def _get_points(morph, method, neurite_type, target_point):
"""Extract relevant points of dendrite to align the morphology, see align_morphology."""
_to_type = {
'apical': SectionType.apical_dendrite,
'axon': SectionType.axon
}
for root_section in morph.root_sections:
if root_section.type == _to_type[neurite_type]:
if method == AlignMethod.TRUNK.value:
if target_point is not None:
target_secid = point_to_section_segment(
morph, target_point)[0] - 1
if target_secid is None:
return None
elif neurite_type == 'apical':
target_secid = apical_point_section_segment(morph)[0]
else:
raise Exception(
f"We don't know how to get target point for {neurite_type}."
)
return np.vstack([
section.points for section in
morph.sections[target_secid].iter(IterType.upstream)
])
if method == AlignMethod.FIRST_SECTION.value:
return root_section.points
if method == AlignMethod.FIRST_SEGMENT.value:
return root_section.points[:2]
return np.vstack(
[section.points for section in root_section.iter()])
def test_point_to_section_segment():
neuron = Morphology(os.path.join(DATA, 'apical_test.h5'))
section, segment = spatial.point_to_section_segment(neuron, [0., 25., 0.])
eq_(section, 2)
eq_(segment, 1)
assert_raises(ValueError, spatial.point_to_section_segment, neuron, [24, 0, 0])
def test_point_to_section_segment():
neuron = Morphology(DATA / 'apical_test.h5')
section, segment = spatial.point_to_section_segment(neuron, [0., 25., 0.])
assert section == 1
assert segment == 1
with pytest.raises(ValueError):
spatial.point_to_section_segment(neuron, [24, 0, 0])
section, segment = spatial.point_to_section_segment(neuron, [0., 25.1, 0.],
rtol=1e-1,
atol=1e-1)
assert section == 1
assert segment == 1
section, segment = spatial.point_to_section_segment(
neuron, [0., 25.0001, 0.])
assert section == 1
assert segment == 1
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 apical_point_section_segment(neuron):
'''find the apical point's section and segment
Args:
neuron (morphio.Morphology): a morphology
Returns:
a tuple (MorphIO section ID, point ID) of the apical point
'''
point = apical_point_position(neuron)
if point is None:
L.warning('Could not find apical point')
return None, None
section, segment = point_to_section_segment(neuron, point)
section -= 1 # MorphIO ID = NeuroM ID - 1
return section, segment
def apical_point_section_segment(neuron):
"""Find the apical point's section and segment.
Args:
neuron (morphio.Morphology): a morphology
Returns:
Tuple: (NeuroM/MorphIO section ID, point ID) of the apical point. Since NeuroM v2, section
ids of NeuroM and MorphIO are the same excluding soma.
"""
point = apical_point_position(neuron)
if point is None:
L.warning('Could not find apical point')
return None, None
section, segment = point_to_section_segment(neuron, point)
return section, segment
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 __init__(
self, # pylint: disable=too-many-arguments
inputfile: Path,
axons: Optional[Path] = None,
seed: Optional[int] = 0,
cut_leaves_coordinates: Optional[NDArray[(3, Any)]] = None,
legacy_detection: bool = False,
repair_flags: Optional[Dict[RepairType, bool]] = None,
apical_point: NDArray[3, float] = None,
params: Dict = None):
'''Repair the input morphology
The repair algorithm uses sholl analysis of intact branches to grow new branches from cut
leaves. The algorithm is fairly complex, but can be controled via a few parameters in the
params dictionary. By default, they are:
_PARAMS = {
'seg_length': 5.0, # lenghts of new segments
'sholl_layer_size': 10, # resoluion of the shll profile
'noise_continuation': 0.5, # together with seg_length, this controls the tortuosity
'soma_repulsion': 0.2, # if 0, previous section direction, if 1, radial direction
'bifurcation_angle': 20, # noise amplitude in degree around mean bif angle on the cell
'path_length_ratio': 0.5, # a smaller value will make a strornger taper rate
'children_diameter_ratio': 0.8, # 1: child diam = parent diam, 0: child diam = tip diam
'tip_percentile': 25, # percentile of tip radius distributions to use as tip radius
}
Args:
inputfile: the input neuron to repair
axons: donor axons whose section will be used to repair this axon
seed: the numpy seed
cut_leaves_coordinates: List of 3D coordinates from which to start the repair
legacy_detection: if True, use the legacy cut plane detection
(see neuror.legacy_detection)
repair_flags: a dict of flags where key is a RepairType and value is whether
it should be repaired or not. If not provided, all types will be repaired.
apical_point: 3d vector for apical point, else, the automatic apical detection is used
if apical_point == -1, no automatic detection will be tried
params: repair internal parameters (see comments in code for details)
Note: based on https://bbpcode.epfl.ch/browse/code/platform/BlueRepairSDK/tree/BlueRepairSDK/src/repair.cpp#n469 # noqa, pylint: disable=line-too-long
'''
np.random.seed(seed)
self.legacy_detection = legacy_detection
self.inputfile = inputfile
self.axon_donors = axons or list()
self.donated_intact_axon_sections = list()
self.repair_flags = repair_flags or dict()
self.params = params if params is not None else _PARAMS
if legacy_detection:
self.cut_leaves = CutPlane.find_legacy(inputfile,
'z').cut_leaves_coordinates
elif cut_leaves_coordinates is None:
self.cut_leaves = CutPlane.find(
inputfile, bin_width=15).cut_leaves_coordinates
else:
self.cut_leaves = np.asarray(cut_leaves_coordinates)
self.neuron = load_neuron(inputfile)
self.repair_type_map = dict()
self.max_y_cylindrical_extent = _max_y_dendritic_cylindrical_extent(
self.neuron)
self.max_y_extent = max(
np.max(section.points[:, COLS.Y])
for section in self.neuron.iter())
self.info = dict()
apical_section_id = None
if apical_point != -1:
if apical_point:
# recall MorphIO ID = NeuroM ID - 1
apical_section_id = point_to_section_segment(
self.neuron, apical_point)[0] - 1
else:
apical_section_id, _ = apical_point_section_segment(
self.neuron)
if apical_section_id:
self.apical_section = self.neuron.sections[apical_section_id]
else:
self.apical_section = None
# record the tip radius as a lower bound for diameters with taper, excluding axons
# because they are treated separately, with thinner diameters
_diameters = [
np.mean(leaf.points[:, COLS.R]) for neurite in self.neuron.neurites
if neurite.type is not NeuriteType.axon
for leaf in iter_sections(neurite, iterator_type=Section.ileaf)
]
self.tip_radius = (np.percentile(
_diameters, self.params["tip_percentile"]) if _diameters else None)
self.current_trunk_radius = None
# estimate a global tapering rate of the morphology as a function of trunk radius,
# such that the tip radius is attained on average af max_path_length, defined as a fraction
# of the maximal path length via the parameter path_lengt_ratio. The smaller this parameter
# the faster the radii will convert to tip_radius.
# TODO: maybe we would need this per neurite_type
max_path_length = self.params["path_length_ratio"] * np.max(
nm.get("terminal_path_lengths_per_neurite", self.neuron))
self.taper = (lambda trunk_radius: (trunk_radius - self.tip_radius) *
self.params["seg_length"] / max_path_length)
