mbrubake / cryoem-cvpr2015 Goto Github PK

I tried to plot the current state of the reconstruction using IPython. But when I import visualizer.py using import visualizer, I encountered such report with long long traceback as follows:

IPython 0.12.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
/usr/lib/python2.7/dist-packages/IPython/zmq/__init__.py:37: RuntimeWarning: libzmq 4 detected.
        It is unlikely that IPython's zmq code will work properly.
        Please install libzmq stable, which is 2.1.x or 2.2.x
  RuntimeWarning)

Welcome to pylab, a matplotlib-based Python environment [backend: Qt4Agg].
For more information, type 'help(pylab)'.
In [1]: import visualizer
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/home/yzs/work/cryoEM/3DReconstruction/cryoem-cvpr2015/<ipython-input-1-22c2bba9562b> in <module>()
----> 1 import visualizer

/home/yzs/work/cryoEM/3DReconstruction/cryoem-cvpr2015/visualizer.py in <module>()
      4 # Visualization code for cryoem

      5 
----> 6 from mayavi import mlab
      7 import matplotlib.pyplot as plt
      8 from matplotlib.widgets import Slider

BLABLABLABLABLA

/usr/local/lib/python2.7/dist-packages/pyface/qt/__init__.py in prepare_pyqt4()
     15     # Set PySide compatible APIs.

     16     import sip
---> 17     sip.setapi('QDate', 2)
     18     sip.setapi('QDateTime', 2)
     19     sip.setapi('QString', 2)

ValueError: API 'QDate' has already been set to version 1

and I searched for this problem. The results make me think that this is a problem due to the conflict between qt4 and wxpython2.8. (Just minutes ago, I installed mayavi and run $ mayavi2 in bash, I was told that the mayavi requires wxPython2.8 or greater version. So I installed wxPython2.8 by apt ). Then I set the environment var to make use of qt4 instead of wxpython2.8 : export ETS_TOOLKIT=qt4. And mayavi doesn't report the require for wxPython2.8 or greater problem. Yet at this time the ValueError: API 'QDate' has already been set to version 1 problem when i import visualizer still exists.
How can I solve this conflict？

we run the latest scientific linux 6.7 with the system python and qt bindings and have the following problem:

$ ipython --pylab=qt
Python 2.6.6 (r266:84292, Jul 22 2015, 16:47:47)
Type "copyright", "credits" or "license" for more information.

IPython 0.13.2 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.

Welcome to pylab, a matplotlib-based Python environment [backend: Qt4Agg].
For more information, type 'help(pylab)'.

In [1]: import visualizer
File "monitor.py", line 84
like_timing = {k[len(dset+'like_timing'):] : self.stat[k] for k in ks}
^
SyntaxError: invalid syntax

./runexp.py exp/EMD_2824
ERROR LOADING FFTW! USING NUMPY
Dataset noise profile
Noise: 0.995
Data: 1.03
Signal: 0.25
Signal-to-Noise Ratio: 6.3% (-12.0dB)
Dividing dataset of 40863 images with minisize of 200
Test Images: 200
Train Images: 40663
Minibatches: 203
Batch Size Range: 200 - 201
Estimated DC Component: 0.421 +/- 0.0458
Using positive datasign
Randomly generating initial density (init_random_seed = 0)... done in 5.73230814934s
Windowing and aligning initial density... done in 1.18s
Scaling initial model... estimated modelscale = 0.0032... done in 0.00s
WARNING: the DC component estimate has a high relative variance, it may be inaccurate!
Detected 40 cores, using 40 threads
Iteration 1: freq = 0.02, rad = 0.0708, N_T = 101
Slice Ops: 189, generated in 0.0406110286713 secs.
Inplane Ops: 24, generated in 0.00356101989746 secs.
Shift Ops: 1, generated in 0.000195026397705 secs.
Traceback (most recent call last):
File "./runexp.py", line 22, in
CO.run()
File "/projects/marlovits/lugmayr/cryoem-cvpr2015-master/optimizer.py", line 549, in run
while self.dowork(): pass
File "/projects/marlovits/lugmayr/cryoem-cvpr2015-master/optimizer.py", line 708, in dowork
self.sampler_R.perform_update()
File "/projects/marlovits/lugmayr/cryoem-cvpr2015-master/importancesampler/fixed.py", line 309, in perform_update
self.clear_updates()
File "/projects/marlovits/lugmayr/cryoem-cvpr2015-master/importancesampler/fixed.py", line 302, in clear_updates
self.global_upd[:] = 0
TypeError: 'NoneType' object does not support item assignment

Please tell me how to fix the error of "Building module sincint failed:"?.
I met this error while running this program as README suggested.

Hi,

I tried to run the script vismrc.py but the module qtvis is missing.
Had also the problem with git in the code of runexp.py, I commented out the code.
And finally "vis = visualizer.Visualizer('exp/1AON_sagd_is',extra_plots=True)" is crashing
Best regards,

when downloading this software by pressing "Download ZIP" instead of using git, the following error appears during runtime:

$ ./runexp.py exp/1AON_sagd_is
ERROR LOADING FFTW! USING NUMPY
Dataset noise profile
Noise: 25
Data: 25.3
Signal: 3.6
Signal-to-Noise Ratio: 2.1% (-16.8dB)
Dividing dataset of 40000 images with minisize of 200
Test Images: 200
Train Images: 39800
Minibatches: 199
Batch Size Range: 200 - 200
Estimated DC Component: 54.6 +/- 0.261
Using positive datasign
fatal: Not a git repository (or any of the parent directories): .git
Traceback (most recent call last):
File "./runexp.py", line 20, in
CO = optimizer.CryoOptimizer(expbase, kargs)
File "/clustertmp/lugmayr/cryoem-cvpr2015-master/optimizer.py", line 402, in init
self.ostream("Git SHA1: " + gitutil.git_get_SHA1())
File "/clustertmp/lugmayr/cryoem-cvpr2015-master/util/gitutil.py", line 18, in git_get_SHA1
return subprocess.check_output(args).strip()
File "/opt/python27/lib/python2.7/subprocess.py", line 573, in check_output
raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['git', 'rev-parse', 'HEAD']' returned non-zero exit status 128

Please add to the README file, that a data line in the defocus.txt file must start with a space ' ' before the image number otherwise the whole line is considered as comment. It took me quite a while to analyse your code to find this out.