#UXML: UXML metadata plugin#

Looks for #UXML control line control lines. These lines contain metadata written as XML structures and formatted according to the supplied XML Schema uxml.xsd in the same directory as the uxml.py plugin. The lines which comprise the XML are written as a list in each scan: scan.UXML. If there are no #UXML control lines, then scan.UXML does not exist.

Once the scan has been fully read scan.UXML is converted into an XML document structure (using the lxml.etree package) which is stored in scan.UXML_root. The structure is validated against the XML Schema uxml.xsd. If invalid, the error message is reported by raising a UXML_Error python exception.

A fully-validated structure can be written using the Writer class. The UXML metadata is written to the scan’s NXentry group as subgroup named UXML with NeXus base class NXnote. The hierarchy within this UXML is defined from the content provided in the SPEC scan.

Please consult the XML Schema file for the rules governing the use of #UXML in a SPEC data file: * uxml.xsd

#UXML: UXML structured metadata

exception spec2nexus.plugins.uxml.UXML_Error[source]#

Bases: Exception

Report detected UXML errors.

add_note()#: Exception.add_note(note) – add a note to the exception

args#

with_traceback()#: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class spec2nexus.plugins.uxml.UXML_metadata[source]#

Bases: ControlLineBase

#UXML – XML metadata in scan header

IN-MEMORY REPRESENTATION

(SpecDataFileScan): UXML : XML document root

HDF5/NeXus REPRESENTATION

various items below the NXentry parent group, as indicated in the UXML

Public methods

process(text, scan, *args, **kws)

read #UXML lines from SPEC data file into scan.UXML

Internal methods

`walk_xml_tree`(h5parent, xml_node)	parse the XML node into HDF5 objects
`make_NeXus_links`()	create all the hardlinks as directed
`prune_dict`(d, keys)	remove keys from dictionary d
`dataset`(h5parent, xml_node)	HDF5/NeXus dataset specification
`group`(h5parent, xml_node)	HDF5/NeXus group specification
`hardlink`(h5parent, xml_node)	HDF5/NeXus hard link specification

converters = {'float': <class 'float'>, 'int': <class 'int'>, 'str': <class 'str'>}#

dataset(h5parent, xml_node)[source]#: HDF5/NeXus dataset specification

group(h5parent, xml_node)[source]#: HDF5/NeXus group specification

hardlink(h5parent, xml_node)[source]#: HDF5/NeXus hard link specification

key = '#UXML'#

known_keys = {'#@CHANN': <spec2nexus.plugins.spec_common.SPEC_MCA_ChannelInformation object>, '#@CTIME': <spec2nexus.plugins.spec_common.SPEC_MCA_CountTime object>, '#@MCA': <spec2nexus.plugins.spec_common.SPEC_MCA object>, '#@ROI': <spec2nexus.plugins.spec_common.SPEC_MCA_RegionOfInterest object>, '#@[cC][aA][lL][iI][bB]': <spec2nexus.plugins.spec_common.SPEC_MCA_Calibration object>, '#C': <spec2nexus.plugins.spec_common.SPEC_Comment object>, '#CCD': <spec2nexus.plugins.XPCS.XPCS_CCD object>, '#D': <spec2nexus.plugins.spec_common.SPEC_Date object>, '#E': <spec2nexus.plugins.spec_common.SPEC_Epoch object>, '#F': <spec2nexus.plugins.spec_common.SPEC_File object>, '#G\\d+': <spec2nexus.plugins.spec_common.SPEC_Geometry object>, '#H\\d+': <unicat.UNICAT_MetadataMnemonics object>, '#I': <spec2nexus.plugins.spec_common.SPEC_NormalizingFactor object>, '#J\\d+': <spec2nexus.plugins.spec_common.SPEC_CounterNames object>, '#L': <spec2nexus.plugins.spec_common.SPEC_Labels object>, '#M': <spec2nexus.plugins.spec_common.SPEC_Monitor object>, '#MD\\w*': <spec2nexus.plugins.apstools_specwriter.MD_apstools object>, '#N': <spec2nexus.plugins.spec_common.SPEC_NumColumns object>, '#O\\d+': <spec2nexus.plugins.spec_common.SPEC_PositionerNames object>, '#P\\d+': <spec2nexus.plugins.spec_common.SPEC_Positioners object>, '#Q': <spec2nexus.plugins.spec_common.SPEC_HKL object>, '#R': <spec2nexus.plugins.spec_common.SPEC_UserResults object>, '#S': <spec2nexus.plugins.spec_common.SPEC_Scan object>, '#T': <spec2nexus.plugins.spec_common.SPEC_CountTime object>, '#U': <spec2nexus.plugins.spec_common.SPEC_UserReserved object>, '#UIM\\w*': <spec2nexus.plugins.uim.UIM_generic object>, '#UXML': <uxml.UXML_metadata object>, '#VA\\d+': <spec2nexus.plugins.XPCS.XPCS_VA object>, '#VD\\d+': <spec2nexus.plugins.XPCS.XPCS_VD object>, '#VE\\d+': <spec2nexus.plugins.XPCS.XPCS_VE object>, '#V\\d+': <unicat.UNICAT_MetadataValues object>, '#X': <spec2nexus.plugins.spec_common.SPEC_TemperatureSetPoint object>, '#XPCS': <spec2nexus.plugins.XPCS.XPCS_XPCS object>, '#j\\d+': <spec2nexus.plugins.spec_common.SPEC_CounterMnemonics object>, '#o\\d+': <spec2nexus.plugins.spec_common.SPEC_PositionerMnemonics object>, '@A\\d*': <spec2nexus.plugins.spec_common.SPEC_MCA_Array object>, 'scan_data': <spec2nexus.plugins.spec_common.SPEC_DataLine object>, 'unrecognized_control_line': <spec2nexus.plugins.fallback.UnrecognizedControlLine object>}#

lazy_attributes = ['H', 'V', 'metadata', 'UXML', 'UXML_root', 'MD', '_unrecognized', 'UIM', 'comments', 'G', 'diffractometer', 'I', 'J', 'j', 'L', 'column_first', 'column_last', 'M', 'monitor_name', 'N', 'O', 'o', 'P', 'positioner', 'Q', 'R', 'T', 'time_name', 'U', 'TEMP_SP', 'DEGC_SP', 'data', 'data_lines', 'MCA', 'VA', 'VD', 'VE', 'XPCS', 'CCD']#

make_NeXus_links()[source]#: create all the hardlinks as directed

match_key(text)#

Test if this handler’s key matches text.

Parameters:: text (str) – first word on the line, up to but not including the first whitespace
Returns:: key or None

Applies a regular expression match using each handler’s key as the regular expression to match with text.

plugins = [<spec2nexus.plugins.unicat.UNICAT_MetadataMnemonics object>, <spec2nexus.plugins.unicat.UNICAT_MetadataValues object>, <spec2nexus.plugins.uxml.UXML_metadata object>, <apstools_specwriter.MD_apstools object>, <fallback.UnrecognizedControlLine object>, <unicat.UNICAT_MetadataMnemonics object>, <unicat.UNICAT_MetadataValues object>, <uxml.UXML_metadata object>, <uim.UIM_generic object>, <spec_common.SPEC_File object>, <spec_common.SPEC_Epoch object>, <spec_common.SPEC_Date object>, <spec_common.SPEC_Comment object>, <spec_common.SPEC_Scan object>, <spec_common.SPEC_Geometry object>, <spec_common.SPEC_NormalizingFactor object>, <spec_common.SPEC_CounterNames object>, <spec_common.SPEC_CounterMnemonics object>, <spec_common.SPEC_Labels object>, <spec_common.SPEC_Monitor object>, <spec_common.SPEC_NumColumns object>, <spec_common.SPEC_PositionerNames object>, <spec_common.SPEC_PositionerMnemonics object>, <spec_common.SPEC_Positioners object>, <spec_common.SPEC_HKL object>, <spec_common.SPEC_UserResults object>, <spec_common.SPEC_CountTime object>, <spec_common.SPEC_UserReserved object>, <spec_common.SPEC_TemperatureSetPoint object>, <spec_common.SPEC_DataLine object>, <spec_common.SPEC_MCA object>, <spec_common.SPEC_MCA_Array object>, <spec_common.SPEC_MCA_Calibration object>, <spec_common.SPEC_MCA_ChannelInformation object>, <spec_common.SPEC_MCA_CountTime object>, <spec_common.SPEC_MCA_RegionOfInterest object>, <XPCS.XPCS_VA object>, <XPCS.XPCS_VD object>, <XPCS.XPCS_VE object>, <XPCS.XPCS_XPCS object>, <XPCS.XPCS_CCD object>, <spec2nexus.plugins.uim.UIM_generic object>, <spec2nexus.plugins.apstools_specwriter.MD_apstools object>, <spec2nexus.plugins.XPCS.XPCS_VA object>, <spec2nexus.plugins.XPCS.XPCS_VD object>, <spec2nexus.plugins.XPCS.XPCS_VE object>, <spec2nexus.plugins.XPCS.XPCS_XPCS object>, <spec2nexus.plugins.XPCS.XPCS_CCD object>, <spec2nexus.plugins.fallback.UnrecognizedControlLine object>, <spec2nexus.plugins.spec_common.SPEC_File object>, <spec2nexus.plugins.spec_common.SPEC_Epoch object>, <spec2nexus.plugins.spec_common.SPEC_Date object>, <spec2nexus.plugins.spec_common.SPEC_Comment object>, <spec2nexus.plugins.spec_common.SPEC_Scan object>, <spec2nexus.plugins.spec_common.SPEC_Geometry object>, <spec2nexus.plugins.spec_common.SPEC_NormalizingFactor object>, <spec2nexus.plugins.spec_common.SPEC_CounterNames object>, <spec2nexus.plugins.spec_common.SPEC_CounterMnemonics object>, <spec2nexus.plugins.spec_common.SPEC_Labels object>, <spec2nexus.plugins.spec_common.SPEC_Monitor object>, <spec2nexus.plugins.spec_common.SPEC_NumColumns object>, <spec2nexus.plugins.spec_common.SPEC_PositionerNames object>, <spec2nexus.plugins.spec_common.SPEC_PositionerMnemonics object>, <spec2nexus.plugins.spec_common.SPEC_Positioners object>, <spec2nexus.plugins.spec_common.SPEC_HKL object>, <spec2nexus.plugins.spec_common.SPEC_UserResults object>, <spec2nexus.plugins.spec_common.SPEC_CountTime object>, <spec2nexus.plugins.spec_common.SPEC_UserReserved object>, <spec2nexus.plugins.spec_common.SPEC_TemperatureSetPoint object>, <spec2nexus.plugins.spec_common.SPEC_DataLine object>, <spec2nexus.plugins.spec_common.SPEC_MCA object>, <spec2nexus.plugins.spec_common.SPEC_MCA_Array object>, <spec2nexus.plugins.spec_common.SPEC_MCA_Calibration object>, <spec2nexus.plugins.spec_common.SPEC_MCA_ChannelInformation object>, <spec2nexus.plugins.spec_common.SPEC_MCA_CountTime object>, <spec2nexus.plugins.spec_common.SPEC_MCA_RegionOfInterest object>]#

postprocess(scan, *args, **kws)[source]#

convert the UXML text into an XML object (scan.UXML_root)

Parameters:: scan (SpecDataFileScan) – data from a single SPEC scan

process(text, scan, *args, **kws)[source]#: read #UXML lines from SPEC data file into scan.UXML

prune_dict(d, keys)[source]#: remove keys from dictionary d

scan_attributes_defined = ['UXML', 'UXML_root']#

selector = None#

target_id = {}#

unique_id = {}#

walk_xml_tree(h5parent, xml_node)[source]#: parse the XML node into HDF5 objects

writer(nxentry, writer, scan, *args, **kws)[source]#: Describe how to store this data in an HDF5 NeXus file

#UXML: UXML metadata plugin#

This Page