Posted by
robert atwood on
URL: http://imagej.273.s1.nabble.com/Fiji-compressed-mhd-file-not-working-tp5018786.html
Hi,
In FIJI, I find the capability to use .mhd files, which is useful for me. However I tried saving an (8-bt binary thresholded) image in compressed form , and subsequently opening the file only gives noise or else nothing at all.
However, the file that is written is properly read by other application (using ITK in c++) , and the compressed .mhd file that was created by the ITK application can be read in the Fiji .
In trying to replicated at a smaller scale (original file is 250 Mb -> compressed 9 Mb) I found that sometimes it just silently fails to read the file.
I updated Fiji this morning and it is running on Linux (centOs) platform .
Here is a macro that creates an image to replicate two behaviour modes:
__________________________________
newImage("Untitled", "8-bit white", 150, 150, 100);
makeOval(28, 27, 33, 45);
setBackgroundColor(0, 0, 0);
run("Clear", "stack");
run("MHD/MHA compressed ...", "save=blob_compressed.mhd");
run("Add Specified Noise...", "stack standard=25");
run("MHD/MHA compressed ...", "save=blob_noise_compressed.mhd");
run("Close All");
open("blob_compressed.mhd");
getBoolean("Did any file get opened?");
open("blob_noise_compressed.mhd");
getBoolean("Does this look like the original image?");
_______________________________
Dr. Robert C. Atwood
Diamond Light Source
and
Manchester X-ray Imaging Facility (University of Manchester)
Rm G15, Research Complex at Harwell
Harwell Science and Innovation Campous, Didcot, OX11 0FA
Tel: +44 1235 778 670
www.diamond.ac.uk
www.rc-harwell.ac.uk
www.mxif.manchester.ac.uk
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