Python NeuronGroup.k方法代码示例

# 需要导入模块: from brian2 import NeuronGroup [as 别名]
# 或者: from brian2.NeuronGroup import k [as 别名]
def run_cpp_standalone(params, network_objs):
    import os
    from numpy.fft import rfft, irfft
    from brian2.devices.device import CurrentDeviceProxy
    from brian2.units import Unit
    from brian2 import check_units, implementation, device, prefs, NeuronGroup, Network

    tempdir = os.path.join(params["program_dir"], "cpp_standalone")
    tempdir = os.path.join(tempdir, "c_" + str(params["sigma_c"]) + \
                           "_s_" + str(params["sigma_s"]))
    if not os.path.exists(tempdir):
        os.makedirs(tempdir)


    prefs.codegen.cpp.libraries += ['mkl_gf_lp64', # -Wl,--start-group
                                    'mkl_gnu_thread',
                                    'mkl_core', #  -Wl,--end-group
                                    'iomp5']


    # give extra arguments and path information to the compiler
    extra_incs = ['-I'+os.path.expanduser(s) for s in [ tempdir, "~/intel/mkl/include"]]
    prefs.codegen.cpp.extra_compile_args_gcc = ['-w', '-Ofast', '-march=native'] + extra_incs

    # give extra arguments and path information to the linker
    prefs.codegen.cpp.extra_link_args += ['-L{0}/intel/mkl/lib/intel64'.format(os.path.expanduser('~')),
                                          '-L{0}/intel/lib/intel64'.format(os.path.expanduser('~')),
                                          '-m64', '-Wl,--no-as-needed']

    # Path that the compiled and linked code needs at runtime
    os.environ["LD_LIBRARY_PATH"] = os.path.expanduser('~/intel/mkl/lib/intel64:')
    os.environ["LD_LIBRARY_PATH"] += os.path.expanduser('~/intel/lib/intel64:')

    # Variable definitions
    N = params["NI"] # this is the amount of neurons with variable synaptic strength
    Noffset = params["NE"]
    neurons = network_objs["neurons"]
    params["rho0_dt"] = params["rho_0"]/second * params["rate_interval"]
    mkl_threads = 1


    # Includes the header files in all generated files
    prefs.codegen.cpp.headers += ['<sense.h>',]
    prefs.codegen.cpp.define_macros += [('N_REAL', int(N)),
                                        ('N_CMPLX', int(N/2+1))]
    path_to_sense_hpp = os.path.join(tempdir, 'sense.h')
    path_to_sense_cpp = os.path.join(tempdir, 'sense.cpp')
    with open(path_to_sense_hpp, "w") as f:
        header_code = '''
        #ifndef SENSE_H
        #define SENSE_H
        #include <mkl_service.h>
        #include <mkl_vml.h>
        #include <mkl_dfti.h>
        #include <cstring>
        extern DFTI_DESCRIPTOR_HANDLE hand;
        extern MKL_Complex16 in_cmplx[N_CMPLX], out_cmplx[N_CMPLX], k_cmplx[N_CMPLX];
        DFTI_DESCRIPTOR_HANDLE init_dfti();
        #endif'''
        f.write(header_code)
        #MKL_Complex16 is a type (probably struct)
    with open(path_to_sense_cpp, "w") as f:
        sense_code = '''
        #include <sense.h>
        DFTI_DESCRIPTOR_HANDLE hand;
        MKL_Complex16 in_cmplx[N_CMPLX], out_cmplx[N_CMPLX], k_cmplx[N_CMPLX];
        DFTI_DESCRIPTOR_HANDLE init_dfti()
        {{
            DFTI_DESCRIPTOR_HANDLE hand = 0;
            mkl_set_num_threads({mkl_threads});
            DftiCreateDescriptor(&hand, DFTI_DOUBLE, DFTI_REAL, 1, (MKL_LONG)N_REAL); //MKL_LONG status
            DftiSetValue(hand, DFTI_PLACEMENT, DFTI_NOT_INPLACE);
            DftiSetValue(hand, DFTI_CONJUGATE_EVEN_STORAGE, DFTI_COMPLEX_COMPLEX);
            DftiSetValue(hand, DFTI_BACKWARD_SCALE, 1. / N_REAL);
            //if (0 == status) status = DftiSetValue(hand, DFTI_THREAD_LIMIT, {mkl_threads});
            DftiCommitDescriptor(hand); //if (0 != status) cout << "ERROR, status = " << status << "\\n";
            return hand;
        }} '''.format(mkl_threads=mkl_threads, )
        f.write(sense_code)

    # device_get_array_name will be the function get_array_name() and what it does is getting
    # the string names of brian objects
    device_get_array_name = CurrentDeviceProxy.__getattr__(device, 'get_array_name')
    # instert_code is a function which is used to insert code into the main()
    # function
    insert_code = CurrentDeviceProxy.__getattr__(device, 'insert_code')

    ### Computing the kernel (Owen changed it to a gaussian kernel now)
    # Owen uses a trick here which is he creates a NeuronGroup which doesn't
    # really do anything in the Simulation. It's just a dummy NeuronGroup
    # to hold an array to which he would like to have access to during runtime.
    if params["sigma_s"] == np.infty:
        k = np.ones(N)/N
    elif params["sigma_s"] < 1e-3:
        k = np.zeros(N)
        k[0] = 1
    else:
        intercell = params["x_NI"]
        length = intercell*N
        d = np.linspace(intercell-length/2, length/2, N)
#.........这里部分代码省略.........