def test_legacy_sholl_data():
'''Comparing results with the old repair launch with the following commands:
repair --dounravel 0 --inputdir /gpfs/bbp.cscs.ch/project/proj83/home/gevaert/morph-release/morph_release_old_code-2020-07-27/output/04_ZeroDiameterFix --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')
obj = test_module.Repair(inputfile=DATA_PATH /
'compare-bbpsdk/rp120430_P-2_idA.h5',
legacy_detection=True)
obj._fill_repair_type_map()
obj._fill_statistics_for_intact_subtrees()
key_mapping = {
'basal': RepairType.basal,
'oblique': RepairType.oblique,
'tuft': RepairType.tuft
}
expected_stats = {key_mapping[k]: v for k, v in SHOLL_STATS.items()}
flattened = {(i, j): [
obj.info['sholl'][RepairType.oblique][i][j][action] for action in
[Action.BIFURCATION, Action.CONTINUATION, Action.TERMINATION]
]
for i in obj.info['sholl'][RepairType.oblique].keys()
for j in obj.info['sholl'][RepairType.oblique][i].keys()}
assert_dict_equal(flattened, expected_stats[RepairType.oblique])
def test_legacy_compare_with_legacy_result2():
'''Comparing results with the old repair launch with the following commands:
repair --dounravel 0 --inputdir /gpfs/bbp.cscs.ch/project/proj83/home/gevaert/morph-release/morph_release_old_code-2020-07-27/output/04_ZeroDiameterFix --input vd100714B_idB --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/vd100714B_idB.h5')
obj = test_module.Repair(inputfile=DATA_PATH /
'compare-bbpsdk/vd100714B_idB.h5',
legacy_detection=True)
cut_sections = {
point_to_section_segment(neuron, point)[0]
for point in obj.cut_leaves
}
legacy_cut_sections = {
62, 64, 65, 69, 73, 77, 78, 85, 87, 88, 89, 91, 93, 94, 115, 116, 119,
120, 125, 126, 130, 133, 136, 137, 138, 140, 142, 144, 145, 147, 150,
151, 152, 159, 165, 171, 172, 175, 177, 179, 180, 182, 184, 188, 191,
200, 202, 204, 205, 207, 208, 209, 211, 215, 217, 218, 219, 220, 238,
239, 241, 247, 248, 250, 251, 252, 253, 256, 257, 258, 261, 262, 264,
266, 267, 283, 288, 289, 290, 291, 293, 294, 295, 316, 318, 320, 322,
324, 326, 328, 330, 331, 337, 338, 339, 340, 343, 344, 345, 351, 357,
359, 362, 363, 371, 372, 375, 377, 378, 384, 385, 386, 387, 388, 390,
391, 394, 416, 426, 427, 429, 430, 431, 438, 439, 440, 441, 453, 466,
468, 470, 471, 481, 486, 487, 488, 489, 527, 528, 529, 533, 534, 538,
540, 541, 543, 545, 548, 549, 551, 572, 573, 574, 576, 577, 581, 583,
584, 588, 595, 596, 598, 599, 602, 607, 608, 609, 610, 613, 614, 615,
617, 620, 622, 623, 624, 626, 637, 639, 640, 645, 647, 648, 649, 650,
653, 654, 665, 666, 667, 670, 677, 678, 679, 680, 689, 691, 693, 694,
703, 716, 717, 721, 723, 725, 726
}
assert_equal(cut_sections, legacy_cut_sections)
obj._fill_repair_type_map()
types = defaultdict(list)
for k, v in obj.repair_type_map.items():
types[v].append(k)
# offset due to the first section id in the old soft being the soma
offset = 1
assert_equal(obj.apical_section, None)
assert_equal(
{section.id + offset
for section in types[RepairType.basal]}, {
650, 651, 668, 671, 702, 719, 652, 655, 653, 654, 656, 663, 657,
662, 658, 661, 659, 660, 664, 667, 665, 666, 669, 670, 672, 681,
673, 680, 674, 679, 675, 678, 676, 677, 682, 695, 683, 684, 685,
686, 687, 690, 688, 689, 691, 692, 693, 694, 696, 699, 697, 698,
700, 701, 703, 704, 705, 706, 707, 710, 708, 709, 711, 718, 712,
713, 714, 715, 716, 717, 720, 727, 721, 722, 723, 724, 725, 726,
728, 735, 729, 730, 731, 734, 732, 733, 736, 737, 738
})
assert_array_equal(
[section.id + offset for section in types[RepairType.oblique]], [])
assert_array_equal(
[section.id + offset for section in types[RepairType.trunk]], [])
assert_equal({section.id + offset
for section in types[RepairType.tuft]}, set())
intacts = defaultdict(list)
for sec in obj._find_intact_sub_trees():
intacts[obj.repair_type_map[sec]].append(sec)
# Since there is no apical dendrite, all of those are empty
for extended_type in [
RepairType.trunk, RepairType.oblique, RepairType.tuft
]:
assert_equal(intacts[extended_type], [])
assert_equal({sec.id + offset
for sec in intacts[RepairType.basal]},
{
651, 668, 671, 702, 719, 652, 655, 656, 663, 657, 662,
658, 661, 659, 660, 664, 669, 672, 681, 673, 674, 675,
676, 682, 695, 683, 684, 685, 686, 687, 690, 688, 692,
696, 699, 697, 698, 700, 701, 704, 705, 706, 707, 710,
708, 709, 711, 718, 712, 713, 714, 715, 720, 727, 722,
724, 728, 735, 729, 730, 731, 734, 732, 733, 736, 737, 738
})
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/gevaert/morph-release/morph_release_old_code-2020-07-27/output/04_ZeroDiameterFix --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')
obj = test_module.Repair(inputfile=DATA_PATH /
'compare-bbpsdk/rp120430_P-2_idA.h5',
legacy_detection=True)
cut_sections = {
point_to_section_segment(neuron, point)[0]
for point in obj.cut_leaves
}
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)
obj._fill_repair_type_map()
types = defaultdict(list)
for k, v in obj.repair_type_map.items():
types[v].append(k)
# offset due to the first section id in the old soft being the soma
offset = 1
# These numbers come from the attribute 'apical' from the h5py group 'neuron1'
section_id, segment_id = 134, 8
assert_equal(obj.apical_section.id + offset, section_id)
assert_equal(len(obj.apical_section.points) - 1, segment_id)
assert_array_equal(
[section.id + offset for section in types[RepairType.basal]], [
90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104,
105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117,
118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,
131, 132
])
assert_array_equal(
[0] + [section.id + offset for section in types[RepairType.axon]], [
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52,
53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,
87, 88, 89
])
assert_array_equal(
[section.id + offset for section in types[RepairType.oblique]],
[217, 218, 219])
assert_array_equal(
[section.id + offset for section in types[RepairType.trunk]],
[133, 134])
expected_tufts = {
135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148,
149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162,
163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176,
177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190,
191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204,
205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216
}
actual_tufts = {section.id + offset for section in types[RepairType.tuft]}
assert_equal(actual_tufts, expected_tufts)
expected_axons = {
1, 2, 77, 3, 70, 4, 59, 5, 46, 6, 41, 7, 40, 8, 39, 9, 38, 10, 19, 11,
16, 12, 15, 13, 14, 17, 18, 20, 37, 21, 34, 22, 31, 23, 28, 24, 27, 25,
26, 29, 30, 32, 33, 35, 36, 42, 45, 43, 44, 47, 58, 48, 53, 49, 52, 50,
51, 54, 55, 56, 57, 60, 69, 61, 66, 62, 63, 64, 65, 67, 68, 71, 76, 72,
75, 73, 74, 78, 83, 79, 82, 80, 81, 84, 85, 86, 89, 87, 88
}
actual_axons = {section.id + offset for section in types[RepairType.axon]}
assert_equal(actual_axons, expected_axons)
intacts = defaultdict(list)
for sec in obj._find_intact_sub_trees():
intacts[obj.repair_type_map[sec]].append(sec)
assert_equal([sec.id + offset for sec in intacts[RepairType.trunk]], [])
assert_equal([sec.id + offset for sec in intacts[RepairType.oblique]],
[217])
assert_equal(
{sec.id + offset
for sec in intacts[RepairType.tuft]}, {
135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147,
151, 152, 153, 154, 155, 159, 160, 161, 165, 170, 171, 172, 173,
174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186,
187, 188, 189, 190, 191, 193, 194, 195, 196, 197, 198, 199, 200,
204, 207, 209, 210, 211, 212, 213, 214, 215, 216
})
def test_repair_only_axon():
'''Test repairing a morph which has only an axon (but no dendrites) does not crash'''
test_module.Repair(DATA_PATH / 'just-axon.asc')
ok_(True)