jicbioimage.core.util.array
¶
Module containing utility functions for manipulating numpy arrays.
-
jicbioimage.core.util.array.
check_dtype
(array, allowed)[source]¶ Raises TypeError if the array is not of an allowed dtype.
Parameters: - array – array whose dtype is to be checked
- allowed – instance or list of allowed dtypes
Raises: TypeError
-
jicbioimage.core.util.array.
color_array
(array, color_dict)[source]¶ Return RGB color array.
Assigning a unique RGB color value to each unique element of the input array and return an array of shape (array.shape, 3).
Parameters: - array – input numpy.array
- color_dict – dictionary with keys/values corresponding to identifiers and RGB tuples respectively
-
jicbioimage.core.util.array.
dtype_contract
(input_dtype=None, output_dtype=None)[source]¶ Function decorator for specifying input and/or output array dtypes.
Parameters: - input_dtype – dtype of input array
- output_dtype – dtype of output array
Returns: function decorator
-
jicbioimage.core.util.array.
map_stack
(array3D, z_function)[source]¶ Return 3D array where each z-slice has had the function applied to it.
Parameters: - array3D – 3D numpy.array
- z_function – function to be mapped to each z-slice
-
jicbioimage.core.util.array.
normalise
(array)[source]¶ Return array normalised such that all values are between 0 and 1.
If all the values in the array are the same the function will return: - np.zeros(array.shape, dtype=np.float) if the value is 0 or less - np.ones(array.shape, dtype=np.float) if the value is greater than 0
Parameters: array – numpy.array Returns: numpy.array.astype(numpy.float)
-
jicbioimage.core.util.array.
pretty_color_array
(array, keep_zero_black=True)[source]¶ Return a RGB pretty color array.
Assigning a pretty RGB color value to each unique element of the input array and return an array of shape (array.shape, 3).
Parameters: - array – input numpy.array
- keep_zero_black – whether or not the background should be black
Returns: numpy.array