diff --git a/nd2reader/parser.py b/nd2reader/parser.py
index 3c8c8a16a8293305065e08ce2a9ae729d0a0debd..8534e7996fad76eec9c1e85efe55caefb0d3d4bf 100644
--- a/nd2reader/parser.py
+++ b/nd2reader/parser.py
@@ -8,9 +8,9 @@ from pims.base_frames import Frame
import numpy as np
from nd2reader.common import get_version, read_chunk
-from nd2reader.exceptions import InvalidVersionError
from nd2reader.label_map import LabelMap
from nd2reader.raw_metadata import RawMetadata
+from nd2reader import stitched
class Parser(object):
@@ -232,8 +232,7 @@ class Parser(object):
Returns:
"""
- return (image_group_number - (field_of_view * len(self.metadata["z_levels"]) + z_level)) / (
- len(self.metadata["fields_of_view"]) * len(self.metadata["z_levels"]))
+ return (image_group_number - (field_of_view * len(self.metadata["z_levels"]) + z_level)) / (len(self.metadata["fields_of_view"]) * len(self.metadata["z_levels"]))
@property
def _channel_offset(self):
@@ -268,6 +267,7 @@ class Parser(object):
timestamp = struct.unpack("d", data[:8])[0]
image_group_data = array.array("H", data)
image_data_start = 4 + channel_offset
+ image_group_data = stitched.remove_parsed_unwanted_bytes(image_group_data, image_data_start, height, width)
# The images for the various channels are interleaved within the same array. For example, the second image
# of a four image group will be composed of bytes 2, 6, 10, etc. If you understand why someone would design
@@ -276,7 +276,8 @@ class Parser(object):
try:
image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, width))
except ValueError:
- image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, int(round(len(image_group_data[image_data_start::number_of_true_channels])/height))))
+ new_width = len(image_group_data[image_data_start::number_of_true_channels]) // height
+ image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, new_width))
# Skip images that are all zeros! This is important, since NIS Elements creates blank "gap" images if you
# don't have the same number of images each cycle. We discovered this because we only took GFP images every
@@ -285,11 +286,12 @@ class Parser(object):
if np.any(image_data):
return timestamp, image_data
- # If a blank "gap" image is encountered, generate an array of corresponding height and width to avoid
- # errors with ND2-files with missing frames. Array is filled with nan to reflect that data is missing.
+ # If a blank "gap" image is encountered, generate an array of corresponding height and width to avoid
+ # errors with ND2-files with missing frames. Array is filled with nan to reflect that data is missing.
else:
empty_frame = np.full((height, width), np.nan)
- warnings.warn('ND2 file contains gap frames which are represented by np.nan-filled arrays; to convert to zeros use e.g. np.nan_to_num(array)')
+ warnings.warn(
+ "ND2 file contains gap frames which are represented by np.nan-filled arrays; to convert to zeros use e.g. np.nan_to_num(array)")
return timestamp, image_data
def _get_frame_metadata(self):
diff --git a/nd2reader/stitched.py b/nd2reader/stitched.py
new file mode 100644
index 0000000000000000000000000000000000000000..9721e212d31fe30b1c76675e12c11f0aee637476
--- /dev/null
+++ b/nd2reader/stitched.py
@@ -0,0 +1,54 @@
+# -*- 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
+ # appended at the end of each row. Then, returns the indexes of the unwanted
+ # bytes.
+ number_of_true_channels = int(len(image_group_data[4:]) / (height * width))
+ n_unwanted_bytes = (len(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."
+ )
+ return np.arange(
+ image_data_start + height * number_of_true_channels,
+ len(image_group_data) - n_unwanted_bytes + 1,
+ height * 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
+ # proper reshaping of the data. Hence, here the unwanted zero bytes are
+ # identified and removed.
+ unwanted_byte_ids = get_unwanted_bytes_ids(
+ 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)
+ return image_group_data
diff --git a/tests/test_parser.py b/tests/test_parser.py
index 11dba3830f9b335c7cac4cf7f156a4f9ee0eff0b..c0b4ddfa02ba5e8000bd63c6fd351c92fa508bd5 100644
--- a/tests/test_parser.py
+++ b/tests/test_parser.py
@@ -2,8 +2,8 @@ import unittest
from os import path
from nd2reader.artificial import ArtificialND2
from nd2reader.common import check_or_make_dir
-from nd2reader.exceptions import InvalidVersionError
from nd2reader.parser import Parser
+import urllib.request
class TestParser(unittest.TestCase):
@@ -13,15 +13,24 @@ class TestParser(unittest.TestCase):
def setUp(self):
dir_path = path.dirname(path.realpath(__file__))
- check_or_make_dir(path.join(dir_path, 'test_data/'))
- self.test_file = path.join(dir_path, 'test_data/test.nd2')
+ check_or_make_dir(path.join(dir_path, "test_data/"))
+ self.test_file = path.join(dir_path, "test_data/test.nd2")
self.create_test_nd2()
def test_can_open_test_file(self):
self.create_test_nd2()
- with open(self.test_file, 'rb') as fh:
+ with open(self.test_file, "rb") as fh:
parser = Parser(fh)
self.assertTrue(parser.supported)
-
+ def test_get_image(self):
+ stitched_path = "test_data/test_stitched.nd2"
+ if not path.isfile(stitched_path):
+ file_name, header = urllib.request.urlretrieve(
+ "https://downloads.openmicroscopy.org/images/ND2/karl/sample_image.nd2",
+ stitched_path,
+ )
+ with open(stitched_path, "rb") as fh:
+ parser = Parser(fh)
+ parser.get_image(0)