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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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Issue with running demo #38

Open pawlowac opened 5 years ago

pawlowac commented 5 years ago

Hi, I'm trying to run the provided demo to confirm everything is working on my system. I am using the 1.11.6 version on linux. I am at the merge step and it keeps throwing an error

in StackStitcher::mergeTilesVaa3DRaw: cannot create file mdata.bin in <my_folder>/RES(98x98x0) [reason: in TiledVolume::init(...): unable to find stacks in the given directory]

Error: StackStitcher::mergeTilesVaa3DRaw: 1 errors in creating mdata.bin files

Is there something I'm doing wrong here?

Thanks, Andrew

abria commented 5 years ago

Could you please attach the xml_merging.xml file? The folder name indicates that the stitched volume is empty, so there is nothing to initialize (mdata.bin is an initialization file).

pawlowac commented 5 years ago

Hi Alessandro,

Please see the attached file. I noticed in the user documentation that terastitcher will no longer support merge, which will be done using teraconverter. I also could not get it to work with teraconverter. All previous steps of the demo worked without a problem.

xml_merging.txt

abria commented 5 years ago

From the xml provided, all tiles are placed at the origin (0,0,0), and all computed displacements are invalid. I guess something went wrong with the import step, did you check the test slice?

iannellog commented 5 years ago

Andrew, I too had a look to your xml file. I understand that you are using the dataset we provide for testing the parallel execution of the tool (54 tile arranged in a 6x54 matrix). However the xml_merging.xml file you are using is wrong. I do not know how you could have generated it. The values reported in the xml have not sense: values reported at lines 6-9 are wrong. Have you followed all steps reported in the demo page? If you change manually the values describing how the dataset is configured TeraStitcher cannot import it. To do that you have to precisely understand the meaning of all tags in the file. This is explained in the documentation we provide both in the website pages and in the user's guides in pdf. Best.

-- Giulio

Il giorno mer 17 ott 2018 alle ore 03:08 pawlowac notifications@github.com ha scritto:

Hi Alessandro,

Please see the attached file. I noticed in the user documentation that terastitcher will no longer support merge, which will be done using teraconverter. I also could not get it to work with teraconverter. All previous steps of the demo worked without a problem.

xml_merging.txt https://github.com/abria/TeraStitcher/files/2485443/xml_merging.txt

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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

pawlowac commented 5 years ago

Hi Giulio, Alessandro,

I think I know what went wrong. The google drive folder contains a folder and a zip file. I thought the folder was a '.sub3' file by mistake and ignored it and tried the demo on the 'tostich.zip' file. I'll try it again using the correct rar files.

iannellog commented 5 years ago

Il giorno mer 17 ott 2018 alle ore 17:59 pawlowac notifications@github.com ha scritto:

Hi Giulio, Alessandro,

I think I know what went wrong. The google drive folder contains a folder and a zip file. I thought the folder was a '.sub3' file by mistake and ignored it and tried the demo on the 'tostich.zip' file. I'll try it again using the correct rar files.

I do not understand your mail. There are two demos. One for testing TeraStitcher in a simple way and it consists of 7 .rar files. I do not remember well, but it should be a 3x3 tile matrix. The other demo is in the topstitch.zip file for testing parallel execution. It is 1.3 GB large and a 6x9 tile matrix. For this second dataset and you need to get also the file xml_import.xml (the link on the same page).

I hope this can help.

-- Giulio

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