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unitTests.m
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function tests = unitTests
% This file is part of GPCCA.
%
% Copyright (c) 2018, 2017 Bernhard Reuter
%
% If you use this code or parts of it, cite the following reference:
%
% Reuter, B., Weber, M., Fackeldey, K., R?blitz, S., & Garcia, M. E. (2018). Generalized
% Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on
% Amyloid beta Conformational Dynamics Driven by an Oscillating Electric Field. Journal of
% Chemical Theory and Computation, 14(7), 3579-3594. https://doi.org/10.1021/acs.jctc.8b00079
%
% GPCCA is free software: you can redistribute it and/or modify
% it under the terms of the GNU Lesser General Public License as published
% by the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU Lesser General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
% -------------------------------------------------------------------------
% All test functions written by Bernhard Reuter, Theoretical Physics II,
% University of Kassel, 2017
tests = functiontests(localfunctions) ;
end
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% -------------------------------------------------------------------------
% test do_schur (depends on gram_schmidt_mod, SRSchur_num_t, numeric_t)
% (logic paths: 3) (assertions: 2+12)
% The 12 assertions here can't be tested (its also not necessary, since they
% are tested elsewhere)
function do_Schur_MatrixShapeError1(testCase) % a1
% test for the assertion if P matrix isnt quadratic
d1 = numeric_t('[0,0,0]') ;
d2 = numeric_t('[0,0,0]') ;
d3 = numeric_t('[0,0,0]') ;
d4 = numeric_t('[0,0,0]') ;
P = [ d1; d2; d3; d4 ] ;
sd = numeric_t('[ 0, 0, 0, 0 ]') ;
fileid = 'test_do_schur_MatrixShapeError1' ;
try
[ ~, ~ ] = do_schur( P, sd, fileid, 0 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'do_schur:MatrixShapeError1'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_do_schur_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function do_Schur_MatrixShapeError2(testCase) % a1
% test for the assertion if sd vector length doesnt match with the
% shape of P
d1 = numeric_t('[0,0,0]') ;
d2 = numeric_t('[0,0,0]') ;
d3 = numeric_t('[0,0,0]') ;
P = [ d1; d2; d3 ] ;
sd = numeric_t('[ 0, 0, 0, 0 ]') ;
fileid = 'test_do_schur_MatrixShapeError2' ;
try
[ ~, ~ ] = do_schur( P, sd, fileid, 0 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'do_schur:MatrixShapeError2'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_do_schur_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_do_schur(testCase) % l1
% test normal execution
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_do_schur' ;
[ X, RR ] = do_schur( P, sd, fileid, 0 ) ;
N = 9 ;
verifyTrue(testCase,all(size(P)==[N,N]))
verifyTrue(testCase,all(size(X)==[N,N]))
verifyTrue(testCase,all(size(RR)==[N,N]))
% test, if P*X=X*RR (Schur decomposition)
dummy = ( abs(X*RR - P*X) < (testCase.TestData.abstolfac * eps(numeric_t)) ) ;
verifyTrue(testCase,all(dummy(:)))
% test, if the first column of X is 1
dummy = (abs(X(:,1) - 1) < (testCase.TestData.abstolfac * eps(numeric_t))) ;
verifyTrue(testCase,all(dummy(:)))
end
function test_do_schur_DataTypeError(testCase) % l2
% test the error for the case, that class(P)~=class(sd)
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_do_schur_DataTypeError' ;
if isa(P,'mp') && isa(sd,'mp')
sd = double(sd) ;
elseif isa(P,'double') && isa(sd,'double')
sd = single(sd) ;
else
error('test_do_schur_DataTypeError:DataTypeError', ...
['class(P)=',class(P),' class(sd)=',class(sd)])
end
try
[ ~, ~ ] = do_schur( P, sd, fileid, 0 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'do_schur:DataTypeError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_do_schur_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_do_schur_b_pos(testCase) % l3a
% test normal execution with b>0
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_do_schur' ;
[ X, RR ] = do_schur( P, sd, fileid, 3 ) ;
N = 9 ;
verifyTrue(testCase,all(size(P)==[N,N]))
verifyTrue(testCase,all(size(X)==[N,3]))
verifyTrue(testCase,all(size(RR)==[N,N]))
% test, if P*X=X*RR (Schur decomposition)
dummy = ( abs(X*RR(1:3,1:3) - P*X) < (testCase.TestData.abstolfac * eps(numeric_t)) ) ;
verifyTrue(testCase,all(dummy(:)))
% test, if the first column of X is 1
dummy = (abs(X(:,1) - 1) < (testCase.TestData.abstolfac * eps(numeric_t))) ;
verifyTrue(testCase,all(dummy(:)))
end
function test_do_schur_b_neg(testCase) % l3b
% test normal execution with b<0
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_do_schur' ;
[ X, RR ] = do_schur( P, sd, fileid, -3 ) ;
N = 9 ;
verifyTrue(testCase,all(size(P)==[N,N]))
verifyTrue(testCase,all(size(X)==[N,3]))
verifyTrue(testCase,all(size(RR)==[N,N]))
% test, if P*X=X*RR (Schur decomposition)
dummy = ( abs(X*RR(1:3,1:3) - P*X) < (testCase.TestData.abstolfac * eps(numeric_t)) ) ;
verifyTrue(testCase,all(dummy(:)))
% test, if the first column of X is 1
dummy = (abs(X(:,1) - 1) < (testCase.TestData.abstolfac * eps(numeric_t))) ;
verifyTrue(testCase,all(dummy(:)))
end
% -------------------------------------------------------------------------
% test fillA (depends on do_schur, initialize_A, numeric_t) (logic paths: 6)
% (assertions: 6)
function test_fillA_MatrixShapeError1(testCase) % a1
% test assertion, if A matrix isnt quadratic
d1 = [1,0,0,0] ;
d2 = [1,0,0,0] ;
d3 = [1,0,0,0] ;
svecs = [ d1; d2; d3 ] ;
A = svecs ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:MatrixShapeError1'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_MatchError(testCase) % a2
% test assertion, if second dimension of schur vector matrix doesnt
% match to the dimensions of the A matrix
d1 = [1,0,0,0] ;
d2 = [1,0,0,0] ;
d3 = [1,0,0,0] ;
svecs = [ d1; d2; d3 ] ;
A = zeros(3) ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:MatchError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_MatrixShapeError2(testCase) % a3
% test assertion for A smaller 2x2
svecs = [ 1, 1 ]' ;
A = 0 ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:MatrixShapeError2'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_MatrixShapeError3(testCase) % a4
% test assertion for (N,k)-matrix with k>N
d1 = [1,0,0,0] ;
d2 = [1,0,0,0] ;
d3 = [1,0,0,0] ;
svecs = [ d1; d2; d3 ] ;
A = zeros(4) ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:MatrixShapeError3'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_MatrixShapeError4(testCase) % a5
% test assertion for (N,k)-matrix with k=N
d1 = [1,0,0] ;
d2 = [1,0,0] ;
d3 = [1,0,0] ;
svecs = [ d1; d2; d3 ] ;
A = zeros(3) ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:MatrixShapeError4'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_FirstColumnError(testCase) % a6
% test for the assertion if first column of schur vector matrix isnt
% constantly equal 1
d1 = [0,0,0] ;
d2 = [0,0,0] ;
d3 = [0,0,0] ;
d4 = [0,0,0] ;
svecs = [ d1; d2; d3; d4 ] ;
A = zeros(3) ;
try
[ ~ ] = fillA( A, svecs ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'fillA:FirstColumnError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_fillA_mu0(testCase) % l
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_fillA_mu0' ;
% get Schur vectors
[ X, ~ ] = do_schur( P, sd, fileid, 0 ) ;
svecs = X(:,1:3) ;
% initialize A
[ T, A ] = evalc('initialize_A( svecs, 1 )') ;
% just save
name = 'test_fillA_mu0-initial-A.txt' ;
save_t(name, A, '-ascii')
% fill A
[ T1, A ] = evalc('fillA( A, double(svecs))') ;
% T, T1 is stored to a file
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s\n','test_fillA_mu0') ;
fprintf(fileID,'%s\n',T) ;
fprintf(fileID,'%s\n\n',T1) ;
fclose(fileID) ;
% just save
name = 'test_fillA_mu0-A.txt' ;
save_t(name, A, '-ascii')
name = 'test_fillA_mu0-svecs(N,1-3).txt' ;
save_t(name, double(svecs), '-ascii')
% actaul testing
import matlab.unittest.constraints.IsEqualTo;
import matlab.unittest.constraints.AbsoluteTolerance;
import matlab.unittest.constraints.RelativeTolerance;
% set absolute and relative tolerance for verification
abstol = testCase.TestData.abstolfac * eps ;
reltol = testCase.TestData.reltolfac * eps ;
% check positivity
[ m, k ] = size(A) ;
[ N, n ] = size(svecs) ;
verifyTrue( testCase, m == k )
verifyTrue( testCase, n == k )
A_exp = inf(k) ;
for j = 1:k
dummy = [] ;
for l = 1:N
dummy(l) = svecs(l,2:k)*A(2:k,j) ;
end
A_exp(1,j) = -min(dummy) ;
end
testCase.verifyThat(A(1,:), IsEqualTo(A_exp(1,:), ...
'Within', AbsoluteTolerance(abstol) | RelativeTolerance(reltol)))
% check partition of unity
A_exp(1,1) = 1 - sum(A(1,2:k)) ;
for i = 2:k
A_exp(i,1) = - sum(A(i,2:k)) ;
end
testCase.verifyThat(A(:,1), IsEqualTo(A_exp(:,1), ...
'Within', AbsoluteTolerance(abstol) | RelativeTolerance(reltol)))
end
function test_fillA_mu1000(testCase) % l
% specify the test case data
matrixfile = 'example_matrix_mu1000.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_fillA_mu1000' ;
% get Schur vectors
[ X, ~ ] = do_schur( P, sd, fileid, 0 ) ;
svecs = X(:,1:5) ;
% initialize A
[ T, A ] = evalc('initialize_A( svecs, 1 )') ;
% just save
name = 'test_fillA_mu1000-initial-A.txt' ;
save_t(name, A, '-ascii')
% fill A
[ T1, A ] = evalc('fillA( A, double(svecs))') ;
% T, T1 is stored to a file
fileID = fopen('test_fillA_report.txt','a') ;
fprintf(fileID,'%s\n','test_fillA_mu1000') ;
fprintf(fileID,'%s\n',T) ;
fprintf(fileID,'%s\n\n',T1) ;
fclose(fileID) ;
% just save
name = 'test_fillA_mu1000-A.txt' ;
save_t(name, A, '-ascii')
name = 'test_fillA_mu1000-svecs(N,1-5).txt' ;
save_t(name, double(svecs), '-ascii')
% actaul testing
import matlab.unittest.constraints.IsEqualTo;
import matlab.unittest.constraints.AbsoluteTolerance;
import matlab.unittest.constraints.RelativeTolerance;
% set absolute and relative tolerance for verification
abstol = testCase.TestData.abstolfac * eps ;
reltol = testCase.TestData.reltolfac * eps ;
% check positivity
[ m, k ] = size(A) ;
[ N, n ] = size(svecs) ;
verifyTrue( testCase, m == k )
verifyTrue( testCase, n == k )
A_exp = inf(k) ;
for j = 1:k
dummy = [] ;
for l = 1:N
dummy(l) = svecs(l,2:k)*A(2:k,j) ;
end
A_exp(1,j) = -min(dummy) ;
end
testCase.verifyThat(A(1,:), IsEqualTo(A_exp(1,:), ...
'Within', AbsoluteTolerance(abstol) | RelativeTolerance(reltol)))
% check partition of unity
A_exp(1,1) = 1 - sum(A(1,2:k)) ;
for i = 2:k
A_exp(i,1) = - sum(A(i,2:k)) ;
end
testCase.verifyThat(A(:,1), IsEqualTo(A_exp(:,1), ...
'Within', AbsoluteTolerance(abstol) | RelativeTolerance(reltol)))
end
% -------------------------------------------------------------------------
% test getopt (depends on none) (logic paths: 2) (assertions: 0)
function test_getopt(testCase) % l1 + l2
dummy.field = 111 ;
[ field, dummy ] = getopt( dummy, 'field', 999 ) ;
verifyEqual(testCase,field,111)
verifyTrue(testCase,isstruct(dummy))
verifyEqual(testCase,dummy.field,111)
clearvars dummy
dummy = [] ;
[ field, dummy ] = getopt( dummy, 'field', 999 ) ;
verifyEqual(testCase,field,999)
verifyTrue(testCase,isstruct(dummy))
verifyEqual(testCase,dummy.field,999)
end
% -------------------------------------------------------------------------
% test gram_schmidt_mod (depends on nearly_equal, numeric_t) (logic paths: 3)
% (assertions: 2)
function test_gram_schmidt_mod_MatrixShapeError1(testCase) % a1
% test assertion for matrix with only one row
sys = numeric_t('[ 3, 1 ]') ;
sd = numeric_t('1') ;
try
[ ~ ] = gram_schmidt_mod( sys, sd ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'gram_schmidt_mod:MatrixShapeError1'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_gram_schmidt_mod_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_gram_schmidt_mod_MatrixShapeError2(testCase) % a2
% test assertion for matrix with only one column
sys = numeric_t('[ 3, 1 ]') ;
sys = sys' ;
sd = numeric_t('[ 9/sqrt(10), 1/sqrt(10) ]') ;
try
[ ~ ] = gram_schmidt_mod( sys, sd ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'gram_schmidt_mod:MatrixShapeError2'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_gram_schmidt_mod_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_gram_schmidt_mod_R2_mp(testCase) % l1a
% test basis of R^2, example taken from:
% https://de.wikipedia.org/wiki/Gram-Schmidtsches_Orthogonalisierungsverfahren
prec = testCase.TestData.precision ;
assumeEqual(testCase, prec, 'mp')
x1 = numeric_t('[ 3, 1 ]') ;
x2 = numeric_t('[ 2, 2 ]') ;
sys = [ x1; x2 ] ;
sys = sys' ;
sd = (x1.^2)/norm(x1) ;
Q = gram_schmidt_mod( sys, sd ) ;
u1 = numeric_t('[ 3/sqrt(10), 1/sqrt(10) ]') ;
u2 = numeric_t('[ -1/sqrt(10), 3/sqrt(10) ]') ;
orthosys = [ u1; u2 ] ;
orthosys = orthosys' ;
abstol = testCase.TestData.abstolfac * eps(numeric_t) ;
reltol = testCase.TestData.reltolfac * eps(numeric_t) ;
[ ~, ~, c ] = verifyAlmostEqual(Q, orthosys, abstol, ...
reltol, true) ;
verifyTrue(testCase, c)
end
function test_gram_schmidt_mod_R2_double(testCase) % l1b
% test basis of R^2, example taken from:
% https://de.wikipedia.org/wiki/Gram-Schmidtsches_Orthogonalisierungsverfahren
prec = testCase.TestData.precision ;
assumeEqual(testCase, prec, 'double')
import matlab.unittest.constraints.IsEqualTo;
import matlab.unittest.constraints.AbsoluteTolerance;
import matlab.unittest.constraints.RelativeTolerance;
% set absolute and relative tolerance for verification
abstol = testCase.TestData.abstolfac * eps ;
reltol = testCase.TestData.reltolfac * eps ;
x1 = numeric_t('[ 3, 1 ]') ;
x2 = numeric_t('[ 2, 2 ]') ;
sys = [ x1; x2 ] ;
sys = sys' ;
sd = numeric_t('[ 0.5, 0.5 ]') ;
Q = gram_schmidt_mod( sys, sd ) ;
u1 = numeric_t('[ sqrt(0.5), sqrt(0.5) ]') ;
u2 = numeric_t('[ sqrt(0.5), -sqrt(0.5) ]') ;
orthosys = [ u1; u2 ] ;
orthosys = orthosys' ;
testCase.verifyThat(Q, IsEqualTo(orthosys, ...
'Within', AbsoluteTolerance(abstol) & RelativeTolerance(reltol)))
end
function test_gram_schmidt_mod_R4(testCase) % l1
% test for subspace of R^4, example taken from:
% http://math.bard.edu/~mbelk/math601/GramSchmidtExamples.pdf
x1 = numeric_t('[ 1, 1, 1, 1 ]') ;
x2 = numeric_t('[ -1, 4, 4, 1 ]') ;
x3 = numeric_t('[ 4, -2, 2, 0 ]') ;
sys = [ x1; x2; x3 ] ;
sys = sys' ;
sd = numeric_t('[ 0.25, 0.25, 0.25, 0.25 ]') ;
Q = gram_schmidt_mod( sys, sd ) ;
u1 = numeric_t('[ 1/2, 1/2, 1/2, 1/2 ]') ;
u2 = numeric_t('[ -1/sqrt(2), sqrt(2)/3, sqrt(2)/3, -1/(3*sqrt(2)) ]') ;
u3 = numeric_t('[ 1/(2*sqrt(3)), -5/(6*sqrt(3)), 7/(6*sqrt(3)), -5/(6*sqrt(3)) ]') ;
orthosys = [ u1; u2; u3 ] ;
orthosys = orthosys' ;
abstol = testCase.TestData.abstolfac * eps(numeric_t) ;
reltol = testCase.TestData.reltolfac * eps(numeric_t) ;
[ ~, ~, c ] = verifyAlmostEqual(Q, orthosys, abstol, ...
reltol, true) ;
verifyTrue(testCase, c)
end
% -------------------------------------------------------------------------
% test indexsearch (depends on numeric_t) (logic paths: 6) (assertions: 1)
function test_indexsearch_MatrixShapeError(testCase) % a1
% test assertion for (N,k)-matrix with k>N
v1 = numeric_t('[1,0,0,0]') ;
v2 = numeric_t('[0,1,0,0]') ;
v3 = numeric_t('[0,0,1,0]') ;
sys = [ v1; v2; v3 ] ;
try
[ ~ ] = indexsearch( sys ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'indexsearch:MatrixShapeError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_indexsearch_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_indexsearch(testCase) % l
% test correct function for standard simplex in 6D first
v0 = numeric_t('[0,0,0,0,0,0]') ;
v1 = numeric_t('[1,0,0,0,0,0]') ;
v2 = numeric_t('[0,1,0,0,0,0]') ;
v3 = numeric_t('[0,0,1,0,0,0]') ;
v4 = numeric_t('[0,0,0,1,0,0]') ;
v5 = numeric_t('[0,0,0,0,1,0]') ;
v6 = numeric_t('[0,0,0,0,0,1]') ;
sys = [ v0; v1; v0; v2; v0; v3; v0; v4; v0; v5; v0; v6 ] ;
% find indices
index = indexsearch( sys ) ;
index_exp = numeric_t('[2,4,6,8,10,12]') ;
dummy = ( index == index_exp ) ;
verifyTrue(testCase, all(dummy(:)) )
% define simple system of points in 3D, which all are inside (or on the
% surface) of the 3D-simplex with vertices v0=[0,0,0], v1=[1.5,0,0],
% v2=[0,2,0], v3=[0,0,3]
v3 = numeric_t('[0,0,3]') ;
p1 = numeric_t('[0.75,1,0]') ;
v1 = numeric_t('[1.5,0,0]') ;
v0 = numeric_t('[0,0,0]') ;
p3 = numeric_t('[0.375,0.5,0.75]') ;
v2 = numeric_t('[0,2,0]') ;
p2 = numeric_t('[0,1.2,1.2]') ;
p4 = numeric_t('[0.15,0.2,0.6]') ;
p5 = numeric_t('[0,0.6,0.3]') ;
sys = [ v3; p1; v1; v0; p3; v2; p2; p4; p5 ] ;
% find indices
index = indexsearch( sys ) ;
index_exp = numeric_t('[1,6,3]') ;
dummy = ( index == index_exp ) ;
verifyTrue(testCase, all(dummy(:)) )
end
% -------------------------------------------------------------------------
% test initialize_A (depends on do_schur, indexsearch, numeric_t) (logic paths: 4)
% (assertions: 4)
function test_initialize_A_FirstColumnError(testCase) % a1
% test for the assertion if first column of schur vector matrix isnt
% constantly equal 1
d1 = numeric_t('[0,0,0]') ;
d2 = numeric_t('[0,0,0]') ;
d3 = numeric_t('[0,0,0]') ;
d4 = numeric_t('[0,0,0]') ;
dummy = [ d1; d2; d3; d4 ] ;
try
[ ~ ] = initialize_A( dummy, 1 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_A:FirstColumnError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_A_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_initialize_A_MatrixShapeError1(testCase) % a2
% test assertion for (N,k)-matrix with k>N
d1 = numeric_t('[1,0,0,0]') ;
d2 = numeric_t('[1,0,0,0]') ;
d3 = numeric_t('[1,0,0,0]') ;
dummy = [ d1; d2; d3 ] ;
try
[ ~ ] = initialize_A( dummy, 1 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_A:MatrixShapeError1'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_initialize_A_MatrixShapeError2(testCase) % a3
% test assertion for (N,k)-matrix with k=N
d1 = numeric_t('[1,0,0]') ;
d2 = numeric_t('[1,0,0]') ;
d3 = numeric_t('[1,0,0]') ;
dummy = [ d1; d2; d3 ] ;
try
[ ~ ] = initialize_A( dummy, 1 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_A:MatrixShapeError2'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_initialize_A_condition(testCase) % a4
% test assertion for too high matrix condition
dummy = hilb(14) ;
dummy(:,14) = [] ;
dummy(:,1) = numeric_t('1') ;
try
[ ~ ] = initialize_A( dummy, 1 ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_A:A_ConditionError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_initialize_A_init(testCase) % l1
% test for the error if init isnt 0 or 1
d1 = numeric_t('[1,0,0]') ;
d2 = numeric_t('[1,0,0]') ;
d3 = numeric_t('[1,0,0]') ;
d4 = numeric_t('[1,0,0]') ;
dummy = [ d1; d2; d3; d4 ] ;
init = 2 ;
try
[ ~ ] = initialize_A( dummy, init ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_A:InputError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
function test_initialize_A(testCase) % l2
import matlab.unittest.constraints.IsEqualTo;
import matlab.unittest.constraints.AbsoluteTolerance;
import matlab.unittest.constraints.RelativeTolerance;
% specify the test case data
matrixfile = 'example_matrix_mu0.txt' ;
% get the known test case data
[ P, sd ] = get_knownInput( matrixfile ) ;
fileid = 'test_fillA' ;
% get Schur vectors
[ X, ~ ] = do_schur( P, sd, fileid, 0 ) ;
evs = X(:,1:4) ;
% initialize A
[ T, A ] = evalc('initialize_A( evs, 1 )') ;
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s\n','test_initialize_A') ;
fprintf(fileID,'%s\n\n',T) ;
fclose(fileID) ;
% set absolute and relative tolerance for verification
abstol = testCase.TestData.abstolfac * eps ;
reltol = testCase.TestData.reltolfac * eps ;
% find indices
index = indexsearch( evs ) ;
A_exp = double( pinv( X(index,1:4) ) ) ;
testCase.verifyThat(A, IsEqualTo(A_exp, ...
'Within', AbsoluteTolerance(abstol) | RelativeTolerance(reltol)))
end
function test_initialize_A_conditionWarning(testCase) % l3
% test warning for high matrix condition
dummy = hilb(6) ;
dummy(:,6) = [] ;
dummy(:,1) = numeric_t('1') ;
[ T, ~ ] = evalc('initialize_A( dummy, 1 )') ;
fileID = fopen('test_initialize_A_report.txt','a') ;
fprintf(fileID,'%s\n','test_initialize_A_conditionWarning') ;
fprintf(fileID,'%s\n\n',T) ;
fclose(fileID) ;
warning = ['Warning for 5 clusters: The condition ' ...
'number of the initial guess for A is > 1e4'] ;
C = strsplit(T, '\n') ;
verifyTrue( testCase, strcmp(C(1), warning) )
end
function test_initialize_A_loadOldfile(testCase) % l4
% test initialization by loading of an already existing matrix from
% file.
% set global variable to indicate testrun (no display output, no
% interactive input): 'minChiON' indicates that minChi criterion is
% used and input is taken from testInput_minChiON.mat. 'minChiOFF'
% indicates that minChi criterion isnt used and input is taken from
% testInput_minChiOFF.mat.
global testmode
testmode = 'minChiON' ;
d1 = [1,0,0] ;
d2 = [1,0,0] ;
d3 = [1,0,0] ;
d4 = [1,0,0] ;
dummy = [ d1; d2; d3 ; d4 ] ;
actVal = initialize_A( dummy, 0 ) ;
e1 = [0,1,0] ;
e2 = [0,1,0] ;
e3 = [0,1,0] ;
e4 = [0,1,0] ;
expVal = [ e1; e2; e3 ; e4 ] ;
verifyEqual(testCase, actVal, expVal, 'AbsTol', eps)
end
% -------------------------------------------------------------------------
% test initialize_optional (depends on none) (logic paths: 5) (assertions: 0)
% test for valid initialization of iopt in case of empty iopt
function test_initialize_optional_empty_iopt(testCase) % l1
% set the ID-string for file-naming
id = 'test_initialize_optional_empty_iopt' ;
[ iopt, fileid, final_opt ] = initialize_optional( [], id ) ;
verifyEqual(testCase, isempty(iopt), true)
verifyEqual(testCase, final_opt, false)
verifyEqual(testCase, fileid, '')
end
function test_initialize_optional_SolverError(testCase)
id = 'test_initialize_optional_SolverError' ;
iopt.solver = 'Newton' ;
try
[ ~, ~, ~ ] = initialize_optional( iopt, id ) ;
actVal = 0 ;
catch ME
switch ME.identifier
case 'initialize_optional:SolverError'
actVal = 1 ;
otherwise
rethrow(ME)
end
end
fileID = fopen('test_initialize_optional_report.txt','w') ;
fprintf(fileID,'%s',ME.identifier) ;
fprintf(fileID,'%s',': ') ;
fprintf(fileID,'%s\n\n',ME.message) ;
fclose(fileID) ;
expVal = 1 ;
verifyEqual(testCase, actVal, expVal)
end
% test for valid initialization of iopt in case of only
% iopt.solver='gauss-newton' defined
function test_initialize_optional_gauss_newton(testCase) % l3
% set the optional solver and ID-string for file-naming
iopt.solver = 'gauss-newton' ;
id = 'test_initialize_optional_gauss_newton' ;
[ iopt, fileid, final_opt ] = initialize_optional( iopt, id ) ;
verifyEqual(testCase, isstruct(iopt), true)
verifyEqual(testCase, iopt.solver, 'gauss-newton')
verifyEqual(testCase, iopt.init, 1)
verifyEqual(testCase, iopt.parallel, 0)
verifyEqual(testCase, iopt.maxiter, 100)
verifyEqual(testCase, iopt.display, 0)
verifyEqual(testCase, iopt.xtol, 1e-4)
verifyEqual(testCase, iopt.xscale, 1e-06)
fileid_exp = strcat(id,'-',iopt.solver,'-','maxiter','_', ...
num2str(iopt.maxiter),'-','xscale','_', num2str(iopt.xscale), ...
'-','xtol','_',num2str(iopt.xtol),'-',numeric_t) ;
verifyEqual(testCase, fileid, fileid_exp)
verifyEqual(testCase, final_opt, true)
end
% test for valid initialization of iopt in case of only
% iopt.solver='nelder-mead' defined
function test_initialize_optional_nelder_mead(testCase) % l4
% set the optional solver and ID-string for file-naming
iopt.solver = 'nelder-mead' ;
id = 'test_initialize_optional_nelder_mead' ;
[ iopt, fileid, final_opt ] = initialize_optional( iopt, id ) ;
verifyEqual(testCase, isstruct(iopt), true)
verifyEqual(testCase, iopt.solver, 'nelder-mead')
verifyEqual(testCase, iopt.init, 1)
verifyEqual(testCase, iopt.parallel, 0)
verifyEqual(testCase, iopt.maxiter, 2000)
verifyEqual(testCase, iopt.display, 0)
verifyEqual(testCase, iopt.tolfun, 1e-8)
verifyEqual(testCase, iopt.tolx, 1e-8)
fileid_exp = strcat(id,'-',iopt.solver,'-','maxiter','_', ...
num2str(iopt.maxiter),'-','tolfun','_', num2str(iopt.tolfun), ...
'-','tolx','_',num2str(iopt.tolx),'-',numeric_t) ;
verifyEqual(testCase, fileid, fileid_exp)
verifyEqual(testCase, final_opt, true)
end
% test for valid initialization of iopt in case of only
% iopt.solver='levenberg-marquardt' defined
function test_initialize_optional_levenberg_marquardt(testCase) % l5
% set the optional solver and ID-string for file-naming
iopt.solver = 'levenberg-marquardt' ;
id = 'test_initialize_optional_levenberg_marquardt' ;
[ iopt, fileid, final_opt ] = initialize_optional( iopt, id ) ;
verifyEqual(testCase, isstruct(iopt), true)
verifyEqual(testCase, iopt.solver, 'levenberg-marquardt')
verifyEqual(testCase, iopt.init, 1)
verifyEqual(testCase, iopt.parallel, 0)
verifyEqual(testCase, iopt.maxiter, 500)
verifyEqual(testCase, iopt.display, 0)
verifyEqual(testCase, iopt.tolfun, 1e-8)
verifyEqual(testCase, iopt.tolx, 1e-10)
fileid_exp = strcat(id,'-',iopt.solver,'-','maxiter','_', ...
num2str(iopt.maxiter),'-','tolfun','_', num2str(iopt.tolfun), ...
'-','tolx','_',num2str(iopt.tolx),'-',numeric_t) ;
verifyEqual(testCase, fileid, fileid_exp)
verifyEqual(testCase, final_opt, true)
end
% -------------------------------------------------------------------------
% test initialize_workspace (depends on none) (logic paths: 4) (assertions: 0)
% test for valid initialization of wk in case of empty wk
function test_initialize_workspace_empty_wk(testCase)
% set the solver, optional solver and ID-string for file-naming
[ wk, fileid ] = initialize_workspace( [] ) ;
verifyEqual(testCase, isstruct(wk), true)
verifyEqual(testCase, wk.id, 'gpcca')
verifyEqual(testCase, wk.schur, 1)
verifyEqual(testCase, wk.b, 0)
verifyEqual(testCase, wk.init, 1)
verifyEqual(testCase, wk.solver, 'gauss-newton')
verifyEqual(testCase, wk.maxiter, 100)
verifyEqual(testCase, wk.display, 0)
verifyEqual(testCase, wk.xtol, 1e-4)
verifyEqual(testCase, wk.xscale, 1e-06)
fileid_exp = strcat(wk.id,'-',wk.solver,'-','maxiter','_', ...
num2str(wk.maxiter),'-','xscale','_', num2str(wk.xscale), ...
'-','xtol','_',num2str(wk.xtol),'-',numeric_t) ;