def generate_ome_fromimc(imc_acquisition):
"""
:param imc_acquisition:
:return:
"""
y, x, c = imc_acquisition.shape
print(x, y, c)
metadata = MetadataTools.createOMEXMLMetadata()
filename = '/home/vitoz/temp/test.ome.tiff'
MetadataTools.populateMetadata(metadata, 0, filename, True, "XYZTC",
FormatTools.getPixelTypeString(6), x, y, 1,
c, 1, 1)
if imc_acquisition.origin == 'mcd':
ac_id = imc_acquisition.image_ID
meta_xml = et.XML(imc_acquisition.original_metadata)
ns = '{' + meta_xml.tag.split('}')[0].strip('{') + '}'
channel_xml = [
channel_xml
for channel_xml in meta_xml.findall(ns + 'AcquisitionChannel')
if channel_xml.find(ns + 'AcquisitionID').text == ac_id
]
ac_xml = [
tx for tx in meta_xml.findall(ns + 'Acquisition')
if tx.find(ns + 'ID').text == ac_id
][0]
# AcquisitionDate = ac_xml.find(ns+'StartTimeStamp').text
# Description = ac_xml.find(ns+'Description').text
# AblationPower = ac_xml.find(ns + 'AblationPower').text
# AblationDistanceBetweenShots = ac_xml.find(ns + 'AblationDistanceBetweenShots').text
# AblationFrequency = ac_xml.find(ns + 'AblationFrequency').text
# ROIID = ac_xml.find(ns + 'ROIID').text
# OrderNumber = ac_xml.find(ns + 'OrderNumber').text
# SignalType = ac_xml.find(ns + 'SignalType').text
# DataStartOffset = ac_xml.find(ns + 'DataStartOffset').text
# DataEndOffset = ac_xml.find(ns + 'DataEndOffset').text
# StartTimeStamp = ac_xml.find(ns + 'StartTimeStamp').text
# EndTimeStamp = ac_xml.find(ns + 'EndTimeStamp').text
# SegmentDataFormat = ac_xml.find(ns + 'SegmentDataFormat').text
# ValueBytes = ac_xml.find(ns + 'ValueBytes').text
#
# chan_order = [int(cxml.find(ns+'OrderNumber').text) for cxml in channel_xml]
metadata.setImageID(ac_id, 0)
metadata.setImageName(ac_id, 0)
metadata.setPixelsDimensionOrder(DimensionOrder.XYCZT, 0)
metadata.setPixelsSizeX(PositiveInteger(x), 0)
metadata.setPixelsSizeY(PositiveInteger(y), 0)
metadata.setPixelsSizeC(PositiveInteger(c), 0)
metadata.setPixelsSizeZ(PositiveInteger(1), 0)
metadata.setPixelsSizeT(PositiveInteger(1), 0)
metadata.setPixelsPhysicalSizeX(Length(1, units.MICROM), 0)
metadata.setPixelsPhysicalSizeY(Length(1, units.MICROM), 0)
metadata.setPixelsPhysicalSizeZ(Length(1, units.MICROM), 0)
metadata.setPixelsID(ac_id, 0)
metadata.setPixelsType(PixelType.FLOAT, 0)
metadata.setPixelsInterleaved(False, 0)
# metadata.setTiffDataFirstC(NonNegativeInteger(0), 0, 0)
# metadata.setTiffDataFirstZ(NonNegativeInteger(0), 0, 0)
# metadata.setTiffDataFirstT(NonNegativeInteger(0), 0, 0)
print(c)
for i in range(c):
metadata.setChannelSamplesPerPixel(PositiveInteger(1), 0, i)
for cxml in channel_xml:
cnr = int(cxml.find(ns + 'OrderNumber').text) - 3
if cnr >= 0:
name = cxml.find(ns + 'ChannelName').text
label = cxml.find(ns + 'ChannelLabel')
if label.text is None:
label = name
else:
print(label.text)
label = label.text
print(label)
print(name)
cid = '_'.join([label, name])
cid = cid.strip('(').strip(')')
name = name.replace('(', '').strip(')')
metadata.setChannelFluor(name, 0, cnr)
metadata.setChannelName(cid, 0, cnr)
metadata.setChannelID(cid, 0, cnr)
# for i in range(c):
# metadata.setPlaneTheC(NonNegativeInteger(i),0,i)
# metadata.setPlaneTheZ(NonNegativeInteger(0), 0, i)
# metadata.setPlaneTheT(NonNegativeInteger(0), 0, i)
return metadata
else:
ac_id = imc_acquisition.image_ID
metadata.setImageID(ac_id, 0)
metadata.setImageName(ac_id, 0)
metadata.setPixelsDimensionOrder(DimensionOrder.XYCZT, 0)
metadata.setPixelsSizeX(PositiveInteger(x), 0)
metadata.setPixelsSizeY(PositiveInteger(y), 0)
metadata.setPixelsSizeC(PositiveInteger(c), 0)
metadata.setPixelsSizeZ(PositiveInteger(1), 0)
metadata.setPixelsSizeT(PositiveInteger(1), 0)
metadata.setPixelsPhysicalSizeX(Length(1, units.MICROM), 0)
metadata.setPixelsPhysicalSizeY(Length(1, units.MICROM), 0)
metadata.setPixelsPhysicalSizeZ(Length(1, units.MICROM), 0)
metadata.setPixelsID(ac_id, 0)
metadata.setPixelsType(PixelType.FLOAT, 0)
metadata.setPixelsInterleaved(False, 0)
# metadata.setTiffDataFirstC(NonNegativeInteger(0), 0, 0)
# metadata.setTiffDataFirstZ(NonNegativeInteger(0), 0, 0)
# metadata.setTiffDataFirstT(NonNegativeInteger(0), 0, 0)
print(c)
for i in range(c):
metadata.setChannelSamplesPerPixel(PositiveInteger(1), 0, i)
for cnr, metal, label in zip(range(c), imc_acquisition.channel_metals,
imc_acquisition.channel_labels):
metadata.setChannelFluor(metal, 0, cnr)
metadata.setChannelName(label, 0, cnr)
metadata.setChannelID(label, 0, cnr)
return metadata
