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jonathfjonathf
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added missing file
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‎.circleci/config.yml

Lines changed: 15 additions & 2 deletions
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@@ -6,9 +6,22 @@ jobs:
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- image: circleci/python:2.7.14
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steps:
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- checkout
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- restore_cache:
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key: reqs-{{ checksum "requirements.txt" }}
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- run:
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name: "Install Python requirements"
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command: pip install --user -Ur requirements.txt
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command: |
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virtualenv venv
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. venv/bin/activate
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pip install -Ur requirements.txt
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pip install -e .
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- save_cache:
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key: reqs-{{ checksum "requirements.txt" }}
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paths:
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- venv
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- run:
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name: "Run tests"
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command: python setup.py test
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command: |
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. venv/bin/activate
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python setup.py test
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‎conftest.py

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"""Global configuration."""
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import os
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import inspect
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import shutil
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import pytest
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import matlab2cpp
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from matlab2cpp import collection
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@pytest.fixture(scope="session")
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def workspace_folder(tmpdir_factory):
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"""Create a temporary folder to perform tests from."""
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return str(tmpdir_factory.mktemp("workspace"))
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@pytest.fixture(scope="function", autouse=True)
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def workspace(workspace_folder, doctest_namespace):
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"""Fill temporary folder for each test."""
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# move data to workspace:
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source = os.path.join(os.path.dirname(inspect.stack()[0][1]), "test", "data")
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if os.path.isdir(workspace_folder):
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shutil.rmtree(workspace_folder)
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shutil.copytree(source, workspace_folder)
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# add content to doctest namespace:
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doctest_namespace["workspace"] = workspace_folder
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doctest_namespace["matlab2cpp"] = matlab2cpp
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doctest_namespace["collection"] = collection
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# change to workspace:
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curdir = os.path.abspath(os.path.curdir)
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os.chdir(workspace_folder)
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yield workspace_folder
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# clean up:
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os.chdir(curdir)
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shutil.rmtree(workspace_folder)

‎src/matlab2cpp/configure/frontend.py

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def configure(root, suggest=True, **kws):
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"""
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configure backend
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See also:
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:py:func:`matlab2cpp.Builder.configure <Builder.configure>`
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"""
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from .. import tree
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if isinstance(root, tree.Builder):
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root = root.project
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loop(root, suggest)
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loop(root, suggest)
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def loop(root, suggest):
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from . import datatypes, backends, reserved
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nodes = root.flatten(False, True, True)
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while True:
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# loop and configure
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for node in nodes:
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# reserved stuff
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if node.cls + "_" + node.name in reserved.__dict__:
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rule = reserved.__dict__[node.cls+"_"+node.name]
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if isinstance(rule, str):
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node.type = rule
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else:
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rule(node)
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# Datatype stuff
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if node.prop["type"] != "TYPE":
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pass
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elif node.cls in datatypes.__dict__:
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datatype = datatypes.__dict__[node.cls]
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if isinstance(datatype, str):
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node.type = datatype
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else:
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datatype(node)
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# Backend stuff
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if node.backend != "unknown":
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pass
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elif node.cls in backends.__dict__:
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backend = backends.__dict__[node.cls]
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if isinstance(backend, str):
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node.backend = backend
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else:
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backend(node)
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# determine if done
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if suggest:
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complete = True
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for program in root.project:
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suggests = program.suggest
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program.stypes = suggests
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program.ftypes = suggests
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complete = complete and not any([any(v) for v in suggests.values()])
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if complete:
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break
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else:
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break
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# delete log, if any (create on translate)
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for program in root.project:
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program[-1].children = []

‎test/data/function_reference.hpp

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#ifndef F_M_HPP
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#define F_M_HPP
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#include <armadillo>
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using namespace arma ;
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irowvec f(irowvec x) ;
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void g() ;
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irowvec f(irowvec x)
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{
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irowvec y ;
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y = x+2 ;
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return y ;
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}
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void g()
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{
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irowvec x, y ;
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sword _x [] = {1, 2, 3} ;
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x = irowvec(_x, 3, false) ;
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y = f(x) ;
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}
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#endif

‎test/data/function_reference.m

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function y=f(x)
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y = x+2
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end
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function g()
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x = [1,2,3]
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y = f(x)
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end

‎test/data/function_reference_2.hpp

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#ifndef F_M_HPP
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#define F_M_HPP
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#include <armadillo>
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using namespace arma ;
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void f(irowvec a, ivec b, irowvec& y, ivec& z) ;
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void g() ;
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void f(irowvec a, ivec b, irowvec& y, ivec& z)
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{
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y = a+2 ;
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z = b-3 ;
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}
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void g()
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{
18+
irowvec a, y ;
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ivec b, z ;
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sword _a [] = {1, 2, 3} ;
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a = irowvec(_a, 3, false) ;
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sword _b [] = {4, 5, 6} ;
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b = ivec(_b, 3, false) ;
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f(a, b, y, z) ;
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}
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#endif

‎test/data/function_reference_2.m

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function [y,z]=f(a,b)
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y = a+2
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z = b-3
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end
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function g()
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a = [1,2,3]
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b = [4;5;6]
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[y,z] = f(a,b)
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end

‎test/data/fx_decon.cpp

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#ifndef FX_DECON_M_HPP
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#define FX_DECON_M_HPP
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#include <armadillo>
5+
#include "mconvert.h"
6+
#include <cmath>
7+
using namespace arma ;
8+
9+
mat fx_decon(mat DATA, double dt, int lf, double mu, double flow, int fhigh) ;
10+
void ar_modeling(cx_vec x, int lf, double mu, cx_vec& yf, cx_vec& yb) ;
11+
12+
mat fx_decon(mat DATA, double dt, int lf, double mu, double flow, int fhigh)
13+
{
14+
cx_mat DATA_FX, DATA_FX_b, DATA_FX_f ;
15+
cx_vec aux_in, aux_out_b, aux_out_f ;
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int ihigh, ilow, k, nf, nt, ntraces ;
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mat DATA_b, DATA_f ;
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nt = DATA.n_rows;
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ntraces = DATA.n_cols;
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nf = pow(2, m2cpp::nextpow2(nt)) ;
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DATA_FX_f = arma::zeros<cx_mat>(nf, ntraces) ;
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DATA_FX_b = arma::zeros<cx_mat>(nf, ntraces) ;
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ilow = std::floor(flow*dt*nf)+1 ;
25+
if (ilow<1)
26+
{
27+
ilow = 1 ;
28+
}
29+
ihigh = std::floor(fhigh*dt*nf)+1 ;
30+
if (ihigh>std::floor(nf/2.0)+1)
31+
{
32+
ihigh = std::floor(nf/2.0)+1 ;
33+
}
34+
DATA_FX = m2cpp::fft<mat>(DATA, nf, 1) ;
35+
for (k=ilow; k<=ihigh; k++)
36+
{
37+
aux_in = arma::trans(DATA_FX.row(k-1)) ;
38+
ar_modeling(aux_in, lf, mu, aux_out_f, aux_out_b) ;
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DATA_FX_f.row(k-1) = arma::trans(aux_out_f) ;
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DATA_FX_b.row(k-1) = arma::trans(aux_out_b) ;
41+
}
42+
for (k=nf/2.0+2; k<=nf; k++)
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{
44+
DATA_FX_f.row(k-1) = arma::conj(DATA_FX_f.row(nf-k+1)) ;
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DATA_FX_b.row(k-1) = arma::conj(DATA_FX_b.row(nf-k+1)) ;
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}
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DATA_f = arma::real(m2cpp::ifft<cx_mat>(DATA_FX_f, 1)) ;
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DATA_f = DATA_f.rows(arma::span(0, nt-1)) ;
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DATA_b = arma::real(m2cpp::ifft<cx_mat>(DATA_FX_b, 1)) ;
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DATA_b = DATA_b.rows(arma::span(0, nt-1)) ;
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DATA_f = (DATA_f+DATA_b) ;
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DATA_f.cols(arma::span(lf, ntraces-lf-1)) = DATA_f.cols(arma::span(lf, ntraces-lf-1))/2.0 ;
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return DATA_f ;
54+
}
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void ar_modeling(cx_vec x, int lf, double mu, cx_vec& yf, cx_vec& yb)
57+
{
58+
cx_double beta ;
59+
cx_mat B, M, temp ;
60+
cx_vec C, R, ab, af, y ;
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uword nx ;
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nx = m2cpp::length(x) ;
63+
y = x(arma::span(0, nx-lf-1)) ;
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C = x(arma::span(1, nx-lf)) ;
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R = x(arma::span(nx-lf, nx-1)) ;
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M = m2cpp::hankel(C, R) ;
67+
B = arma::trans(M)*M ;
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beta = B(0, 0)*(cx_double) mu/100.0 ;
69+
ab = arma::solve((B+beta*arma::eye<cx_mat>(lf, lf)), arma::trans(M), solve_opts::fast)*y ;
70+
temp = M*ab ;
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temp = arma::join_cols(temp, arma::zeros<cx_mat>(lf, 1)) ;
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yb = temp ;
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y = x(arma::span(lf, nx-1)) ;
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C = x(arma::span(lf-1, nx-2)) ;
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R = arma::flipud(x(arma::span(0, lf-1))) ;
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M = toeplitz(C, R) ;
77+
B = arma::trans(M)*M ;
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beta = B(0, 0)*(cx_double) mu/100.0 ;
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af = arma::solve((B+beta*arma::eye<cx_mat>(lf, lf)), arma::trans(M), solve_opts::fast)*y ;
80+
temp = M*af ;
81+
temp = arma::join_cols(arma::zeros<cx_mat>(lf, 1), temp) ;
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yf = temp ;
83+
return ;
84+
}
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#endif

‎test/data/fx_decon.m

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function [DATA_f] = fx_decon(DATA,dt,lf,mu,flow,fhigh);
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[nt,ntraces] = size(DATA);
3+
nf = 2^nextpow2(nt);
4+
DATA_FX_f = zeros(nf,ntraces);
5+
DATA_FX_b = zeros(nf,ntraces);
6+
ilow = floor(flow*dt*nf)+1;
7+
if ilow<1;
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ilow=1;
9+
end;
10+
ihigh = floor(fhigh*dt*nf)+1;
11+
if ihigh > floor(nf/2)+1;
12+
ihigh=floor(nf/2)+1;
13+
end
14+
DATA_FX = fft(DATA,nf,1);
15+
for k = ilow:ihigh;
16+
aux_in = DATA_FX(k,:)';
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[aux_out_f,aux_out_b] = ar_modeling(aux_in,lf,mu);
18+
DATA_FX_f(k,:) = aux_out_f';
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DATA_FX_b(k,:) = aux_out_b';
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end;
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for k=nf/2+2:nf
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DATA_FX_f(k,:) = conj(DATA_FX_f(nf-k+2,:));
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DATA_FX_b(k,:) = conj(DATA_FX_b(nf-k+2,:));
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end
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DATA_f = real(ifft(DATA_FX_f,[],1));
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DATA_f = DATA_f(1:nt,:);
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DATA_b = real(ifft(DATA_FX_b,[],1));
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DATA_b = DATA_b(1:nt,:);
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DATA_f = (DATA_f + DATA_b);
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DATA_f(:,lf+1:ntraces-lf)= DATA_f(:,lf+1:ntraces-lf)/2;
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return
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function [yf,yb] = ar_modeling(x,lf,mu);
33+
nx = length(x);
34+
y = x(1:nx-lf,1);
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C = x(2:nx-lf+1,1);
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R = x(nx-lf+1:nx,1);
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M = hankel(C,R);
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B = M'*M; beta = B(1,1)*mu/100;
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ab = (B + beta*eye(lf))\M'*y;
40+
temp = M*ab;
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temp = [temp;zeros(lf,1)];
42+
yb = temp;
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y = x(lf+1:nx,1);
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C = x(lf:nx-1,1);
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R = flipud(x(1:lf,1));
46+
M = toeplitz(C,R);
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B = M'*M; beta = B(1,1)*mu/100;
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af = (B + beta*eye(lf))\M'*y;
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temp = M*af;
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temp = [zeros(lf,1);temp];
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yf = temp;
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return

‎test/data/fx_decon.m.py

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functions = {
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"ar_modeling" : {
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"B" : "cx_mat",
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"C" : "cx_vec",
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"M" : "cx_mat",
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"R" : "cx_vec",
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"ab" : "cx_vec",
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"af" : "cx_vec",
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"beta" : "cx_double",
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"lf" : "int",
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"mu" : "double",
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"nx" : "uword",
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"temp" : "cx_mat",
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"x" : "cx_vec",
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"y" : "cx_vec",
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"yb" : "cx_vec",
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"yf" : "cx_vec",
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},
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"fx_decon" : {
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"DATA" : "mat",
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"DATA_FX" : "cx_mat",
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"DATA_FX_b" : "cx_mat",
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"DATA_FX_f" : "cx_mat",
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"DATA_b" : "mat",
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"DATA_f" : "mat",
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"aux_in" : "cx_vec",
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"aux_out_b" : "cx_vec",
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"aux_out_f" : "cx_vec",
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"dt" : "double",
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"fhigh" : "int",
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"flow" : "double",
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"ihigh" : "int",
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"ilow" : "int",
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"k" : "int",
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"lf" : "int",
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"mu" : "double",
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"nf" : "int",
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"nt" : "int",
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"ntraces" : "int",
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},
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}
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includes = [
43+
'#include <armadillo>',
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'using namespace arma ;',
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]

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