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