Open hackermd opened 9 years ago
Generating an OMLXML string
metadata = bioformats.OMEXML() metadata.to_xml()
produces the following output
'<ome:OME xmlns:ns2="%(NS_BINARY_FILE)s" xmlns:ome="http://www.openmicroscopy.org/Schemas/ome/2013-06s" xmlns:sa="http://www.openmicroscopy.org/Schemas/sa/2013-06s" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2013-06 http://www.openmicroscopy.org/Schemas/OME/2012-03/ome.xsd">\n <ome:Image ID="Image:0" Name="default.png">\n <ome:AcquiredDate>%(DEFAULT_NOW)s</ome:AcquiredDate>\n <ome:Pixels DimensionOrder="XYCTZ" ID="Pixels:0" SizeC="1" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" Type="uint8">\n<ome:Channel ID="Channel:0:0" SamplesPerPixel="1">\n <ome:LightPath />\n </ome:Channel>\n <ns2:BinData BigEndian="false" Length="0" />\n </ome:Pixels>\n </ome:Image>\n <sa:StructuredAnnotations />\n</ome:OME>'
This string cannot be parsed
from lxml import etree root = etree.fromstring(metadata)
gives
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-6-e1da52d13adb> in <module>() ----> 1 root = etree.fromstring(metadata) lxml.etree.pyx in lxml.etree.fromstring (src/lxml/lxml.etree.c:70569)() parser.pxi in lxml.etree._parseMemoryDocument (src/lxml/lxml.etree.c:106392)() ValueError: can only parse strings
I'm using python-bioformats (1.0.5) installed via pip.
python-bioformats (1.0.5)
Generating an OMLXML string
produces the following output
This string cannot be parsed
gives
I'm using
python-bioformats (1.0.5)
installed via pip.