From 078bba08a281566de2cb9eece4621bfa96f0234c Mon Sep 17 00:00:00 2001
From: William Niu <87096829+zjniu@users.noreply.github.com>
Date: Mon, 3 Jan 2022 11:37:41 -0500
Subject: [PATCH] Update stitched.py
Fixes rbnvrw/nd2reader#56.
---
nd2reader/stitched.py | 31 +++++++------------------------
1 file changed, 7 insertions(+), 24 deletions(-)
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
--
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