Exemple #1
0
  //! Compute automatic stretch for a portion of the cube
  void ChipViewport::computeStretch(Stretch &stretch, bool force) {
    if (p_stretchLocked && !force) {
      stretch = *p_stretch;
    }
    else {
      Statistics stats;
      for (int line = 1; line < p_chip->Lines(); line++) {
        for (int samp = 1; samp < p_chip->Samples(); samp++) {
          double value = p_chip->GetValue(samp, line);
          stats.AddData(&value, 1);
        }
      }

      Histogram hist(stats.BestMinimum(), stats.BestMaximum());
      for (int line = 1; line <= p_chip->Lines(); line++) {
        for (int samp = 1; samp <= p_chip->Samples(); samp++) {
          double value = p_chip->GetValue(samp, line);
          hist.AddData(&value, 1);
        }
      }

      stretch.ClearPairs();
      if (hist.Percent(0.5) != hist.Percent(99.5)) {
        stretch.AddPair(hist.Percent(0.5), 0.0);
        stretch.AddPair(hist.Percent(99.5), 255.0);
      }
      else {
        stretch.AddPair(-DBL_MAX, 0.0);
        stretch.AddPair(DBL_MAX, 255.0);
      }

      *p_stretch = stretch;
    }
  }
Exemple #2
0
void IsisMain() {

    // Setup the input and output cubes
    ProcessByLine p;  // used for getting histograms from input cubes
    Cube *icube = p.SetInputCube("FROM", Isis::OneBand);
    p.SetOutputCube ("TO");

    // Histogram parameters
    UserInterface &ui = Application::GetUserInterface(); 
    double minimum = ui.GetDouble("MINPER");
    double maximum = ui.GetDouble("MAXPER");
    int increment = ui.GetInteger("INCREMENT");

    // Histograms from input cubes
    Histogram *from = icube->Histogram();
    Histogram *match = icube->Histogram();

    double fromMin = from->Percent(minimum);
    double fromMax = from->Percent(maximum);
    int fromBins = from->Bins();
    double data[fromBins];
    double slope = (fromMax - fromMin) / (fromBins - 1);

    // Set "match" to have the same data range and number of bins as "to"
    match->SetBins(fromBins);
    match->SetValidRange(fromMin, fromMax);
    for (int i = 0; i < fromBins; i++) {
        data[i] = fromMin + (slope * i);
    }
    match->AddData(data, fromBins);

		stretch.ClearPairs();
		double lastPer = from->Percent(minimum);
    stretch.AddPair(lastPer, match->Percent(minimum));
    for (double i = increment+minimum; i < maximum; i += increment) {
				double curPer = from->Percent(i);
        if (lastPer < curPer) {
						if(abs(lastPer - curPer) > DBL_EPSILON) {
  	          stretch.AddPair(curPer, match->Percent(i));
							lastPer = curPer;
						}
				}
    }
		double curPer = from->Percent(maximum);
		if (lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
			stretch.AddPair(curPer, match->Percent(maximum));
		}

    // Start the processing
    p.StartProcess(remap);
    p.EndProcess();
}
Exemple #3
0
// The input buffer has a raw 16 bit buffer but the values are still 0 to 255
void FixDns8 (Buffer &buf) {

    // Convert all 8bit image values of =255 (xFF) to 16bit NULL, count as gap
    // Convert all 8bit image values of =254 (xFE) to 16bit HIS, count as HIS
    // Convert all 8bit image values of =0 (x00) to 16bit LIS, count as NULL
    // Convert 8bit image data to 16bit by applying the LUT

    short int *raw = (short int*)(buf.RawBuffer());

    for (int i=0; i<buf.size(); i++) {

        if (raw[i] == (short int)255) {
            buf[i] = Isis::NULL8;
            gapCount[section]++;
        }
        else if (raw[i] == (short int)254) {
            buf[i] = Isis::HIGH_INSTR_SAT8;
            hisCount[section]++;
        }
        else if (raw[i] == (short int)0) {
            buf[i] = Isis::LOW_INSTR_SAT8;
            lisCount[section]++;
        }
        else { // It's valid so just run it thru the lookup table to get a 16 bit dn
            buf[i] = stretch.Map(buf[i]);
            validCount[section]++;
        }
    }
}
Exemple #4
0
// Adjust FROM histogram to resemble MATCH's histogram
void remap(vector<Buffer *> &in, vector<Buffer *> &out) {
  Buffer &from = *in[0];
  Buffer &to = *out[0];

  for(int i = 0; i < from.size(); i++) {
    to[i] = stretch.Map(from[i]);
  }
}   // end remap
Exemple #5
0
// Basic tests for the low-level SkRecord code.
DEF_TEST(Record, r) {
    SkRecord record;

    // Add a simple DrawRect command.
    SkRect rect = SkRect::MakeWH(10, 10);
    SkPaint paint;
    SkNEW_PLACEMENT_ARGS(record.append<SkRecords::DrawRect>(), SkRecords::DrawRect, (paint, rect));

    // Its area should be 100.
    AreaSummer summer;
    summer.apply(record);
    REPORTER_ASSERT(r, summer.area() == 100);

    // Scale 2x.
    Stretch stretch;
    stretch.apply(&record);

    // Now its area should be 100 + 400.
    summer.apply(record);
    REPORTER_ASSERT(r, summer.area() == 500);
}
Exemple #6
0
void IsisMain() {
  // Setup the input and output cubes along with histograms
  ProcessByLine p;
  Cube *mcube = p.SetInputCube("MATCH", Isis::OneBand);
  Histogram *match = mcube->histogram();
  p.ClearInputCubes();
  Cube *icube = p.SetInputCube("FROM", Isis::OneBand);
  Histogram *from = icube->histogram();
  p.SetOutputCube("TO");

  // Histogram specifications
  UserInterface &ui = Application::GetUserInterface();
  double minimum = ui.GetDouble("MINPER");
  double maximum = ui.GetDouble("MAXPER");

  stretch.ClearPairs();

  // CDF mode selected
  if(ui.GetString("STRETCH") == "CDF") {
    int increment = ui.GetInteger("INCREMENT");
    double lastPer = from->Percent(minimum);
    stretch.AddPair(lastPer, match->Percent(minimum));
    for(double i = increment + minimum; i < maximum; i += increment) {
      double curPer = from->Percent(i);
      if(lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
        stretch.AddPair(curPer, match->Percent(i));
        lastPer = curPer;
      }
    }
    double curPer = from->Percent(maximum);
    if(lastPer < curPer && abs(lastPer - curPer) > DBL_EPSILON) {
      stretch.AddPair(curPer, match->Percent(maximum));
    }
  }

  // Modal mode is selected
  else {
    stretch.AddPair(from->Percent(minimum), match->Percent(minimum));
    stretch.AddPair(from->Mode(), match->Mode());
    stretch.AddPair(from->Percent(maximum), match->Percent(maximum));
  }

  // Start the processing
  p.StartProcess(remap);
  p.EndProcess();
}
Exemple #7
0
// Adjust FROM cumulative distribution to be flatter
void remap(Buffer &in, Buffer &out) {
    for (int i = 0; i < in.size(); i++) {
        out[i] = stretch.Map(in[i]);
    }
}   // end remap .
Exemple #8
0
void IsisMain ()
{
    stretch.ClearPairs();

    for (int i=0; i<6; i++) {
        gapCount[i] = 0;
        suspectGapCount[i] = 0;
        invalidCount[i] = 0;
        lisCount[i] = 0;
        hisCount[i] = 0;
        validCount[i] = 0;
    }

    void TranslateHiriseEdrLabels (Filename &labelFile, Cube *);
    void SaveHiriseCalibrationData (ProcessImportPds &process, Cube *,
                                    Pvl &pdsLabel);
    void SaveHiriseAncillaryData (ProcessImportPds &process, Cube *);
    void FixDns8 (Buffer &buf);
    void FixDns16 (Buffer &buf);

    ProcessImportPds p;
    Pvl pdsLabel;
    UserInterface &ui = Application::GetUserInterface();

    // Get the input filename and make sure it is a HiRISE EDR
    Filename inFile = ui.GetFilename("FROM");
    iString id;
    bool projected;
    try {
        Pvl lab(inFile.Expanded());
        id = (string) lab.FindKeyword ("DATA_SET_ID");
        projected = lab.HasObject("IMAGE_MAP_PROJECTION");
    }
    catch (iException &e) {
        string msg = "Unable to read [DATA_SET_ID] from input file [" +
                     inFile.Expanded() + "]";
        throw iException::Message(iException::Io,msg, _FILEINFO_);
    }

    //Checks if in file is rdr
    if( projected ) {
        string msg = "[" + inFile.Name() + "] appears to be an rdr file.";
        msg += " Use pds2isis.";
        throw iException::Message(iException::User,msg, _FILEINFO_);
    }

    id.ConvertWhiteSpace();
    id.Compress();
    id.Trim(" ");
    if (id != "MRO-M-HIRISE-2-EDR-V1.0") {
        string msg = "Input file [" + inFile.Expanded() + "] does not appear to be " +
                     "in HiRISE EDR format. DATA_SET_ID is [" + id + "]";
        throw iException::Message(iException::Io,msg, _FILEINFO_);
    }

    p.SetPdsFile (inFile.Expanded(), "", pdsLabel);

    // Make sure the data we need for the BLOBs is saved by the Process
    p.SaveFileHeader();
    p.SaveDataPrefix();
    p.SaveDataSuffix();

    // Let the Process create the output file but override any commandline
    // output bit type and min/max. It has to be 16bit for the rest of hi2isis
    // to run.
    // Setting the min/max to the 16 bit min/max keeps all the dns (including
    // the 8 bit special pixels from changing their value when they are mapped
    // to the 16 bit output.
    CubeAttributeOutput &outAtt = ui.GetOutputAttribute("TO");
    outAtt.PixelType (Isis::SignedWord);
    outAtt.Minimum((double)VALID_MIN2);
    outAtt.Maximum((double)VALID_MAX2);
    Cube *ocube = p.SetOutputCube(ui.GetFilename("TO"), outAtt);
    p.StartProcess ();
    TranslateHiriseEdrLabels (inFile, ocube);

    // Pull out the lookup table so we can apply it in the second pass
    // and remove it from the labels.
    // Add the UNLUTTED keyword to the instrument group so we know
    // if the lut has been used to convert back to 14 bit data
    PvlGroup &instgrp = ocube->GetGroup("Instrument");
    PvlKeyword lutKey = instgrp["LookupTable"];
    PvlSequence lutSeq;
    lutSeq = lutKey;

    // Set up the Stretch object with the info from the lookup table
    // If the first entry is (0,0) then no lut was applied.
    if ((lutKey.IsNull()) ||
            (lutSeq.Size()==1 && lutSeq[0][0]=="0" && lutSeq[0][1]=="0")) {
        stretch.AddPair(0.0, 0.0);
        stretch.AddPair(65536.0, 65536.0);
        instgrp.AddKeyword(PvlKeyword("Unlutted","TRUE"));
        instgrp.DeleteKeyword ("LookupTable");
    }
    // The user wants it unlutted
    else if (ui.GetBoolean("UNLUT")) {
        for (int i=0; i<lutSeq.Size(); i++) {
            stretch.AddPair(i, (((double)lutSeq[i][0] + (double)lutSeq[i][1]) / 2.0));
        }
        instgrp.AddKeyword(PvlKeyword("Unlutted","TRUE"));
        instgrp.DeleteKeyword ("LookupTable");
    }
    // The user does not want the data unlutted
    else {
        stretch.AddPair(0.0, 0.0);
        stretch.AddPair(65536.0, 65536.0);
        instgrp.AddKeyword(PvlKeyword("Unlutted","FALSE"));
    }
    ocube->PutGroup(instgrp);

    // Save the calibration and ancillary data as BLOBs. Both get run thru the
    // lookup table just like the image data.
    SaveHiriseCalibrationData (p, ocube, pdsLabel);
    SaveHiriseAncillaryData (p, ocube);

    // Save off the input bit type so we know how to process it on the
    // second pass below.
    Isis::PixelType inType = p.PixelType();

    // All finished with the ImportPds object
    p.EndProcess ();


    // Make another pass thru the data using the output file in read/write mode
    // This allows us to correct gaps, remap special pixels and accumulate some
    // counts
    lsbGap = ui.GetBoolean("LSBGAP");
    ProcessByLine p2;
    string ioFile = ui.GetFilename("TO");
    CubeAttributeInput att;
    p2.SetInputCube(ioFile, att, ReadWrite);
    p2.Progress()->SetText("Converting special pixels");
    section = 4;
    p2.StartProcess((inType == Isis::UnsignedByte) ? FixDns8 : FixDns16);
    p2.EndProcess();


    // Log the results of the image conversion
    PvlGroup results("Results");
    results += PvlKeyword ("From", inFile.Expanded());

    results += PvlKeyword ("CalibrationBufferGaps", gapCount[0]);
    results += PvlKeyword ("CalibrationBufferLIS", lisCount[0]);
    results += PvlKeyword ("CalibrationBufferHIS", hisCount[0]);
    results += PvlKeyword ("CalibrationBufferPossibleGaps", suspectGapCount[0]);
    results += PvlKeyword ("CalibrationBufferInvalid", invalidCount[0]);
    results += PvlKeyword ("CalibrationBufferValid", validCount[0]);

    results += PvlKeyword ("CalibrationImageGaps", gapCount[1]);
    results += PvlKeyword ("CalibrationImageLIS", lisCount[1]);
    results += PvlKeyword ("CalibrationImageHIS", hisCount[1]);
    results += PvlKeyword ("CalibrationImagePossibleGaps", suspectGapCount[1]);
    results += PvlKeyword ("CalibrationImageInvalid", invalidCount[1]);
    results += PvlKeyword ("CalibrationImageValid", validCount[1]);

    results += PvlKeyword ("CalibrationDarkGaps", gapCount[2]);
    results += PvlKeyword ("CalibrationDarkLIS", lisCount[2]);
    results += PvlKeyword ("CalibrationDarkHIS", hisCount[2]);
    results += PvlKeyword ("CalibrationDarkPossibleGaps", suspectGapCount[2]);
    results += PvlKeyword ("CalibrationDarkInvalid", invalidCount[2]);
    results += PvlKeyword ("CalibrationDarkValid", validCount[2]);

    results += PvlKeyword ("ObservationBufferGaps", gapCount[3]);
    results += PvlKeyword ("ObservationBufferLIS", lisCount[3]);
    results += PvlKeyword ("ObservationBufferHIS", hisCount[3]);
    results += PvlKeyword ("ObservationBufferPossibleGaps", suspectGapCount[3]);
    results += PvlKeyword ("ObservationBufferInvalid", invalidCount[3]);
    results += PvlKeyword ("ObservationBufferValid", validCount[3]);

    results += PvlKeyword ("ObservationImageGaps", gapCount[4]);
    results += PvlKeyword ("ObservationImageLIS", lisCount[4]);
    results += PvlKeyword ("ObservationImageHIS", hisCount[4]);
    results += PvlKeyword ("ObservationImagePossibleGaps", suspectGapCount[4]);
    results += PvlKeyword ("ObservationImageInvalid", invalidCount[4]);
    results += PvlKeyword ("ObservationImageValid", validCount[4]);

    results += PvlKeyword ("ObservationDarkGaps", gapCount[5]);
    results += PvlKeyword ("ObservationDarkLIS", lisCount[5]);
    results += PvlKeyword ("ObservationDarkHIS", hisCount[5]);
    results += PvlKeyword ("ObservationDarkPossibleGaps", suspectGapCount[5]);
    results += PvlKeyword ("ObservationDarkInvalid", invalidCount[5]);
    results += PvlKeyword ("ObservationDarkValid", validCount[5]);

    // Write the results to the log
    Application::Log(results);

    return;
}
Exemple #9
0
void IsisMain() {
  colorOffset = 0;
  frameletLines.clear();
  outputCubes.clear();

  uveven = NULL;
  uvodd = NULL;
  viseven = NULL;
  visodd = NULL;

  ProcessImportPds p;
  Pvl pdsLab;

  UserInterface &ui = Application::GetUserInterface();
  QString fromFile = ui.GetFileName("FROM");

  flip = false;//ui.GetBoolean("FLIP");

  p.SetPdsFile(fromFile, "", pdsLab);
  ValidateInputLabels(pdsLab);
  inputCubeLines = p.Lines();

  lookupTable = Stretch();

  // read the lut if the option is on
  if(ui.GetBoolean("UNLUT") && pdsLab["LRO:LOOKUP_TABLE_TYPE"][0] == "STORED") {
    PvlKeyword lutKeyword = pdsLab["LRO:LOOKUP_CONVERSION_TABLE"];

    for(int i = 0; i < lutKeyword.size(); i ++) {
      IString lutPair = lutKeyword[i];
      lutPair.ConvertWhiteSpace();
      lutPair.Remove("() ");
      QString outValueMin = lutPair.Token(" ,").ToQt();
      QString outValueMax = lutPair.Token(" ,").ToQt();
      lookupTable.AddPair(i, (toDouble(outValueMin) + toDouble(outValueMax)) / 2.0);
    }
  }

  QString instModeId = pdsLab["INSTRUMENT_MODE_ID"];

  // this will be used to convert num input lines to num output lines,
  //   only changed for when both uv and vis exist (varying summing)
  double visOutputLineRatio = 1.0;
  double uvOutputLineRatio = 1.0;

  int numFilters = 0;
  if(ui.GetBoolean("COLOROFFSET")) {
    colorOffset = ui.GetInteger("COLOROFFSETSIZE");
  }

  // Determine our band information based on
  // INSTRUMENT_MODE_ID - FILTER_NUMBER is
  // only going to be used for BW images
  if(instModeId == "COLOR") {
    numFilters = 7;
    frameletLines.push_back(4);
    frameletLines.push_back(4);
    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);

    uveven  = new Cube();
    uvodd   = new Cube();
    viseven = new Cube();
    visodd  = new Cube();

    // 14 output lines (1 framelet) from 5vis/2uv lines
    visOutputLineRatio = 14.0 / (14.0 * 5.0 + 4.0 * 2.0);

    // 4 output lines (1 framelet) from 5vis/2uv lines
    uvOutputLineRatio = 4.0 / (14.0 * 5.0 + 4.0 * 2.0);
  }
  else if(instModeId == "VIS") {
    numFilters = 5;

    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);
    frameletLines.push_back(14);

    viseven = new Cube();
    visodd  = new Cube();

    // 14 output lines (1 framelet) from 5vis/2uv lines
    visOutputLineRatio = 14.0 / (14.0 * 5.0);
  }
  else if(instModeId == "UV") {
    numFilters = 2;

    frameletLines.push_back(4);
    frameletLines.push_back(4);

    uveven = new Cube();
    uvodd  = new Cube();

    // 4 output lines (1 framelet) from 2uv lines
    uvOutputLineRatio = 4.0 / (4.0 * 2.0);
  }
  else if(instModeId == "BW") {
    numFilters = 1;

    frameletLines.push_back(14);

    viseven = new Cube();
    visodd  = new Cube();
  }

  padding.resize(numFilters);


  for(int filter = 0; filter < numFilters; filter++) {
    padding[filter] = (colorOffset * frameletLines[filter]) * filter;

    // dont count UV for VIS offsetting
    if(instModeId == "COLOR" && filter > 1) {
      padding[filter] -= 2 * colorOffset * frameletLines[filter];
    }
  }

  FileName baseFileName(ui.GetFileName("TO"));

  if(uveven && uvodd) {
    // padding[1] is max padding for UV
    int numSamples = ((viseven) ? p.Samples() / 4 : p.Samples());
    numSamples     = 128; // UV is alway sum 4 so it is 128 samples
    int numLines   = (int)(uvOutputLineRatio * inputCubeLines + 0.5) + padding[1];
    int numBands   = 2;

    uveven->setDimensions(numSamples, numLines, numBands);
    uveven->setPixelType(Isis::Real);

    QString filename = baseFileName.path() + "/" + baseFileName.baseName() + ".uv.even.cub";
    uveven->create(filename);

    uvodd->setDimensions(numSamples, numLines, numBands);
    uvodd->setPixelType(Isis::Real);

    filename = baseFileName.path() + "/" + baseFileName.baseName() + ".uv.odd.cub";
    uvodd->create(filename);
  }

  if(viseven && visodd) {
    // padding[size-1] is max padding for vis (padding[0] or padding[4] or padding[6])
    int numSamples = p.Samples();
    int numLines   = (int)(visOutputLineRatio * inputCubeLines + 0.5) + padding[padding.size()-1];
    int numBands   = ((uveven) ? padding.size() - 2 : padding.size());

    viseven->setDimensions(numSamples, numLines, numBands);
    viseven->setPixelType(Isis::Real);

    QString filename = baseFileName.path() + "/" + baseFileName.baseName() + ".vis.even.cub";
    viseven->create(filename);

    visodd->setDimensions(numSamples, numLines, numBands);
    visodd->setPixelType(Isis::Real);

    filename = baseFileName.path() + "/" + baseFileName.baseName() + ".vis.odd.cub";
    visodd->create(filename);
  }

  Pvl isis3VisEvenLab, isis3VisOddLab, isis3UvEvenLab, isis3UvOddLab;
  TranslateLabels(pdsLab, isis3VisEvenLab, isis3VisOddLab, isis3UvEvenLab, isis3UvOddLab);

  writeNullsToFile();
  p.StartProcess(separateFramelets);
  p.EndProcess();

  // Add original labels
  OriginalLabel origLabel(pdsLab);

  int numFramelets = padding.size();
  PvlKeyword numFrameletsKeyword("NumFramelets", toString(numFramelets));

  if(uveven) {
    for(int grp = 0; grp < isis3UvEvenLab.groups(); grp++) {
      uveven->putGroup(isis3UvEvenLab.group(grp));
    }

    History history("IsisCube");
    history.AddEntry();
    uveven->write(history);
    uveven->write(origLabel);

    uveven->close();
    delete uveven;
    uveven = NULL;
  }

  if(uvodd) {
    for(int grp = 0; grp < isis3UvOddLab.groups(); grp++) {
      uvodd->putGroup(isis3UvOddLab.group(grp));
    }

    History history("IsisCube");
    history.AddEntry();
    uvodd->write(history);
    uvodd->write(origLabel);

    uvodd->close();
    delete uvodd;
    uvodd = NULL;
  }

  if(viseven) {
    for(int grp = 0; grp < isis3VisEvenLab.groups(); grp++) {
      viseven->putGroup(isis3VisEvenLab.group(grp));
    }

    History history("IsisCube");
    history.AddEntry();
    viseven->write(history);
    viseven->write(origLabel);

    viseven->close();
    delete viseven;
    viseven = NULL;
  }

  if(visodd) {
    for(int grp = 0; grp < isis3VisOddLab.groups(); grp++) {
      visodd->putGroup(isis3VisOddLab.group(grp));
    }

    History history("IsisCube");
    history.AddEntry();
    visodd->write(history);
    visodd->write(origLabel);

    visodd->close();
    delete visodd;
    visodd = NULL;
  }
}
Exemple #10
0
//! Separates each of the individual WAC framelets into the right place
void separateFramelets(Buffer &in) {
  // this is true if uv is summed and mixed with unsummed vis
  bool extractMiddleSamples = false;
  // This is the framelet set the line belongs to
  int frameletSet = 0;
  // this is the offset into the set
  int frameletSetOffset = 0;
  // this is true if framelet belongs in an even cube
  bool even = false;
  // line # in current framelet
  int frameletLineOffset = 0;
  // this is the framelet number the current line belongs in
  int framelet = getFrameletNumber(in.Line(), frameletSet, frameletSetOffset, frameletLineOffset, even);
  // this is the output file the current line belongs in
  Cube *outfile = NULL;

  // uv and vis outputs
  if(viseven && uveven) {
    if(framelet < 2 && even) {
      outfile = uveven;
      extractMiddleSamples = true;
    }
    else if(framelet < 2) {
      outfile = uvodd;
      extractMiddleSamples = true;
    }
    else if(even) {
      outfile = viseven;
    }
    else {
      outfile = visodd;
    }
  }
  // vis output
  else if(viseven) {
    if(even) {
      outfile = viseven;
    }
    else {
      outfile = visodd;
    }
  }
  // uv output
  else {
    extractMiddleSamples = true;

    if(even) {
      outfile = uveven;
    }
    else {
      outfile = uvodd;
    }
  }

  // We know our output file now, so get a linemanager for writing
  LineManager mgr(*outfile);

  // line is framelet * frameletLineOffset + frameletSetOffset
  int outLine = 1;
  int outBand = framelet + 1;

  // if both vis & uv on, outLine is a calculation based on the current line
  //   being uv or vis and the general calculation (above) does not work
  if(viseven && uveven) {
    // uv file
    if(framelet < 2) {
      outLine = frameletSet * 4 + 1 + padding[framelet];
    }
    // vis file
    else {
      outLine = frameletSet * 14 + 1 + padding[framelet];
      outBand -= 2; // uv is not in vis file
    }
  }
  // only vis on
  else if(viseven) {
    outLine = frameletSet * 14 + 1 + padding[framelet];
  }
  // only uv on
  else {
    outLine = frameletSet * 4 + 1 + padding[framelet];
  }

  if(flip) {
    outLine = outfile->lineCount() - (outLine - 1);
  }

  outLine += frameletLineOffset;

  mgr.SetLine(outLine, outBand);

  if(!extractMiddleSamples) {
    for(int i = 0; i < in.size(); i++) {
      if(i >= mgr.size()) {
        QString msg = "The input file has an unexpected number of samples";
        throw IException(IException::Unknown, msg, _FILEINFO_);
      }

      mgr[i] = lookupTable.Map(in[i]);
    }
  }
  else {
    // read middle of input...
    int startSamp = (in.size() / 2) - mgr.size() / 2;
    int endSamp = (in.size() / 2) + mgr.size() / 2;

    if(mgr.size() > in.size()) {
      QString msg = "Output number of samples calculated is invalid";
      throw IException(IException::Unknown, msg, _FILEINFO_);
    }

    for(int inputSamp = startSamp; inputSamp < endSamp; inputSamp++) {
      mgr[inputSamp - startSamp] = lookupTable.Map(in[inputSamp]);
    }
  }

  outfile->write(mgr);
}