view()

Complexity

Conditions

2

Size

Total Lines

25

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	0

from niprov.dependencies import Dependencies
def view(img, dependencies=Dependencies()):
    libs = dependencies.getLibraries()
    plt = libs.pyplot
    nibabel = libs.nibabel
    data = nibabel.load(img.path).get_data()

    ## 3D
    ndims = len(data.shape)
    sliceOrder = [1, 0, 2]

    fig, axs = plt.subplots(nrows=1, ncols=ndims)

    for d in range(ndims):
        slicing = [slice(None)]*ndims
        slicing[sliceOrder[d]] = int(data.shape[d]/2)
        axs[d].matshow(data[slicing].T, origin='lower', 
            cmap = plt.get_cmap('gray'), vmin = 0, vmax = data.max())
        axs[d].locator_params(nbins=3)
        axs[d].tick_params(axis='both', which='major', labelsize=8)

    plt.tight_layout()

    fname = 'myplot.png'
    plt.savefig(fname)
    webbrowser.open(fname)