import os
import numpy as np
from bmtk.utils.reports import CompartmentReport
try:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nhosts = comm.Get_size()
barrier = comm.Barrier
except Exception as exc:
rank = 0
nhosts = 1
barrier = lambda: None
cpath = os.path.dirname(os.path.realpath(__file__))
output_file = os.path.join(cpath, 'compartment_files/multi_population_report.h5')
[docs]
def build_file():
rank_cells = [(0, 10, 'v1'), (1, 50, 'v1'), (2, 100, 'v1'), (3, 1, 'v1'), (4, 200, 'v1'), (0, 100, 'v2'), (1, 50, 'v2')]
cr = CompartmentReport(output_file, mode='w', tstart=0.0, tstop=100.0, dt=0.1, variable='Vm', units='mV')
for node_id, n_elements, pop in rank_cells:
cr.add_cell(node_id=node_id, population=pop, element_ids=np.arange(n_elements),
element_pos=np.zeros(n_elements))
for i in range(1000):
for node_id, n_elements, pop in rank_cells:
cr.record_cell(node_id, population=pop, vals=[node_id]*n_elements, tstep=i)
cr.close()
[docs]
def test_compartment_reader():
report = CompartmentReport(output_file, 'r')
assert(len(report.populations) == 2)
# Check v1 population
assert('v1' in report.populations)
v1_grp = report['v1']
assert(np.all(np.sort(v1_grp.node_ids()) == np.arange(5)))
assert(v1_grp.tstart() == 0.0)
assert(v1_grp.tstop() == 100.0)
assert(v1_grp.dt() == 0.1)
assert(v1_grp.units() == 'mV')
assert(v1_grp.n_elements() == 361)
assert(v1_grp.element_pos().size == 361)
assert(v1_grp.element_ids().size == 361)
assert(v1_grp.data().shape == (1000, 361))
assert(v1_grp.data(0).shape == (1000, 10))
assert(v1_grp.data(0, time_window=(0.0, 50.0)).shape == (500, 10))
assert(np.all(np.unique(v1_grp.data(0)) == [0.0]))
assert(v1_grp.data(1).shape == (1000, 50))
assert(np.all(np.unique(v1_grp.data(1)) == [1.0]))
assert(v1_grp.data(2).shape == (1000, 100))
assert(np.all(np.unique(v1_grp.data(2)) == [2.0]))
assert(v1_grp.data(3).shape == (1000, 1))
assert(np.all(np.unique(v1_grp.data(3)) == [3.0]))
assert(v1_grp.data(4).shape == (1000, 200))
assert(np.all(np.unique(v1_grp.data(4)) == [4.0]))
# Check v2 population
assert('v2' in report.populations)
v1_grp = report['v2']
assert(np.all(np.sort(v1_grp.node_ids()) == np.arange(2)))
assert(v1_grp.tstart() == 0.0)
assert(v1_grp.tstop() == 100.0)
assert(v1_grp.dt() == 0.1)
assert(v1_grp.units() == 'mV')
assert(v1_grp.n_elements() == 150)
assert(v1_grp.element_pos().size == 150)
assert(v1_grp.element_ids().size == 150)
assert(v1_grp.data().shape == (1000, 150))
assert(v1_grp.data(0).shape == (1000, 100))
assert(v1_grp.data(0, time_window=(0.0, 50.0)).shape == (500, 100))
assert(np.all(np.unique(v1_grp.data(0)) == [0.0]))
assert(v1_grp.data(1).shape == (1000, 50))
assert(np.all(np.unique(v1_grp.data(1)) == [1.0]))
[docs]
def test_compartment_reader2():
report = CompartmentReport(output_file, 'r', default_population='v1')
assert(len(report.populations) == 2)
assert('v1' in report.populations)
assert(np.all(np.sort(report.node_ids()) == np.arange(5)))
assert(report.tstart() == 0.0)
assert(report.tstop() == 100.0)
assert(report.dt() == 0.1)
assert(report.units() == 'mV')
assert(report.n_elements() == 361)
assert(report.element_pos().size == 361)
assert(report.element_ids().size == 361)
assert(report.data().shape == (1000, 361))
assert(report.data(0).shape == (1000, 10))
assert(report.data(0, time_window=(0.0, 50.0)).shape == (500, 10))
assert(np.all(np.unique(report.data(0)) == [0.0]))
assert(report.data(1).shape == (1000, 50))
assert(np.all(np.unique(report.data(1)) == [1.0]))
assert(report.data(2).shape == (1000, 100))
assert(np.all(np.unique(report.data(2)) == [2.0]))
assert(report.data(3).shape == (1000, 1))
assert(np.all(np.unique(report.data(3)) == [3.0]))
assert(report.data(4).shape == (1000, 200))
assert(np.all(np.unique(report.data(4)) == [4.0]))
# Check v2 population
assert('v2' in report.populations)
assert(np.all(np.sort(report.node_ids(population='v2')) == np.arange(2)))
assert(report.tstart(population='v2') == 0.0)
assert(report.tstop(population='v2') == 100.0)
assert(report.dt(population='v2') == 0.1)
assert(report.units(population='v2') == 'mV')
assert(report.n_elements(population='v2') == 150)
assert(report.element_pos(population='v2').size == 150)
assert(report.element_ids(population='v2').size == 150)
assert(report.data(population='v2').shape == (1000, 150))
assert(report.data(0, population='v2').shape == (1000, 100))
assert(report.data(0, population='v2', time_window=(0.0, 50.0)).shape == (500, 100))
assert(np.all(np.unique(report.data(0, population='v2')) == [0.0]))
assert(report.data(1, population='v2').shape == (1000, 50))
assert(np.all(np.unique(report.data(1, population='v2')) == [1.0]))
if __name__ == '__main__':
#build_file()
#test_compartment_reader()
test_compartment_reader2()
