void ReadModelList(void)
{
if (templateModelList.lLength > 0) return;
_String modelListFile (_HYStandardDirectory (HY_HBL_DIRECTORY_TEMPLATE_MODELS) & "models.lst");
FILE* modelList = doFileOpen (modelListFile.getStr(),"rb");
if (!modelList) {
return;
}
_String theData (modelList);
fclose (modelList);
if (theData.sLength) {
_ElementaryCommand::ExtractConditions(theData,0,templateModelList);
for (unsigned long i = 0; i<templateModelList.countitems(); i++) {
_String* thisString = (_String*)templateModelList(i);
_List thisModel;
_ElementaryCommand::ExtractConditions(*thisString,thisString->FirstNonSpaceIndex(),thisModel,',');
if (thisModel.lLength!=5) {
templateModelList.Delete(i);
i--;
continue;
}
for (long j = 0; j<5; j++) {
((_String*)thisModel(j))->StripQuotes();
}
((_String*)thisModel(0))->UpCase();
templateModelList.Replace(i,&thisModel,true);
}
}
}
void _HYConsoleWindow::_SetMenuBar(void)
{
if (menu_items && !gtk_item_factory_get_item(menu_items,"<HY_WINDOW>/Analysis")) {
gtk_item_factory_delete_item (menu_items, "<HY_WINDOW>/File/Open");
gtk_item_factory_delete_item (menu_items, "<HY_WINDOW>/File/Close");
gtk_item_factory_delete_item (menu_items, "<HY_WINDOW>/File/Switch to console");
gtk_item_factory_create_items (menu_items, sizeof (hyphy_console_window_menu_file) / sizeof (hyphy_console_window_menu_file[0]), hyphy_console_window_menu_file, this);
GtkMenu * fileMenu = GTK_MENU (gtk_item_factory_get_widget (menu_items, "<HY_WINDOW>/File"));
gtk_menu_reorder_child (fileMenu, gtk_item_factory_get_item (menu_items, "<HY_WINDOW>/File/New"), 0);
gtk_menu_reorder_child (fileMenu, gtk_item_factory_get_item (menu_items, "<HY_WINDOW>/File/Open"), 1);
gtk_menu_reorder_child (fileMenu, gtk_item_factory_get_item (menu_items, "<HY_WINDOW>/File/sep1"), 2);
gtk_widget_set_sensitive(gtk_item_factory_get_widget (menu_items,"<HY_WINDOW>/Edit/Clear"), true);
gtk_widget_set_sensitive(gtk_item_factory_get_widget (menu_items,"<HY_WINDOW>/Edit/Select All"), true);
gtk_widget_set_sensitive(gtk_item_factory_get_widget_by_action(menu_items,21), false);
gtk_widget_set_sensitive(gtk_item_factory_get_widget_by_action(menu_items,22), false);
gtk_widget_set_sensitive(gtk_item_factory_get_item (menu_items,"<HY_WINDOW>/Analysis/Results"), false);
gtk_widget_set_sensitive(gtk_item_factory_get_widget_by_action(menu_items,30), false);
for (long counter=0; counter<availablePostProcessors.countitems(); counter++) {
_String * postItem = (_String*)(*(_List*)availablePostProcessors(counter))(0);
if (!postItem->Equal (&menuSeparator)) {
postItem = (_String*)(*(_List*)availablePostProcessors(counter))(1);
_String tryFileName (*postItem);
FILE * tryFile = doFileOpen (tryFileName.getStr(), "r");
if (tryFile) {
fclose(tryFile);
} else {
availablePostProcessors.Delete(counter);
counter--;
}
}
}
if (availablePostProcessors.lLength) {
long sepCount = 0;
for (long counter=0; counter<availablePostProcessors.countitems(); counter++) {
_String * postItem = (_String*)(*(_List*)availablePostProcessors(counter))(0),
chopped = _String("/Analysis/Results/")&*postItem;
if (postItem->Equal (&menuSeparator)) {
GtkItemFactoryEntry aProcEntry = {NULL,NULL,NULL,0,"<Separator>"};
chopped = chopped & sepCount++;
aProcEntry.path = chopped.sData;
gtk_item_factory_create_items (menu_items, 1, &aProcEntry, this);
} else {
GtkItemFactoryEntry aProcEntry = {NULL,NULL,hyphy_menu_item_callback,1000+counter,"<Item>"};
aProcEntry.path = chopped.sData;
gtk_item_factory_create_items (menu_items, 1, &aProcEntry, this);
}
}
}
}
}
void SaveConsole (void)
{
_String sDP = dialogPrompt;
dialogPrompt = "Save HyPhy console to:";
_String fileName(WriteFileDialogInput ());
if (fileName.sLength == 0)
return;
FILE * f = doFileOpen (fileName.getStr(),"w");
if (!f)
{
fileName = _String ("Could not open '") & fileName & "' for writing.";
ProblemReport (fileName, (Ptr)hyphyConsoleWindow);
}
else
{
fileName = GetVersionString () & " console saved on " & GetTimeStamp () & "\n\n";
fwrite (fileName.sData,1,fileName.sLength, f);
_String *cS;
((_HYTextBox*)hyphyConsoleWindow->GetObject (0))->StoreText (cS);
#ifdef __WINDOZE__
for (long k=0; k<cS->sLength; k++)
{
char c = cS->sData[k];
if (c=='\r')
fprintf (f,"\n");
else
fputc (c,f);
}
#else
fprintf (f,"%s",cS->sData);
#endif
fclose (f);
DeleteObject (cS);
}
dialogPrompt = sDP;
}
void TrainModelNN (_String* model, _String* matrix)
{
_String errMsg;
long modelIdx = modelNames.Find(model);
_Parameter verbI;
checkParameter (VerbosityLevelString, verbI, 0.0);
char buffer [128];
if (modelIdx < 0) {
errMsg = *model & " did not refer to an existring model";
} else {
_Variable* boundsMatrix = FetchVar (LocateVarByName (*matrix));
if (boundsMatrix && (boundsMatrix->ObjectClass() == MATRIX)) {
_Matrix * bmatrix = (_Matrix*) boundsMatrix->GetValue ();
if (bmatrix->IsAStringMatrix() && (bmatrix->GetVDim () == 3)) {
_Variable* modelMatrix = LocateVar (modelMatrixIndices.lData[modelIdx]);
_SimpleList modelVariableList;
{
_AVLList mvla (&modelVariableList);
modelMatrix->ScanForVariables (mvla, true);
mvla.ReorderList();
}
if (bmatrix->GetHDim () == modelVariableList.lLength) {
// now map model variables to bounds matrix
_SimpleList variableMap;
_String *myName;
for (long k = 0; k < modelVariableList.lLength; k++) {
myName = ((_FString*)bmatrix->GetFormula(k,0)->Compute())->theString;
long vID = LocateVarByName (*myName);
if (vID < 0) {
break;
}
vID = variableNames.GetXtra (vID);
vID = modelVariableList.Find(vID);
if (vID < 0) {
break;
}
variableMap << vID;
}
if (variableMap.lLength == modelVariableList.lLength) {
_Matrix vBounds (variableMap.lLength,2, false, true);
long k2 = 0;
for (; k2 < variableMap.lLength; k2++) {
_Parameter lb = ((_FString*)bmatrix->GetFormula(k2,1)->Compute())->theString->toNum(),
ub = ((_FString*)bmatrix->GetFormula(k2,2)->Compute())->theString->toNum();
if ( ub>lb || k2) {
vBounds.Store (k2,0,lb);
vBounds.Store (k2,1,ub);
if (ub<=lb && vBounds (k2-1,0) <= vBounds (k2-1,1) && (!CheckEqual(vBounds (k2-1,0),0.0) || !CheckEqual(vBounds (k2-1,1),1.0))) {
break;
}
}
}
if (k2 == modelVariableList.lLength) {
// set up the sampling now
_String fName = ProcessLiteralArgument (&ModelNNFile,nil);
FILE* nnFile = doFileOpen (fName.getStr(), "w");
if (nnFile) {
_Matrix* modelMatrix = (_Matrix*) LocateVar(modelMatrixIndices.lData[modelIdx])->GetValue();
_Parameter mainSteps,
checkSteps,
errorTerm,
loopMax,
hiddenNodes,
absError,
nn1,
nn2;
long fullDimension = modelMatrix->GetHDim() * modelMatrix->GetVDim();
checkParameter (ModelNNTrainingSteps, mainSteps, 10000.0);
checkParameter (ModelNNVerificationSample, checkSteps, 500.0);
checkParameter (ModelNNPrecision, errorTerm, 0.01);
checkParameter (ModelNNTrainingSteps, loopMax, 10);
checkParameter (ModelNNHiddenNodes, hiddenNodes, 5);
checkParameter (ModelNNLearningRate, nn1, .3);
checkParameter (ModelNNPersistenceRate, nn2, .1);
Net** matrixNet = new Net* [fullDimension] ;
for (long i = 0; i < fullDimension; i++) {
checkPointer (matrixNet [i] = new Net (variableMap.lLength,(long)hiddenNodes,1,errorTerm,nn1,nn2,100,200,true));
//matrixNet[i]->verbose = true;
}
checkPointer (matrixNet);
_List tIn,
tOut;
FILE* varSamples = doFileOpen ("variableSamples.out", "w");
fprintf (varSamples, "%s" ,LocateVar(modelVariableList.lData[0])->GetName()->getStr());
for (long vc = 1; vc < modelVariableList.lLength; vc++) {
fprintf (varSamples, ",%s" ,LocateVar(modelVariableList.lData[variableMap.lData[vc]])->GetName()->getStr());
}
fprintf (varSamples, "\n");
for (long itCount = 0; itCount < loopMax; itCount ++) {
if (verbI > 5) {
snprintf (buffer, sizeof(buffer), "\nNeural Network Pass %ld. Building a training set...\n", itCount);
BufferToConsole (buffer);
}
while (tIn.countitems() < mainSteps) {
NNMatrixSampler (0, vBounds, modelVariableList, variableMap, modelMatrix, tIn, tOut);
}
_Matrix inData (mainSteps, variableMap.lLength, false, true);
_Parameter *md = inData.theData;
for (long matrixC = 0; matrixC < mainSteps; matrixC++) {
_Parameter * ed = ((_Matrix*)tIn (matrixC))->theData;
fprintf (varSamples, "\n%g",*ed);
*md = *ed;
ed++;
md++;
for (long entryC = 1; entryC < variableMap.lLength; entryC++, ed++, md++) {
*md = *ed;
fprintf (varSamples, ",%g", *md);
}
}
tIn.Clear();
if (verbI > 5) {
BufferToConsole ( "Done Building Training Set. Training...\n");
}
long lastDone = 0;
for (long cellCount = 0; cellCount < fullDimension; cellCount++) {
Net* thisCell = matrixNet[cellCount];
_Matrix outVector (mainSteps, 1, false, true);
for (long oc = 0; oc < mainSteps; oc++) {
outVector.theData[oc] = ((_Matrix*)tOut(oc))->theData[cellCount];
}
thisCell->studyAll (inData.theData, outVector.theData, mainSteps);
long nowDone = (cellCount+1)*100./fullDimension;
if (nowDone > lastDone) {
snprintf (buffer, sizeof(buffer),"%ld%% done\n", lastDone = nowDone);
BufferToConsole (buffer);
}
}
tOut.Clear();
if (verbI > 5) {
BufferToConsole ( "Done Training. Resampling...\n");
}
_PMathObj tObj = _Constant(0).Time();
_Parameter time1 = tObj->Value(),
time2;
while (tIn.countitems() < checkSteps) {
NNMatrixSampler (0, vBounds, modelVariableList, variableMap, modelMatrix, tIn, tOut);
}
absError = 0.0;
DeleteObject (tObj);
tObj = _Constant(0).Time();
time2 = tObj->Value();
if (verbI > 5) {
snprintf (buffer, sizeof(buffer),"Done Resampling in %g seconds. Computing Error...\n", time2-time1);
BufferToConsole (buffer);
}
_Parameter maxValT,
maxValE;
for (long verCount = 0; verCount < checkSteps; verCount++) {
_Parameter* inData = ((_Matrix*)tIn(verCount))->theData,
* outData = ((_Matrix*)tOut(verCount))->theData;
for (long cellCount = 0; cellCount < fullDimension; cellCount++) {
Net *thisCell = matrixNet[cellCount];
_Parameter estVal = thisCell->eval(inData)[0],
trueVal = outData[cellCount],
localError;
localError = estVal-trueVal;
if (localError < 0) {
localError = -localError;
}
if (absError < localError) {
maxValT = trueVal;
maxValE = estVal;
absError = localError;
}
}
}
DeleteObject (tObj);
tObj = _Constant(0).Time();
time1 = tObj->Value();
DeleteObject (tObj);
if (verbI > 5) {
snprintf (buffer, sizeof(buffer), "Done Error Checking in %g seconds. Got max abs error %g on the pair %g %g\n", time1-time2, absError, maxValT, maxValE);
BufferToConsole (buffer);
}
if (absError <= errorTerm) {
break;
}
}
if (absError > errorTerm) {
ReportWarning (_String("Couldn't achive desired precision in TrainModelNN. Achieved error of ") & absError);
}
fclose (varSamples);
fprintf (nnFile,"{{\n\"%s\"", LocateVar(modelVariableList.lData[0])->GetName()->getStr());
_Matrix newBounds (modelVariableList.lLength, 2, false, true);
if (vBounds(0,0)>vBounds(0,1)) {
newBounds.Store (variableMap.lData[0],0,0.);
newBounds.Store (variableMap.lData[0],1,1.);
} else {
newBounds.Store (variableMap.lData[0],0,vBounds(0,0));
newBounds.Store (variableMap.lData[0],1,vBounds(0,1));
}
for (long varCounter = 1; varCounter < modelVariableList.lLength; varCounter ++) {
fprintf (nnFile,",\n\"%s\"", LocateVar(modelVariableList.lData[varCounter])->GetName()->getStr());
if (vBounds(varCounter,0)>vBounds(varCounter,1)) {
newBounds.Store (variableMap.lData[varCounter],0,0.);
newBounds.Store (variableMap.lData[varCounter],1,1.);
} else {
newBounds.Store (variableMap.lData[varCounter],0,vBounds(varCounter,0));
newBounds.Store (variableMap.lData[varCounter],1,vBounds(varCounter,1));
}
}
fprintf (nnFile,"\n}}\n");
newBounds.toFileStr (nnFile);
for (long i2 = 0; i2 < fullDimension; i2++) {
matrixNet[i2]->save(nnFile);
delete matrixNet [i2];
}
fclose (nnFile);
delete matrixNet;
} else {
errMsg = _String ("Failed to open ") & fName & " for writing";
}
} else {
errMsg = _String ("Invalid variable bounds in row ") & (k2+1) & " of the bounds matrix";
}
} else {
errMsg = *myName & " was not one of the model parameters";
}
} else {
errMsg = *matrix & " must be a have the same number of rows as the number of model parameters";
}
} else {
errMsg = *matrix & " must be a string matrix with 3 columns";
}
} else {
errMsg = *matrix & " was not the identifier of a valid matrix variable";
}
}
if (errMsg.sLength) {
errMsg = errMsg & _String(" in call to TrainModelNN.");
WarnError (errMsg);
}
}
void _HYConsoleWindow::DoEcho (void)
{
_List menuChoices;
if (!echoFileRef)
{
menuChoices && & startEchoing;
}
else
{
menuChoices && & stopEchoing;
if (echoStatus == 0) // paused
menuChoices && & resumeEchoing;
else
menuChoices && & pauseEchoing;
}
int h,v;
_HYButtonBar * bb = (_HYButtonBar*)GetObject (2);
bb->GetButtonLoc(2,h,v,true);
_String choice = HandlePullDown (menuChoices,h,v,0);
if (choice.Equal (&startEchoing))
{
_String saveDP (dialogPrompt),
fileName;
dialogPrompt = "Echo HyPhy console to:";
fileName = WriteFileDialogInput ();
if (fileName.sLength)
{
echoFileRef = doFileOpen (fileName.sData,"w");
if (!echoFileRef)
{
fileName = _String ("File '")&fileName& "' couldn't be opened for writing.";
ProblemReport (fileName);
}
}
dialogPrompt = saveDP;
echoStatus = 1;
}
else
if (choice.Equal (&stopEchoing))
{
fclose (echoFileRef);
echoFileRef = nil;
echoStatus = 0;
}
else
if (choice.Equal (&pauseEchoing))
echoStatus = 0;
else
if (choice.Equal (&resumeEchoing))
echoStatus = 1;
bb->_UnpushButton();
_PaintStatusBar();
}
