def setUp(self): self.ref_pop = Population([load_pt_neuron(f, mt.set_tree_type) for f in NRN_PATHS]) self.fst_pop = Population([nm.load_neuron(f) for f in NRN_PATHS]) self.ref_types = [t.type for t in self.ref_pop.neurites]
def setUp(self): self.ref_nrn = load_pt_neuron(os.path.join(SWC_DATA_PATH, SWC_MORPH_FILENAME), mt.set_tree_type) self.sec_nrn = nm.load_neuron(os.path.join(SWC_DATA_PATH, SWC_MORPH_FILENAME)) self.sec_nrn_trees = [n.root_node for n in self.sec_nrn.neurites] self.ref_types = [n.type for n in self.ref_nrn.neurites]
import os import numpy as np from nose import tools as nt from neurom.view import _compat from neurom.view._dendrogram import Dendrogram from neurom.point_neurite.io.utils import load_neuron as load_pt_neuron from neurom.point_neurite.dendrogram import Dendrogram as PointDendrogram from neurom.core.types import NeuriteType from neurom import load_neuron from neurom.morphmath import segment_radius as segrad _PWD = os.path.dirname(os.path.abspath(__file__)) DATA_PATH = os.path.join(_PWD, '../../../test_data/h5/v1/Neuron.h5') NRN0 = load_pt_neuron(DATA_PATH) NRN1 = load_neuron(DATA_PATH) def _close(a, b, debug=False): if debug: print '\na.shape: %s\nb.shape: %s\n' % (a.shape, b.shape) print '\na: %s\nb:%s\n' % (a, b) print '\na - b:%s\n' % (a - b) nt.assert_equal(len(a), len(b)) nt.assert_true(np.allclose(a, b)) def _equal(a, b, debug=False): if debug: print '\na.shape: %s\nb.shape: %s\n' % (a.shape, b.shape)
from neurom.core.tree import i_chain2 from neurom.point_neurite.io.utils import load_neuron as load_pt_neuron from neurom.point_neurite.features import get from neurom.point_neurite import treefunc as mt _PWD = os.path.dirname(os.path.abspath(__file__)) SWC_DATA_PATH = os.path.join(_PWD, '../../../test_data/swc') H5V1_DATA_PATH = os.path.join(_PWD, '../../../test_data/h5/v1') H5V2_DATA_PATH = os.path.join(_PWD, '../../../test_data/h5/v2') MORPH_FILENAME = 'Neuron.h5' SWC_MORPH_FILENAME = 'Neuron.swc' # Arbitrarily use h5 v1 as reference always REF_NRN = load_pt_neuron(os.path.join(H5V1_DATA_PATH, MORPH_FILENAME), mt.set_tree_type) REF_NEURITE_TYPES = [NeuriteType.apical_dendrite, NeuriteType.basal_dendrite, NeuriteType.basal_dendrite, NeuriteType.axon] def _close(a, b, debug=False): if debug: print 'a: %s\nb:%s\n' % (a, b) nt.assert_equal(len(a), len(b)) nt.assert_true(np.allclose(a, b)) def _equal(a, b, debug=False): if debug: print 'a: %s\nb:%s\n' % (a, b) nt.assert_equal(len(a), len(b))
from neurom import viewer from neurom.point_neurite.io.utils import load_neuron as load_pt_neuron import os from matplotlib import pyplot as plt class Dummy(object): pass _PWD = os.path.dirname(os.path.abspath(__file__)) DATA_PATH = os.path.join(_PWD, '../../test_data/swc') MORPH_FILENAME = os.path.join(DATA_PATH, 'Neuron.swc') nrn = load_neuron(MORPH_FILENAME) pt_nrn = load_pt_neuron(MORPH_FILENAME) def test_draw_neuron(): viewer.draw(pt_nrn) viewer.draw(nrn) plt.close('all') def test_draw_neuron3d(): viewer.draw(pt_nrn, mode='3d') viewer.draw(nrn, mode='3d') plt.close('all') def test_draw_tree():