Skip to content

Commit

Permalink
New way combine pre and postChl
Browse files Browse the repository at this point in the history
  • Loading branch information
@ccwang92
ccwang92 committed Jun 8, 2020
1 parent 4e21453 commit be59dee
Show file tree
Hide file tree
Showing 28 changed files with 218 additions and 128 deletions.
6 changes: 0 additions & 6 deletions .classpath
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,6 @@
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
<attributes>
<attribute name="maven.pomderived" value="true"/>
<attribute name="test" value="true"/>
</attributes>
</classpathentry>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5">
<attributes>
<attribute name="maven.pomderived" value="true"/>
Expand Down
1 change: 1 addition & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
/target/
2 changes: 2 additions & 0 deletions .settings/org.eclipse.jdt.core.prefs
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
org.eclipse.jdt.core.compiler.compliance=1.5
org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
org.eclipse.jdt.core.compiler.release=disabled
org.eclipse.jdt.core.compiler.source=1.5
188 changes: 116 additions & 72 deletions src/main/java/SynQuantVid_.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,11 @@ public class SynQuantVid_ implements PlugIn, DialogListener{
protected double minFill, maxWHRatio;
protected int NumSynSite=0;
protected ImagePlus outputImp=null; // detection results output
int[][][][] synIdx;
double[][][][] synZscore;
int [][][][] synIdx;
double [][][][] synZscore;
double slideThrZ;
int [][][] sliderSynMap; // synapse map after post-processing
int way2combinePostPre = 1; // the way to combine pre- and post-channel, 0:intersect, 1: add pre-zscore to post-zscore


boolean fastflag = true; //true: no use because we only use fast version
Expand Down Expand Up @@ -85,6 +86,8 @@ public boolean showDialog()
openData[activeImageIDs.length] = "Null";
gd.addChoice("Post-synapse:", openData, openData[0]);
gd.addChoice("Pre-synapse:", openData, openData[activeImageIDs.length]);
String[] combinePrePostChl = {"intersect", "post_channel_mainly","Null"};
gd.addChoice("Way to combine:", combinePrePostChl, combinePrePostChl[combinePrePostChl.length-1]);
gd.addChoice("Dendrite channel", openData, openData[activeImageIDs.length]);
gd.showDialog();
if (gd.wasCanceled()){
Expand All @@ -102,6 +105,9 @@ public boolean showDialog()
}
int post_chl = gd.getNextChoiceIndex();
int pre_chl = gd.getNextChoiceIndex();
way2combinePostPre = gd.getNextChoiceIndex();
if (way2combinePostPre>1) //user forget to set or single channel
way2combinePostPre = 1;
int den_chl = gd.getNextChoiceIndex();

numChannels = 2; // we only care two channels: post- and pre-synaptic channel
Expand Down Expand Up @@ -153,13 +159,9 @@ public boolean showDialog()
* ***/
public void synQuant3D_real() {
//// parameter initialization
paraQ3D q = new paraQ3D(numChannels, 0.8);
paraQ3D q = new paraQ3D(numChannels, way2combinePostPre, 0.8);
BasicMath bm = new BasicMath();
//// data saving final results
// timePts = imp.getNFrames();
// synIdx = new int [timePts][zSlice][height][width];
// synZscore = new double [timePts][zSlice][height][width];
// q.synZscore = new double [timePts][zSlice][height][width];
slideThrZ = 1000;
ppsd3D particle3D_det = null;
//short[][] Arr3D = null;
Expand All @@ -178,9 +180,7 @@ public void synQuant3D_real() {
synIdx = new int [timePts][zSlice][height][width];
synZscore = new double [timePts][zSlice][height][width];
}
//if (q._NumChannel == q.NumChannelProcessed + 1 ) {

//}

double vox_x = imp.getCalibration().pixelWidth;
if(vox_x==1)//simulated data
vox_x = 2.0757e-7;
Expand All @@ -191,33 +191,28 @@ public void synQuant3D_real() {

long startTime1=System.nanoTime();
////particle detection
for (int i=1; i <= timePts; i++){
for (int i=1; i <= timePts; i++)
{
q.curTps = i-1;
short[][] Arr3D = stack2array(type, stack, i); // #zstack*#pixels in one slice
paraP3D p = new paraP3D(fdr, zscore_thres,(int)bm.matrix2DMin(Arr3D),(int)bm.matrix2DMax(Arr3D),MinSize, MaxSize, minFill, maxWHRatio);
particle3D_det = new ppsd3D(Arr3D, width, height, vox_x, p,q);
// synIdx[i-1] = particle3D_det.ppsd_main.kMap;
// synZscore[i-1] = particle3D_det.ppsd_main.zMap;
// for the final channel, we save the output results
if (q._NumChannel == q.NumChannelProcessed + 1 ) { // last one

// for the post channel, we save the output results
if (q._NumChannel == q.NumChannelProcessed + 1 )
{ // last one
synIdx[i-1] = particle3D_det.ppsd_main.kMap;
synZscore[i-1] = particle3D_det.ppsd_main.zMap;
double tmpThrZ = particle3D_det.ppsd_main.thrZ;
if (slideThrZ > tmpThrZ)
slideThrZ = tmpThrZ;
}else {// not last one
}else
{// pre-channel
q.synZscore[q.curTps] = particle3D_det.ppsd_main.zMap;
// if (q.NumChannelProcessed == 0) { // first one
// q.synZscore[q.curTps] = particle3D_det.ppsd_main.zMap;
// }else { //not first, not last
// q.synZscore[q.curTps] = bm.matrix3DAdd(q.synZscore[q.curTps], particle3D_det.ppsd_main.zMap);
// }
}
}
long endTime1=System.nanoTime();
System.out.println("Finished. Data size: "+zSlice+" * "+height+" * "+width+" * "+timePts+" Total running time: "+(endTime1-startTime1)/1e9);
//// results display

q.NumChannelProcessed ++;
q.var = 0; // reset variance, preparing for new channel
}
Expand Down Expand Up @@ -261,28 +256,39 @@ public void synQuant3D_real() {

// display the results of puncta detection results
ImageHandling IH = new ImageHandling();
if (imp.getNSlices() == 1) { //for 2d data use ROI manager to display results
if (imp.getNSlices() == 1)
{ //for 2d data use ROI manager to display results
boolean [][] synMap2dBin = new boolean[synZscore[0][0].length][synZscore[0][0][0].length];
if (sliderSynMap == null) {
for (int i=0; i<synZscore[0][0].length; i++) {
for (int j=0; j<synZscore[0][0][0].length;j++) {
if(synZscore[0][0][i][j]>=zscore_thres) {
if (sliderSynMap == null)
{
for (int i=0; i<synZscore[0][0].length; i++)
{
for (int j=0; j<synZscore[0][0][0].length;j++)
{
if(synZscore[0][0][i][j]>=zscore_thres)
{
synMap2dBin[i][j] = true;
}
else {
else
{
synMap2dBin[i][j] = false;
}
}
}
}
else {
else
{
//boolean [][] synMap2dBin = new boolean[sliderSynMap[0].length][sliderSynMap[0][0].length];
for (int i=0; i<sliderSynMap[0].length; i++) {
for (int j=0; j<sliderSynMap[0][0].length;j++) {
if(sliderSynMap[0][i][j]>0) {
for (int i=0; i<sliderSynMap[0].length; i++)
{
for (int j=0; j<sliderSynMap[0][0].length;j++)
{
if(sliderSynMap[0][i][j]>0)
{
synMap2dBin[i][j] = true;
}
else {
else
{
synMap2dBin[i][j] = false;
}
}
Expand All @@ -295,30 +301,43 @@ public void synQuant3D_real() {
ROIImp.show();
IH.DisplayROI(IH.NextLabel,height,width,synMap2d, ROIImp,"Synapse detection results");
}
else {//for 3d data use table to display statistics results
else
{//for 3d data use table to display statistics results
boolean [][][] synMap3dBin = new boolean[synZscore[0].length][synZscore[0][0].length][synZscore[0][0][0].length];
if (sliderSynMap == null) {
for (int k = 0; k<synZscore[0].length; k++) {
for (int i=0; i<synZscore[0][0].length; i++) {
for (int j=0; j<synZscore[0][0][0].length;j++) {
if(synZscore[0][k][i][j]>=zscore_thres) {
if (sliderSynMap == null)
{
for (int k = 0; k<synZscore[0].length; k++)
{
for (int i=0; i<synZscore[0][0].length; i++)
{
for (int j=0; j<synZscore[0][0][0].length;j++)
{
if(synZscore[0][k][i][j]>=zscore_thres)
{
synMap3dBin[k][i][j] = true;
}
else {
else
{
synMap3dBin[k][i][j] = false;
}
}
}
}
}
else {
for (int k = 0; k<sliderSynMap.length; k++) {
for (int i=0; i<sliderSynMap[0].length; i++) {
for (int j=0; j<sliderSynMap[0][0].length;j++) {
if(sliderSynMap[k][i][j]>0) {
else
{
for (int k = 0; k<sliderSynMap.length; k++)
{
for (int i=0; i<sliderSynMap[0].length; i++)
{
for (int j=0; j<sliderSynMap[0][0].length;j++)
{
if(sliderSynMap[k][i][j]>0)
{
synMap3dBin[k][i][j] = true;
}
else {
else
{
synMap3dBin[k][i][j] = false;
}
}
Expand All @@ -327,19 +346,24 @@ public void synQuant3D_real() {
}
int[][][] synMap3d = IH.bwlabel3D(synMap3dBin,26);
double [][] puncta_feats = new double [IH.NextLabel][4]; // volume, Mean, Max, Min intensity
for (int i=0; i < IH.NextLabel; i++) {
for (int i=0; i < IH.NextLabel; i++)
{
puncta_feats[i][0] = 0;
puncta_feats[i][1] = 0;
puncta_feats[i][2] = 0;
puncta_feats[i][3] = 65536;
}
double[][] ArrDouble3D = stack2DoubleArray(imp.getType(), imp.getStack(), 1);
System.out.println(bm.matrix2DMax(ArrDouble3D));
for (int k = 0; k<synMap3d.length; k++) {
for (int i=0; i<synMap3d[0].length; i++) {
for (int j=0; j<synMap3d[0][0].length;j++) {
for (int k = 0; k<synMap3d.length; k++)
{
for (int i=0; i<synMap3d[0].length; i++)
{
for (int j=0; j<synMap3d[0][0].length;j++)
{
int punctum_id = synMap3d[k][i][j]-1;
if (punctum_id >= 0) {
if (punctum_id >= 0)
{
if (punctum_id >= puncta_feats.length)
System.out.print(true);
puncta_feats[punctum_id][0] += 1;
Expand Down Expand Up @@ -368,21 +392,27 @@ public void synQuant3D_real() {
det_ft_table.showRowNumbers(false);
det_ft_table.show("Puncta statistics on 3D data");
}
if(den_imp != null) {
if (den_imp.getNSlices() == 1 & imp.getNSlices() == 1) { //do quantification
if(den_imp != null)
{
if (den_imp.getNSlices() == 1 & imp.getNSlices() == 1)
{ //do quantification
boolean [][] kSynR1 = new boolean [synZscore[0][0].length][synZscore[0][0][0].length];
if (sliderSynMap == null) {
if (sliderSynMap == null)
{
for (int i=0; i<kSynR1.length; i++)
{
for(int j=0; j<kSynR1[0].length;j++) {
for(int j=0; j<kSynR1[0].length;j++)
{
kSynR1[i][j] = synZscore[0][0][i][j]>zscore_thres;
}
}
}
else {
else
{
for (int i=0; i<kSynR1.length; i++)
{
for(int j=0; j<kSynR1[0].length;j++) {
for(int j=0; j<kSynR1[0].length;j++)
{
kSynR1[i][j] = sliderSynMap[0][i][j] > 0;
}
}
Expand All @@ -391,7 +421,8 @@ public void synQuant3D_real() {
//show features
ResultsTable Ft_table = new ResultsTable();
int DenCnt = 0;
for (int i=0;i<den_det.CurNum;i++) {
for (int i=0;i<den_det.CurNum;i++)
{
Ft_table.incrementCounter();
DenCnt = DenCnt+1;
Ft_table.addLabel("Dendrite piece #"+DenCnt);
Expand Down Expand Up @@ -444,12 +475,17 @@ public boolean dialogItemChanged (GenericDialog gd, AWTEvent e) {
//System.out.println("-th Frame SynNum: " + zscore_thres);
//outputImp = IJ.createHyperStack("Found Particles", width, height, 1, zSlice, timePts,16/*bitdepth*/);
outputImp.show();
for (int i=1; i <= timePts; i++){
for (int i=1; i <= timePts; i++)
{
sliderSynMap = new int [zSlice][height][width];
for (int zz=0;zz<zSlice; zz++) {
for(int yy=0;yy<height; yy++) {
for(int xx=0;xx<width; xx++) {
if(synZscore[i-1][zz][yy][xx] >= zscore_thres) {
for (int zz=0;zz<zSlice; zz++)
{
for(int yy=0;yy<height; yy++)
{
for(int xx=0;xx<width; xx++)
{
if(synZscore[i-1][zz][yy][xx] >= zscore_thres)
{
sliderSynMap[zz][yy][xx] = 1;//synZscore[i-1][zz][yy][xx];
}
}
Expand Down Expand Up @@ -585,21 +621,28 @@ public void SynapticDisplay(int [][][] kSynR1, int curTimePt){
// }
// }
double max_intensity = 0;
if(imp.getType() == ImagePlus.GRAY16) {
for(int stackNum=1; stackNum<=curStack.getSize(); stackNum++) {
if(imp.getType() == ImagePlus.GRAY16)
{
for(int stackNum=1; stackNum<=curStack.getSize(); stackNum++)
{
double tmp_max = curInStack.getProcessor(stackNum).getStatistics().max;
if (max_intensity < tmp_max) {
if (max_intensity < tmp_max)
{
max_intensity = tmp_max;
}
}
}
for(int stackNum=1; stackNum<=curStack.getSize(); stackNum++) {
for(int stackNum=1; stackNum<=curStack.getSize(); stackNum++)
{
outIP = curStack.getProcessor(stackNum);
inIP = curInStack.getProcessor(stackNum);
for (int i = 0; i < width; i++) {
for(int j = 0;j<height;j++){
for (int i = 0; i < width; i++)
{
for(int j = 0;j<height;j++)
{
// put channel values in an integer
if(imp.getType() == ImagePlus.GRAY8) {
if(imp.getType() == ImagePlus.GRAY8)
{
int tmp_val = (int)inIP.get(i, j) & 0xff;
if(kSynR1[stackNum-1][j][i]>0)
outIP.set(i, j, (((int)200 & 0xff) << 16)
Expand All @@ -609,7 +652,8 @@ public void SynapticDisplay(int [][][] kSynR1, int curTimePt){
outIP.set(i, j, (((int)0 & 0xff) << 16)
+ (tmp_val << 8)
+ ((int)0 & 0xff));
}else {
}else
{
// if(inIP.get(i, j)>255*10)
// System.out.println(" "+inIP.get(i, j));
byte tmp_float_val = (byte) ((((double)inIP.get(i, j))/max_intensity)*255);
Expand Down
Loading

0 comments on commit be59dee

Please sign in to comment.