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)
{
return fileA < fileB;
}
struct RPlot
{
QString basename, suffix;
QFile file;
QStringList pivotHeaders;
QVector< QSet<QString> > pivotItems;
float confidence; // confidence interval for plotting across splits
int ncol; // Number of columns for plot legends
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)
{
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);
confidence = destination.get<float>("confidence", 95) / 100.0;
ncol = destination.get<int>("ncol", major.size > 1 ? major.size : (minor.header.isEmpty() ? major.size : minor.size));
flip = minor.header == "Algorithm";
// 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");
}
void qplot(QString geom, QString data, bool flipY, File opts)
{
file.write(qPrintable(QString("qplot(X, %1, data=%2, geom=\"%3\", main=\"%4\"").arg(flipY ? "1-Y" : "Y", data, geom, opts.get<QString>("title", "")) +
(opts.contains("size") ? QString(", size=I(%1)").arg(opts.get<QString>("size")) : QString()) +
(major.size > 1 ? QString(", colour=factor(%1)").arg(major.header) : QString()) +
(minor.size > 1 ? QString(", linetype=factor(%1)").arg(minor.header) : QString()) +
(QString(", xlab=\"%1\", ylab=\"%2\") + theme_minimal()").arg(opts.get<QString>("xTitle"), opts.get<QString>("yTitle"))) +
((major.smooth || minor.smooth) && confidence != 0 && data != "CMC" ? QString(" + geom_errorbar(data=%1[seq(1, NROW(%1), by = 29),], aes(x=X, ymin=%2), width=0.1, alpha=I(1/2))").arg(data, flipY ? "(1-lower), ymax=(1-upper)" : "lower, ymax=upper") : QString()) +
(major.size > 1 ? getScale("colour", major.header, major.size) : QString()) +
(minor.size > 1 ? QString(" + scale_linetype_discrete(\"%1\")").arg(minor.header) : QString()) +
(opts.getBool("xLog") ? QString(" + scale_x_log10(labels=%1, breaks=%2) + annotation_logticks(sides=\"b\")").arg(opts.get<QString>("xLabels", "trans_format(\"log10\", math_format())"), opts.get<QString>("xBreaks", "waiver()"))
: QString(" + scale_x_continuous(labels=%1, breaks=%2)").arg(opts.get<QString>("xLabels", "percent"), opts.get<QString>("xBreaks", "pretty_breaks(n=10)"))) +
(opts.getBool("yLog") ? QString(" + scale_y_log10(labels=%1, breaks=%2) + annotation_logticks(sides=\"l\")").arg(opts.get<QString>("yLabels", "trans_format(\"log10\", math_format())"), opts.get<QString>("yBreaks", "waiver()"))
: QString(" + scale_y_continuous(labels=%1, breaks=%2)").arg(opts.get<QString>("yLabels", "percent"), opts.get<QString>("yBreaks", "pretty_breaks(n=10)"))) +
(opts.contains("xLimits") ? QString(" + xlim%1").arg(QtUtils::toString(opts.get<QPointF>("xLimits", QPointF()))) : QString()) +
(opts.contains("yLimits") ? QString(" + ylim%1").arg(QtUtils::toString(opts.get<QPointF>("yLimits", QPointF()))) : QString()) +
QString(" + theme(legend.title = element_text(size = %1), legend.text = element_text(size = %1), plot.title = element_text(size = %1), axis.text = element_text(size = %1), axis.title.x = element_text(size = %1), axis.title.y = element_text(size = %1),").arg(QString::number(opts.get<float>("textSize",12))) +
QString(" legend.position=%1, legend.background = element_rect(fill = 'white'), panel.grid.major = element_line(colour = \"gray\"), panel.grid.minor = element_line(colour = \"gray\", linetype = \"dashed\"))").arg(opts.contains("legendPosition") ? "c"+QtUtils::toString(opts.get<QPointF>("legendPosition")) : "'bottom'") +
QString(" + guides(col=guide_legend(ncol=%1))\n\n").arg(ncol)));
}
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("\nevalFormatting()\n\n");
// Set variables in R
p.file.write(qPrintable(QString("basename <- \"%1\"\n").arg(p.basename)));
p.file.write(qPrintable(QString("errBars <- %1\n").arg((p.major.smooth || p.minor.smooth) && p.confidence != 0 ? "TRUE" : "FALSE")));
p.file.write(qPrintable(QString("csv <- %1\n").arg(destination.getBool("csv") ? "TRUE" : "FALSE")));
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 &type, QStringList() << "DET" << "IET" << "CMC" << "TF" << "FT" << "CT") {
p.file.write(qPrintable(QString("%1 <- summarySE(%1, measurevar=\"Y\", groupvars=c(\"%2\", \"X\"), conf.interval=%3)"
"\n").arg(type, groupvar, QString::number(p.confidence))));
}
p.file.write(qPrintable(QString("%1 <- summarySE(%1, measurevar=\"X\", groupvars=c(\"Error\", \"%2\", \"Y\"), conf.interval=%3)"
"\n\n").arg("ERR", groupvar, QString::number(p.confidence))));
}
// 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=c(1,5,10,50,100),xBreaks=c(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(data=data, title=\"%1 - %2\")\n").arg(PRODUCT_NAME, PRODUCT_VERSION)));
if (!destination.getBool("csv")) p.file.write("plot.new()\n");
QString table = "plotTable(data=%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");
}
p.qplot("line", "DET", true, optMap["rocOptions"]);
p.qplot("line", "DET", false, optMap["detOptions"]);
p.qplot("line", "IET", false, optMap["ietOptions"]);
p.qplot("line", "CMC", false, optMap["cmcOptions"]);
p.file.write(qPrintable(QString("qplot(X, data=SD, geom=\"histogram\", fill=Y, position=\"identity\", alpha=I(1/2)") +
QString(", xlab=\"Score\", ylab=\"Frequency\"") +
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("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=\"False Accept Rate\", ylab=\"True Accept Rate\") + theme_minimal()") +
(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, geom=\"line\", linetype=Error") +
((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\", ylab=\"Error Rate\") + theme_minimal()") +
((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")));
p.file.write(qPrintable(QString("if (nrow(IM) != 0) {\n\tlibrary(jpeg)\n\tlibrary(png)\n\tlibrary(grid)\n\t")));
p.file.write(qPrintable(QString("\t# Print impostor matches above the EER\n\tfor (i in 1:nrow(IM)) {\n\t\tscore <- IM[i,1]\n\t\tfiles <- IM[i,2]\n\t\talg <- IM[i,3]\n\t\tfiles <- unlist(strsplit(files, \"[:]\"))\n\n\t\text1 <- unlist(strsplit(files[2], \"[.]\"))[2]\n\t\text2 <- unlist(strsplit(files[4], \"[.]\"))[2]\n\t\t") +
QString("if (ext1 == \"jpg\" || ext1 == \"JPEG\" || ext1 == \"jpeg\" || ext1 == \"JPG\") {\n\t\t\timg1 <- readJPEG(files[2])\n\t\t} else if (ext1 == \"PNG\" || ext1 == \"png\") {\n\t\t\timg1 <- readPNG(files[2])\n\t\t} else if (ext1 == \"TIFF\" || ext1 == \"tiff\" || ext1 == \"TIF\" || ext1 == \"tif\") {\n\t\t\timg1 <- readTIFF(files[2])\n\t\t} else {\n\t\t\tnext\n\t\t}\n\t\tif (ext2 == \"jpg\" || ext2 == \"JPEG\" || ext2 == \"jpeg\" || ext2 == \"JPG\") {\n\t\t\timg2 <- readJPEG(files[4])\n\t\t} ") +
QString("else if (ext2 == \"PNG\" || ext2 == \"png\") {\n\t\t\timg2 <- readPNG(files[4])\n\t\t} else if (ext2 == \"TIFF\" || ext2 == \"tiff\" || ext2 == \"TIF\" || ext2 == \"tif\") {\n\t\t\timg2 <- readTIFF(files[4])\n\t\t} else {\n\t\t\tnext\n\t\t}") +
QString("\n\t\tname1 <- files[1]\n\t\tname2 <- files[3]\n\n\t\tg1 <- rasterGrob(img1, interpolate=TRUE)\n\t\tg2 <- rasterGrob(img2, interpolate=TRUE)\n\n\t\t") +
QString("plot1 <- qplot(1:10, 1:10, geom=\"blank\") + annotation_custom(g1, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) + theme(axis.line=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks=element_blank(), panel.background=element_blank()) + labs(title=alg) + ylab(unlist(strsplit(files[2], \"[/]\"))[length(unlist(strsplit(files[2], \"[/]\")))]) + xlab(name1)\n\t\t") +
QString("plot2 <- qplot(1:10, 1:10, geom=\"blank\") + annotation_custom(g2, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) + theme(axis.line=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks=element_blank(), panel.background=element_blank()) + labs(title=paste(\"Impostor score =\", score)) + ylab(unlist(strsplit(files[4], \"[/]\"))[length(unlist(strsplit(files[4], \"[/]\")))]) + xlab(name2)\n\n\t\t") +
QString("multiplot(plot1, plot2, cols=2)\n\t}")));
p.file.write(qPrintable(QString("\n\n\t# Print genuine matches below the EER\n\tfor (i in 1:nrow(GM)) {\n\t\tscore <- GM[i,1]\n\t\tfiles <- GM[i,2]\n\t\talg <- GM[i,3]\n\t\tfiles <- unlist(strsplit(files, \"[:]\"))\n\n\t\text1 <- unlist(strsplit(files[2], \"[.]\"))[2]\n\t\text2 <- unlist(strsplit(files[4], \"[.]\"))[2]\n\t\t") +
QString("if (ext1 == \"jpg\" || ext1 == \"JPEG\" || ext1 == \"jpeg\" || ext1 == \"JPG\") {\n\t\t\timg1 <- readJPEG(files[2])\n\t\t} else if (ext1 == \"PNG\" || ext1 == \"png\") {\n\t\t\timg1 <- readPNG(files[2])\n\t\t} else if (ext1 == \"TIFF\" || ext1 == \"tiff\" || ext1 == \"TIF\" || ext1 == \"tif\") {\n\t\t\timg1 <- readTIFF(files[2])\n\t\t} else {\n\t\t\tnext\n\t\t}\n\t\tif (ext2 == \"jpg\" || ext2 == \"JPEG\" || ext2 == \"jpeg\" || ext2 == \"JPG\") {\n\t\t\timg2 <- readJPEG(files[4])\n\t\t} ") +
QString("else if (ext2 == \"PNG\" || ext2 == \"png\") {\n\t\t\timg2 <- readPNG(files[4])\n\t\t} else if (ext2 == \"TIFF\" || ext2 == \"tiff\" || ext2 == \"TIF\" || ext2 == \"tif\") {\n\t\t\timg2 <- readTIFF(files[4])\n\t\t} else {\n\t\t\tnext\n\t\t}") +
QString("\n\t\tname1 <- files[1]\n\t\tname2 <- files[3]\n\n\t\tg1 <- rasterGrob(img1, interpolate=TRUE)\n\t\tg2 <- rasterGrob(img2, interpolate=TRUE)\n\n\t\t") +
QString("plot1 <- qplot(1:10, 1:10, geom=\"blank\") + annotation_custom(g1, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) + theme(axis.line=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks=element_blank(), panel.background=element_blank()) + labs(title=alg) + ylab(unlist(strsplit(files[2], \"[/]\"))[length(unlist(strsplit(files[2], \"[/]\")))]) + xlab(name1)\n\t\t") +
QString("plot2 <- qplot(1:10, 1:10, geom=\"blank\") + annotation_custom(g2, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) + theme(axis.line=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), axis.ticks=element_blank(), panel.background=element_blank()) + labs(title=paste(\"Genuine score =\", score)) + ylab(unlist(strsplit(files[4], \"[/]\"))[length(unlist(strsplit(files[4], \"[/]\")))]) + xlab(name2)\n\n\t\t") +
QString("multiplot(plot1, plot2, cols=2)\n\t}\n}\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);
// 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]);
}
}
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$Plot),-c(1)]\n"
"AverageOverlap <- data[grep(\"AverageOverlap\",data$Plot),-c(1)]\n"
"rm(data)\n"
"\n");
QString plotType("line");
if (filesHaveSinglePoint(files))
plotType = QString("point");
foreach (const QString &type, QStringList() << "Discrete" << "Continuous") {
optMap["rocOptions"].set("title", type);
p.qplot(plotType, type + "ROC", false, optMap["rocOptions"]);
}
foreach (const QString &type, QStringList() << "Discrete" << "Continuous") {
optMap["prOptions"].set("title", type);
p.qplot(plotType, type + "PR", false, optMap["prOptions"]);
}
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, legend.position=\"bottom\")\n\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\") + 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(qPrintable(QString("# Split data into individual plots\n"
"plot_index = which(names(data)==\"Plot\")\n"
"Box <- data[grep(\"Box\",data$Plot),-c(1)]\n"
"Box$X <- factor(Box$X, levels = Box$X, ordered = TRUE)\n"
"Sample <- data[grep(\"Sample\",data$Plot),-c(1)]\n"
"Sample$X <- as.character(Sample$X)\n"
"EXT <- data[grep(\"EXT\",data$Plot),-c(1)]\n"
"EXT$X <- as.character(EXT$X)\n"
"EXP <- data[grep(\"EXP\",data$Plot),-c(1)]\n"
"EXP$X <- as.character(EXP$X)\n"
"NormLength <- data[grep(\"NormLength\",data$Plot),-c(1)]\n"
"rm(data)\n"
"\n")));
p.file.write(qPrintable(QString("\nreadData <- function(data) {\n\texamples <- list()\n"
"\tfor (i in 1:nrow(data)) {\n"
"\t\tpath <- data[i,1]\n"
"\t\tvalue <- data[i,2]\n"
"\t\tfile <- unlist(strsplit(path, \"[.]\"))[1]\n"
"\t\text <- unlist(strsplit(path, \"[.]\"))[2]\n"
"\t\tif (ext == \"jpg\" || ext == \"JPEG\" || ext == \"jpeg\" || ext == \"JPG\") {\n"
"\t\t\timg <- readJPEG(path)\n"
"\t\t} else if (ext == \"PNG\" || ext == \"png\") {\n"
"\t\t\timg <- readPNG(path)\n"
"\t\t} else if (ext == \"TIFF\" || ext == \"tiff\" || ext == \"TIF\" || ext == \"tif\") { \n"
"\t\t\timg <- readTIFF(path)\n"
"}else {\n"
"\t\t\tnext\n"
"\t\t}\n"
"\t\texample <- list(file = file, value = value, image = img)\n"
"\t\texamples[[i]] <- example\n"
"\t}\n"
"\treturn(examples)\n"
"}\n")));
p.file.write(qPrintable(QString("\nlibrary(jpeg)\n"
"library(png)\n"
"library(grid)\n")));
p.file.write(qPrintable(QString("\nplotImage <- function(image, title=NULL, label=NULL) { \n"
"\tp <- qplot(1:10, 1:10, geom=\"blank\") + annotation_custom(rasterGrob(image$image), xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) + theme(axis.line=element_blank(), axis.title.y=element_blank(), axis.text.x=element_blank(), axis.text.y=element_blank(), line=element_blank(), axis.ticks=element_blank(), panel.background=element_blank()) + labs(title=title) + xlab(label)\n"
"\treturn(p)"
"}\n")));
p.file.write(qPrintable(QString("\nsample <- readData(Sample) \n"
"rows <- sample[[1]]$value\n"
"algs <- unique(Box$%1)\n"
"algs <- algs[!duplicated(algs)]\n"
"print(plotImage(sample[[1]],\"Sample Landmarks\",sprintf(\"Total Landmarks: %s\",sample[[1]]$value))) \n"
"if (nrow(EXT) != 0 && nrow(EXP)) {\n"
"\tfor (j in 1:length(algs)) {\n"
"\ttruthSample <- readData(EXT[EXT$. == algs[[j]],])\n"
"\tpredictedSample <- readData(EXP[EXP$. == algs[[j]],])\n"
"\t\tfor (i in 1:length(predictedSample)) {\n"
"\t\t\tmultiplot(plotImage(predictedSample[[i]],sprintf(\"%s\\nPredicted Landmarks\",algs[[j]]),sprintf(\"Average Landmark Error: %.3f\",predictedSample[[i]]$value)),plotImage(truthSample[[i]],\"Ground Truth\\nLandmarks\",\"\"),cols=2)\n"
"\t\t}\n"
"\t}\n"
"}\n").arg(p.major.size > 1 ? p.major.header : (p.minor.header.isEmpty() ? p.major.header : p.minor.header))));
p.file.write(qPrintable(QString("\n"
"# Code to format error table\n"
"StatBox <- summarySE(Box, measurevar=\"Y\", groupvars=c(\"%1\",\"X\"))\n"
"OverallStatBox <- summarySE(Box, measurevar=\"Y\", groupvars=c(\"%1\"))\n"
"mat <- matrix(paste(as.character(round(StatBox$Y, 3)), round(StatBox$ci, 3), sep=\" \\u00b1 \"),nrow=rows,ncol=length(algs),byrow=FALSE)\n"
"mat <- rbind(mat, paste(as.character(round(OverallStatBox$Y, 3)), round(OverallStatBox$ci, 3), sep=\" \\u00b1 \"))\n"
"mat <- rbind(mat, as.character(round(NormLength$Y, 3)))\n"
"colnames(mat) <- algs\n"
"rownames(mat) <- c(seq(0,rows-1),\"Aggregate\",\"Average IPD\")\n"
"ETable <- as.table(mat)\n").arg(p.major.size > 1 ? p.major.header : (p.minor.header.isEmpty() ? p.major.header : p.minor.header))));
p.file.write(qPrintable(QString("\n"
"print(textplot(ETable))\n"
"print(title(\"Landmarking Error Rates\"))\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