Compressed MHD reads incorrectly

[ctrueden]

A bug report from Robert Atwood on the ImageJ mailing list:

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?");

It is likely a bug in the compression logic of MetaImage_Reader.