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Update stitched.py

Fixes rbnvrw/nd2reader#56.
upstream/backport/20220103
William Niu 3 years ago
committed by Lorenzo ZOLFANELLI
parent
commit
078bba08a2
1 changed files with 7 additions and 24 deletions
  1. +7
    -24
      nd2reader/stitched.py

+ 7
- 24
nd2reader/stitched.py View File

@ -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

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