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Fixes #37 + test - the default xml was misformatted #40

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Fixes #37 + test - the default xml was misformatted #40

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16 changes: 10 additions & 6 deletions bioformats/omexml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,11 +32,11 @@ def xsd_now():
NS_RE = r"http://www.openmicroscopy.org/Schemas/(?P<ns_key>.*)/[0-9/-]"

default_xml = """<?xml version="1.0" encoding="UTF-8"?>
<OME xmlns="{ns_ome_default}s"
<OME xmlns="{ns_ome_default}"
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">
xsi:schemaLocation="{ns_ome_default} {ns_ome_default}/ome.xsd">
<Image ID="Image:0" Name="default.png">
<AcquiredDate>%(DEFAULT_NOW)s</AcquiredDate>
<AcquiredDate>{DEFAULT_NOW}</AcquiredDate>
<Pixels DimensionOrder="XYCTZ"
ID="Pixels:0"
SizeC="1"
Expand All @@ -48,12 +48,16 @@ def xsd_now():
<Channel ID="Channel:0:0" SamplesPerPixel="1">
<LightPath/>
</Channel>
<BinData xmlns="%(NS_BINARY_FILE)s"
<BinData xmlns="{ns_binary_file}"
BigEndian="false" Length="0"/>
</Pixels>
</Image>
<StructuredAnnotations xmlns="{ns_sa_default}s"/>
</OME>""".format(ns_ome_default=NS_DEFAULT.format(ns_key='ome'), ns_sa_default=NS_DEFAULT.format(ns_key='sa'))
<StructuredAnnotations xmlns="{ns_sa_default}"/>
</OME>""".format(
ns_ome_default=NS_DEFAULT.format(ns_key='OME'),
ns_sa_default=NS_DEFAULT.format(ns_key='sa'),
ns_binary_file=NS_DEFAULT.format(ns_key="BinaryFile"),
DEFAULT_NOW=DEFAULT_NOW)

#
# These are the OME-XML pixel types - not all supported by subimager
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18 changes: 18 additions & 0 deletions bioformats/tests/test_omexml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,11 @@

import datetime
import os
import re
import unittest
import urllib
import xml.dom
import xml.etree.ElementTree

import bioformats.omexml as O

Expand All @@ -32,6 +34,22 @@ def test_00_00_init(self):
self.assertEquals(o.root_node.tag, O.qn(o.get_ns("ome"), "OME"))
self.assertEquals(o.image_count, 1)

def test_00_01_ns_binary_file(self):
# regression test of issue #37
o = O.OMEXML()
xmlstr = o.to_xml()
tree = xml.etree.ElementTree.fromstring(xmlstr)
bfelements = tree.findall(".//*[@BigEndian]")
self.assertEqual(len(bfelements), 1)
#
# Try to find BinData with the namespace,
# http://www.openmicroscopy.org/Schemas/BinaryFile/YYYY-MM
#
match = re.match(
"\\{http://www.openmicroscopy.org/Schemas/BinaryFile/"
"\\d{4}-\\d{2}\\}BinData", bfelements[0].tag)
self.assertTrue(match is not None)

def test_01_01_read(self):
for xml in (self.GROUPFILES_XML, TIFF_XML):
o = O.OMEXML(xml)
Expand Down