image.size does not correspond to image.shape sometimes

[FrickTobias]

Some nd2 images has images seem to miss one data point, making it impossible to reshape their array which also makes the file non-iterable.

Notably 18105583 == 18105584 - 1, where 18105584 == 3892 * 4651 so it would seem one data point is missing.

NIS-viewer can open the file without issues.

Error

ValueError: cannot reshape array of size 18105583 into shape (3892,4651)

Code to reproduce

#! /bin/python3

from nd2reader import ND2Reader

INPUT = "/Users/tobiasfrick/PycharmProjects/demos/test-data/multiple-channels.nd2"


def iterate():
    with ND2Reader(INPUT) as images:
        for _ in images:
            pass


if __name__ == '__main__':
    iterate()

Versions

% python --version
Python 3.8.10
% conda list | grep nd2reader
nd2reader                 3.3.0              pyhd8ed1ab_0    conda-forge

Traceback

python main.py
Traceback (most recent call last):
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/nd2reader/parser.py", line 277, in _get_raw_image_data
    image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, width))
  File "<__array_function__ internals>", line 5, in reshape
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 298, in reshape
    return _wrapfunc(a, 'reshape', newshape, order=order)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
    result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 18105583 into shape (3892,4652)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "main.py", line 18, in <module>
    main()
  File "main.py", line 13, in main
    for i in images:
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/slicerator/__init__.py", line 227, in <genexpr>
    return (self._get(i) for i in self.indices)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/slicerator/__init__.py", line 207, in _get
    return self._ancestor[key]
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/slicerator/__init__.py", line 188, in __getitem__
    return self._get(indices)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/pims/base_frames.py", line 98, in __getitem__
    return self.get_frame(key)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/pims/base_frames.py", line 592, in get_frame
    result = self._get_frame_wrapped(**coords)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/nd2reader/reader.py", line 88, in get_frame_2D
    return self._parser.get_image_by_attributes(t, v, c, z, y, x)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/nd2reader/parser.py", line 103, in get_image_by_attributes
    timestamp, raw_image_data = self._get_raw_image_data(image_group_number, channel,
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/nd2reader/parser.py", line 280, in _get_raw_image_data
    image_data = np.reshape(image_group_data[image_data_start::number_of_true_channels], (height, new_width))
  File "<__array_function__ internals>", line 5, in reshape
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 298, in reshape
    return _wrapfunc(a, 'reshape', newshape, order=order)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 54, in _wrapfunc
    return _wrapit(obj, method, *args, **kwds)
  File "/Users/tobiasfrick/miniconda3/envs/demos/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 43, in _wrapit
    result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: cannot reshape array of size 18105583 into shape (3892,4651)