I am getting an error message “Vis request failed when requesting get_individual_data_mic (Error: Internal server error [500])” after motion-correction and ctf completes processing a exposure. It re-appears when selecting any other exposures too.
Also no image appears in the 2D display field.
Everything about the processing seems to be functioning correctly and works with images from another microscope.
My suspicions are the images are oriented with a longer vertical height then horizontal width leaving the images to appear taller than wider, but that is mostly a guess.
I am running cryosparc live v2.14.1
cryosparcm status
CryoSPARC System master node installed at
Current cryoSPARC version: v2.14.1
cryosparcm process status:
app RUNNING pid 6094, uptime 7:56:50
app_dev STOPPED Not started
command_core RUNNING pid 5862, uptime 7:57:05
command_proxy RUNNING pid 5904, uptime 7:57:02
command_rtp RUNNING pid 5908, uptime 7:57:01
command_vis RUNNING pid 5927, uptime 7:56:59
database RUNNING pid 5785, uptime 7:57:08
watchdog_dev STOPPED Not started
webapp RUNNING pid 6051, uptime 7:56:51
webapp_dev STOPPED Not started
Here is the message from command_vis Log that is genereated when I click on an exposure and the error mesages pops up.
2020-03-16 09:58:07,527 VIS.MAIN INFO Receieved request for get_individual_data_mic
2020-03-16 09:58:07,542 RTP.PLOTTING INFO Current exposure viewer cache size: 10 micrographs
2020-03-16 09:58:07,696 RTP.PLOTTING INFO Pruned exposure viewer cache. New size: 10 micrographs
[2020-03-16 09:58:07,708] ERROR in app: Exception on /get_individual_data_mic [POST]
Traceback (most recent call last):
File "/opt/packages/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
response = self.full_dispatch_request()
File "/opt/packages/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/opt/packages/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/opt/packages/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
rv = self.dispatch_request()
File "/opt/packages/cryosparc/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "cryosparc2_command/command_vis/__init__.py", line 121, in wrapper
res = func(*args, **kwargs)
File "cryosparc2_command/command_vis/__init__.py", line 417, in get_individual_data_mic
return make_file_response(read_mrc_image_data(project_uid, micrograph_blob['path'][0], psize=micrograph_blob['psize_A'][0], lp_filter_A=lp_filter_A, cache_key=exposure_uid))
File "cryosparc2_command/command_vis/__init__.py", line 380, in read_mrc_image_data
arr_tile = arr_view[tile_start_y[y]:tile_end_y[y], tile_start_x[x]:tile_end_x[x]]
IndexError: index 8 is out of bounds for axis 0 with size 8
We’ve identified this is indeed a bug. It never revealed itself since the code still works in all situations where the micrograph is longer in x than it is in y. I’ll be releasing the fix for this bug in the next version of cryoSPARC Live.
Thanks for your help!
