Update tensorstore zarr writer to write sequences #12
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JesseMckinzie
commented
Jul 2, 2024
JesseMckinzie
commented
- Update tensorstore zarr writer to writer sequences
JesseMckinzie
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src/cpp/writer/tswriter.cpp
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| switch(_dtype_code) | ||
| { | ||
| case (1): { | ||
| auto data_array = tensorstore::Array(py_image.mutable_unchecked<std::uint8_t, 1>().data(0), _image_shape, tensorstore::c_order); |
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I don't think _image_shape is correct here. What if the data we are writing is only a part of the image? IMO, it should be deduced from rows, cols...etc.
| rows = Seq(0, br._Y - 1, 1) | ||
| cols = Seq(0, br._X - 1, 1) | ||
| layers = Seq(0, 0, 1) | ||
| channels = Seq(0, 0, 1) | ||
| tsteps = Seq(0, 0, 1) |
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Add a test where you are writing two different part of the image. May be a 2D image where you write two part of the images separately.
Also, another 3D image, where you write the channels separately.
src/python/bfiocpp/tswriter.py
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| def write_image_data( | ||
| self, | ||
| image_data: np.ndarray, | ||
| rows: int, | ||
| cols: int, | ||
| layers: int, | ||
| channels: int, | ||
| tsteps: int, | ||
| ): |
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This interface should support 2D-5D images. We should not have a restriction of only 5D image
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| void TsWriterCPP::WriteImageData(py::array& py_image) { | ||
| auto position = dimension_order.find("X"); |
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Since "YX" will always be in dimension_order, this check can be improved.
Instead of this, check if dimenstion_order is of length between 2 and 5 and ends with YX. If not, throw an exception. Also, _x_index is always 0 and '_y_indexis always1`. These don't need to be member variable.
| rows: int, | ||
| cols: int, | ||
| layers: Optional[int] = None, | ||
| channels: Optional[int] = None, | ||
| tsteps: Optional[int] = None, | ||
| ): |
