pyKst/pykst.py

@@ -419,7 +419,6 @@ def new_spectrum(self,
                    apodize_function = 0,
                    sigma = 1.0,
                    output_type = 0,
-                   interpolate_over_holes = True,
                    name=""):
     """ Create a new Spectrum in kst.
     
@@ -437,7 +436,6 @@ def new_spectrum(self,
                     apodize_function,
                     sigma,
                     output_type,
-                    interpolate_over_holes,
                     name)
 
   def spectrum(self, name):
@@ -1862,7 +1860,6 @@ class Spectrum(Object) :
     :param apodize_function: index of the apodization function - see apodize_function()
     :param sigma: only used if gausian apodization is selected.
     :param output_type: index for the output type - see output_type()
-    :param interpolate_over_holes: interpolate over NaNs, if true.
 
     The apodize funcition is::
     
@@ -1891,7 +1888,6 @@ def __init__(self, client,
                apodize_function = 0,
                sigma = 1.0,
                output_type = 0,
-               interpolate_over_holes = True,
                name="", new=True) :
 
     Object.__init__(self,client)
@@ -1909,8 +1905,7 @@ def __init__(self, client,
                        rate_units + "," +
                        b2str(apodize_function) + "," +
                        b2str(sigma) + "," +
-                       b2str(output_type) + "," +
-                       b2str(interpolate_over_holes) + ")")
+                       b2str(output_type) + "," + ")")
 
       self.handle=self.client.send("endEdit()")
       self.handle.remove(0,self.handle.indexOf("ing ")+4)
@@ -2002,12 +1997,6 @@ def output_type(self):
     retval = self.client.send_si(self.handle, "outputTypeIndex()")
     return retval
 
-  def interpolate_over_holes(self):
-    """ replace NaNs with an interpolation, if true. """
-    retval = self.client.send_si(self.handle, "interpolateOverHoles()")
-    return retval
-
-
 # FIT ###################################################################
 class Fit(Object) :
   """ This is a class which provides some methods common to all fits """

src/libkst/editablevector.cpp

@@ -58,9 +58,10 @@ void EditableVector::setValue(const int &i, const double &val) { //sa Vector::ch
     _scalars["sum"]->setValue(_sum+val-_v[i]);
     _scalars["sumsquared"]->setValue(_sum*_sum);
     _scalars["max"]->setValue(qMax(_max,val));
-    _scalars["min"]->setValue(qMin(_min,_min));
-    double b=qMax(double(0.0),_minPos);
-    _scalars["minpos"]->setValue(qMin(_min,b));
+    _scalars["min"]->setValue(qMin(_min,val));
+    if (val>=0.0) {
+      _scalars["minpos"]->setValue(qMin(_minPos,val));
+    }
     _scalars["last"]->setValue(_v[_size-1]);
     _scalars["first"]->setValue(_v[0]);
     _v[i]=val;

src/libkst/vector.cpp

@@ -72,6 +72,9 @@ Vector::Vector(ObjectStore *store)
     _size = size;
   }
   _is_rising = false;
+  _has_nan = false;
+  _v_no_nans_dirty = true;
+  _v_no_nans_size = 0;
 
   _scalars.clear();
   _strings.clear();
@@ -156,7 +159,7 @@ double Vector::interpolate(int in_i, int ns_i) const {
   GENERATE_INTERPOLATION
 }
 
-
+/** same as above, but as a function for use in plugins, etc */
 double kstInterpolate(double *_v, int _size, int in_i, int ns_i) {
   GENERATE_INTERPOLATION
 }
@@ -193,7 +196,6 @@ double kstInterpolate(double *_v, int _size, int in_i, int ns_i) {
       }                                     \
     }
 
-
 #define GENERATE_INTERPOLATION              \
   assert(_size > 0);                        \
   /** Limits checks - optional? **/         \
@@ -244,9 +246,12 @@ double Vector::interpolateNoHoles(int in_i, int ns_i) const {
 }
 
 
+#if 0
 double kstInterpolateNoHoles(double *_v, int _size, int in_i, int ns_i) {
   GENERATE_INTERPOLATION
 }
+#endif
+
 
 #undef FIND_LEFT
 #undef FIND_RIGHT
@@ -261,6 +266,19 @@ double Vector::value(int i) const {
   return _v[i];
 }
 
+double Vector::noNanValue(int i) {
+  if (i < 0 || i >= _size) { // can't look before beginning or past end
+    return 0.0;
+  }
+  if (_has_nan) {
+    if (_v_no_nans_dirty) {
+      updateVNoNans();
+    }
+    return _v_no_nans[i];
+  }
+  return _v[i];
+}
+
 void Vector::CreateScalars(ObjectStore *store) {
   if (!_isScalarList) {
     _min = _max = _mean = _minPos = 0.0;
@@ -345,6 +363,8 @@ void Vector::updateScalars() {
   }
 }
 
+
+#if 0
 double* Vector::realloced(double *memptr, int newSize) {
   double *old = _v;
   _v = memptr;
@@ -357,14 +377,57 @@ double* Vector::realloced(double *memptr, int newSize) {
   updateScalars();
   return old;
 }
-
+#endif
 
 void Vector::setV(double *memptr, int newSize) {
   _v = memptr;
   NumNew = newSize;
   _size = newSize;
 }
 
+#define FIND_LEFT(val, idx)                 \
+    for (; idx >= 0; --idx) {               \
+      if (_v[idx] == _v[idx]) {             \
+        val = _v[idx]; break;               \
+      }                                     \
+    }
+
+#define FIND_RIGHT(val, idx)                \
+    for (; idx < _size; ++idx) {            \
+      if (_v[idx] == _v[idx]) {             \
+        val = _v[idx]; break;               \
+      }                                     \
+    }
+
+void Vector::updateVNoNans()  {
+
+  if (_size != _v_no_nans_size) {
+    kstrealloc(_v_no_nans, _size*sizeof(double));
+    _v_no_nans_size = _size;
+  }
+
+  for (int in_i = 0; in_i < _size; in_i++) {
+    if (_v[in_i] == _v[in_i]) {
+      _v_no_nans[in_i] = _v[in_i];
+    } else {
+      double left = 0., right = 0.;
+      int leftIndex = in_i, rightIndex = in_i;
+      FIND_LEFT(left, leftIndex);
+      FIND_RIGHT(right, rightIndex);
+      if (leftIndex == -1) {
+        _v_no_nans[in_i] = right;
+      } else if (rightIndex == _size) {
+        _v_no_nans[in_i] = left;
+      } else {
+        _v_no_nans[in_i] = left + (right - left) * double(in_i - leftIndex) / double(rightIndex - leftIndex);
+      }
+    }
+  }
+  _v_no_nans_dirty = false;
+}
+#undef FIND_LEFT
+#undef FIND_RIGHT
+
 
 void Vector::zero() {
   _ns_min = _ns_max = 0.0;
@@ -428,6 +491,9 @@ void Vector::internalUpdate() {
   _imax = _imin = 0;
   _nsum = 0;
 
+  _has_nan = false;
+  _v_no_nans_dirty = true;
+
   if (_size > 0) {
     _is_rising = true;
 
@@ -436,6 +502,10 @@ void Vector::internalUpdate() {
       // do nothing
     }
 
+    if (i>0) {
+      _has_nan = true;
+    }
+
     if (i == _size) { // there were no finite points:
       if (!_isScalarList) {
         _scalars["sum"]->setValue(sum);
@@ -506,6 +576,7 @@ void Vector::internalUpdate() {
         }
       } else {
         _is_rising = false;
+        _has_nan = true;
       }
     }
 
@@ -586,6 +657,16 @@ double *Vector::value() const {
   return _v;
 }
 
+double *Vector::noNanValue() {
+  if (_has_nan) {
+    if (_v_no_nans_dirty) {
+      updateVNoNans();
+    }
+    return _v_no_nans;
+  }
+  return _v;
+}
+
 
 void Vector::newSync() {
   NumNew = NumShifted = 0;

src/libkst/vector.h

@@ -41,7 +41,7 @@ class KstDataObject;
 
 // KST::interpolate is still too polluting
 KSTCORE_EXPORT double kstInterpolate(double *v, int _size, int in_i, int ns_i);
-KSTCORE_EXPORT double kstInterpolateNoHoles(double *v, int _size, int in_i, int ns_i);
+//KSTCORE_EXPORT double kstInterpolateNoHoles(double *v, int _size, int in_i, int ns_i);
 
 class Vector;
 typedef SharedPtr<Vector> VectorPtr;
@@ -77,11 +77,16 @@ class KSTCORE_EXPORT Vector : public Primitive
     /** Return V[i], interpolated/decimated to have ns_i total samples */
     double interpolate(int i, int ns_i) const;
 
-    /** Return V[i], interpolated/decimated to have ns_i total samples, without any holes */
+    /** Return V[i], interpolated/decimated to have ns_i total samples, without any NaNs */
     double interpolateNoHoles(int i, int ns_i) const;
 
     /** Return V[i] uninterpolated */
     double value(int i) const;
+    double noNanValue(int i);
+
+    /** Return a pointer to the raw vector */
+    double *value() const;
+    double *noNanValue();
 
     /** Return Minimum value in Vector */
     inline double min() const { return _min; }
@@ -139,9 +144,6 @@ class KSTCORE_EXPORT Vector : public Primitive
     /** Save vector information */
     virtual void save(QXmlStreamWriter &s);
 
-    /** Return a pointer to the raw vector */
-    double *value() const;
-
     /** access functions for _isScalarList */
     bool isScalarList() const { return _isScalarList; }
 
@@ -196,6 +198,11 @@ class KSTCORE_EXPORT Vector : public Primitive
     /** Where the vector is held */
     double *_v;
 
+    /** _v with nans removed **/
+    double *_v_no_nans;
+    bool _v_no_nans_dirty : 1;
+    int _v_no_nans_size;
+
     /** number of samples shifted since last newSync */
     int NumShifted;
 
@@ -205,6 +212,9 @@ class KSTCORE_EXPORT Vector : public Primitive
     /** is the vector monotonically rising */
     bool _is_rising : 1;
 
+    /** the vector has at least one NaN */
+    bool _has_nan : 1;
+
     /** if true then we have a scalar list and do not want to be able to
     use it in a curve, display statistics for it, etc. */
     bool _isScalarList : 1;
@@ -232,13 +242,14 @@ class KSTCORE_EXPORT Vector : public Primitive
 
     friend class DataObject;
     friend class Matrix;
-    virtual double* realloced(double *memptr, int newSize);
+    //virtual double* realloced(double *memptr, int newSize);
     virtual void setV(double *memptr, int newSize);
 
     ObjectMap<Scalar> _scalars;
     ObjectMap<String> _strings;
 
-
+private:
+    void updateVNoNans();
 };
 
 

src/libkstapp/csddialog.cpp

@@ -121,7 +121,6 @@ void CSDTab::clearTabValues() {
   _vector->clearSelection();
   _windowSize->clear();
   _FFTOptions->clearValues();
-  _FFTOptions->disableInterpolateOverHoles();
 }
 
 
@@ -140,8 +139,6 @@ CSDDialog::CSDDialog(ObjectPtr dataObject, QWidget *parent)
     configureTab(dataObject);
   }
 
-  _CSDTab->FFTOptionsWidget()->disableInterpolateOverHoles();
-
   connect(_CSDTab, SIGNAL(optionsChanged()), this, SLOT(updateButtons()));  
   connect(this, SIGNAL(editMultipleMode()), this, SLOT(editMultipleMode()));
   connect(this, SIGNAL(editSingleMode()), this, SLOT(editSingleMode()));

src/libkstapp/datawizard.cpp

@@ -1219,8 +1219,7 @@ void DataWizard::finished() {
                                 _pageDataPresentation->getFFTOptions()->rateUnits(),
                                 _pageDataPresentation->getFFTOptions()->apodizeFunction(),
                                 _pageDataPresentation->getFFTOptions()->sigma(),
-                                _pageDataPresentation->getFFTOptions()->output(),
-                                _pageDataPresentation->getFFTOptions()->interpolateOverHoles());
+                                _pageDataPresentation->getFFTOptions()->output());
 
           powerspectrum->registerChange();
           powerspectrum->unlock();

src/libkstapp/powerspectrumdialog.cpp

@@ -176,7 +176,6 @@ void PowerSpectrumDialog::configureTab(ObjectPtr object) {
     _powerSpectrumTab->FFTOptionsWidget()->setApodizeFunction(psd->apodizeFxn());
     _powerSpectrumTab->FFTOptionsWidget()->setSigma(psd->gaussianSigma());
     _powerSpectrumTab->FFTOptionsWidget()->setOutput(psd->output());
-    _powerSpectrumTab->FFTOptionsWidget()->setInterpolateOverHoles(psd->interpolateHoles());
     _powerSpectrumTab->hideCurveOptions();
     if (_editMultipleWidget) {
       PSDList objects = _document->objectStore()->getObjects<PSD>();
@@ -215,8 +214,7 @@ ObjectPtr PowerSpectrumDialog::createNewDataObject() {
                         _powerSpectrumTab->FFTOptionsWidget()->rateUnits(),
                         _powerSpectrumTab->FFTOptionsWidget()->apodizeFunction(),
                         _powerSpectrumTab->FFTOptionsWidget()->sigma(),
-                        _powerSpectrumTab->FFTOptionsWidget()->output(),
-                        _powerSpectrumTab->FFTOptionsWidget()->interpolateOverHoles());
+                        _powerSpectrumTab->FFTOptionsWidget()->output());
 
   if (DataDialog::tagStringAuto()) {
      powerspectrum->setDescriptiveName(QString());
@@ -315,7 +313,6 @@ ObjectPtr PowerSpectrumDialog::editExistingDataObject() const {
 
           const bool apodize = options->apodizeDirty() ? options->apodize() : powerspectrum->apodize();
           const bool removeMean = options->removeMeanDirty() ? options->removeMean() : powerspectrum->removeMean();
-          const bool interpolateOverHoles = options->interpolateOverHolesDirty() ? options->interpolateOverHoles() : powerspectrum->interpolateHoles();
           const bool interleavedAverage = options->interleavedAverageDirty() ? options->interleavedAverage() : powerspectrum->average();
           const int FFTLength = options->FFTLengthDirty() ? options->FFTLength() : powerspectrum->length();
           const ApodizeFunction apodizeFunction = options->apodizeFunctionDirty() ? options->apodizeFunction() : powerspectrum->apodizeFxn();
@@ -335,7 +332,6 @@ ObjectPtr PowerSpectrumDialog::editExistingDataObject() const {
           powerspectrum->setApodizeFxn(apodizeFunction);
           powerspectrum->setGaussianSigma(sigma);
           powerspectrum->setOutput(output);
-          powerspectrum->setInterpolateHoles(interpolateOverHoles);
 
           powerspectrum->registerChange();
           powerspectrum->unlock();
@@ -354,7 +350,6 @@ ObjectPtr PowerSpectrumDialog::editExistingDataObject() const {
       powerspectrum->setApodizeFxn(_powerSpectrumTab->FFTOptionsWidget()->apodizeFunction());
       powerspectrum->setGaussianSigma(_powerSpectrumTab->FFTOptionsWidget()->sigma());
       powerspectrum->setOutput(_powerSpectrumTab->FFTOptionsWidget()->output());
-      powerspectrum->setInterpolateHoles(_powerSpectrumTab->FFTOptionsWidget()->interpolateOverHoles());
       if (DataDialog::tagStringAuto()) {
         powerspectrum->setDescriptiveName(QString());
       } else {