diff --git a/nd2reader/stitched.py b/nd2reader/stitched.py index a2f6850..a62e5a2 100644 --- a/nd2reader/stitched.py +++ b/nd2reader/stitched.py @@ -1,12 +1,11 @@ # -*- coding: utf-8 -*- import numpy as np # type: ignore -import warnings def get_unwanted_bytes_ids(image_group_data, image_data_start, height, width): # Check if the byte array size conforms to the image axes size. If not, check # that the number of unexpected (unwanted) bytes is a multiple of the number of - # rows (height), as the same unmber of unwanted bytes is expected to be + # rows (height), as the same number of unwanted bytes is expected to be # appended at the end of each row. Then, returns the indexes of the unwanted # bytes. # Skip the first 4 elements that correspond to the time stamp @@ -15,27 +14,16 @@ def get_unwanted_bytes_ids(image_group_data, image_data_start, height, width): if not n_unwanted_bytes: return np.arange(0) assert 0 == n_unwanted_bytes % height, ( - "An unexpected number of extra bytes was encountered based on the expected" - + " frame size, therefore the file could not be parsed." + "An unexpected number of extra bytes was encountered based on the expected" + + " frame size, therefore the file could not be parsed." ) return np.arange( - image_data_start + height * number_of_true_channels, + image_data_start + width * number_of_true_channels, len(image_group_data) - n_unwanted_bytes + 1, - height * number_of_true_channels, + width * number_of_true_channels, ) -def remove_bytes_by_id(byte_ids, image_group_data, height): - # Remove bytes by ID. - bytes_per_row = len(byte_ids) // height - warnings.warn( - f"{len(byte_ids)} ({bytes_per_row}*{height}) unexpected zero " - + "bytes were found in the ND2 file and removed to allow further parsing." - ) - for i in range(len(byte_ids)): - del image_group_data[byte_ids[i] : (byte_ids[i] + bytes_per_row)] - - def remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, width): # Stitched ND2 files have been reported to contain unexpected (according to # image shape) zero bytes at the end of each image data row. This hinders @@ -45,11 +33,6 @@ def remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, wid image_group_data, image_data_start, height, width ) if 0 != len(unwanted_byte_ids): - assert np.all( - image_group_data[unwanted_byte_ids + np.arange(len(unwanted_byte_ids))] == 0 - ), ( - f"{len(unwanted_byte_ids)} unexpected non-zero bytes were found" - + " in the ND2 file, the file could not be parsed." - ) - remove_bytes_by_id(unwanted_byte_ids, image_group_data, height) + image_group_data = np.delete(np.array(image_group_data), unwanted_byte_ids) + return image_group_data