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
{
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("_");
}
static QString getScale(const QString &mode, const QString &title, int vals)
{
if (vals > 12) return " + scale_"+mode+"_discrete(\""+title+"\")";
else if (vals > 11) return " + scale_"+mode+"_brewer(\""+title+"\", palette=\"Set3\")";
else if (vals > 9) return " + scale_"+mode+"_brewer(\""+title+"\", palette=\"Paired\")";
else return " + scale_"+mode+"_brewer(\""+title+"\", palette=\"Set1\")";
}
// Custom sorting method to ensure datasets are ordered nicely
static bool sortFiles(const QString &fileA, const QString &fileB)
{
QFileInfo fileInfoA(fileA);
QFileInfo fileInfoB(fileB);
if (fileInfoA.fileName().contains("Good")) return true;
if (fileInfoB.fileName().contains("Good")) return false;
if (fileInfoA.fileName().contains("Bad")) return true;
if (fileInfoB.fileName().contains("Bad")) return false;
if (fileInfoA.fileName().contains("Ugly")) return true;
if (fileInfoB.fileName().contains("Ugly")) return false;
if (fileInfoA.fileName().contains("MEDS")) return true;
if (fileInfoB.fileName().contains("MEDS")) return false;
if (fileInfoA.fileName().contains("PCSO")) return true;
if (fileInfoB.fileName().contains("PCSO")) return false;
return fileA < fileB;
}
struct RPlot
{
QString basename, suffix;
QFile file;
QStringList pivotHeaders;
QVector< QSet<QString> > pivotItems;
bool flip;
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, bool isEvalFormat = true)
{
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()));
file.write("# Load libraries\n"
"library(ggplot2)\n"
"library(gplots)\n"
"library(reshape)\n"
"library(scales)\n"
"\n"
"# 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$%1 <- \"%2\"\n").arg(pivotHeaders[i], pivots[i])));
}
file.write("data <- rbind(data, tmp)\n");
}
// Format data
if (isEvalFormat)
file.write("\n"
"# Split data into individual plots\n"
"plot_index = which(names(data)==\"Plot\")\n"
"Metadata <- data[grep(\"Metadata\",data$Plot),-c(1)]\n"
"DET <- data[grep(\"DET\",data$Plot),-c(1)]\n"
"FAR <- data[grep(\"FAR\",data$Plot),-c(1)]\n"
"FRR <- data[grep(\"FRR\",data$Plot),-c(1)]\n"
"SD <- data[grep(\"SD\",data$Plot),-c(1)]\n"
"BC <- data[grep(\"BC\",data$Plot),-c(1)]\n"
"CMC <- data[grep(\"CMC\",data$Plot),-c(1)]\n"
"FAR$Error <- \"FAR\"\n"
"FRR$Error <- \"FRR\"\n"
"ERR <- rbind(FAR, FRR)\n"
"rm(data, FAR, FRR)\n"
"\n"
"# Format data\n"
"Metadata$Y<-factor(Metadata$Y, levels=c(\"Genuine\",\"Impostor\",\"Ignored\",\"Gallery\",\"Probe\"))\n"
"DET$Y <- as.numeric(as.character(DET$Y))\n"
"ERR$Y <- as.numeric(as.character(ERR$Y))\n"
"SD$Y <- as.factor(unique(as.character(SD$Y)))\n"
"BC$Y <- as.numeric(as.character(BC$Y))\n"
"CMC$Y <- as.numeric(as.character(CMC$Y))\n"
"\n"
"# Code to format FAR values\n"
"far_names <- list('0.001'=\"FAR = 0.1%\", '0.01'=\"FAR = 1%\")\n"
"far_labeller <- function(variable,value) { return(far_names[as.character(value)]) }\n");
// Open output device
file.write(qPrintable(QString("\n"
"# Open output device\n"
"%1(\"%2.%1\")\n").arg(suffix, basename)));
// Write metadata table
if ((suffix == "pdf") && isEvalFormat) {
file.write("\n"
"# Write metadata table\n");
QString MT = "MT <- as.data.frame(recast(Metadata, %1 ~ Y, id.var=c(\"%2\",\"Y\"), measure.var=c(\"X\")))\n";
file.write(qPrintable(MT.arg(pivotHeaders.join(" + "), pivotHeaders.join("\",\""))));
QString textplot = "par(mfrow=c(4,1))\n"
"plot.new()\n"
"print(title(paste(\"%1 - %2\",date(),sep=\"\\n\")))\n"
"print(textplot(MT[,!(names(MT) %in% c(\"Genuine\", \"Impostor\", \"Ignored\"))], show.rownames=FALSE))\n"
"print(title(\"Images\"))\n"
"print(textplot(MT[,!(names(MT) %in% c(\"Gallery\", \"Probe\"))], show.rownames=FALSE))\n"
"print(title(\"Matches\"))\n"
"plot.new()\n"
"print(title(\"Gallery * Probe = Genuine + Impostor + Ignored\"))\n";
file.write(qPrintable(textplot.arg(PRODUCT_NAME, PRODUCT_VERSION)));
}
// Write figures
file.write("\n"
"# Write figures\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);
flip = minor.header == "Algorithm";
}
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));
const bool minimalist = destination.getBool("minimalist");
RPlot p(files, destination);
p.file.write(qPrintable(QString("qplot(X, 1-Y, data=DET%1").arg((p.major.smooth || p.minor.smooth) ? ", geom=\"smooth\", method=loess, level=0.99" : ", geom=\"line\"") +
(p.major.size > 1 ? QString(", colour=factor(%1)").arg(p.major.header) : QString()) +
(p.minor.size > 1 ? QString(", linetype=factor(%1)").arg(p.minor.header) : QString()) +
QString(", xlab=\"False Accept Rate\", ylab=\"True Accept Rate\") + theme_minimal()") +
(p.major.size > 1 ? getScale("colour", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(p.minor.header) : QString()) +
QString(" + scale_x_log10(labels=percent, limits=c(min(DET$X),1)) + scale_y_continuous(labels=percent) + annotation_logticks(sides=\"b\")\n\n")));
p.file.write(qPrintable(QString("qplot(X, Y, data=DET%1").arg((p.major.smooth || p.minor.smooth) ? ", geom=\"smooth\", method=loess, level=0.99" : ", geom=\"line\"") +
(p.major.size > 1 ? QString(", colour=factor(%1)").arg(p.major.header) : QString()) +
(p.minor.size > 1 ? QString(", linetype=factor(%1)").arg(p.minor.header) : QString()) +
QString(", xlab=\"False Accept Rate\", ylab=\"False Reject Rate\") + geom_abline(alpha=0.5, colour=\"grey\", linetype=\"dashed\") + theme_minimal()") +
(p.major.size > 1 ? getScale("colour", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(p.minor.header) : QString()) +
QString(" + scale_x_log10(labels=percent, limits=c(min(DET$X),1)) + scale_y_continuous(labels=percent)\n\n")));
p.file.write(qPrintable(QString("qplot(X, data=SD, geom=\"histogram\", fill=Y, position=\"identity\", alpha=I(1/2)") +
QString(", xlab=\"Score%1\"").arg((p.flip ? p.major.size : p.minor.size) > 1 ? " / " + (p.flip ? p.major.header : p.minor.header) : QString()) +
QString(", ylab=\"Frequency%1\"").arg((p.flip ? p.minor.size : p.major.size) > 1 ? " / " + (p.flip ? p.minor.header : p.major.header) : QString()) +
QString(") + scale_fill_manual(\"Ground Truth\", values=c(\"blue\", \"red\")) + theme_minimal() + scale_x_continuous(minor_breaks=NULL) + scale_y_continuous(minor_breaks=NULL) + theme(axis.text.y=element_blank(), axis.ticks=element_blank(), axis.text.x=element_text(angle=-90, hjust=0))") +
(p.major.size > 1 ? (p.minor.size > 1 ? QString(" + facet_grid(%2 ~ %1, scales=\"free\")").arg((p.flip ? p.major.header : p.minor.header), (p.flip ? p.minor.header : p.major.header)) : QString(" + facet_wrap(~ %1, scales = \"free\")").arg(p.major.header)) : QString()) +
QString(" + theme(aspect.ratio=1)\n\n")));
p.file.write(qPrintable(QString("ggplot(CMC, aes(x=X, y=Y%1%2)) + xlab(\"Rank\") + ylab(\"Retrieval Rate\")").arg(p.major.size > 1 ? QString(" ,colour=factor(%1)").arg(p.major.header) : QString(), p.minor.size > 1 ? QString(", linetype=factor(%1)").arg(p.minor.header) : QString()) +
((p.major.smooth || p.minor.smooth) ? (minimalist ? " + stat_summary(geom=\"line\", fun.y=mean)" : " + stat_summary(geom=\"line\", fun.y=min, aes(linetype=\"Min/Max\")) + stat_summary(geom=\"line\", fun.y=max, aes(linetype=\"Min/Max\")) + stat_summary(geom=\"line\", fun.y=mean, aes(linetype=\"Mean\")) + scale_linetype_manual(\"Legend\", values=c(\"Mean\"=1, \"Min/Max\"=2))") : " + geom_line()") +
(minimalist ? "" : " + scale_x_log10(labels=c(1,5,10,50,100), breaks=c(1,5,10,50,100)) + annotation_logticks(sides=\"b\")") +
(p.major.size > 1 ? getScale("colour", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(p.minor.header) : QString()) +
QString(" + theme_minimal() + scale_y_continuous(labels=percent)\n\n")));
p.file.write(qPrintable(QString("qplot(factor(%1)%2, data=BC, %3").arg(p.major.smooth ? (p.minor.header.isEmpty() ? "Algorithm" : p.minor.header) : p.major.header, (p.major.smooth || p.minor.smooth) ? ", Y" : "", (p.major.smooth || p.minor.smooth) ? "geom=\"boxplot\"" : "geom=\"bar\", position=\"dodge\", weight=Y") +
(p.major.size > 1 ? QString(", fill=factor(%1)").arg(p.major.header) : QString()) +
QString(", xlab=\"%1False Accept Rate\"").arg(p.major.size > 1 ? p.major.header + " / " : QString()) +
QString(", ylab=\"True Accept Rate%1\") + theme_minimal()").arg(p.minor.size > 1 ? " / " + p.minor.header : QString()) +
(p.major.size > 1 ? getScale("fill", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + facet_grid(%2 ~ X)").arg(p.minor.header) : QString(" + facet_grid(. ~ X, labeller=far_labeller)")) +
QString(" + scale_y_continuous(labels=percent) + theme(legend.position=\"none\", axis.text.x=element_text(angle=-90, hjust=0))%1").arg((p.major.smooth || p.minor.smooth) ? "" : " + geom_text(data=BC, aes(label=Y, y=0.05))\n\n")));
p.file.write(qPrintable(QString("qplot(X, Y, data=ERR%1, linetype=Error").arg((p.major.smooth || p.minor.smooth) ? ", geom=\"smooth\", method=loess, level=0.99" : ", geom=\"line\"") +
((p.flip ? p.major.size : p.minor.size) > 1 ? QString(", colour=factor(%1)").arg(p.flip ? p.major.header : p.minor.header) : QString()) +
QString(", xlab=\"Score%1\", ylab=\"Error Rate\") + theme_minimal()").arg((p.flip ? p.minor.size : p.major.size) > 1 ? " / " + (p.flip ? p.minor.header : p.major.header) : QString()) +
((p.flip ? p.major.size : p.minor.size) > 1 ? getScale("colour", p.flip ? p.major.header : p.minor.header, p.flip ? p.major.size : p.minor.size) : QString()) +
QString(" + scale_y_log10(labels=percent) + annotation_logticks(sides=\"l\")") +
((p.flip ? p.minor.size : p.major.size) > 1 ? QString(" + facet_wrap(~ %1, scales=\"free_x\")").arg(p.flip ? p.minor.header : p.major.header) : QString()) +
QString(" + theme(aspect.ratio=1)\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;
}
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, false);
p.file.write("# Split data into individual plots\n"
"plot_index = which(names(data)==\"Plot\")\n"
"DiscreteROC <- data[grep(\"DiscreteROC\",data$Plot),-c(1)]\n"
"ContinuousROC <- data[grep(\"ContinuousROC\",data$Plot),-c(1)]\n"
"DiscretePR <- data[grep(\"DiscretePR\",data$Plot),-c(1)]\n"
"ContinuousPR <- data[grep(\"ContinuousPR\",data$Plot),-c(1)]\n"
"Overlap <- data[grep(\"Overlap\",data$Plot),-c(1)]\n"
"rm(data)\n"
"\n");
QString plotType("line");
if (filesHaveSinglePoint(files))
plotType = QString("point");
foreach (const QString &type, QStringList() << "Discrete" << "Continuous")
p.file.write(qPrintable(QString("qplot(X, Y, data=%1ROC%2").arg(type, (p.major.smooth || p.minor.smooth) ? ", geom=\"smooth\", method=loess, level=0.99" : QString(", geom=\"%1\"").arg(plotType)) +
(p.major.size > 1 ? QString(", colour=factor(%1)").arg(p.major.header) : QString()) +
(p.minor.size > 1 ? QString(", linetype=factor(%1)").arg(p.minor.header) : QString()) +
QString(", xlab=\"False Accepts\", ylab=\"True Accept Rate\") + theme_minimal()") +
(p.major.size > 1 ? getScale("colour", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(p.minor.header) : QString()) +
QString(" + scale_x_log10() + scale_y_continuous(labels=percent) + annotation_logticks(sides=\"b\") + ggtitle(\"%1\")\n\n").arg(type)));
foreach (const QString &type, QStringList() << "Discrete" << "Continuous")
p.file.write(qPrintable(QString("qplot(X, Y, data=%1PR%2").arg(type, (p.major.smooth || p.minor.smooth) ? ", geom=\"smooth\", method=loess, level=0.99" : QString(", geom=\"%1\"").arg(plotType)) +
(p.major.size > 1 ? QString(", colour=factor(%1)").arg(p.major.header) : QString()) +
(p.minor.size > 1 ? QString(", linetype=factor(%1)").arg(p.minor.header) : QString()) +
QString(", xlab=\"Recall\", ylab=\"Precision\") + theme_minimal()") +
(p.major.size > 1 ? getScale("colour", p.major.header, p.major.size) : QString()) +
(p.minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(p.minor.header) : QString()) +
QString(" + scale_x_continuous(labels=percent) + scale_y_continuous(labels=percent) + ggtitle(\"%1\")\n\n").arg(type)));
p.file.write(qPrintable(QString("qplot(X, data=Overlap, geom=\"histogram\", position=\"identity\", xlab=\"Overlap\", ylab=\"Frequency\")") +
QString(" + theme_minimal() + scale_x_continuous(minor_breaks=NULL) + scale_y_continuous(minor_breaks=NULL) + theme(axis.text.y=element_blank(), axis.ticks=element_blank(), axis.text.x=element_text(angle=-90, hjust=0))") +
(p.major.size > 1 ? (p.minor.size > 1 ? QString(" + facet_grid(%2 ~ %1, scales=\"free\")").arg(p.minor.header, p.major.header) : QString(" + facet_wrap(~ %1, scales = \"free\")").arg(p.major.header)) : QString()) +
QString(" + theme(aspect.ratio=1)\n\n")));
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, false);
p.file.write("# Split data into individual plots\n"
"plot_index = which(names(data)==\"Plot\")\n"
"Box <- data[grep(\"Box\",data$Plot),-c(1)]\n"
"rm(data)\n"
"\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(0.01,0.1,1,10)) + 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", false);
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