segrefine3Dplot error

[cyanpku]

Dear Carsten,

I would like to use the segrefine3Dplot to monitor how well the refinement goes. However the program stopped immediately with an error in the report log:

---------

TypeError: ufunc 'invert' not supported for the input types, and the inputs could not be safely coerced 

to any supported types according to the casting rule ''safe''

---------

I used tried spring.db from either the segmentrefine3D folder or the segment folder, it didn't make any different. The only "invert" I've noticed is during segmentation. I run the segmentrefine3D using un-inverted segments but still get the same error. 

What's your advice to get pass this problem? Thanks a lot.

Here's my spring version:

Spring environment loaded.

GUI from package Emspring-0.84.1470

Spring environment loaded.

EMAN 2.1 alpha2 (CVS 2013/08/07 17:01:09)

Your EMAN2 is running on:  NAME="Red Hat Enterprise Linux Server"

VERSION="7.2 (Maipo)"

ID="rhel"

ID_LIKE="fedora"

VERSION_ID="7.2"

PRETTY_NAME="Red Hat Enterprise Linux Server 7.2 (Maipo)"

ANSI_COLOR="0;31"

CPE_NAME="cpe:/o:redhat:enterprise_linux:7.2:GA:server"

HOME_URL="https://www.redhat.com/"

BUG_REPORT_URL="https://bugzilla.redhat.com/"

REDHAT_BUGZILLA_PRODUCT="Red Hat Enterprise Linux 7"

REDHAT_BUGZILLA_PRODUCT_VERSION=7.2

REDHAT_SUPPORT_PRODUCT="Red Hat Enterprise Linux"

REDHAT_SUPPORT_PRODUCT_VERSION="7.2"

Red Hat Enterprise Linux Server release 7.2 (Maipo)

Red Hat Enterprise Linux Server release 7.2 (Maipo) 3.10.0-327.el7.x86_64 x86_64

Your Python version is:  2.7.2

Jing Wang

Dr. Marek Basler's group

University of Basel

[Carsten Sachse]

Dear Jing,

I am not entirely sure on the origin of the error message. Have you provided the grid.db generated by SEGREFINE3DGRID? A common problem is did some SEGMENTREFINE3D jobs of the grid did not complete properly. You can check the contents of the grid.db by:

% sqlite3 grid.db .dump 

Best wishes,

Carsten

[cyanpku]

Hi Carsten,
Thank you very much for the advice! I skipped the segrefine3dgrid and just want to monitor the refinement with the 3Drefineplot while the segmentrefine3D is still running. Sorry I didn't see any part of the 3Drefineplot requiring for a grid.db, I guess you mean the error arises from the spring.db because the segmentrefine3D program should complete before launching the 3Drefineplot?
Bests,
Jing

[Carsten Sachse]

Dear Jing,

On Wednesday, February 24, 2016 at 8:10:46 PM UTC+1, cyanpku wrote:

Hi Carsten,
Thank you very much for the advice! I skipped the segrefine3dgrid and just want to monitor the refinement with the 3Drefineplot while the segmentrefine3D is still running.

Unfortunately, you cannot monitor progress while SEGREFINE3DGRID is running. You will have to provide a completed grid.db 

Sorry I didn't see any part of the 3Drefineplot requiring for a grid.db, I guess you mean the error arises from the spring.db because the segmentrefine3D program should complete before launching the 3Drefineplot?

I meant you will need to wait until SEGREFINE3DGRID is completed until you can analyze the grid.db using SEGREFINE3DPLOT.

Best wishes,

Carsten 

[cyanpku]

Hi Carsten,

Question about the Segrefine3Dplot again .... The same error at 1% progress, although I used a spring.db and refinement.db from segmentrefine3D program completed:

TypeError: ufunc 'invert' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

I kind of gave up on it until I switched the sequence of refinement.db and spring.db in the parameter file and the progress bar made it to 20%! Then a window "segrefine3Dplot: spring.db" popped up demanding  "the program to plot refinement parameters from segmentrefine3d", followed by a blank option tab and the spring exit sign. 

Do you have any clue about what went wrong?

Thanks a lot for your help as always,

Jing

[Carsten Sachse]

Dear Jing,

 Is it possible that you are using only a subset of all segments by applying some selection criteria? If this is the case, this may create confusion for SEGREFINE3DPLOT. Try to apply the exact same criteria to SEGREFINE3DPLOT as well. I hope it helps.

Best wishes,

Carsten

On Tuesday, February 23, 2016 at 11:45:54 AM UTC+1, cyanpku wrote:

[cyanpku]

Hi Carsten,

Thanks a lot for the suggestion!

I used several selection criteria during segrefine3d, such as defocus, astigmatism, class, out of plane tilt etc. On the segrefine3Dplot interface, the parameter options include only micrographs and helices list. The spring version I'm using is Emspring-0.84.1470. I'm gonna run the segrefine3d without any selection and see if that solves the error.

Cheers,

Jing