Refactored.

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):
@@ -247,38 +246,6 @@ class Parser(object):
         """
         return {channel: n for n, channel in enumerate(self.metadata["channels"])}
 
-    def _get_unwanted_bytes_ids(
-        self, 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(self, 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 _get_raw_image_data(self, image_group_number, channel_offset, height, width):
         """Reads the raw bytes and the timestamp of an image.
 
@@ -300,42 +267,17 @@ class Parser(object):
         timestamp = struct.unpack("d", data[:8])[0]
         image_group_data = array.array("H", data)
         image_data_start = 4 + channel_offset
-
-        # 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 = self._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."
-            )
-            self._remove_bytes_by_id(unwanted_byte_ids, image_group_data, height)
+        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
         # a data structure that way, please send the author of this library a message.
         number_of_true_channels = int(len(image_group_data[4:]) / (height * width))
         try:
-            image_data = np.reshape(
-                image_group_data[image_data_start::number_of_true_channels],
-                (height, width),
-            )
+            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,
-                    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
@@ -349,9 +291,7 @@ class Parser(object):
         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)"
-            )
+                "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):

nd2reader/stitched.py

@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+import numpy as np  # type: ignore
+import warnings
+
+
+def get_unwanted_bytes_ids(self, 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(self, 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

tests/test_parser.py

@@ -2,7 +2,6 @@ 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