demo3D12

[needonature]

when run demo3D12 in lane cluster:

Checking if image collections are present.
Image collections already present. Skipping download.
demo3D12
The estimated running time is 12 minutes. Please wait.
Checking selection of nuclear model class/type
Checking selection of cell membrane model class/type
Checking selection of protein model class/type
Checking the existence of temporary folder
Reading file ../../../images/HeLa/3D/processed/LAM_cell1_ch0_t1.tif
Reading file ../../../images/HeLa/3D/processed/LAM_cell1_ch1_t1.tif
Reading file ../../../images/HeLa/3D/processed/LAM_cell1_ch2_t1.tif
Reading file ../../../images/HeLa/3D/processed/LAM_cell1_mask_update_t1.tif
Warning: uigetfile is no longer supported when MATLAB is started with the -nodisplay or -noFigureWindows option or there is no display. For more information, see "Changes to -nodisplay and -noFigureWindows
Startup Options" in the MATLAB Release Notes. To view the release note in your system browser, run web('www.mathworks.com/help/matlab/release-notes.html#br5ktrh-3', '-browser')
> In warnfiguredialog (line 21)
  In uigetfile (line 121)
  In bfopen (line 105)
  In ml_readimage (line 96)
  In img2model>readfileifnonblank (line 282)
  In img2model (line 129)
  In img2slml (line 475)
  In demo3D12 (line 144)
Error using javaObjectEDT
Scalar input must be a java object

Error in matlab.ui.internal.dialog.Dialog/getParentFrame (line 46)
               obj.ParentFrame = javaObjectEDT(com.mathworks.hg.peer.utils.DialogUtilities.createParentWindow);

Error in matlab.ui.internal.dialog.FileSystemChooser/getParentFrame (line 129)
                parframe = getParentFrame@matlab.ui.internal.dialog.Dialog(obj);

Error in matlab.ui.internal.dialog.FileChooser/showPeerAndBlockMATLAB (line 113)
            parFrame = getParentFrame(obj);

Error in matlab.ui.internal.dialog.FileChooser/show (line 122)
            obj.showPeerAndBlockMATLAB();

Error in uigetputfile_helper (line 46)
ufd.show();

Error in uigetfile (line 122)
[filename, pathname, filterindex] = uigetputfile_helper(0, varargin{:});

Error in bfopen (line 105)
  [file, path] = uigetfile(bfGetFileExtensions, 'Choose a file to open');

Error in ml_readimage (line 96)
                bfimg = bfopen( filename );

Error in img2model>readfileifnonblank (line 282)
    img = ml_readimage(filename);

Error in img2model (line 129)
    [immask,options.crop_image_path] = readfileifnonblank(options.masks,i);

Error in img2slml (line 475)
model = img2model(dnaImagesDirectoryPath, ...

Error in demo3D12 (line 144)
answer = img2slml( dimensionality, dna, cellm, protein, options );

Exception in thread "AWT-EventQueue-0" java.awt.HeadlessException
    at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
    at java.awt.Window.<init>(Unknown Source)
    at java.awt.Frame.<init>(Unknown Source)
    at javax.swing.JFrame.<init>(Unknown Source)
    at com.mathworks.mwswing.MJFrame.<init>(MJFrame.java:108)
    at com.mathworks.mwswing.MJFrame.<init>(MJFrame.java:101)
    at com.mathworks.hg.peer.utils.DialogUtilities$1.runWithOutput(DialogUtilities.java:58)
    at com.mathworks.jmi.AWTUtilities$Invoker$2.watchedRun(AWTUtilities.java:475)
    at com.mathworks.jmi.AWTUtilities$WatchedRunnable.run(AWTUtilities.java:436)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$200(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

[needonature]

in jupyternote book:

Warning: Name is nonexistent or not a directory: /home/jovyan/.mcrCache9.2/img2sl0/home/bteo/cellorganizer3/utilities/3D/LDDMM_fast/imrender/vgg
> In path (line 109)
  In addpath (line 88)
  In startup (line 3)
Warning: Name is nonexistent or not a directory: /home/jovyan/.mcrCache9.2/img2sl0/home/bteo/cellorganizer3/utilities/3D/LDDMM_fast/imrender/ojw
> In path (line 109)
  In addpath (line 88)
  In startup (line 4)
Running deployed version of slml2img
Attempting to read input file input.txt
Evaluating lines from input file
Checking selection of nuclear model class/type
Checking selection of cell membrane model class/type
Checking selection of protein model class/type
Checking the existence of temporary folder
Warning: Cell parameterization is empty. Either images not found or unable to extract parameters from images.
> In param2model_3D (line 45)
  In param2model (line 42)
  In img2model (line 171)
  In img2slml (line 475)
Warning: Model is empty.
> In param2model (line 49)
  In img2model (line 171)
  In img2slml (line 475)
Warning: CellOrganizer: img2model returned an empty model. Exiting program.
> In img2slml (line 482)

[needonature]

have create branch: 12-demo3D12

[icaoberg]

@needonature the first error you see with the open dialog is because it couldn't find the images and then bfopen was called and tried to open a dialog so you can select a file.

This either happens because

1. the files do not exist on disk
2. there is a typo on the filename

[needonature]

@icaoberg first bug is in demo3D12 itself, mask file typo, I fixed it. second bug is because docker build.sh doesn't have 3D images downloaded, I don't know what link should be used to download 3D images...

[icaoberg]

@needonature the issue with the lack of images can be fixed by @RuijiaChen she knows what to do

_{Sent with GitHawk}

[RuijiaChen]

@icaoberg Fixed the bug, please see branch "12-demo3D12"

[icaoberg]

@RuijiaChen check the latest version of the demo on

• http://repositories.compbio.cs.cmu.edu/cellorganizer/cellorganizer3

and update Jupyter notebook.