http://imagej.273.s1.nabble.com/Problem-saving-PNG-files-in-particular-order-tp5011977p5011999.html
Michael, that worked - in development mode at least. Sunday I tried to
failed. It takes between 380 and 400 milliseconds for the 640,000 file to
be non-zero. That's transferring from memory to a RAM disk!
Georg C. Lichtenberg
> Hi Robert,
>
> in case the problem occurs because the file has not been written yet while
> the next command is executed:
> Maybe have a loop, waiting until the file exists?
>
> In ImageJ macro language, something like the following:
>
> for (i=0; i<100; i++) {
> if (File.exists(path) && File.length(path)>100) i=100; //break the loop
> if (i==99) exit("timeout, did not save so far");
> wait(50);
> }
>
> It won't tell you whether the file is has been completely written. Some
> operating systems might report zero length for a file that is unfinished,
> but I would not rely on that.
>
> Michael
> ________________________________________________________________
> On Mar 16, 2015, at 00:33, Robert Lockwood wrote:
>
> > I have been writing software that controls a one-of-a-kind research grade
> > aerial infrared camera running the Java code from the Eclipse editor
> > (Ubuntu 14.04). When deployed scripts initialize all the code and start
> the
> > various pieces running.
> >
> > I import the data, 16 bit unsigned, into IJ and save it as 16 bit
> unsigned
> > PNG ('raw' data). Then I use the data already in IJ, assign a LUT, etc.
> > and save this now displayable PMG file to different folder and tell my
> > webpage GUI to get and display the file for the operator to view.
> >
> > This works fine when I run the code from Eclipse but fails when I use the
> > scripts to automatically start the code when the (headless) computer
> boots.
> >
> > What I think is happening is that IJ tells the OS to save the 16 bit data
> > file and the OS says, OK it's a write - that's not a priority. Then the
> > displayable file is saved and now there may be two files in the queue.
> The
> > message is sent to the webpage, the webpage requests the displayable file
> > but it's not yet saved. The notebook, iPad, etc. that is the webpage
> > client is either connected directly to the server or to the router,
> there's
> > no traffic going across the internet so it's quite fast.
> >
> > There are a couple code snippets following.
> >
> > I'd like to try to force the OS to save the files quickly, but don't know
> > if that's possible in IJ. I'd also like to save the displayable file
> with
> > its LUT first but don't know how to do that without making a second copy
> of
> > the raw data.
> >
> > Is it possible to use the IJ objects after the LUT has been applied and
> > 'recover' (so to speak) the 16 bit data and save it?
> >
> > I'd appreciate any suggestions ...
> >
> > // ----- save 'raw' data as 16 bit unsigned short as PNG -----
> > ImagePlus imp = IJ.createImage("Untitled", imageWidth, imageHeight, 1
> > ,imageBitsPerPix );
> > ShortProcessor ip = (ShortProcessor) imp.getProcessor();
> > short[] data = (short[]) ip.getPixels();
> > // copy pixel data to IJ ip
> > imageByteBuffer.position(0);
> > int index = 0;
> > while(imageByteBuffer.hasRemaining())
> > data[index++] = imageByteBuffer.getShort();
> > if(State.isRecording()) {
> > IJ.saveAs(imp, "PNG", imageFullPathName);
> >
> > // ---- apply LUT to data already in IJ and save it ----
> > if (useLUT) {
> > ImageStatistics stats = ip.getStatistics();
> > ip.setMinAndMax(stats.histMin, stats.histMax);
> > ip.setLut(Shared.getLUT());
> > imp.setProcessor("LUT", ip);
> > final String imageName = getDisplayFileName();
> > final String imageFullPathname = imageDisplyFolderPath + imageName;
> > IJ.saveAs(imp, "PNG", imageFullPathname);
> > }
> >
> > Thanks in advance
> > Nate
> >
> > One's first step in wisdom is to question everything - and one's last is
> to
> > come to terms with everything.
> >
> > Georg C. Lichtenberg
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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