void IsisMain() {
// Open the input cube
UserInterface &ui = Application::GetUserInterface();
Filename fname = ui.GetFilename("FROM");
string name = fname.Basename();
bool rmv = ui.GetBoolean("REMOVE");
// Run a standard deviation filter on the cube
string inFile = ui.GetFilename("FROM");
string outFile = name + ".step1.cub";
string parameters = "FROM=" + inFile + " TO=" + outFile
+ " toldef=stddev flattol=10 line=9 samp=9 minimum=9 tolmin=4.0 tolmax=4.0"
+ " replace=null";
Isis::iApp ->Exec("noisefilter",parameters);
// Run a standard deviation filter on the cube
inFile = outFile;
outFile = name + ".step2.cub";
parameters = "FROM=" + inFile + " TO=" + outFile +
" toldef=stddev flattol=10 line=3 samp=3 minimum=3 tolmin=3.5 tolmax=3.5";
Isis::iApp ->Exec("noisefilter",parameters);
if (rmv) remove(inFile.c_str());
// Run a standard deviation filter on the cube
inFile = outFile;
outFile = name + ".step3.cub";
parameters = "FROM=" + inFile + " TO=" + outFile
+ " toldef=stddev flattol=10 samp=9 line=9 minimum=9 tolmin=4.0 tolmax=4.0"
+ " replace=null";
Isis::iApp ->Exec("noisefilter",parameters);
if (rmv) remove(inFile.c_str());
// Run a standard deviation filter on the cube
inFile = outFile;
outFile = name + ".step4.cub";
parameters = "FROM=" + inFile + " TO=" + outFile +
" toldef=stddev samp=3 line=3 minimum=3 tolmin=3.5 tolmax=3.5";
Isis::iApp ->Exec("noisefilter",parameters);
if (rmv) remove(inFile.c_str());
// Run a lowpass filter on the cube
inFile = outFile;
outFile = ui.GetFilename("TO");
parameters = "FROM=" + inFile + " TO=" + outFile +
" filter=outside samp=3 line=3 minimum=5 replacement=null";
Isis::iApp ->Exec("lowpass",parameters);
if (rmv) remove(inFile.c_str());
}
void IsisMain() {
//Get user parameters
UserInterface &ui = Application::GetUserInterface();
Filename inFile = ui.GetFilename("FROM");
int numberOfLines = ui.GetInteger("NL");
int lineOverlap = ui.GetInteger("OVERLAP");
//Throws exception if user is dumb
if ( lineOverlap >= numberOfLines ) {
throw iException::Message( iException::User, "The Line Overlap (OVERLAP) must be less than the Number of Lines (LN).", _FILEINFO_ );
}
//Opens the cube
Cube cube;
cube.Open( inFile.Expanded() );
//Loops through, cropping as desired
int cropNum = 1;
int startLine = 1;
bool hasReachedEndOfCube = false;
while ( startLine <= cube.Lines() && not hasReachedEndOfCube ) {
//! Sets up the proper paramaters for running the crop program
string parameters = "FROM=" + inFile.Expanded() +
" TO=" + inFile.Path() + "/" + inFile.Basename() + ".segment" + iString(cropNum) + ".cub"
+ " LINE=" + iString(startLine) + " NLINES=";
if ( startLine + numberOfLines > cube.Lines() ) {
parameters += iString( cube.Lines() - ( startLine - 1 ) );
hasReachedEndOfCube = true;
}
else {
parameters += iString(numberOfLines);
}
Isis::iApp ->Exec("crop",parameters);
//The starting line for next crop
startLine = 1 + cropNum * ( numberOfLines - lineOverlap );
cropNum++;
}
}
void IsisMain() {
// Get the list of cubes to mosaic
FileList imageList;
UserInterface &ui = Application::GetUserInterface();
imageList.Read(ui.GetFilename("FROMLIST"));
if (imageList.size() < 1) {
std::string msg = "The list file [" + ui.GetFilename("FROMLIST") +
"] does not contain any data";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Make sure the user enters a "OUTSTATS" file if the CALCULATE option
// is selected
std::string processOpt = ui.GetString("PROCESS");
if (processOpt == "CALCULATE") {
if (!ui.WasEntered("OUTSTATS")) {
std::string msg = "If the CALCULATE option is selected, you must enter";
msg += " an OUTSTATS file";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
// Make sure number of bands and projection parameters match for all cubes
for (unsigned int i=0; i<imageList.size(); i++) {
Cube cube1;
cube1.Open(imageList[i]);
g_maxBand = cube1.Bands();
for (unsigned int j=(i+1); j<imageList.size(); j++) {
Cube cube2;
cube2.Open(imageList[j]);
// Make sure number of bands match
if (g_maxBand != cube2.Bands()) {
string msg = "Number of bands do not match between cubes [" +
imageList[i] + "] and [" + imageList[j] + "]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
//Create projection from each cube
Projection *proj1 = cube1.Projection();
Projection *proj2 = cube2.Projection();
// Test to make sure projection parameters match
if (*proj1 != *proj2) {
string msg = "Mapping groups do not match between cubes [" +
imageList[i] + "] and [" + imageList[j] + "]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Read hold list if one was entered
std::vector<int> hold;
if (ui.WasEntered("HOLD")) {
FileList holdList;
holdList.Read(ui.GetFilename("HOLD"));
// Make sure each file in the holdlist matches a file in the fromlist
for (int i=0; i<(int)holdList.size(); i++) {
bool matched = false;
for (int j=0; j<(int)imageList.size(); j++) {
if (holdList[i] == imageList[j]) {
matched = true;
hold.push_back(j);
break;
}
}
if (!matched) {
std::string msg = "The hold list file [" + holdList[i] +
"] does not match a file in the from list";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Read to list if one was entered
FileList outList;
if (ui.WasEntered("TOLIST")) {
outList.Read(ui.GetFilename("TOLIST"));
// Make sure each file in the tolist matches a file in the fromlist
if (outList.size() != imageList.size()) {
std::string msg = "Each input file in the FROM LIST must have a ";
msg += "corresponding output file in the TO LIST.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Make sure that all output files do not have the same names as their
// corresponding input files
for (unsigned i = 0; i < outList.size(); i++) {
if (outList[i].compare(imageList[i]) == 0) {
std::string msg = "The to list file [" + outList[i] +
"] has the same name as its corresponding from list file.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Test to ensure sampling percent in bound
double sampPercent = ui.GetDouble("PERCENT");
if (sampPercent <= 0.0 || sampPercent > 100.0) {
string msg = "The sampling percent must be a decimal (0.0, 100.0]";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
int mincnt = ui.GetInteger("MINCOUNT");
bool wtopt = ui.GetBoolean("WEIGHT");
if (processOpt != "APPLY") {
// Loop through all the input cubes, calculating statistics for each cube to use later
iString maxCubeStr ((int)imageList.size());
for (int band=1; band<=g_maxBand; band++) {
std::vector<Statistics> statsList;
for (int img=0; img<(int)imageList.size(); img++) {
Process p;
const CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
// Add a Statistics object to the list for every band of every input cube
g_imageIndex = img;
Statistics stats = GatherStatistics(*icube, band, sampPercent, maxCubeStr);
statsList.push_back(stats);
p.EndProcess();
}
// Create a separate OverlapNormalization object for every band
OverlapNormalization *oNorm = new OverlapNormalization (statsList);
for (int h=0; h<(int)hold.size(); h++) oNorm->AddHold(hold[h]);
g_oNormList.push_back(oNorm);
}
// A list for keeping track of which input cubes are known to overlap another
std::vector<bool> doesOverlapList;
for (unsigned int i=0; i<imageList.size(); i++) doesOverlapList.push_back(false);
// Find overlapping areas and add them to the set of known overlaps for each
// band shared amongst cubes
for (unsigned int i=0; i<imageList.size(); i++){
Cube cube1;
cube1.Open(imageList[i]);
for (unsigned int j=(i+1); j<imageList.size(); j++) {
Cube cube2;
cube2.Open(imageList[j]);
iString cubeStr1 ((int)(i+1));
iString cubeStr2 ((int)(j+1));
string statMsg = "Gathering Overlap Statisitcs for Cube " +
cubeStr1 + " vs " + cubeStr2 + " of " + maxCubeStr;
// Get overlap statistics for cubes
OverlapStatistics oStats(cube1, cube2, statMsg, sampPercent);
// Only push the stats onto the oList vector if there is an overlap in at
// least one of the bands
if (oStats.HasOverlap()) {
oStats.SetMincount(mincnt);
g_overlapList.push_back(oStats);
for (int band=1; band<=g_maxBand; band++) {
// Fill wt vector with 1's if the overlaps are not to be weighted, or
// fill the vector with the number of valid pixels in each overlap
int weight = 1;
if (wtopt) weight = oStats.GetMStats(band).ValidPixels();
// Make sure overlap has at least MINCOUNT pixels and add
if (oStats.GetMStats(band).ValidPixels() >= mincnt) {
g_oNormList[band-1]->AddOverlap(oStats.GetMStats(band).X(), i,
oStats.GetMStats(band).Y(), j, weight);
doesOverlapList[i] = true;
doesOverlapList[j] = true;
}
}
}
}
}
// Print an error if one or more of the images does not overlap another
{
std::string badFiles = "";
for (unsigned int img=0; img<imageList.size(); img++) {
// Print the name of each input cube without an overlap
if (!doesOverlapList[img]) {
badFiles += "[" + imageList[img] + "] ";
}
}
if (badFiles != "") {
std::string msg = "File(s) " + badFiles;
msg += " do(es) not overlap any other input images with enough valid pixels";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
// Determine whether to calculate gains or offsets
std::string adjust = ui.GetString("ADJUST");
OverlapNormalization::SolutionType sType = OverlapNormalization::Both;
if (adjust == "CONTRAST") sType = OverlapNormalization::Gains;
if (adjust == "BRIGHTNESS") sType = OverlapNormalization::Offsets;
// Loop through each band making all necessary calculations
for (int band=0; band<g_maxBand; band++) {
g_oNormList[band]->Solve(sType);
}
}
// Print gathered statistics to the gui and the print file
int validCnt = 0;
int invalidCnt = 0;
if (processOpt != "APPLY") {
PvlGroup results("Results");
// Compute the number valid and invalid overlaps
for (unsigned int o=0; o<g_overlapList.size(); o++) {
for (int band=1; band<=g_maxBand; band++) {
if (g_overlapList[o].IsValid(band)) validCnt++;
else invalidCnt++;
}
}
results += PvlKeyword("TotalOverlaps", validCnt+invalidCnt);
results += PvlKeyword("ValidOverlaps", validCnt);
results += PvlKeyword("InvalidOverlaps", invalidCnt);
std::string weightStr = "false";
if (wtopt) weightStr = "true";
results += PvlKeyword("Weighted", weightStr);
results += PvlKeyword("MinCount", mincnt);
// Name and band modifiers for each image
for (unsigned int img=0; img<imageList.size(); img++) {
results += PvlKeyword("FileName", imageList[img]);
// Band by band statistics
for (int band=1; band<=g_maxBand; band++) {
iString mult (g_oNormList[band-1]->Gain(img));
iString base (g_oNormList[band-1]->Offset(img));
iString avg (g_oNormList[band-1]->Average(img));
iString bandNum (band);
std::string bandStr = "Band" + bandNum;
PvlKeyword bandStats(bandStr);
bandStats += mult;
bandStats += base;
bandStats += avg;
results += bandStats;
}
}
// Write the results to the log
Application::Log(results);
}
// Setup the output text file if the user requested one
if (ui.WasEntered("OUTSTATS")) {
PvlObject equ("EqualizationInformation");
PvlGroup gen("General");
gen += PvlKeyword("TotalOverlaps", validCnt+invalidCnt);
gen += PvlKeyword("ValidOverlaps", validCnt);
gen += PvlKeyword("InvalidOverlaps", invalidCnt);
std::string weightStr = "false";
if (wtopt) weightStr = "true";
gen += PvlKeyword("Weighted", weightStr);
gen += PvlKeyword("MinCount", mincnt);
equ.AddGroup(gen);
for (unsigned int img=0; img<imageList.size(); img++) {
// Format and name information
PvlGroup norm("Normalization");
norm.AddComment("Formula: newDN = (oldDN - AVERAGE) * GAIN + AVERAGE + OFFSET");
norm.AddComment("BandN = (GAIN, OFFSET, AVERAGE)");
norm += PvlKeyword("FileName", imageList[img]);
// Band by band statistics
for (int band=1; band<=g_maxBand; band++) {
iString mult (g_oNormList[band-1]->Gain(img));
iString base (g_oNormList[band-1]->Offset(img));
iString avg (g_oNormList[band-1]->Average(img));
iString bandNum (band);
std::string bandStr = "Band" + bandNum;
PvlKeyword bandStats(bandStr);
bandStats += mult;
bandStats += base;
bandStats += avg;
norm += bandStats;
}
equ.AddGroup(norm);
}
// Write the equalization and overlap statistics to the file
std::string out = Filename(ui.GetFilename("OUTSTATS")).Expanded();
std::ofstream os;
os.open(out.c_str(),std::ios::app);
Pvl p;
p.SetTerminator("");
p.AddObject(equ);
os << p << std::endl;
for (unsigned int i=0; i<g_overlapList.size(); i++) {
os << g_overlapList[i];
if (i != g_overlapList.size()-1) os << std::endl;
}
os << "End";
}
// Check for errors with the input statistics
if (processOpt == "APPLY") {
Pvl inStats (ui.GetFilename("INSTATS"));
PvlObject &equalInfo = inStats.FindObject("EqualizationInformation");
// Make sure each file in the instats matches a file in the fromlist
if (imageList.size() > (unsigned)equalInfo.Groups()-1) {
std::string msg = "Each input file in the FROM LIST must have a ";
msg += "corresponding input file in the INPUT STATISTICS.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
// Check that each file in the FROM LIST is present in the INPUT STATISTICS
for (unsigned i = 0; i < imageList.size(); i++) {
std::string fromFile = imageList[i];
bool foundFile = false;
for (int j = 1; j < equalInfo.Groups(); j++) {
PvlGroup &normalization = equalInfo.Group(j);
std::string normFile = normalization["Filename"][0];
if (fromFile == normFile) {
// Store the index in INPUT STATISTICS file corresponding to the
// current FROM LIST file
normIndices.push_back(j);
foundFile = true;
}
}
if (!foundFile) {
std::string msg = "The from list file [" + fromFile +
"] does not have any corresponding file in the stats list.";
throw iException::Message(iException::User,msg,_FILEINFO_);
}
}
}
// Apply the correction to the images if the user wants this done
if (processOpt != "CALCULATE") {
iString maxCubeStr ((int)imageList.size());
for (int img=0; img<(int)imageList.size(); img++) {
// Set up for progress bar
ProcessByLine p;
iString curCubeStr (img+1);
p.Progress()->SetText("Equalizing Cube " + curCubeStr + " of " + maxCubeStr);
// Open input cube
CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
// Establish the output file depending upon whether or not a to list
// was entered
std::string out;
if (ui.WasEntered("TOLIST")) {
out = outList[img];
}
else {
Filename file = imageList[img];
out = file.Path() + "/" + file.Basename() + ".equ." + file.Extension();
}
// Allocate output cube
CubeAttributeOutput outAtt;
p.SetOutputCube(out,outAtt,icube->Samples(),icube->Lines(),icube->Bands());
// Apply gain/offset to the image
g_imageIndex = img;
if (processOpt == "APPLY") {
// Apply correction based on pre-determined statistics information
Pvl inStats (ui.GetFilename("INSTATS"));
PvlObject &equalInfo = inStats.FindObject("EqualizationInformation");
PvlGroup &normalization = equalInfo.Group(normIndices[g_imageIndex]);
gains.clear();
offsets.clear();
avgs.clear();
// Get and store the modifiers for each band
for (int band = 1; band < normalization.Keywords(); band++) {
gains.push_back(normalization[band][0]);
offsets.push_back(normalization[band][1]);
avgs.push_back(normalization[band][2]);
}
p.StartProcess(ApplyViaFile);
}
else {
// Apply correction based on the statistics gathered in this run
p.StartProcess(ApplyViaObject);
}
p.EndProcess();
}
}
// Clean-up for batch list runs
for (unsigned int o=0; o<g_oNormList.size(); o++) delete g_oNormList[o];
g_oNormList.clear();
g_overlapList.clear();
normIndices.clear();
gains.clear();
offsets.clear();
avgs.clear();
}
void IsisMain() {
// Get the list of cubes to process
FileList imageList;
UserInterface &ui = Application::GetUserInterface();
imageList.Read(ui.GetFilename("FROMLIST"));
// Read to list if one was entered
FileList outList;
if (ui.WasEntered("TOLIST")) {
outList.Read(ui.GetFilename("TOLIST"));
}
// Check for user input errors and return the file list sorted by CCD numbers
ErrorCheck(imageList, outList);
// Adds statistics for whole and side regions of every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_s.Reset();
g_sl.Reset();
g_sr.Reset();
iString maxCube ((int)imageList.size());
iString curCube (img+1);
ProcessByLine p;
p.Progress()->SetText("Gathering Statistics for Cube " +
curCube + " of " + maxCube);
CubeAttributeInput att;
const std::string inp = imageList[img];
p.SetInputCube(inp, att);
p.StartProcess(GatherStatistics);
p.EndProcess();
g_allStats.push_back(g_s);
g_leftStats.push_back(g_sl);
g_rightStats.push_back(g_sr);
}
// Initialize the object that will calculate the gains and offsets
g_oNorm = new OverlapNormalization(g_allStats);
// Add the known overlaps between two cubes, and apply a weight to each
// overlap equal the number of pixels in the overlapping area
for (int i=0; i<(int)imageList.size()-1; i++) {
int j = i+1;
g_oNorm->AddOverlap(g_rightStats[i], i, g_leftStats[j], j,
g_rightStats[i].ValidPixels());
}
// Read in and then set the holdlist
FileList holdList;
holdList.Read(ui.GetFilename("HOLD"));
for (unsigned i=0; i<holdList.size(); i++) {
int index = -1;
for (unsigned j=0; j<imageList.size(); j++) {
std::string curName = imageList.at(j);
if (curName.compare(holdList[i]) == 0) {
index = j;
g_oNorm->AddHold(index);
}
}
}
// Attempt to solve the least squares equation
g_oNorm->Solve(OverlapNormalization::Both);
// Apply correction to the cubes if desired
bool applyopt = ui.GetBoolean("APPLY");
if (applyopt) {
// Loop through correcting the gains and offsets by line for every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_imageNum = img;
ProcessByLine p;
iString max_cube ((int)imageList.size());
iString cur_cube (img+1);
p.Progress()->SetText("Equalizing Cube " + cur_cube + " of " + max_cube);
CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
Filename file = imageList[img];
// Establish the output file depending upon whether or not a to list
// was entered
std::string out;
if (ui.WasEntered("TOLIST")) {
out = outList[img];
}
else {
Filename file = imageList[img];
out = file.Path() + "/" + file.Basename() + ".equ." + file.Extension();
}
CubeAttributeOutput outAtt;
p.SetOutputCube(out,outAtt,icube->Samples(),icube->Lines(),icube->Bands());
p.StartProcess(Apply);
p.EndProcess();
}
}
// Setup the output text file if the user requested one
if (ui.WasEntered("OUTSTATS")) {
std::string out = Filename(ui.GetFilename("OUTSTATS")).Expanded();
std::ofstream os;
os.open(out.c_str(),std::ios::app);
// Get statistics for each cube with PVL
Pvl p;
PvlObject equ("EqualizationInformation");
for (int img=0; img<(int)imageList.size(); img++) {
std::string cur = imageList[img];
PvlGroup a("Adjustment");
a += PvlKeyword("FileName", cur);
a += PvlKeyword("Average", g_oNorm->Average(img));
a += PvlKeyword("Base", g_oNorm->Offset(img));
a += PvlKeyword("Multiplier", g_oNorm->Gain(img));
equ.AddGroup(a);
}
p.AddObject(equ);
os << p << std::endl;
}
PvlGroup results ("Results");
for (int img=0; img<(int)imageList.size(); img++) {
results += PvlKeyword("FileName", imageList[img]);
results += PvlKeyword("Average", g_oNorm->Average(img));
results += PvlKeyword("Base", g_oNorm->Offset(img));
results += PvlKeyword("Multiplier", g_oNorm->Gain(img));
}
Application::Log(results);
// Clean-up for batch list runs
delete g_oNorm;
g_oNorm = NULL;
g_allStats.clear();
g_leftStats.clear();
g_rightStats.clear();
}