diff --git a/src/libkstmath/psd.cpp b/src/libkstmath/psd.cpp
@@ -89,8 +89,7 @@ ScriptInterface* PSD::createScriptInterface() {
 void PSD::change(VectorPtr in_V,
                                double in_freq, bool in_average, int in_averageLen, bool in_apodize,
                                bool in_removeMean, const QString& in_VUnits, const QString& in_RUnits,
-                               ApodizeFunction in_apodizeFxn, double in_gaussianSigma, PSDType in_output,
-                               bool interpolateHoles) {
+                               ApodizeFunction in_apodizeFxn, double in_gaussianSigma, PSDType in_output) {
 
   if (in_V) {
     _inputVectors[INVECTOR] = in_V;
@@ -105,7 +104,6 @@ void PSD::change(VectorPtr in_V,
   _vectorUnits = in_VUnits;
   _rateUnits = in_RUnits;
   _Output = in_output;
-  _interpolateHoles = interpolateHoles;
   _averageLength = in_averageLen;
 
   _last_n_subsets = 0;
@@ -174,7 +172,7 @@ void PSD::internalUpdate() {
   }
   //f[0] = -1E-280; // really 0 (this shouldn't be needed...)
 
-  _psdCalculator.calculatePowerSpectrum(iv->value(), v_len, psd, _PSDLength, _RemoveMean,  _interpolateHoles, _Average, _averageLength, _Apodize, _apodizeFxn, _gaussianSigma, _Output, _Frequency);
+  _psdCalculator.calculatePowerSpectrum(iv->noNanValue(), v_len, psd, _PSDLength, _RemoveMean, _Average, _averageLength, _Apodize, _apodizeFxn, _gaussianSigma, _Output, _Frequency);
 
   _last_n_subsets = n_subsets;
   _last_n_new = 0;
@@ -221,7 +219,6 @@ void PSD::save(QXmlStreamWriter &s) {
   s.writeAttribute("removemean", QVariant(_RemoveMean).toString());
   s.writeAttribute("apodize", QVariant(_Apodize).toString());
   s.writeAttribute("apodizefunction", QString::number(_apodizeFxn));
-  s.writeAttribute("interpolateholes", QVariant(_interpolateHoles).toString());
   s.writeAttribute("vectorunits", _vectorUnits);
   s.writeAttribute("rateunits", _rateUnits);
   s.writeAttribute("outputtype", QString::number(_Output));
@@ -411,7 +408,6 @@ DataObjectPtr PSD::makeDuplicate() const {
   powerspectrum->setApodizeFxn(_apodizeFxn);
   powerspectrum->setGaussianSigma(_gaussianSigma);
   powerspectrum->setOutput(_Output);
-  powerspectrum->setInterpolateHoles(_interpolateHoles);
   if (descriptiveNameIsManual()) {
     powerspectrum->setDescriptiveName(descriptiveName());
   }
@@ -422,18 +418,6 @@ DataObjectPtr PSD::makeDuplicate() const {
 }
 
 
-bool PSD::interpolateHoles() const {
-  return _interpolateHoles;
-}
-
-
-void PSD::setInterpolateHoles(bool interpolate) {
-  if (interpolate != _interpolateHoles) {
-    _interpolateHoles = interpolate;
-  }
-  _changed = true;
-}
-
 void PSD::updateVectorLabels() {
   LabelInfo label_info;
 

diff --git a/src/libkstmath/psd.h b/src/libkstmath/psd.h
@@ -74,9 +74,6 @@ class KSTMATH_EXPORT PSD : public DataObject {
     PSDType output() const;
     void setOutput(PSDType in_output);
 
-    bool interpolateHoles() const;
-    void setInterpolateHoles(bool interpolate);
-
     virtual bool slaveVectorsUsed() const;
 
     virtual void showNewDialog();
@@ -94,7 +91,7 @@ class KSTMATH_EXPORT PSD : public DataObject {
     void change(VectorPtr in_V,
         double freq, bool average, int average_len, bool apodize, bool removeMean,
         const QString& VUnits, const QString& RUnits, ApodizeFunction in_apodizeFxn = WindowOriginal, 
-        double in_gaussianSigma = 3.0, PSDType in_output = PSDAmplitudeSpectralDensity, bool interpolateHoles = false);
+        double in_gaussianSigma = 3.0, PSDType in_output = PSDAmplitudeSpectralDensity);
     virtual void internalUpdate();
 
     void setChanged() { _changed=true;}
@@ -120,7 +117,6 @@ class KSTMATH_EXPORT PSD : public DataObject {
     bool _Apodize;
     bool _RemoveMean;
     bool _Average;
-    bool _interpolateHoles;
     PSDType _Output;
     PSDType _prevOutput;
     int _last_n_subsets;

diff --git a/src/libkstmath/psdcalculator.cpp b/src/libkstmath/psdcalculator.cpp
@@ -159,7 +159,7 @@ void PSDCalculator::updateWindowFxn(ApodizeFunction apodizeFxn, double gaussianS
 int PSDCalculator::calculatePowerSpectrum(
   double *input, int inputLen, 
   double *output, int outputLen, 
-  bool removeMean, bool interpolateHoles,
+  bool removeMean,
   bool average, int averageLen, 
   bool apodize, ApodizeFunction apodizeFxn, double gaussianSigma,
   PSDType outputType, double inputSamplingFreq) {
@@ -225,22 +225,10 @@ int PSDCalculator::calculatePowerSpectrum(
 
     // apply the PSD options (removeMean, apodize, etc.)
     // separate cases for speed- although this shouldn't really matter- the rdft should be the most time consuming step by far for any large data set.
-    if (removeMean && apodize && interpolateHoles) {
-      for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
-        _a[i_samp] = (Kst::kstInterpolateNoHoles(input, inputLen, i_samp + ioffset, inputLen) - mean)*_w[i_samp];
-      }
-    } else if (removeMean && apodize) {
+    if (removeMean && apodize) {
       for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
         _a[i_samp] = (input[i_samp + ioffset] - mean)*_w[i_samp];
       }
-    } else if (removeMean && interpolateHoles) {
-      for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
-        _a[i_samp] = Kst::kstInterpolateNoHoles(input, inputLen, i_samp + ioffset, inputLen) - mean;
-      }
-    } else if (apodize && interpolateHoles) {
-      for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
-        _a[i_samp] = Kst::kstInterpolateNoHoles(input, inputLen, i_samp + ioffset, inputLen)*_w[i_samp];
-      }
     } else if (removeMean) {
       for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
         _a[i_samp] = input[i_samp + ioffset] - mean;
@@ -249,10 +237,6 @@ int PSDCalculator::calculatePowerSpectrum(
       for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
         _a[i_samp] = input[i_samp + ioffset]*_w[i_samp];
       }
-    } else if (interpolateHoles) {
-      for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
-        _a[i_samp] = Kst::kstInterpolateNoHoles(input, inputLen, i_samp + ioffset, inputLen);
-      }
     } else {
       for (i_samp = 0; i_samp < currentCopyLen; ++i_samp) {
         _a[i_samp] = input[i_samp + ioffset];

diff --git a/src/libkstmath/psdcalculator.h b/src/libkstmath/psdcalculator.h
@@ -51,7 +51,7 @@ class PSDCalculator {
     PSDCalculator();
     ~PSDCalculator();
 
-    int calculatePowerSpectrum(double *input, int inputLen, double *output, int outputLen, bool removeMean,  bool interpolateHoles, bool average, int averageLen, bool apodize, ApodizeFunction apodizeFxn, double gaussianSigma, PSDType outputType, double inputSamplingFreq);
+    int calculatePowerSpectrum(double *input, int inputLen, double *output, int outputLen, bool removeMean, bool average, int averageLen, bool apodize, ApodizeFunction apodizeFxn, double gaussianSigma, PSDType outputType, double inputSamplingFreq);
 
     static int calculateOutputVectorLength(int inputLen, bool average, int averageLen);
 

diff --git a/src/libkstmath/psdfactory.cpp b/src/libkstmath/psdfactory.cpp
@@ -35,7 +35,7 @@ DataObjectPtr PSDFactory::generateObject(ObjectStore *store, QXmlStreamReader& x
   double frequency=1.0, gaussianSigma=1.0;
   int length=8, apodizeFunction=0, outputType=0;
   QString vectorName, vectorUnits, rateUnits, descriptiveName;
-  bool average=false, removeMean=false, apodize=false, interpolateHoles=false;
+  bool average=false, removeMean=false, apodize=false;
 
   while (!xml.atEnd()) {
       const QString n = xml.name().toString();
@@ -54,7 +54,6 @@ DataObjectPtr PSDFactory::generateObject(ObjectStore *store, QXmlStreamReader& x
         outputType = attrs.value("outputtype").toString().toInt();
 
         average = attrs.value("average").toString() == "true" ? true : false;
-        interpolateHoles = attrs.value("interpolateholes").toString() == "true" ? true : false;
         removeMean = attrs.value("removemean").toString() == "true" ? true : false;
         apodize = attrs.value("apodize").toString() == "true" ? true : false;
         if (attrs.value("descriptiveNameIsManual").toString() == "true") {
@@ -97,7 +96,7 @@ DataObjectPtr PSDFactory::generateObject(ObjectStore *store, QXmlStreamReader& x
   powerspectrum->change(vector, frequency,
         average, length, apodize, removeMean,
         vectorUnits, rateUnits, (ApodizeFunction)apodizeFunction, 
-        gaussianSigma, (PSDType)outputType, interpolateHoles);
+        gaussianSigma, (PSDType)outputType);
 
   powerspectrum->setDescriptiveName(descriptiveName);
 

diff --git a/src/plugins/dataobject/convolution/convolve/convolve.cpp b/src/plugins/dataobject/convolution/convolve/convolve.cpp
@@ -198,22 +198,22 @@ bool ConvolveSource::algorithm() {
     memset( pdResponse, 0, iLength * sizeof( double ) );
 
     for (int i = 0; i < iResponseMidpoint; i++) {
-      pdResponse[i]                           = response->value()[iResponseMidpoint+i];
-      pdResponse[iLength-iResponseMidpoint+i] = response->value()[i];
+      pdResponse[i]                           = response->noNanValue()[iResponseMidpoint+i];
+      pdResponse[iLength-iResponseMidpoint+i] = response->noNanValue()[i];
     }
 
     //
     // handle the case where the response function has an odd number of points...
     //
     if (iResponseMidpoint % 2 == 1) {
-      pdResponse[iResponseMidpoint]           = response->value()[response->length()-1];
+      pdResponse[iResponseMidpoint]           = response->noNanValue()[response->length()-1];
     }
 
     //
     // zero-pad the convolve array...
     //
     memset( pdConvolve, 0, iLength * sizeof( double ) );
-    memcpy( pdConvolve, convolve->value(), convolve->length() * sizeof( double ) );
+    memcpy( pdConvolve, convolve->noNanValue(), convolve->length() * sizeof( double ) );
 
     //
     // calculate the FFTs of the two functions...

diff --git a/src/plugins/dataobject/convolution/deconvolve/deconvolve.cpp b/src/plugins/dataobject/convolution/deconvolve/deconvolve.cpp
@@ -199,23 +199,23 @@ bool DeconvolveSource::algorithm() {
     memset( pdResponse, 0, iLength * sizeof( double ) );
 
     for ( int i=0; i < iResponseMidpoint; i++) {
-      pdResponse[i]                           = response->value()[iResponseMidpoint+i];
-      pdResponse[iLength-iResponseMidpoint+i] = response->value()[i];
+      pdResponse[i]                           = response->noNanValue()[iResponseMidpoint+i];
+      pdResponse[iLength-iResponseMidpoint+i] = response->noNanValue()[i];
     }
 
     //
     // handle the case where the response function has an odd number of points...
     //
     if (iResponseMidpoint % 2 == 1) {
-      pdResponse[iResponseMidpoint]           = response->value()[response->length()];
+      pdResponse[iResponseMidpoint]           = response->noNanValue()[response->length()];
 
     }
 
     //
     // zero-pad the convolve array...
     //
     memset( pdConvolve, 0, iLength * sizeof( double ) );
-    memcpy( pdConvolve, deconvolve->value(), deconvolve->length() * sizeof( double ) );
+    memcpy( pdConvolve, deconvolve->noNanValue(), deconvolve->length() * sizeof( double ) );
 
     //
     // calculate the FFTs of the two functions...

diff --git a/src/plugins/dataobject/correlation/autocorrelation/autocorrelation.cpp b/src/plugins/dataobject/correlation/autocorrelation/autocorrelation.cpp
@@ -174,7 +174,7 @@ bool AutoCorrelationSource::algorithm() {
     // zero-pad the two arrays...
     //
     memset( pdArrayOne, 0, iLength * sizeof( double ) );
-    memcpy( pdArrayOne, inputVector->value(), inputVector->length() * sizeof( double ) );
+    memcpy( pdArrayOne, inputVector->noNanValue(), inputVector->length() * sizeof( double ) );
 
     //
     // calculate the FFTs of the two functions...

diff --git a/src/plugins/dataobject/crossspectrum/crossspectrum.cpp b/src/plugins/dataobject/crossspectrum/crossspectrum.cpp
@@ -241,11 +241,11 @@ bool CrossSpectrumSource::algorithm() {
     for (i_samp = 0; i_samp < copyLen; ++i_samp) {
       i = ( i_samp + i_subset*xps_len )/dv0;
       mean_a += (
-        a[i_samp] = inputVectorOne->value()[i]
+        a[i_samp] = inputVectorOne->noNanValue()[i]
         );
       i = ( i_samp + i_subset*xps_len )/dv1;
       mean_b += (
-        b[i_samp] = inputVectorTwo->value()[i]
+        b[i_samp] = inputVectorTwo->noNanValue()[i]
         );
     }
     if (copyLen>1) {

diff --git a/src/plugins/dataobject/genericfilter/genericfilter.cpp b/src/plugins/dataobject/genericfilter/genericfilter.cpp
@@ -222,10 +222,13 @@ bool GenericFilterSource::algorithm() {
   double in = 0.0;
   theFilter.ConnectTo(in); // the filter keeps a pointer to "in"
   theFilter.Reset();
+
+  double *v_in = inputVector->noNanValue();
+  double *v_out = outputVector->value();
   for (int i=0; i<length; i++) {
-    in = inputVector->value()[i];
+    in = v_in[i];
     theFilter.NextTimeStep();
-    outputVector->value()[i] = theFilter.out;
+    v_out[i] = theFilter.out;
   }
 
   return true;

diff --git a/src/plugins/dataobject/interpolations/interpolations.h b/src/plugins/dataobject/interpolations/interpolations.h
@@ -58,9 +58,11 @@ bool interpolate(Kst::VectorPtr xVector,
           if (pAccel != NULL) {
             pSpline = gsl_spline_alloc( pType, iLengthData );
             if (pSpline != NULL) {
-              if (!gsl_spline_init( pSpline, xVector->value(), yVector->value(), iLengthData )) {
+              if (!gsl_spline_init( pSpline, xVector->noNanValue(), yVector->noNanValue(), iLengthData )) {
+                double *xV1 = x1Vector->noNanValue();
+                double *yVout = yOutVector->value();
                 for( int i=0; i<iLengthInterp; i++) {
-                  yOutVector->value()[i] = gsl_spline_eval( pSpline, x1Vector->value()[i], pAccel );
+                  yVout[i] = gsl_spline_eval( pSpline, xV1[i], pAccel );
                 }
 
                 bReturn = true;

diff --git a/src/plugins/dataobject/linefit/linefit.cpp b/src/plugins/dataobject/linefit/linefit.cpp
@@ -172,12 +172,17 @@ bool LineFitSource::algorithm() {
   outputVectorX->resize( 2, false );
   outputVectorY->resize( 2, false );
 
+  double* vX_in = inputVectorX->noNanValue();
+  double* vY_in = inputVectorY->noNanValue();
+  double* vX_out = outputVectorX->value();
+  double* vY_out = outputVectorY->value();
+
   if (inputVectorY->length() == 1) {
-    outputVectorX->value()[0] = inputVectorX->value()[0];
-    outputVectorX->value()[1] = inputVectorX->value()[inputVectorX->length() - 1];
-    outputVectorY->value()[0] = inputVectorY->value()[0];
-    outputVectorY->value()[1] = inputVectorY->value()[0];
-    outputScalarA->setValue( inputVectorY->value()[0] );
+    vX_out[0] = vX_in[0];
+    vX_out[1] = vX_in[inputVectorX->length() - 1];
+    vY_out[0] = vY_in[0];
+    vY_out[1] = vY_in[0];
+    outputScalarA->setValue( vY_in[0] );
     outputScalarB->setValue( 0 );
     outputScalarChi->setValue( chi2 );
     return true;
@@ -190,30 +195,30 @@ bool LineFitSource::algorithm() {
     long int idx = long(Kst::roundDouble(z));
     double skew = z - floor(z); /* [0..1] */
     long int idx2 = idx + 1;
-    sy += inputVectorY->value()[i];
+    sy += vY_in[i];
     while (idx2 >= inputVectorY->length()) {
       idx2--;
     }
-    sx += inputVectorX->value()[idx] + (inputVectorX->value()[idx2] - inputVectorX->value()[idx])*skew;
+    sx += vX_in[idx] + (vX_in[idx2] - vX_in[idx])*skew;
   }
 
   sxoss = sx / inputVectorX->length();
 
   for (i = 0; i < inputVectorX->length(); ++i) {
-    double t = inputVectorX->value()[i] - sxoss;
+    double t = vX_in[i] - sxoss;
     st2 += t * t;
-    b += t * inputVectorY->value()[i];
+    b += t * vY_in[i];
   }
 
   b /= st2;
   a = (sy - sx*b)/inputVectorX->length();
 
   /* could put goodness of fit, etc, in here */
 
-  outputVectorX->value()[0] = inputVectorX->value()[0];
-  outputVectorX->value()[1] = inputVectorX->value()[inputVectorX->length()-1];
-  outputVectorY->value()[0] = a+b*outputVectorX->value()[0];
-  outputVectorY->value()[1] = a+b*outputVectorX->value()[1];
+  vX_out[0] = vX_in[0];
+  vX_out[1] = vX_in[inputVectorX->length()-1];
+  vY_out[0] = a+b*vX_out[0];
+  vY_out[1] = a+b*vX_out[1];
 
   for (i = 0; i < inputVectorX->length(); ++i) {
     double z = xScale*i;
@@ -225,8 +230,8 @@ bool LineFitSource::algorithm() {
     while (idx2 >= inputVectorX->length()) {
       idx2--;
     }
-    newX = inputVectorX->value()[idx] + (inputVectorX->value()[idx2] - inputVectorX->value()[idx])*skew;
-    ci = inputVectorY->value()[i] - a - b*newX;
+    newX = vX_in[idx] + (vX_in[idx2] - vX_in[idx])*skew;
+    ci = vY_in[i] - a - b*newX;
     chi2 += ci*ci;
   }
 

diff --git a/src/plugins/filters/cumulativeaverage/cumulativeaverage.cpp b/src/plugins/filters/cumulativeaverage/cumulativeaverage.cpp
@@ -158,10 +158,12 @@ bool CumulativeAverageSource::algorithm() {
   /* Memory allocation */
   outputVector->resize(inputVector->length(), true);
 
-  outputVector->value()[0] = inputVector->value()[0]; // i = 1
+  double *v_in = inputVector->noNanValue();
+  double *v_out = outputVector->value();
+  v_out[0] = v_in[0]; // i = 1
 
   for (int i = 1; i < inputVector->length(); ++i) {
-    outputVector->value()[i] = (inputVector->value()[i] + (i * outputVector->value()[i-1])) / (i+1);
+    v_out[i] = (v_in[i] + (i * v_out[i-1])) / (i+1);
   }
 
   return true;

diff --git a/src/plugins/filters/cumulativesum/cumulativesum.cpp b/src/plugins/filters/cumulativesum/cumulativesum.cpp
@@ -170,10 +170,15 @@ bool CumulativeSumSource::algorithm() {
   /* Memory allocation */
   outputVector->resize(inputVector->length(), true);
 
-  outputVector->value()[0] = inputVector->value()[0];
+  double *v_in = inputVector->noNanValue();
+  double *v_out = outputVector->value();
+  double s_in = inputScalar->value();
+  int len = inputVector->length();
 
-  for (int i = 1; i < inputVector->length(); i++) {
-    outputVector->value()[i] = inputVector->value()[i]*inputScalar->value() + outputVector->value()[i-1];
+  v_out[0] = v_in[0];
+
+  for (int i = 1; i < len; i++) {
+    v_out[i] = v_in[i]*s_in + v_out[i-1];
   }
 
   return true;

diff --git a/src/plugins/filters/filters.h b/src/plugins/filters/filters.h
@@ -99,7 +99,7 @@ bool kst_pass_filter(
         if( real != NULL ) {
           work = gsl_fft_real_workspace_alloc( iLengthDataPadded );
           if( work != NULL ) {
-            memcpy( pPadded, vector->value(), iLengthData * sizeof( double ) );
+            memcpy( pPadded, vector->noNanValue(), iLengthData * sizeof( double ) );
 
             // We are going to do a cubic spline extrapolation on the data
             // to improve behavior for high pass filters.

diff --git a/src/plugins/filters/unwind/filterunwind.cpp b/src/plugins/filters/unwind/filterunwind.cpp
@@ -218,11 +218,11 @@ bool FilterUnwindSource::algorithm() {
   step *= (max-min)/100.0;
 
 
-  last_x_in = inputVector->value(0);
+  last_x_in = inputVector->noNanValue(0);
   outputVector->value()[0] = last_x_in;
 
   for (i=1; i<N; ++i) {
-    x = inputVector->value(i);
+    x = inputVector->noNanValue(i);
     if ((x>max) || (x<min)) { // invalid/spike... ignore.
       x = last_x_in;
     }

diff --git a/src/plugins/fits/common.h b/src/plugins/fits/common.h
@@ -78,24 +78,28 @@ bool precursor( Kst::VectorPtr xVector, Kst::VectorPtr yVector, Kst::VectorPtr w
     // do any necessary interpolations...
     //
         pInputs[XVALUES] = (double*)malloc(*piLength * sizeof( double ));
+
+        double *v_x = xVector->noNanValue();
+        double *v_y = yVector->noNanValue();
+
         if (xVector->length() == *piLength) {
           for( i=0; i<*piLength; i++) {
-            pInputs[XVALUES][i] = xVector->value()[i];
+            pInputs[XVALUES][i] = v_x[i];
           }
         } else {
           for( i=0; i<*piLength; i++) {
-            pInputs[XVALUES][i] = interpolate( i, *piLength, xVector->value(), xVector->length() );
+            pInputs[XVALUES][i] = interpolate( i, *piLength, v_x, xVector->length() );
           }
         }
 
         pInputs[YVALUES] = (double*)malloc(*piLength * sizeof( double ));
         if (yVector->length() == *piLength) {
           for( i=0; i<*piLength; i++) {
-            pInputs[YVALUES][i] = yVector->value()[i];
+            pInputs[YVALUES][i] = v_y[i];
           }
         } else {
           for( i=0; i<*piLength; i++) {
-            pInputs[YVALUES][i] = interpolate( i, *piLength, yVector->value(), yVector->length() );
+            pInputs[YVALUES][i] = interpolate( i, *piLength, v_y, yVector->length() );
           }
         }
 

diff --git a/src/plugins/fits/linear.h b/src/plugins/fits/linear.h
@@ -73,8 +73,8 @@ bool kstfit_linear_unweighted(
                 // fill in the matrices and vectors...
                 //
                 for( i=0; i<iLength; i++ ) {
-                  gsl_vector_set( pVectorY, i, interpolate(i, iLength, yVector->value(), yVector->length()));
-                  dXInterpolated = interpolate(i, iLength, xVector->value(), xVector->length());
+                  gsl_vector_set( pVectorY, i, interpolate(i, iLength, yVector->noNanValue(), yVector->length()));
+                  dXInterpolated = interpolate(i, iLength, xVector->noNanValue(), xVector->length());
                   for( j=0; j<iNumParams; j++ ) {
                     dX = calculate_matrix_entry( dXInterpolated, j );
                     gsl_matrix_set( pMatrixX, i, j, dX );
@@ -99,7 +99,7 @@ bool kstfit_linear_unweighted(
                             gsl_vector_get( pVectorParameters, j );
                     }
                     vectorOutYFitted->value()[i] = dY;
-                    vectorOutYResiduals->value()[i] = interpolate(i, iLength, yVector->value(), yVector->length()) - dY;
+                    vectorOutYResiduals->value()[i] = interpolate(i, iLength, yVector->noNanValue(), yVector->length()) - dY;
                   }
 
                   for( i=0; i<iNumParams; i++ ) {

diff --git a/src/plugins/fits/linear_weighted.h b/src/plugins/fits/linear_weighted.h
@@ -76,10 +76,10 @@ bool kstfit_linear_weighted(
                   // fill in the matrices and vectors...
                   //
                   for( i=0; i<iLength; i++ ) {
-                    gsl_vector_set( pVectorY, i, interpolate(i, iLength, yVector->value(), yVector->length()));
-                    gsl_vector_set( pVectorWeights, i, interpolate(i, iLength, weightsVector->value(), weightsVector->length()));
+                    gsl_vector_set( pVectorY, i, interpolate(i, iLength, yVector->noNanValue(), yVector->length()));
+                    gsl_vector_set( pVectorWeights, i, interpolate(i, iLength, weightsVector->noNanValue(), weightsVector->length()));
                     for( j=0; j<iNumParams; j++ ) {
-                      dX = calculate_matrix_entry( interpolate(i, iLength, xVector->value(), xVector->length()), j );
+                      dX = calculate_matrix_entry( interpolate(i, iLength, xVector->noNanValue(), xVector->length()), j );
                       gsl_matrix_set( pMatrixX, i, j, dX );
                     }
                   }
@@ -102,7 +102,7 @@ bool kstfit_linear_weighted(
                               gsl_vector_get( pVectorParameters, j );
                       }
                       vectorOutYFitted->value()[i] = dY;
-                      vectorOutYResiduals->value()[i] = interpolate(i, iLength, yVector->value(), yVector->length()) - dY;
+                      vectorOutYResiduals->value()[i] = interpolate(i, iLength, yVector->noNanValue(), yVector->length()) - dY;
                     }
 
                     for( i=0; i<iNumParams; i++ ) {

diff --git a/src/plugins/fits/non_linear.h b/src/plugins/fits/non_linear.h
@@ -119,24 +119,28 @@ bool kstfit_nonlinear(
     }
 
     pInputX = (double*)malloc(iLength * sizeof( double ));
+
+    double *v_x = xVector->noNanValue();
+    double *v_y = yVector->noNanValue();
+
     if (xVector->length() == iLength) {
       for( i=0; i<iLength; i++) {
-        pInputX[i] = xVector->value()[i];
+        pInputX[i] = v_x[i];
       }
     } else {
       for( i=0; i<iLength; i++) {
-        pInputX[i] = interpolate( i, iLength, xVector->value(), xVector->length() );
+        pInputX[i] = interpolate( i, iLength, v_x, xVector->length() );
       }
     }
 
     pInputY = (double*)malloc(iLength * sizeof( double ));
     if (yVector->length() == iLength) {
       for( i=0; i<iLength; i++) {
-        pInputY[i] = yVector->value()[i];
+        pInputY[i] = v_y[i];
       }
     } else {
       for( i=0; i<iLength; i++) {
-        pInputY[i] = interpolate( i, iLength, yVector->value(), yVector->length() );
+        pInputY[i] = interpolate( i, iLength, v_y, yVector->length() );
       }
     }
 

diff --git a/src/plugins/fits/non_linear_weighted.h b/src/plugins/fits/non_linear_weighted.h
@@ -121,24 +121,28 @@ bool kstfit_nonlinear_weighted(
 
     // do any necessary interpolation...
     pInputs[XVALUES] = (double*)malloc(iLength * sizeof( double ));
+
+    double *v_x = xVector->noNanValue();
+    double *v_y = yVector->noNanValue();
+
     if (xVector->length() == iLength) {
       for( i=0; i<iLength; i++) {
-        pInputs[XVALUES][i] = xVector->value()[i];
+        pInputs[XVALUES][i] = v_x[i];
       }
     } else {
       for( i=0; i<iLength; i++) {
-        pInputs[XVALUES][i] = interpolate( i, iLength, xVector->value(), xVector->length() );
+        pInputs[XVALUES][i] = interpolate( i, iLength, v_x, xVector->length() );
       }
     }
 
     pInputs[YVALUES] = (double*)malloc(iLength * sizeof( double ));
     if (yVector->length() == iLength) {
       for( i=0; i<iLength; i++) {
-        pInputs[YVALUES][i] = yVector->value()[i];
+        pInputs[YVALUES][i] = v_y[i];
       }
     } else {
       for( i=0; i<iLength; i++) {
-        pInputs[YVALUES][i] = interpolate( i, iLength, yVector->value(), yVector->length() );
+        pInputs[YVALUES][i] = interpolate( i, iLength, v_y, yVector->length() );
       }
     }
 

diff --git a/src/widgets/fftoptions.cpp b/src/widgets/fftoptions.cpp
@@ -30,7 +30,6 @@ FFTOptions::FFTOptions(QWidget *parent)
   connect(_apodize, SIGNAL(clicked()), this, SIGNAL(modified()));
   connect(_removeMean, SIGNAL(clicked()), this, SIGNAL(modified()));
   connect(_interleavedAverage, SIGNAL(clicked()), this, SIGNAL(modified()));
-  connect(_interpolateOverHoles, SIGNAL(clicked()), this, SIGNAL(modified()));
   connect(_sampleRate, SIGNAL(textChanged(QString)), this, SIGNAL(modified()));
   connect(_vectorUnits, SIGNAL(textChanged(QString)), this, SIGNAL(modified()));
   connect(_rateUnits, SIGNAL(textChanged(QString)), this, SIGNAL(modified()));
@@ -46,7 +45,6 @@ FFTOptions::FFTOptions(QWidget *parent)
   _removeMean->setProperty("si","Remo&ve mean");
   _FFTLengthLabel->setProperty("si","FFT &length: 2^");
   _interleavedAverage->setProperty("si","Interleave&d average");
-  _interpolateOverHoles->setProperty("si","Interpolate over &holes");
   TextLabel1_9_2->setProperty("si","Sa&mple rate:");
   TextLabel1_9_3->setProperty("si","Vector units:");
   TextLabel1_9_2_2->setProperty("si","Rate units:");
@@ -138,21 +136,6 @@ void FFTOptions::setRemoveMean(const bool removeMean) {
 }
 
 
-bool FFTOptions::interpolateOverHoles() const {
-  return _interpolateOverHoles->isChecked();
-}
-
-
-bool FFTOptions::interpolateOverHolesDirty() const {
-  return _interpolateOverHoles->checkState() == Qt::PartiallyChecked;
-}
-
-
-void FFTOptions::setInterpolateOverHoles(const bool interpolateOverHoles) {
-  _interpolateOverHoles->setChecked(interpolateOverHoles);
-}
-
-
 int FFTOptions::FFTLength() const {
   return _FFTLength->value();
 }
@@ -237,18 +220,11 @@ void FFTOptions::clearValues() {
   _apodize->setCheckState(Qt::PartiallyChecked);
   _interleavedAverage->setCheckState(Qt::PartiallyChecked);
   _removeMean->setCheckState(Qt::PartiallyChecked);
-  _interpolateOverHoles->setCheckState(Qt::PartiallyChecked);
   _apodizeFunction->setCurrentIndex(-1);
   _output->setCurrentIndex(-1);
 }
 
 
-void FFTOptions::disableInterpolateOverHoles() {
-  _interpolateOverHoles->setChecked(false);
-  _interpolateOverHoles->setEnabled(false);
-}
-
-
 void FFTOptions::changedApodizeFxn() {
   int gaussianIndex = 5;
   if (_apodizeFunction->itemText(0).isEmpty()) {
@@ -305,7 +281,6 @@ void FFTOptions::setWidgetDefaults() {
   dialogDefaults().setValue("spectrum/apodizeFxn", apodizeFunction());
   dialogDefaults().setValue("spectrum/gaussianSigma", sigma());
   dialogDefaults().setValue("spectrum/output", output());
-  dialogDefaults().setValue("spectrum/interpolateHoles", interpolateOverHoles());
 }
 
 // set the widget to the stored default values
@@ -320,7 +295,6 @@ void FFTOptions::loadWidgetDefaults() {
   setApodizeFunction(ApodizeFunction(dialogDefaults().value("spectrum/apodizeFxn",WindowOriginal).toInt()));
   setSigma(dialogDefaults().value("spectrum/gaussianSigma",1.0).toDouble());
   setOutput(PSDType(dialogDefaults().value("spectrum/output",PSDPowerSpectralDensity).toInt()));
-  setInterpolateOverHoles(dialogDefaults().value("spectrum/interpolateHoles",true).toInt());
 }
 
 }

diff --git a/src/widgets/fftoptions.h b/src/widgets/fftoptions.h
@@ -70,11 +70,6 @@ class KSTWIDGETS_EXPORT FFTOptions : public QWidget, public Ui::FFTOptions
     bool outputDirty() const;
     void setOutput(const PSDType output);
 
-    bool interpolateOverHoles() const;
-    bool interpolateOverHolesDirty() const;
-    void setInterpolateOverHoles(const bool interpolateOverHoles);
-
-    void disableInterpolateOverHoles();
     void clearValues();
 
     void setWidgetDefaults();

diff --git a/src/widgets/fftoptions.ui b/src/widgets/fftoptions.ui
@@ -11,7 +11,16 @@
    </rect>
   </property>
   <layout class="QGridLayout" name="gridLayout_2">
-   <property name="margin">
+   <property name="leftMargin">
+    <number>0</number>
+   </property>
+   <property name="topMargin">
+    <number>0</number>
+   </property>
+   <property name="rightMargin">
+    <number>0</number>
+   </property>
+   <property name="bottomMargin">
     <number>0</number>
    </property>
    <property name="spacing">
@@ -31,7 +40,16 @@
      <layout class="QGridLayout" name="gridLayout">
       <item row="0" column="0">
        <layout class="QGridLayout">
-        <property name="margin">
+        <property name="leftMargin">
+         <number>0</number>
+        </property>
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <property name="rightMargin">
+         <number>0</number>
+        </property>
+        <property name="bottomMargin">
          <number>0</number>
         </property>
         <item row="0" column="3">
@@ -167,7 +185,16 @@
       </item>
       <item row="1" column="0">
        <layout class="QGridLayout">
-        <property name="margin">
+        <property name="leftMargin">
+         <number>0</number>
+        </property>
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <property name="rightMargin">
+         <number>0</number>
+        </property>
+        <property name="bottomMargin">
          <number>0</number>
         </property>
         <item row="0" column="2">
@@ -218,21 +245,20 @@
           </property>
          </widget>
         </item>
-        <item row="0" column="4">
-         <widget class="QCheckBox" name="_interpolateOverHoles">
-          <property name="text">
-           <string>Interpolate over &amp;holes</string>
-          </property>
-          <property name="checked">
-           <bool>false</bool>
-          </property>
-         </widget>
-        </item>
        </layout>
       </item>
       <item row="2" column="0">
        <layout class="QHBoxLayout">
-        <property name="margin">
+        <property name="leftMargin">
+         <number>0</number>
+        </property>
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <property name="rightMargin">
+         <number>0</number>
+        </property>
+        <property name="bottomMargin">
          <number>0</number>
         </property>
         <item>
@@ -338,7 +364,16 @@
       </item>
       <item row="3" column="0">
        <layout class="QHBoxLayout">
-        <property name="margin">
+        <property name="leftMargin">
+         <number>0</number>
+        </property>
+        <property name="topMargin">
+         <number>0</number>
+        </property>
+        <property name="rightMargin">
+         <number>0</number>
+        </property>
+        <property name="bottomMargin">
          <number>0</number>
         </property>
         <item>
@@ -399,7 +434,6 @@
   <tabstop>_sigma</tabstop>
   <tabstop>_interleavedAverage</tabstop>
   <tabstop>_FFTLength</tabstop>
-  <tabstop>_interpolateOverHoles</tabstop>
   <tabstop>_sampleRate</tabstop>
   <tabstop>_vectorUnits</tabstop>
   <tabstop>_rateUnits</tabstop>

diff --git a/tests/dirfile_maker/dirfile_maker.c b/tests/dirfile_maker/dirfile_maker.c
@@ -15,14 +15,15 @@ struct DFEntryType {
   char type;
 };
 
-#define NDF 15
+#define NDF 16
 #define SCOUNT 0
 #define FCOUNT 1
 #define SINE 2
 #define SSINE 3
 #define COS 4
 #define TIME 5
-#define EXTRA 6
+#define HASNANS 6
+#define EXTRA 7
 
 struct DFEntryType df[NDF] = {
   {"scount", 1, -1, 'f'},
@@ -31,6 +32,7 @@ struct DFEntryType df[NDF] = {
   {"ssine", 1, -1, 'f'},
   {"cos", 20, -1, 'f'},
   {"time", 20, -1, 'd'},
+  {"hasnans", 20, -1, 'f'},
   {"E0", 20, -1, 'f'},
   {"E1", 20, -1, 'f'},
   {"E2", 20, -1, 'f'},
@@ -146,7 +148,20 @@ int main() {
       }
 
     }
-
+
+    /* write 'hasnans' */
+    for (i=0; i<df[HASNANS].spf; i++) {
+      dx = count*df[HASNANS].spf+i;
+      x = (double)rand()/(double)RAND_MAX;
+      if (x<0.01) {
+        x = NAN;
+      }
+      nw = write(df[HASNANS].fp, &x, sizeof(float));
+      if (nw<0) {
+        fprintf(stderr, "error writing cos\n");
+      }
+    }
+
     /* write extras */
     for (j=6; j<NDF; j++) {
       for (i=0; i<df[j].spf; i++) {