From 1ed1f0bb24c5d15c93cdc582345e178737abc592 Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Sat, 15 Aug 2020 11:52:03 +0200 Subject: [PATCH] Removed empty bytes at channel subchunk ends Checks if the chunk data size does not match the expected, based on image axes size. Verifies that all unwanted bytes are zero-bytes and removes them. Two triggered warnings: one for unwanted bytes and one for bytes removed (more of an INFO though). --- nd2reader/parser.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/nd2reader/parser.py b/nd2reader/parser.py index 3c8c8a1..8df38cd 100644 --- a/nd2reader/parser.py +++ b/nd2reader/parser.py @@ -273,6 +273,17 @@ class Parser(object): # of a four image group will be composed of bytes 2, 6, 10, etc. If you understand why someone would design # a data structure that way, please send the author of this library a message. number_of_true_channels = int(len(image_group_data[4:]) / (height * width)) + + # Remove unwanted 0-bytes that can appear in stitched images + unwanted_bytes_len = (len(image_group_data[image_data_start:]))%(height*width) + if unwanted_bytes_len: + warnings.warn('Identified unwanted bytes in the ND2 file, possibly stitched.') + byte_ids = range(image_data_start+height*number_of_true_channels, len(image_group_data)-unwanted_bytes_len+1, height*number_of_true_channels) + if all([0 == image_group_data[byte_ids[i]+i] for i in range(len(byte_ids))]): + warnings.warn('All unwanted bytes are zero-bytes, correctly removed.') + for i in range(len(byte_ids)): + del image_group_data[byte_ids[i]] + try: image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, width)) except ValueError: