Concatenated sequence automatic bounds update

[Masoud Ramuz]

Dear all,

I'm concatenating sequences on the Z axis through

            concS = SequenceUtil.concatZ(seqBundle, false, false, true);
The completed sequence shows the following:

Auto-bounds/Refresh on the histogram is not working despite looking ticked.

Unticking and reticking the box fixes it:

I'm wondering if there's a way to just have it start with the properly working auto bounds?

I've tried setting

            concS.setAutoUpdateChannelBounds(true);

but this does not solve the issue.

[Stephane]

Dear Masoud,

That should fix your problem:

concS.updateChannelsBounds(true);

- Stephane

[Masoud Ramuz]

Dear Stephane,

Sorry for getting back to this so late, I hadn't had much chance to properly test this solution before.

Sadly this doesn't work for me, no matter where in my code I try to implement your solution.

To clarify things further, please see the image below. I'm creating a concatenated sequence out of isolations of images created from specific locations of my acquisition. This is done by stacking the images from these 4 ROI (green) into one sequence's Z axis (Pos1), using

SequenceUtil.concatZ()

As you can see, the Pos1 sequence's histogram settings do not match auto-bounds for any of the images inside of it despite setting

concS.updateChannelsBounds(true);

I've tried to set this after concatenation of the sequence, as well as much later in my code.

Right now I'm forced to manually turn auto-bounds off and on again for each concS (we have about 5 to 8 of these during an experiment), so it would be nice if there was a way to solve this issue.

Cheers,

Masoud

[Stephane]

Dear Masoud,

Sometime it's a bit tricky to understand why the bounds didn't got updated correctly, specially when you create the sequence or/and the viewer before setting the data into it.

What you can try is to use concs.beginUpdate() / concs.endUpdate()  before and after changing sequence data.

It would be nice to have, if possible, the piece of code generating concs (just that part) as i cannot reproduce the issue here.

- Stephane

[Masoud Ramuz]

Dear Stephane, the begin/endUpdate doesn't help.

I'll post some code below:

Initial setup of the image splitter gets sequences with ROIs drawn on them and will crop to these ROIs and concatenate the resulting images into one sequence:

    Splitter (ArrayList<Sequence> acquiredSeqs, File transfoFile) throws InterruptedException{
        System.out.println("started S1");
        rois = new ArrayList<ROI>();
        cropImages = new ArrayList<IcyBufferedImage>();
        seqBundleList = new ArrayList<>();
        concSeqList = new ArrayList<Sequence>();
        fuck = false;
        SU1 = null;
        doneSU = false;
        init = true;
        ArrayList<Sequence>    seqBundle = null;

        System.out.println("splitter checkpoint 1");
        for (int r = 0; r < rois.size(); r++) {
            rois.get(r).setName(rois.get(r).getName() + " Channel#" + Integer.toString(r));
            rois.get(r).setShowName(true);
        }
       
        for (Sequence acquiredSeq : acquiredSeqs) {            
        // get current position
        String pos = ExtractPos(acquiredSeq);        
       
        // get image type
        dataType = acquiredSeq.getDataType_();
       
        // get contours for splitting
        rois = acquiredSeqs.get(0).getROIs();
        possibilities = new String[rois.size()];
       
        //Create image per ROI
        seqBundle = new ArrayList<Sequence>();
            for(int r = 0; r < rois.size(); r++)
            {
                ROI roi = rois.get(r);
                Rectangle5D bnd = roi.getBounds5D();
                IcyBufferedImage img = new IcyBufferedImage((int)Math.round(bnd.getSizeX()), (int) Math.round(bnd.getSizeY()), 1, dataType);
             
                //TODO: Before each crop, apply transform. After each crop, reset base image
                //change bnd to after-transform corners
                IcyBufferedImage copyImg = acquiredSeq.getLastImage();
               
                // store image
                cropImages.add(r, img);
             
                // create sequence
                Sequence s = new Sequence(img);
               
                // change sequence name
                s.setName(roi.getName());
               
                // show it
//                Icy.getMainInterface().addSequence(s);
               
                // ready ROI options
                possibilities[r] = s.getName();
               
                // create bundle of split images from single sequence(position)
                seqBundle.add(s);
            }
            // pair bundles with their pos name
            seqBundleList.add(new BPpair(seqBundle, pos));

        //Concatenate split images
        if (!MultiFretIcy.PS.offlineBool) {
            Sequence[] seqBundle2 = new Sequence[seqBundle.size()];
            seqBundle2 = seqBundle.toArray(seqBundle2);
           
            // create sequence
            Sequence concS = new Sequence();
            concS.beginUpdate();
            concS = SequenceUtil.concatZ(seqBundle2, false, false, true);
            concS.endUpdate();
           
            // set sequence name
            concS.setName(pos);
           
            // set channel names
            for(int r = 0; r < rois.size(); r++)  {
                concS.setChannelName(r, rois.get(r).getName());
            }
           
            // show it
            concS.updateChannelsBounds(true);
            Icy.getMainInterface().addSequence(concS);
           
            // List
            concSeqList.add(concS);

            System.out.println("made thing");
            System.out.println("Triggered split");    
           
            // Initial split so SU has something to work with
            Split(new AcquiredObject(acquiredSeq.getLastImage(),System.nanoTime(),pos),transfoFile,false);            

        }
    }

The following Split method is called every time a new acquisition is made, and will crop the acquisition in the same way as before and put the image data in the right concatenated sequence:

    public void Split(AcquiredObject acqObj, File transfoFile,boolean x) {
        // Update images
        IcyBufferedImage newImage = null;
        try {
            newImage = acqObj.acqImg;
        } catch (Exception e) {
            MessageDialog.showDialog("ERROR ACQUIRING IMAGE");
            e.printStackTrace();
        }
       
        for(int q = 0; q < seqBundleList.size(); q++) {
            if(seqBundleList.get(q).Pos.equals(acqObj.position)) {
                ArrayList<Sequence> seqBundle = seqBundleList.get(q).Bundle;
                for(int r = 0; r < rois.size(); r++)  {            
                    seqBundle.get(r).beginUpdate();
                   
                    ROI roi = rois.get(r);
                    Rectangle bnd = roi.getBounds5D().toRectangle2D().getBounds();
                    IcyBufferedImage img = cropImages.get(r);
                    img.copyData(newImage, bnd, null);
                   
                    seqBundle.get(r).removeAllImages();
                    seqBundle.get(r).addImage(img);
                   
                    Sequence concS = null;
                    for (Sequence s : concSeqList) {
                        if (s.getName().equals(acqObj.position)) {
                            concS = s;
                        }
                    }
                   
                    if (concS == null) {System.out.println("No Matching concS");}
                   
                    concS.beginUpdate();                  
                    concS.setImage(0, r, IcyBufferedImageUtil.scale(img, concS.getWidth(), concS.getHeight())); init = false;
                    concS.endUpdate();
                    concS.updateChannelsBounds(true);                  

                    // x is true after the initial split
                    if (x==true) {
                        String roiN = rois.get(r).getName();
                        System.out.println("Split made: " + roiN);
                        if (roiN != base && MultiFretIcy.PS.transformEnabled == true) {
                        Transform(seqBundle.get(r), transfoFile, roiN);
                        }
                    }
                    seqBundle.get(r).endUpdate();      
                }
            }
        }

Apologies if it's a bit messy, please ask for any clarification needed.