Visualize the example data and start roi_buddy

[Chongxi Lai]

Dear SIMA-Team,

I've loaded example data but have no idea how to visualize it. 

One way I saw in the document is use roi_buddy. I run it but get the below error:

Chongxi@fileindexdrives:~/.local/lib/python2.7/site-packages/ROIBuddy$ python roi_buddy.py

/Users/Chongxi/anaconda/lib/python2.7/site-packages/skimage/filter/__init__.py:6: skimage_deprecation: The `skimage.filter` module has been renamed to `skimage.filters`.  This placeholder module will be removed in v0.13.

  warn(skimage_deprecation('The `skimage.filter` module has been renamed '

Traceback (most recent call last):

  File "roi_buddy.py", line 34, in <module>

    import guiqwt.baseplot

  File "/Users/Chongxi/anaconda/lib/python2.7/site-packages/guiqwt/baseplot.py", line 60, in <module>

    from guiqwt.transitional import (QwtPlot, QwtLinearScaleEngine,

  File "/Users/Chongxi/anaconda/lib/python2.7/site-packages/guiqwt/transitional.py", line 19, in <module>

    from PyQt4.Qwt5 import (QwtPlot, QwtSymbol, QwtLinearScaleEngine,

ImportError: No module named Qwt5

It reminds me that I need Qwt5 under PyQt4 module. However, I use anaconda Mac OS X version, its original PyQt4 module does not has Qwt5. Could you recommend a PyQt4 library that contains Qwt5 under Mac OS X for anaconda python 2.7.10? 

Best,

Chongxi

[Patrick Kaifosh]

If you want to visualize the dataset within Python, you can use the
matplotlib package and view such things as individual frames or time
averages (see the dataset API for how to get the frames and time
averages: http://losonczylab.org/sima/1.3/api/datasets.html). Otherwise,
you can export data, as shown here
(https://github.com/losonczylab/sima/blob/master/examples/workflow.py)

Regarding ROI Buddy, yes it seems the problem is that your versions of
guiqwt and PyQt4 are not fully compatible with each other. I'm not a Mac
OS X user, but hopefully someone who is will be able to help you out, or
you will be able to figure it out. In fact, someone had a very similar
issue on linux, and perhaps their solution will work for you:
https://github.com/losonczylab/roibuddy/issues/17

Chongxi Lai wrote:
> Dear SIMA-Team,
>
> I've loaded example data but have no idea how to visualize it.
>
> One way I saw in the document is use roi_buddy. I run it but get the
> below error:
>
> Chongxi@fileindexdrives:~/.local/lib/python2.7/site-packages/ROIBuddy$
> python roi_buddy.py
> /Users/Chongxi/anaconda/lib/python2.7/site-packages/skimage/filter/__init__.py:6:
> skimage_deprecation: The `skimage.filter` module has been renamed to
> `skimage.filters`. This placeholder module will be removed in v0.13.
> warn(skimage_deprecation('The `skimage.filter` module has been renamed '
> Traceback (most recent call last):
> File "roi_buddy.py", line 34, in <module>
> import guiqwt.baseplot
> File
> "/Users/Chongxi/anaconda/lib/python2.7/site-packages/guiqwt/baseplot.py",
> line 60, in <module>
> from guiqwt.transitional import (QwtPlot, QwtLinearScaleEngine,
> File
> "/Users/Chongxi/anaconda/lib/python2.7/site-packages/guiqwt/transitional.py",
> line 19, in <module>
> from PyQt4.Qwt5 import (QwtPlot, QwtSymbol, QwtLinearScaleEngine,
> ImportError: No module named Qwt5
>

> It reminds me that I need /Qwt5 /under/PyQt4 /module. However, I use

> anaconda Mac OS X version, its original PyQt4 module does not has
> Qwt5. Could you recommend a PyQt4 library that contains Qwt5 under

> *Mac OS X *for *anaconda python 2.7.10*?
>
> Best,
> Chongxi
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