def write_fused(output_path,channel,sizeZ,theC,physX,physY,physZ):
IJ.log("Writing fused data")
# number of slices will determine filename format
digits = "00"
if sizeZ < 100:
digits = "0"
if sizeZ < 10:
digits = ""
# get the base metadata from the first fused image
meta = MetadataTools.createOMEXMLMetadata()
reader = get_reader(output_path+"img_t1_z%s1_c1"%digits,meta)
reader.close()
# reset some metadata
meta.setPixelsPhysicalSizeX(physX,0)
meta.setPixelsPhysicalSizeY(physY,0)
meta.setPixelsPhysicalSizeZ(physZ,0)
meta.setPixelsSizeZ(PositiveInteger(sizeZ),0)
meta.setChannelID("Channel:0:" + str(0), 0, 0)
spp = channel['spp']
meta.setChannelSamplesPerPixel(spp, 0, 0)
name = channel['name']
color = channel['color']
meta.setChannelName(name,0,0)
meta.setChannelColor(color,0,0)
# determine the number of subsets that need to be written
slices_per_subset = 200
num_output_files = divmod(sizeZ,slices_per_subset)
fpaths = []
if num_output_files[0] == 0:
nslices = [sizeZ]
num_output_files = 1
fpaths.append("%sfused_C%s.ome.tif"%(output_path,str(theC-1)))
else:
nslices = []
for n in range(num_output_files[0]):
nslices.append(slices_per_subset)
if num_output_files[1] > 0:
nslices.append(num_output_files[1])
for s in range(len(nslices)):
fpaths.append("%sfused_C%s_subset%s.ome.tif"%(output_path,str(theC-1),str(s)))
# setup a writer
writer = ImageWriter()
writer.setCompression('LZW')
writer.setMetadataRetrieve(meta)
writer.setId(fpaths[0])
# write the slices, changing the output file when necessary
theZ = 0
for f in range(len(fpaths)):
meta.setImageName(os.path.basename(fpaths[f]),0)
writer.changeOutputFile(fpaths[f])
for s in range(nslices[f]):
fpath = output_path+"img_t1_z%s%s_c1"%(digits,str(theZ+1))
if (len(digits) == 1) and (theZ+1 > 9):
fpath = output_path+"img_t1_z%s_c1"%(str(theZ+1))
if (len(digits) == 2) and (theZ+1 > 9):
fpath = output_path+"img_t1_z0%s_c1"%(str(theZ+1))
if (len(digits) == 2) and (theZ+1 > 99):
fpath = output_path+"img_t1_z%s_c1"%(str(theZ+1))
IJ.log("writing slice %s"%os.path.basename(fpath))
m = MetadataTools.createOMEXMLMetadata()
r = get_reader(fpath,m)
m.setPixelsPhysicalSizeX(physX,0)
m.setPixelsPhysicalSizeY(physY,0)
m.setPixelsPhysicalSizeZ(physZ,0)
m.setChannelID("Channel:0:" + str(0), 0, 0)
spp = channel['spp']
m.setChannelSamplesPerPixel(spp, 0, 0)
name = channel['name']
color = channel['color']
m.setChannelName(name,0,0)
m.setChannelColor(color,0,0)
writer.saveBytes(theZ,r.openBytes(0))
r.close()
theZ += 1
writer.close()
