How to use the aicsimageio.constants.Dimensions.Scene function in aicsimageio

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github AllenCellModeling / aicsimageio / aicsimageio / aics_image.py View on Github external
def size_s(self) -> int:
        """
        Returns
        -------
        size: int
            The size of the Scene dimension.
        """
        return self.size(Dimensions.Scene)[0]
github AllenCellModeling / aicsimageio / aicsimageio / readers / czi_reader.py View on Github external
try:
            # Get image dims indicies
            image_dim_indices = czi.dims_shape()

            # Catch inconsistent scene dimension sizes
            if len(image_dim_indices) > 1:
                # Choose the provided scene
                log.info(
                    f"File contains variable dimensions per scene, "
                    f"selected scene: {self.specific_s_index} for data retrieval."
                )

                # Get the specific scene
                if self.specific_s_index < len(image_dim_indices):
                    data, _ = czi.read_image(
                        **{Dimensions.Scene: self.specific_s_index}
                    )
                else:
                    raise exceptions.InconsistentShapeError(
                        f"The CZI image provided has variable dimensions per scene. "
                        f"Please provide a valid index to the 'S' parameter to create "
                        f"a dask array for the index provided. "
                        f"Provided scene index: {self.specific_s_index}. "
                        f"Scene index range: 0-{len(image_dim_indices)}."
                    )

            else:
                # If the list is length one that means that all the scenes in the image
                # have the same dimensions
                # Read all data in the image
                data, _ = czi.read_image()
github AllenCellModeling / aicsimageio / aicsimageio / readers / lif_reader.py View on Github external
def size_s(self) -> int:
        return self._size_of_dimension(Dimensions.Scene)
github AllenCellModeling / aicsimageio / aicsimageio / aics_image.py View on Github external
def size_s(self) -> int:
        """
        Returns
        -------
        size: int
            The size of the Scene dimension.
        """
        return self.size(Dimensions.Scene)[0]
github AllenCellModeling / aicsimageio / aicsimageio / readers / tiff_reader.py View on Github external
f"Replaced with guess: {guessed_dim}"
                                    )
                                    break

                            # All of our guess dims were already in the dim list,
                            # append the dim read from meta
                            if not appended_dim:
                                best_guess.append(dim_from_meta)

                    best_guess = "".join(best_guess)

                    # Add scene dimension only if there are multiple scenes
                    if len(tiff.series) == 1:
                        self._dims = best_guess
                    else:
                        self._dims = f"{Dimensions.Scene}{best_guess}"

        return self._dims
github AllenCellModeling / aicsimageio / aicsimageio / readers / lif_reader.py View on Github external
The list of locked dimensions

        Returns
        -------
        Dict[Dimension: range]
            These ranges can then be used to iterate through the specified YX images

        """
        if read_dims is None:
            read_dims = {}

        data_shape = LifReader._dims_shape(lif=lif)

        # If S is in read_dims then use the specified value and the specified dims for
        # that scene
        if Dimensions.Scene in read_dims:
            s_range = range(
                read_dims[Dimensions.Scene], read_dims[Dimensions.Scene] + 1
            )
            s_dict = data_shape[s_range[0]]
        else:
            s_range = range(*data_shape[0][Dimensions.Scene])
            s_dict = data_shape[0]

        # Map the dims over to ranges and if the dim is in read_dims make the range
        # over the single dim
        integrated_dims = {Dimensions.Scene: s_range}
        for dim in [Dimensions.Time, Dimensions.Channel, Dimensions.SpatialZ]:
            if dim in read_dims:
                integrated_dims[dim] = range(read_dims[dim], read_dims[dim] + 1)
            else:
                integrated_dims[dim] = range(*s_dict[dim])
github AllenCellModeling / aicsimageio / aicsimageio / readers / lif_reader.py View on Github external
-------
        numpy.ndarray
            a stack of images as a numpy.ndarray
        List[Tuple[str, int]]
            The shape of the data being returned
        """
        if read_dims is None:
            read_dims = {}

        lif = LifFile(im_path)

        # Data has already been checked for consistency. The dims are either consistent
        # or S is specified selected_ranges get's the ranges for the Dimension for the
        # range unless the dim is explicitly specified
        selected_ranges = LifReader._read_dims_to_ranges(lif, read_dims)
        s_index = read_dims[Dimensions.Scene] if Dimensions.Scene in read_dims else 0
        lif_img = lif.get_image(img_n=s_index)
        x_size = lif_img.dims[0]
        y_size = lif_img.dims[1]
        pixel_type = LifReader.get_pixel_type(meta, s_index)

        # The ranged dims
        ranged_dims = [
            (dim, len(selected_ranges[dim]))
            for dim in [
                Dimensions.Scene,
                Dimensions.Time,
                Dimensions.Channel,
                Dimensions.SpatialZ,
            ]
        ]
github AllenCellModeling / aicsimageio / aicsimageio / readers / czi_reader.py View on Github external
def size_s(self) -> int:
        return self._size_of_dimension(Dimensions.Scene)