ERROR: Cannot find 3D I/O plugin "auto" or it is not a 3D I/O plugin

[ghost]

I'm trying to run the demo and I'm currently on Step 8. The command I'm running is:

terastitcher --merge --projin=./data/tomo300511_subv3/xml_merging.xml --volout=./stitched_data --resolutions=01234 --volout_plugin="TiledXY|3Dseries" --imout_plugin="tiff3D" --imout_format="tif"

I have Tiff 2D/3D installed and I tried using both the TeraStitcher-portable binary and TeraStitcher-installer hoping the latter would install a dependency I'm missing. I also tried installing Terastitcher through the link on the homepage http://abria.github.io/TeraStitcher/. Yet I'm still getting this error in all cases:

OPERATION:  Multiresolution tile merging
PHASE:      Saving to disc resolution 1
TIME REMAINING: 2 minutes and 1 seconds
PROGRESS:   1%  *:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

ERROR: Cannot find 3D I/O plugin "auto" or it is not a 3D I/O plugin

Interestingly this output cycles with a different output when I try to run the command multiple times. This is the other output I get:

OPERATION:  Multiresolution tile merging
PHASE:      Initializing...
TIME REMAINING: 0 minutes and 0 seconds
PROGRESS:   0%  ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in ./stitched_data/RES(1277x1265x992) [reason: in Block[0,0]::init(): stack in "./stitched_data/RES(1277x1265x992)/068936/068936_161088" is empty]

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in ./stitched_data/RES(638x632x496) [reason: in TiledVolume::init(...): Unable to find stacks in the given directory]

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in ./stitched_data/RES(319x316x248) [reason: in TiledVolume::init(...): Unable to find stacks in the given directory]

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in ./stitched_data/RES(159x158x124) [reason: in TiledVolume::init(...): Unable to find stacks in the given directory]

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in ./stitched_data/RES(79x79x62) [reason: in TiledVolume::init(...): Unable to find stacks in the given directory]

ERROR: StackStitcher::mergeTilesVaa3DRaw: 5 errors in creating mdata.bin files

I can't find this "auto" plug-in is online. I am running Ubuntu 16.04.2 LTS (GNU/Linux 4.10.0-40-generic x86_64). Any help would be appreciated. Thank you!

[abria]

Hi,

you are right, we found a bug in the latest build (only on the command line version - the GUI still works).

To solve this issue, you should avoid the --volout_plugin parameter. We are fixing this bug so it will not be present in the next release.

Please, let us know.

Thanks.

[ghost]

Hi abria, thanks for your reply. I tried your suggestion by running: terastitcher --merge --projin=./data/tomo300511_subv3/xml_merging.xml --volout=./stitched_data --resolutions=01234 --imout_plugin="tiff3D" --imout_format="tif" and ran into the exception

PHASE:      Initializing...
TIME REMAINING: 0 minutes and 0 seconds
PROGRESS:   0%  ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

terminate called after throwing an instance of 'IconImageManager::IOException'
Aborted (core dumped)

Any idea what's wrong? Is it something with my xml file?

[iannellog]

Before running again the merge step of TeraStitcher you must delete all the files created in the './stitched_data' folder (in particular you must delete the file 'resume_status.bin'). Then you can launch the command

terastitcher --merge --projin=./data/tomo300511_subv3/xml_merging.xml --volout=./stitched_data --resolutions=01234 --volout_plugin="TiledXY|3Dseries"

(option --volout_plugin alone is sufficient and, for a bug, it is alternative to --imout_plugin, you can avoid the option --imout_format).

This way the merge step should work. Consider however that to perform the merge step you can use the tool TeraConverter (included in the distribution) which is more flexible and is able to generate the stitched image in many different formats.

Attached you will found the draft of a more detailed guide (even though not complete yet) to the TeraTools. I hope this can help.

-- Giulio

2017-12-02 23:58 GMT+01:00 jyim6 notifications@github.com:

Hi abria, thanks for your reply. I tried your suggestion by running: terastitcher --merge --projin=./data/tomo300511_subv3/xml_merging.xml --volout=./stitched_data --resolutions=01234 --imout_plugin="tiff3D" --imout_format="tif" and ran into the exception

PHASE: Initializing... TIME REMAINING: 0 minutes and 0 seconds PROGRESS: 0% ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

terminate called after throwing an instance of 'IconImageManager::IOException' Aborted (core dumped)```

Any idea what's wrong? Is it something with my xml file?

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Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

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[ghost]

Hi Giulio, thanks for your reply. I tried teraconverter and it did work. Thank you for the help!