Replies Created

  •
    deborakeller0@gmail.com November 14, 2019 at 10:24 am

    I did another trial overnight (still running) with 3 images (193 time points, 900mB) and an output in TXT and it seems to have worked for the first time ever…

    though if I try and touch the program it will freeze

    However, it took a looong time and I have no clue why the 2nd image took so long

    Image1:
    Active contour: 1h20 (5521 ROI)
    spot detector: 8 min (199247 detected scale 1 90%, 109151 filtered >4px)
    ROI inclusion analysis: 1h42 min

    image 2:
    active contour 8h49min (5617 ROI – 5061 filtered)
    spot detector 10 min (189 961 ROI detected scale 1 90%, 98529 filtered >4px)
    ROI inclusion analysis: 58 min

    image 3 is still running active contour….
    deborakeller0@gmail.com November 13, 2019 at 4:44 pm

    one idea… could the available RAM limit the writing? ie I guess the intermediate results are stored somewhere, if there is not enough RAM dedicated to the storing for big images, could that play a role?

    I currenlty have 34.2Gb of RAM for icy and it does not seem to be using cache memory or disk…

    just a thought
    deborakeller0@gmail.com November 13, 2019 at 11:25 am

    it again did not work… I get emtpy excel xlsx files – below the screenshot of the last image… snif
    deborakeller0@gmail.com November 8, 2019 at 9:54 am

    files where spot stats could not get exported are 1kb
    deborakeller0@gmail.com November 7, 2019 at 3:18 pm

    well, i am running into the excel xlsx limit quite often (and get empty excel file at the end for spot statistics, not roi inclusion)… hence switching over to .txt (where I think there should be no limit on file size / line numbers)

    The text export in ROI statistics is tab delimited and has a header on top. I found a work-around now, but if it were possible to have the CSV format as an option to export ROI stats or ROI inclusion stats ( or any measurements), it would be great (if easily doable).

     

    Thanks for the micron sign!
    deborakeller0@gmail.com November 6, 2019 at 2:19 pm

    ok – I found a libary we can import to deal with special characters (though I am still in favor of removing them coz it also causes problems when saving in txt).

    speaking of .txt …

    is it possible to add an export to a legit CSV format and ideally WITHOUT the additional first line (that specifies ==ROI inclusion == or == ROI stats== ?

    don’t know how much work it is but I am running into the excel limitations for numbers but the .txt format is a bit xombersome as well.

    cheers

    Debbi
    deborakeller0@gmail.com September 12, 2019 at 2:59 pm

    bug ROI number
    deborakeller0@gmail.com September 6, 2019 at 3:59 pm

    HI Stephane,

    does this work for all timepoints?

    I have the following script (I guess from you before  you made it as a protocol) – it works, but only at the first time point.

    Any way to make it work at all timepoints ? cheers

    Debbi

    // Click on the button
    // to edit in a frame.

    bounds = input0.getBounds2D()
    output0 = []
    ind = 0;

    for(i = 0; i < input1.length; i++)
    {
    r = input1[i]

    rbounds = r.getBounds5D().toRectangle2D();
    if ((rbounds.getMinX() == bounds.getMinX()) ||
    (rbounds.getMinY() == bounds.getMinY()) ||
    (rbounds.getMaxX() == bounds.getMaxX()) ||
    (rbounds.getMaxY() == bounds.getMaxY()))
    continue;

    output0[ind++] = r;
    }
    deborakeller0@gmail.com June 13, 2019 at 11:04 am

    This happened on multiple cells and with multiple parameters.. and even after fresh Icy installation
    deborakeller0@gmail.com June 4, 2019 at 10:52 am

     
    deborakeller0@gmail.com May 31, 2019 at 10:35 am

    he following error is reported only on first occurence :
    org.pushingpixels.substance.api.UiThreadingViolationException: State tracking must be done on Event Dispatch Thread
    at org.pushingpixels.substance.internal.utils.SubstanceCoreUtilities.testThreadingViolation(SubstanceCoreUtilities.java:2117)
    at org.pushingpixels.substance.internal.animation.StateTransitionTracker$ModelStateInfo.clear(StateTransitionTracker.java:171)
    at org.pushingpixels.substance.internal.animation.StateTransitionTracker.onModelStateChanged(StateTransitionTracker.java:337)
    at org.pushingpixels.substance.internal.animation.StateTransitionTracker$4.stateChanged(StateTransitionTracker.java:262)
    at javax.swing.DefaultButtonModel.fireStateChanged(DefaultButtonModel.java:349)
    at javax.swing.JToggleButton$ToggleButtonModel.setSelected(JToggleButton.java:269)
    at javax.swing.AbstractButton.setSelected(AbstractButton.java:348)
    at plugins.adufour.roi.ROIMeasures$MeasureSelector.loadParameters(ROIMeasures.java:1295)
    at plugins.adufour.roi.ROIMeasures$MeasureSelector.valueChanged(ROIMeasures.java:1363)
    at plugins.adufour.roi.ROIMeasures$MeasureSelector.valueChanged(ROIMeasures.java:1)
    at plugins.adufour.vars.lang.Var.fireVariableChanged(Var.java:328)
    at plugins.adufour.vars.lang.Var.setValue(Var.java:791)
    at plugins.adufour.vars.lang.Var.loadFromXML(Var.java:530)
    at plugins.adufour.blocks.util.BlocksML.loadWorkFlow_V4(BlocksML.java:1430)
    at plugins.adufour.blocks.util.BlocksML.loadWorkFlow_V4(BlocksML.java:1306)
    at plugins.adufour.blocks.util.BlocksML.loadWorkFlow(BlocksML.java:773)
    at plugins.adufour.protocols.gui.ProtocolPanel.loadWorkFlow(ProtocolPanel.java:454)
    at plugins.adufour.protocols.gui.MainFrame$2.run(MainFrame.java:597)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)
    deborakeller0@gmail.com May 29, 2019 at 2:33 pm

    obviously you can clean up afterwards but it’d be good if it can be done before it generates additional areas..

    maybe it’s a feature request: restrict size of entering objects and min and/or max intensity