Unverified Commit b953e984 authored by Amy Stamile's avatar Amy Stamile Committed by GitHub
Browse files

Fixed hist outputs to N/A when all DNs are special pixels (#4412) 

* Updated bad stats to NA.

* Added gtests and removed old makefile tests.

* Updated changelog.

* Addressed PR feedback
parent 6c5176f8

CHANGELOG.md

+1 −0
Original line number Diff line number Diff line
@@ -52,6 +52,7 @@ release. 
- Fixed bug where the time bias was not being added to the ephemeris times in ckwriter. [4129](https://github.com/USGS-Astrogeology/ISIS3/issues/4129)

- Fixed logging in FindFeatures where we were trying to get a non-existent Pvl group from the Pvl log. [#4375](https://github.com/USGS-Astrogeology/ISIS3/issues/4375)

- Fixed an arccos evaluating a double close to either 1, -1 when calculating the ground azimuth in camera.cpp. [#4393](https://github.com/USGS-Astrogeology/ISIS3/issues/4393)

- Fixed hist outputs to N/A when all DNs are special pixels. [#3709](https://github.com/USGS-Astrogeology/ISIS3/issues/3709)



### Changed

isis/src/base/apps/hist/hist.cpp

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#include "hist.h"



#include <QDockWidget>

#include <QMenuBar>

#include <QString>



#include "CubePlotCurve.h"

#include "Histogram.h"

#include "ImageHistogram.h"

#include "HistogramItem.h"

#include "HistogramPlotWindow.h"

#include "LineManager.h"

#include "Process.h"

#include "Progress.h"

#include "QHistogram.h"

#include "UserInterface.h"





using namespace std;



namespace Isis {



  void hist(UserInterface &ui) {

    Cube cube;

    CubeAttributeInput inAtt = ui.GetInputAttribute("FROM");

    if (inAtt.bands().size() != 0) {

      cube.setVirtualBands(inAtt.bands());

    }

    cube.open(ui.GetFileName("FROM"));

    hist(&cube, ui);

  }



  void hist(Cube *icube, UserInterface &ui) {

    Process p;



    if (!ui.WasEntered("TO") && !ui.IsInteractive()) {

      QString msg = "The [TO] parameter must be entered";

      throw IException(IException::User, msg, _FILEINFO_);

    }



    Histogram *hist;

    if (ui.WasEntered("MINIMUM") && ui.WasEntered("MAXIMUM")) {

      int nbins = 0;



      if (ui.WasEntered("NBINS")){

        nbins = ui.GetInteger("NBINS");

      }

      else {

        // Calculate bins based on data type.

        // Bin calculations are based on logic in Histogram::InitializeFromCube

        if (icube->pixelType() == UnsignedByte) {

          nbins = 256;

        }

        else if (icube->pixelType() == SignedWord ||

                 icube->pixelType() == UnsignedWord ||

                 icube->pixelType() == UnsignedInteger ||

                 icube->pixelType() == SignedInteger ||

                 icube->pixelType() == Real) {

          nbins = 65536;

        }

        else {

          IString msg = "Unsupported pixel type";

          throw IException(IException::Programmer, msg, _FILEINFO_);

        }

      }

      hist = new Histogram(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"), nbins);

    }

    else {



      if (ui.WasEntered("NBINS")){

        hist = new ImageHistogram(*icube, 1, p.Progress(), 1, 1, Null, Null, ui.GetInteger("NBINS"));

      }

      else {

        hist = new ImageHistogram(*icube, 1, p.Progress());

      }

    }



    // Setup the histogram



    // Loop and accumulate histogram

    p.Progress()->SetText("Gathering Histogram");

    p.Progress()->SetMaximumSteps(icube->lineCount());

    p.Progress()->CheckStatus();

    LineManager line(*icube);



    for (int i = 1; i <= icube->lineCount(); i++) {

      line.SetLine(i);

      icube->read(line);

      hist->AddData(line.DoubleBuffer(), line.size());

      p.Progress()->CheckStatus();

    }



    if (!ui.IsInteractive() || ui.WasEntered("TO") ) {

      // Write the results

      QString outfile = ui.GetFileName("TO");

      ofstream fout;

      fout.open(outfile.toLatin1().data());



      fout << "Cube:              " << icube->fileName() << endl;

      fout << "Band:              " << icube->bandCount() << endl;



      if(hist->ValidPixels() != 0) {

        fout << "Average:           " << hist->Average() << endl;

        fout << "Std Deviation:     " << hist->StandardDeviation() << endl;

        fout << "Variance:          " << hist->Variance() << endl;

        fout << "Median:            " << hist->Median() << endl;

        fout << "Mode:              " << hist->Mode() << endl;

        fout << "Skew:              " << hist->Skew() << endl;

        fout << "Minimum:           " << hist->Minimum() << endl;

        fout << "Maximum:           " << hist->Maximum() << endl;

      }

      else {

        fout << "Average:           " << "N/A" << endl;

        fout << "Std Deviation:     " << "N/A" << endl;

        fout << "Variance:          " << "N/A" << endl;

        fout << "Median:            " << "N/A" << endl;

        fout << "Mode:              " << "N/A" << endl;

        fout << "Skew:              " << "N/A" << endl;

        fout << "Minimum:           " << "N/A" << endl;

        fout << "Maximum:           " << "N/A" << endl;

      }



      fout << endl;

      fout << "Total Pixels:      " << hist->TotalPixels() << endl;

      fout << "Valid Pixels:      " << hist->ValidPixels() << endl;

      fout << "Pixels Below Min:  " << hist->UnderRangePixels() << endl;

      fout << "Pixels Above Max:  " << hist->OverRangePixels() << endl;

      fout << "Null Pixels:       " << hist->NullPixels() << endl;

      fout << "Lis Pixels:        " << hist->LisPixels() << endl;

      fout << "Lrs Pixels:        " << hist->LrsPixels() << endl;

      fout << "His Pixels:        " << hist->HisPixels() << endl;

      fout << "Hrs Pixels:        " << hist->HrsPixels() << endl;



      //  Write histogram in tabular format

      fout << endl;

      fout << endl;

      fout << "MinInclusive,MaxExclusive,Pixels,CumulativePixels,Percent,CumulativePercent" << endl;



      Isis::BigInt total = 0;

      double cumpct = 0.0;

      double low;

      double high;



      for (int i = 0; i < hist->Bins(); i++) {

        if (hist->BinCount(i) > 0) {

          total += hist->BinCount(i);

          double pct = (double)hist->BinCount(i) / hist->ValidPixels() * 100.;

          cumpct += pct;



          hist->BinRange(i, low, high);



          fout << low << ",";

          fout << high << ",";

          fout << hist->BinCount(i) << ",";

          fout << total << ",";

          fout << pct << ",";

          fout << cumpct << endl;

        }

      }

      fout.close();

    }

    // If we are in gui mode, create a histogram plot

    if (ui.IsInteractive()) {

      // Set the title for the dialog

      QString title;

      if (ui.WasEntered("TITLE") ) {

        title = ui.GetString("TITLE");

      }

      else {

        title = "Histogram Plot for " + FileName(ui.GetAsString("FROM")).name();

      }



      // Create the QHistogram, set the title & load the Isis::Histogram into it



      HistogramPlotWindow *plot = new HistogramPlotWindow(title.toLatin1().data(),

                                                          ui.TheGui());



      // Set the xaxis title if they entered one

      if (ui.WasEntered("XAXIS") ) {

        QString xaxis(ui.GetString("XAXIS"));

        plot->setAxisLabel(QwtPlot::xBottom, xaxis.toLatin1().data());

      }



      // Set the yLeft axis title if they entered one

      if (ui.WasEntered("FREQAXIS") ) {

        QString yaxis(ui.GetString("FREQAXIS"));

        plot->setAxisLabel(QwtPlot::yRight, yaxis.toLatin1().data());

      }



      // Set the yRight axis title if they entered one

      if (ui.WasEntered("PERCENTAXIS") ) {

        QString y2axis(ui.GetString("PERCENTAXIS") );

        plot->setAxisLabel(QwtPlot::yLeft, y2axis.toLatin1().data());

      }



      //Transfer data from histogram to the plotcurve

      QVector<QPointF> binCountData;

      QVector<QPointF> cumPctData;

      double cumpct = 0.0;

      double low;

      double high;

      for (int i = 0; i < hist->Bins(); i++) {

        if (hist->BinCount(i) > 0) {

          hist->BinRange(i, low, high);

          binCountData.append(QPointF(low, hist->BinCount(i) ) );



          double pct = (double)hist->BinCount(i) / hist->ValidPixels() * 100.0;

          cumpct += pct;

          cumPctData.append(QPointF(low, cumpct) );

        }

      }



      HistogramItem *histCurve = new HistogramItem();

      histCurve->setColor(Qt::darkCyan);

      histCurve->setTitle("Frequency");



      CubePlotCurve *cdfCurve = new CubePlotCurve(CubePlotCurve::CubeDN,

                                                  CubePlotCurve::Percentage);

      cdfCurve->setStyle(QwtPlotCurve::Lines);

      cdfCurve->setTitle("Percentage");



      QPen *pen = new QPen(Qt::red);

      pen->setWidth(2);

      histCurve->setYAxis(QwtPlot::yRight);

      cdfCurve->setYAxis(QwtPlot::yLeft);

      cdfCurve->setPen(*pen);



      QVector<QwtIntervalSample> intervals(binCountData.size() );

      for (int y = 0; y < binCountData.size(); y++) {



        intervals[y].interval = QwtInterval(binCountData[y].x(),

                                            binCountData[y].x() + hist->BinSize());



        intervals[y].value = binCountData[y].y();

      }



      QPen percentagePen(Qt::red);

      percentagePen.setWidth(2);

      cdfCurve->setColor(Qt::red);

      cdfCurve->setMarkerSymbol(QwtSymbol::NoSymbol);



      histCurve->setData(QwtIntervalSeriesData(intervals));

      cdfCurve->setData(new QwtPointSeriesData(cumPctData));



      plot->add(histCurve);

      plot->add(cdfCurve);



      QLabel *label;

      if(hist->ValidPixels() != 0) {

        label = new QLabel("  Average = " + QString::number(hist->Average()) + '\n' +

               "\n  Minimum = " + QString::number(hist->Minimum()) + '\n' +

               "\n  Maximum = " + QString::number(hist->Maximum()) + '\n' +

               "\n  Stand. Dev.= " + QString::number(hist->StandardDeviation()) + '\n' +

               "\n  Variance = " + QString::number(hist->Variance()) + '\n' +

               "\n  Median = " + QString::number(hist->Median()) + '\n' +

               "\n  Mode = " + QString::number(hist->Mode()) + '\n' +

               "\n  Skew = " + QString::number(hist->Skew()), plot);

      }

      else {

        label = new QLabel("  Average = N/A"

                           "\n\n  Minimum = N/A"

                           "\n\n  Maximum = N/A"

                           "\n\n  Stand. Dev.= N/A"

                           "\n\n  Variance = N/A"

                           "\n\n  Median = N/A"

                           "\n\n  Mode = N/A"

                           "\n\n  Skew = N/A" , plot);

      }



      plot->getDockWidget()->setWidget(label);



      plot->showWindow();

    }

    delete hist;

    p.EndProcess();

  }

}

isis/src/base/apps/hist/hist.h

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Original line number Diff line number Diff line 
#ifndef hist_h

#define hist_h



/** This is free and unencumbered software released into the public domain.



The authors of ISIS do not claim copyright on the contents of this file.

For more details about the LICENSE terms and the AUTHORS, you will

find files of those names at the top level of this repository. **/



/* SPDX-License-Identifier: CC0-1.0 */



#include "Cube.h"

#include "UserInterface.h"



namespace Isis{

  extern void hist(Cube *cube, UserInterface &ui);

  extern void hist(UserInterface &ui);

}



#endif

isis/src/base/apps/hist/main.cpp

+4 −231
Original line number Diff line number Diff line 
#define GUIHELPERS

#include "Isis.h"



#include <QDockWidget>

#include <QMenuBar>

#include <QString>



#include "CubePlotCurve.h"

#include "Histogram.h"

#include "Application.h"

#include "ImageHistogram.h"

#include "HistogramItem.h"

#include "HistogramPlotWindow.h"

#include "LineManager.h"

#include "Process.h"

#include "Progress.h"

#include "QHistogram.h"

#include "UserInterface.h"



#include "hist.h"



using namespace std;

using namespace Isis;

using namespace std;



void helperButtonCalcMinMax();
@@ -28,226 +17,10 @@ map <QString, void *> GuiHelpers() { 
  return helper;

}





void IsisMain() {

  Process p;

  Cube *icube = p.SetInputCube("FROM");



  UserInterface &ui = Application::GetUserInterface();

  if (!ui.WasEntered("TO") && !ui.IsInteractive()) {

    QString msg = "The [TO] parameter must be entered";

    throw IException(IException::User, msg, _FILEINFO_);

  }



  Histogram *hist;

  if (ui.WasEntered("MINIMUM") && ui.WasEntered("MAXIMUM")) {

    int nbins = 0;



    if (ui.WasEntered("NBINS")){

      nbins = ui.GetInteger("NBINS");

    }

    else {

      // Calculate bins based on data type.

      // Bin calculations are based on logic in Histogram::InitializeFromCube

      if (icube->pixelType() == UnsignedByte) {

        nbins = 256;

      }

      else if (icube->pixelType() == SignedWord ||

               icube->pixelType() == UnsignedWord ||

               icube->pixelType() == UnsignedInteger ||

               icube->pixelType() == SignedInteger ||

               icube->pixelType() == Real) {

        nbins = 65536;

      }

      else {

        IString msg = "Unsupported pixel type";

        throw IException(IException::Programmer, msg, _FILEINFO_);

      }

    }

    hist = new Histogram(ui.GetDouble("MINIMUM"), ui.GetDouble("MAXIMUM"), nbins);

  }

  else {



    if (ui.WasEntered("NBINS")){

      hist = new ImageHistogram(*icube, 1, p.Progress(), 1, 1, Null, Null, ui.GetInteger("NBINS"));

    }

    else {

      hist = new ImageHistogram(*icube, 1, p.Progress());

    }

  }



  // Setup the histogram



  // Loop and accumulate histogram

  p.Progress()->SetText("Gathering Histogram");

  p.Progress()->SetMaximumSteps(icube->lineCount());

  p.Progress()->CheckStatus();

  LineManager line(*icube);



  for (int i = 1; i <= icube->lineCount(); i++) {

    line.SetLine(i);

    icube->read(line);

    hist->AddData(line.DoubleBuffer(), line.size());

    p.Progress()->CheckStatus();

  }



  if (!ui.IsInteractive() || ui.WasEntered("TO") ) {

    // Write the results

    QString outfile = ui.GetFileName("TO");

    ofstream fout;

    fout.open(outfile.toLatin1().data());



    fout << "Cube:              " << ui.GetFileName("FROM") << endl;

    fout << "Band:              " << icube->bandCount() << endl;

    fout << "Average:           " << hist->Average() << endl;

    fout << "Std Deviation:     " << hist->StandardDeviation() << endl;

    fout << "Variance:          " << hist->Variance() << endl;

    fout << "Median:            " << hist->Median() << endl;

    fout << "Mode:              " << hist->Mode() << endl;

    fout << "Skew:              " << hist->Skew() << endl;

    fout << "Minimum:           " << hist->Minimum() << endl;

    fout << "Maximum:           " << hist->Maximum() << endl;

    fout << endl;

    fout << "Total Pixels:      " << hist->TotalPixels() << endl;

    fout << "Valid Pixels:      " << hist->ValidPixels() << endl;

    fout << "Pixels Below Min:  " << hist->UnderRangePixels() << endl;

    fout << "Pixels Above Max:  " << hist->OverRangePixels() << endl;

    fout << "Null Pixels:       " << hist->NullPixels() << endl;

    fout << "Lis Pixels:        " << hist->LisPixels() << endl;

    fout << "Lrs Pixels:        " << hist->LrsPixels() << endl;

    fout << "His Pixels:        " << hist->HisPixels() << endl;

    fout << "Hrs Pixels:        " << hist->HrsPixels() << endl;



    //  Write histogram in tabular format

    fout << endl;

    fout << endl;

    fout << "MinInclusive,MaxExclusive,Pixels,CumulativePixels,Percent,CumulativePercent" << endl;



    Isis::BigInt total = 0;

    double cumpct = 0.0;

    double low;

    double high;



    for (int i = 0; i < hist->Bins(); i++) {

      if (hist->BinCount(i) > 0) {

        total += hist->BinCount(i);

        double pct = (double)hist->BinCount(i) / hist->ValidPixels() * 100.;

        cumpct += pct;



        hist->BinRange(i, low, high);



        fout << low << ",";

        fout << high << ",";

        fout << hist->BinCount(i) << ",";

        fout << total << ",";

        fout << pct << ",";

        fout << cumpct << endl;

  hist(ui);

}

    }

    fout.close();

  }

  // If we are in gui mode, create a histogram plot

  if (ui.IsInteractive()) {

    // Set the title for the dialog

    QString title;

    if (ui.WasEntered("TITLE") ) {

      title = ui.GetString("TITLE");

    }

    else {

      title = "Histogram Plot for " + FileName(ui.GetAsString("FROM")).name();

    }



    // Create the QHistogram, set the title & load the Isis::Histogram into it



    HistogramPlotWindow *plot = new HistogramPlotWindow(title.toLatin1().data(),

                                                        ui.TheGui());



    // Set the xaxis title if they entered one

    if (ui.WasEntered("XAXIS") ) {

      QString xaxis(ui.GetString("XAXIS"));

      plot->setAxisLabel(QwtPlot::xBottom, xaxis.toLatin1().data());

    }



    // Set the yLeft axis title if they entered one

    if (ui.WasEntered("FREQAXIS") ) {

      QString yaxis(ui.GetString("FREQAXIS"));

      plot->setAxisLabel(QwtPlot::yRight, yaxis.toLatin1().data());

    }



    // Set the yRight axis title if they entered one

    if (ui.WasEntered("PERCENTAXIS") ) {

      QString y2axis(ui.GetString("PERCENTAXIS") );

      plot->setAxisLabel(QwtPlot::yLeft, y2axis.toLatin1().data());

    }



    //Transfer data from histogram to the plotcurve

    QVector<QPointF> binCountData;

    QVector<QPointF> cumPctData;

    double cumpct = 0.0;

    double low;

    double high;

    for (int i = 0; i < hist->Bins(); i++) {

      if (hist->BinCount(i) > 0) {

        hist->BinRange(i, low, high);

        binCountData.append(QPointF(low, hist->BinCount(i) ) );



        double pct = (double)hist->BinCount(i) / hist->ValidPixels() * 100.0;

        cumpct += pct;

        cumPctData.append(QPointF(low, cumpct) );

      }

    }



    HistogramItem *histCurve = new HistogramItem();

    histCurve->setColor(Qt::darkCyan);

    histCurve->setTitle("Frequency");



    CubePlotCurve *cdfCurve = new CubePlotCurve(CubePlotCurve::CubeDN,

                                                CubePlotCurve::Percentage);

    cdfCurve->setStyle(QwtPlotCurve::Lines);

    cdfCurve->setTitle("Percentage");



    QPen *pen = new QPen(Qt::red);

    pen->setWidth(2);

    histCurve->setYAxis(QwtPlot::yRight);

    cdfCurve->setYAxis(QwtPlot::yLeft);

    cdfCurve->setPen(*pen);



    QVector<QwtIntervalSample> intervals(binCountData.size() );

    for (int y = 0; y < binCountData.size(); y++) {



      intervals[y].interval = QwtInterval(binCountData[y].x(),

                                          binCountData[y].x() + hist->BinSize());



      intervals[y].value = binCountData[y].y();

    }



    QPen percentagePen(Qt::red);

    percentagePen.setWidth(2);

    cdfCurve->setColor(Qt::red);

    cdfCurve->setMarkerSymbol(QwtSymbol::NoSymbol);



    histCurve->setData(QwtIntervalSeriesData(intervals));

    cdfCurve->setData(new QwtPointSeriesData(cumPctData));



    plot->add(histCurve);

    plot->add(cdfCurve);



    QLabel *label = new QLabel("  Average = " + QString::number(hist->Average()) + '\n' +

           "\n  Minimum = " + QString::number(hist->Minimum()) + '\n' +

           "\n  Maximum = " + QString::number(hist->Maximum()) + '\n' +

           "\n  Stand. Dev.= " + QString::number(hist->StandardDeviation()) + '\n' +

           "\n  Variance = " + QString::number(hist->Variance()) + '\n' +

           "\n  Median = " + QString::number(hist->Median()) + '\n' +

           "\n  Mode = " + QString::number(hist->Mode()) + '\n' +

           "\n  Skew = " + QString::number(hist->Skew()), plot);

    plot->getDockWidget()->setWidget(label);



    plot->showWindow();

  }

  delete hist;

  p.EndProcess();

}





// Helper function to fill in the auto calculated min/max.

void helperButtonCalcMinMax() {

isis/src/base/apps/hist/tsts/Makefile

deleted100644 → 0
+0 −4
Original line number Diff line number Diff line 
BLANKS = "%-6s"    

LENGTH = "%-40s"



include $(ISISROOT)/make/isismake.tststree