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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,<br>
<br>
I have done some more investigating and it seems that the issue appeared in going from version 4.4.4 (OK) to version 4.4.5 (not OK).<br>
<br>
Cheers,<br>
<br>
Tjelvar<br>
<br>
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<div style="direction: ltr;" id="divRpF142277"><font face="Tahoma" size="2" color="#000000"><b>From:</b> ome-users [ome-users-bounces@lists.openmicroscopy.org.uk] on behalf of Tjelvar Olsson (JIC)<br>
<b>Sent:</b> 24 June 2015 09:02<br>
<b>To:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> [ome-users] bfconvert query<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi,<br>
<br>
First of all I'd like to thank you for the "bfconvert" BioFormats tool. It makes my life so much easier.<br>
<br>
However, it seems that in version 5.x it produces corrupted png files (I have tried it on versions 5.0.6 and 5.1.2).<br>
<br>
The problem can be reproduced using the command below on your sample ome.tiff file.<br>
<br>
$ bfconvert multi-channel-4D-series.ome.tif S%s_C%c_Z%z_T%t.png<br>
<br>
If I try to open these png files using a simply Python script (attached). I get the error:<br>
<br>
$ python open_png.py 5.1.2/S0_C0_Z0_T0.png<br>
Traceback (most recent call last):<br>
File "open_png.py", line 3, in <module><br>
im = Image.open(sys.argv[1])<br>
File "/usr/lib64/python2.7/site-packages/PIL/Image.py", line 2013, in open<br>
raise IOError("cannot identify image file")<br>
IOError: cannot identify image file<br>
<br>
Whereas if I doe the same with one of the images converted using bfconvert version 4.4.2 everything works fine.<br>
<br>
Opening the files using an in-house tool that makes use of libpng gives some more descriptive feedback:<br>
<br>
libpng warning: acTL: CRC error<br>
<br>
Comparing the sizes of the files generated using version bfconvert 5.1.2 and 4.4.2 reveal that the former is smaller.<br>
<font size="2"><span style="font-size:10pt"><br>
</span></font>$ ls -l 5.1.2/S0_C0_Z0_T0.png <br>
-rw-r--r-- 1 olssont olssont 2226 Jun 24 08:50 5.1.2/S0_C0_Z0_T0.png<br>
$ ls -l 4.4.2/S0_C0_Z0_T0.png <br>
-rw-r--r-- 1 olssont olssont 2238 Jun 24 08:30 4.4.2/S0_C0_Z0_T0.png<br>
<br>
I have attached the sample converted png files.<br>
<br>
Any ideas what is going on?<br>
<br>
Cheers,<br>
<br>
Tjelvar<br>
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