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