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Adding getter and setter for m_ranges christiaanjs/beast-validation#2 #95

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Merged
rbouckaert merged 1 commit into from
May 5, 2025
Merged

Adding getter and setter for m_ranges christiaanjs/beast-validation#2 #95

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53 changes: 29 additions & 24 deletions src/beastfx/app/tools/LogAnalyser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,11 @@ protected enum type {
*/
protected List<String>[] m_ranges;

public List<String>[] getRanges() {return m_ranges;}

public void setRanges(List<String>[] ranges) {this.m_ranges = ranges;}


/**
* data from log file with burn-in removed *
*/
Expand Down Expand Up @@ -152,7 +157,7 @@ public LogAnalyser() {
*
* @param args
* @param burnInPercentage burnInPercentage typical = 10; percentage of data that can be ignored
* @throws IOException
* @throws IOException
*/
public LogAnalyser(String[] args, int burnInPercentage) throws IOException {
this(args, burnInPercentage, false, true);
Expand All @@ -178,11 +183,11 @@ public LogAnalyser(String fileName, int burnInPercentage) throws IOException {
public LogAnalyser(String fileName, int burnInPercentage, String [] tags) throws IOException {
this(fileName, burnInPercentage, false, true, tags);
}

public LogAnalyser(String fileName, int burnInPercentage, boolean quiet) throws IOException {
this(fileName, burnInPercentage, quiet, true, null);
}

public LogAnalyser(String fileName, int burnInPercentage, boolean quiet, String [] tags) throws IOException {
this(fileName, burnInPercentage, quiet, true, tags);
}
Expand All @@ -194,7 +199,7 @@ public LogAnalyser(String fileName) throws IOException {
public LogAnalyser(String fileName, int burnInPercentage, boolean quiet, boolean calcStats) throws IOException {
this(fileName, burnInPercentage, quiet, calcStats, null);
}

public LogAnalyser(String fileName, int burnInPercentage, boolean quiet, boolean calcStats, String [] tags) throws IOException {
this.fileName = fileName;
this.quiet = quiet;
Expand Down Expand Up @@ -238,7 +243,7 @@ protected void readLogFile(String fileName, int burnInPercentage) throws IOExcep
// grab data from the log, ignoring burn in samples
m_types = new type[items];
Arrays.fill(m_types, type.INTEGER);
int reported = 0;
int reported = 0;
while (fin.ready()) {
str = fin.readLine();
int i = 0;
Expand Down Expand Up @@ -275,7 +280,7 @@ protected void readLogFile(String fileName, int burnInPercentage) throws IOExcep
m_types[i] = type.BOOL;
else
m_types[i] = type.NOMINAL;

fin.close();
} // readLogFile

Expand All @@ -286,7 +291,7 @@ protected void readLogFile(String fileName, int burnInPercentage) throws IOExcep
public void calcStats() {
calcStats(null);
}

public void calcStats(String [] tags) {
logln("\nCalculating statistics\n\n" + BAR);
int stars = 0;
Expand Down Expand Up @@ -317,7 +322,7 @@ public void calcStats(String [] tags) {
m_fMean[i] = Double.NaN;
m_fStdDev[i] = Double.NaN;
}

if (m_types[i] == type.REAL || m_types[i] == type.INTEGER) {
// calc median, and 95% HPD interval
Double[] sorted = trace.clone();
Expand All @@ -336,12 +341,12 @@ public void calcStats(String [] tags) {
}
m_f95HPDlow[i] = sorted[hpdIndex];
m_f95HPDup[i] = sorted[hpdIndex + n];

// calc effective sample size
m_fACT[i] = ESS.ACT(m_fTraces[i], sampleInterval);
m_fStdError[i] = ESS.stdErrorOfMean(trace, sampleInterval);
m_fESS[i] = trace.length / (m_fACT[i] / sampleInterval);

// calc geometric mean
if (sorted[0] > 0) {
// geometric mean is only defined when all elements are positive
Expand Down Expand Up @@ -530,7 +535,7 @@ public String getLogFile() {
public void print(PrintStream out) {
print(out, null);
}

public void print(PrintStream out, String [] tags) {
// set up header for prefix, if any is specified
String prefix = System.getProperty("prefix");
Expand All @@ -544,7 +549,7 @@ public void print(PrintStream out, String [] tags) {
}
}
}

try {
// delay so that stars can be flushed from stderr
Thread.sleep(100);
Expand Down Expand Up @@ -598,7 +603,7 @@ public void printOneLineHeader(PrintStream out, String [] tags) {
out.println("\t");
}


private boolean matchesTags(String [] tags, int paramIdx) {
if (tags == null) {
return true;
Expand All @@ -611,7 +616,7 @@ private boolean matchesTags(String [] tags, int paramIdx) {
}
return false;
}

/**
* Display results for single log on one line.
*
Expand All @@ -620,7 +625,7 @@ private boolean matchesTags(String [] tags, int paramIdx) {
public void printOneLine(PrintStream out) {
printOneLine(out, null);
}

public void printOneLine(PrintStream out, String [] tags) {
for (int paramIdx=1; paramIdx<m_sLabels.length; paramIdx++) {
if (matchesTags(tags, paramIdx)) {
Expand Down Expand Up @@ -666,7 +671,7 @@ static void printUsageAndExit() {
System.out.println("[fileX] log file to analyse. Multiple files are allowed, each is analysed separately");
System.exit(0);
}

class CoreRunnable implements java.lang.Runnable {
static private boolean headerPrinted = false;
static private int lineNr = 0;
Expand All @@ -675,7 +680,7 @@ class CoreRunnable implements java.lang.Runnable {
List<String> files;
int burnInPercentage;
String [] tags;

CoreRunnable(int start, int end, List<String> files, CountDownLatch countDown, int burnInPercentage, String [] tags) {
this.start = start;
this.end = end;
Expand All @@ -698,12 +703,12 @@ public void run() {
while (!headerPrinted) {
Thread.sleep(500);
}

synchronized (countDown) {
System.out.print(lineNr + "\t" + files.get(i) + "\t");
lineNr++;
analyser.printOneLine(System.out, tags);
}
}
} catch (IOException | InterruptedException e) {
e.printStackTrace();
}
Expand All @@ -713,7 +718,7 @@ public void run() {

} // CoreRunnable


/**
* @param args
*/
Expand Down Expand Up @@ -808,19 +813,19 @@ public static void main(String[] args) {

}
countDown.await();

// gracefully exit
exec.shutdownNow();
System.exit(0);

} else {
for (int idx=0; idx<files.size(); idx++) {
analyser = new LogAnalyser(files.get(idx), burninPercentage, true, tags);

if (idx == 0) {
analyser.printOneLineHeader(System.out, tags);
}

System.out.print(idx + "\t" + files.get(idx) + "\t");
analyser.printOneLine(System.out, tags);
}
Expand Down