def test_legacy():
points, sign = test_module.internal_cut_detection(SIMPLE, 'y')
assert_array_equal(points,
[[ 6., -4., 0.],
[-5., -4., 0.]])
assert_equal(sign, -1)
assert_raises(Exception, test_module.cut_detect, SIMPLE, 'z')
def test_legacy_compare_with_legacy_result():
'''Comparing results with the old repair launch with the following commands:
repair --dounravel 0 --inputdir /gpfs/bbp.cscs.ch/project/proj83/home/bcoste/release/out-new/01_ConvertMorphologies --input rp120430_P-2_idA --overlap=true --incremental=false --restrict=true --distmethod=mirror
The arguments are the one used in the legacy morphology workflow.
'''
neuron = load_neuron(DATA_PATH / 'compare-bbpsdk/rp120430_P-2_idA.h5')
points, sign = test_module.internal_cut_detection(neuron, 'z')
assert_equal(sign, 1)
cut_sections = {point_to_section_segment(neuron, point)[0]
for point in points}
legacy_cut_sections = {13,14,17,18,38,39,40,45,58,67,68,69,73,75,76,93,94,101,102,103,105,106,109,110,111,120,124,125,148,149,150,156,157,158,162,163,164,166,167,168,169,192,201,202,203,205,206,208}
assert_equal(cut_sections, legacy_cut_sections)
def find_legacy(cls, neuron, axis):
'''Find the cut points according to the legacy algorithm
As implemented in:
https://bbpcode.epfl.ch/source/xref/platform/BlueRepairSDK/BlueRepairSDK/src/repair.cpp#263
'''
if not isinstance(neuron, Neuron):
neuron = load_neuron(neuron)
cut_leaves, side = internal_cut_detection(neuron, axis)
plane = cls([int(axis.upper() == 'X'), int(axis.upper() == 'Y'),
int(axis.upper() == 'Z'), 0],
upward=(side < 0),
morphology=None,
bin_width=0)
plane.morphology = load_neuron(neuron)
plane.cut_leaves_coordinates = cut_leaves
return plane