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Build fixes. Closes #821 
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3 files changed

+45
-63
lines changed

3 files changed

+45
-63
lines changed

‎src/Core/Algorithms/BrainStimulator/ElectrodeCoilSetupAlgorithm.cc‎

Lines changed: 33 additions & 44 deletions
Original file line numberDiff line numberDiff line change
@@ -52,8 +52,6 @@
5252
#include <boost/algorithm/string/trim.hpp>
5353
#include <boost/algorithm/string/split.hpp>
5454
#include <boost/format.hpp>
55-
#include <boost/assign.hpp>
56-
#include <math.h>
5755
#include <Core/Math/MiscMath.h>
5856

5957
using namespace SCIRun::Core::Algorithms;
@@ -62,9 +60,6 @@ using namespace SCIRun::Core::Algorithms::Fields;
6260
using namespace SCIRun::Core::Datatypes;
6361
using namespace SCIRun::Core::Geometry;
6462
using namespace SCIRun;
65-
using namespace boost;
66-
using namespace boost::assign;
67-
using namespace Eigen;
6863

6964
ALGORITHM_PARAMETER_DEF(BrainStimulator, NumberOfPrototypes);
7065
ALGORITHM_PARAMETER_DEF(BrainStimulator, TableValues);
@@ -141,7 +136,7 @@ VariableHandle ElectrodeCoilSetupAlgorithm::fill_table(FieldHandle, DenseMatrixH
141136

142137
if (tab_values.size() < locations->nrows())
143138
{
144-
row +=
139+
row = {
145140
Variable(columnNames[0], boost::str(boost::format("%s") % "0")),
146141
Variable(columnNames[1], boost::str(boost::format("%s") % "0")),
147142
Variable(columnNames[2], boost::str(boost::format("%.3f") % (*locations)(i, 0))),
@@ -151,7 +146,7 @@ VariableHandle ElectrodeCoilSetupAlgorithm::fill_table(FieldHandle, DenseMatrixH
151146
Variable(columnNames[6], std::string("???")),
152147
Variable(columnNames[7], std::string("???")),
153148
Variable(columnNames[8], std::string("???")),
154-
Variable(columnNames[9], std::string("???"));
149+
Variable(columnNames[9], std::string("???")) };
155150
/*
156151
//TODO: this compiles but needs testing by user. Not sure it's an improvement.
157152
row = makeNamedVariableList(columnNames,
@@ -212,7 +207,7 @@ VariableHandle ElectrodeCoilSetupAlgorithm::fill_table(FieldHandle, DenseMatrixH
212207
Variable var8 = makeVariable("NY", boost::str(boost::format("%s") % str8));
213208
Variable var9 = makeVariable("NZ", boost::str(boost::format("%s") % str9));
214209
Variable var10 = makeVariable("thickness", boost::str(boost::format("%s") % str10));
215-
row += var1, var2, var3, var4, var5, var6, var7, var8, var9, var10;
210+
row = { var1, var2, var3, var4, var5, var6, var7, var8, var9, var10 };
216211

217212
}
218213
}
@@ -230,9 +225,9 @@ DenseMatrixHandle ElectrodeCoilSetupAlgorithm::make_rotation_matrix(const double
230225
DenseMatrixHandle result(new DenseMatrix(3, 3));
231226

232227
double normal_vector_norm = sqrt(normal[0] * normal[0] + normal[1] * normal[1] + normal[2] * normal[2]);
233-
Vector3d normal_vector((double)normal[0] / normal_vector_norm, (double)normal[1] / normal_vector_norm, (double)normal[2] / normal_vector_norm);
228+
Eigen::Vector3d normal_vector((double)normal[0] / normal_vector_norm, (double)normal[1] / normal_vector_norm, (double)normal[2] / normal_vector_norm);
234229

235-
Vector3d tan_vector1, tan_vector2;
230+
Eigen::Vector3d tan_vector1, tan_vector2;
236231
if (normal_vector(0) != 0 || normal_vector(2) != 0)
237232
{
238233
tan_vector1(0) = normal_vector(2);
@@ -254,8 +249,6 @@ DenseMatrixHandle ElectrodeCoilSetupAlgorithm::make_rotation_matrix(const double
254249
tan_vector2 = normal_vector.cross(tan_vector1);
255250
normal_vector_norm = sqrt(tan_vector2(0)*tan_vector2(0) + tan_vector2(1)*tan_vector2(1) + tan_vector2(2)*tan_vector2(2));
256251
tan_vector2(0) /= normal_vector_norm; tan_vector2(1) /= normal_vector_norm; tan_vector2(2) /= normal_vector_norm;
257-
DenseMatrixHandle rotation_matrix2;
258-
Matrix3d rotation_matrix(3, 3), rotation_matrix1(3, 3);
259252

260253
(*result)(0, 2) = normal_vector(0);
261254
(*result)(1, 2) = normal_vector(1);
@@ -299,7 +292,7 @@ FieldHandle ElectrodeCoilSetupAlgorithm::make_tms(FieldHandle scalp, const std::
299292
VMesh* tms_coils_vmesh = tms_coils_field->vmesh();
300293
VField* tms_coils_vfld = tms_coils_field->vfield();
301294
std::vector<Point> tms_coils_field_values;
302-
295+
303296
for (int i = 0; i < coil_prototyp_map.size(); i++)
304297
{
305298
if (coil_prototyp_map[i] <= elc_coil_proto.size() && coil_prototyp_map[i] >= 0)
@@ -340,7 +333,7 @@ FieldHandle ElectrodeCoilSetupAlgorithm::make_tms(FieldHandle scalp, const std::
340333
THROW_ALGORITHM_PROCESSING_ERROR("Internal error: could not retrieve coil prototype positions ");
341334
}
342335

343-
DenseMatrixHandle magnetic_dipoles(boost::make_shared<DenseMatrix>(fielddata->nrows(), 3));
336+
auto magnetic_dipoles(boost::make_shared<DenseMatrix>(fielddata->nrows(), 3ul));
344337

345338
/// subtract the mean from the coil positions to move them accourding to GUI table entries
346339
double mean_loc_x = 0, mean_loc_y = 0, mean_loc_z = 0;
@@ -524,7 +517,6 @@ FieldHandle ElectrodeCoilSetupAlgorithm::make_tms(FieldHandle scalp, const std::
524517

525518
boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm::make_table_row(int i, double x, double y, double z, double nx, double ny, double nz) const
526519
{
527-
Variable::List row;
528520
double out_nx, out_ny, out_nz;
529521
auto tab_values = get(Parameters::TableValues).toVector();
530522
auto col = tab_values[i].toVector();
@@ -552,7 +544,7 @@ boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm
552544
{
553545
out_nx = boost::lexical_cast<double>(col[6].toString());
554546
}
555-
catch (bad_lexical_cast&) {}
547+
catch (boost::bad_lexical_cast&) {}
556548
}
557549

558550
if (str8.compare("???") == 0)
@@ -566,7 +558,7 @@ boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm
566558
{
567559
out_ny = boost::lexical_cast<double>(col[7].toString());
568560
}
569-
catch (bad_lexical_cast&) {}
561+
catch (boost::bad_lexical_cast&) {}
570562
}
571563

572564
if (str9.compare("???") == 0)
@@ -580,7 +572,7 @@ boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm
580572
{
581573
out_nz = boost::lexical_cast<double>(col[8].toString());
582574
}
583-
catch (bad_lexical_cast&) {}
575+
catch (boost::bad_lexical_cast&) {}
584576
}
585577

586578
Variable var1 = makeVariable("Input #", boost::str(boost::format("%s") % str1));
@@ -609,9 +601,9 @@ boost::tuple<Variable::List, double, double, double> ElectrodeCoilSetupAlgorithm
609601
Variable var7 = makeVariable("NX", boost::str(boost::format("%s") % str7));
610602
Variable var8 = makeVariable("NY", boost::str(boost::format("%s") % str8));
611603
Variable var9 = makeVariable("NZ", boost::str(boost::format("%s") % str9));
612-
613604
Variable var10 = makeVariable("thickness", boost::str(boost::format("%s") % str10));
614-
row += var1, var2, var3, var4, var5, var6, var7, var8, var9, var10;
605+
606+
Variable::List row{ var1, var2, var3, var4, var5, var6, var7, var8, var9, var10 };
615607

616608
return boost::make_tuple(row, out_nx, out_ny, out_nz);
617609
}
@@ -724,12 +716,10 @@ boost::tuple<DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> Electr
724716
{
725717
THROW_ALGORITHM_PROCESSING_ERROR("Internal error: could not retrieve positions from assigned prototype ");
726718
}
727-
728-
if (fieldnodes->nrows() <= 0) // put this to tms as well
719+
if (fieldnodes->nrows() == 0) // put this to tms as well
729720
{
730721
THROW_ALGORITHM_PROCESSING_ERROR("Internal error: could not retrieve positions from assigned prototype ");
731722
}
732-
733723
///second, subtract the mean of the prototyp positions to center it in origin
734724
double mean_loc_x = 0, mean_loc_y = 0, mean_loc_z = 0;
735725
for (int j = 0; j < fieldnodes->nrows(); j++)
@@ -768,7 +758,6 @@ boost::tuple<DenseMatrixHandle, FieldHandle, FieldHandle, VariableHandle> Electr
768758
(*fieldnodes)(j, 1) = (*rotated_positions)(1, 0) + elc_y[i];
769759
(*fieldnodes)(j, 2) = (*rotated_positions)(2, 0) + elc_z[i];
770760
}
771-
772761
VMesh* prototype_vmesh = prototype->vmesh();
773762

774763
FieldInformation fieldinfo("TriSurfMesh", CONSTANTDATA_E, "double"); /// this is the final moved prototype for elc i
@@ -1433,19 +1422,19 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
14331422

14341423
try
14351424
{
1436-
c1 = lexical_cast<int>(row[0].toString());
1425+
c1 = boost::lexical_cast<int>(row[0].toString());
14371426
}
1438-
catch (bad_lexical_cast &)
1427+
catch (boost::bad_lexical_cast &)
14391428
{
14401429
c1 = std::numeric_limits<double>::quiet_NaN();
14411430
row_valid = false;
14421431
}
14431432

14441433
try
14451434
{
1446-
c2 = lexical_cast<int>(row[1].toString());
1435+
c2 = boost::lexical_cast<int>(row[1].toString());
14471436
}
1448-
catch (bad_lexical_cast &)
1437+
catch (boost::bad_lexical_cast &)
14491438
{
14501439
c2 = std::numeric_limits<double>::quiet_NaN();
14511440
row_valid = false;
@@ -1460,9 +1449,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
14601449
{
14611450
try
14621451
{
1463-
c3 = lexical_cast<double>(str_x);
1452+
c3 = boost::lexical_cast<double>(str_x);
14641453
}
1465-
catch (bad_lexical_cast &)
1454+
catch (boost::bad_lexical_cast &)
14661455
{
14671456
c3 = std::numeric_limits<double>::quiet_NaN();
14681457
valid_position = false;
@@ -1478,9 +1467,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
14781467
{
14791468
try ///get the electrode thickness from GUI
14801469
{
1481-
c4 = lexical_cast<double>(str_y);
1470+
c4 = boost::lexical_cast<double>(str_y);
14821471
}
1483-
catch (bad_lexical_cast &)
1472+
catch (boost::bad_lexical_cast &)
14841473
{
14851474
c4 = std::numeric_limits<double>::quiet_NaN();
14861475
valid_position = false;
@@ -1496,9 +1485,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
14961485
{
14971486
try ///get the electrode thickness from GUI
14981487
{
1499-
c5 = lexical_cast<double>(str_z);
1488+
c5 = boost::lexical_cast<double>(str_z);
15001489
}
1501-
catch (bad_lexical_cast &)
1490+
catch (boost::bad_lexical_cast &)
15021491
{
15031492
c5 = std::numeric_limits<double>::quiet_NaN();
15041493
valid_position = false;
@@ -1511,9 +1500,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
15111500
{
15121501
try
15131502
{
1514-
c6 = lexical_cast<double>(row[5].toString());
1503+
c6 = boost::lexical_cast<double>(row[5].toString());
15151504
}
1516-
catch (bad_lexical_cast &)
1505+
catch (boost::bad_lexical_cast &)
15171506
{
15181507
c6 = std::numeric_limits<double>::quiet_NaN();
15191508
}
@@ -1583,9 +1572,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
15831572
/// get NX
15841573
try
15851574
{
1586-
c7 = lexical_cast<double>(row[6].toString());
1575+
c7 = boost::lexical_cast<double>(row[6].toString());
15871576
}
1588-
catch (bad_lexical_cast &)
1577+
catch (boost::bad_lexical_cast &)
15891578
{
15901579
c7 = std::numeric_limits<double>::quiet_NaN();
15911580
valid_normal = false;
@@ -1594,9 +1583,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
15941583
/// get NY
15951584
try
15961585
{
1597-
c8 = lexical_cast<double>(row[7].toString());
1586+
c8 = boost::lexical_cast<double>(row[7].toString());
15981587
}
1599-
catch (bad_lexical_cast &)
1588+
catch (boost::bad_lexical_cast &)
16001589
{
16011590
c8 = std::numeric_limits<double>::quiet_NaN();
16021591
valid_normal = false;
@@ -1605,9 +1594,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
16051594
/// get NZ
16061595
try
16071596
{
1608-
c9 = lexical_cast<double>(row[8].toString());
1597+
c9 = boost::lexical_cast<double>(row[8].toString());
16091598
}
1610-
catch (bad_lexical_cast &)
1599+
catch (boost::bad_lexical_cast &)
16111600
{
16121601
c9 = std::numeric_limits<double>::quiet_NaN();
16131602
valid_normal = false;
@@ -1616,9 +1605,9 @@ boost::tuple<VariableHandle, DenseMatrixHandle, FieldHandle, FieldHandle, FieldH
16161605
/// get electrode thickness
16171606
try
16181607
{
1619-
c10 = lexical_cast<double>(row[9].toString());
1608+
c10 = boost::lexical_cast<double>(row[9].toString());
16201609
}
1621-
catch (bad_lexical_cast &)
1610+
catch (boost::bad_lexical_cast &)
16221611
{
16231612
c10 = std::numeric_limits<double>::quiet_NaN();
16241613
}

‎src/Core/Algorithms/BrainStimulator/Tests/ElectrodeCoilSetupAlgorithmTests.cc‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -51,8 +51,6 @@ using namespace SCIRun::Core::Datatypes;
5151
using namespace SCIRun::Core::Algorithms::BrainStimulator;
5252
using namespace SCIRun::Core::Algorithms;
5353
using namespace SCIRun::TestUtils;
54-
using namespace boost;
55-
using namespace boost::assign;
5654

5755
namespace
5856
{
@@ -97,8 +95,7 @@ TEST(ElectrodeCoilSetupAlgorithmTests, AlgoCorrect)
9795
var8=makeVariable("NY", boost::str(boost::format("%s") % "???"));
9896
var9=makeVariable("NZ", boost::str(boost::format("%s") % "???"));
9997
var10=makeVariable("thickness",boost::str(boost::format("%s") % "2"));
100-
Variable::List tmp;
101-
tmp += var1,var2,var3,var4,var5,var6,var7,var8,var9,var10;
98+
Variable::List tmp{ var1, var2, var3, var4, var5, var6, var7, var8, var9, var10 };
10299
table.push_back(makeVariable("row" + boost::lexical_cast<std::string>(0), tmp));
103100
VariableHandle output(new Variable(Name("Table"), table));
104101
///@Dan: I dont know how to set the table to the GUI so that the module can executed properly.

‎src/Dataflow/Engine/Scheduler/Tests/SchedulingWithBoostGraph.cc‎

Lines changed: 11 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -51,14 +51,14 @@
5151
#include <Core/Algorithms/Base/AlgorithmVariableNames.h>
5252
#include <Core/Logging/Log.h>
5353

54-
#include <boost/assign.hpp>
5554
#include <boost/config.hpp> // put this first to suppress some VC++ warnings
5655
#include <boost/lockfree/spsc_queue.hpp>
5756

5857
#include <iostream>
5958
#include <iterator>
6059
#include <algorithm>
6160
#include <numeric>
61+
#include <queue>
6262
#include <ctime>
6363

6464
#include <boost/utility.hpp>
@@ -88,10 +88,6 @@ using ::testing::NiceMock;
8888
using ::testing::DefaultValue;
8989
using ::testing::Return;
9090

91-
using namespace std;
92-
using namespace boost;
93-
using namespace boost::assign;
94-
9591
namespace
9692
{
9793
class InstanceCountIdGenerator : public ModuleIdGenerator
@@ -309,16 +305,16 @@ TEST_F(SchedulingWithBoostGraph, SerialNetworkOrder)
309305
BoostGraphSerialScheduler scheduler;
310306
ModuleExecutionOrder order = scheduler.schedule(matrixMathNetwork);
311307

312-
std::list<ModuleId> expected = list_of
313-
(ModuleId("CreateMatrix:1"))
314-
(ModuleId("EvaluateLinearAlgebraUnary:4"))
315-
(ModuleId("CreateMatrix:0"))
316-
(ModuleId("EvaluateLinearAlgebraUnary:3"))
317-
(ModuleId("EvaluateLinearAlgebraBinary:5"))
318-
(ModuleId("EvaluateLinearAlgebraUnary:2"))
319-
(ModuleId("EvaluateLinearAlgebraBinary:6"))
320-
(ModuleId("ReportMatrixInfo:8"))
321-
(ModuleId("ReportMatrixInfo:7"));
308+
std::list<ModuleId> expected{
309+
ModuleId("CreateMatrix:1"),
310+
ModuleId("EvaluateLinearAlgebraUnary:4"),
311+
ModuleId("CreateMatrix:0"),
312+
ModuleId("EvaluateLinearAlgebraUnary:3"),
313+
ModuleId("EvaluateLinearAlgebraBinary:5"),
314+
ModuleId("EvaluateLinearAlgebraUnary:2"),
315+
ModuleId("EvaluateLinearAlgebraBinary:6"),
316+
ModuleId("ReportMatrixInfo:8"),
317+
ModuleId("ReportMatrixInfo:7") };
322318
EXPECT_EQ(ModuleExecutionOrder(expected), order);
323319
}
324320

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