def run(): t_start = datetime.now() image_paths = glob(os.path.join(str(import_dir.getPath()), '*tif')) print '\tread image metadata' reader = ImageReader() in_meta = MetadataTools.createOMEXMLMetadata() reader.setMetadataStore(in_meta) x_dims = [] y_dims = [] z_dims = [] c_dims = [] t_dims = [] eff = [] spp = [] for image_path in image_paths: print '\t parse %s' % (image_path) reader.setId(image_path) x_dims.append(reader.getSizeX()) y_dims.append(reader.getSizeY()) z_dims.append(reader.getSizeZ()) c_dims.append(reader.getSizeC()) t_dims.append(reader.getSizeT()) eff.append(reader.imageCount / z_dims[-1] / t_dims[-1]) spp.append(reader.getSizeC() / eff[-1]) format = FormatTools.getPixelTypeString(reader.getPixelType()) series = reader.getSeries() big_endian = Boolean.FALSE order = reader.getDimensionOrder() reader.close() # Compute the dimensions of the output file x_dim = max(x_dims) y_dim = max(y_dims) z_dim = max(z_dims) c_dim = max(c_dims) t_dim = max(t_dims) print '\t series: %i' % series print '\t format: %s' % format print '\t dimension order: %s' % order print '\t x: %s -> %i' % (x_dims, x_dim) print '\t y: %s -> %i' % (y_dims, y_dim) print '\t z: %s -> %i' % (z_dims, z_dim) print '\t c: %s -> %i' % (c_dims, c_dim) print '\t t: %s -> %i' % (t_dims, t_dim) print '\t effective size c: %s' % eff print '\t samples per pixel: %s' % spp # Get the time dimension from the number of input files t_dim = len(image_paths) # TODO: Tried to work out the order with Axes class, got something weird though. dimensions = [Short(x_dim), Short(y_dim), Short(c_dim), Short(z_dim)] pixels_per_plane = x_dim * y_dim # Assemble the metadata for the output file out_meta = MetadataTools.createOMEXMLMetadata() out_meta.setImageID(MetadataTools.createLSID('Image', series), series) out_meta.setPixelsID(MetadataTools.createLSID('Pixels', series), series) out_meta.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0) out_meta.setPixelsDimensionOrder(DimensionOrder.fromString(order), series) out_meta.setPixelsType(PixelType.fromString(format), series) out_meta.setPixelsSizeX(PositiveInteger(x_dim), series) out_meta.setPixelsSizeY(PositiveInteger(y_dim), series) out_meta.setPixelsSizeZ(PositiveInteger(z_dim), series) out_meta.setPixelsSizeC(PositiveInteger(c_dim), series) out_meta.setPixelsSizeT(PositiveInteger(t_dim), series) for c in range(c_dim): out_meta.setChannelID(MetadataTools.createLSID('Channel', series, c), series, c) out_meta.setChannelSamplesPerPixel(PositiveInteger(1), series, c) # Initialize the BF writer result_path = os.path.join(result_dir.getPath(), result_name) writer = ImageWriter() writer.setMetadataRetrieve(out_meta) writer.setId(result_path) print '\tcreated to %s' % (result_path) # Write the stacks into the output file N = len(image_paths) for i, image_path in enumerate(image_paths): status.showStatus(i, N, "catenating %i of %i time-points" % (i, N)) print '\t processing %s' % (image_path) ds = io.open(image_path) xi = ds.dimensionIndex(Axes.X) xv = ds.dimension(xi) yi = ds.dimensionIndex(Axes.Y) yv = ds.dimension(yi) zi = ds.dimensionIndex(Axes.Z) zv = ds.dimension(zi) ti = ds.dimensionIndex(Axes.TIME) tv = ds.dimension(ti) ci = ds.dimensionIndex(Axes.CHANNEL) cv = ds.dimension(ci) dx = float(x_dim - xv) / 2.0 dy = float(y_dim - yv) / 2.0 dz = float(z_dim - zv) / 2.0 print '\t translation vector (dx, dy, dz) = (%f, %f, %f)' % ( dx, dy, dz) if (dx != 0) or (dy != 0) or (dz != 0): stk = Views.translate(ds, long(dx), long(dy), long(0), long(dz)) stk = Views.extendZero(stk) else: stk = Views.extendZero(ds.getImgPlus().getImg()) print '\t writing planes ', n = 0 plane = 1 byte_array = [] interval_view = Views.interval(stk, \ [Long(0), Long(0), Long(0), Long(0)], \ [Long(x_dim - 1), Long(y_dim - 1), Long(c_dim - 1), Long(z_dim - 1)]) cursor = interval_view.cursor() while cursor.hasNext(): n += 1 cursor.fwd() value = cursor.get().getInteger() bytes = DataTools.shortToBytes(value, big_endian) byte_array.extend(bytes) if n == pixels_per_plane: writer.saveBytes(plane - 1, byte_array) print '.', if ((plane) % 10) == 0: print '\n\t ', byte_array = [] plane += 1 n = 0 print ' ' writer.close() t = datetime.now() - t_start print '\twrote %i planes to %s in %i sec.' % (plane - 1, result_path, t.total_seconds()) print '... done.'