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treescaper.cpp
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treescaper.cpp
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//##########################################################################
//# This software is part of the Treescaper i
//# -- Version 0.1
//# Copyright (C) 2010 Wen Huang
//#
//# This program is free software; you can redistribute it and/or
//# modify it under the terms of the GNU General Public License
//# as published by the Free Software Foundation; either version 2
//# of the License, or (at your option) any later version.
//#
//# This program is distributed in the hope that it will be useful,
//# but WITHOUT ANY WARRANTY; without even the implied warranty of
//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//# GNU General Public License for more details.
//# http://www.gnu.org/copyleft/gpl.html
//##########################################################################
//#include"DIST.h"
//#include "Bipartition.h"
#include <QtCore>
#include "wdef.h"
#include "wImage.h"
#include "treescaper.h"
#include "ui_treescaper.h"
#include <iostream>
#include <fstream>
#include <sstream>
#include "wstring.h"
#include "wNLDR.h"
#include <QFile>
#include <QTextStream>
#include "wNLDRthread.h"
#include "warray.cpp"
#include "setting.h"
#include "NLDRsetting.h"
#include "QMessageBox"
#include "sys/stat.h"
#include "QFileDialog"
#include <QStringList>
#include <QString>
#include <QChar>
#include "plot2d.h"
#include "plot2d_AWTY.h"
#include <QDebug>
#include <QFileInfo>
/*
"No data in memory": empty memory
"Unweighted treeset" : Unweighted treeset in memory
"Weighted treeset" : Weighted treeset in memory
"Bipartition Matrix": Bipartitin matrix
"Covariance Matrix": Covariance matrix
"Unweighted RF-distance": Unweighted Robinson-Foulds distance
"Weighted RF-distance": Weighted Robinson-Foulds distance
"Matching-distance": Matching distance
"SPR-distance": Subtree Prune and Regraft distance
"Geodesic-distance": Geodesic distance (to do)
"File-distance": distance from load file
"File-coordinate": distance coordinates from load file
"Affinity-URF": Affinity matrix for unweighted Robinson-Foulds distance
"Affinity-RF": Affinity matrix for weighted Robinson-Foulds distance
"Affinity-match": Affinity matrix for matching distance
"Affinity-SPR": Affinity matrix for subtree prune and regraft distance
"Affinity-geodesic": Affinity matrix for geodisic distance
"Affinity-filedist": Affinity matrix for file distance
*/
namespace paras{
nldr_parameters nldrparas;
image_parameters imageparas;
String plot_type;
bool plot_makemovie;
bool is_sort_volume;
};
TreeScaper::TreeScaper(QWidget *parent, Qt::WindowFlags flags) :
QMainWindow(parent, flags),
ui(new Ui::TreeScaper)
{
#ifdef _MAC
QDir curDir("./");
QString CurrentDirName = curDir.canonicalPath();
QDir dir = QDir(QApplication::applicationDirPath());
QString ModifiedDirName = dir.canonicalPath();
QString logfileName;
if(CurrentDirName == ModifiedDirName)
{
// Running App inside Qt Creator
logfileName = CurrentDirName.append("/log.txt");
}
else
{
// Running App outside Qt Creator
dir.cdUp();
dir.cdUp();
dir.cdUp();
ModifiedDirName = dir.canonicalPath();
dir.setCurrent(ModifiedDirName);
logfileName = ModifiedDirName.append("/log.txt");
}
freopen(logfileName.toLocal8Bit().data(),"w",stdout);
setvbuf(stdout, NULL, _IONBF, 0);
#elif defined(_WINDOWS)
freopen("./log.txt","w",stdout);
#elif defined(_LINUX)
freopen("./log.txt","w",stdout);
#endif
// freopen("./log.txt","w",stdout);
// setvbuf(stdout, NULL, _IONBF, 0);
// QFileSystemWatcher * watcher = new QFileSystemWatcher(this);
// watcher->addPath("./log.txt");
// connect(watcher,SIGNAL(fileChanged(QString)),this,SLOT(HandleFileChange(QString)));
// qDebug() << "hsdf\n";//---
// setWindowFlags(Qt::CustomizeWindowHint | Qt::WindowTitleHint);//-- | Qt::WindowMinMaxButtonsHint);
ui->setupUi(this);
timer = new QTimer(this);
connect(timer,SIGNAL(timeout()),this,SLOT(timerloadlog()));
// connect(this,SIGNAL(sendplottree(const NEWICKTREE *, String)),this,SLOT(plottree(const NEWICKTREE *, String)), Qt::QueuedConnection);
connect(this,SIGNAL(sendplottree(const NEWICKTREE *, char *, bool , bool , const LabelMap *)),
this,SLOT(plottree(const NEWICKTREE *, char *, bool , bool , const LabelMap *)), Qt::QueuedConnection);
connect(&nldrthd, SIGNAL(sendbuttonvisible(int)), this, SLOT(buttonvisible(int)));
connect(&communitythd, SIGNAL(sendbuttonCommunityPlotenable(int)), this, SLOT(buttonCommunityPlotenable(int)));
// connect(ui->buttonCONVcomboBox, SIGNAL(activated(int)), this, SLOT(buttonCONVcomboBox(int)));
connect(ui->comboBoxTreeData, SIGNAL(activated(int)), this, SLOT(comboBoxTreeData(int)));
connect(ui->comboBoxCD, SIGNAL(activated(int)), this, SLOT(comboBoxCD(int)));
connect(ui->comboBoxDimNLDR, SIGNAL(activated(int)), this, SLOT(comboBoxDimNLDR(int)));
timer->start(500);
TreesData = new Trees;
initialize_paras(paras::nldrparas, paras::imageparas);
ui->pushNLDRplot->setEnabled(false);
ui->pushNLDRplottrees->setEnabled(false);
ui->pushNLDRsaveindices->setEnabled(false);
ui->comboBoxdimtype->setCurrentIndex(0);
ui->comboboxNLDRmethod->setCurrentIndex(4);
ui->comboBoxNLDRalgo->setCurrentIndex(2);
ui->textdimstart->setReadOnly(true);
ui->textdimend->setReadOnly(true);
ui->textdimdimest->setReadOnly(true);
// ui->pushDISToutput->setEnabled(false);
// ui->pushDISTcleardata->setEnabled(false);
ui->pushDISTcomm->setEnabled(false);
ui->pushCOVAcomm->setEnabled(false);
ui->labelDATAlistname->setEnabled(false);
ui->textDATAlistfile->setEnabled(false);
ui->pushDATAButtonlistbrowse->setEnabled(false);
const char *cnull = "";
QString qsnull(cnull);
ui->textBrowserNLDRlog->setHtml(qsnull);
// ui->textBrowserdimlog->setHtml(qsnull);
// ui->textBrowserDISTlog->setHtml(qsnull);
ui->textBrowserDATAlog->setHtml(qsnull);
// ui->textBrowserCONVlog->setHtml(qsnull);
ui->labelDISTaffinity->setEnabled(true);
ui->comboBoxDISTaffinity->setEnabled(true);
ui->pushDISTaffinity->setEnabled(false);
// ui->labelDISTHighfreq->setEnabled(false);
// ui->labelDISTLowfreq->setEnabled(false);
// ui->textDISThighfreq->setEnabled(false);
// ui->textDISTlowfreq->setEnabled(false);
ui->pushCOVAplotcom->setEnabled(false);
ui->pushDISTplotcom->setEnabled(false);
this->resize(800, 500);
qout = NULL;
// qout = new QDebugStream (std::cout, ui->textBrowserDATAlog,
// ui->textBrowserCONSlog,
// ui->textBrowserCONVlog,
// ui->textBrowserCOVAlog,
// ui->textBrowserDISTlog,
// ui->textBrowserdimlog,
// ui->textBrowserNLDRlog,"./log.txt");
// ui->textBrowserDATAlog->ensureCursorVisible();
// ui->textBrowserCONSlog->ensureCursorVisible();
// ui->textBrowserCONVlog->ensureCursorVisible();
// ui->textBrowserCOVAlog->ensureCursorVisible();
// ui->textBrowserDISTlog->ensureCursorVisible();
// ui->textBrowserdimlog->ensureCursorVisible();
// ui->textBrowserNLDRlog->ensureCursorVisible();
// ui->labelCOVAlambda_2->setVisible(false);
// ui->radioButtonCOVALp->setVisible(false);
// ui->radioButtonCOVALn->setVisible(false);
// ui->textCOVALfixed->setVisible(false);
// ui->labelCOVAlambda->setVisible(false);
// ui->labelCOVAfrom->setVisible(false);
// ui->textCOVALstart->setVisible(false);
// ui->labelCOVAto->setVisible(false);
// ui->textCOVALend->setVisible(false);
// ui->labelCOVAintv->setVisible(false);
// ui->textCOVALinterval->setVisible(false);
ui->labelCOVAlambda_2->setEnabled(false);
ui->radioButtonCOVALp->setEnabled(false);
ui->radioButtonCOVALn->setEnabled(false);
ui->textCOVALfixed->setEnabled(false);
ui->labelCOVAlambda->setEnabled(false);
ui->labelCOVAfrom->setEnabled(false);
ui->textCOVALstart->setEnabled(false);
ui->labelCOVAto->setEnabled(false);
ui->textCOVALend->setEnabled(false);
ui->labelCOVAintv->setEnabled(false);
ui->textCOVALinterval->setEnabled(false);
ui->labelDISTlambda_2->setEnabled(false);
ui->labelDISTfrom->setEnabled(false);
ui->textDISTLstart->setEnabled(false);
ui->labelDISTto->setEnabled(false);
ui->textDISTLend->setEnabled(false);
ui->labelDISTto_2->setEnabled(false);
ui->textDISTLinterval->setEnabled(false);
}
void TreeScaper::buttonCommunityPlotenable(int input)
{
if(input == 0)
{
ui->pushCOVAplotcom->setEnabled(false);
ui->pushDISTplotcom->setEnabled(false);
}
if(input == 1)
{
ui->pushCOVAplotcom->setEnabled(false);
ui->pushDISTplotcom->setEnabled(true);
}
if(input == 2)
{
ui->pushCOVAplotcom->setEnabled(true);
ui->pushDISTplotcom->setEnabled(false);
}
}
void TreeScaper::buttonvisible(int input)
{
ui->pushNLDRplot->setEnabled(true);
ui->pushNLDRplottrees->setEnabled(false);
ui->pushNLDRsaveindices->setEnabled(true);
}
TreeScaper::~TreeScaper()
{
if(qout != NULL)
delete qout;
delete timer;
delete TreesData;
delete [] paras::imageparas.cluster_index;
delete ui;
}
void TreeScaper::initialize_paras(nldr_parameters &nldrparas, image_parameters &imageparas)
{
QMessageBox msgBox;
//=====================load nldrparas==================
// File nldrfparas("nldrparas");
// if(!nldrfparas.is_open())
// {
// msgBox.setText("Error: Cannot open parameter file \"nldrparas\"!");
// msgBox.exec();
// return;
// }
// Array<String> nldrentries;
// String nldrelement;
// nldrfparas >> nldrelement;
// int countnldrelements = 1; // Skip newline at the end of the file
// while(! nldrfparas.is_end())
// {
// nldrentries.add(nldrelement);
// if(countnldrelements > 101)
// break;
// else
// nldrfparas >> nldrelement;
// countnldrelements += 1;
// }
ifstream nldrfparas;
nldrfparas.open("nldrparas");
if(!nldrfparas.is_open())
{
msgBox.setText("Error: Cannot open parameter file \"nldrparas\"!");
msgBox.exec();
return;
}
string nldrlinefromfile;
string nldrelementfromline;
Array<String> nldrentries;
while(getline(nldrfparas, nldrlinefromfile))
{
std::istringstream nldriss(nldrlinefromfile);
while(nldriss >> nldrelementfromline)
{
String nldrelement(nldrelementfromline.c_str());
nldrentries.add(nldrelement);
}
}
QString nldrqtstr[51];
for(int i = 0; i < 51; i++)
nldrqtstr[i] = (char *) nldrentries[2 * i + 1];
nldrparas.random_start = nldrqtstr[0].toDouble();
nldrparas.random_end = nldrqtstr[1].toDouble();
nldrparas.length_tru = nldrqtstr[2].toInt();
nldrparas.interval_tru = nldrqtstr[3].toInt();
nldrparas.length_con = nldrqtstr[4].toInt();
nldrparas.iterval_con = nldrqtstr[5].toInt();
nldrparas.KRU_LIN_e = nldrqtstr[6].toDouble();
nldrparas.KRU_LIN_max_iter = nldrqtstr[7].toInt();
nldrparas.KRU_LIN_run_time = nldrqtstr[8].toInt();
nldrparas.KRU_MAJ_e = nldrqtstr[9].toDouble();
nldrparas.KRU_MAJ_max_iter = nldrqtstr[10].toInt();
nldrparas.KRU_MAJ_run_time = nldrqtstr[11].toInt();
nldrparas.KRU_GAU_e = nldrqtstr[12].toDouble();
nldrparas.KRU_GAU_max_iter = nldrqtstr[13].toInt();
nldrparas.KRU_GAU_run_time = nldrqtstr[14].toInt();
nldrparas.KRU_STO_epochs = nldrqtstr[15].toInt();
nldrparas.KRU_STO_alpha0 = nldrqtstr[16].toDouble();
nldrparas.KRU_STO_alphan = nldrqtstr[17].toDouble();
nldrparas.NOR_MAJ_e = nldrqtstr[18].toDouble();
nldrparas.NOR_MAJ_max_iter = nldrqtstr[19].toInt();
nldrparas.NOR_MAJ_run_time = nldrqtstr[20].toInt();
nldrparas.NOR_GAU_e = nldrqtstr[21].toDouble();
nldrparas.NOR_GAU_max_iter = nldrqtstr[22].toInt();
nldrparas.NOR_GAU_run_time = nldrqtstr[23].toInt();
nldrparas.NOR_STO_epochs = nldrqtstr[24].toInt();
nldrparas.NOR_STO_alpha0 = nldrqtstr[25].toDouble();
nldrparas.NOR_STO_alphan = nldrqtstr[26].toDouble();
nldrparas.NLM_MAJ_e = nldrqtstr[27].toDouble();
nldrparas.NLM_MAJ_max_iter = nldrqtstr[28].toInt();
nldrparas.NLM_MAJ_run_time = nldrqtstr[29].toInt();
nldrparas.NLM_GAU_e = nldrqtstr[30].toDouble();
nldrparas.NLM_GAU_max_iter = nldrqtstr[31].toInt();
nldrparas.NLM_GAU_run_time = nldrqtstr[32].toInt();
nldrparas.NLM_STO_epochs = nldrqtstr[33].toInt();
nldrparas.NLM_STO_alpha0 = nldrqtstr[34].toDouble();
nldrparas.NLM_STO_alphan = nldrqtstr[35].toDouble();
nldrparas.CCA_MAJ_e = nldrqtstr[36].toDouble();
nldrparas.CCA_MAJ_max_iter = nldrqtstr[37].toInt();
nldrparas.CCA_MAJ_run_time = nldrqtstr[38].toInt();
nldrparas.CCA_MAJ_lambda0 = nldrqtstr[39].toDouble();
nldrparas.CCA_MAJ_lambdan = nldrqtstr[40].toDouble();
nldrparas.CCA_GAU_e = nldrqtstr[41].toDouble();
nldrparas.CCA_GAU_max_iter = nldrqtstr[42].toInt();
nldrparas.CCA_GAU_run_time = nldrqtstr[43].toInt();
nldrparas.CCA_GAU_lambda0 = nldrqtstr[44].toDouble();
nldrparas.CCA_GAU_lambdan = nldrqtstr[45].toDouble();
nldrparas.CCA_STO_epochs = nldrqtstr[46].toInt();
nldrparas.CCA_STO_lambda0 = nldrqtstr[47].toDouble();
nldrparas.CCA_STO_lambdan = nldrqtstr[48].toDouble();
nldrparas.CCA_STO_alpha0 = nldrqtstr[49].toDouble();
nldrparas.CCA_STO_alphan = nldrqtstr[50].toDouble();
//================plotparas========================
ifstream plotfparas;
plotfparas.open("plotparas");
if(!plotfparas.is_open())
{
msgBox.setText("Error: Cannot open parameter file \"plotparas\"!");
msgBox.exec();
return;
}
string linefromfile;
string elementfromline;
Array<String> entries;
while(getline(plotfparas, linefromfile))
{
std::istringstream iss(linefromfile);
while(iss >> elementfromline)
{
String element(elementfromline.c_str());
entries.add(element);
}
}
paras::plot_type = entries[1];
if(entries[3] == (String) "1")
paras::plot_makemovie = true;
else
paras::plot_makemovie = false;
QString qtstr(entries[5]);
imageparas.cluster_num = qtstr.toInt();
qtstr = (char *) entries[7];
if(qtstr.toInt() == 1)
paras::is_sort_volume = true;
else
paras::is_sort_volume = false;
qtstr = (char *) entries[9];
imageparas.color_type = qtstr.toInt();
qtstr = (char *) entries[11];
imageparas.outlier_e = qtstr.toDouble();
qtstr = (char *) entries[13];
imageparas.outlierpercent = qtstr.toDouble();
qtstr = (char *) entries[15];
imageparas.sep_factor = qtstr.toDouble();
qtstr = (char *) entries[17];
imageparas.point_size = qtstr.toDouble();
qtstr = (char *) entries[19];
imageparas.moviesizex = qtstr.toInt();
qtstr = (char *) entries[21];
imageparas.moviesizey = qtstr.toInt();
qtstr = (char *) entries[23];
imageparas.zoom = qtstr.toDouble();
qtstr = (char *) entries[25];
imageparas.frame_num = qtstr.toInt();
int max_index = 0;
QStringList indices, range;
QString qtelement;
for(int i = 0; i < imageparas.cluster_num; i++)
{
if(i * 2 + 27 >= entries.get_length())
{
msgBox.setText("Error: The index setting of NLDR plot is wrong, please set again.");
msgBox.exec();
return;
}
qtelement = (char *) entries[i * 2 + 27];
indices = qtelement.split(",", QString::SkipEmptyParts);
for(int j = 0; j < indices.size(); j++)
{
range = indices[j].split("-", QString::SkipEmptyParts);
for(int k = 0; k < range.size(); k++)
if(range[k].toInt() > max_index)
max_index = range[k].toInt();
}
}
imageparas.cluster_index = new int [max_index + 1];
for(int i = 0; i <= max_index; i++)
imageparas.cluster_index[i] = -1;
imageparas.index_size = max_index + 1;
for(int i = 0; i < imageparas.cluster_num; i++)
{
qtelement = (char *) entries[i * 2 + 27];
indices = qtelement.split(",", QString::SkipEmptyParts);
for(int j = 0; j < indices.size(); j++)
{
range = indices[j].split("-", QString::SkipEmptyParts);
if(range.size() == 1)
paras::imageparas.cluster_index[range[0].toInt()] = i;
else
{
for(int k = 0; k < range.size(); k = k + 2)
{
for(int h = range[k].toInt(); h <= range[k + 1].toInt(); h++)
paras::imageparas.cluster_index[h] = i;
}
}
/*for(int k = 0; k < range.size(); k = k + 2)
{
for(int h = range[k].toInt(); h <= range[k + 1].toInt(); h++)
imageparas.cluster_index[h] = i;
}*/
}
}
}
void TreeScaper::on_pushNLDRrun_clicked()
{
if(nldrthd.isRunning())
{
QMessageBox::warning(NULL, "Warning", "NLDR is running!", 0, 0);
return;
}
double **dist = NULL;
int **distint = NULL;
int size = 0;
QString qtcost = ui->comboboxNLDRmethod->currentText();
string stdcost = qtcost.toStdString();
String cost(stdcost.c_str());
if(cost == (String) "Classic Scaling")
cost = "CLASSIC_MDS";
else
if(cost == (String) "Kruskal-1")
cost = "KRUSKAL1";
else
if(cost == (String) "Normalized")
cost = "NORMALIZED";
else
if(cost == (String) "NLM")
cost = "SAMMON";
QString qtalgo = ui->comboBoxNLDRalgo->currentText();
string stdalgo = qtalgo.toStdString();
String algo(stdalgo.c_str());
if(algo == (String) "Linear Iteration MDS")
algo = "LINEAR_ITERATION";
else
if(algo == (String) "Majorization")
algo = "MAJORIZATION";
else
if(algo == (String) "Gauss Seidel")
algo = "GAUSS_SEIDEL";
else
if(algo == (String) "Stochastic")
algo = "STOCHASTIC";
else
if(algo == (String) "Metropolis")
algo = "METROPOLIS";
QString qtdim = ui->textNLDRdim->toPlainText();
string stddim = qtdim.toStdString();
String dim(stddim.c_str());
QString qtflag = ui->textNLDRflag->toPlainText();
string stdflag = qtflag.toStdString();
String flag(stdflag.c_str());
QString qtinit = ui->comboBoxNLDRinit->currentText();
string stdinit = qtinit.toStdString();
String init(stdinit.c_str());
if(init == (String) "Random")
init = "RAND";
else
init = "CLASSIC_MDS";
QString qtseed = ui->textNLDRrandseed->toPlainText();
int seed = qtseed.toInt();
if(nldrthd.isRunning())
{
cout << "Warning: NLDR is running already!\n\n";
return;
}
QString qtNLDRdata = ui->comboBoxNLDRdata->currentText();
string stdNLDRdata = qtNLDRdata.toStdString();
String NLDRdata(stdNLDRdata.c_str());
QString qtfname = ui->textDATAfile->toPlainText();
string stdfname = qtfname.toStdString();
// Choose Directory
string rawfilename = stdfname.substr(stdfname.find_last_of("/") + 1);
QString dir = QFileDialog::getExistingDirectory(this, tr("Open Directory"), "", QFileDialog::ShowDirsOnly | QFileDialog::DontResolveSymlinks);
string dirfname = dir.toStdString();
if(dirfname.empty()) // cancel
return;
dirfname.append("/");
dirfname.append(rawfilename);
String fname(dirfname.c_str());
File file(fname);
CORplot = file.prefix_name_lastof();
size = TreesData->Get_n_trees();
if(NLDRdata == (String) "Unweighted RF-distance")
{
dist = TreesData->GetdistURF();
CORplot += "_URF";
} else if(NLDRdata == (String) "Weighted RF-distance")
{
dist = TreesData->GetdistRF();
CORplot += "_RF";
} else if(NLDRdata == (String) "Matching-distance")
{
distint = TreesData->GetdistMatch();
CORplot += "_Match";
} else if(NLDRdata == (String) "SPR-distance")
{
distint = TreesData->GetdistSPR();
CORplot += "_SPR";
}
else if(NLDRdata == (String) "Geodesic-distance")
{
dist = TreesData->GetdistGeo();
CORplot += "_Geo";
} else if(NLDRdata == (String) "File-distance")
{
dist = TreesData->GetdistFile();
size = TreesData->Get_filedistsize();
QString qtdistfname = ui->textDISTfile_2->toPlainText();
string stddistfname = qtdistfname.toStdString();
// Save files in chosen directory
string rawdistfilename = stddistfname.substr(stddistfname.find_last_of("/") + 1);
string dirdistfname = dirfname.substr(0, dirfname.find_last_of("/"));
dirdistfname.append("/");
dirdistfname.append(rawdistfilename);
String fdistname(dirdistfname.c_str());
fname = fdistname;
File filedist(fdistname);
CORplot = filedist.prefix_name_lastof();
} else
{
cout << "Warning: There is no distance matrix in memory!\n\n";
return;
}
if(NLDRdata == (String) "Matching-distance"
|| NLDRdata == (String) "SPR-distance")
{
dist = new double *[size];
for(int i = 0; i < size; i++)
dist[i] = new double [size];
for(int i = 0; i < size; i++)
for(int j = 0; j <= i; j++)
{
dist[i][j] = (double) distint[i][j];
dist[j][i] = dist[i][j];
}
}
/*
QString qttttfname = ui->textNLDRfile->toPlainText();
string stdtttfname = qttttfname.toStdString();
String ftttname(stdtttfname.c_str());
File tttfile(ftttname);
if(! tttfile.is_open())
{
cout << "error: can not open the data file!" << endl;
return;
}
nldrthd.initialization(ftttname, (double **) NULL, 0, dim, cost, algo, init, flag, seed, paras::nldrparas);
*/
cout << "\nRunning NLDR..." << endl;
nldrthd.initialization(CORplot, dist, size, dim, cost, algo, init, flag, seed, paras::nldrparas);
nldrthd.start();
CORplot += "_";
CORplot += dim;
CORplot += "D_";
CORplot += cost;
CORplot += "_COR_";
CORplot += algo;
CORplot += ".out";
if(NLDRdata == (String) "Matching-distance"
|| NLDRdata == (String) "SPR-distance")
{
for(int i = 0; i < size; i++)
delete [] dist[i];
delete [] dist;
}
}
void TreeScaper::on_pushNLDRclear_clicked()
{
File fout("log.txt");
fout.clean();
fout.close();
ui->textBrowserDATAlog->setText("");
// ui->textBrowserCONSlog->setText("");
// ui->textBrowserCONVlog->setText("");
ui->textBrowserCOVAlog->setText("");
// ui->textBrowserDISTlog->setText("");
// ui->textBrowserdimlog->setText("");
ui->textBrowserNLDRlog->setText("");
}
void TreeScaper::timerloadlog()
{
char element;
String line;
Array<String> lines;
int length = 0;
String logtext;
struct stat fstat;
stat("log.txt",&fstat);
#ifdef _LINUX
static long prensec = 0;
static long presec = 0;
if(prensec == fstat.st_mtim.tv_nsec && presec == fstat.st_mtim.tv_sec)
return;
prensec = fstat.st_mtim.tv_nsec;
presec = fstat.st_mtim.tv_sec;
#endif
#ifdef _MAC
static long prensec = 0;
if(prensec == (long) fstat.st_size)
return;
prensec = (long) fstat.st_size;
#endif
#ifdef _WINDOWS
static long prensec = 0;
static long presec = 0;
if(prensec == fstat.st_mtime && presec == fstat.st_size)
return;
prensec = fstat.st_mtime;
presec = fstat.st_size;
#endif
fstream file("log.txt", ios::out | ios::in);
while(file.get(element))
{
if(element != '\n' && element != 13)
line.add(element);
if((element == '\n' || element == 13))
{
if(line != EMPTY_STRING)
{
lines.add(line);
line = EMPTY_STRING;
}
else
lines.add("\n");
}
}
length = lines.get_length();
for(int i = 0; i < length; i++)
{
logtext += lines[i];//--[length - 1 - i];
logtext += "<br>";
}
const char *str = logtext;
QString qtlogtext(str);
// ui->textBrowserNLDRlog->setHtml(qtlogtext);
// ui->textBrowserdimlog->setHtml(qtlogtext);
// ui->textBrowserDISTlog->setHtml(qtlogtext);
// ui->textBrowserDATAlog->setHtml(qtlogtext);
ui->textBrowserNLDRlog->clear();
// ui->textBrowserdimlog->clear();
// ui->textBrowserDISTlog->clear();
ui->textBrowserDATAlog->clear();
// ui->textBrowserCONSlog->clear();
// ui->textBrowserCONVlog->clear();
ui->textBrowserCOVAlog->clear();
ui->textBrowserNLDRlog->append(qtlogtext);
// ui->textBrowserdimlog->append(qtlogtext);
// ui->textBrowserDISTlog->append(qtlogtext);
ui->textBrowserDATAlog->append(qtlogtext);
// ui->textBrowserCONSlog->append(qtlogtext);
// ui->textBrowserCONVlog->append(qtlogtext);
ui->textBrowserCOVAlog->append(qtlogtext);
}
/*
void TreeScaper::HandleFileChange(QString qtlogtext)
{
ui->textBrowserNLDRlog->setHtml(qtlogtext);
ui->textBrowserdimlog->setHtml(qtlogtext);
ui->textBrowserDISTlog->setHtml(qtlogtext);
ui->textBrowserDATAlog->setHtml(qtlogtext);
}*/
void TreeScaper::on_pushNLDRplot_clicked()
{
if(plotthd.isRunning())
{
cout << "Warning: The figure has already been plotted!\n\n";
return;
}
String filename;
// if(!ui->checkBoxNLDRplot->isChecked())
filename = CORplot;
// else
// {
// QString qtfname = ui->textNLDRplotfile->toPlainText();
// string stdfname = qtfname.toStdString();
// filename = stdfname.c_str();
// }
File file(filename);
if(! file.is_open())
{
cout << "Error: The coordinates file \""<< filename << "\" cannot be found! Run NLDR first!\n\n";//--- or select the coordinate file first by checking the box!" << endl;
return;
}
if(file.lines() < paras::imageparas.index_size)
{
cout << "Error: The largest index should not be greater than the number of points!\n\n";
return;
}
Array<int> selected_trees;
if(TreesData->Get_n_trees() == 0)
{
selected_trees.resize(paras::imageparas.index_size + 1);
selected_trees[0] = -1;
plotthd.initialization(filename, paras::imageparas, selected_trees);
plotthd.start();
return;
}
ui->pushNLDRplottrees->setEnabled(true);
cout << "\nTo plot the trees, press SHIFT + R and circle points from the figure. Then, click the 'Plot Trees' button.\n\n";
plotthd.initialization(filename, paras::imageparas, TreesData->selected_trees);
plotthd.start();
}
void TreeScaper::on_pushNLDRsetting_clicked()
{
NLDRsetting nldrst(this);
nldrst.show();
nldrst.exec();
}
void TreeScaper::on_pushPlotsetting_clicked()
{
setting st(this);
st.show();
st.exec();
}
void TreeScaper::on_pushdimrun_clicked()
{
if(dimestthd.isRunning())
{
QMessageBox::warning(NULL, "Warning", "Dimension estimation is running!", 0, 0);
return;
}
double **dist = NULL;
int ** distint = NULL;
int size = 0;
int dim = 0;
String type;
QString qtest = ui->comboBoxdimestimator->currentText();
string stdest = qtest.toStdString();
String est(stdest.c_str());
if(est == (String) "Correlation dimension")
est = "CORR_DIM";
else
if(est == (String) "Maximum likelihood")
est = "MLE_DIM";
else
est = "NN_DIM";
QString qtnum = ui->textdimnumber->toPlainText();
if(qtnum.toInt() < 2)
{
cout << "Warning: The number is at least 2!\n\n";
return;
}
QString qtDIMdata = ui->comboBoxDIMdata->currentText();
string stdDIMdata = qtDIMdata.toStdString();
String DIMdata(stdDIMdata.c_str());
QString qtfname = ui->textDATAfile->toPlainText();
string stdfname = qtfname.toStdString();
// Choose Directory
string rawfilename = stdfname.substr(stdfname.find_last_of("/") + 1);
QString dir = QFileDialog::getExistingDirectory(this, tr("Open Directory"), "", QFileDialog::ShowDirsOnly);
string dirfname = dir.toStdString();
if(dirfname.empty()) // cancel
return;
dirfname.append("/");
dirfname.append(rawfilename);
String fname(dirfname.c_str());
File file(fname);
DIMplot = file.prefix_name_lastof();
if(DIMdata == (String) "Unweighted RF-distance")
{
dist = TreesData->GetdistURF();
size = TreesData->Get_n_trees();
DIMplot += "_URF";
type = "DIS";
} else if(DIMdata == (String) "Weighted RF-distance")
{
dist = TreesData->GetdistRF();
size = TreesData->Get_n_trees();
DIMplot += "_RF";
type = "DIS";
} else if(DIMdata == (String) "Matching-distance")
{
distint = TreesData->GetdistMatch();
size = TreesData->Get_n_trees();
DIMplot += "_Match";
type = "DIS";
} else if(DIMdata == (String) "SPR-distance")
{
distint = TreesData->GetdistSPR();
size = TreesData->Get_n_trees();
DIMplot += "_SPR";
type = "DIS";
}
else if(DIMdata == (String) "Geodesic-distance")
{
dist = TreesData->GetdistGeo();
size = TreesData->Get_n_trees();
DIMplot += "_Geo";
type = "DIS";
}
else if(DIMdata == (String) "File-distance")
{
dist = TreesData->GetdistFile();
size = TreesData->Get_filedistsize();
type = "DIS";
QString qtdistfname = ui->textDISTfile_2->toPlainText();
string stddistfname = qtdistfname.toStdString();
// Save files in chosen directory
string rawdistfilename = stddistfname.substr(stddistfname.find_last_of("/") + 1);
string dirdistfname = dirfname.substr(0, dirfname.find_last_of("/"));
dirdistfname.append("/");
dirdistfname.append(rawdistfilename);
String fdistname(dirdistfname.c_str());
File filedist(fdistname);
DIMplot = filedist.prefix_name_lastof();
}
else if(DIMdata == (String) "File-coordinate")
{
dist = TreesData->GetcoordFile();
size = TreesData->Get_filedcoordinatesize();
dim = TreesData->Get_filedcoordinatedim();
cout << "size: " << size << " dim: " << dim << endl;
type = "COR";
QString qtcoordfname = ui->textDISTfile_2->toPlainText();
string stdcoordfname = qtcoordfname.toStdString();
// Save files in chosen directory
string rawcoordfilename = stdcoordfname.substr(stdcoordfname.find_last_of("/") + 1);
string dircoordfname = dirfname.substr(0, dirfname.find_last_of("/"));
dircoordfname.append("/");
dircoordfname.append(rawcoordfilename);
String fcoordname(dircoordfname.c_str());
File filecoord(fcoordname);
DIMplot = filecoord.prefix_name();
}
else
{
cout << "Warning: There is no distance matrix or coordinate data in memory!\n\n";
return;
}
if(DIMdata == (String) "Matching-distance" || DIMdata == (String) "SPR-distance")
{
dist = new double *[size];
for(int i = 0; i < size; i++)
dist[i] = new double [size];
for(int i = 0; i < size; i++)
for(int j = 0; j < size; j++)
{
dist[i][j] = (double) distint[i][j];
}
}
cout << "\nRunning Dimension Estimation..." << endl;
dimestthd.initialization(DIMplot, dist, size, dim, est, type, qtnum.toInt());
dimestthd.start();
// DIMplot = file.prefix_name();
DIMplot += "_";
DIMplot += est;
if(est == (String) "MLE_DIM")
DIMplot += "_k.out";
else
DIMplot += "_logvslog.out";
ui->textdimstart->setReadOnly(false);
ui->textdimend->setReadOnly(false);
if(ui->textdimstart->toPlainText() == "(disable)")
{
ui->textdimstart->setText("(input)");
ui->textdimend->setText("(input)");