search

informatics-isi-edu / synspy

Synaptic segmentation and visualization with fluorescence microscopy
BSD 3-Clause "New" or "Revised" License
4 stars 1 forks source link

"Viewer subprocess Execution Failed" Error for Synspy #36

Closed BDemps closed 7 years ago

BDemps commented 7 years ago

An interesting error occurred on the Linux computer, preventing one user (Kwa) from performing segmentation. SynImgZfDsy20170505A3C brings up an error ("viewer subprocess execution failed") when synspy tries to run it. Here's the catch - the issue ONLY occurs when you do 3D view mode. On 2D slicer mode on either Linux or Mac computers, the image seems to open fine.

Any idea what could be the problem?

karlcz commented 7 years ago

The easiest way to debug this would be to manually launch synspy-viewer on the spim image file giving the proper crop box as a runtime parameter. Then the crash should show more diagnostics in the terminal.

It might be worth testing against a freshly downloaded copy of the image file as well as the one in the launcher's download cache folder. The 2D viewer uses a completely different file (the pre-processed NPZ), so if there was a problem downloading or storing the spim image, it would only affect the 3D viewer.

karlcz commented 7 years ago

@BDemps I'm not sure if you saw that I responded here and co-assigned you, so I thought I'd ping you explicitly...

BDemps commented 7 years ago

Yup, I saw. Was gonna do this this afternoon! Thanks for the reminder though

On Sep 5, 2017 10:23 AM, "Karl Czajkowski" notifications@github.com wrote:

@BDemps https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bdemps&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=xsMnGXLi7Ahx1lbLAYsXiuJDWV0Gdgk8PEwHnQtC6ag&s=7vUq4YwjtIZkmhneFCxgfhxI9wocqF6Djk18IFg5Ubw&e= I'm not sure if you saw that I responded here and co-assigned you, so I thought I'd ping you explicitly...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_informatics-2Disi-2Dedu_synspy_issues_36-23issuecomment-2D327245756&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=xsMnGXLi7Ahx1lbLAYsXiuJDWV0Gdgk8PEwHnQtC6ag&s=cCp5e0BdPSjDieRvK1_9TFiLZFHUndhkUNZ3nHI_YvQ&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AbQStwRNClHYYc4A-2DGbT0AerMQ-5FQFeTvks5sfYNIgaJpZM4PGbQT&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=xsMnGXLi7Ahx1lbLAYsXiuJDWV0Gdgk8PEwHnQtC6ag&s=yxJ2YzcEBjuN1vWLHmm0gH4YrgvMRedckG9n35g5hq0&e= .

karlcz commented 7 years ago

I tested SynImgZfDsy20170505A3C with the 3D viewer both via manual download and via the launcher and it worked both times. So, I am pretty sure you must have had a botched download and your download cache is corrupt.

So, please try clearing it out and re-testing. If it still fails, run synspy-viewer manually on the file with the correct XYZ_SLICE parameter and provide the console outputs from the crash.

BDemps commented 7 years ago

So, I tested it and still had issues. Here's how I resolved that one (very strange):

I downloaded the file and opened it in Fiji. It had incorrect ZYX voxel sizes. I changed them to the correct voxel size and then saved as a different file name as .ome.tiff in Fiji. Then, I opened that file, it had correct numbers but incorrect scale (it had four orders of magnitude off of what it should be for some reason). I changed it back to the correct scale again and then just clicked save (instead of save as). Then, I used bfconvert to change it to a different filename with .ome.tiff. Then, I was able to open it with synspy-launcher!

I think the student will need to re-check this one, as I don't think it was ever properly opening before. In fact, I'm not sure how she was able to segment it at all. Maybe she started before the cache got corrupt? Anyway, it is an odd solution but maybe it will be the case for some number of images in the future. At least we have a fix...

On Wed, Sep 6, 2017 at 2:54 PM, Karl Czajkowski notifications@github.com wrote:

I tested SynImgZfDsy20170505A3C with the 3D viewer both via manual download and via the launcher and it worked both times. So, I am pretty sure you must have had a botched download and your download cache is corrupt.

So, please try clearing it out and re-testing. If it still fails, run synspy-viewer manually on the file with the correct XYZ_SLICE parameter and provide the console outputs from the crash.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_informatics-2Disi-2Dedu_synspy_issues_36-23issuecomment-2D327615611&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=jFQ3llPAnHV-Zi_y2PPd9DUdIyrJ-JsIx9GmQxaCdPk&s=AFEqJtRf06uGgTjhpSDpXqzlMc0LO8QjeDyoDadcTbY&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AbQStxwHiRsCF4xFUHg0qm4K0hDsdVzzks5sfwxkgaJpZM4PGbQT&d=DwMFaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Lssj6JKak_DaRnExGYcKnQ&m=jFQ3llPAnHV-Zi_y2PPd9DUdIyrJ-JsIx9GmQxaCdPk&s=gx8vBTSMLqQvw6fXRUR2GY_L3RsJs-DtcBD8VFPlY5o&e= .

-- William Dempsey, Ph.D. Postdoctoral Scholar Molecular and Computational Biology Dana and David Dornsife College of Letters, Arts and Sciences University of Southern California wdempsey@usc.edu Lab #: 213-821-1818