[d26dea0] | 1 | import logging |
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| 2 | import os |
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| 3 | import sys |
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| 4 | import datetime |
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| 5 | import inspect |
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[574adc7] | 6 | |
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| 7 | import numpy as np |
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[d26dea0] | 8 | |
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[682c432] | 9 | # The following 2 imports *ARE* used. Do not remove either. |
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| 10 | import xml.dom.minidom |
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| 11 | from xml.dom.minidom import parseString |
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| 12 | |
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[7477fb9] | 13 | from lxml import etree |
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| 14 | |
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[574adc7] | 15 | from sas.sascalc.data_util.nxsunit import Converter |
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| 16 | |
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| 17 | # For saving individual sections of data |
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| 18 | from ..data_info import Data1D, Data2D, DataInfo, plottable_1D, plottable_2D, \ |
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| 19 | Collimation, TransmissionSpectrum, Detector, Process, Aperture, \ |
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| 20 | combine_data_info_with_plottable as combine_data |
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| 21 | from ..loader_exceptions import FileContentsException, DefaultReaderException, \ |
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| 22 | DataReaderException |
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| 23 | from . import xml_reader |
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| 24 | from .xml_reader import XMLreader |
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| 25 | from .cansas_constants import CansasConstants, CurrentLevel |
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| 26 | |
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[463e7ffc] | 27 | logger = logging.getLogger(__name__) |
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[c155a16] | 28 | |
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[d26dea0] | 29 | PREPROCESS = "xmlpreprocess" |
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| 30 | ENCODING = "encoding" |
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| 31 | RUN_NAME_DEFAULT = "None" |
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[250fec92] | 32 | INVALID_SCHEMA_PATH_1_1 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_1.xsd" |
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| 33 | INVALID_SCHEMA_PATH_1_0 = "{0}/sas/sascalc/dataloader/readers/schema/cansas1d_invalid_v1_0.xsd" |
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| 34 | INVALID_XML = "\n\nThe loaded xml file, {0} does not fully meet the CanSAS v1.x specification. SasView loaded " + \ |
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| 35 | "as much of the data as possible.\n\n" |
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[d26dea0] | 36 | |
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| 37 | CONSTANTS = CansasConstants() |
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| 38 | CANSAS_FORMAT = CONSTANTS.format |
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| 39 | CANSAS_NS = CONSTANTS.names |
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| 40 | ALLOW_ALL = True |
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| 41 | |
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| 42 | class Reader(XMLreader): |
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| 43 | cansas_version = "1.0" |
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| 44 | base_ns = "{cansas1d/1.0}" |
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[250fec92] | 45 | cansas_defaults = None |
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[d26dea0] | 46 | type_name = "canSAS" |
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[250fec92] | 47 | invalid = True |
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[654e8e0] | 48 | frm = "" |
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[af08e55] | 49 | # Log messages and errors |
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[250fec92] | 50 | logging = None |
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| 51 | errors = set() |
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[af08e55] | 52 | # Namespace hierarchy for current xml_file object |
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[250fec92] | 53 | names = None |
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| 54 | ns_list = None |
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[af08e55] | 55 | # Temporary storage location for loading multiple data sets in a single file |
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[250fec92] | 56 | current_data1d = None |
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| 57 | data = None |
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[af08e55] | 58 | # Wildcards |
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[d26dea0] | 59 | type = ["XML files (*.xml)|*.xml", "SasView Save Files (*.svs)|*.svs"] |
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[af08e55] | 60 | # List of allowed extensions |
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[d26dea0] | 61 | ext = ['.xml', '.XML', '.svs', '.SVS'] |
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[af08e55] | 62 | # Flag to bypass extension check |
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[d26dea0] | 63 | allow_all = True |
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| 64 | |
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[250fec92] | 65 | def reset_state(self): |
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| 66 | """ |
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| 67 | Resets the class state to a base case when loading a new data file so previous |
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| 68 | data files do not appear a second time |
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| 69 | """ |
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[61f329f0] | 70 | super(Reader, self).reset_state() |
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[250fec92] | 71 | self.data = [] |
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| 72 | self.process = Process() |
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| 73 | self.transspectrum = TransmissionSpectrum() |
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| 74 | self.aperture = Aperture() |
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| 75 | self.collimation = Collimation() |
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| 76 | self.detector = Detector() |
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| 77 | self.names = [] |
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| 78 | self.cansas_defaults = {} |
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| 79 | self.ns_list = None |
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[d26dea0] | 80 | self.logging = [] |
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| 81 | self.encoding = None |
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| 82 | |
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[250fec92] | 83 | def read(self, xml_file, schema_path="", invalid=True): |
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[2469df7] | 84 | if schema_path != "" or not invalid: |
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[bc570f4] | 85 | # read has been called from self.get_file_contents because xml file doens't conform to schema |
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| 86 | _, self.extension = os.path.splitext(os.path.basename(xml_file)) |
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| 87 | return self.get_file_contents(xml_file=xml_file, schema_path=schema_path, invalid=invalid) |
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[250fec92] | 88 | |
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[bc570f4] | 89 | # Otherwise, read has been called by the data loader - file_reader_base_class handles this |
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| 90 | return super(XMLreader, self).read(xml_file) |
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| 91 | |
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| 92 | def get_file_contents(self, xml_file=None, schema_path="", invalid=True): |
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[7477fb9] | 93 | # Reset everything since we're loading a new file |
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[250fec92] | 94 | self.reset_state() |
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| 95 | self.invalid = invalid |
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[bc570f4] | 96 | if xml_file is None: |
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| 97 | xml_file = self.f_open.name |
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[7477fb9] | 98 | # We don't sure f_open since lxml handles opnening/closing files |
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[bc570f4] | 99 | try: |
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[8dec7e7] | 100 | # Raises FileContentsException |
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| 101 | self.load_file_and_schema(xml_file, schema_path) |
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[7477fb9] | 102 | # Parse each SASentry |
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[7b07fbe] | 103 | entry_list = self.xmlroot.xpath('/ns:SASroot/ns:SASentry', |
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| 104 | namespaces={ |
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| 105 | 'ns': self.cansas_defaults.get( |
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| 106 | "ns") |
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| 107 | }) |
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| 108 | self.is_cansas(self.extension) |
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[bc570f4] | 109 | self.set_processing_instructions() |
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| 110 | for entry in entry_list: |
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| 111 | self._parse_entry(entry) |
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[c54c965] | 112 | self.data_cleanup() |
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[bc570f4] | 113 | except FileContentsException as fc_exc: |
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[7477fb9] | 114 | # File doesn't meet schema - try loading with a less strict schema |
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| 115 | base_name = xml_reader.__file__ |
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| 116 | base_name = base_name.replace("\\", "/") |
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| 117 | base = base_name.split("/sas/")[0] |
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| 118 | if self.cansas_version == "1.1": |
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| 119 | invalid_schema = INVALID_SCHEMA_PATH_1_1.format(base, self.cansas_defaults.get("schema")) |
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| 120 | else: |
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| 121 | invalid_schema = INVALID_SCHEMA_PATH_1_0.format(base, self.cansas_defaults.get("schema")) |
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| 122 | self.set_schema(invalid_schema) |
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| 123 | if self.invalid: |
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[250fec92] | 124 | try: |
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[7477fb9] | 125 | # Load data with less strict schema |
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| 126 | self.read(xml_file, invalid_schema, False) |
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| 127 | |
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| 128 | # File can still be read but doesn't match schema, so raise exception |
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| 129 | self.load_file_and_schema(xml_file) # Reload strict schema so we can find where error are in file |
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[250fec92] | 130 | invalid_xml = self.find_invalid_xml() |
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[527a190] | 131 | if invalid_xml != "": |
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[7b07fbe] | 132 | basename, _ = os.path.splitext( |
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| 133 | os.path.basename(self.f_open.name)) |
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[cd57c7d4] | 134 | invalid_xml = INVALID_XML.format(basename + self.extension) + invalid_xml |
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| 135 | raise DataReaderException(invalid_xml) # Handled by base class |
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[7477fb9] | 136 | except FileContentsException as fc_exc: |
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[0615d54] | 137 | msg = "CanSAS Reader could not load the file {}".format(xml_file) |
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[7477fb9] | 138 | if fc_exc.message is not None: # Propagate error messages from earlier |
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[0615d54] | 139 | msg = fc_exc.message |
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[dcb91cf] | 140 | if not self.extension in self.ext: # If the file has no associated loader |
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| 141 | raise DefaultReaderException(msg) |
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[7477fb9] | 142 | raise FileContentsException(msg) |
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| 143 | pass |
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| 144 | else: |
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| 145 | raise fc_exc |
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| 146 | except Exception as e: # Convert all other exceptions to FileContentsExceptions |
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[574adc7] | 147 | raise FileContentsException(str(e)) |
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[7b07fbe] | 148 | finally: |
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| 149 | if not self.f_open.closed: |
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| 150 | self.f_open.close() |
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[7477fb9] | 151 | |
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| 152 | def load_file_and_schema(self, xml_file, schema_path=""): |
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| 153 | base_name = xml_reader.__file__ |
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| 154 | base_name = base_name.replace("\\", "/") |
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| 155 | base = base_name.split("/sas/")[0] |
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| 156 | |
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| 157 | # Try and parse the XML file |
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| 158 | try: |
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| 159 | self.set_xml_file(xml_file) |
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| 160 | except etree.XMLSyntaxError: # File isn't valid XML so can't be loaded |
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[dcb91cf] | 161 | msg = "SasView cannot load {}.\nInvalid XML syntax".format(xml_file) |
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[7477fb9] | 162 | raise FileContentsException(msg) |
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| 163 | |
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| 164 | self.cansas_version = self.xmlroot.get("version", "1.0") |
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| 165 | self.cansas_defaults = CANSAS_NS.get(self.cansas_version, "1.0") |
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| 166 | |
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| 167 | if schema_path == "": |
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| 168 | schema_path = "{}/sas/sascalc/dataloader/readers/schema/{}".format( |
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| 169 | base, self.cansas_defaults.get("schema").replace("\\", "/") |
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| 170 | ) |
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| 171 | self.set_schema(schema_path) |
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| 172 | |
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| 173 | def is_cansas(self, ext="xml"): |
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[250fec92] | 174 | """ |
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[7477fb9] | 175 | Checks to see if the XML file is a CanSAS file |
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[250fec92] | 176 | |
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[7477fb9] | 177 | :param ext: The file extension of the data file |
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| 178 | :raises FileContentsException: Raised if XML file isn't valid CanSAS |
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[250fec92] | 179 | """ |
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[7477fb9] | 180 | if self.validate_xml(): # Check file is valid XML |
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| 181 | name = "{http://www.w3.org/2001/XMLSchema-instance}schemaLocation" |
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| 182 | value = self.xmlroot.get(name) |
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| 183 | # Check schema CanSAS version matches file CanSAS version |
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| 184 | if CANSAS_NS.get(self.cansas_version).get("ns") == value.rsplit(" ")[0]: |
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| 185 | return True |
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| 186 | if ext == "svs": |
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| 187 | return True # Why is this required? |
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| 188 | # If we get to this point then file isn't valid CanSAS |
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[dcb91cf] | 189 | logger.warning("File doesn't meet CanSAS schema. Trying to load anyway.") |
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[7477fb9] | 190 | raise FileContentsException("The file is not valid CanSAS") |
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[250fec92] | 191 | |
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[7477fb9] | 192 | def _parse_entry(self, dom, recurse=False): |
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[654e8e0] | 193 | if not self._is_call_local() and not recurse: |
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[1686a333] | 194 | self.reset_state() |
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[7b07fbe] | 195 | if not recurse: |
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[7477fb9] | 196 | self.current_datainfo = DataInfo() |
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[7b07fbe] | 197 | # Raises FileContentsException if file doesn't meet CanSAS schema |
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| 198 | self.invalid = False |
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| 199 | # Look for a SASentry |
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| 200 | self.data = [] |
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[1686a333] | 201 | self.parent_class = "SASentry" |
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[7b07fbe] | 202 | self.names.append("SASentry") |
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| 203 | self.current_datainfo.meta_data["loader"] = "CanSAS XML 1D" |
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| 204 | self.current_datainfo.meta_data[ |
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| 205 | PREPROCESS] = self.processing_instructions |
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| 206 | if self._is_call_local() and not recurse: |
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| 207 | basename, _ = os.path.splitext(os.path.basename(self.f_open.name)) |
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| 208 | self.current_datainfo.filename = basename + self.extension |
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[7477fb9] | 209 | # Create an empty dataset if no data has been passed to the reader |
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| 210 | if self.current_dataset is None: |
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[7b07fbe] | 211 | self._initialize_new_data_set(dom) |
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[7477fb9] | 212 | self.base_ns = "{" + CANSAS_NS.get(self.cansas_version).get("ns") + "}" |
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[250fec92] | 213 | |
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[7477fb9] | 214 | # Loop through each child in the parent element |
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[250fec92] | 215 | for node in dom: |
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[5f26aa4] | 216 | attr = node.attrib |
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| 217 | name = attr.get("name", "") |
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| 218 | type = attr.get("type", "") |
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[250fec92] | 219 | # Get the element name and set the current names level |
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| 220 | tagname = node.tag.replace(self.base_ns, "") |
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| 221 | tagname_original = tagname |
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| 222 | # Skip this iteration when loading in save state information |
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[7b07fbe] | 223 | if tagname in ["fitting_plug_in", "pr_inversion", "invariant", "corfunc"]: |
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[250fec92] | 224 | continue |
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| 225 | # Get where to store content |
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| 226 | self.names.append(tagname_original) |
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| 227 | self.ns_list = CONSTANTS.iterate_namespace(self.names) |
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| 228 | # If the element is a child element, recurse |
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| 229 | if len(node.getchildren()) > 0: |
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| 230 | self.parent_class = tagname_original |
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| 231 | if tagname == 'SASdata': |
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[af08e55] | 232 | self._initialize_new_data_set(node) |
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| 233 | if isinstance(self.current_dataset, plottable_2D): |
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| 234 | x_bins = attr.get("x_bins", "") |
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| 235 | y_bins = attr.get("y_bins", "") |
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| 236 | if x_bins is not "" and y_bins is not "": |
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| 237 | self.current_dataset.shape = (x_bins, y_bins) |
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| 238 | else: |
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| 239 | self.current_dataset.shape = () |
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[7477fb9] | 240 | # Recurse to access data within the group |
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| 241 | self._parse_entry(node, recurse=True) |
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[5f26aa4] | 242 | if tagname == "SASsample": |
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| 243 | self.current_datainfo.sample.name = name |
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| 244 | elif tagname == "beam_size": |
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| 245 | self.current_datainfo.source.beam_size_name = name |
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| 246 | elif tagname == "SAScollimation": |
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| 247 | self.collimation.name = name |
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| 248 | elif tagname == "aperture": |
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| 249 | self.aperture.name = name |
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| 250 | self.aperture.type = type |
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[7477fb9] | 251 | self._add_intermediate() |
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[250fec92] | 252 | else: |
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[7b07fbe] | 253 | # TODO: Clean this up to make it faster (fewer if/elifs) |
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[1905128] | 254 | if isinstance(self.current_dataset, plottable_2D): |
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| 255 | data_point = node.text |
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| 256 | unit = attr.get('unit', '') |
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| 257 | else: |
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| 258 | data_point, unit = self._get_node_value(node, tagname) |
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[250fec92] | 259 | |
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[af08e55] | 260 | # If this is a dataset, store the data appropriately |
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[250fec92] | 261 | if tagname == 'Run': |
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[5f26aa4] | 262 | self.current_datainfo.run_name[data_point] = name |
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[250fec92] | 263 | self.current_datainfo.run.append(data_point) |
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| 264 | elif tagname == 'Title': |
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| 265 | self.current_datainfo.title = data_point |
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| 266 | elif tagname == 'SASnote': |
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| 267 | self.current_datainfo.notes.append(data_point) |
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| 268 | |
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[0b79323] | 269 | # I and Q points |
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[af08e55] | 270 | elif tagname == 'I' and isinstance(self.current_dataset, plottable_1D): |
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[527a190] | 271 | self.current_dataset.yaxis("Intensity", unit) |
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[250fec92] | 272 | self.current_dataset.y = np.append(self.current_dataset.y, data_point) |
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[af08e55] | 273 | elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_1D): |
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[250fec92] | 274 | self.current_dataset.dy = np.append(self.current_dataset.dy, data_point) |
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| 275 | elif tagname == 'Q': |
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[527a190] | 276 | self.current_dataset.xaxis("Q", unit) |
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[250fec92] | 277 | self.current_dataset.x = np.append(self.current_dataset.x, data_point) |
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| 278 | elif tagname == 'Qdev': |
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| 279 | self.current_dataset.dx = np.append(self.current_dataset.dx, data_point) |
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| 280 | elif tagname == 'dQw': |
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[590b5c2] | 281 | self.current_dataset.dxw = np.append(self.current_dataset.dxw, data_point) |
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[250fec92] | 282 | elif tagname == 'dQl': |
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| 283 | self.current_dataset.dxl = np.append(self.current_dataset.dxl, data_point) |
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[1686a333] | 284 | elif tagname == 'Qmean': |
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| 285 | pass |
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| 286 | elif tagname == 'Shadowfactor': |
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| 287 | pass |
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[ad4632c] | 288 | elif tagname == 'Sesans': |
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| 289 | self.current_datainfo.isSesans = bool(data_point) |
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[527a190] | 290 | self.current_dataset.xaxis(attr.get('x_axis'), |
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| 291 | attr.get('x_unit')) |
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| 292 | self.current_dataset.yaxis(attr.get('y_axis'), |
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| 293 | attr.get('y_unit')) |
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[63d773c] | 294 | elif tagname == 'yacceptance': |
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| 295 | self.current_datainfo.sample.yacceptance = (data_point, unit) |
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[ad4632c] | 296 | elif tagname == 'zacceptance': |
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| 297 | self.current_datainfo.sample.zacceptance = (data_point, unit) |
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[250fec92] | 298 | |
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[af08e55] | 299 | # I and Qx, Qy - 2D data |
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| 300 | elif tagname == 'I' and isinstance(self.current_dataset, plottable_2D): |
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| 301 | self.current_dataset.yaxis("Intensity", unit) |
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[1905128] | 302 | self.current_dataset.data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 303 | elif tagname == 'Idev' and isinstance(self.current_dataset, plottable_2D): |
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[1905128] | 304 | self.current_dataset.err_data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 305 | elif tagname == 'Qx': |
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| 306 | self.current_dataset.xaxis("Qx", unit) |
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[1905128] | 307 | self.current_dataset.qx_data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 308 | elif tagname == 'Qy': |
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| 309 | self.current_dataset.yaxis("Qy", unit) |
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[1905128] | 310 | self.current_dataset.qy_data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 311 | elif tagname == 'Qxdev': |
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| 312 | self.current_dataset.xaxis("Qxdev", unit) |
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[1905128] | 313 | self.current_dataset.dqx_data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 314 | elif tagname == 'Qydev': |
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| 315 | self.current_dataset.yaxis("Qydev", unit) |
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[1905128] | 316 | self.current_dataset.dqy_data = np.fromstring(data_point, dtype=float, sep=",") |
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[af08e55] | 317 | elif tagname == 'Mask': |
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[bcabf4e] | 318 | inter = [item == "1" for item in data_point.split(",")] |
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[1905128] | 319 | self.current_dataset.mask = np.asarray(inter, dtype=bool) |
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[af08e55] | 320 | |
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| 321 | # Sample Information |
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[250fec92] | 322 | elif tagname == 'ID' and self.parent_class == 'SASsample': |
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| 323 | self.current_datainfo.sample.ID = data_point |
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| 324 | elif tagname == 'Title' and self.parent_class == 'SASsample': |
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| 325 | self.current_datainfo.sample.name = data_point |
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| 326 | elif tagname == 'thickness' and self.parent_class == 'SASsample': |
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| 327 | self.current_datainfo.sample.thickness = data_point |
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| 328 | self.current_datainfo.sample.thickness_unit = unit |
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| 329 | elif tagname == 'transmission' and self.parent_class == 'SASsample': |
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| 330 | self.current_datainfo.sample.transmission = data_point |
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| 331 | elif tagname == 'temperature' and self.parent_class == 'SASsample': |
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| 332 | self.current_datainfo.sample.temperature = data_point |
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| 333 | self.current_datainfo.sample.temperature_unit = unit |
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| 334 | elif tagname == 'details' and self.parent_class == 'SASsample': |
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| 335 | self.current_datainfo.sample.details.append(data_point) |
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| 336 | elif tagname == 'x' and self.parent_class == 'position': |
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| 337 | self.current_datainfo.sample.position.x = data_point |
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| 338 | self.current_datainfo.sample.position_unit = unit |
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| 339 | elif tagname == 'y' and self.parent_class == 'position': |
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| 340 | self.current_datainfo.sample.position.y = data_point |
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| 341 | self.current_datainfo.sample.position_unit = unit |
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| 342 | elif tagname == 'z' and self.parent_class == 'position': |
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| 343 | self.current_datainfo.sample.position.z = data_point |
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| 344 | self.current_datainfo.sample.position_unit = unit |
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| 345 | elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
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| 346 | self.current_datainfo.sample.orientation.x = data_point |
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| 347 | self.current_datainfo.sample.orientation_unit = unit |
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| 348 | elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
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| 349 | self.current_datainfo.sample.orientation.y = data_point |
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| 350 | self.current_datainfo.sample.orientation_unit = unit |
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| 351 | elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASsample' in self.names: |
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| 352 | self.current_datainfo.sample.orientation.z = data_point |
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| 353 | self.current_datainfo.sample.orientation_unit = unit |
---|
| 354 | |
---|
[af08e55] | 355 | # Instrumental Information |
---|
[250fec92] | 356 | elif tagname == 'name' and self.parent_class == 'SASinstrument': |
---|
| 357 | self.current_datainfo.instrument = data_point |
---|
[7477fb9] | 358 | |
---|
[af08e55] | 359 | # Detector Information |
---|
[250fec92] | 360 | elif tagname == 'name' and self.parent_class == 'SASdetector': |
---|
| 361 | self.detector.name = data_point |
---|
| 362 | elif tagname == 'SDD' and self.parent_class == 'SASdetector': |
---|
| 363 | self.detector.distance = data_point |
---|
| 364 | self.detector.distance_unit = unit |
---|
| 365 | elif tagname == 'slit_length' and self.parent_class == 'SASdetector': |
---|
| 366 | self.detector.slit_length = data_point |
---|
| 367 | self.detector.slit_length_unit = unit |
---|
| 368 | elif tagname == 'x' and self.parent_class == 'offset': |
---|
| 369 | self.detector.offset.x = data_point |
---|
| 370 | self.detector.offset_unit = unit |
---|
| 371 | elif tagname == 'y' and self.parent_class == 'offset': |
---|
| 372 | self.detector.offset.y = data_point |
---|
| 373 | self.detector.offset_unit = unit |
---|
| 374 | elif tagname == 'z' and self.parent_class == 'offset': |
---|
| 375 | self.detector.offset.z = data_point |
---|
| 376 | self.detector.offset_unit = unit |
---|
| 377 | elif tagname == 'x' and self.parent_class == 'beam_center': |
---|
| 378 | self.detector.beam_center.x = data_point |
---|
| 379 | self.detector.beam_center_unit = unit |
---|
| 380 | elif tagname == 'y' and self.parent_class == 'beam_center': |
---|
| 381 | self.detector.beam_center.y = data_point |
---|
| 382 | self.detector.beam_center_unit = unit |
---|
| 383 | elif tagname == 'z' and self.parent_class == 'beam_center': |
---|
| 384 | self.detector.beam_center.z = data_point |
---|
| 385 | self.detector.beam_center_unit = unit |
---|
| 386 | elif tagname == 'x' and self.parent_class == 'pixel_size': |
---|
| 387 | self.detector.pixel_size.x = data_point |
---|
| 388 | self.detector.pixel_size_unit = unit |
---|
| 389 | elif tagname == 'y' and self.parent_class == 'pixel_size': |
---|
| 390 | self.detector.pixel_size.y = data_point |
---|
| 391 | self.detector.pixel_size_unit = unit |
---|
| 392 | elif tagname == 'z' and self.parent_class == 'pixel_size': |
---|
| 393 | self.detector.pixel_size.z = data_point |
---|
| 394 | self.detector.pixel_size_unit = unit |
---|
| 395 | elif tagname == 'roll' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
---|
| 396 | self.detector.orientation.x = data_point |
---|
| 397 | self.detector.orientation_unit = unit |
---|
| 398 | elif tagname == 'pitch' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
---|
| 399 | self.detector.orientation.y = data_point |
---|
| 400 | self.detector.orientation_unit = unit |
---|
| 401 | elif tagname == 'yaw' and self.parent_class == 'orientation' and 'SASdetector' in self.names: |
---|
| 402 | self.detector.orientation.z = data_point |
---|
| 403 | self.detector.orientation_unit = unit |
---|
[7477fb9] | 404 | |
---|
[af08e55] | 405 | # Collimation and Aperture |
---|
[250fec92] | 406 | elif tagname == 'length' and self.parent_class == 'SAScollimation': |
---|
| 407 | self.collimation.length = data_point |
---|
| 408 | self.collimation.length_unit = unit |
---|
| 409 | elif tagname == 'name' and self.parent_class == 'SAScollimation': |
---|
| 410 | self.collimation.name = data_point |
---|
| 411 | elif tagname == 'distance' and self.parent_class == 'aperture': |
---|
| 412 | self.aperture.distance = data_point |
---|
| 413 | self.aperture.distance_unit = unit |
---|
| 414 | elif tagname == 'x' and self.parent_class == 'size': |
---|
| 415 | self.aperture.size.x = data_point |
---|
| 416 | self.collimation.size_unit = unit |
---|
| 417 | elif tagname == 'y' and self.parent_class == 'size': |
---|
| 418 | self.aperture.size.y = data_point |
---|
| 419 | self.collimation.size_unit = unit |
---|
| 420 | elif tagname == 'z' and self.parent_class == 'size': |
---|
| 421 | self.aperture.size.z = data_point |
---|
| 422 | self.collimation.size_unit = unit |
---|
| 423 | |
---|
[af08e55] | 424 | # Process Information |
---|
[250fec92] | 425 | elif tagname == 'name' and self.parent_class == 'SASprocess': |
---|
| 426 | self.process.name = data_point |
---|
| 427 | elif tagname == 'description' and self.parent_class == 'SASprocess': |
---|
| 428 | self.process.description = data_point |
---|
| 429 | elif tagname == 'date' and self.parent_class == 'SASprocess': |
---|
| 430 | try: |
---|
| 431 | self.process.date = datetime.datetime.fromtimestamp(data_point) |
---|
| 432 | except: |
---|
| 433 | self.process.date = data_point |
---|
| 434 | elif tagname == 'SASprocessnote': |
---|
| 435 | self.process.notes.append(data_point) |
---|
| 436 | elif tagname == 'term' and self.parent_class == 'SASprocess': |
---|
[5f26aa4] | 437 | unit = attr.get("unit", "") |
---|
[7477fb9] | 438 | dic = { "name": name, "value": data_point, "unit": unit } |
---|
[5f26aa4] | 439 | self.process.term.append(dic) |
---|
[250fec92] | 440 | |
---|
[af08e55] | 441 | # Transmission Spectrum |
---|
[250fec92] | 442 | elif tagname == 'T' and self.parent_class == 'Tdata': |
---|
| 443 | self.transspectrum.transmission = np.append(self.transspectrum.transmission, data_point) |
---|
| 444 | self.transspectrum.transmission_unit = unit |
---|
| 445 | elif tagname == 'Tdev' and self.parent_class == 'Tdata': |
---|
| 446 | self.transspectrum.transmission_deviation = np.append(self.transspectrum.transmission_deviation, data_point) |
---|
| 447 | self.transspectrum.transmission_deviation_unit = unit |
---|
| 448 | elif tagname == 'Lambda' and self.parent_class == 'Tdata': |
---|
| 449 | self.transspectrum.wavelength = np.append(self.transspectrum.wavelength, data_point) |
---|
| 450 | self.transspectrum.wavelength_unit = unit |
---|
| 451 | |
---|
[af08e55] | 452 | # Source Information |
---|
[250fec92] | 453 | elif tagname == 'wavelength' and (self.parent_class == 'SASsource' or self.parent_class == 'SASData'): |
---|
| 454 | self.current_datainfo.source.wavelength = data_point |
---|
| 455 | self.current_datainfo.source.wavelength_unit = unit |
---|
| 456 | elif tagname == 'wavelength_min' and self.parent_class == 'SASsource': |
---|
| 457 | self.current_datainfo.source.wavelength_min = data_point |
---|
| 458 | self.current_datainfo.source.wavelength_min_unit = unit |
---|
| 459 | elif tagname == 'wavelength_max' and self.parent_class == 'SASsource': |
---|
| 460 | self.current_datainfo.source.wavelength_max = data_point |
---|
| 461 | self.current_datainfo.source.wavelength_max_unit = unit |
---|
| 462 | elif tagname == 'wavelength_spread' and self.parent_class == 'SASsource': |
---|
| 463 | self.current_datainfo.source.wavelength_spread = data_point |
---|
| 464 | self.current_datainfo.source.wavelength_spread_unit = unit |
---|
| 465 | elif tagname == 'x' and self.parent_class == 'beam_size': |
---|
| 466 | self.current_datainfo.source.beam_size.x = data_point |
---|
| 467 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 468 | elif tagname == 'y' and self.parent_class == 'beam_size': |
---|
| 469 | self.current_datainfo.source.beam_size.y = data_point |
---|
| 470 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 471 | elif tagname == 'z' and self.parent_class == 'pixel_size': |
---|
| 472 | self.current_datainfo.source.data_point.z = data_point |
---|
| 473 | self.current_datainfo.source.beam_size_unit = unit |
---|
| 474 | elif tagname == 'radiation' and self.parent_class == 'SASsource': |
---|
| 475 | self.current_datainfo.source.radiation = data_point |
---|
| 476 | elif tagname == 'beam_shape' and self.parent_class == 'SASsource': |
---|
| 477 | self.current_datainfo.source.beam_shape = data_point |
---|
| 478 | |
---|
[af08e55] | 479 | # Everything else goes in meta_data |
---|
[250fec92] | 480 | else: |
---|
| 481 | new_key = self._create_unique_key(self.current_datainfo.meta_data, tagname) |
---|
| 482 | self.current_datainfo.meta_data[new_key] = data_point |
---|
| 483 | |
---|
| 484 | self.names.remove(tagname_original) |
---|
| 485 | length = 0 |
---|
| 486 | if len(self.names) > 1: |
---|
| 487 | length = len(self.names) - 1 |
---|
| 488 | self.parent_class = self.names[length] |
---|
[654e8e0] | 489 | if not self._is_call_local() and not recurse: |
---|
| 490 | self.frm = "" |
---|
[7477fb9] | 491 | self.current_datainfo.errors = set() |
---|
| 492 | for error in self.errors: |
---|
| 493 | self.current_datainfo.errors.add(error) |
---|
[c54c965] | 494 | self.data_cleanup() |
---|
[2b3eb3d] | 495 | self.sort_data() |
---|
[c54c965] | 496 | self.reset_data_list() |
---|
[7b07fbe] | 497 | return self.output[0], None |
---|
[c54c965] | 498 | |
---|
[654e8e0] | 499 | def _is_call_local(self): |
---|
| 500 | if self.frm == "": |
---|
| 501 | inter = inspect.stack() |
---|
| 502 | self.frm = inter[2] |
---|
| 503 | mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") |
---|
[1686a333] | 504 | mod_name = mod_name.replace(".py", "") |
---|
| 505 | mod = mod_name.split("sas/") |
---|
| 506 | mod_name = mod[1] |
---|
| 507 | if mod_name != "sascalc/dataloader/readers/cansas_reader": |
---|
| 508 | return False |
---|
| 509 | return True |
---|
| 510 | |
---|
[7477fb9] | 511 | def _add_intermediate(self): |
---|
[250fec92] | 512 | """ |
---|
| 513 | This method stores any intermediate objects within the final data set after fully reading the set. |
---|
| 514 | """ |
---|
| 515 | if self.parent_class == 'SASprocess': |
---|
| 516 | self.current_datainfo.process.append(self.process) |
---|
| 517 | self.process = Process() |
---|
| 518 | elif self.parent_class == 'SASdetector': |
---|
| 519 | self.current_datainfo.detector.append(self.detector) |
---|
| 520 | self.detector = Detector() |
---|
| 521 | elif self.parent_class == 'SAStransmission_spectrum': |
---|
| 522 | self.current_datainfo.trans_spectrum.append(self.transspectrum) |
---|
| 523 | self.transspectrum = TransmissionSpectrum() |
---|
| 524 | elif self.parent_class == 'SAScollimation': |
---|
| 525 | self.current_datainfo.collimation.append(self.collimation) |
---|
| 526 | self.collimation = Collimation() |
---|
[5f26aa4] | 527 | elif self.parent_class == 'aperture': |
---|
[250fec92] | 528 | self.collimation.aperture.append(self.aperture) |
---|
| 529 | self.aperture = Aperture() |
---|
| 530 | elif self.parent_class == 'SASdata': |
---|
| 531 | self.data.append(self.current_dataset) |
---|
| 532 | |
---|
| 533 | def _get_node_value(self, node, tagname): |
---|
| 534 | """ |
---|
| 535 | Get the value of a node and any applicable units |
---|
| 536 | |
---|
| 537 | :param node: The XML node to get the value of |
---|
| 538 | :param tagname: The tagname of the node |
---|
| 539 | """ |
---|
| 540 | #Get the text from the node and convert all whitespace to spaces |
---|
| 541 | units = '' |
---|
| 542 | node_value = node.text |
---|
| 543 | if node_value is not None: |
---|
| 544 | node_value = ' '.join(node_value.split()) |
---|
| 545 | else: |
---|
| 546 | node_value = "" |
---|
| 547 | |
---|
| 548 | # If the value is a float, compile with units. |
---|
| 549 | if self.ns_list.ns_datatype == "float": |
---|
| 550 | # If an empty value is given, set as zero. |
---|
| 551 | if node_value is None or node_value.isspace() \ |
---|
| 552 | or node_value.lower() == "nan": |
---|
| 553 | node_value = "0.0" |
---|
| 554 | #Convert the value to the base units |
---|
| 555 | node_value, units = self._unit_conversion(node, tagname, node_value) |
---|
| 556 | |
---|
| 557 | # If the value is a timestamp, convert to a datetime object |
---|
| 558 | elif self.ns_list.ns_datatype == "timestamp": |
---|
| 559 | if node_value is None or node_value.isspace(): |
---|
| 560 | pass |
---|
| 561 | else: |
---|
| 562 | try: |
---|
| 563 | node_value = \ |
---|
| 564 | datetime.datetime.fromtimestamp(node_value) |
---|
| 565 | except ValueError: |
---|
| 566 | node_value = None |
---|
| 567 | return node_value, units |
---|
| 568 | |
---|
| 569 | def _unit_conversion(self, node, tagname, node_value): |
---|
[d26dea0] | 570 | """ |
---|
| 571 | A unit converter method used to convert the data included in the file |
---|
| 572 | to the default units listed in data_info |
---|
| 573 | |
---|
[250fec92] | 574 | :param node: XML node |
---|
| 575 | :param tagname: name of the node |
---|
[d26dea0] | 576 | :param node_value: The value of the current dom node |
---|
| 577 | """ |
---|
| 578 | attr = node.attrib |
---|
| 579 | value_unit = '' |
---|
| 580 | err_msg = None |
---|
[682c432] | 581 | default_unit = None |
---|
[5f26aa4] | 582 | if not isinstance(node_value, float): |
---|
| 583 | node_value = float(node_value) |
---|
| 584 | if 'unit' in attr and attr.get('unit') is not None: |
---|
[d26dea0] | 585 | try: |
---|
[62160509] | 586 | unit = attr['unit'] |
---|
[2b538cd] | 587 | # Split the units to retain backwards compatibility with |
---|
| 588 | # projects, analyses, and saved data from v4.1.0 |
---|
[62160509] | 589 | unit_list = unit.split("|") |
---|
| 590 | if len(unit_list) > 1: |
---|
| 591 | local_unit = unit_list[1] |
---|
| 592 | else: |
---|
| 593 | local_unit = unit |
---|
[250fec92] | 594 | unitname = self.ns_list.current_level.get("unit", "") |
---|
| 595 | if "SASdetector" in self.names: |
---|
| 596 | save_in = "detector" |
---|
| 597 | elif "aperture" in self.names: |
---|
| 598 | save_in = "aperture" |
---|
| 599 | elif "SAScollimation" in self.names: |
---|
| 600 | save_in = "collimation" |
---|
| 601 | elif "SAStransmission_spectrum" in self.names: |
---|
| 602 | save_in = "transspectrum" |
---|
| 603 | elif "SASdata" in self.names: |
---|
| 604 | x = np.zeros(1) |
---|
| 605 | y = np.zeros(1) |
---|
| 606 | self.current_data1d = Data1D(x, y) |
---|
| 607 | save_in = "current_data1d" |
---|
| 608 | elif "SASsource" in self.names: |
---|
| 609 | save_in = "current_datainfo.source" |
---|
| 610 | elif "SASsample" in self.names: |
---|
| 611 | save_in = "current_datainfo.sample" |
---|
| 612 | elif "SASprocess" in self.names: |
---|
| 613 | save_in = "process" |
---|
| 614 | else: |
---|
| 615 | save_in = "current_datainfo" |
---|
[e6e89c4] | 616 | default_unit = getattrchain(self, '.'.join((save_in, unitname))) |
---|
[574adc7] | 617 | if (local_unit and default_unit |
---|
| 618 | and local_unit.lower() != default_unit.lower() |
---|
| 619 | and local_unit.lower() != "none"): |
---|
[9efdb29] | 620 | # Check local units - bad units raise KeyError |
---|
| 621 | #print("loading", tagname, node_value, local_unit, default_unit) |
---|
| 622 | data_conv_q = Converter(local_unit) |
---|
| 623 | value_unit = default_unit |
---|
| 624 | node_value = data_conv_q(node_value, units=default_unit) |
---|
[d26dea0] | 625 | else: |
---|
| 626 | value_unit = local_unit |
---|
| 627 | except KeyError: |
---|
[527a190] | 628 | # Do not throw an error for loading Sesans data in cansas xml |
---|
| 629 | # This is a temporary fix. |
---|
| 630 | if local_unit != "A" and local_unit != 'pol': |
---|
| 631 | err_msg = "CanSAS reader: unexpected " |
---|
| 632 | err_msg += "\"{0}\" unit [{1}]; " |
---|
| 633 | err_msg = err_msg.format(tagname, local_unit) |
---|
| 634 | err_msg += "expecting [{0}]".format(default_unit) |
---|
[d26dea0] | 635 | value_unit = local_unit |
---|
[574adc7] | 636 | except Exception: |
---|
[d26dea0] | 637 | err_msg = "CanSAS reader: unknown error converting " |
---|
| 638 | err_msg += "\"{0}\" unit [{1}]" |
---|
| 639 | err_msg = err_msg.format(tagname, local_unit) |
---|
| 640 | value_unit = local_unit |
---|
| 641 | elif 'unit' in attr: |
---|
| 642 | value_unit = attr['unit'] |
---|
| 643 | if err_msg: |
---|
| 644 | self.errors.add(err_msg) |
---|
| 645 | return node_value, value_unit |
---|
| 646 | |
---|
[0b79323] | 647 | def _initialize_new_data_set(self, node=None): |
---|
| 648 | if node is not None: |
---|
| 649 | for child in node: |
---|
| 650 | if child.tag.replace(self.base_ns, "") == "Idata": |
---|
| 651 | for i_child in child: |
---|
| 652 | if i_child.tag.replace(self.base_ns, "") == "Qx": |
---|
| 653 | self.current_dataset = plottable_2D() |
---|
| 654 | return |
---|
| 655 | self.current_dataset = plottable_1D(np.array(0), np.array(0)) |
---|
| 656 | |
---|
| 657 | ## Writing Methods |
---|
[250fec92] | 658 | def write(self, filename, datainfo): |
---|
[d26dea0] | 659 | """ |
---|
[250fec92] | 660 | Write the content of a Data1D as a CanSAS XML file |
---|
[d26dea0] | 661 | |
---|
[250fec92] | 662 | :param filename: name of the file to write |
---|
| 663 | :param datainfo: Data1D object |
---|
| 664 | """ |
---|
| 665 | # Create XML document |
---|
| 666 | doc, _ = self._to_xml_doc(datainfo) |
---|
| 667 | # Write the file |
---|
[e6e89c4] | 668 | file_ref = open(filename, 'wb') |
---|
[235f514] | 669 | if self.encoding is None: |
---|
[250fec92] | 670 | self.encoding = "UTF-8" |
---|
| 671 | doc.write(file_ref, encoding=self.encoding, |
---|
| 672 | pretty_print=True, xml_declaration=True) |
---|
| 673 | file_ref.close() |
---|
[d26dea0] | 674 | |
---|
[250fec92] | 675 | def _to_xml_doc(self, datainfo): |
---|
[d26dea0] | 676 | """ |
---|
[250fec92] | 677 | Create an XML document to contain the content of a Data1D |
---|
[d26dea0] | 678 | |
---|
[250fec92] | 679 | :param datainfo: Data1D object |
---|
[d26dea0] | 680 | """ |
---|
[af08e55] | 681 | is_2d = False |
---|
[83c09af] | 682 | if issubclass(datainfo.__class__, Data2D): |
---|
| 683 | is_2d = True |
---|
[d26dea0] | 684 | |
---|
[250fec92] | 685 | # Get PIs and create root element |
---|
| 686 | pi_string = self._get_pi_string() |
---|
| 687 | # Define namespaces and create SASroot object |
---|
| 688 | main_node = self._create_main_node() |
---|
| 689 | # Create ElementTree, append SASroot and apply processing instructions |
---|
| 690 | base_string = pi_string + self.to_string(main_node) |
---|
| 691 | base_element = self.create_element_from_string(base_string) |
---|
| 692 | doc = self.create_tree(base_element) |
---|
| 693 | # Create SASentry Element |
---|
| 694 | entry_node = self.create_element("SASentry") |
---|
| 695 | root = doc.getroot() |
---|
| 696 | root.append(entry_node) |
---|
[d26dea0] | 697 | |
---|
[250fec92] | 698 | # Add Title to SASentry |
---|
| 699 | self.write_node(entry_node, "Title", datainfo.title) |
---|
| 700 | # Add Run to SASentry |
---|
| 701 | self._write_run_names(datainfo, entry_node) |
---|
| 702 | # Add Data info to SASEntry |
---|
[83c09af] | 703 | if is_2d: |
---|
| 704 | self._write_data_2d(datainfo, entry_node) |
---|
| 705 | else: |
---|
| 706 | self._write_data(datainfo, entry_node) |
---|
[250fec92] | 707 | # Transmission Spectrum Info |
---|
[8434365] | 708 | # TODO: fix the writer to linearize all data, including T_spectrum |
---|
| 709 | # self._write_trans_spectrum(datainfo, entry_node) |
---|
[250fec92] | 710 | # Sample info |
---|
| 711 | self._write_sample_info(datainfo, entry_node) |
---|
| 712 | # Instrument info |
---|
| 713 | instr = self._write_instrument(datainfo, entry_node) |
---|
| 714 | # Source |
---|
| 715 | self._write_source(datainfo, instr) |
---|
| 716 | # Collimation |
---|
| 717 | self._write_collimation(datainfo, instr) |
---|
| 718 | # Detectors |
---|
| 719 | self._write_detectors(datainfo, instr) |
---|
| 720 | # Processes info |
---|
| 721 | self._write_process_notes(datainfo, entry_node) |
---|
| 722 | # Note info |
---|
| 723 | self._write_notes(datainfo, entry_node) |
---|
| 724 | # Return the document, and the SASentry node associated with |
---|
| 725 | # the data we just wrote |
---|
| 726 | # If the calling function was not the cansas reader, return a minidom |
---|
| 727 | # object rather than an lxml object. |
---|
[654e8e0] | 728 | self.frm = inspect.stack()[1] |
---|
| 729 | doc, entry_node = self._check_origin(entry_node, doc) |
---|
[250fec92] | 730 | return doc, entry_node |
---|
[d26dea0] | 731 | |
---|
[250fec92] | 732 | def write_node(self, parent, name, value, attr=None): |
---|
| 733 | """ |
---|
| 734 | :param doc: document DOM |
---|
| 735 | :param parent: parent node |
---|
| 736 | :param name: tag of the element |
---|
| 737 | :param value: value of the child text node |
---|
| 738 | :param attr: attribute dictionary |
---|
[d26dea0] | 739 | |
---|
[250fec92] | 740 | :return: True if something was appended, otherwise False |
---|
| 741 | """ |
---|
| 742 | if value is not None: |
---|
| 743 | parent = self.ebuilder(parent, name, value, attr) |
---|
| 744 | return True |
---|
| 745 | return False |
---|
[d26dea0] | 746 | |
---|
| 747 | def _get_pi_string(self): |
---|
| 748 | """ |
---|
| 749 | Creates the processing instructions header for writing to file |
---|
| 750 | """ |
---|
| 751 | pis = self.return_processing_instructions() |
---|
| 752 | if len(pis) > 0: |
---|
| 753 | pi_tree = self.create_tree(pis[0]) |
---|
| 754 | i = 1 |
---|
| 755 | for i in range(1, len(pis) - 1): |
---|
| 756 | pi_tree = self.append(pis[i], pi_tree) |
---|
| 757 | pi_string = self.to_string(pi_tree) |
---|
| 758 | else: |
---|
| 759 | pi_string = "" |
---|
| 760 | return pi_string |
---|
| 761 | |
---|
| 762 | def _create_main_node(self): |
---|
| 763 | """ |
---|
| 764 | Creates the primary xml header used when writing to file |
---|
| 765 | """ |
---|
| 766 | xsi = "http://www.w3.org/2001/XMLSchema-instance" |
---|
| 767 | version = self.cansas_version |
---|
| 768 | n_s = CANSAS_NS.get(version).get("ns") |
---|
| 769 | if version == "1.1": |
---|
| 770 | url = "http://www.cansas.org/formats/1.1/" |
---|
| 771 | else: |
---|
| 772 | url = "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/" |
---|
| 773 | schema_location = "{0} {1}cansas1d.xsd".format(n_s, url) |
---|
| 774 | attrib = {"{" + xsi + "}schemaLocation" : schema_location, |
---|
| 775 | "version" : version} |
---|
| 776 | nsmap = {'xsi' : xsi, None: n_s} |
---|
| 777 | |
---|
| 778 | main_node = self.create_element("{" + n_s + "}SASroot", |
---|
| 779 | attrib=attrib, nsmap=nsmap) |
---|
| 780 | return main_node |
---|
| 781 | |
---|
| 782 | def _write_run_names(self, datainfo, entry_node): |
---|
| 783 | """ |
---|
| 784 | Writes the run names to the XML file |
---|
| 785 | |
---|
| 786 | :param datainfo: The Data1D object the information is coming from |
---|
| 787 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 788 | """ |
---|
[235f514] | 789 | if datainfo.run is None or datainfo.run == []: |
---|
[d26dea0] | 790 | datainfo.run.append(RUN_NAME_DEFAULT) |
---|
| 791 | datainfo.run_name[RUN_NAME_DEFAULT] = RUN_NAME_DEFAULT |
---|
| 792 | for item in datainfo.run: |
---|
| 793 | runname = {} |
---|
| 794 | if item in datainfo.run_name and \ |
---|
| 795 | len(str(datainfo.run_name[item])) > 1: |
---|
| 796 | runname = {'name': datainfo.run_name[item]} |
---|
| 797 | self.write_node(entry_node, "Run", item, runname) |
---|
| 798 | |
---|
| 799 | def _write_data(self, datainfo, entry_node): |
---|
| 800 | """ |
---|
[83c09af] | 801 | Writes 1D I and Q data to the XML file |
---|
[d26dea0] | 802 | |
---|
| 803 | :param datainfo: The Data1D object the information is coming from |
---|
| 804 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 805 | """ |
---|
| 806 | node = self.create_element("SASdata") |
---|
| 807 | self.append(node, entry_node) |
---|
| 808 | |
---|
| 809 | for i in range(len(datainfo.x)): |
---|
| 810 | point = self.create_element("Idata") |
---|
| 811 | node.append(point) |
---|
| 812 | self.write_node(point, "Q", datainfo.x[i], |
---|
[058f6c3] | 813 | {'unit': datainfo._xunit}) |
---|
[d26dea0] | 814 | if len(datainfo.y) >= i: |
---|
| 815 | self.write_node(point, "I", datainfo.y[i], |
---|
[058f6c3] | 816 | {'unit': datainfo._yunit}) |
---|
[5f26aa4] | 817 | if datainfo.dy is not None and len(datainfo.dy) > i: |
---|
[d26dea0] | 818 | self.write_node(point, "Idev", datainfo.dy[i], |
---|
[058f6c3] | 819 | {'unit': datainfo._yunit}) |
---|
[5f26aa4] | 820 | if datainfo.dx is not None and len(datainfo.dx) > i: |
---|
[d26dea0] | 821 | self.write_node(point, "Qdev", datainfo.dx[i], |
---|
[058f6c3] | 822 | {'unit': datainfo._xunit}) |
---|
[5f26aa4] | 823 | if datainfo.dxw is not None and len(datainfo.dxw) > i: |
---|
[d26dea0] | 824 | self.write_node(point, "dQw", datainfo.dxw[i], |
---|
[058f6c3] | 825 | {'unit': datainfo._xunit}) |
---|
[5f26aa4] | 826 | if datainfo.dxl is not None and len(datainfo.dxl) > i: |
---|
[d26dea0] | 827 | self.write_node(point, "dQl", datainfo.dxl[i], |
---|
[058f6c3] | 828 | {'unit': datainfo._xunit}) |
---|
[ad4632c] | 829 | if datainfo.isSesans: |
---|
[527a190] | 830 | sesans_attrib = {'x_axis': datainfo._xaxis, |
---|
| 831 | 'y_axis': datainfo._yaxis, |
---|
| 832 | 'x_unit': datainfo.x_unit, |
---|
| 833 | 'y_unit': datainfo.y_unit} |
---|
| 834 | sesans = self.create_element("Sesans", attrib=sesans_attrib) |
---|
[ad4632c] | 835 | sesans.text = str(datainfo.isSesans) |
---|
[527a190] | 836 | entry_node.append(sesans) |
---|
[6a455cd3] | 837 | self.write_node(entry_node, "yacceptance", datainfo.sample.yacceptance[0], |
---|
[63d773c] | 838 | {'unit': datainfo.sample.yacceptance[1]}) |
---|
[527a190] | 839 | self.write_node(entry_node, "zacceptance", datainfo.sample.zacceptance[0], |
---|
[ad4632c] | 840 | {'unit': datainfo.sample.zacceptance[1]}) |
---|
| 841 | |
---|
[d26dea0] | 842 | |
---|
[83c09af] | 843 | def _write_data_2d(self, datainfo, entry_node): |
---|
| 844 | """ |
---|
| 845 | Writes 2D data to the XML file |
---|
| 846 | |
---|
| 847 | :param datainfo: The Data2D object the information is coming from |
---|
| 848 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 849 | """ |
---|
[af08e55] | 850 | attr = {} |
---|
| 851 | if datainfo.data.shape: |
---|
[1905128] | 852 | attr["x_bins"] = str(len(datainfo.x_bins)) |
---|
| 853 | attr["y_bins"] = str(len(datainfo.y_bins)) |
---|
| 854 | node = self.create_element("SASdata", attr) |
---|
[83c09af] | 855 | self.append(node, entry_node) |
---|
| 856 | |
---|
[1905128] | 857 | point = self.create_element("Idata") |
---|
| 858 | node.append(point) |
---|
[574adc7] | 859 | qx = ','.join(str(v) for v in datainfo.qx_data) |
---|
| 860 | qy = ','.join(str(v) for v in datainfo.qy_data) |
---|
| 861 | intensity = ','.join(str(v) for v in datainfo.data) |
---|
[1905128] | 862 | |
---|
| 863 | self.write_node(point, "Qx", qx, |
---|
| 864 | {'unit': datainfo._xunit}) |
---|
| 865 | self.write_node(point, "Qy", qy, |
---|
| 866 | {'unit': datainfo._yunit}) |
---|
| 867 | self.write_node(point, "I", intensity, |
---|
| 868 | {'unit': datainfo._zunit}) |
---|
| 869 | if datainfo.err_data is not None: |
---|
[574adc7] | 870 | err = ','.join(str(v) for v in datainfo.err_data) |
---|
[1905128] | 871 | self.write_node(point, "Idev", err, |
---|
[83c09af] | 872 | {'unit': datainfo._zunit}) |
---|
[1905128] | 873 | if datainfo.dqy_data is not None: |
---|
[574adc7] | 874 | dqy = ','.join(str(v) for v in datainfo.dqy_data) |
---|
[1905128] | 875 | self.write_node(point, "Qydev", dqy, |
---|
| 876 | {'unit': datainfo._yunit}) |
---|
| 877 | if datainfo.dqx_data is not None: |
---|
[574adc7] | 878 | dqx = ','.join(str(v) for v in datainfo.dqx_data) |
---|
[1905128] | 879 | self.write_node(point, "Qxdev", dqx, |
---|
| 880 | {'unit': datainfo._xunit}) |
---|
| 881 | if datainfo.mask is not None: |
---|
[574adc7] | 882 | mask = ','.join("1" if v else "0" for v in datainfo.mask) |
---|
[1905128] | 883 | self.write_node(point, "Mask", mask) |
---|
[83c09af] | 884 | |
---|
[d26dea0] | 885 | def _write_trans_spectrum(self, datainfo, entry_node): |
---|
| 886 | """ |
---|
| 887 | Writes the transmission spectrum data to the XML file |
---|
| 888 | |
---|
| 889 | :param datainfo: The Data1D object the information is coming from |
---|
| 890 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 891 | """ |
---|
| 892 | for i in range(len(datainfo.trans_spectrum)): |
---|
| 893 | spectrum = datainfo.trans_spectrum[i] |
---|
| 894 | node = self.create_element("SAStransmission_spectrum", |
---|
| 895 | {"name" : spectrum.name}) |
---|
| 896 | self.append(node, entry_node) |
---|
| 897 | if isinstance(spectrum.timestamp, datetime.datetime): |
---|
| 898 | node.setAttribute("timestamp", spectrum.timestamp) |
---|
| 899 | for i in range(len(spectrum.wavelength)): |
---|
| 900 | point = self.create_element("Tdata") |
---|
| 901 | node.append(point) |
---|
| 902 | self.write_node(point, "Lambda", spectrum.wavelength[i], |
---|
| 903 | {'unit': spectrum.wavelength_unit}) |
---|
| 904 | self.write_node(point, "T", spectrum.transmission[i], |
---|
| 905 | {'unit': spectrum.transmission_unit}) |
---|
[7432acb] | 906 | if spectrum.transmission_deviation is not None \ |
---|
[d26dea0] | 907 | and len(spectrum.transmission_deviation) >= i: |
---|
| 908 | self.write_node(point, "Tdev", |
---|
| 909 | spectrum.transmission_deviation[i], |
---|
| 910 | {'unit': |
---|
| 911 | spectrum.transmission_deviation_unit}) |
---|
| 912 | |
---|
| 913 | def _write_sample_info(self, datainfo, entry_node): |
---|
| 914 | """ |
---|
| 915 | Writes the sample information to the XML file |
---|
| 916 | |
---|
| 917 | :param datainfo: The Data1D object the information is coming from |
---|
| 918 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 919 | """ |
---|
| 920 | sample = self.create_element("SASsample") |
---|
| 921 | if datainfo.sample.name is not None: |
---|
| 922 | self.write_attribute(sample, "name", |
---|
| 923 | str(datainfo.sample.name)) |
---|
| 924 | self.append(sample, entry_node) |
---|
| 925 | self.write_node(sample, "ID", str(datainfo.sample.ID)) |
---|
| 926 | self.write_node(sample, "thickness", datainfo.sample.thickness, |
---|
| 927 | {"unit": datainfo.sample.thickness_unit}) |
---|
| 928 | self.write_node(sample, "transmission", datainfo.sample.transmission) |
---|
| 929 | self.write_node(sample, "temperature", datainfo.sample.temperature, |
---|
| 930 | {"unit": datainfo.sample.temperature_unit}) |
---|
| 931 | |
---|
| 932 | pos = self.create_element("position") |
---|
| 933 | written = self.write_node(pos, |
---|
| 934 | "x", |
---|
| 935 | datainfo.sample.position.x, |
---|
| 936 | {"unit": datainfo.sample.position_unit}) |
---|
| 937 | written = written | self.write_node( \ |
---|
| 938 | pos, "y", datainfo.sample.position.y, |
---|
| 939 | {"unit": datainfo.sample.position_unit}) |
---|
| 940 | written = written | self.write_node( \ |
---|
| 941 | pos, "z", datainfo.sample.position.z, |
---|
| 942 | {"unit": datainfo.sample.position_unit}) |
---|
[2469df7] | 943 | if written: |
---|
[d26dea0] | 944 | self.append(pos, sample) |
---|
| 945 | |
---|
| 946 | ori = self.create_element("orientation") |
---|
| 947 | written = self.write_node(ori, "roll", |
---|
| 948 | datainfo.sample.orientation.x, |
---|
| 949 | {"unit": datainfo.sample.orientation_unit}) |
---|
| 950 | written = written | self.write_node( \ |
---|
| 951 | ori, "pitch", datainfo.sample.orientation.y, |
---|
| 952 | {"unit": datainfo.sample.orientation_unit}) |
---|
| 953 | written = written | self.write_node( \ |
---|
| 954 | ori, "yaw", datainfo.sample.orientation.z, |
---|
| 955 | {"unit": datainfo.sample.orientation_unit}) |
---|
[2469df7] | 956 | if written: |
---|
[d26dea0] | 957 | self.append(ori, sample) |
---|
| 958 | |
---|
| 959 | for item in datainfo.sample.details: |
---|
| 960 | self.write_node(sample, "details", item) |
---|
| 961 | |
---|
| 962 | def _write_instrument(self, datainfo, entry_node): |
---|
| 963 | """ |
---|
| 964 | Writes the instrumental information to the XML file |
---|
| 965 | |
---|
| 966 | :param datainfo: The Data1D object the information is coming from |
---|
| 967 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 968 | """ |
---|
| 969 | instr = self.create_element("SASinstrument") |
---|
| 970 | self.append(instr, entry_node) |
---|
| 971 | self.write_node(instr, "name", datainfo.instrument) |
---|
| 972 | return instr |
---|
| 973 | |
---|
| 974 | def _write_source(self, datainfo, instr): |
---|
| 975 | """ |
---|
| 976 | Writes the source information to the XML file |
---|
| 977 | |
---|
| 978 | :param datainfo: The Data1D object the information is coming from |
---|
| 979 | :param instr: instrument node to be appended to |
---|
| 980 | """ |
---|
| 981 | source = self.create_element("SASsource") |
---|
| 982 | if datainfo.source.name is not None: |
---|
| 983 | self.write_attribute(source, "name", |
---|
| 984 | str(datainfo.source.name)) |
---|
| 985 | self.append(source, instr) |
---|
[235f514] | 986 | if datainfo.source.radiation is None or datainfo.source.radiation == '': |
---|
[d26dea0] | 987 | datainfo.source.radiation = "neutron" |
---|
| 988 | self.write_node(source, "radiation", datainfo.source.radiation) |
---|
| 989 | |
---|
| 990 | size = self.create_element("beam_size") |
---|
| 991 | if datainfo.source.beam_size_name is not None: |
---|
| 992 | self.write_attribute(size, "name", |
---|
| 993 | str(datainfo.source.beam_size_name)) |
---|
| 994 | written = self.write_node( \ |
---|
| 995 | size, "x", datainfo.source.beam_size.x, |
---|
| 996 | {"unit": datainfo.source.beam_size_unit}) |
---|
| 997 | written = written | self.write_node( \ |
---|
| 998 | size, "y", datainfo.source.beam_size.y, |
---|
| 999 | {"unit": datainfo.source.beam_size_unit}) |
---|
| 1000 | written = written | self.write_node( \ |
---|
| 1001 | size, "z", datainfo.source.beam_size.z, |
---|
| 1002 | {"unit": datainfo.source.beam_size_unit}) |
---|
[2469df7] | 1003 | if written: |
---|
[d26dea0] | 1004 | self.append(size, source) |
---|
| 1005 | |
---|
| 1006 | self.write_node(source, "beam_shape", datainfo.source.beam_shape) |
---|
| 1007 | self.write_node(source, "wavelength", |
---|
| 1008 | datainfo.source.wavelength, |
---|
| 1009 | {"unit": datainfo.source.wavelength_unit}) |
---|
| 1010 | self.write_node(source, "wavelength_min", |
---|
| 1011 | datainfo.source.wavelength_min, |
---|
| 1012 | {"unit": datainfo.source.wavelength_min_unit}) |
---|
| 1013 | self.write_node(source, "wavelength_max", |
---|
| 1014 | datainfo.source.wavelength_max, |
---|
| 1015 | {"unit": datainfo.source.wavelength_max_unit}) |
---|
| 1016 | self.write_node(source, "wavelength_spread", |
---|
| 1017 | datainfo.source.wavelength_spread, |
---|
| 1018 | {"unit": datainfo.source.wavelength_spread_unit}) |
---|
| 1019 | |
---|
| 1020 | def _write_collimation(self, datainfo, instr): |
---|
| 1021 | """ |
---|
| 1022 | Writes the collimation information to the XML file |
---|
| 1023 | |
---|
| 1024 | :param datainfo: The Data1D object the information is coming from |
---|
| 1025 | :param instr: lxml node ElementTree object to be appended to |
---|
| 1026 | """ |
---|
[235f514] | 1027 | if datainfo.collimation == [] or datainfo.collimation is None: |
---|
[d26dea0] | 1028 | coll = Collimation() |
---|
| 1029 | datainfo.collimation.append(coll) |
---|
| 1030 | for item in datainfo.collimation: |
---|
| 1031 | coll = self.create_element("SAScollimation") |
---|
| 1032 | if item.name is not None: |
---|
| 1033 | self.write_attribute(coll, "name", str(item.name)) |
---|
| 1034 | self.append(coll, instr) |
---|
| 1035 | |
---|
| 1036 | self.write_node(coll, "length", item.length, |
---|
| 1037 | {"unit": item.length_unit}) |
---|
| 1038 | |
---|
| 1039 | for aperture in item.aperture: |
---|
| 1040 | apert = self.create_element("aperture") |
---|
| 1041 | if aperture.name is not None: |
---|
| 1042 | self.write_attribute(apert, "name", str(aperture.name)) |
---|
| 1043 | if aperture.type is not None: |
---|
| 1044 | self.write_attribute(apert, "type", str(aperture.type)) |
---|
| 1045 | self.append(apert, coll) |
---|
| 1046 | |
---|
| 1047 | size = self.create_element("size") |
---|
| 1048 | if aperture.size_name is not None: |
---|
| 1049 | self.write_attribute(size, "name", |
---|
| 1050 | str(aperture.size_name)) |
---|
| 1051 | written = self.write_node(size, "x", aperture.size.x, |
---|
| 1052 | {"unit": aperture.size_unit}) |
---|
| 1053 | written = written | self.write_node( \ |
---|
| 1054 | size, "y", aperture.size.y, |
---|
| 1055 | {"unit": aperture.size_unit}) |
---|
| 1056 | written = written | self.write_node( \ |
---|
| 1057 | size, "z", aperture.size.z, |
---|
| 1058 | {"unit": aperture.size_unit}) |
---|
[2469df7] | 1059 | if written: |
---|
[d26dea0] | 1060 | self.append(size, apert) |
---|
| 1061 | |
---|
| 1062 | self.write_node(apert, "distance", aperture.distance, |
---|
| 1063 | {"unit": aperture.distance_unit}) |
---|
| 1064 | |
---|
| 1065 | def _write_detectors(self, datainfo, instr): |
---|
| 1066 | """ |
---|
| 1067 | Writes the detector information to the XML file |
---|
| 1068 | |
---|
| 1069 | :param datainfo: The Data1D object the information is coming from |
---|
| 1070 | :param inst: lxml instrument node to be appended to |
---|
| 1071 | """ |
---|
[235f514] | 1072 | if datainfo.detector is None or datainfo.detector == []: |
---|
[d26dea0] | 1073 | det = Detector() |
---|
| 1074 | det.name = "" |
---|
| 1075 | datainfo.detector.append(det) |
---|
| 1076 | |
---|
| 1077 | for item in datainfo.detector: |
---|
| 1078 | det = self.create_element("SASdetector") |
---|
| 1079 | written = self.write_node(det, "name", item.name) |
---|
| 1080 | written = written | self.write_node(det, "SDD", item.distance, |
---|
| 1081 | {"unit": item.distance_unit}) |
---|
[2469df7] | 1082 | if written: |
---|
[d26dea0] | 1083 | self.append(det, instr) |
---|
| 1084 | |
---|
| 1085 | off = self.create_element("offset") |
---|
| 1086 | written = self.write_node(off, "x", item.offset.x, |
---|
| 1087 | {"unit": item.offset_unit}) |
---|
| 1088 | written = written | self.write_node(off, "y", item.offset.y, |
---|
| 1089 | {"unit": item.offset_unit}) |
---|
| 1090 | written = written | self.write_node(off, "z", item.offset.z, |
---|
| 1091 | {"unit": item.offset_unit}) |
---|
[2469df7] | 1092 | if written: |
---|
[d26dea0] | 1093 | self.append(off, det) |
---|
| 1094 | |
---|
| 1095 | ori = self.create_element("orientation") |
---|
| 1096 | written = self.write_node(ori, "roll", item.orientation.x, |
---|
| 1097 | {"unit": item.orientation_unit}) |
---|
| 1098 | written = written | self.write_node(ori, "pitch", |
---|
| 1099 | item.orientation.y, |
---|
| 1100 | {"unit": item.orientation_unit}) |
---|
| 1101 | written = written | self.write_node(ori, "yaw", |
---|
| 1102 | item.orientation.z, |
---|
| 1103 | {"unit": item.orientation_unit}) |
---|
[2469df7] | 1104 | if written: |
---|
[d26dea0] | 1105 | self.append(ori, det) |
---|
| 1106 | |
---|
| 1107 | center = self.create_element("beam_center") |
---|
| 1108 | written = self.write_node(center, "x", item.beam_center.x, |
---|
| 1109 | {"unit": item.beam_center_unit}) |
---|
| 1110 | written = written | self.write_node(center, "y", |
---|
| 1111 | item.beam_center.y, |
---|
| 1112 | {"unit": item.beam_center_unit}) |
---|
| 1113 | written = written | self.write_node(center, "z", |
---|
| 1114 | item.beam_center.z, |
---|
| 1115 | {"unit": item.beam_center_unit}) |
---|
[2469df7] | 1116 | if written: |
---|
[d26dea0] | 1117 | self.append(center, det) |
---|
| 1118 | |
---|
| 1119 | pix = self.create_element("pixel_size") |
---|
| 1120 | written = self.write_node(pix, "x", item.pixel_size.x, |
---|
| 1121 | {"unit": item.pixel_size_unit}) |
---|
| 1122 | written = written | self.write_node(pix, "y", item.pixel_size.y, |
---|
| 1123 | {"unit": item.pixel_size_unit}) |
---|
| 1124 | written = written | self.write_node(pix, "z", item.pixel_size.z, |
---|
| 1125 | {"unit": item.pixel_size_unit}) |
---|
[2469df7] | 1126 | if written: |
---|
[d26dea0] | 1127 | self.append(pix, det) |
---|
[3a9801f] | 1128 | self.write_node(det, "slit_length", item.slit_length, |
---|
| 1129 | {"unit": item.slit_length_unit}) |
---|
| 1130 | |
---|
[d26dea0] | 1131 | |
---|
| 1132 | def _write_process_notes(self, datainfo, entry_node): |
---|
| 1133 | """ |
---|
| 1134 | Writes the process notes to the XML file |
---|
| 1135 | |
---|
| 1136 | :param datainfo: The Data1D object the information is coming from |
---|
| 1137 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 1138 | |
---|
| 1139 | """ |
---|
| 1140 | for item in datainfo.process: |
---|
| 1141 | node = self.create_element("SASprocess") |
---|
| 1142 | self.append(node, entry_node) |
---|
| 1143 | self.write_node(node, "name", item.name) |
---|
| 1144 | self.write_node(node, "date", item.date) |
---|
| 1145 | self.write_node(node, "description", item.description) |
---|
| 1146 | for term in item.term: |
---|
[1686a333] | 1147 | if isinstance(term, list): |
---|
| 1148 | value = term['value'] |
---|
| 1149 | del term['value'] |
---|
[5f26aa4] | 1150 | elif isinstance(term, dict): |
---|
| 1151 | value = term.get("value") |
---|
| 1152 | del term['value'] |
---|
[1686a333] | 1153 | else: |
---|
| 1154 | value = term |
---|
[d26dea0] | 1155 | self.write_node(node, "term", value, term) |
---|
| 1156 | for note in item.notes: |
---|
| 1157 | self.write_node(node, "SASprocessnote", note) |
---|
| 1158 | if len(item.notes) == 0: |
---|
| 1159 | self.write_node(node, "SASprocessnote", "") |
---|
| 1160 | |
---|
| 1161 | def _write_notes(self, datainfo, entry_node): |
---|
| 1162 | """ |
---|
| 1163 | Writes the notes to the XML file and creates an empty note if none |
---|
| 1164 | exist |
---|
| 1165 | |
---|
| 1166 | :param datainfo: The Data1D object the information is coming from |
---|
| 1167 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 1168 | |
---|
| 1169 | """ |
---|
| 1170 | if len(datainfo.notes) == 0: |
---|
| 1171 | node = self.create_element("SASnote") |
---|
| 1172 | self.append(node, entry_node) |
---|
| 1173 | else: |
---|
| 1174 | for item in datainfo.notes: |
---|
| 1175 | node = self.create_element("SASnote") |
---|
| 1176 | self.write_text(node, item) |
---|
| 1177 | self.append(node, entry_node) |
---|
| 1178 | |
---|
[654e8e0] | 1179 | def _check_origin(self, entry_node, doc): |
---|
[d26dea0] | 1180 | """ |
---|
| 1181 | Return the document, and the SASentry node associated with |
---|
| 1182 | the data we just wrote. |
---|
| 1183 | If the calling function was not the cansas reader, return a minidom |
---|
| 1184 | object rather than an lxml object. |
---|
| 1185 | |
---|
| 1186 | :param entry_node: lxml node ElementTree object to be appended to |
---|
| 1187 | :param doc: entire xml tree |
---|
| 1188 | """ |
---|
[654e8e0] | 1189 | if not self.frm: |
---|
| 1190 | self.frm = inspect.stack()[1] |
---|
| 1191 | mod_name = self.frm[1].replace("\\", "/").replace(".pyc", "") |
---|
[d26dea0] | 1192 | mod_name = mod_name.replace(".py", "") |
---|
| 1193 | mod = mod_name.split("sas/") |
---|
| 1194 | mod_name = mod[1] |
---|
[45d90b9] | 1195 | if mod_name != "sascalc/dataloader/readers/cansas_reader": |
---|
[d26dea0] | 1196 | string = self.to_string(doc, pretty_print=False) |
---|
| 1197 | doc = parseString(string) |
---|
| 1198 | node_name = entry_node.tag |
---|
| 1199 | node_list = doc.getElementsByTagName(node_name) |
---|
| 1200 | entry_node = node_list.item(0) |
---|
[5ce7f17] | 1201 | return doc, entry_node |
---|
[d26dea0] | 1202 | |
---|
| 1203 | # DO NOT REMOVE - used in saving and loading panel states. |
---|
| 1204 | def _store_float(self, location, node, variable, storage, optional=True): |
---|
| 1205 | """ |
---|
| 1206 | Get the content of a xpath location and store |
---|
| 1207 | the result. Check that the units are compatible |
---|
| 1208 | with the destination. The value is expected to |
---|
| 1209 | be a float. |
---|
| 1210 | |
---|
| 1211 | The xpath location might or might not exist. |
---|
| 1212 | If it does not exist, nothing is done |
---|
| 1213 | |
---|
| 1214 | :param location: xpath location to fetch |
---|
| 1215 | :param node: node to read the data from |
---|
| 1216 | :param variable: name of the data member to store it in [string] |
---|
| 1217 | :param storage: data object that has the 'variable' data member |
---|
| 1218 | :param optional: if True, no exception will be raised |
---|
| 1219 | if unit conversion can't be done |
---|
| 1220 | |
---|
| 1221 | :raise ValueError: raised when the units are not recognized |
---|
| 1222 | """ |
---|
| 1223 | entry = get_content(location, node) |
---|
| 1224 | try: |
---|
| 1225 | value = float(entry.text) |
---|
[574adc7] | 1226 | except ValueError: |
---|
[d26dea0] | 1227 | value = None |
---|
| 1228 | |
---|
| 1229 | if value is not None: |
---|
| 1230 | # If the entry has units, check to see that they are |
---|
| 1231 | # compatible with what we currently have in the data object |
---|
| 1232 | units = entry.get('unit') |
---|
| 1233 | if units is not None: |
---|
| 1234 | toks = variable.split('.') |
---|
[e6e89c4] | 1235 | local_unit = getattr(storage, toks[0]+"_unit") |
---|
[7432acb] | 1236 | if local_unit is not None and units.lower() != local_unit.lower(): |
---|
[9efdb29] | 1237 | try: |
---|
| 1238 | conv = Converter(units) |
---|
| 1239 | setattrchain(storage, variable, conv(value, units=local_unit)) |
---|
| 1240 | except Exception: |
---|
| 1241 | _, exc_value, _ = sys.exc_info() |
---|
| 1242 | err_mess = "CanSAS reader: could not convert" |
---|
| 1243 | err_mess += " %s unit [%s]; expecting [%s]\n %s" \ |
---|
| 1244 | % (variable, units, local_unit, exc_value) |
---|
[d26dea0] | 1245 | self.errors.add(err_mess) |
---|
| 1246 | if optional: |
---|
[c155a16] | 1247 | logger.info(err_mess) |
---|
[d26dea0] | 1248 | else: |
---|
[574adc7] | 1249 | raise ValueError(err_mess) |
---|
[d26dea0] | 1250 | else: |
---|
[e6e89c4] | 1251 | setattrchain(storage, variable, value) |
---|
[d26dea0] | 1252 | else: |
---|
[e6e89c4] | 1253 | setattrchain(storage, variable, value) |
---|
[d26dea0] | 1254 | |
---|
| 1255 | # DO NOT REMOVE - used in saving and loading panel states. |
---|
| 1256 | def _store_content(self, location, node, variable, storage): |
---|
| 1257 | """ |
---|
| 1258 | Get the content of a xpath location and store |
---|
| 1259 | the result. The value is treated as a string. |
---|
| 1260 | |
---|
| 1261 | The xpath location might or might not exist. |
---|
| 1262 | If it does not exist, nothing is done |
---|
| 1263 | |
---|
| 1264 | :param location: xpath location to fetch |
---|
| 1265 | :param node: node to read the data from |
---|
| 1266 | :param variable: name of the data member to store it in [string] |
---|
| 1267 | :param storage: data object that has the 'variable' data member |
---|
| 1268 | |
---|
| 1269 | :return: return a list of errors |
---|
| 1270 | """ |
---|
| 1271 | entry = get_content(location, node) |
---|
| 1272 | if entry is not None and entry.text is not None: |
---|
[9efdb29] | 1273 | setattrchain(storage, variable, entry.text.strip()) |
---|
[250fec92] | 1274 | |
---|
| 1275 | # DO NOT REMOVE Called by outside packages: |
---|
| 1276 | # sas.sasgui.perspectives.invariant.invariant_state |
---|
| 1277 | # sas.sasgui.perspectives.fitting.pagestate |
---|
| 1278 | def get_content(location, node): |
---|
| 1279 | """ |
---|
| 1280 | Get the first instance of the content of a xpath location. |
---|
| 1281 | |
---|
| 1282 | :param location: xpath location |
---|
| 1283 | :param node: node to start at |
---|
| 1284 | |
---|
| 1285 | :return: Element, or None |
---|
| 1286 | """ |
---|
| 1287 | nodes = node.xpath(location, |
---|
| 1288 | namespaces={'ns': CANSAS_NS.get("1.0").get("ns")}) |
---|
| 1289 | if len(nodes) > 0: |
---|
| 1290 | return nodes[0] |
---|
| 1291 | else: |
---|
| 1292 | return None |
---|
| 1293 | |
---|
| 1294 | # DO NOT REMOVE Called by outside packages: |
---|
| 1295 | # sas.sasgui.perspectives.fitting.pagestate |
---|
| 1296 | def write_node(doc, parent, name, value, attr=None): |
---|
| 1297 | """ |
---|
| 1298 | :param doc: document DOM |
---|
| 1299 | :param parent: parent node |
---|
| 1300 | :param name: tag of the element |
---|
| 1301 | :param value: value of the child text node |
---|
| 1302 | :param attr: attribute dictionary |
---|
| 1303 | |
---|
| 1304 | :return: True if something was appended, otherwise False |
---|
| 1305 | """ |
---|
| 1306 | if attr is None: |
---|
| 1307 | attr = {} |
---|
| 1308 | if value is not None: |
---|
| 1309 | node = doc.createElement(name) |
---|
| 1310 | node.appendChild(doc.createTextNode(str(value))) |
---|
| 1311 | for item in attr: |
---|
| 1312 | node.setAttribute(item, attr[item]) |
---|
| 1313 | parent.appendChild(node) |
---|
| 1314 | return True |
---|
| 1315 | return False |
---|
[e6e89c4] | 1316 | |
---|
| 1317 | def getattrchain(obj, chain, default=None): |
---|
| 1318 | """Like getattr, but the attr may contain multiple parts separated by '.'""" |
---|
| 1319 | for part in chain.split('.'): |
---|
| 1320 | if hasattr(obj, part): |
---|
| 1321 | obj = getattr(obj, part, None) |
---|
| 1322 | else: |
---|
| 1323 | return default |
---|
| 1324 | return obj |
---|
| 1325 | |
---|
| 1326 | def setattrchain(obj, chain, value): |
---|
| 1327 | """Like setattr, but the attr may contain multiple parts separated by '.'""" |
---|
| 1328 | parts = list(chain.split('.')) |
---|
| 1329 | for part in parts[-1]: |
---|
| 1330 | obj = getattr(obj, part, None) |
---|
| 1331 | if obj is None: |
---|
| 1332 | raise ValueError("missing parent object "+part) |
---|
| 1333 | setattr(obj, value) |
---|