5. Input/Output (processor.utilities.io)

processor.utilities.io.array_to_tiff(array, filename)

Save array to imageJ compatible tiff stack.

Args:

array (np.array): array to save. 2D,3D or 4D filename (str): full path and name of file to save.

processor.utilities.io.res_to_xarray(res, binNames, binAxes, metadata=None)

creates a BinnedArray (xarray subclass) out of the given np.array

Parameters:

res: np.array

nd array of binned data

binNames (list): list of names of the binned axes binAxes (list): list of np.arrays with the values of the axes

Returns:

ba: BinnedArray (xarray)

an xarray-like container with binned data, axis, and all available metadata

processor.utilities.io.save_binned(data, file_name, format='h5', path=None, mode='w')

Save a binned numpy array to h5 file. The file includes the axes (taken from the scheduled bins) and the delay stage histogram, if it exists.

Parameters:

file_name: str

Name of the saved file. The extension ‘.h5’ is automatically added.

path: str | None

File path.

mode: str | ‘w’

Write mode of h5 file (‘w’ = write).

processor.utilities.io.to_tiff(data, filename, axis_dict=None)

save array to imagej tiff sack.

processor.utilities.io.xarray_to_h5(data, faddr, mode='w')

Save xarray formatted data to hdf5

Args:

data (xarray.DataArray): input data faddr (str): complete file name (including path) mode (str): hdf5 read/write mode

Returns:

processor.utilities.io.xarray_to_tiff(data, filename, axis_dict=None)

Save data to tiff file.

Args:

data: xarray.DataArray

data to be saved. ImageJ likes tiff files with axis order as TZCYXS. Therefore, best axis order in input should be: Time, Energy, posY, posX. The channels ‘C’ and ‘S’ are automatically added and can be ignored.

filename: str

full path and name of file to save.

axis_dict: dict

name pairs for correct axis ordering. Keys should be any of T,Z,C,Y,X,S. The Corresponding value will be searched among the dimensions of the xarray, and placed in the right order for imagej stacks metadata.

units: bool

Not implemented. Will be used to set units in the tif stack TODO: expand imagej metadata to include physical units