int testioparams(PV_Init* initObj, int rank) {
initObj->resetState();
// Ignore -r and -c switches
initObj->setRestartFlag(false);
initObj->setCheckpointReadDir(NULL);
HyPerCol * hc = build(initObj, NULL, 0);
if (hc == NULL) {
pvError().printf("testioparams error: unable to build HyPerCol.\n");
}
int status = hc->run(); // Needed to generate pv.params file
if (status != PV_SUCCESS) {
pvError().printf("testioparams error: run to generate pv.params file failed.\n");
}
const char * paramsfile = hc->getPrintParamsFilename();
std::string paramsfileString = paramsfile;
if (paramsfile[0]!='/') {
const char * outputPath = hc->getOutputPath();
paramsfileString.insert(0, "/");
paramsfileString.insert(0, outputPath);
}
delete hc;
initObj->setParams(paramsfileString.c_str());
if (rank==0) {
pvInfo().printf("Running --testioparams with effective command line\n");
initObj->printState();
}
status = rebuildandrun(initObj, NULL, &assertAllZeroes, NULL, 0);
return status;
}
int testioparams(PV_Init* initObj, int rank) {
PV_Arguments * arguments = initObj->getArguments();
arguments->resetState();
// Ignore -r and -c switches
arguments->setRestartFlag(false);
arguments->setCheckpointReadDir(NULL);
initObj->initialize();
HyPerCol * hc = build(initObj, NULL, 0);
if (hc == NULL) {
fprintf(stderr, "testioparams error: unable to build HyPerCol.\n");
exit(EXIT_FAILURE);
}
int status = hc->run(); // Needed to generate pv.params file
if (status != PV_SUCCESS) {
fprintf(stderr, "testioparams error: run to generate pv.params file failed.\n");
exit(EXIT_FAILURE);
}
const char * paramsfile = hc->getPrintParamsFilename();
std::string paramsfileString = paramsfile;
if (paramsfile[0]!='/') {
const char * outputPath = hc->getOutputPath();
paramsfileString.insert(0, "/");
paramsfileString.insert(0, outputPath);
}
delete hc;
arguments->setParamsFile(paramsfileString.c_str());
if (rank==0) {
printf("%s --testioparams running PetaVision with arguments\n", arguments->getProgramName());
arguments->printState();
}
status = rebuildandrun(initObj, NULL, &assertAllZeroes, NULL, 0);
return status;
}
int StochasticReleaseTestProbe::computePValues(long int step, int f) {
int status = PV_SUCCESS;
assert(step >=0 && step < INT_MAX);
int nf = getTargetLayer()->getLayerLoc()->nf;
assert(f >= 0 && f < nf);
int idx = (step-1)*nf + f;
pvwdata_t wgt = conn->get_wDataStart(0)[f*(nf+1)]; // weights should be one-to-one weights
HyPerLayer * pre = conn->preSynapticLayer();
const pvdata_t * preactPtr = pre->getLayerData();
const PVLayerLoc * preLoc = pre->getLayerLoc();
const int numPreNeurons = pre->getNumNeurons();
bool found=false;
pvdata_t preact = 0.0f;
for (int n=f; n<numPreNeurons; n+=nf) {
int nExt = kIndexExtended(n, preLoc->nx, preLoc->ny, preLoc->nf, preLoc->halo.lt, preLoc->halo.rt, preLoc->halo.dn, preLoc->halo.up);
pvdata_t a = preactPtr[nExt];
if (a!=0.0f) {
if (found) {
assert(preact==a);
}
else {
found = true;
preact = a;
}
}
}
preact *= getParent()->getDeltaTime();
if (preact < 0.0f) preact = 0.0f;
if (preact > 1.0f) preact = 1.0f;
const PVLayerLoc * loc = getTargetLayer()->getLayerLoc();
const pvdata_t * activity = getTargetLayer()->getLayerData();
int nnzf = 0;
const int numNeurons = getTargetLayer()->getNumNeurons();
for (int n=f; n<numNeurons; n+=nf) {
int nExt = kIndexExtended(n, loc->nx, loc->ny, loc->nf, loc->halo.lt, loc->halo.rt, loc->halo.dn, loc->halo.up);
assert(activity[nExt]==0 || activity[nExt]==wgt);
if (activity[nExt]!=0) nnzf++;
}
HyPerLayer * l = getTargetLayer();
HyPerCol * hc = l->getParent();
MPI_Allreduce(MPI_IN_PLACE, &nnzf, 1, MPI_INT, MPI_SUM, hc->icCommunicator()->communicator());
if (hc->columnId()==0) {
const int neuronsPerFeature = l->getNumGlobalNeurons()/nf;
double mean = preact * neuronsPerFeature;
double stddev = sqrt(neuronsPerFeature*preact*(1-preact));
double numdevs = (nnzf-mean)/stddev;
pvalues[idx] = erfc(fabs(numdevs)/sqrt(2));
fprintf(outputstream->fp, " Feature %d, nnz=%5d, expectation=%7.1f, std.dev.=%5.1f, discrepancy of %f deviations, p-value %f\n",
f, nnzf, mean, stddev, numdevs, pvalues[idx]);
}
assert(status==PV_SUCCESS);
return status;
}
int main(int argc, char * argv[])
{
int status = 0;
int rank=0;
PV_Init* initObj = new PV_Init(&argc, &argv, false/*allowUnrecognizedArguments*/);
PV_Arguments * arguments = initObj->getArguments();
if (arguments->getParamsFile() != NULL) {
if (rank==0) {
fprintf(stderr, "%s does not take -p as an option. Instead the necessary params file is hard-coded.\n", argv[0]);
}
MPI_Barrier(MPI_COMM_WORLD);
exit(EXIT_FAILURE);
}
arguments->setParamsFile("input/test_border_activity.params");
initObj->initialize();
HyPerCol * hc = new HyPerCol("column", initObj);
const char * imageLayerName = "test_border_activity image";
const char * retinaLayerName = "test_border_activity retina";
const char * l1LayerName = "test_border_activity layer";
Image * image = new Image(imageLayerName, hc); assert(image);
Retina * retina = new Retina(retinaLayerName, hc); assert(retina);
ANNLayer * l1 = new ANNLayer(l1LayerName, hc); assert(l1);
HyPerConn * conn1 = new HyPerConn("test_border_activity connection 1", hc);
assert(conn1);
HyPerConn * conn2 = new HyPerConn("test_border_activity connection 2", hc);
assert(conn2);
#ifdef DEBUG_OUTPUT
PointProbe * p1 = new PointProbe( 0, 0, 0, "L1 (0,0,0):");
PointProbe * p2 = new PointProbe(32, 32, 32, "L1 (32,32,0):");
l1->insertProbe(p1);
l1->insertProbe(p2);
#endif
// run the simulation
hc->run();
status = check_activity(l1);
delete hc;
delete initObj;
return status;
}
int main(int argc, char* argv[])
{
int status = 0;
PV_Init* initObj = new PV_Init(&argc, &argv);
initObj->initialize(argc, argv);
// create the managing hypercolumn
//
HyPerCol* hc = new HyPerCol("test_constant_input column", argc, argv, initObj);
// create the image
//
TestImage * image = new TestImage("test_constant_input image", hc);
// create the layers
//
HyPerLayer * retina = new Retina("test_constant_input retina", hc);
// create the connections
//
HyPerConn * conn = new HyPerConn("test_constant_input connection", hc);
const int nxp = conn->xPatchSize();
const int nyp = conn->yPatchSize();
const PVLayerLoc * imageLoc = image->getLayerLoc();
const PVLayerLoc * retinaLoc = image->getLayerLoc();
const int nfPre = imageLoc->nf;
float sumOfWeights = (float) (nxp*nyp*nfPre);
if (imageLoc->nx > retinaLoc->nx) { sumOfWeights *= imageLoc->nx/retinaLoc->nx;}
if (imageLoc->ny > retinaLoc->ny) { sumOfWeights *= imageLoc->ny/retinaLoc->ny;}
hc->run();
const int rank = hc->columnId();
#ifdef DEBUG_OUTPUT
printf("[%d]: column: ", rank);
printLoc(hc->getImageLoc());
printf("[%d]: image : ", rank);
printLoc(image->getImageLoc());
printf("[%d]: retina: ", rank);
printLoc(*retina->getLayerLoc());
printf("[%d]: l1 : ", rank);
printLoc(*l1->getLayerLoc());
#endif
status = checkLoc(hc, image->getLayerLoc());
if (status != PV_SUCCESS) {
fprintf(stderr, "[%d]: test_constant_input: ERROR in image loc\n", rank);
exit(status);
}
status = checkLoc(hc, retina->getLayerLoc());
if (status != PV_SUCCESS) {
fprintf(stderr, "[%d]: test_constant_input: ERROR in retina loc\n", rank);
exit(status);
}
status = checkInput(image->getLayerLoc(), image->getActivity(), image->getConstantVal(), true);
if (status != PV_SUCCESS) {
fprintf(stderr, "[%d]: test_constant_input: ERROR in image data\n", rank);
exit(status);
}
float retinaVal = sumOfWeights * image->getConstantVal();
status = checkInput(retina->getLayerLoc(), retina->getActivity(), retinaVal, false);
if (status != 0) {
fprintf(stderr, "[%d]: test_constant_input: ERROR in retina data\n", rank);
exit(status);
}
status = checkInput(retina->getLayerLoc(), retina->getLayerData(), retinaVal, true);
if (status != 0) {
fprintf(stderr, "[%d]: test_constant_input: ERROR in retina data\n", rank);
exit(status);
}
delete hc;
delete initObj;
return status;
}
int main(int argc, char * argv[]) {
PV_Init* initObj = new PV_Init(&argc, &argv, false/*allowUnrecognizedArguments*/);
InterColComm * icComm = new InterColComm(initObj->getArguments());
PV_Arguments * arguments = initObj->getArguments();
if (arguments->getParamsFile() != NULL) {
int rank = icComm->globalCommRank();
if (rank==0) {
fprintf(stderr, "%s does not take -p as an option. Instead the necessary params file is hard-coded.\n", arguments->getProgramName());
}
MPI_Barrier(MPI_COMM_WORLD);
exit(EXIT_FAILURE);
}
arguments->setParamsFile("input/TransposeHyPerConnTest.params");
initObj->initialize();
// Don't call buildandrun because it will delete hc before returning. (I could use the customexit hook)
HyPerCol * hc = build(initObj);
hc->run(); // Weight values are initialized when run calls allocateDataStructures
int status = PV_SUCCESS;
HyPerConn * originalMap = NULL;
TransposeConn * transpose = NULL;
TransposeConn * transposeOfTranspose = NULL;
BaseConnection * baseConn;
baseConn = hc->getConnFromName("Original Map for One to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to One Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to One Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-one case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for Many to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for Many to One Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for Many to One Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "Many-to-one case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for One to Many Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to Many Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to Many Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-many case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for One to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to One Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to One Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-one case, FeedbackConn");
baseConn = hc->getConnFromName("Original Map for Many to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for Many to One Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for Many to One Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "Many-to-one case, FeedbackConn");
baseConn = hc->getConnFromName("Original Map for One to Many Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to Many Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to Many Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-many case, FeedbackConn");
delete hc;
delete initObj;
return status;
}
int main(int argc, char * argv[]) {
PV_Init* initObj = new PV_Init(&argc, &argv);
InterColComm * icComm = new InterColComm(argc, argv);
PVParams * params = new PVParams("input/TransposeHyPerConnTest.params", 2*(INITIAL_LAYER_ARRAY_SIZE+INITIAL_CONNECTION_ARRAY_SIZE), icComm);
initObj->initialize(params, icComm);
// Don't call buildandrun because it will delete hc before returning. (I could use the customexit hook)
HyPerCol * hc = build(argc, argv, initObj);
hc->run(); // Weight values are initialized when run calls allocateDataStructures
int status = PV_SUCCESS;
HyPerConn * originalMap = NULL;
TransposeConn * transpose = NULL;
TransposeConn * transposeOfTranspose = NULL;
BaseConnection * baseConn;
baseConn = hc->getConnFromName("Original Map for One to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to One Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to One Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-one case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for Many to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for Many to One Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for Many to One Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "Many-to-one case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for One to Many Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to Many Test of TransposeConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to Many Test of TransposeConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-many case, TransposeConn");
baseConn = hc->getConnFromName("Original Map for One to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to One Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to One Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-one case, FeedbackConn");
baseConn = hc->getConnFromName("Original Map for Many to One Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for Many to One Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for Many to One Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "Many-to-one case, FeedbackConn");
baseConn = hc->getConnFromName("Original Map for One to Many Test");
originalMap = dynamic_cast<HyPerConn *>(baseConn);
//assert(originalMap->usingSharedWeights());
transpose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose for One to Many Test of FeedbackConn"));
transposeOfTranspose = dynamic_cast<TransposeConn *>(hc->getConnFromName("Transpose of Transpose for One to Many Test of FeedbackConn"));
status = testTransposeOfTransposeWeights(originalMap, transpose, transposeOfTranspose, "One-to-many case, FeedbackConn");
delete hc;
delete initObj;
return status;
}
int StochasticReleaseTestProbe::outputState(double timed) {
// Set conn. Can't do that in initStochasticReleaseTestProbe because we need to search for a conn with the given post, and connections' postLayerName is not necessarily set.
if (conn==NULL) {
HyPerCol * hc = getTargetLayer()->getParent();
int numconns = hc->numberOfConnections();
for (int c=0; c<numconns; c++) {
if (!strcmp(hc->getConnection(c)->getPostLayerName(),getTargetLayer()->getName())) {
assert(conn==NULL); // Only one connection can go to this layer for this probe to work
BaseConnection * baseConn = hc->getConnection(c);
conn = dynamic_cast<HyPerConn *>(baseConn);
}
}
assert(conn!=NULL);
}
assert(conn->numberOfAxonalArborLists()==1);
assert(conn->xPatchSize()==1);
assert(conn->yPatchSize()==1);
assert(conn->getNumDataPatches()==conn->fPatchSize());
int status = StatsProbe::outputState(timed);
assert(status==PV_SUCCESS);
HyPerLayer * l = getTargetLayer();
HyPerCol * hc = l->getParent();
int nf = l->getLayerLoc()->nf;
if (timed>0.0) {
for (int f=0; f < nf; f++) {
if (computePValues(hc->getCurrentStep(), f)!=PV_SUCCESS) status = PV_FAILURE;
}
assert(status == PV_SUCCESS);
if (hc->columnId()==0 && hc->simulationTime()+hc->getDeltaTime()/2>=hc->getStopTime()) {
// This is the last timestep
// sort the p-values and apply Holm-Bonferroni method since there is one for each timestep and each feature.
long int num_steps = hc->getFinalStep() - hc->getInitialStep();
long int N = num_steps * nf;
qsort(pvalues, (size_t) N, sizeof(*pvalues), compar);
while(N>0 && isnan(pvalues[N-1])) {
N--;
}
for (long int k=0; k<N; k++) {
if (pvalues[k]*(N-k)<0.05) {
fprintf(stderr, "layer \"%s\" FAILED: p-value %ld out of %ld (ordered by size) with Holm-Bonferroni correction = %f\n", getTargetLayer()->getName(), k, N, pvalues[k]*(N-k));
status = PV_FAILURE;
}
}
}
}
assert(status==PV_SUCCESS);
return status;
}
