if verbose:
print "Initialize stacks"
avg_stack = None
max_int_stack = None
max_dev_stack = None
max_col_diff_stack = None
median_stack = None
if avg_stack_file is not None:
avg_stack = np.zeros((h,w,c), dtype='double')
avg_stack = avg_stack + img
if max_int_stack_file is not None:
max_int_stack = np.zeros((h,w,c), dtype=img.dtype)
max_int_stack = max_int_stack + img
# Maximum intensities need to be 32-bit to prevent overflow
max_pix_intensities = np.zeros((h,w), dtype='uint32')
max_pix_intensities = max_pix_intensities + img.sum(axis=2)
if max_dev_stack_file is not None:
max_dev_stack = np.zeros((h,w,c), dtype=img.dtype)
max_dev_stack = max_dev_stack + img
max_pix_deviations = np.zeros((h,w), dtype='uint16')
max_pix_deviations = max_pix_deviations + img.std(axis=2)
if max_col_diff_stack_file is not None:
max_col_diff_stack = np.zeros((h,w,c), dtype=img.dtype)
max_col_diff_stack = max_col_diff_stack + img
max_col_diffs = img.max(axis=2)-img.min(axis=2)
if median_stack_file is not None:
# Import HDF5 library
import h5py
median_stack = np.zeros((h,w,c), dtype=img.dtype)
# Create a HDF5 file for temporary storage space for median stack
# calculations. The file is memorymapped, so access from the
