diff --git a/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java b/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java
index b24368184e1934275a557eb4c48ee189a11dfb8d..2f1fac8c4a5f44ececd3659c1d1a424b21ea1038 100644
--- a/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java
+++ b/src/main/java/plugins/fab/trackmanager/processors/TrackProcessorMSD.java
@@ -105,14 +105,19 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
{
XYSeries series = new XYSeries("Track " + trackPool.getTrackIndex(ts));
- if (ts.isAllDetectionEnabled())
+ // Better to allow partially clipped tracks otherwise we cannot get MSD for them (Stephane)
+ // TODO: check that it doesn't bring any regression
+ // if (ts.isAllDetectionEnabled())
{
double[] msd = scaledMeanSquaredDisplacement(seq, ts);
- for (int i = 0; i < msd.length; i++)
- series.add(i * tScale, msd[i]);
+ if (msd.length > 0)
+ {
+ for (int i = 0; i < msd.length; i++)
+ series.add(i * tScale, msd[i]);
- xyDataset.addSeries(series);
+ xyDataset.addSeries(series);
+ }
}
}
}
@@ -122,14 +127,19 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
{
XYSeries series = new XYSeries("Track " + trackPool.getTrackIndex(ts));
- if (ts.isAllDetectionEnabled())
+ // Better to allow partially clipped tracks otherwise we cannot get MSD for them (Stephane)
+ // TODO: check that it doesn't bring any regression
+ // if (ts.isAllDetectionEnabled())
{
double[] msd = scaledMeanSquaredDisplacement(null, ts);
- for (int i = 0; i < msd.length; i++)
- series.add(i, msd[i]);
+ if (msd.length > 0)
+ {
+ for (int i = 0; i < msd.length; i++)
+ series.add(i, msd[i]);
- xyDataset.addSeries(series);
+ xyDataset.addSeries(series);
+ }
}
}
}
@@ -203,9 +213,11 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
outputName = trackPool.getDisplaySequence().getFilename();
outputName += ".msd.xls";
}
- else outputName = SaveDialog.chooseFileForResult("XLS MSD export", "tracks-msd", ".xls");
+ else
+ outputName = SaveDialog.chooseFileForResult("XLS MSD export", "tracks-msd", ".xls");
- if (StringUtil.isEmpty(outputName)) return;
+ if (StringUtil.isEmpty(outputName))
+ return;
try
{
@@ -229,25 +241,31 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
int row = 0;
for (TrackSegment ts : trackPool.getTrackSegmentList())
{
- if (ts.isAllDetectionEnabled())
+ // Better to allow partially clipped tracks otherwise we cannot get MSD for them (Stephane)
+ // TODO: check that it doesn't bring any regression
+ // if (ts.isAllDetectionEnabled())
{
- System.out.println("track " + cnt);
-
- if (page != null)
- XLSUtil.setCellString(page, 0, row, "track " + cnt);
-
double[] msd = scaledMeanSquaredDisplacement(seq, ts);
- for (int i = 0; i < msd.length; i++)
+
+ if (msd.length > 0)
{
- System.out.println((i * tScale) + "\t" + msd[i]);
- // System.out.println(i + "\t" + msd[i]);
+ System.out.println("track " + cnt);
if (page != null)
- XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
- }
+ XLSUtil.setCellString(page, 0, row, "track " + cnt);
+
+ for (int i = 0; i < msd.length; i++)
+ {
+ System.out.println((i * tScale) + "\t" + msd[i]);
+ // System.out.println(i + "\t" + msd[i]);
+
+ if (page != null)
+ XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
+ }
- cnt++;
- row++;
+ cnt++;
+ row++;
+ }
}
}
}
@@ -258,26 +276,30 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
for (TrackSegment ts : trackPool.getTrackSegmentList())
{
- if (ts.isAllDetectionEnabled())
+ // Better to allow partially clipped tracks otherwise we cannot get MSD for them (Stephane)
+ // TODO: check that it doesn't bring any regression
+ // if (ts.isAllDetectionEnabled())
{
- System.out.println("track " + cnt);
-
- if (page != null)
- XLSUtil.setCellString(page, 0, row, "track " + cnt);
-
double[] msd = scaledMeanSquaredDisplacement(null, ts);
- // double[] msd = meanSquaredDisplacement(ts);
- for (int i = 0; i < msd.length; i++)
+ if (msd.length > 0)
{
- System.out.println(i + "\t" + msd[i]);
+ System.out.println("track " + cnt);
if (page != null)
- XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
- }
+ XLSUtil.setCellString(page, 0, row, "track " + cnt);
+
+ for (int i = 0; i < msd.length; i++)
+ {
+ System.out.println(i + "\t" + msd[i]);
- cnt++;
- row++;
+ if (page != null)
+ XLSUtil.setCellNumber(page, i + 1, row, msd[i]);
+ }
+
+ cnt++;
+ row++;
+ }
}
}
}
@@ -320,65 +342,96 @@ public class TrackProcessorMSD extends PluginTrackManagerProcessor implements Ac
sz = 1d;
}
- int nMSD = ts.getDetectionList().size();
- // double[] dt_n = new double[nMSD];
- double[] msd = new double[nMSD];
+ final int numDetection = ts.getDetectionList().size();
+ int firstEnabledDetectionIndex = -1;
+ int numEnabledDetection = 0;
+ int lastFirstEnabledDetectionIndex = -1;
+ int lastNumEnabledDetection = 0;
- for (int t = 1; t < nMSD; t++)
+ // Find partially enabled/clipped tracks otherwise we cannot get MSD for them (Stephane)
+ // TODO: check that it doesn't bring any regression
+ for (int i = 0; i < numDetection; i++)
{
- msd[t] = 0d;
- for (int j = 1; j <= t; j++)
- msd[t] += scaledSquaredDistance(ts.getDetectionAt(0), ts.getDetectionAt(j), sx, sy, sz);
-
- msd[t] /= t;
- }
-
- // for (int dt = 1; dt < nMSD; dt++)
- // {
- // for (int j = 0; (j + dt) < nMSD; j += dt)
- // {
- // msd[dt] += scaledSquaredDistance(ts.getDetectionAt(j), ts.getDetectionAt(j + dt), sx, sy, sz);
- // dt_n[dt]++;
- // }
- // }
- //
- // for (int dt = 1; dt < nMSD; dt++)
- // msd[dt] = (dt_n[dt] != 0) ? msd[dt] / dt_n[dt] : 0;
+ final Detection d = ts.getDetectionAt(i);
- return msd;
- }
-
- // mean squared displacement
- private double[] meanSquaredDisplacement(TrackSegment ts)
- {
- int nMSD = ts.getDetectionList().size();
+ if (d.isEnabled())
+ {
+ // start of track
+ if (lastFirstEnabledDetectionIndex == -1)
+ {
+ lastFirstEnabledDetectionIndex = i;
+ lastNumEnabledDetection = 1;
+ }
+ else
+ lastNumEnabledDetection++;
+ }
+ else
+ {
+ // check if last track is the longest found
+ if (lastNumEnabledDetection > numEnabledDetection)
+ {
+ numEnabledDetection = lastNumEnabledDetection;
+ firstEnabledDetectionIndex = lastFirstEnabledDetectionIndex;
+ }
- double[] dt_n = new double[nMSD];
- double[][] msd = new double[nMSD][2];
+ // reset track
+ lastFirstEnabledDetectionIndex = -1;
+ lastNumEnabledDetection = 0;
+ }
+ }
- for (int dt = 1; dt < nMSD; dt++)
+ // check if last track is the longest found
+ if (lastNumEnabledDetection > numEnabledDetection)
{
- msd[dt][0] = dt * 1;
-
- for (int j = 0; j + dt < ts.getDetectionList().size(); j += dt)
- {
- msd[dt][1] += squaredDistance(ts.getDetectionAt(j), ts.getDetectionAt(j + dt));
- dt_n[dt]++;
- }
+ numEnabledDetection = lastNumEnabledDetection;
+ firstEnabledDetectionIndex = lastFirstEnabledDetectionIndex;
}
- for (int dt = 1; dt < nMSD; dt++)
- msd[dt][1] = (dt_n[dt] != 0) ? msd[dt][1] / dt_n[dt] : 0;
+ double[] msd = new double[numEnabledDetection];
- double[] resultmsd = new double[nMSD];
- resultmsd[0] = 0;
- for (int dt = 1; dt < nMSD; dt++)
- resultmsd[dt] = msd[dt][1];
+ for (int t = 1; t < numEnabledDetection; t++)
+ {
+ msd[t] = 0d;
+ for (int j = 1; j <= t; j++)
+ msd[t] += scaledSquaredDistance(ts.getDetectionAt(firstEnabledDetectionIndex), ts.getDetectionAt(firstEnabledDetectionIndex + j), sx, sy, sz);
- return resultmsd;
+ msd[t] /= t;
+ }
+ return msd;
}
+ // mean squared displacement
+// private double[] meanSquaredDisplacement(TrackSegment ts)
+// {
+// int nMSD = ts.getDetectionList().size();
+//
+// double[] dt_n = new double[nMSD];
+// double[][] msd = new double[nMSD][2];
+//
+// for (int dt = 1; dt < nMSD; dt++)
+// {
+// msd[dt][0] = dt * 1;
+//
+// for (int j = 0; j + dt < ts.getDetectionList().size(); j += dt)
+// {
+// msd[dt][1] += squaredDistance(ts.getDetectionAt(j), ts.getDetectionAt(j + dt));
+// dt_n[dt]++;
+// }
+// }
+//
+// for (int dt = 1; dt < nMSD; dt++)
+// msd[dt][1] = (dt_n[dt] != 0) ? msd[dt][1] / dt_n[dt] : 0;
+//
+// double[] resultmsd = new double[nMSD];
+// resultmsd[0] = 0;
+// for (int dt = 1; dt < nMSD; dt++)
+// resultmsd[dt] = msd[dt][1];
+//
+// return resultmsd;
+//
+// }
+
private static double squaredDistance(Detection d1, Detection d2)
{
return scaledSquaredDistance(d1, d2, 1d, 1d, 1d);