Hi CS community
Is there a way to export 2D classification result at a higher resolution than the png or pdf files provided by 2D classification job? I would like to export a publication quality 2D classification result from Select 2D Classes job, however the images are lower resolution than the actual pixel size of the particles.
Thank you.
Alpay
Hi @alburse,
You can use the plotting function used by the 2D Classification job itself. Check out the function parameters for more info (found in cryosparc2_worker/cryosparc2_compute/plotutils.py)
The .mrc file is from the âparticles_selectedâ output of the Select 2D job:
Thank you, I will try this.
Hi
I tried this but could not get it to work. I guess CRYOSPARC_ROOT_DIR is not right, I tried the master folder and worker too. I found this link but not sure if this solution will effect other operations.
Thank you
import os
os.chdir(os.environ[â/share/PI/yiorgo/alpay/modules/alpaysprograms/cryosparc/2.9â])
from cryosparc2_compute import plotutil
from cryosparc2_compute.blobio import mrc
KeyErrorTraceback (most recent call last)
in ()
1 import os
----> 2 os.chdir(os.environ[â/share/PI/yiorgo/alpay/modules/alpaysprograms/cryosparc/2.9â])
3 from cryosparc2_compute import plotutil
4 from cryosparc2_compute.blobio import mrc
/share/software/user/open/python/2.7.13/lib/python2.7/UserDict.pyc in getitem(self, key)
38 if hasattr(self.class, âmissingâ):
39 return self.class.missing(self, key)
â> 40 raise KeyError(key)
41 def setitem(self, key, item): self.data[key] = item
42 def delitem(self, key): del self.data[key]
KeyError: â/share/PI/yiorgo/alpay/modules/alpaysprograms/cryosparc/2.9â
Check your system environment that if âCRYOSPARC_ROOT_DIRâ is set
env | grep âCRYOSPARC_ROOT_DIRâ
You may set it by
echo âexport CRYOSPARC_ROOT_DIR=/path/to/cryosparc/root/dirâ >> ~/.bashrc && . ~/.bashrc
Thank you. I gave the directory (CRYOSPARC_RROT_DIR) directly to Jupyter notebook and it did not work. System environment worked. Thank you
Hi sarulthasan,
Iâm also struggling with this. Unfortuantely, I donât really understand what you meant. Where should I use this plotting function?
Also, is there a reason why this is relatively difficult, compared to a downloading or displaying a 3d map? It seems to me 2D classes are an important (intermediate) result?
Many thanks,
Maarten
Hi Maarten
@stephan showed an example on Jupyter Notebook. You can start a Jupyter notebook and use it as a python environment. I believe cryosparc itself has the jupyter notebook setup and has all the necessary python libraries but I could not find how to start Jupyter notebook from cryosparc environment. Therefore I used my own Jupyter notebook. You will need at least the following python 2.7 libraries installed.
py-numpy py-scipy py-numba py-matplotlib pyFFTW
and CRYOSPARC_ROOT_DIR defined in your bashrc or bash_profile or equivalent file for other shells.
Below worked for me on my bash_profile file.
export CRYOSPARC_ROOT_DIR="/directory-to-cryosparc/cryosparc/2.11/cryosparc2_worker"
If @stephan tells us how to use the jupyter notebook from cryosparc that would be great.
More importantly, I could not really find what parameter to change on the plotutils.py to get the native resolution on the 2D-class averages. If you find it, please let me know.
Hi @maarten.tuijtel,
Youâre right- weâre planning on adding a âdownload imagesâ button that will output a compressed folder of individual class images at full resolution. Iâll keep you updated on this!
