http://imagej.273.s1.nabble.com/Problem-saving-PNG-files-in-particular-order-tp5011977p5012010.html
> 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>>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html