def process_time_points(root, files, outdir):
'''Concatenate images and write ome.tiff file. If image contains already multiple time points just copy the image'''
concat = 1
files.sort()
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
image = BF.openImagePlus(options)
image = image[0]
if image.getNFrames() > 1:
IJ.log(files[0] + " Contains multiple time points. Can only concatenate single time points! Don't do anything!")
image.close()
return
width = image.getWidth()
height = image.getHeight()
for patt in pattern:
outName = re.match(patt, os.path.basename(files[0]))
if outName is None:
continue
if outdir is None:
outfile = os.path.join(root, outName.group(1) + '.ome.tif')
else:
outfile = os.path.join(outdir, outName.group(1) + '.ome.tif')
reader = ImageReader()
reader.setMetadataStore(MetadataTools.createOMEXMLMetadata())
reader.setId(files[0])
timeInfo = []
omeOut = reader.getMetadataStore()
omeOut = setUpXml(omeOut, image, files)
reader.close()
image.close()
IJ.log ('Concatenates ' + os.path.join(root, outName.group(1) + '.ome.tif'))
itime = 0
try:
for ifile, fileName in enumerate(files):
print fileName
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(fileName)
#print omeMeta.getPlaneDeltaT(0,0)
#print omeMeta.getPixelsTimeIncrement(0)
if fileName.endswith('.czi'):
if ifile == 0:
T0 = omeMeta.getPlaneDeltaT(0,0).value()
dT = omeMeta.getPlaneDeltaT(0,0).value() - T0
unit = omeMeta.getPlaneDeltaT(0,0).unit()
else:
timeInfo.append(getTimePoint(reader, omeMeta))
unit = omeMeta.getPixelsTimeIncrement(0).unit()
try:
dT = round(timeInfo[files.index(fileName)]-timeInfo[0],2)
except:
dT = (timeInfo[files.index(fileName)]-timeInfo[0]).seconds
nrImages = reader.getImageCount()
for i in range(0, reader.getImageCount()):
try:
omeOut.setPlaneDeltaT(dT, 0, i + itime*nrImages)
except TypeError:
omeOut.setPlaneDeltaT(Time(dT, unit),0, i + itime*nrImages)
omeOut.setPlanePositionX(omeOut.getPlanePositionX(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionY(omeOut.getPlanePositionY(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionZ(omeOut.getPlanePositionZ(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheC(omeOut.getPlaneTheC(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheT(NonNegativeInteger(itime), 0, i + itime*nrImages)
omeOut.setPlaneTheZ(omeOut.getPlaneTheZ(0,i), 0, i + itime*nrImages)
itime = itime + 1
reader.close()
IJ.showProgress(files.index(fileName), len(files))
try:
incr = float(dT/(len(files)-1))
except:
incr = 0
try:
omeOut.setPixelsTimeIncrement(incr, 0)
except TypeError:
#new Bioformats >5.1.x
omeOut.setPixelsTimeIncrement(Time(incr, unit),0)
outfile = concatenateImagePlus(files, outfile)
if outfile is not None:
filein = RandomAccessInputStream(outfile)
fileout = RandomAccessOutputStream(outfile)
saver = TiffSaver(fileout, outfile)
saver.overwriteComment(filein,omeOut.dumpXML())
fileout.close()
filein.close()
except:
traceback.print_exc()
finally:
#close all possible open files
try:
reader.close()
except:
pass
try:
filein.close()
except:
pass
try:
fileout.close()
except:
def processMovie(root, files, outfile):
"""Concatenate images and write ome.tiff file.
If image contains already multiple time points just copy the image"""
files.sort()
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
image = BF.openImagePlus(options)
image = image[0]
if image.getNFrames() > 1:
msg = ("%s Contains multiple time points. Can only concatenate"
" single time points!" %files[0])
raise RuntimeError(msg)
image.close()
reader = ImageReader()
reader.setMetadataStore(MetadataTools.createOMEXMLMetadata())
reader.setId(files[0])
timeInfo = []
omeOut = reader.getMetadataStore()
omeOut = setUpXml(omeOut, image, files)
reader.close()
image.close()
itime = 0
for fileName in files:
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(fileName)
timeInfo.append(getTimePoint(reader, omeMeta))
nrImages = reader.getImageCount()
for i in range(0, reader.getImageCount()):
try:
dT = round(timeInfo[files.index(fileName)]-timeInfo[0],2)
except:
dT = (timeInfo[files.index(fileName)]-timeInfo[0]).seconds
omeOut.setPlaneDeltaT(dT, 0, i + itime*nrImages)
omeOut.setPlanePositionX(omeOut.getPlanePositionX(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionY(omeOut.getPlanePositionY(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionZ(omeOut.getPlanePositionZ(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheC(omeOut.getPlaneTheC(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheT(omeOut.getPlaneTheT(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheZ(omeOut.getPlaneTheZ(0,i), 0, i + itime*nrImages)
itime = itime + 1
reader.close()
IJ.showProgress(files.index(fileName), len(files))
try:
omeOut.setPixelsTimeIncrement(float(dT/(len(files)-1)), 0)
except:
omeOut.setPixelsTimeIncrement(0, 0)
if len(files) <= 1:
raise RuntimeError('Found only one file. Nothing to concatenate')
outfile = concatenateImagePlus(files, outfile)
filein = RandomAccessInputStream(outfile)
fileout = RandomAccessOutputStream(outfile)
saver = TiffSaver(fileout, outfile)
saver.overwriteComment(filein, omeOut.dumpXML())
fileout.close()
filein.close()
writer.setMetadataRetrieve(omeMeta) tileSizeX = writer.setTileSizeX(tileSizeX) tileSizeY = writer.setTileSizeY(tileSizeY) writer.setId(outFile) type = reader.getPixelType() # create image scaler for downsampling scaler = SimpleImageScaler() # convert to Pyramidal OME-TIFF using tiling for series in range(reader.getSeriesCount()): reader.setSeries(series) writer.setSeries(series) # convert each image in the current series for image in range(reader.getImageCount()): width = reader.getSizeX() height = reader.getSizeY() # Determined the number of tiles to read and write nXTiles = int(math.floor(width / tileSizeX)) nYTiles = int(math.floor(height / tileSizeY)) if nXTiles * tileSizeX != width: nXTiles = nXTiles + 1 if nYTiles * tileSizeY != height: nYTiles = nYTiles + 1; # Convert the main image for y in range(nYTiles): for x in range(nXTiles): writer.setResolution(0);
