saving as TIFF 2D series fails in v1.10.0

[pawlowska]

I donwloaded the newest GUI version. Reading and aligning data looks good, but when I try to save as "TIFF (series, 2D)" I get all sorts of errors, "invalid volume ranges" or "saved resolutions differ from requested resolutions", screenshots below.

[pawlowska]

...interestingly, when I restarted Terastitcher and imported data from XML, skipping the Align step and going straight to Merge, saving started (with only the highest resolution ticked and 'isotropic' off). This is something I noticed before: if an error occurs with certain settings A, then changing the settings to B doesn't help, but starting again and choosing B from the beginning does. Besides, some of the error messages are rather cryptic. This makes it very difficult for the user to understand what's going wrong.

[iannellog]

Monika, thanks for your warnings.

The second error is caused by the presence in the save folder of the file 'resume_status.bin'. This is a feature we introduced to resume interrupted operations on very large images. Actually I should disable it in the GUI version (but I didn't yet). If you have troubles with this file you can simply delete it before restarting the operation.

As to the first error I have to check. It is due to the range [15,1] in D dimension, but I cannot understand why it happens. Have you tried to use a different output format? It is likely the error remains because it probably depends on the computed alignments. If you have the xml file that originally caused the error "invalid volume ranges", i.e. the xml_placetiles.xml file generated after the alignment step, could you send it to me together with the xml_import.xml initially used to import the volume?

Thanks again.

-- Giulio

2017-05-15 12:09 GMT+02:00 Monika Pawlowska notifications@github.com:

...interestingly, when I restarted Terastitcher and imported data from XML, skipping the Align step and going straight to Merge, saving started (with only the highest resolution ticked and 'isotropic' off). This is something I noticed before: if an error occurs with certain settings A, then changing the settings to B doesn't help, but starting again and choosing B from the beginning does. Besides, some of the error messages are rather cryptic. This makes it very difficult for the user to understand what's going wrong.

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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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[pawlowska]

I will try to reproduce the error and keep the xml_placetiles when I do my next dataset, perhaps tomorrow.

I think I couldn't delete the resume_status.bin because it was in use, but I can try picking a different saving folder.

[pawlowska]

I don't find a file "xml_placetiles" anywhere when I reproduce the error and neither in the previous dataset that got merged after restarting. The latest file is xml_displproj. What I do see is that now in the error message it says [45,1], and 45 was the Z search region, while in the previous dataset I think I set Z search region to 15. It seems the error happens when trying to compute the resolution of the merged stack after rejecting the outer bits that can't be aligned with anything? The numbers -21 and -4 appear as displacements of some stacks in xml_displproj (I can email this file to you if that helps).

[iannellog]

Monika, I apologize: the file I was looking for is xml_merging.xml and not xml_placetiles.xml. It should be produced when the Align step is executed.

The behavior you observe should depend on the information contained in the xml files. The coincidence that the search region corresponds to the wrong interval in Z seems to suggest that it is a problem of alignment along Z. You can try to set the Z search region to 0, just to check if this is the problem.

If you could send me all the xml files (xml_import.xml, xml_displcomp.xml, xml_displproj.xml, xml_displthresh.xml, xml_merging.xml) together with the 'mdata.bin' file that is generated in the root directory of the unstitched dataset I am confident I can understand which is the problem. Even only the files xml_displproj.xml and data.bin would be enough (the latter is needed to completely reproduce your setup).

I have one more question: this problem happens always or only with some datasets and/or when the output format "TIFF (series, 2D)" is chosen?

Thanks.

-- Giulio

2017-05-17 11:43 GMT+02:00 Monika Pawlowska notifications@github.com:

I don't find a file "xml_placetiles" anywhere when I reproduce the error and neither in the previous dataset that got merged after restarting. The latest file is xml_displproj. What I do see is that now in the error message it says [45,1], and 45 was the Z search region, while in the previous dataset I think I set Z search region to 15. It seems the error happens when trying to compute the resolution of the merged stack after rejecting the outer bits that can't be aligned with anything? The numbers -21 and -4 appear as displacements of some stacks in xml_displproj (I can email this file to you if that helps). [image: computevolumedims2] https://cloud.githubusercontent.com/assets/11158300/26147722/aac0f4a0-3af4-11e7-8629-a86ae348c9c5.PNG

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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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[pawlowska]

I have one more question: this problem happens always or only with some datasets and/or when the output format "TIFF (series, 2D)" is chosen?

With all data sets so far, choosing HDF5 (and new saving directory) generated an identical error.

Today I tried a smaller dataset and got a new error:

Unfortunately, this time the trick of restarting Terastitcher generates another funny error:

Finally, deleting mdata.bin and restarting Terastitcher again - now I can import the data and merge, but now with the smaller and nicer specimen I can see that when I skip Align (because I already have all the xml files), then merging is wrong, the delays are not taken into account at all.

I sent you xml files by email.