| 1 | """ |
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| 2 | CanSAS data reader - new recursive cansas_version. |
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| 3 | """ |
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| 4 | ############################################################################ |
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| 5 | #This software was developed by the University of Tennessee as part of the |
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| 6 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 7 | #project funded by the US National Science Foundation. |
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| 8 | #If you use DANSE applications to do scientific research that leads to |
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| 9 | #publication, we ask that you acknowledge the use of the software with the |
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| 10 | #following sentence: |
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| 11 | #This work benefited from DANSE software developed under NSF award DMR-0520547. |
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| 12 | #copyright 2008,2009 University of Tennessee |
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| 13 | ############################################################################# |
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| 14 | |
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| 15 | import logging |
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| 16 | import numpy as np |
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| 17 | import os |
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| 18 | import sys |
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| 19 | import datetime |
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| 20 | import inspect |
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| 21 | # For saving individual sections of data |
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| 22 | from sas.sascalc.dataloader.data_info import Data1D, Data2D, DataInfo, \ |
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| 23 | plottable_1D, plottable_2D |
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| 24 | from sas.sascalc.dataloader.data_info import Collimation, TransmissionSpectrum, \ |
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| 25 | Detector, Process, Aperture |
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| 26 | from sas.sascalc.dataloader.data_info import \ |
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| 27 | combine_data_info_with_plottable as combine_data |
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| 28 | import sas.sascalc.dataloader.readers.xml_reader as xml_reader |
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| 29 | from sas.sascalc.dataloader.readers.xml_reader import XMLreader |
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| 30 | from sas.sascalc.dataloader.readers.cansas_constants import CansasConstants, CurrentLevel |
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| 31 | |
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| 32 | # The following 2 imports *ARE* used. Do not remove either. |
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| 33 | import xml.dom.minidom |
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| 34 | from xml.dom.minidom import parseString |
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| 35 | |
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| 36 | logger = logging.getLogger(__name__) |
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| 37 | |
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| 38 | PREPROCESS = "xmlpreprocess" |
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| 39 | ENCODING = "encoding" |
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| 40 | RUN_NAME_DEFAULT = "None" |
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| 41 | INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd" |
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| 42 | INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd" |
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| 43 | INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \ |
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| 44 | "as much of the data as possible.\n\n" |
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| 45 | HAS_CONVERTER = True |
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| 46 | try: |
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| 47 | from sas.sascalc.data_util.nxsunit import Converter |
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| 48 | except ImportError: |
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| 49 | HAS_CONVERTER = False |
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| 50 | |
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| 51 | CONSTANTS = CansasConstants() |
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| 52 | CANSAS_FORMAT = CONSTANTS.format |
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| 53 | CANSAS_NS = CONSTANTS.names |
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| 54 | ALLOW_ALL = True |
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| 55 | |
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| 56 | class Reader(XMLreader): |
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| 57 | """ |
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| 58 | Class to load cansas 1D XML files |
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| 59 | |
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| 60 | :Dependencies: |
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| 61 | The CanSAS reader requires PyXML 0.8.4 or later. |
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| 62 | """ |
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| 63 | # CanSAS version - defaults to version 1.0 |
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| 64 | cansas_version = "1.0" |
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| 65 | base_ns = "{cansas1d/1.0}" |
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| 66 | cansas_defaults = None |
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| 67 | type_name = "canSAS" |
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| 68 | invalid = True |
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| 69 | frm = "" |
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| 70 | # Log messages and errors |
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| 71 | logging = None |
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| 72 | errors = set() |
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| 73 | # Namespace hierarchy for current xml_file object |
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| 74 | names = None |
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| 75 | ns_list = None |
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| 76 | # Temporary storage location for loading multiple data sets in a single file |
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| 77 | current_datainfo = None |
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| 78 | current_dataset = None |
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| 79 | current_data1d = None |
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| 80 | data = None |
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| 81 | # List of data1D objects to be sent back to SasView |
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| 82 | output = None |
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| 83 | # Wildcards |
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| 84 | type = ["XML files (*.xml)|*.xml", "SasView Save Files (*.svs)|*.svs"] |
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| 85 | # List of allowed extensions |
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| 86 | ext = ['.xml', '.XML', '.svs', '.SVS'] |
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| 87 | # Flag to bypass extension check |
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| 88 | allow_all = True |
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| 89 | |
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| 90 | def reset_state(self): |
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| 91 | """ |
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| 92 | Resets the class state to a base case when loading a new data file so previous |
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| 93 | data files do not appear a second time |
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| 94 | """ |
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| 95 | self.current_datainfo = None |
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| 96 | self.current_dataset = None |
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| 97 | self.current_data1d = None |
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| 98 | self.data = [] |
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| 99 | self.process = Process() |
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| 100 | self.transspectrum = TransmissionSpectrum() |
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| 101 | self.aperture = Aperture() |
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| 102 | self.collimation = Collimation() |
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| 103 | self.detector = Detector() |
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| 104 | self.names = [] |
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| 105 | self.cansas_defaults = {} |
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| 106 | self.output = [] |
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| 107 | self.ns_list = None |
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| 108 | self.logging = [] |
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| 109 | self.encoding = None |
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| 110 | |
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| 111 | def read(self, xml_file, schema_path="", invalid=True): |
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| 112 | """ |
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| 113 | Validate and read in an xml_file file in the canSAS format. |
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| 114 | |
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| 115 | :param xml_file: A canSAS file path in proper XML format |
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| 116 | :param schema_path: A file path to an XML schema to validate the xml_file against |
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| 117 | """ |
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| 118 | # For every file loaded, reset everything to a base state |
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| 119 | self.reset_state() |
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| 120 | self.invalid = invalid |
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| 121 | # Check that the file exists |
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| 122 | if os.path.isfile(xml_file): |
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| 123 | basename, extension = os.path.splitext(os.path.basename(xml_file)) |
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| 124 | # If the file type is not allowed, return nothing |
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| 125 | if extension in self.ext or self.allow_all: |
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| 126 | # Get the file location of |
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| 127 | self.load_file_and_schema(xml_file, schema_path) |
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| 128 | self.add_data_set() |
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| 129 | # Try to load the file, but raise an error if unable to. |
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| 130 | # Check the file matches the XML schema |
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| 131 | try: |
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| 132 | self.is_cansas(extension) |
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| 133 | self.invalid = False |
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| 134 | # Get each SASentry from XML file and add it to a list. |
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| 135 | entry_list = self.xmlroot.xpath( |
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| 136 | '/ns:SASroot/ns:SASentry', |
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| 137 | namespaces={'ns': self.cansas_defaults.get("ns")}) |
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| 138 | self.names.append("SASentry") |
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| 139 | |
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| 140 | # Get all preprocessing events and encoding |
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| 141 | self.set_processing_instructions() |
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| 142 | |
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| 143 | # Parse each <SASentry> item |
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| 144 | for entry in entry_list: |
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| 145 | # Create a new DataInfo object for every <SASentry> |
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| 146 | |
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| 147 | # Set the file name and then parse the entry. |
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| 148 | self.current_datainfo.filename = basename + extension |
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| 149 | self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D" |
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| 150 | self.current_datainfo.meta_data[PREPROCESS] = \ |
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| 151 | self.processing_instructions |
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| 152 | |
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| 153 | # Parse the XML SASentry |
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| 154 | self._parse_entry(entry) |
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| 155 | # Combine datasets with datainfo |
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| 156 | self.add_data_set() |
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| 157 | except RuntimeError: |
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| 158 | # If the file does not match the schema, raise this error |
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| 159 | invalid_xml = self.find_invalid_xml() |
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| 160 | invalid_xml = INVALID_XML.format(basename + extension) + invalid_xml |
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| 161 | self.errors.add(invalid_xml) |
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| 162 | # Try again with an invalid CanSAS schema, that requires only a data set in each |
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| 163 | base_name = xml_reader.__file__ |
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| 164 | base_name = base_name.replace("\\", "/") |
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| 165 | base = base_name.split("/sas/")[0] |
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| 166 | if self.cansas_version == "1.1": |
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| 167 | invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema")) |
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| 168 | else: |
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| 169 | invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema")) |
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| 170 | self.set_schema(invalid_schema) |
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| 171 | try: |
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| 172 | if self.invalid: |
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| 173 | if self.is_cansas(): |
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| 174 | self.output = self.read(xml_file, invalid_schema, False) |
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| 175 | else: |
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| 176 | raise RuntimeError |
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| 177 | else: |
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| 178 | raise RuntimeError |
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| 179 | except RuntimeError: |
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| 180 | x = np.zeros(1) |
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| 181 | y = np.zeros(1) |
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| 182 | self.current_data1d = Data1D(x,y) |
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| 183 | self.current_data1d.errors = self.errors |
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| 184 | return [self.current_data1d] |
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| 185 | else: |
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| 186 | self.output.append("Not a valid file path.") |
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| 187 | # Return a list of parsed entries that dataloader can manage |
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| 188 | return self.output |
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| 189 | |
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| 190 | def _parse_entry(self, dom, recurse=False): |
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| 191 | """ |
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| 192 | Parse a SASEntry - new recursive method for parsing the dom of |
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| 193 | the CanSAS data format. This will allow multiple data files |
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| 194 | and extra nodes to be read in simultaneously. |
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| 195 | |
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| 196 | :param dom: dom object with a namespace base of names |
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| 197 | """ |
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| 198 | |
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| 199 | self._check_for_empty_data() |
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| 200 | self._initialize_new_data_set(dom) |
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| 201 | |
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| 202 | self.names.append("SASentry") |
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| 203 | self.parent_class = "SASentry" |
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| 204 | |
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| 205 | self.base_ns = "{0}{1}{2}".format("{", \ |
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| 206 | CANSAS_NS.get(self.cansas_version).get("ns"), "}") |
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| 207 | |
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| 208 | self.ns_list = CONSTANTS.iterate_namespace(self.names) |
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| 209 | |
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| 210 | # Go through each child in the parent element |
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| 211 | for sasNode in dom: |
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| 212 | # Get the element name and set the current name's level |
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| 213 | currentTagName = sasNode.tag.replace(self.base_ns, "") |
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| 214 | # As this is the most likely tag to examine, lets put it first! |
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| 215 | if currentTagName == "SASdata": |
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| 216 | # Are there multiple entries here? |
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| 217 | if len(sasNode) <= 1: |
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| 218 | multipleEntries = False |
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| 219 | else: |
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| 220 | multipleEntries = True |
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| 221 | |
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| 222 | for setupNode in sasNode[0]: |
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| 223 | # Iterating through the tags in the unit node, getting their tag name and respective unit |
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| 224 | setupTagName = setupNode.tag.replace(self.base_ns, "") |
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| 225 | units = setupNode.attrib.get("unit", "") |
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| 226 | |
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| 227 | # Creating our data array first, if there's only one dataNode we will handle this... |
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| 228 | startArray = np.fromstring(setupNode.text, dtype=float, sep=",") |
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| 229 | |
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| 230 | if multipleEntries == True: |
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| 231 | setupArray = np.zeros((len(sasNode), len(startArray))) |
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| 232 | setupArray[0] = startArray |
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| 233 | else: |
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| 234 | setupArray = startArray |
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| 235 | |
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| 236 | # Now put this into the relevant location |
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| 237 | if setupTagName == "I": |
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| 238 | self.current_dataset.yaxis("Intensity", units) |
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| 239 | self.current_dataset.y = setupArray |
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| 240 | elif setupTagName == "Q": |
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| 241 | self.current_dataset.xaxis("Q", units) |
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| 242 | self.current_dataset.x = setupArray |
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| 243 | |
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| 244 | elif setupTagName == "Idev": |
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| 245 | self.current_dataset.dy = setupArray |
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| 246 | elif setupTagName == "Qdev": |
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| 247 | self.current_dataset.dx = setupArray |
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| 248 | |
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| 249 | elif setupTagName == "Qx": |
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| 250 | self.current_dataset.xaxis("Qx", units) |
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| 251 | self.current_dataset.qx_data = setupArray |
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| 252 | elif setupTagName == "Qy": |
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| 253 | self.current_dataset.yaxis("Qy", units) |
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| 254 | self.current_dataset.qy_data = setupArray |
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| 255 | elif setupTagName == "Qxdev": |
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| 256 | self.current_dataset.xaxis("Qxdev", units) |
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| 257 | self.current_dataset.dqx_data = setupArray |
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| 258 | elif setupTagName == "Qydev": |
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| 259 | self.current_dataset.yaxis("Qydev", units) |
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| 260 | self.current_dataset.dqy_data = setupArray |
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| 261 | elif setupTagName == "dQw": |
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| 262 | self.current_dataset.dxw = setupArray |
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| 263 | elif setupTagName == "dQl": |
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| 264 | self.current_dataset.dxl = setupArray |
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| 265 | |
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| 266 | elif setupTagName == "Mask": |
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| 267 | self.current_dataset.mask = np.ndarray.astype(setupArray, dtype=bool) |
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| 268 | elif setupTagName == "Sesans": |
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| 269 | self.current_datainfo.isSesans = bool(setupNode.text) |
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| 270 | |
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| 271 | elif setupTagName == "zacceptance": |
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| 272 | self.current_datainfo.sample.zacceptance = (setupNode.text, units) |
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| 273 | elif setupTagName == "Qmean": |
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| 274 | pass |
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| 275 | elif setupTagName == "Shadowfactor": |
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| 276 | pass |
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| 277 | |
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| 278 | # If there's more data present, let's deal with that too |
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| 279 | for loopIter in range(1, len(sasNode)): |
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| 280 | for dataNode in sasNode[loopIter]: |
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| 281 | # Iterating through the tags in the unit node, getting their tag name and respective unit |
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| 282 | dataTagName = dataNode.tag.replace(self.base_ns, "") |
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| 283 | # Creating our data array first |
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| 284 | dataArray = np.fromstring(dataNode.text, dtype=float, sep=",") |
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| 285 | |
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| 286 | if dataTagName == "I": |
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| 287 | self.current_dataset.y[loopIter] = dataArray |
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| 288 | elif dataTagName == "Q": |
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| 289 | self.current_dataset.x[loopIter] = dataArray |
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| 290 | elif dataTagName == "Idev": |
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| 291 | self.current_dataset.dy[loopIter] = dataArray |
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| 292 | elif dataTagName == "Qdev": |
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| 293 | self.current_dataset.dx[loopIter] = dataArray |
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| 294 | elif dataTagName == "Qx": |
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| 295 | self.current_dataset.qx_data[loopIter] = dataArray |
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| 296 | elif dataTagName == "Qy": |
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| 297 | self.current_dataset.qy_data[loopIter] = dataArray |
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| 298 | elif dataTagName == "Qxdev": |
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| 299 | self.current_dataset.dqx_data[loopIter] = dataArray |
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| 300 | elif dataTagName == "Qydev": |
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| 301 | self.current_dataset.dqy_data[loopIter] = dataArray |
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| 302 | elif dataTagName == "dQw": |
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| 303 | self.current_dataset.dxw[loopIter] = dataArray |
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| 304 | elif dataTagName == "dQl": |
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| 305 | self.current_dataset.dxl[loopIter] = dataArray |
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| 306 | |
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| 307 | self._check_for_empty_resolution() |
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| 308 | self.data.append(self.current_dataset) |
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| 309 | |
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| 310 | # If it's not data, let's check for other tags starting with skippable ones... |
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| 311 | elif currentTagName == "fitting_plug_in" or currentTagName == "pr_inversion" or currentTagName == "invariant": |
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| 312 | continue |
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| 313 | |
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| 314 | # If we'e dealing with a title node then extract the text of the node and put it in the right place |
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| 315 | elif currentTagName == "Title": |
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| 316 | self.current_datainfo.title = sasNode.text |
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| 317 | |
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| 318 | |
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| 319 | # If we'e dealing with a run node then extract the name and text of the node and put it in the right place |
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| 320 | elif currentTagName == "Run": |
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| 321 | self.current_datainfo.run_name[sasNode.text] = sasNode.attrib.get("name", "") |
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| 322 | self.current_datainfo.run.append(sasNode.text) |
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| 323 | |
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| 324 | # If we'e dealing with a sample node |
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| 325 | elif currentTagName == "SASsample": |
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| 326 | for sampleNode in sasNode: |
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| 327 | # Get the variables |
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| 328 | sampleTagName = sampleNode.tag.replace(self.base_ns, "") |
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| 329 | sampleUnits = sampleNode.attrib.get("unit", "") |
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| 330 | sampleData = sampleNode.text |
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| 331 | |
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| 332 | # Populate it via if switching |
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| 333 | if sampleTagName == "ID": |
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| 334 | self.current_datainfo.sample.ID = sampleData |
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| 335 | elif sampleTagName == "Title": |
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| 336 | self.current_datainfo.sample.name = sampleData |
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| 337 | elif sampleTagName == "thickness": |
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| 338 | self.current_datainfo.sample.thickness = sampleData |
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| 339 | self.current_datainfo.sample.thickness_unit = sampleUnits |
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| 340 | elif sampleTagName == "transmission": |
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| 341 | self.current_datainfo.sample.transmission = sampleData |
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| 342 | elif sampleTagName == "temperature": |
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| 343 | self.current_datainfo.sample.temperature = sampleData |
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| 344 | self.current_datainfo.sample.temperature_unit = sampleUnits |
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| 345 | elif sampleTagName == "details": |
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| 346 | self.current_datainfo.sample.details.append(sampleData) |
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| 347 | |
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| 348 | # Extract the positional data |
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| 349 | elif sampleTagName == "position": |
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| 350 | for positionNode in sampleNode: |
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| 351 | positionTagName = positionNode.tag.replace(self.base_ns, "") |
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| 352 | positionUnits = positionNode.attrib.get("unit", "") |
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| 353 | positionData = positionNode.text |
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| 354 | |
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| 355 | # Extract specific tags |
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| 356 | if positionTagName == "x": |
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| 357 | self.current_datainfo.sample.position.x = positionData |
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| 358 | self.current_datainfo.sample.position_unit = positionUnits |
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| 359 | elif positionTagName == "y": |
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| 360 | self.current_datainfo.sample.position.y = positionData |
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| 361 | self.current_datainfo.sample.position_unit = positionUnits |
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| 362 | elif positionTagName == "z": |
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| 363 | self.current_datainfo.sample.position.z = positionData |
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| 364 | self.current_datainfo.sample.position_unit = positionUnits |
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| 365 | |
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| 366 | # Extract the orientation data |
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| 367 | elif sampleTagName == "orientation": |
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| 368 | for orientationNode in sampleNode: |
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| 369 | orientationTagName = orientationNode.tag.replace(self.base_ns, "") |
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| 370 | orientationUnits = orientationNode.attrib.get("unit", "") |
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| 371 | orientationData = orientationNode.text |
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| 372 | |
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| 373 | # Extract specific tags |
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| 374 | if orientationTagName == "roll": |
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| 375 | self.current_datainfo.sample.orientation.x = orientationData |
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| 376 | self.current_datainfo.sample.orientation_unit = orientationUnits |
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| 377 | elif orientationTagName == "pitch": |
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| 378 | self.current_datainfo.sample.orientation.y = orientationData |
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| 379 | self.current_datainfo.sample.orientation_unit = orientationUnits |
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| 380 | elif orientationTagName == "yaw": |
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| 381 | self.current_datainfo.sample.orientation.z = orientationData |
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| 382 | self.current_datainfo.sample.orientation_unit = orientationUnits |
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| 383 | |
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| 384 | # If we're dealing with an instrument node |
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| 385 | elif currentTagName == "SASinstrument": |
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| 386 | for instrumentNode in sasNode: |
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| 387 | instrumentTagName = instrumentNode.tag.replace(self.base_ns, "") |
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| 388 | instrumentUnits = instrumentNode.attrib.get("unit", "") |
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| 389 | instrumentData = instrumentNode.text |
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| 390 | |
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| 391 | # Extract the source name |
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| 392 | if instrumentTagName == "SASsource": |
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| 393 | self.name = instrumentNode.attrib.get("name", "") |
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| 394 | |
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| 395 | for sourceNode in instrumentNode: |
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| 396 | sourceTagName = sourceNode.tag.replace(self.base_ns, "") |
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| 397 | sourceUnits = sourceNode.attrib.get("unit", "") |
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| 398 | sourceData = sourceNode.text |
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| 399 | |
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| 400 | ## Source Information |
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| 401 | if sourceTagName == "wavelength": |
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| 402 | self.current_datainfo.source.wavelength = sourceData |
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| 403 | self.current_datainfo.source.wavelength_unit = sourceUnits |
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| 404 | elif sourceTagName == "wavelength_min": |
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| 405 | self.current_datainfo.source.wavelength_min = sourceData |
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| 406 | self.current_datainfo.source.wavelength_min_unit = sourceUnits |
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| 407 | elif sourceTagName == "wavelength_max": |
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| 408 | self.current_datainfo.source.wavelength_max = sourceData |
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| 409 | self.current_datainfo.source.wavelength_max_unit = sourceUnits |
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| 410 | elif sourceTagName == "wavelength_spread": |
|---|
| 411 | self.current_datainfo.source.wavelength_spread = sourceData |
|---|
| 412 | self.current_datainfo.source.wavelength_spread_unit = sourceUnits |
|---|
| 413 | elif sourceTagName == "radiation": |
|---|
| 414 | self.current_datainfo.source.radiation = sourceData |
|---|
| 415 | elif sourceTagName == "beam_shape": |
|---|
| 416 | self.current_datainfo.source.beam_shape = sourceData |
|---|
| 417 | |
|---|
| 418 | elif sourceTagName == "beam_size": |
|---|
| 419 | for beamNode in sourceNode: |
|---|
| 420 | beamTagName = beamNode.tag.replace(self.base_ns, "") |
|---|
| 421 | beamUnits = beamNode.attrib.get("unit", "") |
|---|
| 422 | beamData = beamNode.text |
|---|
| 423 | |
|---|
| 424 | if beamTagName == "x" and self.parent_class == "beam_size": |
|---|
| 425 | self.current_datainfo.source.beam_size.x = beamData |
|---|
| 426 | self.current_datainfo.source.beam_size_unit = beamUnits |
|---|
| 427 | elif beamTagName == "y" and self.parent_class == "beam_size": |
|---|
| 428 | self.current_datainfo.source.beam_size.y = beamData |
|---|
| 429 | self.current_datainfo.source.beam_size_unit = beamUnits |
|---|
| 430 | |
|---|
| 431 | elif sourceTagName == "pixel_size": |
|---|
| 432 | for pixelNode in sourceNode: |
|---|
| 433 | pixelTagName = pixelNode.tag.replace(self.base_ns, "") |
|---|
| 434 | pixelUnits = pixelNode.attrib.get("unit", "") |
|---|
| 435 | pixelData = pixelNode.text |
|---|
| 436 | |
|---|
| 437 | if pixelTagName == "z": |
|---|
| 438 | self.current_datainfo.source.data_point.z = pixelData |
|---|
| 439 | self.current_datainfo.source.beam_size_unit = pixelUnits |
|---|
| 440 | |
|---|
| 441 | # Extract the collimation |
|---|
| 442 | elif instrumentTagName == "SAScollimation": |
|---|
| 443 | self.collimation.name = instrumentNode.attrib.get("name", "") |
|---|
| 444 | |
|---|
| 445 | for collimationNode in instrumentNode: |
|---|
| 446 | collimationTagName = pixelNode.tag.replace(self.base_ns, "") |
|---|
| 447 | collimationUnits = pixelNode.attrib.get("unit", "") |
|---|
| 448 | collimationData = pixelNode.text |
|---|
| 449 | |
|---|
| 450 | if collimationTagName == "length": |
|---|
| 451 | self.collimation.length = collimationData |
|---|
| 452 | self.collimation.length_unit = collimationUnits |
|---|
| 453 | elif collimationTagName == "name": |
|---|
| 454 | self.collimation.name = collimationData |
|---|
| 455 | |
|---|
| 456 | if collimationTagName == "aperture": |
|---|
| 457 | for apertureNode in collimationNode: |
|---|
| 458 | apertureTagName = apertureNode.tag.replace(self.base_ns, "") |
|---|
| 459 | apertureUnits = apertureNode.attrib.get("unit", "") |
|---|
| 460 | apertureData = apertureNode.text |
|---|
| 461 | |
|---|
| 462 | if tagname == "distance": |
|---|
| 463 | self.aperture.distance = apertureData |
|---|
| 464 | self.aperture.distance_unit = apertureUnits |
|---|
| 465 | |
|---|
| 466 | if collimationTagName == "size": |
|---|
| 467 | for sizeNode in collimationNode: |
|---|
| 468 | sizeTagName = sizeNode.tag.replace(self.base_ns, "") |
|---|
| 469 | sizeUnits = sizeNode.attrib.get("unit", "") |
|---|
| 470 | sizeData = sizeNode.text |
|---|
| 471 | |
|---|
| 472 | if tagname == "x": |
|---|
| 473 | self.aperture.size.x = sizeData |
|---|
| 474 | self.collimation.size_unit = sizeUnits |
|---|
| 475 | elif tagname == "y": |
|---|
| 476 | self.aperture.size.y = sizeData |
|---|
| 477 | self.collimation.size_unit = sizeUnits |
|---|
| 478 | elif tagname == "z": |
|---|
| 479 | self.aperture.size.z = sizeData |
|---|
| 480 | self.collimation.size_unit = sizeUnits |
|---|
| 481 | |
|---|
| 482 | self.current_datainfo.collimation.append(self.collimation) |
|---|
| 483 | self.collimation = Collimation() |
|---|
| 484 | |
|---|
| 485 | # Extract the detector |
|---|
| 486 | elif instrumentTagName == "SASdetector": |
|---|
| 487 | self.name = instrumentNode.attrib.get("name", "") |
|---|
| 488 | |
|---|
| 489 | for detectorNode in instrumentNode: |
|---|
| 490 | detectorTagName = detectorNode.tag.replace(self.base_ns, "") |
|---|
| 491 | detectorUnits = detectorNode.attrib.get("unit", "") |
|---|
| 492 | detectorData = detectorNode.text |
|---|
| 493 | |
|---|
| 494 | if detectorTagName == "name": |
|---|
| 495 | self.detector.name = detectorData |
|---|
| 496 | elif detectorTagName == "SDD": |
|---|
| 497 | self.detector.distance = detectorData |
|---|
| 498 | self.detector.distance_unit = detectorUnits |
|---|
| 499 | elif detectorTagName == "slit_length": |
|---|
| 500 | self.detector.slit_length = detectorData |
|---|
| 501 | self.detector.slit_length_unit = detectorUnits |
|---|
| 502 | |
|---|
| 503 | elif detectorTagName == "offset": |
|---|
| 504 | for offsetNode in detectorNode: |
|---|
| 505 | offsetTagName = offsetNode.tag.replace(self.base_ns, "") |
|---|
| 506 | offsetUnits = offsetNode.attrib.get("unit", "") |
|---|
| 507 | offsetData = offsetNode.text |
|---|
| 508 | |
|---|
| 509 | if offsetTagName == "x": |
|---|
| 510 | self.detector.offset.x = offsetData |
|---|
| 511 | self.detector.offset_unit = offsetUnits |
|---|
| 512 | elif offsetTagName == "y": |
|---|
| 513 | self.detector.offset.y = offsetData |
|---|
| 514 | self.detector.offset_unit = offsetUnits |
|---|
| 515 | elif offsetTagName == "z": |
|---|
| 516 | self.detector.offset.z = offsetData |
|---|
| 517 | self.detector.offset_unit = offsetUnits |
|---|
| 518 | |
|---|
| 519 | elif detectorTagName == "beam_center": |
|---|
| 520 | for beamCenterNode in detectorNode: |
|---|
| 521 | beamCenterTagName = beamCenterNode.tag.replace(self.base_ns, "") |
|---|
| 522 | beamCenterUnits = beamCenterNode.attrib.get("unit", "") |
|---|
| 523 | beamCenterData = beamCenterNode.text |
|---|
| 524 | |
|---|
| 525 | if beamCenterTagName == "x": |
|---|
| 526 | self.detector.beam_center.x = beamCenterData |
|---|
| 527 | self.detector.beam_center_unit = beamCenterUnits |
|---|
| 528 | elif beamCenterTagName == "y": |
|---|
| 529 | self.detector.beam_center.y = beamCenterData |
|---|
| 530 | self.detector.beam_center_unit = beamCenterUnits |
|---|
| 531 | elif beamCenterTagName == "z": |
|---|
| 532 | self.detector.beam_center.z = beamCenterData |
|---|
| 533 | self.detector.beam_center_unit = beamCenterUnits |
|---|
| 534 | |
|---|
| 535 | elif detectorTagName == "pixel_size": |
|---|
| 536 | for pixelSizeNode in detectorNode: |
|---|
| 537 | pixelSizeTagName = pixelSizeNode.tag.replace(self.base_ns, "") |
|---|
| 538 | pixelSizeUnits = pixelSizeNode.attrib.get("unit", "") |
|---|
| 539 | pixelSizeData = pixelSizeNode.text |
|---|
| 540 | |
|---|
| 541 | if pixelSizeTagName == "x": |
|---|
| 542 | self.detector.pixel_size.x = pixelSizeData |
|---|
| 543 | self.detector.pixel_size_unit = pixelSizeUnits |
|---|
| 544 | elif pixelSizeTagName == "y": |
|---|
| 545 | self.detector.pixel_size.y = pixelSizeData |
|---|
| 546 | self.detector.pixel_size_unit = pixelSizeUnits |
|---|
| 547 | elif pixelSizeTagName == "z": |
|---|
| 548 | self.detector.pixel_size.z = pixelSizeData |
|---|
| 549 | self.detector.pixel_size_unit = pixelSizeUnits |
|---|
| 550 | |
|---|
| 551 | elif detectorTagName == "orientation": |
|---|
| 552 | for orientationNode in detectorNode: |
|---|
| 553 | orientationTagName = orientationNode.tag.replace(self.base_ns, "") |
|---|
| 554 | orientationUnits = orientationNode.attrib.get("unit", "") |
|---|
| 555 | orientationData = orientationNode.text |
|---|
| 556 | |
|---|
| 557 | if orientationTagName == "roll": |
|---|
| 558 | self.detector.orientation.x = orientationData |
|---|
| 559 | self.detector.orientation_unit = orientationUnits |
|---|
| 560 | elif orientationTagName == "pitch": |
|---|
| 561 | self.detector.orientation.y = orientationData |
|---|
| 562 | self.detector.orientation_unit = orientationUnits |
|---|
| 563 | elif orientationTagName == "yaw": |
|---|
| 564 | self.detector.orientation.z = orientationData |
|---|
| 565 | self.detector.orientation_unit = orientationUnits |
|---|
| 566 | |
|---|
| 567 | self.current_datainfo.detector.append(self.detector) |
|---|
| 568 | self.detector = Detector() |
|---|
| 569 | |
|---|
| 570 | ## If we'e dealing with a process node |
|---|
| 571 | elif currentTagName == "SASprocess": |
|---|
| 572 | for processNode in sasNode: |
|---|
| 573 | setupTagName = setupNode.tag.replace(self.base_ns, "") |
|---|
| 574 | units = setupNode.attrib.get("unit", "") |
|---|
| 575 | |
|---|
| 576 | if processTagName == "name": |
|---|
| 577 | self.process.name = processNode.text |
|---|
| 578 | elif processTagName == "description": |
|---|
| 579 | self.process.description = processNode.text |
|---|
| 580 | elif processTagName == "date": |
|---|
| 581 | try: |
|---|
| 582 | self.process.date = datetime.datetime.fromtimestamp(processNode.text) |
|---|
| 583 | except: |
|---|
| 584 | self.process.date = processNode.text |
|---|
| 585 | elif processTagName == "term": |
|---|
| 586 | unit = attr.get("unit", "") |
|---|
| 587 | dic = {} |
|---|
| 588 | dic["name"] = processNode.attrib.get("name", "") |
|---|
| 589 | dic["value"] = processNode.text |
|---|
| 590 | dic["unit"] = processNode.attrib.get("unit", "") |
|---|
| 591 | self.process.term.append(dic) |
|---|
| 592 | |
|---|
| 593 | self.current_datainfo.process.append(self.process) |
|---|
| 594 | self.process = Process() |
|---|
| 595 | |
|---|
| 596 | # If we're dealing with a process note node |
|---|
| 597 | elif currentTagName == "SASprocessnote": |
|---|
| 598 | for processNoteNode in sasNode: |
|---|
| 599 | self.process.notes.append(processNoteNode.text) |
|---|
| 600 | |
|---|
| 601 | # If we're dealing with a sas note node |
|---|
| 602 | elif currentTagName == "SASnote": |
|---|
| 603 | for noteNode in sasNode: |
|---|
| 604 | self.current_datainfo.notes.append(noteNode.text) |
|---|
| 605 | |
|---|
| 606 | # If we're dealing with a transmission data node |
|---|
| 607 | elif currentTagName == "Tdata": |
|---|
| 608 | for transmissionDataNode in sasNode: |
|---|
| 609 | transmissionDataTagName = transmissionDataNode.tag.replace(self.base_ns, "") |
|---|
| 610 | transmissionDataUnits = transmissionDataNode.attrib.get("unit", "") |
|---|
| 611 | transmissionDataData = transmissionDataNode.text |
|---|
| 612 | |
|---|
| 613 | # Are there multiple entries here? |
|---|
| 614 | if len(sasNode) <= 1: |
|---|
| 615 | multipleEntries == False |
|---|
| 616 | else: |
|---|
| 617 | multipleEntries == True |
|---|
| 618 | |
|---|
| 619 | for setupNode in sasNode[0]: |
|---|
| 620 | # Iterating through the tags in the unit node, getting their tag name and respective unit |
|---|
| 621 | setupTagName = setupNode.tag.replace(self.base_ns, "") |
|---|
| 622 | transmissionDataUnits = setupNode.attrib.get("unit", "") |
|---|
| 623 | |
|---|
| 624 | # Creating our data array first, if there's only one dataNode we will handle this... |
|---|
| 625 | startArray = np.fromstring(setupNode.text, dtype=float, sep=",") |
|---|
| 626 | |
|---|
| 627 | if multipleEntries == True: |
|---|
| 628 | setupArray = np.zeros((len(sasNode), len(startArray))) |
|---|
| 629 | setupArray[0] = startArray |
|---|
| 630 | else: |
|---|
| 631 | <<<<<<< HEAD |
|---|
| 632 | setupArray = startArray |
|---|
| 633 | |
|---|
| 634 | ## Transmission Spectrum |
|---|
| 635 | if setupTagName == "T": |
|---|
| 636 | self.transspectrum.transmission = setupArray |
|---|
| 637 | self.transspectrum.transmission_unit = transmissionDataUnits |
|---|
| 638 | elif setupTagName == "Tdev": |
|---|
| 639 | self.transspectrum.transmission_deviation = setupArray |
|---|
| 640 | self.transspectrum.transmission_deviation_unit = transmissionDataUnits |
|---|
| 641 | elif setupTagName == "Lambda": |
|---|
| 642 | self.transspectrum.wavelength = setupArray |
|---|
| 643 | self.transspectrum.wavelength_unit = transmissionDataUnits |
|---|
| 644 | |
|---|
| 645 | # If there's more data present, let's deal with that too |
|---|
| 646 | for loopIter in range(1, len(sasNode)): |
|---|
| 647 | for dataNode in sasNode[loopIter]: |
|---|
| 648 | dataTagName = dataNode.tag.replace(self.base_ns, "") |
|---|
| 649 | dataArray = np.fromstring(dataNode.text, dtype=float, sep=",") |
|---|
| 650 | |
|---|
| 651 | if dataTagName == "T": |
|---|
| 652 | self.transspectrum.transmission[loopIter] = setupArray |
|---|
| 653 | elif dataTagName == "Tdev": |
|---|
| 654 | self.transspectrum.transmission_deviation[loopIter] = setupArray |
|---|
| 655 | elif dataTagName == "Lambda": |
|---|
| 656 | self.transspectrum.wavelength[loopIter] = setupArray |
|---|
| 657 | |
|---|
| 658 | self.current_datainfo.trans_spectrum.append(self.transspectrum) |
|---|
| 659 | self.transspectrum = TransmissionSpectrum() |
|---|
| 660 | |
|---|
| 661 | |
|---|
| 662 | ## Everything else goes in meta_data |
|---|
| 663 | else: |
|---|
| 664 | new_key = self._create_unique_key(self.current_datainfo.meta_data, currentTagName) |
|---|
| 665 | self.current_datainfo.meta_data[new_key] = sasNode.text |
|---|
| 666 | ======= |
|---|
| 667 | self.current_dataset.xaxis("Q", unit) |
|---|
| 668 | self.current_dataset.x = np.append(self.current_dataset.x, data_point) |
|---|
| 669 | elif tagname == 'Qdev': |
|---|
| 670 | self.current_dataset.dx = np.append(self.current_dataset.dx, data_point) |
|---|
| 671 | elif tagname == 'dQw': |
|---|
| 672 | self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point) |
|---|
| 673 | elif tagname == 'dQl': |
|---|
| 674 | self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point) |
|---|
| 675 | elif tagname == 'Qmean': |
|---|
| 676 | pass |
|---|
| 677 | elif tagname == 'Shadowfactor': |
|---|
| 678 | pass |
|---|
| 679 | elif tagname == 'Sesans': |
|---|
| 680 | self.current_datainfo.isSesans = bool(data_point) |
|---|
| 681 | elif tagname == 'yacceptance': |
|---|
| 682 | self.current_datainfo.sample.yacceptance = (data_point, unit) |
|---|
| 683 | elif tagname == 'zacceptance': |
|---|
| 684 | self.current_datainfo.sample.zacceptance = (data_point, unit) |
|---|
| 685 | |
|---|
| 686 | # I and Qx, Qy - 2D data |
|---|
| 687 | elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D): |
|---|
| 688 | self.current_dataset.yaxis("Intensity", unit) |
|---|
| 689 | self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 690 | elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D): |
|---|
| 691 | self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 692 | elif tagname == 'Qx': |
|---|
| 693 | self.current_dataset.xaxis("Qx", unit) |
|---|
| 694 | self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 695 | elif tagname == 'Qy': |
|---|
| 696 | self.current_dataset.yaxis("Qy", unit) |
|---|
| 697 | self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 698 | elif tagname == 'Qxdev': |
|---|
| 699 | self.current_dataset.xaxis("Qxdev", unit) |
|---|
| 700 | self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 701 | elif tagname == 'Qydev': |
|---|
| 702 | self.current_dataset.yaxis("Qydev", unit) |
|---|
| 703 | self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",") |
|---|
| 704 | elif tagname == 'Mask': |
|---|
| 705 | inter = [item == "1" for item in data_point.split(",")] |
|---|
| 706 | self.current_dataset.mask = np.asarray(inter, dtype=bool) |
|---|
| 707 | |
|---|
| 708 | # Sample Information |
|---|
| 709 | elif tagname == 'ID' and self.parent_class == 'SASsample': |
|---|
| 710 | self.current_datainfo.sample.ID = data_point |
|---|
| 711 | elif tagname == 'Title' and self.parent_class == 'SASsample': |
|---|
| 712 | self.current_datainfo.sample.name = data_point |
|---|
| 713 | elif tagname == 'thickness' and self.parent_class == 'SASsample': |
|---|
| 714 | self.current_datainfo.sample.thickness = data_point |
|---|
| 715 | self.current_datainfo.sample.thickness_unit = unit |
|---|
| 716 | elif tagname == 'transmission' and self.parent_class == 'SASsample': |
|---|
| 717 | self.current_datainfo.sample.transmission = data_point |
|---|
| 718 | elif tagname == 'temperature' and self.parent_class == 'SASsample': |
|---|
| 719 | self.current_datainfo.sample.temperature = data_point |
|---|
| 720 | self.current_datainfo.sample.temperature_unit = unit |
|---|
| 721 | elif tagname == 'details' and self.parent_class == 'SASsample': |
|---|
| 722 | self.current_datainfo.sample.details.append(data_point) |
|---|
| 723 | elif tagname == 'x' and self.parent_class == 'position': |
|---|
| 724 | self.current_datainfo.sample.position.x = data_point |
|---|
| 725 | self.current_datainfo.sample.position_unit = unit |
|---|
| 726 | elif tagname == 'y' and self.parent_class == 'position': |
|---|
| 727 | self.current_datainfo.sample.position.y = data_point |
|---|
| 728 | self.current_datainfo.sample.position_unit = unit |
|---|
| 729 | elif tagname == 'z' and self.parent_class == 'position': |
|---|
| 730 | self.current_datainfo.sample.position.z = data_point |
|---|
| 731 | self.current_datainfo.sample.position_unit = unit |
|---|
| 732 | elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
|---|
| 733 | self.current_datainfo.sample.orientation.x = data_point |
|---|
| 734 | self.current_datainfo.sample.orientation_unit = unit |
|---|
| 735 | elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
|---|
| 736 | self.current_datainfo.sample.orientation.y = data_point |
|---|
| 737 | self.current_datainfo.sample.orientation_unit = unit |
|---|
| 738 | elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
|---|
| 739 | self.current_datainfo.sample.orientation.z = data_point |
|---|
| 740 | self.current_datainfo.sample.orientation_unit = unit |
|---|
| 741 | |
|---|
| 742 | # Instrumental Information |
|---|
| 743 | elif tagname == 'name' and self.parent_class == 'SASinstrument': |
|---|
| 744 | self.current_datainfo.instrument = data_point |
|---|
| 745 | # Detector Information |
|---|
| 746 | elif tagname == 'name' and self.parent_class == 'SASdetector': |
|---|
| 747 | self.detector.name = data_point |
|---|
| 748 | elif tagname == 'SDD' and self.parent_class == 'SASdetector': |
|---|
| 749 | self.detector.distance = data_point |
|---|
| 750 | self.detector.distance_unit = unit |
|---|
| 751 | elif tagname == 'slit_length' and self.parent_class == 'SASdetector': |
|---|
| 752 | self.detector.slit_length = data_point |
|---|
| 753 | self.detector.slit_length_unit = unit |
|---|
| 754 | elif tagname == 'x' and self.parent_class == 'offset': |
|---|
| 755 | self.detector.offset.x = data_point |
|---|
| 756 | self.detector.offset_unit = unit |
|---|
| 757 | elif tagname == 'y' and self.parent_class == 'offset': |
|---|
| 758 | self.detector.offset.y = data_point |
|---|
| 759 | self.detector.offset_unit = unit |
|---|
| 760 | elif tagname == 'z' and self.parent_class == 'offset': |
|---|
| 761 | self.detector.offset.z = data_point |
|---|
| 762 | self.detector.offset_unit = unit |
|---|
| 763 | elif tagname == 'x' and self.parent_class == 'beam_center': |
|---|
| 764 | self.detector.beam_center.x = data_point |
|---|
| 765 | self.detector.beam_center_unit = unit |
|---|
| 766 | elif tagname == 'y' and self.parent_class == 'beam_center': |
|---|
| 767 | self.detector.beam_center.y = data_point |
|---|
| 768 | self.detector.beam_center_unit = unit |
|---|
| 769 | elif tagname == 'z' and self.parent_class == 'beam_center': |
|---|
| 770 | self.detector.beam_center.z = data_point |
|---|
| 771 | self.detector.beam_center_unit = unit |
|---|
| 772 | elif tagname == 'x' and self.parent_class == 'pixel_size': |
|---|
| 773 | self.detector.pixel_size.x = data_point |
|---|
| 774 | self.detector.pixel_size_unit = unit |
|---|
| 775 | elif tagname == 'y' and self.parent_class == 'pixel_size': |
|---|
| 776 | self.detector.pixel_size.y = data_point |
|---|
| 777 | self.detector.pixel_size_unit = unit |
|---|
| 778 | elif tagname == 'z' and self.parent_class == 'pixel_size': |
|---|
| 779 | self.detector.pixel_size.z = data_point |
|---|
| 780 | self.detector.pixel_size_unit = unit |
|---|
| 781 | elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
|---|
| 782 | self.detector.orientation.x = data_point |
|---|
| 783 | self.detector.orientation_unit = unit |
|---|
| 784 | elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
|---|
| 785 | self.detector.orientation.y = data_point |
|---|
| 786 | self.detector.orientation_unit = unit |
|---|
| 787 | elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
|---|
| 788 | self.detector.orientation.z = data_point |
|---|
| 789 | self.detector.orientation_unit = unit |
|---|
| 790 | # Collimation and Aperture |
|---|
| 791 | elif tagname == 'length' and self.parent_class == 'SAScollimation': |
|---|
| 792 | self.collimation.length = data_point |
|---|
| 793 | self.collimation.length_unit = unit |
|---|
| 794 | elif tagname == 'name' and self.parent_class == 'SAScollimation': |
|---|
| 795 | self.collimation.name = data_point |
|---|
| 796 | elif tagname == 'distance' and self.parent_class == 'aperture': |
|---|
| 797 | self.aperture.distance = data_point |
|---|
| 798 | self.aperture.distance_unit = unit |
|---|
| 799 | elif tagname == 'x' and self.parent_class == 'size': |
|---|
| 800 | self.aperture.size.x = data_point |
|---|
| 801 | self.collimation.size_unit = unit |
|---|
| 802 | elif tagname == 'y' and self.parent_class == 'size': |
|---|
| 803 | self.aperture.size.y = data_point |
|---|
| 804 | self.collimation.size_unit = unit |
|---|
| 805 | elif tagname == 'z' and self.parent_class == 'size': |
|---|
| 806 | self.aperture.size.z = data_point |
|---|
| 807 | self.collimation.size_unit = unit |
|---|
| 808 | |
|---|
| 809 | # Process Information |
|---|
| 810 | elif tagname == 'name' and self.parent_class == 'SASprocess': |
|---|
| 811 | self.process.name = data_point |
|---|
| 812 | elif tagname == 'description' and self.parent_class == 'SASprocess': |
|---|
| 813 | self.process.description = data_point |
|---|
| 814 | elif tagname == 'date' and self.parent_class == 'SASprocess': |
|---|
| 815 | try: |
|---|
| 816 | self.process.date = datetime.datetime.fromtimestamp(data_point) |
|---|
| 817 | except: |
|---|
| 818 | self.process.date = data_point |
|---|
| 819 | elif tagname == 'SASprocessnote': |
|---|
| 820 | self.process.notes.append(data_point) |
|---|
| 821 | elif tagname == 'term' and self.parent_class == 'SASprocess': |
|---|
| 822 | unit = attr.get("unit", "") |
|---|
| 823 | dic = {} |
|---|
| 824 | dic["name"] = name |
|---|
| 825 | dic["value"] = data_point |
|---|
| 826 | dic["unit"] = unit |
|---|
| 827 | self.process.term.append(dic) |
|---|
| 828 | |
|---|
| 829 | # Transmission Spectrum |
|---|
| 830 | elif tagname == 'T' and self.parent_class == 'Tdata': |
|---|
| 831 | self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point) |
|---|
| 832 | self.transspectrum.transmission_unit = unit |
|---|
| 833 | elif tagname == 'Tdev' and self.parent_class == 'Tdata': |
|---|
| 834 | self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point) |
|---|
| 835 | self.transspectrum.transmission_deviation_unit = unit |
|---|
| 836 | elif tagname == 'Lambda' and self.parent_class == 'Tdata': |
|---|
| 837 | self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point) |
|---|
| 838 | self.transspectrum.wavelength_unit = unit |
|---|
| 839 | |
|---|
| 840 | # Source Information |
|---|
| 841 | elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'): |
|---|
| 842 | self.current_datainfo.source.wavelength = data_point |
|---|
| 843 | self.current_datainfo.source.wavelength_unit = unit |
|---|
| 844 | elif tagname == 'wavelength_min' and self.parent_class == 'SASsource': |
|---|
| 845 | self.current_datainfo.source.wavelength_min = data_point |
|---|
| 846 | self.current_datainfo.source.wavelength_min_unit = unit |
|---|
| 847 | elif tagname == 'wavelength_max' and self.parent_class == 'SASsource': |
|---|
| 848 | self.current_datainfo.source.wavelength_max = data_point |
|---|
| 849 | self.current_datainfo.source.wavelength_max_unit = unit |
|---|
| 850 | elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource': |
|---|
| 851 | self.current_datainfo.source.wavelength_spread = data_point |
|---|
| 852 | self.current_datainfo.source.wavelength_spread_unit = unit |
|---|
| 853 | elif tagname == 'x' and self.parent_class == 'beam_size': |
|---|
| 854 | self.current_datainfo.source.beam_size.x = data_point |
|---|
| 855 | self.current_datainfo.source.beam_size_unit = unit |
|---|
| 856 | elif tagname == 'y' and self.parent_class == 'beam_size': |
|---|
| 857 | self.current_datainfo.source.beam_size.y = data_point |
|---|
| 858 | self.current_datainfo.source.beam_size_unit = unit |
|---|
| 859 | elif tagname == 'z' and self.parent_class == 'pixel_size': |
|---|
| 860 | self.current_datainfo.source.data_point.z = data_point |
|---|
| 861 | self.current_datainfo.source.beam_size_unit = unit |
|---|
| 862 | elif tagname == 'radiation' and self.parent_class == 'SASsource': |
|---|
| 863 | self.current_datainfo.source.radiation = data_point |
|---|
| 864 | elif tagname == 'beam_shape' and self.parent_class == 'SASsource': |
|---|
| 865 | self.current_datainfo.source.beam_shape = data_point |
|---|
| 866 | |
|---|
| 867 | # Everything else goes in meta_data |
|---|
| 868 | else: |
|---|
| 869 | new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname) |
|---|
| 870 | self.current_datainfo.meta_data[new_key] = data_point |
|---|
| 871 | >>>>>>> master |
|---|
| 872 | |
|---|
| 873 | self.add_intermediate() |
|---|
| 874 | |
|---|
| 875 | # As before in the code, I guess in case we have to return a tuple for some reason... |
|---|
| 876 | return self.output, None |
|---|
| 877 | |
|---|
| 878 | def _is_call_local(self): |
|---|
| 879 | """ |
|---|
| 880 | |
|---|
| 881 | """ |
|---|
| 882 | if self.frm == "": |
|---|
| 883 | inter = inspect.stack() |
|---|
| 884 | self.frm = inter[2] |
|---|
| 885 | mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") |
|---|
| 886 | mod_name = mod_name.replace(".py", "") |
|---|
| 887 | mod = mod_name.split("sas/") |
|---|
| 888 | mod_name = mod[1] |
|---|
| 889 | if mod_name != "sascalc/dataloader/readers/cansas_reader": |
|---|
| 890 | return False |
|---|
| 891 | return True |
|---|
| 892 | |
|---|
| 893 | def is_cansas(self, ext="xml"): |
|---|
| 894 | """ |
|---|
| 895 | Checks to see if the xml file is a CanSAS file |
|---|
| 896 | |
|---|
| 897 | :param ext: The file extension of the data file |
|---|
| 898 | """ |
|---|
| 899 | if self.validate_xml(): |
|---|
| 900 | name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation" |
|---|
| 901 | value = self.xmlroot.get(name) |
|---|
| 902 | if CANSAS_NS.get(self.cansas_version).get("ns") == \ |
|---|
| 903 | value.rsplit(" ")[0]: |
|---|
| 904 | return True |
|---|
| 905 | if ext == "svs": |
|---|
| 906 | return True |
|---|
| 907 | raise RuntimeError |
|---|
| 908 | |
|---|
| 909 | def load_file_and_schema(self, xml_file, schema_path=""): |
|---|
| 910 | """ |
|---|
| 911 | Loads the file and associates a schema, if a schema is passed in or if one already exists |
|---|
| 912 | |
|---|
| 913 | :param xml_file: The xml file path sent to Reader.read |
|---|
| 914 | :param schema_path: The path to a schema associated with the xml_file, or find one based on the file |
|---|
| 915 | """ |
|---|
| 916 | base_name = xml_reader.__file__ |
|---|
| 917 | base_name = base_name.replace("\\", "/") |
|---|
| 918 | base = base_name.split("/sas/")[0] |
|---|
| 919 | |
|---|
| 920 | # Load in xml file and get the cansas version from the header |
|---|
| 921 | self.set_xml_file(xml_file) |
|---|
| 922 | self.cansas_version = self.xmlroot.get("version", "1.0") |
|---|
| 923 | |
|---|
| 924 | # Generic values for the cansas file based on the version |
|---|
| 925 | self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0") |
|---|
| 926 | if schema_path == "": |
|---|
| 927 | schema_path = "{0}/sas/sascalc/dataloader/readers/schema/{1}".format \ |
|---|
| 928 | (base, self.cansas_defaults.get("schema")).replace("\\", "/") |
|---|
| 929 | |
|---|
| 930 | # Link a schema to the XML file. |
|---|
| 931 | self.set_schema(schema_path) |
|---|
| 932 | |
|---|
| 933 | def add_data_set(self): |
|---|
| 934 | """ |
|---|
| 935 | Adds the current_dataset to the list of outputs after preforming final processing on the data and then calls a |
|---|
| 936 | private method to generate a new data set. |
|---|
| 937 | |
|---|
| 938 | :param key: NeXus group name for current tree level |
|---|
| 939 | """ |
|---|
| 940 | |
|---|
| 941 | if self.current_datainfo and self.current_dataset: |
|---|
| 942 | self._final_cleanup() |
|---|
| 943 | self.data = [] |
|---|
| 944 | self.current_datainfo = DataInfo() |
|---|
| 945 | |
|---|
| 946 | def _initialize_new_data_set(self, node=None): |
|---|
| 947 | """ |
|---|
| 948 | A private class method to generate a new 1D data object. |
|---|
| 949 | Outside methods should call add_data_set() to be sure any existing data is stored properly. |
|---|
| 950 | |
|---|
| 951 | :param node: XML node to determine if 1D or 2D data |
|---|
| 952 | """ |
|---|
| 953 | x = np.array(0) |
|---|
| 954 | y = np.array(0) |
|---|
| 955 | for child in node: |
|---|
| 956 | if child.tag.replace(self.base_ns, "") == "Idata": |
|---|
| 957 | for i_child in child: |
|---|
| 958 | if i_child.tag.replace(self.base_ns, "") == "Qx": |
|---|
| 959 | self.current_dataset = plottable_2D() |
|---|
| 960 | return |
|---|
| 961 | self.current_dataset = plottable_1D(x, y) |
|---|
| 962 | |
|---|
| 963 | def add_intermediate(self): |
|---|
| 964 | """ |
|---|
| 965 | This method stores any intermediate objects within the final data set after fully reading the set. |
|---|
| 966 | |
|---|
| 967 | :param parent: The NXclass name for the h5py Group object that just finished being processed |
|---|
| 968 | """ |
|---|
| 969 | |
|---|
| 970 | if self.parent_class == 'SASprocess': |
|---|
| 971 | self.current_datainfo.process.append(self.process) |
|---|
| 972 | self.process = Process() |
|---|
| 973 | elif self.parent_class == 'SASdetector': |
|---|
| 974 | self.current_datainfo.detector.append(self.detector) |
|---|
| 975 | self.detector = Detector() |
|---|
| 976 | elif self.parent_class == 'SAStransmission_spectrum': |
|---|
| 977 | self.current_datainfo.trans_spectrum.append(self.transspectrum) |
|---|
| 978 | self.transspectrum = TransmissionSpectrum() |
|---|
| 979 | elif self.parent_class == 'SAScollimation': |
|---|
| 980 | self.current_datainfo.collimation.append(self.collimation) |
|---|
| 981 | self.collimation = Collimation() |
|---|
| 982 | elif self.parent_class == 'aperture': |
|---|
| 983 | self.collimation.aperture.append(self.aperture) |
|---|
| 984 | self.aperture = Aperture() |
|---|
| 985 | elif self.parent_class == 'SASdata': |
|---|
| 986 | self._check_for_empty_resolution() |
|---|
| 987 | self.data.append(self.current_dataset) |
|---|
| 988 | |
|---|
| 989 | def _final_cleanup(self): |
|---|
| 990 | """ |
|---|
| 991 | Final cleanup of the Data1D object to be sure it has all the |
|---|
| 992 | appropriate information needed for perspectives |
|---|
| 993 | """ |
|---|
| 994 | |
|---|
| 995 | # Append errors to dataset and reset class errors |
|---|
| 996 | self.current_datainfo.errors = set() |
|---|
| 997 | for error in self.errors: |
|---|
| 998 | self.current_datainfo.errors.add(error) |
|---|
| 999 | self.errors.clear() |
|---|
| 1000 | |
|---|
| 1001 | # Combine all plottables with datainfo and append each to output |
|---|
| 1002 | # Type cast data arrays to float64 and find min/max as appropriate |
|---|
| 1003 | for dataset in self.data: |
|---|
| 1004 | if isinstance(dataset, plottable_1D): |
|---|
| 1005 | if dataset.x is not None: |
|---|
| 1006 | dataset.x = np.delete(dataset.x, [0]) |
|---|
| 1007 | dataset.x = dataset.x.astype(np.float64) |
|---|
| 1008 | dataset.xmin = np.min(dataset.x) |
|---|
| 1009 | dataset.xmax = np.max(dataset.x) |
|---|
| 1010 | if dataset.y is not None: |
|---|
| 1011 | dataset.y = np.delete(dataset.y, [0]) |
|---|
| 1012 | dataset.y = dataset.y.astype(np.float64) |
|---|
| 1013 | dataset.ymin = np.min(dataset.y) |
|---|
| 1014 | dataset.ymax = np.max(dataset.y) |
|---|
| 1015 | if dataset.dx is not None: |
|---|
| 1016 | dataset.dx = np.delete(dataset.dx, [0]) |
|---|
| 1017 | dataset.dx = dataset.dx.astype(np.float64) |
|---|
| 1018 | if dataset.dxl is not None: |
|---|
| 1019 | dataset.dxl = np.delete(dataset.dxl, [0]) |
|---|
| 1020 | dataset.dxl = dataset.dxl.astype(np.float64) |
|---|
| 1021 | if dataset.dxw is not None: |
|---|
| 1022 | dataset.dxw = np.delete(dataset.dxw, [0]) |
|---|
| 1023 | dataset.dxw = dataset.dxw.astype(np.float64) |
|---|
| 1024 | if dataset.dy is not None: |
|---|
| 1025 | dataset.dy = np.delete(dataset.dy, [0]) |
|---|
| 1026 | dataset.dy = dataset.dy.astype(np.float64) |
|---|
| 1027 | np.trim_zeros(dataset.x) |
|---|
| 1028 | np.trim_zeros(dataset.y) |
|---|
| 1029 | np.trim_zeros(dataset.dy) |
|---|
| 1030 | elif isinstance(dataset, plottable_2D): |
|---|
| 1031 | dataset.data = dataset.data.astype(np.float64) |
|---|
| 1032 | dataset.qx_data = dataset.qx_data.astype(np.float64) |
|---|
| 1033 | dataset.xmin = np.min(dataset.qx_data) |
|---|
| 1034 | dataset.xmax = np.max(dataset.qx_data) |
|---|
| 1035 | dataset.qy_data = dataset.qy_data.astype(np.float64) |
|---|
| 1036 | dataset.ymin = np.min(dataset.qy_data) |
|---|
| 1037 | dataset.ymax = np.max(dataset.qy_data) |
|---|
| 1038 | dataset.q_data = np.sqrt(dataset.qx_data * dataset.qx_data |
|---|
| 1039 | + dataset.qy_data * dataset.qy_data) |
|---|
| 1040 | if dataset.err_data is not None: |
|---|
| 1041 | dataset.err_data = dataset.err_data.astype(np.float64) |
|---|
| 1042 | if dataset.dqx_data is not None: |
|---|
| 1043 | dataset.dqx_data = dataset.dqx_data.astype(np.float64) |
|---|
| 1044 | if dataset.dqy_data is not None: |
|---|
| 1045 | dataset.dqy_data = dataset.dqy_data.astype(np.float64) |
|---|
| 1046 | if dataset.mask is not None: |
|---|
| 1047 | dataset.mask = dataset.mask.astype(dtype=bool) |
|---|
| 1048 | |
|---|
| 1049 | if len(dataset.shape) == 2: |
|---|
| 1050 | n_rows, n_cols = dataset.shape |
|---|
| 1051 | dataset.y_bins = dataset.qy_data[0::int(n_cols)] |
|---|
| 1052 | dataset.x_bins = dataset.qx_data[:int(n_cols)] |
|---|
| 1053 | dataset.data = dataset.data.flatten() |
|---|
| 1054 | else: |
|---|
| 1055 | dataset.y_bins = [] |
|---|
| 1056 | dataset.x_bins = [] |
|---|
| 1057 | dataset.data = dataset.data.flatten() |
|---|
| 1058 | |
|---|
| 1059 | final_dataset = combine_data(dataset, self.current_datainfo) |
|---|
| 1060 | self.output.append(final_dataset) |
|---|
| 1061 | |
|---|
| 1062 | def _create_unique_key(self, dictionary, name, numb=0): |
|---|
| 1063 | """ |
|---|
| 1064 | Create a unique key value for any dictionary to prevent overwriting |
|---|
| 1065 | Recurse until a unique key value is found. |
|---|
| 1066 | |
|---|
| 1067 | :param dictionary: A dictionary with any number of entries |
|---|
| 1068 | :param name: The index of the item to be added to dictionary |
|---|
| 1069 | :param numb: The number to be appended to the name, starts at 0 |
|---|
| 1070 | """ |
|---|
| 1071 | if dictionary.get(name) is not None: |
|---|
| 1072 | numb += 1 |
|---|
| 1073 | name = name.split("_")[0] |
|---|
| 1074 | name += "_{0}".format(numb) |
|---|
| 1075 | name = self._create_unique_key(dictionary, name, numb) |
|---|
| 1076 | return name |
|---|
| 1077 | |
|---|
| 1078 | def _get_node_value_from_text(self, node, node_text): |
|---|
| 1079 | """ |
|---|
| 1080 | Get the value of a node and any applicable units |
|---|
| 1081 | |
|---|
| 1082 | :param node: The XML node to get the value of |
|---|
| 1083 | :param tagname: The tagname of the node |
|---|
| 1084 | """ |
|---|
| 1085 | units = "" |
|---|
| 1086 | # If the value is a float, compile with units. |
|---|
| 1087 | if self.ns_list.ns_datatype == "float": |
|---|
| 1088 | # If an empty value is given, set as zero. |
|---|
| 1089 | if node_text is None or node_text.isspace() \ |
|---|
| 1090 | or node_text.lower() == "nan": |
|---|
| 1091 | node_text = "0.0" |
|---|
| 1092 | # Convert the value to the base units |
|---|
| 1093 | tag = node.tag.replace(self.base_ns, "") |
|---|
| 1094 | node_text, units = self._unit_conversion(node, tag, node_text) |
|---|
| 1095 | |
|---|
| 1096 | # If the value is a timestamp, convert to a datetime object |
|---|
| 1097 | elif self.ns_list.ns_datatype == "timestamp": |
|---|
| 1098 | if node_text is None or node_text.isspace(): |
|---|
| 1099 | pass |
|---|
| 1100 | else: |
|---|
| 1101 | try: |
|---|
| 1102 | node_text = \ |
|---|
| 1103 | datetime.datetime.fromtimestamp(node_text) |
|---|
| 1104 | except ValueError: |
|---|
| 1105 | node_text = None |
|---|
| 1106 | return node_text, units |
|---|
| 1107 | |
|---|
| 1108 | def _get_node_value(self, node): |
|---|
| 1109 | """ |
|---|
| 1110 | Get the value of a node and any applicable units |
|---|
| 1111 | |
|---|
| 1112 | :param node: The XML node to get the value of |
|---|
| 1113 | :param tagname: The tagname of the node |
|---|
| 1114 | """ |
|---|
| 1115 | #Get the text from the node and convert all whitespace to spaces |
|---|
| 1116 | units = '' |
|---|
| 1117 | node_value = node.text |
|---|
| 1118 | if node_value is not None: |
|---|
| 1119 | node_value = ' '.join(node_value.split()) |
|---|
| 1120 | else: |
|---|
| 1121 | node_value = "" |
|---|
| 1122 | node_value, units = self._get_node_value_from_text(node, node_value) |
|---|
| 1123 | return node_value, units |
|---|
| 1124 | |
|---|
| 1125 | def _unit_conversion(self, node, tagname, node_value): |
|---|
| 1126 | """ |
|---|
| 1127 | A unit converter method used to convert the data included in the file |
|---|
| 1128 | to the default units listed in data_info |
|---|
| 1129 | |
|---|
| 1130 | :param node: XML node |
|---|
| 1131 | :param tagname: name of the node |
|---|
| 1132 | :param node_value: The value of the current dom node |
|---|
| 1133 | """ |
|---|
| 1134 | attr = node.attrib |
|---|
| 1135 | value_unit = '' |
|---|
| 1136 | err_msg = None |
|---|
| 1137 | default_unit = None |
|---|
| 1138 | if not isinstance(node_value, float): |
|---|
| 1139 | node_value = float(node_value) |
|---|
| 1140 | if 'unit' in attr and attr.get('unit') is not None: |
|---|
| 1141 | try: |
|---|
| 1142 | local_unit = attr['unit'] |
|---|
| 1143 | unitname = self.ns_list.current_level.get("unit", "") |
|---|
| 1144 | if "SASdetector" in self.names: |
|---|
| 1145 | save_in = "detector" |
|---|
| 1146 | elif "aperture" in self.names: |
|---|
| 1147 | save_in = "aperture" |
|---|
| 1148 | elif "SAScollimation" in self.names: |
|---|
| 1149 | save_in = "collimation" |
|---|
| 1150 | elif "SAStransmission_spectrum" in self.names: |
|---|
| 1151 | save_in = "transspectrum" |
|---|
| 1152 | elif "SASdata" in self.names: |
|---|
| 1153 | x = np.zeros(1) |
|---|
| 1154 | y = np.zeros(1) |
|---|
| 1155 | self.current_data1d = Data1D(x, y) |
|---|
| 1156 | save_in = "current_data1d" |
|---|
| 1157 | elif "SASsource" in self.names: |
|---|
| 1158 | save_in = "current_datainfo.source" |
|---|
| 1159 | elif "SASsample" in self.names: |
|---|
| 1160 | save_in = "current_datainfo.sample" |
|---|
| 1161 | elif "SASprocess" in self.names: |
|---|
| 1162 | save_in = "process" |
|---|
| 1163 | else: |
|---|
| 1164 | save_in = "current_datainfo" |
|---|
| 1165 | exec "default_unit = self.{0}.{1}".format(save_in, unitname) |
|---|
| 1166 | if local_unit and default_unit and local_unit.lower() != default_unit.lower() \ |
|---|
| 1167 | and local_unit.lower() != "none": |
|---|
| 1168 | if HAS_CONVERTER == True: |
|---|
| 1169 | # Check local units - bad units raise KeyError |
|---|
| 1170 | data_conv_q = Converter(local_unit) |
|---|
| 1171 | value_unit = default_unit |
|---|
| 1172 | node_value = data_conv_q(node_value, units=default_unit) |
|---|
| 1173 | else: |
|---|
| 1174 | value_unit = local_unit |
|---|
| 1175 | err_msg = "Unit converter is not available.\n" |
|---|
| 1176 | else: |
|---|
| 1177 | value_unit = local_unit |
|---|
| 1178 | except KeyError: |
|---|
| 1179 | err_msg = "CanSAS reader: unexpected " |
|---|
| 1180 | err_msg += "\"{0}\" unit [{1}]; " |
|---|
| 1181 | err_msg = err_msg.format(tagname, local_unit) |
|---|
| 1182 | err_msg += "expecting [{0}]".format(default_unit) |
|---|
| 1183 | value_unit = local_unit |
|---|
| 1184 | except: |
|---|
| 1185 | err_msg = "CanSAS reader: unknown error converting " |
|---|
| 1186 | err_msg += "\"{0}\" unit [{1}]" |
|---|
| 1187 | err_msg = err_msg.format(tagname, local_unit) |
|---|
| 1188 | value_unit = local_unit |
|---|
| 1189 | elif 'unit' in attr: |
|---|
| 1190 | value_unit = attr['unit'] |
|---|
| 1191 | if err_msg: |
|---|
| 1192 | self.errors.add(err_msg) |
|---|
| 1193 | return node_value, value_unit |
|---|
| 1194 | |
|---|
| 1195 | def _check_for_empty_data(self): |
|---|
| 1196 | """ |
|---|
| 1197 | Creates an empty data set if no data is passed to the reader |
|---|
| 1198 | |
|---|
| 1199 | :param data1d: presumably a Data1D object |
|---|
| 1200 | """ |
|---|
| 1201 | if self.current_dataset is None: |
|---|
| 1202 | x_vals = np.empty(0) |
|---|
| 1203 | y_vals = np.empty(0) |
|---|
| 1204 | dx_vals = np.empty(0) |
|---|
| 1205 | dy_vals = np.empty(0) |
|---|
| 1206 | dxl = np.empty(0) |
|---|
| 1207 | dxw = np.empty(0) |
|---|
| 1208 | self.current_dataset = plottable_1D(x_vals, y_vals, dx_vals, dy_vals) |
|---|
| 1209 | self.current_dataset.dxl = dxl |
|---|
| 1210 | self.current_dataset.dxw = dxw |
|---|
| 1211 | |
|---|
| 1212 | def _check_for_empty_resolution(self): |
|---|
| 1213 | """ |
|---|
| 1214 | A method to check all resolution data sets are the same size as I and Q |
|---|
| 1215 | """ |
|---|
| 1216 | if isinstance(self.current_dataset, plottable_1D): |
|---|
| 1217 | dql_exists = False |
|---|
| 1218 | dqw_exists = False |
|---|
| 1219 | dq_exists = False |
|---|
| 1220 | di_exists = False |
|---|
| 1221 | if self.current_dataset.dxl is not None: |
|---|
| 1222 | dql_exists = True |
|---|
| 1223 | if self.current_dataset.dxw is not None: |
|---|
| 1224 | dqw_exists = True |
|---|
| 1225 | if self.current_dataset.dx is not None: |
|---|
| 1226 | dq_exists = True |
|---|
| 1227 | if self.current_dataset.dy is not None: |
|---|
| 1228 | di_exists = True |
|---|
| 1229 | if dqw_exists and not dql_exists: |
|---|
| 1230 | array_size = self.current_dataset.dxw.size - 1 |
|---|
| 1231 | self.current_dataset.dxl = np.append(self.current_dataset.dxl, |
|---|
| 1232 | np.zeros([array_size])) |
|---|
| 1233 | elif dql_exists and not dqw_exists: |
|---|
| 1234 | array_size = self.current_dataset.dxl.size - 1 |
|---|
| 1235 | self.current_dataset.dxw = np.append(self.current_dataset.dxw, |
|---|
| 1236 | np.zeros([array_size])) |
|---|
| 1237 | elif not dql_exists and not dqw_exists and not dq_exists: |
|---|
| 1238 | array_size = self.current_dataset.x.size - 1 |
|---|
| 1239 | self.current_dataset.dx = np.append(self.current_dataset.dx, |
|---|
| 1240 | np.zeros([array_size])) |
|---|
| 1241 | if not di_exists: |
|---|
| 1242 | array_size = self.current_dataset.y.size - 1 |
|---|
| 1243 | self.current_dataset.dy = np.append(self.current_dataset.dy, |
|---|
| 1244 | np.zeros([array_size])) |
|---|
| 1245 | elif isinstance(self.current_dataset, plottable_2D): |
|---|
| 1246 | dqx_exists = False |
|---|
| 1247 | dqy_exists = False |
|---|
| 1248 | di_exists = False |
|---|
| 1249 | mask_exists = False |
|---|
| 1250 | if self.current_dataset.dqx_data is not None: |
|---|
| 1251 | dqx_exists = True |
|---|
| 1252 | if self.current_dataset.dqy_data is not None: |
|---|
| 1253 | dqy_exists = True |
|---|
| 1254 | if self.current_dataset.err_data is not None: |
|---|
| 1255 | di_exists = True |
|---|
| 1256 | if self.current_dataset.mask is not None: |
|---|
| 1257 | mask_exists = True |
|---|
| 1258 | if not dqy_exists: |
|---|
| 1259 | array_size = self.current_dataset.qy_data.size - 1 |
|---|
| 1260 | self.current_dataset.dqy_data = np.append( |
|---|
| 1261 | self.current_dataset.dqy_data, np.zeros([array_size])) |
|---|
| 1262 | if not dqx_exists: |
|---|
| 1263 | array_size = self.current_dataset.qx_data.size - 1 |
|---|
| 1264 | self.current_dataset.dqx_data = np.append( |
|---|
| 1265 | self.current_dataset.dqx_data, np.zeros([array_size])) |
|---|
| 1266 | if not di_exists: |
|---|
| 1267 | array_size = self.current_dataset.data.size - 1 |
|---|
| 1268 | self.current_dataset.err_data = np.append( |
|---|
| 1269 | self.current_dataset.err_data, np.zeros([array_size])) |
|---|
| 1270 | if not mask_exists: |
|---|
| 1271 | array_size = self.current_dataset.data.size - 1 |
|---|
| 1272 | self.current_dataset.mask = np.append( |
|---|
| 1273 | self.current_dataset.mask, |
|---|
| 1274 | np.ones([array_size] ,dtype=bool)) |
|---|
| 1275 | |
|---|
| 1276 | ####### All methods below are for writing CanSAS XML files ####### |
|---|
| 1277 | |
|---|
| 1278 | def write(self, filename, datainfo): |
|---|
| 1279 | """ |
|---|
| 1280 | Write the content of a Data1D as a CanSAS XML file |
|---|
| 1281 | |
|---|
| 1282 | :param filename: name of the file to write |
|---|
| 1283 | :param datainfo: Data1D object |
|---|
| 1284 | """ |
|---|
| 1285 | # Create XML document |
|---|
| 1286 | doc, _ = self._to_xml_doc(datainfo) |
|---|
| 1287 | # Write the file |
|---|
| 1288 | file_ref = open(filename, 'w') |
|---|
| 1289 | if self.encoding is None: |
|---|
| 1290 | self.encoding = "UTF-8" |
|---|
| 1291 | doc.write(file_ref, encoding=self.encoding, |
|---|
| 1292 | pretty_print=True, xml_declaration=True) |
|---|
| 1293 | file_ref.close() |
|---|
| 1294 | |
|---|
| 1295 | def _to_xml_doc(self, datainfo): |
|---|
| 1296 | """ |
|---|
| 1297 | Create an XML document to contain the content of a Data1D |
|---|
| 1298 | |
|---|
| 1299 | :param datainfo: Data1D object |
|---|
| 1300 | """ |
|---|
| 1301 | is_2d = False |
|---|
| 1302 | if issubclass(datainfo.__class__, Data2D): |
|---|
| 1303 | is_2d = True |
|---|
| 1304 | |
|---|
| 1305 | # Get PIs and create root element |
|---|
| 1306 | pi_string = self._get_pi_string() |
|---|
| 1307 | # Define namespaces and create SASroot object |
|---|
| 1308 | main_node = self._create_main_node() |
|---|
| 1309 | # Create ElementTree, append SASroot and apply processing instructions |
|---|
| 1310 | base_string = pi_string + self.to_string(main_node) |
|---|
| 1311 | base_element = self.create_element_from_string(base_string) |
|---|
| 1312 | doc = self.create_tree(base_element) |
|---|
| 1313 | # Create SASentry Element |
|---|
| 1314 | entry_node = self.create_element("SASentry") |
|---|
| 1315 | root = doc.getroot() |
|---|
| 1316 | root.append(entry_node) |
|---|
| 1317 | |
|---|
| 1318 | # Add Title to SASentry |
|---|
| 1319 | self.write_node(entry_node, "Title", datainfo.title) |
|---|
| 1320 | # Add Run to SASentry |
|---|
| 1321 | self._write_run_names(datainfo, entry_node) |
|---|
| 1322 | # Add Data info to SASEntry |
|---|
| 1323 | if is_2d: |
|---|
| 1324 | self._write_data_2d(datainfo, entry_node) |
|---|
| 1325 | else: |
|---|
| 1326 | if self._check_root(): |
|---|
| 1327 | self._write_data(datainfo, entry_node) |
|---|
| 1328 | else: |
|---|
| 1329 | self._write_data_linearized(datainfo, entry_node) |
|---|
| 1330 | # Transmission Spectrum Info |
|---|
| 1331 | # TODO: fix the writer to linearize all data, including T_spectrum |
|---|
| 1332 | # self._write_trans_spectrum(datainfo, entry_node) |
|---|
| 1333 | # Sample info |
|---|
| 1334 | self._write_sample_info(datainfo, entry_node) |
|---|
| 1335 | # Instrument info |
|---|
| 1336 | instr = self._write_instrument(datainfo, entry_node) |
|---|
| 1337 | # Source |
|---|
| 1338 | self._write_source(datainfo, instr) |
|---|
| 1339 | # Collimation |
|---|
| 1340 | self._write_collimation(datainfo, instr) |
|---|
| 1341 | # Detectors |
|---|
| 1342 | self._write_detectors(datainfo, instr) |
|---|
| 1343 | # Processes info |
|---|
| 1344 | self._write_process_notes(datainfo, entry_node) |
|---|
| 1345 | # Note info |
|---|
| 1346 | self._write_notes(datainfo, entry_node) |
|---|
| 1347 | # Return the document, and the SASentry node associated with |
|---|
| 1348 | # the data we just wrote |
|---|
| 1349 | # If the calling function was not the cansas reader, return a minidom |
|---|
| 1350 | # object rather than an lxml object. |
|---|
| 1351 | self.frm = inspect.stack()[1] |
|---|
| 1352 | doc, entry_node = self._check_origin(entry_node, doc) |
|---|
| 1353 | return doc, entry_node |
|---|
| 1354 | |
|---|
| 1355 | def write_node(self, parent, name, value, attr=None): |
|---|
| 1356 | """ |
|---|
| 1357 | :param doc: document DOM |
|---|
| 1358 | :param parent: parent node |
|---|
| 1359 | :param name: tag of the element |
|---|
| 1360 | :param value: value of the child text node |
|---|
| 1361 | :param attr: attribute dictionary |
|---|
| 1362 | |
|---|
| 1363 | :return: True if something was appended, otherwise False |
|---|
| 1364 | """ |
|---|
| 1365 | if value is not None: |
|---|
| 1366 | parent = self.ebuilder(parent, name, value, attr) |
|---|
| 1367 | return True |
|---|
| 1368 | return False |
|---|
| 1369 | |
|---|
| 1370 | def _get_pi_string(self): |
|---|
| 1371 | """ |
|---|
| 1372 | Creates the processing instructions header for writing to file |
|---|
| 1373 | """ |
|---|
| 1374 | pis = self.return_processing_instructions() |
|---|
| 1375 | if len(pis) > 0: |
|---|
| 1376 | pi_tree = self.create_tree(pis[0]) |
|---|
| 1377 | i = 1 |
|---|
| 1378 | for i in range(1, len(pis) - 1): |
|---|
| 1379 | pi_tree = self.append(pis[i], pi_tree) |
|---|
| 1380 | pi_string = self.to_string(pi_tree) |
|---|
| 1381 | else: |
|---|
| 1382 | pi_string = "" |
|---|
| 1383 | return pi_string |
|---|
| 1384 | |
|---|
| 1385 | def _create_main_node(self): |
|---|
| 1386 | """ |
|---|
| 1387 | Creates the primary xml header used when writing to file |
|---|
| 1388 | """ |
|---|
| 1389 | xsi = "http://www.w3.org/2001/XMLSchema-instance" |
|---|
| 1390 | version = self.cansas_version |
|---|
| 1391 | n_s = CANSAS_NS.get(version).get("ns") |
|---|
| 1392 | if version == "1.1": |
|---|
| 1393 | url = "http://www.cansas.org/formats/1.1/" |
|---|
| 1394 | else: |
|---|
| 1395 | url = "http://www.cansas.org/formats/1.0/" |
|---|
| 1396 | schema_location = "{0} {1}cansas1d.xsd".format(n_s, url) |
|---|
| 1397 | attrib = {"{" + xsi + "}schemaLocation" : schema_location, |
|---|
| 1398 | "version" : version} |
|---|
| 1399 | nsmap = {'xsi' : xsi, None: n_s} |
|---|
| 1400 | |
|---|
| 1401 | main_node = self.create_element("{" + n_s + "}SASroot", |
|---|
| 1402 | attrib=attrib, nsmap=nsmap) |
|---|
| 1403 | return main_node |
|---|
| 1404 | |
|---|
| 1405 | def _write_run_names(self, datainfo, entry_node): |
|---|
| 1406 | """ |
|---|
| 1407 | Writes the run names to the XML file |
|---|
| 1408 | |
|---|
| 1409 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1410 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1411 | """ |
|---|
| 1412 | if datainfo.run is None or datainfo.run == []: |
|---|
| 1413 | datainfo.run.append(RUN_NAME_DEFAULT) |
|---|
| 1414 | datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT |
|---|
| 1415 | for item in datainfo.run: |
|---|
| 1416 | runname = {} |
|---|
| 1417 | if item in datainfo.run_name and \ |
|---|
| 1418 | len(str(datainfo.run_name[item])) > 1: |
|---|
| 1419 | runname = {'name': datainfo.run_name[item]} |
|---|
| 1420 | self.write_node(entry_node, "Run", item, runname) |
|---|
| 1421 | |
|---|
| 1422 | def _write_data(self, datainfo, entry_node): |
|---|
| 1423 | """ |
|---|
| 1424 | Writes 1D I and Q data to the XML file |
|---|
| 1425 | |
|---|
| 1426 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1427 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1428 | """ |
|---|
| 1429 | node = self.create_element("SASdata") |
|---|
| 1430 | self.append(node, entry_node) |
|---|
| 1431 | |
|---|
| 1432 | for i in range(len(datainfo.x)): |
|---|
| 1433 | point = self.create_element("Idata") |
|---|
| 1434 | node.append(point) |
|---|
| 1435 | self.write_node(point, "Q", datainfo.x[i], |
|---|
| 1436 | {'unit': datainfo._xaxis + " | " + datainfo._xunit}) |
|---|
| 1437 | if len(datainfo.y) >= i: |
|---|
| 1438 | self.write_node(point, "I", datainfo.y[i], |
|---|
| 1439 | {'unit': datainfo._yaxis + " | " + datainfo._yunit}) |
|---|
| 1440 | if datainfo.dy is not None and len(datainfo.dy) > i: |
|---|
| 1441 | self.write_node(point, "Idev", datainfo.dy[i], |
|---|
| 1442 | {'unit': datainfo._yaxis + " | " + datainfo._yunit}) |
|---|
| 1443 | if datainfo.dx is not None and len(datainfo.dx) > i: |
|---|
| 1444 | self.write_node(point, "Qdev", datainfo.dx[i], |
|---|
| 1445 | {'unit': datainfo._xaxis + " | " + datainfo._xunit}) |
|---|
| 1446 | if datainfo.dxw is not None and len(datainfo.dxw) > i: |
|---|
| 1447 | self.write_node(point, "dQw", datainfo.dxw[i], |
|---|
| 1448 | {'unit': datainfo._xaxis + " | " + datainfo._xunit}) |
|---|
| 1449 | if datainfo.dxl is not None and len(datainfo.dxl) > i: |
|---|
| 1450 | self.write_node(point, "dQl", datainfo.dxl[i], |
|---|
| 1451 | {'unit': datainfo._xaxis + " | " + datainfo._xunit}) |
|---|
| 1452 | if datainfo.isSesans: |
|---|
| 1453 | sesans = self.create_element("Sesans") |
|---|
| 1454 | sesans.text = str(datainfo.isSesans) |
|---|
| 1455 | node.append(sesans) |
|---|
| 1456 | self.write_node(node, "yacceptance", datainfo.sample.yacceptance[0], |
|---|
| 1457 | {'unit': datainfo.sample.yacceptance[1]}) |
|---|
| 1458 | self.write_node(node, "zacceptance", datainfo.sample.zacceptance[0], |
|---|
| 1459 | {'unit': datainfo.sample.zacceptance[1]}) |
|---|
| 1460 | |
|---|
| 1461 | |
|---|
| 1462 | def _write_data_2d(self, datainfo, entry_node): |
|---|
| 1463 | """ |
|---|
| 1464 | Writes 2D data to the XML file |
|---|
| 1465 | |
|---|
| 1466 | :param datainfo: The Data2D object the information is coming from |
|---|
| 1467 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1468 | """ |
|---|
| 1469 | attr = {} |
|---|
| 1470 | if datainfo.data.shape: |
|---|
| 1471 | attr["x_bins"] = str(len(datainfo.x_bins)) |
|---|
| 1472 | attr["y_bins"] = str(len(datainfo.y_bins)) |
|---|
| 1473 | node = self.create_element("SASdata", attr) |
|---|
| 1474 | self.append(node, entry_node) |
|---|
| 1475 | |
|---|
| 1476 | point = self.create_element("Idata") |
|---|
| 1477 | node.append(point) |
|---|
| 1478 | qx = ','.join([str(datainfo.qx_data[i]) for i in xrange(len(datainfo.qx_data))]) |
|---|
| 1479 | qy = ','.join([str(datainfo.qy_data[i]) for i in xrange(len(datainfo.qy_data))]) |
|---|
| 1480 | intensity = ','.join([str(datainfo.data[i]) for i in xrange(len(datainfo.data))]) |
|---|
| 1481 | |
|---|
| 1482 | self.write_node(point, "Qx", qx, |
|---|
| 1483 | {'unit': datainfo._xunit}) |
|---|
| 1484 | self.write_node(point, "Qy", qy, |
|---|
| 1485 | {'unit': datainfo._yunit}) |
|---|
| 1486 | self.write_node(point, "I", intensity, |
|---|
| 1487 | {'unit': datainfo._zunit}) |
|---|
| 1488 | if datainfo.err_data is not None: |
|---|
| 1489 | err = ','.join([str(datainfo.err_data[i]) for i in |
|---|
| 1490 | xrange(len(datainfo.err_data))]) |
|---|
| 1491 | self.write_node(point, "Idev", err, |
|---|
| 1492 | {'unit': datainfo._zunit}) |
|---|
| 1493 | if datainfo.dqy_data is not None: |
|---|
| 1494 | dqy = ','.join([str(datainfo.dqy_data[i]) for i in |
|---|
| 1495 | xrange(len(datainfo.dqy_data))]) |
|---|
| 1496 | self.write_node(point, "Qydev", dqy, |
|---|
| 1497 | {'unit': datainfo._yunit}) |
|---|
| 1498 | if datainfo.dqx_data is not None: |
|---|
| 1499 | dqx = ','.join([str(datainfo.dqx_data[i]) for i in |
|---|
| 1500 | xrange(len(datainfo.dqx_data))]) |
|---|
| 1501 | self.write_node(point, "Qxdev", dqx, |
|---|
| 1502 | {'unit': datainfo._xunit}) |
|---|
| 1503 | if datainfo.mask is not None: |
|---|
| 1504 | mask = ','.join( |
|---|
| 1505 | ["1" if datainfo.mask[i] else "0" |
|---|
| 1506 | for i in xrange(len(datainfo.mask))]) |
|---|
| 1507 | self.write_node(point, "Mask", mask) |
|---|
| 1508 | |
|---|
| 1509 | def _write_trans_spectrum(self, datainfo, entry_node): |
|---|
| 1510 | """ |
|---|
| 1511 | Writes the transmission spectrum data to the XML file |
|---|
| 1512 | |
|---|
| 1513 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1514 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1515 | """ |
|---|
| 1516 | for i in range(len(datainfo.trans_spectrum)): |
|---|
| 1517 | spectrum = datainfo.trans_spectrum[i] |
|---|
| 1518 | node = self.create_element("SAStransmission_spectrum", |
|---|
| 1519 | {"name" : spectrum.name}) |
|---|
| 1520 | self.append(node, entry_node) |
|---|
| 1521 | if isinstance(spectrum.timestamp, datetime.datetime): |
|---|
| 1522 | node.setAttribute("timestamp", spectrum.timestamp) |
|---|
| 1523 | for i in range(len(spectrum.wavelength)): |
|---|
| 1524 | point = self.create_element("Tdata") |
|---|
| 1525 | node.append(point) |
|---|
| 1526 | self.write_node(point, "Lambda", spectrum.wavelength[i], |
|---|
| 1527 | {'unit': spectrum.wavelength_unit}) |
|---|
| 1528 | self.write_node(point, "T", spectrum.transmission[i], |
|---|
| 1529 | {'unit': spectrum.transmission_unit}) |
|---|
| 1530 | if spectrum.transmission_deviation is not None \ |
|---|
| 1531 | and len(spectrum.transmission_deviation) >= i: |
|---|
| 1532 | self.write_node(point, "Tdev", |
|---|
| 1533 | spectrum.transmission_deviation[i], |
|---|
| 1534 | {'unit': |
|---|
| 1535 | spectrum.transmission_deviation_unit}) |
|---|
| 1536 | |
|---|
| 1537 | def _write_sample_info(self, datainfo, entry_node): |
|---|
| 1538 | """ |
|---|
| 1539 | Writes the sample information to the XML file |
|---|
| 1540 | |
|---|
| 1541 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1542 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1543 | """ |
|---|
| 1544 | sample = self.create_element("SASsample") |
|---|
| 1545 | if datainfo.sample.name is not None: |
|---|
| 1546 | self.write_attribute(sample, "name", |
|---|
| 1547 | str(datainfo.sample.name)) |
|---|
| 1548 | self.append(sample, entry_node) |
|---|
| 1549 | self.write_node(sample, "ID", str(datainfo.sample.ID)) |
|---|
| 1550 | self.write_node(sample, "thickness", datainfo.sample.thickness, |
|---|
| 1551 | {"unit": datainfo.sample.thickness_unit}) |
|---|
| 1552 | self.write_node(sample, "transmission", datainfo.sample.transmission) |
|---|
| 1553 | self.write_node(sample, "temperature", datainfo.sample.temperature, |
|---|
| 1554 | {"unit": datainfo.sample.temperature_unit}) |
|---|
| 1555 | |
|---|
| 1556 | pos = self.create_element("position") |
|---|
| 1557 | written = self.write_node(pos, |
|---|
| 1558 | "x", |
|---|
| 1559 | datainfo.sample.position.x, |
|---|
| 1560 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1561 | written = written | self.write_node( \ |
|---|
| 1562 | pos, "y", datainfo.sample.position.y, |
|---|
| 1563 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1564 | written = written | self.write_node( \ |
|---|
| 1565 | pos, "z", datainfo.sample.position.z, |
|---|
| 1566 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1567 | if written == True: |
|---|
| 1568 | self.append(pos, sample) |
|---|
| 1569 | |
|---|
| 1570 | ori = self.create_element("orientation") |
|---|
| 1571 | written = self.write_node(ori, "roll", |
|---|
| 1572 | datainfo.sample.orientation.x, |
|---|
| 1573 | {"unit": datainfo.sample.orientation_unit}) |
|---|
| 1574 | written = written | self.write_node( \ |
|---|
| 1575 | ori, "pitch", datainfo.sample.orientation.y, |
|---|
| 1576 | {"unit": datainfo.sample.orientation_unit}) |
|---|
| 1577 | written = written | self.write_node( \ |
|---|
| 1578 | ori, "yaw", datainfo.sample.orientation.z, |
|---|
| 1579 | {"unit": datainfo.sample.orientation_unit}) |
|---|
| 1580 | if written == True: |
|---|
| 1581 | self.append(ori, sample) |
|---|
| 1582 | |
|---|
| 1583 | for item in datainfo.sample.details: |
|---|
| 1584 | self.write_node(sample, "details", item) |
|---|
| 1585 | |
|---|
| 1586 | def _write_instrument(self, datainfo, entry_node): |
|---|
| 1587 | """ |
|---|
| 1588 | Writes the instrumental information to the XML file |
|---|
| 1589 | |
|---|
| 1590 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1591 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1592 | """ |
|---|
| 1593 | instr = self.create_element("SASinstrument") |
|---|
| 1594 | self.append(instr, entry_node) |
|---|
| 1595 | self.write_node(instr, "name", datainfo.instrument) |
|---|
| 1596 | return instr |
|---|
| 1597 | |
|---|
| 1598 | def _write_source(self, datainfo, instr): |
|---|
| 1599 | """ |
|---|
| 1600 | Writes the source information to the XML file |
|---|
| 1601 | |
|---|
| 1602 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1603 | :param instr: instrument node to be appended to |
|---|
| 1604 | """ |
|---|
| 1605 | source = self.create_element("SASsource") |
|---|
| 1606 | if datainfo.source.name is not None: |
|---|
| 1607 | self.write_attribute(source, "name", |
|---|
| 1608 | str(datainfo.source.name)) |
|---|
| 1609 | self.append(source, instr) |
|---|
| 1610 | if datainfo.source.radiation is None or datainfo.source.radiation == '': |
|---|
| 1611 | datainfo.source.radiation = "neutron" |
|---|
| 1612 | self.write_node(source, "radiation", datainfo.source.radiation) |
|---|
| 1613 | |
|---|
| 1614 | size = self.create_element("beam_size") |
|---|
| 1615 | if datainfo.source.beam_size_name is not None: |
|---|
| 1616 | self.write_attribute(size, "name", |
|---|
| 1617 | str(datainfo.source.beam_size_name)) |
|---|
| 1618 | written = self.write_node( \ |
|---|
| 1619 | size, "x", datainfo.source.beam_size.x, |
|---|
| 1620 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1621 | written = written | self.write_node( \ |
|---|
| 1622 | size, "y", datainfo.source.beam_size.y, |
|---|
| 1623 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1624 | written = written | self.write_node( \ |
|---|
| 1625 | size, "z", datainfo.source.beam_size.z, |
|---|
| 1626 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1627 | if written == True: |
|---|
| 1628 | self.append(size, source) |
|---|
| 1629 | |
|---|
| 1630 | self.write_node(source, "beam_shape", datainfo.source.beam_shape) |
|---|
| 1631 | self.write_node(source, "wavelength", |
|---|
| 1632 | datainfo.source.wavelength, |
|---|
| 1633 | {"unit": datainfo.source.wavelength_unit}) |
|---|
| 1634 | self.write_node(source, "wavelength_min", |
|---|
| 1635 | datainfo.source.wavelength_min, |
|---|
| 1636 | {"unit": datainfo.source.wavelength_min_unit}) |
|---|
| 1637 | self.write_node(source, "wavelength_max", |
|---|
| 1638 | datainfo.source.wavelength_max, |
|---|
| 1639 | {"unit": datainfo.source.wavelength_max_unit}) |
|---|
| 1640 | self.write_node(source, "wavelength_spread", |
|---|
| 1641 | datainfo.source.wavelength_spread, |
|---|
| 1642 | {"unit": datainfo.source.wavelength_spread_unit}) |
|---|
| 1643 | |
|---|
| 1644 | def _write_collimation(self, datainfo, instr): |
|---|
| 1645 | """ |
|---|
| 1646 | Writes the collimation information to the XML file |
|---|
| 1647 | |
|---|
| 1648 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1649 | :param instr: lxml node ElementTree object to be appended to |
|---|
| 1650 | """ |
|---|
| 1651 | if datainfo.collimation == [] or datainfo.collimation is None: |
|---|
| 1652 | coll = Collimation() |
|---|
| 1653 | datainfo.collimation.append(coll) |
|---|
| 1654 | for item in datainfo.collimation: |
|---|
| 1655 | coll = self.create_element("SAScollimation") |
|---|
| 1656 | if item.name is not None: |
|---|
| 1657 | self.write_attribute(coll, "name", str(item.name)) |
|---|
| 1658 | self.append(coll, instr) |
|---|
| 1659 | |
|---|
| 1660 | self.write_node(coll, "length", item.length, |
|---|
| 1661 | {"unit": item.length_unit}) |
|---|
| 1662 | |
|---|
| 1663 | for aperture in item.aperture: |
|---|
| 1664 | apert = self.create_element("aperture") |
|---|
| 1665 | if aperture.name is not None: |
|---|
| 1666 | self.write_attribute(apert, "name", str(aperture.name)) |
|---|
| 1667 | if aperture.type is not None: |
|---|
| 1668 | self.write_attribute(apert, "type", str(aperture.type)) |
|---|
| 1669 | self.append(apert, coll) |
|---|
| 1670 | |
|---|
| 1671 | size = self.create_element("size") |
|---|
| 1672 | if aperture.size_name is not None: |
|---|
| 1673 | self.write_attribute(size, "name", |
|---|
| 1674 | str(aperture.size_name)) |
|---|
| 1675 | written = self.write_node(size, "x", aperture.size.x, |
|---|
| 1676 | {"unit": aperture.size_unit}) |
|---|
| 1677 | written = written | self.write_node( \ |
|---|
| 1678 | size, "y", aperture.size.y, |
|---|
| 1679 | {"unit": aperture.size_unit}) |
|---|
| 1680 | written = written | self.write_node( \ |
|---|
| 1681 | size, "z", aperture.size.z, |
|---|
| 1682 | {"unit": aperture.size_unit}) |
|---|
| 1683 | if written == True: |
|---|
| 1684 | self.append(size, apert) |
|---|
| 1685 | |
|---|
| 1686 | self.write_node(apert, "distance", aperture.distance, |
|---|
| 1687 | {"unit": aperture.distance_unit}) |
|---|
| 1688 | |
|---|
| 1689 | def _write_detectors(self, datainfo, instr): |
|---|
| 1690 | """ |
|---|
| 1691 | Writes the detector information to the XML file |
|---|
| 1692 | |
|---|
| 1693 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1694 | :param inst: lxml instrument node to be appended to |
|---|
| 1695 | """ |
|---|
| 1696 | if datainfo.detector is None or datainfo.detector == []: |
|---|
| 1697 | det = Detector() |
|---|
| 1698 | det.name = "" |
|---|
| 1699 | datainfo.detector.append(det) |
|---|
| 1700 | |
|---|
| 1701 | for item in datainfo.detector: |
|---|
| 1702 | det = self.create_element("SASdetector") |
|---|
| 1703 | written = self.write_node(det, "name", item.name) |
|---|
| 1704 | written = written | self.write_node(det, "SDD", item.distance, |
|---|
| 1705 | {"unit": item.distance_unit}) |
|---|
| 1706 | if written == True: |
|---|
| 1707 | self.append(det, instr) |
|---|
| 1708 | |
|---|
| 1709 | off = self.create_element("offset") |
|---|
| 1710 | written = self.write_node(off, "x", item.offset.x, |
|---|
| 1711 | {"unit": item.offset_unit}) |
|---|
| 1712 | written = written | self.write_node(off, "y", item.offset.y, |
|---|
| 1713 | {"unit": item.offset_unit}) |
|---|
| 1714 | written = written | self.write_node(off, "z", item.offset.z, |
|---|
| 1715 | {"unit": item.offset_unit}) |
|---|
| 1716 | if written == True: |
|---|
| 1717 | self.append(off, det) |
|---|
| 1718 | |
|---|
| 1719 | ori = self.create_element("orientation") |
|---|
| 1720 | written = self.write_node(ori, "roll", item.orientation.x, |
|---|
| 1721 | {"unit": item.orientation_unit}) |
|---|
| 1722 | written = written | self.write_node(ori, "pitch", |
|---|
| 1723 | item.orientation.y, |
|---|
| 1724 | {"unit": item.orientation_unit}) |
|---|
| 1725 | written = written | self.write_node(ori, "yaw", |
|---|
| 1726 | item.orientation.z, |
|---|
| 1727 | {"unit": item.orientation_unit}) |
|---|
| 1728 | if written == True: |
|---|
| 1729 | self.append(ori, det) |
|---|
| 1730 | |
|---|
| 1731 | center = self.create_element("beam_center") |
|---|
| 1732 | written = self.write_node(center, "x", item.beam_center.x, |
|---|
| 1733 | {"unit": item.beam_center_unit}) |
|---|
| 1734 | written = written | self.write_node(center, "y", |
|---|
| 1735 | item.beam_center.y, |
|---|
| 1736 | {"unit": item.beam_center_unit}) |
|---|
| 1737 | written = written | self.write_node(center, "z", |
|---|
| 1738 | item.beam_center.z, |
|---|
| 1739 | {"unit": item.beam_center_unit}) |
|---|
| 1740 | if written == True: |
|---|
| 1741 | self.append(center, det) |
|---|
| 1742 | |
|---|
| 1743 | pix = self.create_element("pixel_size") |
|---|
| 1744 | written = self.write_node(pix, "x", item.pixel_size.x, |
|---|
| 1745 | {"unit": item.pixel_size_unit}) |
|---|
| 1746 | written = written | self.write_node(pix, "y", item.pixel_size.y, |
|---|
| 1747 | {"unit": item.pixel_size_unit}) |
|---|
| 1748 | written = written | self.write_node(pix, "z", item.pixel_size.z, |
|---|
| 1749 | {"unit": item.pixel_size_unit}) |
|---|
| 1750 | if written == True: |
|---|
| 1751 | self.append(pix, det) |
|---|
| 1752 | self.write_node(det, "slit_length", item.slit_length, |
|---|
| 1753 | {"unit": item.slit_length_unit}) |
|---|
| 1754 | |
|---|
| 1755 | def _write_process_notes(self, datainfo, entry_node): |
|---|
| 1756 | """ |
|---|
| 1757 | Writes the process notes to the XML file |
|---|
| 1758 | |
|---|
| 1759 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1760 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1761 | |
|---|
| 1762 | """ |
|---|
| 1763 | for item in datainfo.process: |
|---|
| 1764 | node = self.create_element("SASprocess") |
|---|
| 1765 | self.append(node, entry_node) |
|---|
| 1766 | self.write_node(node, "name", item.name) |
|---|
| 1767 | self.write_node(node, "date", item.date) |
|---|
| 1768 | self.write_node(node, "description", item.description) |
|---|
| 1769 | for term in item.term: |
|---|
| 1770 | if isinstance(term, list): |
|---|
| 1771 | value = term['value'] |
|---|
| 1772 | del term['value'] |
|---|
| 1773 | elif isinstance(term, dict): |
|---|
| 1774 | value = term.get("value") |
|---|
| 1775 | del term['value'] |
|---|
| 1776 | else: |
|---|
| 1777 | value = term |
|---|
| 1778 | self.write_node(node, "term", value, term) |
|---|
| 1779 | for note in item.notes: |
|---|
| 1780 | self.write_node(node, "SASprocessnote", note) |
|---|
| 1781 | if len(item.notes) == 0: |
|---|
| 1782 | self.write_node(node, "SASprocessnote", "") |
|---|
| 1783 | |
|---|
| 1784 | def _write_notes(self, datainfo, entry_node): |
|---|
| 1785 | """ |
|---|
| 1786 | Writes the notes to the XML file and creates an empty note if none |
|---|
| 1787 | exist |
|---|
| 1788 | |
|---|
| 1789 | :param datainfo: The Data1D object the information is coming from |
|---|
| 1790 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1791 | |
|---|
| 1792 | """ |
|---|
| 1793 | if len(datainfo.notes) == 0: |
|---|
| 1794 | node = self.create_element("SASnote") |
|---|
| 1795 | self.append(node, entry_node) |
|---|
| 1796 | else: |
|---|
| 1797 | for item in datainfo.notes: |
|---|
| 1798 | node = self.create_element("SASnote") |
|---|
| 1799 | self.write_text(node, item) |
|---|
| 1800 | self.append(node, entry_node) |
|---|
| 1801 | |
|---|
| 1802 | def _check_root(self): |
|---|
| 1803 | """ |
|---|
| 1804 | Return the document, and the SASentry node associated with |
|---|
| 1805 | the data we just wrote. |
|---|
| 1806 | If the calling function was not the cansas reader, return a minidom |
|---|
| 1807 | object rather than an lxml object. |
|---|
| 1808 | |
|---|
| 1809 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1810 | :param doc: entire xml tree |
|---|
| 1811 | """ |
|---|
| 1812 | if not self.frm: |
|---|
| 1813 | self.frm = inspect.stack()[2] |
|---|
| 1814 | mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") |
|---|
| 1815 | mod_name = mod_name.replace(".py", "") |
|---|
| 1816 | mod = mod_name.split("sas/") |
|---|
| 1817 | mod_name = mod[1] |
|---|
| 1818 | return mod_name == "sascalc/dataloader/readers/cansas_reader" |
|---|
| 1819 | |
|---|
| 1820 | def _check_origin(self, entry_node, doc): |
|---|
| 1821 | """ |
|---|
| 1822 | Return the document, and the SASentry node associated with |
|---|
| 1823 | the data we just wrote. |
|---|
| 1824 | If the calling function was not the cansas reader, return a minidom |
|---|
| 1825 | object rather than an lxml object. |
|---|
| 1826 | |
|---|
| 1827 | :param entry_node: lxml node ElementTree object to be appended to |
|---|
| 1828 | :param doc: entire xml tree |
|---|
| 1829 | """ |
|---|
| 1830 | if not self._check_root(): |
|---|
| 1831 | string = self.to_string(doc, pretty_print=False) |
|---|
| 1832 | doc = parseString(string) |
|---|
| 1833 | node_name = entry_node.tag |
|---|
| 1834 | node_list = doc.getElementsByTagName(node_name) |
|---|
| 1835 | entry_node = node_list.item(0) |
|---|
| 1836 | return doc, entry_node |
|---|
| 1837 | |
|---|
| 1838 | # DO NOT REMOVE - used in saving and loading panel states. |
|---|
| 1839 | def _store_float(self, location, node, variable, storage, optional=True): |
|---|
| 1840 | """ |
|---|
| 1841 | Get the content of a xpath location and store |
|---|
| 1842 | the result. Check that the units are compatible |
|---|
| 1843 | with the destination. The value is expected to |
|---|
| 1844 | be a float. |
|---|
| 1845 | |
|---|
| 1846 | The xpath location might or might not exist. |
|---|
| 1847 | If it does not exist, nothing is done |
|---|
| 1848 | |
|---|
| 1849 | :param location: xpath location to fetch |
|---|
| 1850 | :param node: node to read the data from |
|---|
| 1851 | :param variable: name of the data member to store it in [string] |
|---|
| 1852 | :param storage: data object that has the 'variable' data member |
|---|
| 1853 | :param optional: if True, no exception will be raised |
|---|
| 1854 | if unit conversion can't be done |
|---|
| 1855 | |
|---|
| 1856 | :raise ValueError: raised when the units are not recognized |
|---|
| 1857 | """ |
|---|
| 1858 | entry = get_content(location, node) |
|---|
| 1859 | try: |
|---|
| 1860 | value = float(entry.text) |
|---|
| 1861 | except: |
|---|
| 1862 | value = None |
|---|
| 1863 | |
|---|
| 1864 | if value is not None: |
|---|
| 1865 | # If the entry has units, check to see that they are |
|---|
| 1866 | # compatible with what we currently have in the data object |
|---|
| 1867 | units = entry.get('unit') |
|---|
| 1868 | if units is not None: |
|---|
| 1869 | toks = variable.split('.') |
|---|
| 1870 | local_unit = None |
|---|
| 1871 | exec "local_unit = storage.%s_unit" % toks[0] |
|---|
| 1872 | if local_unit is not None and units.lower() != local_unit.lower(): |
|---|
| 1873 | if HAS_CONVERTER == True: |
|---|
| 1874 | try: |
|---|
| 1875 | conv = Converter(units) |
|---|
| 1876 | exec "storage.%s = %g" % \ |
|---|
| 1877 | (variable, conv(value, units=local_unit)) |
|---|
| 1878 | except: |
|---|
| 1879 | _, exc_value, _ = sys.exc_info() |
|---|
| 1880 | err_mess = "CanSAS reader: could not convert" |
|---|
| 1881 | err_mess += " %s unit [%s]; expecting [%s]\n %s" \ |
|---|
| 1882 | % (variable, units, local_unit, exc_value) |
|---|
| 1883 | self.errors.add(err_mess) |
|---|
| 1884 | if optional: |
|---|
| 1885 | logger.info(err_mess) |
|---|
| 1886 | else: |
|---|
| 1887 | raise ValueError, err_mess |
|---|
| 1888 | else: |
|---|
| 1889 | err_mess = "CanSAS reader: unrecognized %s unit [%s];"\ |
|---|
| 1890 | % (variable, units) |
|---|
| 1891 | err_mess += " expecting [%s]" % local_unit |
|---|
| 1892 | self.errors.add(err_mess) |
|---|
| 1893 | if optional: |
|---|
| 1894 | logger.info(err_mess) |
|---|
| 1895 | else: |
|---|
| 1896 | raise ValueError, err_mess |
|---|
| 1897 | else: |
|---|
| 1898 | exec "storage.%s = value" % variable |
|---|
| 1899 | else: |
|---|
| 1900 | exec "storage.%s = value" % variable |
|---|
| 1901 | |
|---|
| 1902 | # DO NOT REMOVE - used in saving and loading panel states. |
|---|
| 1903 | def _store_content(self, location, node, variable, storage): |
|---|
| 1904 | """ |
|---|
| 1905 | Get the content of a xpath location and store |
|---|
| 1906 | the result. The value is treated as a string. |
|---|
| 1907 | |
|---|
| 1908 | The xpath location might or might not exist. |
|---|
| 1909 | If it does not exist, nothing is done |
|---|
| 1910 | |
|---|
| 1911 | :param location: xpath location to fetch |
|---|
| 1912 | :param node: node to read the data from |
|---|
| 1913 | :param variable: name of the data member to store it in [string] |
|---|
| 1914 | :param storage: data object that has the 'variable' data member |
|---|
| 1915 | |
|---|
| 1916 | :return: return a list of errors |
|---|
| 1917 | """ |
|---|
| 1918 | entry = get_content(location, node) |
|---|
| 1919 | if entry is not None and entry.text is not None: |
|---|
| 1920 | exec "storage.%s = entry.text.strip()" % variable |
|---|
| 1921 | |
|---|
| 1922 | |
|---|
| 1923 | # DO NOT REMOVE Called by outside packages: |
|---|
| 1924 | # sas.sasgui.perspectives.invariant.invariant_state |
|---|
| 1925 | # sas.sasgui.perspectives.fitting.pagestate |
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| 1926 | def get_content(location, node): |
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| 1927 | """ |
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| 1928 | Get the first instance of the content of a xpath location. |
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| 1929 | |
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| 1930 | :param location: xpath location |
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| 1931 | :param node: node to start at |
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| 1932 | |
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| 1933 | :return: Element, or None |
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| 1934 | """ |
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| 1935 | nodes = node.xpath(location, |
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| 1936 | namespaces={'ns': CANSAS_NS.get("1.0").get("ns")}) |
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| 1937 | if len(nodes) > 0: |
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| 1938 | return nodes[0] |
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| 1939 | else: |
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| 1940 | return None |
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| 1941 | |
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| 1942 | # DO NOT REMOVE Called by outside packages: |
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| 1943 | # sas.sasgui.perspectives.fitting.pagestate |
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| 1944 | def write_node(doc, parent, name, value, attr=None): |
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| 1945 | """ |
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| 1946 | :param doc: document DOM |
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| 1947 | :param parent: parent node |
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| 1948 | :param name: tag of the element |
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| 1949 | :param value: value of the child text node |
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| 1950 | :param attr: attribute dictionary |
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| 1951 | |
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| 1952 | :return: True if something was appended, otherwise False |
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| 1953 | """ |
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| 1954 | if attr is None: |
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| 1955 | attr = {} |
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| 1956 | if value is not None: |
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| 1957 | node = doc.createElement(name) |
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| 1958 | node.appendChild(doc.createTextNode(str(value))) |
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| 1959 | for item in attr: |
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| 1960 | node.setAttribute(item, attr[item]) |
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| 1961 | parent.appendChild(node) |
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| 1962 | return True |
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| 1963 | return False |
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