How to use pynets - 10 common examples

def test_do_dir_path():
    """
    Test do_dir_path functionality
    """
    base_dir = str(Path(__file__).parent/"examples")
    func_path = base_dir + '/002/fmri'
    dwi_path = base_dir + '/002/dmri'
    in_func = func_path + '/002.nii.gz'
    in_dwi = dwi_path + '/std_dmri/iso_eddy_corrected_data_denoised_pre_reor.nii.gz'
    in_files = [in_func, in_dwi]

    atlases = ['Power', 'Shirer', 'Shen', 'Smith']
    for inputs in in_files:
        for atlas in atlases:
            dir_path = utils.do_dir_path(atlas, inputs)
            assert dir_path is not None

def test_normalize(x, thr, cp):
        x = thresholding.threshold_proportional(x, 1, copy=True) # remove diagonal
        s = thresholding.normalize(x)
        assert np.max(s) <= 1 and np.min(s) >= 0
        assert np.max(s) == 1 and np.min(s) == round(min(x.flatten())/max(x.flatten()), 1)

def test_threshold_absolute(x, thr, cp):
        s = thresholding.threshold_absolute(x, thr, copy=cp)
        s_test = [val for arr in s for val in arr if val >= thr] # search for value > thr
        assert round(np.sum(s), 10) == round(np.sum(s_test), 10)

def test_density(x, thr):
        d_known = thresholding.est_density(thresholding.threshold_absolute(x, thr, copy=True))
        x = thresholding.density_thresholding(x, d_known)
        d_test = thresholding.est_density(x)
        assert np.equal(np.round(d_known, 1), np.round(d_test, 1))

def test_normalize(x, thr, cp):
        x = thresholding.threshold_proportional(x, 1, copy=True) # remove diagonal
        s = thresholding.normalize(x)
        assert np.max(s) <= 1 and np.min(s) >= 0
        assert np.max(s) == 1 and np.min(s) == round(min(x.flatten())/max(x.flatten()), 1)

def test_invert(x, thr, cp):
        x_cp = x.copy() # invert modifies array in place and need orig to assert.
        x_cp = thresholding.threshold_proportional(x_cp, thr, copy=cp)
        s = thresholding.invert(x_cp)
        x = x.flatten() # flatten arrays to more easily check s > x.
        s = s.flatten()
        s_gt_x = [inv_val > x[idx] for idx, inv_val in enumerate(s) if inv_val > 0]
        assert False not in s_gt_x

def test_thr2prob(x, thr):
        s = thresholding.threshold_absolute(thresholding.normalize(x), thr)
        s[0][0] = 0.0000001
        t = thresholding.thr2prob(s)
        assert float(len(t[np.logical_and(t < 0.001, t > 0)])) == float(0.0)

def test_applyxfm():
    """
    Test applyxfm functionality
    """
    base_dir = str(Path(__file__).parent/"examples")
    anat_dir = base_dir + '/003/anat'
    
    ## First test: Apply xfm from test_align to orig anat img. 
    inp = anat_dir + '/sub-003_T1w_brain.nii.gz'
    ref = anat_dir + '/MNI152_T1_2mm_brain.nii.gz'
    xfm = anat_dir + '/highres2standard.mat'
    aligned = anat_dir + '/highres2standard_2.nii.gz'
    reg_utils.applyxfm(ref, inp, xfm, aligned, interp='trilinear', dof=6)
    # Check test_applyfxm = test_align outputs
    out_applyxfm = nib.load(aligned)
    out_applyxfm_data = out_applyxfm.get_data()
    out_align_file = anat_dir + '/highres2standard.nii.gz'
    out_align = nib.load(out_align_file)
    out_align_data = out_align.get_data()
    check_eq_arrays = np.array_equal(out_applyxfm_data, out_align_data)
    assert check_eq_arrays is True
    
    ## Second test: Apply xfm to standard space roi (invert xfm first) >> native space roi.
    # ref is native space anat image
    ref = anat_dir + '/sub-003_T1w.nii.gz'
    # input is standard space precuneus mask
    inp = anat_dir + '/precuneous_thr_bin.nii.gz'
    # xfm is standard2native from convert_xfm -omat standard2highres.mat highres2standard.mat
    xfm = anat_dir + '/standard2highres.mat'

def test_thr2prob(x, thr):
        s = thresholding.threshold_absolute(thresholding.normalize(x), thr)
        s[0][0] = 0.0000001
        t = thresholding.thr2prob(s)
        assert float(len(t[np.logical_and(t < 0.001, t > 0)])) == float(0.0)

def test_align():
    """
    Test align functionality
    """
    # Linear registrattion
    base_dir = str(Path(__file__).parent/"examples")
    anat_dir = base_dir + '/003/anat'
    inp = anat_dir + '/sub-003_T1w_brain.nii.gz'
    ref = anat_dir + '/MNI152_T1_2mm_brain.nii.gz'
    out = anat_dir + '/highres2standard.nii.gz'
    xfm_out = anat_dir + '/highres2standard.mat'

    reg_utils.align(inp, ref, xfm=xfm_out, out=out, dof=12, searchrad=True, bins=256, interp=None, cost="mutualinfo",
                    sch=None, wmseg=None, init=None)
    
    highres2standard_linear = nib.load(out)
    assert highres2standard_linear is not None