Commit 79460caa authored by Zhang, Chen's avatar Zhang, Chen
Browse files

make dark field optional

parent 7b511aec

src/imars3d/backend/preparation/normalization.py

+9 −4
Original line number Diff line number Diff line
@@ -41,7 +41,7 @@ class normalization(param.ParameterizedFunction): 
    flats = param.Array(

        doc="3D array of flat field images (aka flat field, open beam), axis=0 is the image number axis.", default=None

    )

    darks = param.Array(doc="3D array of dark field images, axis=0 is the image number axis.", default=None)

    darks = param.Array(doc="3D array of optional dark field images, axis=0 is the image number axis.", default=None)

    max_workers = param.Integer(

        default=0,

        bounds=(0, None),
@@ -59,10 +59,15 @@ class normalization(param.ParameterizedFunction): 
        self.max_workers = clamp_max_workers(params.max_workers)

        logger.debug(f"max_worker={self.max_workers}")



        # use median filter to remove outliers from flats and darks

        # NOTE: this will remove the random noises coming from the environment.

        # process flats (formerly known as open beam, white field)

        self.flats = np.median(params.flats, axis=0)



        # process darks (formerly known as black field)

        if params.darks is None:

            self.darks = np.zeros_like(self.flats)

        else:

            self.darks = np.median(params.darks, axis=0)



        # apply normalization

        _bg = self.flats - self.darks

        _bg[_bg <= 0] = 1e-6