tomopy/tomopy

#!/usr/bin/env python
# -*- coding: utf-8 -*-

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"""
Module for external library wrappers.
"""

import numpy as np

import tomopy.util.dtype as dtype
from . import c_shared_lib


__author__ = "Doga Gursoy"
__copyright__ = "Copyright (c) 2015, UChicago Argonne, LLC."
__docformat__ = 'restructuredtext en'
__all__ = ['c_normalize_bg',
           'c_remove_stripe_sf',
           'c_stripes_detect3d',
           'c_stripesmask3d']

LIB_TOMOPY_PREP = c_shared_lib("tomo-prep")


def c_normalize_bg(tomo, air):
    dt, dy, dx = tomo.shape

    LIB_TOMOPY_PREP.normalize_bg.restype = dtype.as_c_void_p()
    LIB_TOMOPY_PREP.normalize_bg(
        dtype.as_c_float_p(tomo),
        dtype.as_c_int(dt),
        dtype.as_c_int(dy),
        dtype.as_c_int(dx),
        dtype.as_c_int(air))


def c_remove_stripe_sf(tomo, size):

    # TODO: we should fix this elsewhere...
    # TOMO object must be contiguous for c function to work
    contiguous_tomo = np.require(tomo, requirements="AC")
    dx, dy, dz = tomo.shape
    istart = 0
    iend = dy

    LIB_TOMOPY_PREP.remove_stripe_sf.restype = dtype.as_c_void_p()
    LIB_TOMOPY_PREP.remove_stripe_sf(
        dtype.as_c_float_p(contiguous_tomo),
        dtype.as_c_int(dx),
        dtype.as_c_int(dy),
        dtype.as_c_int(dz),
        dtype.as_c_int(size),
        dtype.as_c_int(istart),
        dtype.as_c_int(iend))
    tomo[:] = contiguous_tomo[:]

def c_stripes_detect3d(
    input,
    output,
    size,
    radius,
    ncore,
    dx,
    dy,
    dz,
):
    LIB_TOMOPY_PREP.stripesdetect3d_main_float.restype = dtype.as_c_void_p()
    LIB_TOMOPY_PREP.stripesdetect3d_main_float(
        dtype.as_c_float_p(input),
        dtype.as_c_float_p(output),
        dtype.as_c_int(size),
        dtype.as_c_int(radius),
        dtype.as_c_int(ncore),
        dtype.as_c_int(dx),
        dtype.as_c_int(dy),
        dtype.as_c_int(dz),
    )
    return output

def c_stripesmask3d(
    input,
    output,
    threshold_val,
    min_stripe_length,
    min_stripe_depth,
    min_stripe_width,
    sensitivity_perc,
    ncore,
    dx,
    dy,
    dz,
):
    LIB_TOMOPY_PREP.stripesmask3d_main_float.restype = dtype.as_c_void_p()
    LIB_TOMOPY_PREP.stripesmask3d_main_float(
        dtype.as_c_float_p(input),
        dtype.as_c_bool_p(output),
        dtype.as_c_float(threshold_val),
        dtype.as_c_int(min_stripe_length),
        dtype.as_c_int(min_stripe_depth),
        dtype.as_c_int(min_stripe_width),
        dtype.as_c_float(sensitivity_perc),
        dtype.as_c_int(ncore),
        dtype.as_c_int(dx),
        dtype.as_c_int(dy),
        dtype.as_c_int(dz),
    )
    return output