def add_original_metadata(self, key, value):
'''Create an original data key/value pair
key - the original metadata's key name, for instance OM_PHOTOMETRIC_INTERPRETATION
value - the value, for instance, "RGB"
returns the ID for the structured annotation.
'''
dom = get_dom(self.node)
xml_annotation = dom.createElementNS(NS_SA, "XMLAnnotation")
self.node.appendChild(xml_annotation)
node_id = str(uuid.uuid4())
xml_annotation.setAttribute("ID", node_id)
xa_value = dom.createElementNS(NS_SA, "Value")
xml_annotation.appendChild(xa_value)
ov = dom.createElementNS(NS_ORIGINAL_METADATA, "OriginalMetadata")
xa_value.appendChild(ov)
ov_key = dom.createElementNS(NS_ORIGINAL_METADATA, "Key")
ov.appendChild(ov_key)
set_text(ov_key, key)
ov_value = dom.createElementNS(NS_ORIGINAL_METADATA, "Value")
ov.appendChild(ov_value)
set_text(ov_value, value)
return node_id
def _testElementReprAndStrUnicodeNS():
dom = Document()
el = dom.appendChild(
dom.createElementNS(u"http://www.slashdot.org", u"slash:abc"))
string1 = repr(el)
string2 = str(el)
confirm(string1 == string2)
confirm(string1.find("slash:abc") != -1)
dom.unlink()
def _testElementReprAndStrUnicodeNS():
dom = Document()
el = dom.appendChild(
dom.createElementNS(u"http://www.slashdot.org", u"slash:abc"))
string1 = repr(el)
string2 = str(el)
confirm(string1 == string2)
confirm(string1.find("slash:abc") != -1)
dom.unlink()
def set_AcquiredDate(self, date):
acquired_dates = self.node.getElementsByTagNameNS(NS_OME, "AcquiredDate")
if len(acquired_dates) == 0:
dom = get_dom(self.node)
acquired_date = dom.createElementNS(NS_OME, "AcquiredDate")
self.node.appendChild(acquired_date)
else:
acquired_date = acquired_dates[0]
set_text(acquired_date, date)
def testRemoveAttrNS():
dom = Document()
child = dom.appendChild(
dom.createElementNS("http://www.python.org", "python:abc"))
child.setAttributeNS("http://www.w3.org", "xmlns:python",
"http://www.python.org")
child.setAttributeNS("http://www.python.org", "python:abcattr", "foo")
confirm(len(child.attributes) == 2)
child.removeAttributeNS("http://www.python.org", "abcattr")
confirm(len(child.attributes) == 1)
dom.unlink()
def testRemoveAttrNS():
dom = Document()
child = dom.appendChild(
dom.createElementNS("http://www.python.org", "python:abc"))
child.setAttributeNS("http://www.w3.org", "xmlns:python",
"http://www.python.org")
child.setAttributeNS("http://www.python.org", "python:abcattr", "foo")
confirm(len(child.attributes) == 2)
child.removeAttributeNS("http://www.python.org", "abcattr")
confirm(len(child.attributes) == 1)
dom.unlink()
def set_plane_count(self, value):
assert value >= 0
dom = get_dom(self.node)
while(self.plane_count > value):
last = self.node.getElementsByTagNameNS(NS_OME, "Plane")[-1]
self.node.removeChild(last)
last.unlink()
while(self.plane_count < value):
new_plane = OMEXML.Plane(dom.createElementNS(NS_OME, "Plane"))
if self.plane_count > 0:
last = self.node.getElementsByTagNameNS(NS_OME, "Plane")[-1]
insert_after(last, new_plane.node)
else:
self.node.appendChild(new_plane.node)
def set_channel_count(self, value):
assert value > 0
dom = get_dom(self.node)
while(self.channel_count > value):
last = self.node.getElementsByTagNameNS(NS_OME, "Channel")[-1]
self.node.removeChild(last)
last.unlink()
while(self.channel_count < value):
last = self.node.getElementsByTagNameNS(NS_OME, "Channel")[-1]
new_channel = OMEXML.Channel(dom.createElementNS(NS_OME, "Channel"))
insert_after(last, new_channel.node)
new_channel.ID = str(uuid.uuid4())
new_channel.Name = new_channel.ID
new_channel.SamplesPerPixel = 1
def new(self, row, column, well_id = str(uuid.uuid4())):
'''Create a new well at the given row and column
row - index of well's row
column - index of well's column
well_id - the ID attribute for the well
'''
dom = get_dom(self.plate_node)
well_node = dom.createElementNS(NS_SPW, "Well")
self.plate_node.appendChild(well_node)
well = OMEXML.Well(well_node)
well.Row = row
well.Column = column
well.ID = well_id
return well
