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pyushkevich / alfabis_server

RESTful API for the ALFABIS distributed image segmentation server
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DSS service script #2

Open btsken opened 4 years ago

btsken commented 4 years ago

Hi

I got a problem with "Package and Upload Results" 

 itksnap-wt -i $INPUT_WSP \
    -layers-add-anat $RESLICE_SOURCE_IMG -props-set-nickname "Resliced Source Image" \
    -layers-add-anat $COMBINED_WARP -props-set-nickname "Deformation Field" -props-set-colormap jet \
    -layers-add-seg $RESLICE_SOURCE_SEG -props-set-nickname "Resliced Segmentation" \
    -layers-list -o $RESULT_WSP

error message is

ITK-SNAP exception for command -dssp-tickets-upload : Error: Unsupported or missing image file format. ITK-SNAP failed to create an ImageIO object for the image 'C:/Users/KEN/AppData/Local/Temp/alfF4D9.tmp_d/layer_000_d5a93cf0ff7630d52120c17e11f5d7fd.nii.gz' using format ''.

My itk-snap client is on windows and DSS service is on ubuntu

I think it caused by the image path in the workspace. The file system in windows is different from ubuntu

so I got the error when writing the new workspace

How can I do for this problem

Thanks

pyushkevich commented 4 years ago

Hi

During upload, itksnap-wt "archives" the workspace in the temporary directory. It renames the images (layer_000_d5a93cf0ff7630d52120c17e11f5d7fd) and places them all in the same folder as a temporary workspace file. It seems that the error is happening during workspace upload, where it is trying to create a file in the temporary directory ( C:/Users/KEN/AppData/Local/Temp/alfF4D9.tmp_d) and failing.

What I am really confused about is this: you say you are running the service on ubuntu, but why is the temporary path it is complaining about a windows path? Which OS are you calling the -dssp-tickets-upload command on?

Paul

On Tue, Nov 12, 2019 at 2:45 AM Ken Huang notifications@github.com wrote:

Hi

I got a problem with "Package and Upload Results"

itksnap-wt -i $INPUT_WSP \ -layers-add-anat $RESLICE_SOURCE_IMG -props-set-nickname "Resliced Source Image" \ -layers-add-anat $COMBINED_WARP -props-set-nickname "Deformation Field" -props-set-colormap jet \ -layers-add-seg $RESLICE_SOURCE_SEG -props-set-nickname "Resliced Segmentation" \ -layers-list -o $RESULT_WSP

error message is

ITK-SNAP exception for command -dssp-tickets-upload : Error: Unsupported or missing image file format. ITK-SNAP failed to create an ImageIO object for the image 'C:/Users/KEN/AppData/Local/Temp/alfF4D9.tmp_d/layer_000_d5a93cf0ff7630d52120c17e11f5d7fd.nii.gz' using format ''.

My itk-snap client is on windows and DSS service is on ubuntu

I think it caused by the image path in the workspace. The file system in windows is different from ubuntu

so I got the error when writing the new workspace

How can I do for this problem

Thanks

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-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and Science Laboratory Department of Radiology University of Pennsylvania

btsken commented 4 years ago

Thank you for the quick reply.

I use -dssp-tickets-upload command on Ubuntu

By the way

I use the code to download ticket

itksnap-wt -dssp-tickets-download $TICKET_ID $WORKDIR > $TMPDIR/download.txt

After downloaded, checking the layer list, the path is the windows format

itksnap-wt -i $WORKDIR -layers-list

work/ticket_00000016/ticket_00000016.itksnap
2> Layer  Role  Nickname  Filename                                                                                              Tags
2> 000    Main            C:/Users/KEN/AppData/Local/Temp/alf10CB.tmp_d/layer_000_d5a93cf0ff7630d52120c17e11f5d7fd.nii.gz  Target
pyushkevich commented 4 years ago

Odd... Could you send me the INPUT_WSP and RESULT_WSP workspace files?

On Tue, Nov 12, 2019 at 7:46 PM Ken Huang notifications@github.com wrote:

Thank you for the quick reply.

I use ITK-snap GUI program on windows(v3.8.0) to upload (like this) https://alfabis-server.readthedocs.io/en/sandbox/user_quick_start.html

My service on Ubuntu use the code to download

itksnap-wt -dssp-tickets-download $TICKET_ID $WORKDIR > $TMPDIR/download.txt

After downloaded, checking the layer list, the path is the windows format

itksnap-wt -i $WORKDIR -layers-list

work/ticket_00000016/ticket_00000016.itksnap 2> Layer Role Nickname Filename Tags 2> 000 Main C:/Users/KEN/AppData/Local/Temp/alf10CB.tmp_d/layer_000_d5a93cf0ff7630d52120c17e11f5d7fd.nii.gz Target

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pyushkevich/alfabis_server/issues/2?email_source=notifications&email_token=AAJPEW4W3W7YJAGH3RJTEJDQTNE5NA5CNFSM4JL7Q652YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOED4O7MQ#issuecomment-553185202, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJPEW7WL6VARIGWXE24SODQTNE5NANCNFSM4JL7Q65Q .

-- Paul A. Yushkevich, Ph.D. Associate Professor Penn Image Computing and Science Laboratory Department of Radiology University of Pennsylvania

btsken commented 4 years ago

hi

INPUT_WSP RESULT_WSP

thanks