Saving the current session

[Michael Schmid]

Hi everyone,

does someone out there have a plugin to save the current ImageJ session to disk?  It need not be perfect (I don't care about placing windows to the correct position, etc.)...

I tried a simple macro approach (below), but I got stuck:
- 'Save as zip' does not save FFT data of FFT windows
- No way to determine in a macro whether the front window is a text or Results window.  [getInfo("window.contents") gives unpredictable results if the front window is neither image nor text]
- Plots won't have data behind them (that's a restriction I could live with).

Long time ago, this topic was already discussed on the mailinglist, and it was suggested to have the ImageJ data types implement Serializable.  Is I understand it, however, this would imply the risk that one can't read the session after updating ImageJ, which is also not so nice...

Michael
________________________________________________________________

// SaveSession macro
// Saves images and more of an ImageJ session
// V0.0 M. Schmid 2013-11-05
//
// Restrictions (there are actually more):
// Images do not remember the source file
// FFTs are saved as plain 8-bit images (no Fourier transform behind, can't do inverse FFT)
// Plots are saved as images with no data
// What about texts?
// How to discriminate ResultsTables and text with tabs?
// Settings are not saved (ImageJ saves some settings to the ijPrefs.txt file)
//
basePath=getDirectory("Choose a Directory to Save the Session");
getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
date= dayOfMonth+100*(month+1)+10000* dayOfMonth;
time=second+100* minute+10000*hour;
dirName="IJsavedSession_"+date+"_"+IJ.pad(time,6);
path=basePath+File.separator+dirName;
File.makeDirectory(path);
// ----------------- Images -----------------
while(nImages()>0) {
  selectImage(1);
  fileNoExt=path+File.separator+getTitle;
  uniqueNum="";
  while (File.exists(fileNoExt+uniqueNum +".zip")) {
    if (uniqueNum="") uniqueNum="0";
    uniqueNum = toString(parseInt(uniqueNum)-1); //-1, -2, etc.
  }
  save(fileNoExt+uniqueNum+".zip");
  close();
}
// ----------------- Log Window -----------------
logText=getInfo("log");
if(logText!="") {
  File.saveString(logText, path+File.separator+"log.txt");
  selectWindow("Log");
  run("Close");
}

// ----------------- ROI Manager -----------------
nRois=roiManager("count");
if (nRois>0) {
  roiManager("Save", path+File.separator+"roiSet.zip");
  selectWindow("ROI Manager");
  run("Close");
}
// ----------------- Results -----------------
if (nResults>0) {
  saveAs("results",  path+File.separator+"resultsTable.csv");
}

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jerome Mutterer-3]

Hi Michael,
The 'Workspaces' macro does basically the same thing, and allows to keep
multiple workspaces (or sessions) and restore them. It has the same
limitations that you raised.

see http://rsb.info.nih.gov/ij/macros/Workspaces.txt

Jerome



On 5 November 2013 18:37, Michael Schmid <[hidden email]> wrote:

> Hi everyone,
>
> does someone out there have a plugin to save the current ImageJ session to
> disk?  It need not be perfect (I don't care about placing windows to the
> correct position, etc.)...
>
> I tried a simple macro approach (below), but I got stuck:
> - 'Save as zip' does not save FFT data of FFT windows
> - No way to determine in a macro whether the front window is a text or
> Results window.  [getInfo("window.contents") gives unpredictable results if
> the front window is neither image nor text]
> - Plots won't have data behind them (that's a restriction I could live
> with).
>
> Long time ago, this topic was already discussed on the mailinglist, and it
> was suggested to have the ImageJ data types implement Serializable.  Is I
> understand it, however, this would imply the risk that one can't read the
> session after updating ImageJ, which is also not so nice...
>
> Michael
> ________________________________________________________________
>
> // SaveSession macro
> // Saves images and more of an ImageJ session
> // V0.0 M. Schmid 2013-11-05
> //
> // Restrictions (there are actually more):
> // Images do not remember the source file
> // FFTs are saved as plain 8-bit images (no Fourier transform behind,
> can't do inverse FFT)
> // Plots are saved as images with no data
> // What about texts?
> // How to discriminate ResultsTables and text with tabs?
> // Settings are not saved (ImageJ saves some settings to the ijPrefs.txt
> file)
> //
> basePath=getDirectory("Choose a Directory to Save the Session");
> getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second,
> msec);
> date= dayOfMonth+100*(month+1)+10000* dayOfMonth;
> time=second+100* minute+10000*hour;
> dirName="IJsavedSession_"+date+"_"+IJ.pad(time,6);
> path=basePath+File.separator+dirName;
> File.makeDirectory(path);
> // ----------------- Images -----------------
> while(nImages()>0) {
>   selectImage(1);
>   fileNoExt=path+File.separator+getTitle;
>   uniqueNum="";
>   while (File.exists(fileNoExt+uniqueNum +".zip")) {
>     if (uniqueNum="") uniqueNum="0";
>     uniqueNum = toString(parseInt(uniqueNum)-1); //-1, -2, etc.
>   }
>   save(fileNoExt+uniqueNum+".zip");
>   close();
> }
> // ----------------- Log Window -----------------
> logText=getInfo("log");
> if(logText!="") {
>   File.saveString(logText, path+File.separator+"log.txt");
>   selectWindow("Log");
>   run("Close");
> }
>
> // ----------------- ROI Manager -----------------
> nRois=roiManager("count");
> if (nRois>0) {
>   roiManager("Save", path+File.separator+"roiSet.zip");
>   selectWindow("ROI Manager");
>   run("Close");
> }
> // ----------------- Results -----------------
> if (nResults>0) {
>   saveAs("results",  path+File.separator+"resultsTable.csv");
> }
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Nov 5, 2013, at 12:37 PM, Michael Schmid wrote:

> Hi everyone,
>
> does someone out there have a plugin to save the current ImageJ session to disk?  It need not be perfect (I don't care about placing windows to the correct position, etc.)...
>
> I tried a simple macro approach (below), but I got stuck:
> - 'Save as zip' does not save FFT data of FFT windows

In the latest daily build (1.48g8), File>Save As>ZIP and File>Save As>Tiff save the FFT data of FFT windows, except for FFTs of RGB images.

> - No way to determine in a macro whether the front window is a text or Results window.  [getInfo("window.contents") gives unpredictable results if the front window is neither image nor text]

Use the new getInfo("window.type") macro function to get the type of the front window.

-wayne

> - Plots won't have data behind them (that's a restriction I could live with).
>
> Long time ago, this topic was already discussed on the mailinglist, and it was suggested to have the ImageJ data types implement Serializable.  Is I understand it, however, this would imply the risk that one can't read the session after updating ImageJ, which is also not so nice...
>
> Michael
> ________________________________________________________________
>
> // SaveSession macro
> // Saves images and more of an ImageJ session
> // V0.0 M. Schmid 2013-11-05
> //
> // Restrictions (there are actually more):
> // Images do not remember the source file
> // FFTs are saved as plain 8-bit images (no Fourier transform behind, can't do inverse FFT)
> // Plots are saved as images with no data
> // What about texts?
> // How to discriminate ResultsTables and text with tabs?
> // Settings are not saved (ImageJ saves some settings to the ijPrefs.txt file)
> //
> basePath=getDirectory("Choose a Directory to Save the Session");
> getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);
> date= dayOfMonth+100*(month+1)+10000* dayOfMonth;
> time=second+100* minute+10000*hour;
> dirName="IJsavedSession_"+date+"_"+IJ.pad(time,6);
> path=basePath+File.separator+dirName;
> File.makeDirectory(path);
> // ----------------- Images -----------------
> while(nImages()>0) {
>  selectImage(1);
>  fileNoExt=path+File.separator+getTitle;
>  uniqueNum="";
>  while (File.exists(fileNoExt+uniqueNum +".zip")) {
>    if (uniqueNum="") uniqueNum="0";
>    uniqueNum = toString(parseInt(uniqueNum)-1); //-1, -2, etc.
>  }
>  save(fileNoExt+uniqueNum+".zip");
>  close();
> }
> // ----------------- Log Window -----------------
> logText=getInfo("log");
> if(logText!="") {
>  File.saveString(logText, path+File.separator+"log.txt");
>  selectWindow("Log");
>  run("Close");
> }
>
> // ----------------- ROI Manager -----------------
> nRois=roiManager("count");
> if (nRois>0) {
>  roiManager("Save", path+File.separator+"roiSet.zip");
>  selectWindow("ROI Manager");
>  run("Close");
> }
> // ----------------- Results -----------------
> if (nResults>0) {
>  saveAs("results",  path+File.separator+"resultsTable.csv");
> }
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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