http://imagej.273.s1.nabble.com/Problem-saving-PNG-files-in-particular-order-tp5011977p5012019.html
Thanks, Michael, I'm going to try that as soon as I solve a related problem
Georg C. Lichtenberg
> Hi Robert,
>
> the LUT does not affect the image data.
> I guess that ip.setLut(null) should be fine to set the LUT to grayscale.
> The more explicit way of getting the standard grayscale LUT would be
> ip.setColorModel(ip.getDefaultColorModel())
>
> Michael
> ________________________________________________________________
> On Mar 16, 2015, at 19:58, Robert Lockwood wrote:
>
> > Michael, that worked - in development mode at least. Sunday I tried to
> > detect the file without checking that it had a non-zero length but that
> > 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!
> >
> > I'd like to save this displayable file, with the LUT first and then the
> > 'raw data' second since saving the raw data is not critical.
> >
> > Does setting the LUT actually modify the original data?
> > I'd like to, in a manner of speaking, roll back the maximum, minimum, and
> > LUT that were set to save the original data last:
> >
> > ip.setMinAndMax(stats.histMin, stats.histMax); // 0, 2^16 -1
> > ip.setLut(Shared.getLUT()); // set to null?
> > imp.setProcessor("LUT", ip); //
> >
> > I could just start over, of course, but I'm frugal.
> >
> >
> >
> >
> > One's first step in wisdom is to question everything - and one's last is
> to
> > come to terms with everything.
> >
> > Georg C. Lichtenberg
> >
> > On Mon, Mar 16, 2015 at 9:20 AM, Michael Schmid <
[hidden email]
> >
> > wrote:
> >
> >> 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> >>
> >> --
> >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >>
> >
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