From 2a3c1a317e0bf7b6b371b1160f95a3e304cda351 Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Sat, 15 Aug 2020 12:19:07 +0200 Subject: [PATCH] Changed structure to check/remove method pair --- nd2reader/parser.py | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/nd2reader/parser.py b/nd2reader/parser.py index d9bf593..929774c 100644 --- a/nd2reader/parser.py +++ b/nd2reader/parser.py @@ -247,27 +247,28 @@ class Parser(object): """ return {channel: n for n, channel in enumerate(self.metadata["channels"])} - def _find_unwanted_bytes(self, image_group_data, image_data_start, height, width): + def _check_unwanted_bytes(self, image_group_data, image_data_start, height, width): number_of_true_channels = int(len(image_group_data[4:]) / (height * width)) n_unwanted_bytes = (len(image_group_data[image_data_start:]))%(height*width) if not n_unwanted_bytes: - return n_unwanted_bytes + return False assert 0 == n_unwanted_bytes % height, "Unexpected unwanted bytes distribution." - return n_unwanted_bytes + byte_ids = range(image_data_start+height*number_of_true_channels, len(image_group_data)-n_unwanted_bytes+1, height*number_of_true_channels) + all_zero_bytes = all([0 == image_group_data[byte_ids[i]+i] for i in range(len(byte_ids))]) + if not all_zero_bytes: + warnings.warn(f'Identified {n_unwanted_bytes} unwanted non-zero bytes in the ND2 file.') + return all_zero_bytes def _remove_unwanted_bytes(self, image_group_data, image_data_start, height, width): # Remove unwanted 0-bytes that can appear in stitched images - n_unwanted_bytes = self._find_unwanted_bytes(image_group_data, image_data_start, height, width) number_of_true_channels = int(len(image_group_data[4:]) / (height * width)) + n_unwanted_bytes = (len(image_group_data[image_data_start:]))%(height*width) unwanted_byte_per_step = n_unwanted_bytes // height byte_ids = range(image_data_start+height*number_of_true_channels, len(image_group_data)-n_unwanted_bytes+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(f'Identified {n_unwanted_bytes} ({unwanted_byte_per_step}*{height}) unwanted zero-bytes in the ND2 file, removed.') - for i in range(len(byte_ids)): - del image_group_data[byte_ids[i]:(byte_ids[i]+unwanted_byte_per_step)] - else: - warnings.warn(f'Identified {n_unwanted_bytes} unwanted non-zero bytes in the ND2 file.') - + warnings.warn(f'Identified {n_unwanted_bytes} ({unwanted_byte_per_step}*{height}) unwanted zero-bytes in the ND2 file, removed.') + for i in range(len(byte_ids)): + del image_group_data[byte_ids[i]:(byte_ids[i]+unwanted_byte_per_step)] + def _get_raw_image_data(self, image_group_number, channel_offset, height, width): """Reads the raw bytes and the timestamp of an image. @@ -294,7 +295,8 @@ 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)) - self._remove_unwanted_bytes(image_group_data, image_data_start, height, width) + if self._check_unwanted_bytes(image_group_data, image_data_start, height, width): + self._remove_unwanted_bytes(image_group_data, image_data_start, height, width) try: image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, width)) except ValueError: