DM acquired shape different than received shape

Added by Michael Cianfrocco over 7 years ago

Hi Anchi,

We have older K2 running Digital Micrograph 2.32.888.0 on our Talos Arctica at Michigan.

We are having issues with our leginon installation not being able to collect movie frames in Counted mode. While we are able to take a single image, we cannot take a movie.

In looking into the problem, we realized a discrepancy between the DM acquired shape and received shape:

DM acquire shape (3710, 3838)
received shape (3710, 3710)

Which we received when running pyscope directly from the python command line.

This is in spite of our instruments.cfg file having:

[Gatan K2 Counting]
class: damsel.GatanK2Counting
plane: 50
width: 3710
height: 3838

What is going wrong with this to give us incorrect dimensions?

Thanks,
Mike

Replies (4)

RE: DM acquired shape different than received shape - Added by Michael Cianfrocco over 7 years ago

I should follow up to say that when trying to collect a movie at 3710 x 3710, we notice:

DM acquire shape (3710, 3710)
received shape (0,0)

Which, if we are collecting a single image at 3710 x 3710, we don't get this error.

However, if we instead try to collect a single image at 3710 x 3838, we get:

Traceback (most recent call last):
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/Node.py", line 76, in onSetImage
    self.imagepanel.setImageType(evt.typename, evt.image)
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/ImagePanel.py", line 307, in setImageType
    self.selectiontool.setImage(name, imagedata, **kwargs)
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/SelectionTool.py", line 184, in setImage
    self.parent.setImage(image)
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/ImagePanel.py", line 313, in setImage
    self.setNumericImage(imagedata)
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/ImagePanel.py", line 401, in setNumericImage
    self.setBitmap()
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/ImagePanel.py", line 189, in setBitmap
    wximage = self.numpyToWxImage(self.imagedata)
  File "/usr/lib/python2.7/site-packages/leginon/gui/wx/ImagePanel.py", line 223, in numpyToWxImage
    imagedata = Image.fromstring("L", (w, h), normarray.tostring())
  File "/usr/lib64/python2.7/site-packages/PIL/Image.py", line 1845, in fromstring
    return frombytes(*args, **kw)
  File "/usr/lib64/python2.7/site-packages/PIL/Image.py", line 1835, in frombytes
    im.frombytes(data, decoder_name, args)
  File "/usr/lib64/python2.7/site-packages/PIL/Image.py", line 601, in frombytes
    d.setimage(self.im)
ValueError: tile cannot extend outside image

RE: DM acquired shape different than received shape - Added by Anchi Cheng over 7 years ago

This is a bug with DM that happens eventually to every setup eventually. I don't know the exact origin of it. I don't know how to fix it from my side because we did ask nicely to the camera.

The only way to stop it after it starts happening is to close Digital Micrograph and reopen it. This action must have reset something. You can then restart Leginon Client.

RE: DM acquired shape different than received shape - Added by Michael Cianfrocco over 7 years ago

Hi Anchi,

Thanks for your response - unfortunately, we haven't even gotten the movie collection to work yet on this setup of DM. We can only take single images, but not movies - any suggestions on how to deal with this? It is an older K2 and DM, which maybe is the reson we are having the problem.

Mike

RE: DM acquired shape different than received shape - Added by Anchi Cheng over 7 years ago

Hi, Michael,

DM 2.32 is not too old. It is used even on the newest Bioquantum install. There is a rotation applied for 2.30.xxx versions when acquiring movie. Anything newer than that should not do so.
Check if dmsem.py is parsing your dmsem.cfg correctly.

from pyscope import dmsem
d = dmsem.GatanK2Counting()
d.getDMVersion()

The returned values include:
version_long: an integer number that contains all majoy/minor version information. Yours should be 43288.
version_str: major.minor.sub_version. Yours should be 2.32.88

Maybe for some reason your dmsem.cfg is not read right. Or the dmsem.cfg does not match pyscope/leginon version.

(1-4/4)

Project

General

Profile

Leginon