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);