How to use the stardist.rays3d.Rays_GoldenSpiral function in stardist

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github mpicbg-csbd / stardist / stardist / models / model3d.py View on Github external
def __init__(self, axes='ZYX', rays=None, n_channel_in=1, grid=(1,1,1), anisotropy=None, backbone='resnet', **kwargs):

        if rays is None:
            if 'rays_json' in kwargs:
                rays = rays_from_json(kwargs['rays_json'])
            elif 'n_rays' in kwargs:
                rays = Rays_GoldenSpiral(kwargs['n_rays'])
            else:
                rays = Rays_GoldenSpiral(96)
        elif np.isscalar(rays):
            rays = Rays_GoldenSpiral(rays)

        super().__init__(axes=axes, n_channel_in=n_channel_in, n_channel_out=1+len(rays))

        # directly set by parameters
        self.n_rays                    = len(rays)
        self.grid                      = _normalize_grid(grid,3)
        self.anisotropy                = anisotropy if anisotropy is None else tuple(anisotropy)
        self.backbone                  = str(backbone).lower()
        self.rays_json                 = rays.to_json()

        if 'anisotropy' in self.rays_json['kwargs']:
            if self.rays_json['kwargs']['anisotropy'] is None and self.anisotropy is not None:
                self.rays_json['kwargs']['anisotropy'] = self.anisotropy
                print("Changing 'anisotropy' of rays to %s" % str(anisotropy))
            elif self.rays_json['kwargs']['anisotropy'] != self.anisotropy:
                warnings.warn("Mismatch of 'anisotropy' of rays and 'anisotropy'.")
github mpicbg-csbd / stardist / stardist / models / model3d.py View on Github external
def __init__(self, axes='ZYX', rays=None, n_channel_in=1, grid=(1,1,1), anisotropy=None, backbone='resnet', **kwargs):

        if rays is None:
            if 'rays_json' in kwargs:
                rays = rays_from_json(kwargs['rays_json'])
            elif 'n_rays' in kwargs:
                rays = Rays_GoldenSpiral(kwargs['n_rays'])
            else:
                rays = Rays_GoldenSpiral(96)
        elif np.isscalar(rays):
            rays = Rays_GoldenSpiral(rays)

        super().__init__(axes=axes, n_channel_in=n_channel_in, n_channel_out=1+len(rays))

        # directly set by parameters
        self.n_rays                    = len(rays)
        self.grid                      = _normalize_grid(grid,3)
        self.anisotropy                = anisotropy if anisotropy is None else tuple(anisotropy)
        self.backbone                  = str(backbone).lower()
        self.rays_json                 = rays.to_json()

        if 'anisotropy' in self.rays_json['kwargs']:
            if self.rays_json['kwargs']['anisotropy'] is None and self.anisotropy is not None:
github mpicbg-csbd / stardist / stardist / models / model3d.py View on Github external
def __init__(self, axes='ZYX', rays=None, n_channel_in=1, grid=(1,1,1), anisotropy=None, backbone='resnet', **kwargs):

        if rays is None:
            if 'rays_json' in kwargs:
                rays = rays_from_json(kwargs['rays_json'])
            elif 'n_rays' in kwargs:
                rays = Rays_GoldenSpiral(kwargs['n_rays'])
            else:
                rays = Rays_GoldenSpiral(96)
        elif np.isscalar(rays):
            rays = Rays_GoldenSpiral(rays)

        super().__init__(axes=axes, n_channel_in=n_channel_in, n_channel_out=1+len(rays))

        # directly set by parameters
        self.n_rays                    = len(rays)
        self.grid                      = _normalize_grid(grid,3)
        self.anisotropy                = anisotropy if anisotropy is None else tuple(anisotropy)
        self.backbone                  = str(backbone).lower()
        self.rays_json                 = rays.to_json()

        if 'anisotropy' in self.rays_json['kwargs']:
            if self.rays_json['kwargs']['anisotropy'] is None and self.anisotropy is not None:
                self.rays_json['kwargs']['anisotropy'] = self.anisotropy
                print("Changing 'anisotropy' of rays to %s" % str(anisotropy))