plot.cpp
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright 2012 The MITRE Corporation *
* *
* Licensed under the Apache License, Version 2.0 (the "License"); *
* you may not use this file except in compliance with the License. *
* You may obtain a copy of the License at *
* *
* http://www.apache.org/licenses/LICENSE-2.0 *
* *
* Unless required by applicable law or agreed to in writing, software *
* distributed under the License is distributed on an "AS IS" BASIS, *
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. *
* See the License for the specific language governing permissions and *
* limitations under the License. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "plot.h"
#include "version.h"
#include "openbr/core/qtutils.h"
using namespace cv;
namespace br
{
// Flattens file metadata to an R list()
static QString toRList(const File &opts)
{
QStringList retValues;
QString format = "%1=%2";
foreach (const QString &key, opts.localKeys()) {
const QString value = QtUtils::toString(opts.value(key));
if (value.startsWith("("))
retValues.append(format.arg(key, "\"c" + value + "\""));
else if (value == "true")
retValues.append(format.arg(key, "TRUE"));
else if (value == "false")
retValues.append(format.arg(key, "FALSE"));
else
retValues.append(format.arg(key, "\"" + value + "\""));
}
return retValues.join(",");
}
static QStringList getPivots(const QString &file, bool headers)
{
QString str;
if (headers) str = QFileInfo(file).dir().dirName();
else str = QFileInfo(file).completeBaseName();
return str.split("_");
}
// Custom sorting method to ensure datasets are ordered nicely
static bool sortFiles(const QString &fileA, const QString &fileB)
{
return fileA < fileB;
}
struct RPlot
{
QString basename, suffix;
QFile file;
QStringList pivotHeaders;
QVector< QSet<QString> > pivotItems;
struct Pivot
{
int index, size;
QString header;
bool smooth;
Pivot() : index(-1), size(0), smooth(false) {}
Pivot(int _index, int _size, const QString &_header)
: index(_index), size(_size), header(_header), smooth(false) {}
};
Pivot major, minor;
RPlot(QStringList files, const File &destination)
{
if (files.isEmpty()) qFatal("Empty file list.");
qSort(files.begin(), files.end(), sortFiles);
// Parse destination
QFileInfo fileInfo(destination);
basename = fileInfo.path() + "/" + fileInfo.completeBaseName();
suffix = fileInfo.suffix();
if (suffix.isEmpty()) suffix = "pdf";
file.setFileName(basename+".R");
bool success = file.open(QFile::WriteOnly);
if (!success) qFatal("Failed to open %s for writing.", qPrintable(file.fileName()));
// Copy plot_utils.R into output script with source()
file.write(qPrintable(QString("source(\"%1\")\n\n").arg(Globals->sdkPath + "/share/openbr/plotting/plot_utils.R")));
file.write("# Read CSVs\n"
"data <- NULL\n");
// Read files and retrieve pivots
pivotHeaders = getPivots(files.first(), true);
pivotItems = QVector< QSet<QString> >(pivotHeaders.size());
foreach (const QString &fileName, files) {
QStringList pivots = getPivots(fileName, false);
// If the number of pivots don't match, abandon the directory/filename labeling scheme
if (pivots.size() != pivotHeaders.size()) {
pivots.clear();
pivots.push_back(QFileInfo(fileName).completeBaseName());
pivotHeaders.clear();
pivotHeaders.push_back("File");
}
file.write(qPrintable(QString("tmp <- read.csv(\"%1\")\n").arg(fileName).replace("\\", "\\\\")));
for (int i=0; i<pivots.size(); i++) {
pivotItems[i].insert(pivots[i]);
file.write(qPrintable(QString("tmp$%1 <- \"%2\"\n").arg(pivotHeaders[i], pivots[i])));
}
file.write("data <- rbind(data, tmp)\n");
}
for (int i=0; i<pivotItems.size(); i++) {
const int size = pivotItems[i].size();
if (size > major.size) {
minor = major;
major = Pivot(i, size, pivotHeaders[i]);
} else if (size > minor.size) {
minor = Pivot(i, size, pivotHeaders[i]);
}
}
const QString &smooth = destination.get<QString>("smooth", "");
major.smooth = !smooth.isEmpty() && (major.header == smooth) && (major.size > 1);
minor.smooth = !smooth.isEmpty() && (minor.header == smooth) && (minor.size > 1);
if (major.smooth) major.size = 1;
if (minor.smooth) minor.size = 1;
if (major.size < minor.size)
std::swap(major, minor);
// Set variables in R
file.write(qPrintable(QString("\nconfidence <- %1\n").arg(destination.get<float>("confidence", 95) / 100.0)));
file.write(qPrintable(QString("ncol <- %1\n").arg(destination.get<int>("ncol", major.size > 1 ? major.size : (minor.header.isEmpty() ? major.size : minor.size)))));
file.write(qPrintable(QString("basename <- \"%1\"\n").arg(basename)));
file.write(qPrintable(QString("smooth <- %1\n").arg((major.smooth || minor.smooth) && (destination.get<float>("confidence", 95) / 100.0) != 0 ? "TRUE" : "FALSE")));
file.write(qPrintable(QString("csv <- %1\n").arg(destination.getBool("csv") ? "TRUE" : "FALSE")));
file.write(qPrintable(QString("majorHeader <- \"%1\"\n").arg(major.header)));
file.write(qPrintable(QString("majorSize <- %1\n").arg(major.size)));
file.write(qPrintable(QString("majorSmooth <- %1\n").arg(major.smooth ? "TRUE" : "FALSE")));
file.write(qPrintable(QString("minorHeader <- \"%1\"\n").arg(minor.header)));
file.write(qPrintable(QString("minorSize <- %1\n").arg(minor.size)));
file.write(qPrintable(QString("minorSmooth <- %1\n").arg(minor.smooth ? "TRUE" : "FALSE")));
file.write(qPrintable(QString("flip <- %1\n").arg(minor.header == "Algorithm" ? "TRUE" : "FALSE")));
// Open output device
file.write(qPrintable(QString("\n"
"# Open output device\n"
"%1(\"%2.%1\"%3)\n").arg(suffix, basename, suffix != "pdf" ? ", width=800, height=800" : "")));
// Write figures
file.write("\n"
"# Write figures\n");
}
bool finalize(bool show = false)
{
file.write("dev.off()\n");
if (suffix != "pdf") file.write(qPrintable(QString("unlink(\"%1.%2\")").arg(basename, suffix)));
file.close();
bool success = QtUtils::runRScript(file.fileName());
if (success && show) QtUtils::showFile(basename+"."+suffix);
return success;
}
};
// Does not work if dataset folder starts with a number
bool Plot(const QStringList &files, const File &destination, bool show)
{
qDebug("Plotting %d file(s) to %s", files.size(), qPrintable(destination));
RPlot p(files, destination);
p.file.write("\nformatData()\n\n");
p.file.write(qPrintable(QString("algs <- %1\n").arg((p.major.size > 1 && p.minor.size > 1) && !(p.major.smooth || p.minor.smooth) ? QString("paste(TF$%1, TF$%2, sep=\"_\")").arg(p.major.header, p.minor.header)
: QString("TF$%1").arg(p.major.size > 1 ? p.major.header : (p.minor.header.isEmpty() ? p.major.header : p.minor.header)))));
p.file.write("algs <- algs[!duplicated(algs)]\n");
if (p.major.smooth || p.minor.smooth) {
QString groupvar = p.major.size > 1 ? p.major.header : (p.minor.header.isEmpty() ? p.major.header : p.minor.header);
foreach(const QString &data, QStringList() << "DET" << "IET" << "CMC" << "TF" << "FT" << "CT") {
p.file.write(qPrintable(QString("%1 <- summarySE(%1, measurevar=\"Y\", groupvars=c(\"%2\", \"X\"), conf.interval=confidence)"
"\n").arg(data, groupvar)));
}
p.file.write(qPrintable(QString("%1 <- summarySE(%1, measurevar=\"X\", groupvars=c(\"Error\", \"%2\", \"Y\"), conf.interval=confidence)"
"\n\n").arg("ERR", groupvar)));
}
// Use a br::file for simple storage of plot options
QMap<QString,File> optMap;
optMap.insert("rocOptions", File(QString("[xTitle=False Accept Rate,yTitle=True Accept Rate,xLog=true,yLog=false]")));
optMap.insert("detOptions", File(QString("[xTitle=False Accept Rate,yTitle=False Reject Rate,xLog=true,yLog=true]")));
optMap.insert("ietOptions", File(QString("[xTitle=False Positive Identification Rate (FPIR),yTitle=False Negative Identification Rate (FNIR),xLog=true,yLog=true]")));
optMap.insert("cmcOptions", File(QString("[xTitle=Rank,yTitle=Retrieval Rate,xLog=true,yLog=false,size=1,xLabels=(1,5,10,50,100),xBreaks=(1,5,10,50,100)]")));
foreach (const QString &key, optMap.keys()) {
const QStringList options = destination.get<QStringList>(key, QStringList());
foreach (const QString &option, options) {
QStringList words = QtUtils::parse(option, '=');
QtUtils::checkArgsSize(words[0], words, 1, 2);
optMap[key].set(words[0], words[1]);
}
}
// optional plot metadata and accuracy tables
if (destination.getBool("metadata", true)) {
p.file.write("\n# Write metadata table\n");
p.file.write(qPrintable(QString("plotMetadata(metadata=Metadata, title=\"%1 - %2\")\n").arg(PRODUCT_NAME, PRODUCT_VERSION)));
if (!destination.getBool("csv")) p.file.write("plot.new()\n");
QString table = "plotTable(tableData=%1, name=%2, labels=%3)\n";
p.file.write(qPrintable(table.arg("TF", "\"Table of True Accept Rates at various False Accept Rates\"",
"c(\"FAR = 1e-06\", \"FAR = 1e-05\", \"FAR = 1e-04\", \"FAR = 1e-03\", \"FAR = 1e-02\", \"FAR = 1e-01\")")));
p.file.write(qPrintable(table.arg("FT", "\"Table of False Accept Rates at various True Accept Rates\"",
"c(\"TAR = 0.40\", \"TAR = 0.50\", \"TAR = 0.65\", \"TAR = 0.75\", \"TAR = 0.85\", \"TAR = 0.95\")")));
p.file.write(qPrintable(table.arg("CT", "\"Table of retrieval rate at various ranks\"",
"c(\"Rank 1\", \"Rank 5\", \"Rank 10\", \"Rank 20\", \"Rank 50\", \"Rank 100\")")));
p.file.write(qPrintable(table.arg("TS", "\"Template Size by Algorithm\"",
"c(\"Template Size (bytes):\")")));
p.file.write("\n");
}
// Write plots
QString plot = "plot <- plotLine(lineData=%1, options=list(%2), flipY=%3)\nplot\n";
p.file.write(qPrintable(QString(plot).arg("DET", toRList(optMap["rocOptions"]), "TRUE")));
p.file.write(qPrintable(QString(plot).arg("DET", toRList(optMap["detOptions"]), "FALSE")));
p.file.write(qPrintable(QString(plot).arg("IET", toRList(optMap["ietOptions"]), "FALSE")));
p.file.write(qPrintable(QString(plot).arg("CMC", toRList(optMap["cmcOptions"]), "FALSE")));
p.file.write("plot <- plotSD(sdData=SD)\nplot\n");
p.file.write("plot <- plotBC(bcData=BC)\nplot\n");
p.file.write("plot <- plotERR(errData=ERR)\nplot\n");
p.file.write("plotEERSamples(imData=IM, gmData=GM)\n\n");
return p.finalize(show);
}
//Check if only one ROC point is in the file
bool fileHasSinglePoint(const QString &evalFile) {
QFile file(evalFile);
bool success = file.open(QFile::ReadOnly);
if (!success) qFatal("Failed to open %s for reading.", qPrintable(evalFile));
QStringList lines = QString(file.readAll()).split("\n");
file.close();
int rocCnt = 0;
foreach (const QString &line, lines) {
if (line.contains("DiscreteROC")) {
rocCnt++;
}
if (rocCnt > 1)
return false;
}
return true;
}
//Check all files to see if any single file has only have one ROC point
bool filesHaveSinglePoint(const QStringList &files) {
foreach (const File &file, files)
if (fileHasSinglePoint(file))
return true;
return false;
}
// Properly
bool PlotDetection(const QStringList &files, const File &destination, bool show)
{
qDebug("Plotting %d detection file(s) to %s", files.size(), qPrintable(destination));
RPlot p(files, destination);
p.file.write("\nformatData(type=\"detection\")\n\n");
// Use a br::file for simple storage of plot options
QMap<QString,File> optMap;
optMap.insert("rocOptions", File(QString("[xTitle=False Accepts Per Image,yTitle=True Accept Rate,xLog=true,yLog=false]")));
optMap.insert("prOptions", File(QString("[xTitle=False Accept Rate,yTitle=False Reject Rate,xLog=true,yLog=true]")));
foreach (const QString &key, optMap.keys()) {
const QStringList options = destination.get<QStringList>(key, QStringList());
foreach (const QString &option, options) {
QStringList words = QtUtils::parse(option, '=');
QtUtils::checkArgsSize(words[0], words, 1, 2);
optMap[key].set(words[0], words[1]);
}
}
QString plotType("line");
if (filesHaveSinglePoint(files))
plotType = QString("point");
QString plot = "plot <- plotLine(lineData=%1, options=list(%2), flipY=%3, geometry=%4)\nplot\n";
foreach (const QString &type, QStringList() << "Discrete" << "Continuous") {
optMap["rocOptions"].set("title", type);
p.file.write(qPrintable(QString(plot).arg(type + "ROC", toRList(optMap["rocOptions"]), "FALSE", "\"" + plotType + "\"")));
}
foreach (const QString &type, QStringList() << "Discrete" << "Continuous") {
optMap["prOptions"].set("title", type);
p.file.write(qPrintable(QString(plot).arg(type + "PR", toRList(optMap["prOptions"]), "FALSE", "\"" + plotType + "\"")));
}
p.file.write("plot <- plotOverlap(overlapData=Overlap)\nplot\n");
p.file.write(qPrintable(QString("ggplot(AverageOverlap, aes(x=%1, y=%2, label=round(X,3)), main=\"Average Overlap\") + geom_text() + theme_minimal()").arg(p.minor.size > 1 ? p.minor.header : "'X'", p.major.size > 1 ? p.major.header : "'Y'") +
QString("%1%2\n\n").arg(p.minor.size > 1 ? "" : " + xlab(NULL)", p.major.size > 1 ? "" : " + ylab(NULL)")));
p.file.write(qPrintable(QString("ggplot(AverageOverlap, aes(x=%1, y=%2, fill=X)) + geom_tile() + scale_fill_continuous(\"Average Overlap\", guide=FALSE) + theme_minimal()").arg(p.minor.size > 1 ? p.minor.header : "'X'", p.major.size > 1 ? p.major.header : "'Y'") +
QString("%1%2\n\n").arg(p.minor.size > 1 ? "" : " + xlab(NULL)", p.major.size > 1 ? "" : " + ylab(NULL)")));
return p.finalize(show);
}
bool PlotLandmarking(const QStringList &files, const File &destination, bool show)
{
qDebug("Plotting %d landmarking file(s) to %s", files.size(), qPrintable(destination));
RPlot p(files, destination);
p.file.write("\nformatData(type=\"landmarking\")\n\n");
p.file.write(qPrintable(QString("algs <- uniqueBox$%1)\n").arg(p.major.size > 1 ? p.major.header : (p.minor.header.isEmpty() ? p.major.header : p.minor.header))));
p.file.write("algs <- algs[!duplicated(algs)]\n");
p.file.write("plotLandmarkSamples(samples=sample, expData=EXP, extData=EXT)\n");
p.file.write("plotLandmarkTables(tableData=Box)\n");
p.file.write(qPrintable(QString("ggplot(Box, aes(Y,%1%2))").arg(p.major.size > 1 ? QString(", colour=%1").arg(p.major.header) : QString(),
p.minor.size > 1 ? QString(", linetype=%1").arg(p.minor.header) : QString()) +
QString(" + annotation_logticks(sides=\"b\") + stat_ecdf() + scale_x_log10(\"Normalized Error\", breaks=c(0.001,0.01,0.1,1,10)) + scale_y_continuous(\"Cumulative Density\", label=percent) + theme_minimal()\n\n")));
p.file.write(qPrintable(QString("ggplot(Box, aes(factor(X), Y%1%2))").arg(p.major.size > 1 ? QString(", colour=%1").arg(p.major.header) : QString(), p.minor.size > 1 ? QString(", linetype=%1").arg(p.minor.header) : QString()) +
QString("+ annotation_logticks(sides=\"l\") + geom_boxplot(alpha=0.5) + geom_jitter(size=1, alpha=0.5) + scale_x_discrete(\"Landmark\") + scale_y_log10(\"Normalized Error\", breaks=c(0.001,0.01,0.1,1,10)) + theme_minimal()\n\n")));
p.file.write(qPrintable(QString("ggplot(Box, aes(factor(X), Y%1%2))").arg(p.major.size > 1 ? QString(", colour=%1").arg(p.major.header) : QString(), p.minor.size > 1 ? QString(", linetype=%1").arg(p.minor.header) : QString()) +
QString("+ annotation_logticks(sides=\"l\") + geom_violin(alpha=0.5) + scale_x_discrete(\"Landmark\") + scale_y_log10(\"Normalized Error\", breaks=c(0.001,0.01,0.1,1,10))\n\n")));
return p.finalize(show);
}
bool PlotMetadata(const QStringList &files, const QString &columns, bool show)
{
qDebug("Plotting %d metadata file(s) for columns %s", files.size(), qPrintable(columns));
RPlot p(files, "PlotMetadata");
foreach (const QString &column, columns.split(";"))
p.file.write(qPrintable(QString("qplot(%1, %2, data=data, geom=\"violin\", fill=%1) + coord_flip() + theme_minimal()\nggsave(\"%2.pdf\")\n").arg(p.major.header, column)));
return p.finalize(show);
}
} // namespace br