collimationData self.collimation.length_unit = collimationUnits elif collimationTagName == "name": self.collimation.name = collimationData if collimationTagName == "aperture": for apertureNode in collimationNode: apertureTagName = apertureNode.tag.replace(self.base_ns, "") apertureUnits = apertureNode.attrib.get("unit", "") apertureData = apertureNode.text if tagname == "distance": self.aperture.distance = apertureData self.aperture.distance_unit = apertureUnits if collimationTagName == "size": for sizeNode in collimationNode: sizeTagName = sizeNode.tag.replace(self.base_ns, "") sizeUnits = sizeNode.attrib.get("unit", "") sizeData = sizeNode.text if tagname == "x": self.aperture.size.x = sizeData self.collimation.size_unit = sizeUnits elif tagname == "y": self.aperture.size.y = sizeData self.collimation.size_unit = sizeUnits elif tagname == "z": self.aperture.size.z = sizeData self.collimation.size_unit = sizeUnits self.current_datainfo.collimation.append(self.collimation) self.collimation = Collimation() # Extract the detector elif instrumentTagName == "SASdetector": self.name = instrumentNode.attrib.get("name", "") for detectorNode in instrumentNode: detectorTagName = detectorNode.tag.replace(self.base_ns, "") detectorUnits = detectorNode.attrib.get("unit", "") detectorData = detectorNode.text if detectorTagName == "name": self.detector.name = detectorData elif detectorTagName == "SDD": self.detector.distance = detectorData self.detector.distance_unit = detectorUnits elif detectorTagName == "slit_length": self.detector.slit_length = detectorData self.detector.slit_length_unit = detectorUnits elif detectorTagName == "offset": for offsetNode in detectorNode: offsetTagName = offsetNode.tag.replace(self.base_ns, "") offsetUnits = offsetNode.attrib.get("unit", "") offsetData = offsetNode.text if offsetTagName == "x": self.detector.offset.x = offsetData self.detector.offset_unit = offsetUnits elif offsetTagName == "y": self.detector.offset.y = offsetData self.detector.offset_unit = offsetUnits elif offsetTagName == "z": self.detector.offset.z = offsetData self.detector.offset_unit = offsetUnits elif detectorTagName == "beam_center": for beamCenterNode in detectorNode: beamCenterTagName = beamCenterNode.tag.replace(self.base_ns, "") beamCenterUnits = beamCenterNode.attrib.get("unit", "") beamCenterData = beamCenterNode.text if beamCenterTagName == "x": self.detector.beam_center.x = beamCenterData self.detector.beam_center_unit = beamCenterUnits elif beamCenterTagName == "y": self.detector.beam_center.y = beamCenterData self.detector.beam_center_unit = beamCenterUnits elif beamCenterTagName == "z": self.detector.beam_center.z = beamCenterData self.detector.beam_center_unit = beamCenterUnits elif detectorTagName == "pixel_size": for pixelSizeNode in detectorNode: pixelSizeTagName = pixelSizeNode.tag.replace(self.base_ns, "") pixelSizeUnits = pixelSizeNode.attrib.get("unit", "") pixelSizeData = pixelSizeNode.text if pixelSizeTagName == "x": self.detector.pixel_size.x = pixelSizeData self.detector.pixel_size_unit = pixelSizeUnits elif pixelSizeTagName == "y": self.detector.pixel_size.y = pixelSizeData self.detector.pixel_size_unit = pixelSizeUnits elif pixelSizeTagName == "z": self.detector.pixel_size.z = pixelSizeData self.detector.pixel_size_unit = pixelSizeUnits elif detectorTagName == "orientation": for orientationNode in detectorNode: orientationTagName = orientationNode.tag.replace(self.base_ns, "") orientationUnits = orientationNode.attrib.get("unit", "") orientationData = orientationNode.text if orientationTagName == "roll": self.detector.orientation.x = orientationData self.detector.orientation_unit = orientationUnits elif orientationTagName == "pitch": self.detector.orientation.y = orientationData self.detector.orientation_unit = orientationUnits elif orientationTagName == "yaw": self.detector.orientation.z = orientationData self.detector.orientation_unit = orientationUnits self.current_datainfo.detector.append(self.detector) self.detector = Detector() ## If we'e dealing with a process node elif currentTagName == "SASprocess": for processNode in sasNode: setupTagName = setupNode.tag.replace(self.base_ns, "") units = setupNode.attrib.get("unit", "") if processTagName == "name": self.process.name = processNode.text elif processTagName == "description": self.process.description = processNode.text elif processTagName == "date": try: self.process.date = datetime.datetime.fromtimestamp(processNode.text) except: self.process.date = processNode.text elif processTagName == "term": unit = attr.get("unit", "") dic = {} dic["name"] = processNode.attrib.get("name", "") dic["value"] = processNode.text dic["unit"] = processNode.attrib.get("unit", "") self.process.term.append(dic) self.current_datainfo.process.append(self.process) self.process = Process() # If we're dealing with a process note node elif currentTagName == "SASprocessnote": for processNoteNode in sasNode: self.process.notes.append(processNoteNode.text) # If we're dealing with a sas note node elif currentTagName == "SASnote": for noteNode in sasNode: self.current_datainfo.notes.append(noteNode.text) # If we're dealing with a transmission data node elif currentTagName == "Tdata": for transmissionDataNode in sasNode: transmissionDataTagName = transmissionDataNode.tag.replace(self.base_ns, "") transmissionDataUnits = transmissionDataNode.attrib.get("unit", "") transmissionDataData = transmissionDataNode.text # Are there multiple entries here? if len(sasNode) <= 1: multipleEntries == False else: multipleEntries == True for setupNode in sasNode[0]: # Iterating through the tags in the unit node, getting their tag name and respective unit setupTagName = setupNode.tag.replace(self.base_ns, "") transmissionDataUnits = setupNode.attrib.get("unit", "") # Creating our data array first, if there's only one dataNode we will handle this... startArray = np.fromstring(setupNode.text, dtype=float, sep=",") if multipleEntries == True: setupArray = np.zeros((len(sasNode), len(startArray))) setupArray[0] = startArray else: setupArray = startArray ## Transmission Spectrum if setupTagName == "T": self.transspectrum.transmission = setupArray self.transspectrum.transmission_unit = transmissionDataUnits elif setupTagName == "Tdev": self.transspectrum.transmission_deviation = setupArray self.transspectrum.transmission_deviation_unit = transmissionDataUnits elif setupTagName == "Lambda": self.transspectrum.wavelength = setupArray self.transspectrum.wavelength_unit = transmissionDataUnits # If there's more data present, let's deal with that too for loopIter in range(1, len(sasNode)): for dataNode in sasNode[loopIter]: dataTagName = dataNode.tag.replace(self.base_ns, "") dataArray = np.fromstring(dataNode.text, dtype=float, sep=",") if dataTagName == "T": self.transspectrum.transmission[loopIter] = setupArray elif dataTagName == "Tdev": self.transspectrum.transmission_deviation[loopIter] = setupArray elif dataTagName == "Lambda": self.transspectrum.wavelength[loopIter] = setupArray self.current_datainfo.trans_spectrum.append(self.transspectrum) self.transspectrum = TransmissionSpectrum() ## Everything else goes in meta_data else: new_key = self._create_unique_key(self.current_datainfo.meta_data, currentTagName) self.current_datainfo.meta_data[new_key] = sasNode.text self.add_intermediate() # As before in the code, I guess in case we have to return a tuple for some reason... return self.output, 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 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 raise RuntimeError def load_file_and_schema(self, xml_file, schema_path=""): """ Loads the file and associates a schema, if a schema is passed in or if one already exists :param xml_file: The xml file path sent to Reader.read :param schema_path: The path to a schema associated with the xml_file, or find one based on the file """ 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 self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0") if schema_path == "": schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \ (base, self.cansas_defaults.get("schema")).replace("\\", "/") # Link a schema to the XML file. self.set_schema(schema_path) def add_data_set(self): """ Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a private method to generate a new data set. :param key: NeXus group name for current tree level """ if self.current_datainfo and self.current_dataset: self._final_cleanup() self.data = [] self.current_datainfo = DataInfo() def _initialize_new_data_set(self, node=None): """ A private class method to generate a new 1D data object. Outside methods should call add_data_set() to be sure any existing data is stored properly. :param node: XML node to determine if 1D or 2D data """ x = np.array(0) y = np.array(0) 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(x, y) def add_intermediate(self): """ This method stores any intermediate objects within the final data set after fully reading the set. :param parent: The NXclass name for the h5py Group object that just finished being processed """ 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._check_for_empty_resolution() self.data.append(self.current_dataset) def _final_cleanup(self): """ Final cleanup of the Data1D object to be sure it has all the appropriate information needed for perspectives """ # Append errors to dataset and reset class errors self.current_datainfo.errors = set() for error in self.errors: self.current_datainfo.errors.add(error) self.errors.clear() # Combine all plottables with datainfo and append each to output # Type cast data arrays to float64 and find min/max as appropriate for dataset in self.data: if isinstance(dataset, plottable_1D): if dataset.x is not None: dataset.x = np.delete(dataset.x, [0]) dataset.x = dataset.x.astype(np.float64) dataset.xmin = np.min(dataset.x) dataset.xmax = np.max(dataset.x) if dataset.y is not None: dataset.y = np.delete(dataset.y, [0]) dataset.y = dataset.y.astype(np.float64) dataset.ymin = np.min(dataset.y) dataset.ymax = np.max(dataset.y) if dataset.dx is not None: dataset.dx = np.delete(dataset.dx, [0]) dataset.dx = dataset.dx.astype(np.float64) if dataset.dxl is not None: dataset.dxl = np.delete(dataset.dxl, [0]) dataset.dxl = dataset.dxl.astype(np.float64) if dataset.dxw is not None: dataset.dxw = np.delete(dataset.dxw, [0]) dataset.dxw = dataset.dxw.astype(np.float64) if dataset.dy is not None: dataset.dy = np.delete(dataset.dy, [0]) dataset.dy = dataset.dy.astype(np.float64) np.trim_zeros(dataset.x) np.trim_zeros(dataset.y) np.trim_zeros(dataset.dy) elif isinstance(dataset, plottable_2D): dataset.data = dataset.data.astype(np.float64) dataset.qx_data = dataset.qx_data.astype(np.float64) dataset.xmin = np.min(dataset.qx_data) dataset.xmax = np.max(dataset.qx_data) dataset.qy_data = dataset.qy_data.astype(np.float64) dataset.ymin = np.min(dataset.qy_data) dataset.ymax = np.max(dataset.qy_data) dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data + dataset.qy_data * dataset.qy_data) if dataset.err_data is not None: dataset.err_data = dataset.err_data.astype(np.float64) if dataset.dqx_data is not None: dataset.dqx_data = dataset.dqx_data.astype(np.float64) if dataset.dqy_data is not None: dataset.dqy_data = dataset.dqy_data.astype(np.float64) if dataset.mask is not None: dataset.mask = dataset.mask.astype(dtype=bool) if len(dataset.shape) == 2: n_rows, n_cols = dataset.shape dataset.y_bins = dataset.qy_data[0::int(n_cols)] dataset.x_bins = dataset.qx_data[:int(n_cols)] dataset.data = dataset.data.flatten() else: dataset.y_bins = [] dataset.x_bins = [] dataset.data = dataset.data.flatten() final_dataset = combine_data(dataset, self.current_datainfo) self.output.append(final_dataset) def _create_unique_key(self, dictionary, name, numb=0): """ Create a unique key value for any dictionary to prevent overwriting Recurse 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 _get_node_value_from_text(self, node, node_text): """ 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 """ units = "" # 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_text is None or node_text.isspace() \ or node_text.lower() == "nan": node_text = "0.0" # Convert the value to the base units tag = node.tag.replace(self.base_ns, "") node_text, units = self._unit_conversion(node, tag, node_text) # If the value is a timestamp, convert to a datetime object elif self.ns_list.ns_datatype == "timestamp": if node_text is None or node_text.isspace(): pass else: try: node_text = \ datetime.datetime.fromtimestamp(node_text) except ValueError: node_text = None return node_text, units def _get_node_value(self, node): """ 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 = "" node_value, units = self._get_node_value_from_text(node, node_value) 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: local_unit = attr['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" exec "default_unit = self.{0}.{1}".format(save_in, unitname) if local_unit and default_unit 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) return node_value, value_unit def _check_for_empty_data(self): """ Creates an empty data set if no data is passed to the reader :param data1d: presumably a Data1D object """ if self.current_dataset is None: x_vals = np.empty(0) y_vals = np.empty(0) dx_vals = np.empty(0) dy_vals = np.empty(0) dxl = np.empty(0) dxw = np.empty(0) self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals) self.current_dataset.dxl = dxl self.current_dataset.dxw = dxw def _check_for_empty_resolution(self): """ A method to check all resolution data sets are the same size as I and Q """ if isinstance(self.current_dataset, plottable_1D): dql_exists = False dqw_exists = False dq_exists = False di_exists = False if self.current_dataset.dxl is not None: dql_exists = True if self.current_dataset.dxw is not None: dqw_exists = True if self.current_dataset.dx is not None: dq_exists = True if self.current_dataset.dy is not None: di_exists = True if dqw_exists and not dql_exists: array_size = self.current_dataset.dxw.size - 1 self.current_dataset.dxl = np.append(self.current_dataset.dxl, np.zeros([array_size])) elif dql_exists and not dqw_exists: array_size = self.current_dataset.dxl.size - 1 self.current_dataset.dxw = np.append(self.current_dataset.dxw, np.zeros([array_size])) elif not dql_exists and not dqw_exists and not dq_exists: array_size = self.current_dataset.x.size - 1 self.current_dataset.dx = np.append(self.current_dataset.dx, np.zeros([array_size])) if not di_exists: array_size = self.current_dataset.y.size - 1 self.current_dataset.dy = np.append(self.current_dataset.dy, np.zeros([array_size])) elif isinstance(self.current_dataset, plottable_2D): dqx_exists = False dqy_exists = False di_exists = False mask_exists = False if self.current_dataset.dqx_data is not None: dqx_exists = True if self.current_dataset.dqy_data is not None: dqy_exists = True if self.current_dataset.err_data is not None: di_exists = True if self.current_dataset.mask is not None: mask_exists = True if not dqy_exists: array_size = self.current_dataset.qy_data.size - 1 self.current_dataset.dqy_data = np.append( self.current_dataset.dqy_data, np.zeros([array_size])) if not dqx_exists: array_size = self.current_dataset.qx_data.size - 1 self.current_dataset.dqx_data = np.append( self.current_dataset.dqx_data, np.zeros([array_size])) if not di_exists: array_size = self.current_dataset.data.size - 1 self.current_dataset.err_data = np.append( self.current_dataset.err_data, np.zeros([array_size])) if not mask_exists: array_size = self.current_dataset.data.size - 1 self.current_dataset.mask = np.append( self.current_dataset.mask, np.ones([array_size] ,dtype=bool)) ####### All methods below are for writing CanSAS XML files ####### 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 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: if self._check_root(): self._write_data(datainfo, entry_node) else: self._write_data_linearized(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 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://www.cansas.org/formats/1.0/" 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._xaxis + " | " + datainfo._xunit}) if len(datainfo.y) >= i: self.write_node(point, "I", datainfo.y[i], {'unit': datainfo._yaxis + " | " + datainfo._yunit}) if datainfo.dy is not None and len(datainfo.dy) > i: self.write_node(point, "Idev", datainfo.dy[i], {'unit': datainfo._yaxis + " | " + datainfo._yunit}) if datainfo.dx is not None and len(datainfo.dx) > i: self.write_node(point, "Qdev", datainfo.dx[i], {'unit': datainfo._xaxis + " | " + datainfo._xunit}) if datainfo.dxw is not None and len(datainfo.dxw) > i: self.write_node(point, "dQw", datainfo.dxw[i], {'unit': datainfo._xaxis + " | " + datainfo._xunit}) if datainfo.dxl is not None and len(datainfo.dxl) > i: self.write_node(point, "dQl", datainfo.dxl[i], {'unit': datainfo._xaxis + " | " + datainfo._xunit}) if datainfo.isSesans: sesans = self.create_element("Sesans") sesans.text = str(datainfo.isSesans) node.append(sesans) self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0], {'unit': datainfo.sample.yacceptance[1]}) self.write_node(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(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))]) qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))]) intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(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(datainfo.err_data[i]) for i in xrange(len(datainfo.err_data))]) self.write_node(point, "Idev", err, {'unit': datainfo._zunit}) if datainfo.dqy_data is not None: dqy = ','.join([str(datainfo.dqy_data[i]) for i in xrange(len(datainfo.dqy_data))]) self.write_node(point, "Qydev", dqy, {'unit': datainfo._yunit}) if datainfo.dqx_data is not None: dqx = ','.join([str(datainfo.dqx_data[i]) for i in xrange(len(datainfo.dqx_data))]) self.write_node(point, "Qxdev", dqx, {'unit': datainfo._xunit}) if datainfo.mask is not None: mask = ','.join( ["1" if datainfo.mask[i] else "0" for i in xrange(len(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 == 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 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 == 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 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 == 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 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 == 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}) if written == True: 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_root(self): """ 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()[2] mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") mod_name = mod_name.replace(".py", "") mod = mod_name.split("sas/") mod_name = mod[1] return mod_name == "sascalc/dataloader/readers/cansas_reader" 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._check_root(): 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: 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 is not 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: logger.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: logger.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 # 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