Error in Live: 'get_individual_data_mic' request failed

closed

#1

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


#2

Hi @Paul,

Can you please paste the output of the following log:

cryosparcm log command_vis

Thanks,
Suhail


#3

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

#4

Hey @Paul,

Is it possible if you can send us the dimensions (frame size) of your movies?


#5

header 20Mar13_4C_230-7_0009.tif

RO image file on unit 1 : 20Mar13_4C_230-7_0009.tif Size= 522167 K

                This is a TIFF file.

Number of columns, rows, sections … 8184 11520 50
Map mode … 0 (byte)
Start cols, rows, sects, grid x,y,z … 0 0 0 8184 11520 50
Pixel spacing (Angstroms)… 0.4693 0.4693 0.4693
Cell angles … 90.000 90.000 90.000
Fast, medium, slow axes … X Y Z
Origin on x,y,z … 0.000 0.000 0.000
Minimum density … 0.0000
Maximum density … 6.0000
Mean density … 3.0000
tilt angles (original,current) … 0.0 0.0 0.0 0.0 0.0 0.0
Space group,# extra bytes,idtype,lens . 0 0 0 0

 2 Titles :

SerialEMCCD: Dose frac. image, scaled by 1.00 r/f 5
SuperRef_20Mar13_4C_135-1_0004.dm4


#6

Thank you for your help @Paul,

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!


#7

Thank you the notice. I will consider this issue resolved and look forward to the update.