import argparse import h5py if __name__ == '__main__': print("Writing BigDataViewer XML file...") parser = argparse.ArgumentParser() parser.add_argument("--channels", type = int, default = 2, help ="color channels") parser.add_argument("--tiles", type = int, default = 10, help ="imaging tiles") args = parser.parse_args() c = args.channels t = args.tiles f = open('data.xml', 'w') f.write('\n') f.write('\n') f.write('\t.\n') f.write('\t\n') f.write('\t\t\n') f.write('\t\t\tdata.h5\n') f.write('\t\t\n') f.write('\t\t\n') f2 = h5py.File('data.h5','r') dset = f2.get('/t00000/s00/0/cells') x = dset.shape[2] y = dset.shape[1] z = dset.shape[0] for i in range (0, c): for j in range(0, t): f.write('\t\t\t\n') f.write('\t\t\t\t' + str(t*i+j) + '\n') f.write('\t\t\t\t' + str(t*i+j) + '\n') f.write('\t\t\t\t' + str(x) + ' ' + str(y) + ' ' + str(z) + '\n') f.write('\t\t\t\t\n') f.write('\t\t\t\t\tum\n') f.write('\t\t\t\t\t0.4455 0.3151 0.3151\n') f.write('\t\t\t\t\n') f.write('\t\t\t\t\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\t' + str(i) + '\n') f.write('\t\t\t\t\t' + str(j) + '\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\t\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\n') for i in range(0, c): f.write('\t\t\t\t\n') f.write('\t\t\t\t\t' + str(i) + '\n') f.write('\t\t\t\t\t' + str(i) + '\n') f.write('\t\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\n') for i in range(0, t): f.write('\t\t\t\t\n') f.write('\t\t\t\t\t' + str(i) + '\n') f.write('\t\t\t\t\t' + str(i) + '\n') f.write('\t\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\t\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\t0\n') f.write('\t\t\t\t\n') f.write('\t\t\t\n') f.write('\t\t\n') f.write('\t\t\n') f.write('\t\t\t0') f.write('\t\t\n') f.write('\t\t\n') f.write('\t\n') f.write('\t\n') for i in range(0, c*t): f.write('\t\t\n') f.write('\t\t\t\n') f.write('\t\t\t\tcalibration\n') f.write('\t\t\t\t1.0 0.0 0.0 0.0 0.0 0.707 0.0 0.0 0.0 0.0 0.707 0.0\n') f.write('\t\t\t\n') f.write('\t\t') f.write('\t\n') f.write('\t\n') f.write('\t\n') f.write('\t\n') f.write('\t\n') f.write('\t\n') f.write('')