Posted by
Rasband, Wayne (NIH/NIMH) [E] on
Oct 13, 2013; 8:18pm
URL: http://imagej.273.s1.nabble.com/Best-path-to-take-tp5005126p5005154.html
On Oct 10, 2013, at 4:28 PM, Robert Lockwood wrote:
>>> Why not just save the images in TIFF format? Why invent
>>> another file format?
>
> When I saw that I could save the files as TIFF I gave it a try but that
> destroys the original data. What's is apparently saved is the image data,
> that is, it's reduced to BufferedImage. That was a disappointing
> exercise.
>
> I know that it is possible for a TIFF file to have the original data in it
> but AFAIK Fiji doesn't support writing this Scientific data mode, alas.
ImageJ can save 16-bit unsigned scientific data in TIFF format, including metadata (properties). Here is an example:
int w=256, h=256;
short[] data = new short[w*h];
for (int i=0; i<w*h; i++)
data[i] = (short)i;
ImageProcessor ip = new ShortProcessor(w, h, data, null);
ImagePlus imp = new ImagePlus("temp", ip);
String properties = "key1: value1\nkey2: value2";
imp.setProperty("Info", properties);
IJ.saveAsTiff(imp, IJ.getDirectory("home")+"test.tiff");
To save using lossless compression, replace the IJ.saveAsTiff() call with:
IJ.saveAs(imp, "zip", IJ.getDirectory("home")+"test.tiff");
Open and display the file using File>Open and display the metadata by typing "i" (Image>Show Info).
A plugin can open the TIFF file and retrieve the short data using:
ImagePlus imp = IJ.openImage(path);
ImageProcessor ip = imp.getProcessor();
short[] data = (short[])ip.getPixels();
It can retrieve the metadata using:
ImagePlus imp = IJ.openImage();
String properties = imp.getProperty("Info");
-wayne
> ---------- Forwarded message ----------
> From: Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]>
> Date: Thu, Oct 10, 2013 at 1:08 PM
> Subject: Re: Best path to take
> To: Robert Lockwood <
[hidden email]>
>
> Dear Robert,
>
> Why not just save the images in TIFF format? Why invent another file format?
>
> Best regards,
>
> -wayne
>
>
> On Oct 10, 2013, at 3:29 PM, Robert Lockwood wrote:
>
>> Johannes, thanks for your help with my initial attempt to write a plugin.
>>
>> Before I proceed I am asking you and others in the group for some advice.
>>
>> My situation is that we are developing a camera system for in house
>> infrared photography, primarily of wild fires. At this point I need to be
>> able to provide a way for others to view our image data and thought that
>> Fiji would be a good solution.
>>
>> I've decided that our images will all have a metadata header and the first
>> 24 bytes would be identical in function. Our image data is all (C-talk
>> here) unsigned shorts with the 12-14 bits of precision depending on the
>> camera and are monochrome.
>>
>> The size varies greatly among the cameras with a probable minimum of 512
>> lines by 640 pixels up to 11 megapixels. The image data for most of the
>> cameras are very low contrast unless fire is in the image and consist of
>> raw DN values.
>>
>> The common part of the header, the minimum information for the image to be
>> displayed, is" Offset-to-image-data, number-of-lines,
>> number-of-samples-per-line, pixel-size, and time-of-acquisition (Java date
>> time in ms). The first four data are Java ints, and the time is a Java
>> long for a total of 24 bytes.
>>
>> I'd like to tell the few people who need to view the images to just
>> download and install Fiji on their LINUX, Macs, and Windows machines, and
>> then how to load and use the plugin/macro I supply. The object is for the
>> user to use Fiji to browse and display our files (possible extension
>> .rawimage) and not need to enter any image metadata as they may not know
>> those data. Once the image is in Fiji it can be manipulated, saved-as,
>> etc. In essence it should work analogous to importing a raw image without
>> needing to input metadata by hand.
>>
>> TIA for any insight, pointers, etc.
>>
>> Nate
>>
>> --
>> When I was 12 I thought I would live forever.
>> So far, so good.
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
>
>
>
> --
> When I was 12 I thought I would live forever.
> So far, so good.
>
> --
> ImageJ mailing list:
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