installation problem

[jbiofiz]

Hey, I am very eager to try Hooke, however I met some prolemwith
installation. I installed all the required modules in required
versions, but when I try to run hooke.py I get the following:

Traceback (most recent call last):
File "D:\hooke2\hooke.py", line 21, in <module>
import wxmpl
File "C:\Python25\lib\wxmpl.py", line 22, in <module>
import matplotlib
File "C:\Python25\lib\site-packages\matplotlib\__init__.py", line
129, in <module>
from rcsetup import defaultParams, validate_backend,
validate_toolbar
File "C:\Python25\lib\site-packages\matplotlib\rcsetup.py", line 19,
in <module>
from matplotlib.colors import is_color_like
File "C:\Python25\lib\site-packages\matplotlib\colors.py", line 54,
in <module>
import matplotlib.cbook as cbook
File "C:\Python25\lib\site-packages\matplotlib\cbook.py", line 10,
in <module>
import numpy.ma as ma
ImportError: No module named ma

How I can solve the problem? I must warn that I have only marginal
knowledge of Python.

[massimo sandal]

Hi Jbiofiz,

Thanks for your mail. I am answering below:

2009/4/2 jbiofiz <jbi...@gmail.com>:

> Traceback (most recent call last):
> File "D:\hooke2\hooke.py", line 21, in <module>
> import wxmpl
> File "C:\Python25\lib\wxmpl.py", line 22, in <module>
> import matplotlib
> File "C:\Python25\lib\site-packages\matplotlib\__init__.py", line
> 129, in <module>
> from rcsetup import defaultParams, validate_backend,
> validate_toolbar
> File "C:\Python25\lib\site-packages\matplotlib\rcsetup.py", line 19,
> in <module>
> from matplotlib.colors import is_color_like
> File "C:\Python25\lib\site-packages\matplotlib\colors.py", line 54,
> in <module>
> import matplotlib.cbook as cbook
> File "C:\Python25\lib\site-packages\matplotlib\cbook.py", line 10,
> in <module>
> import numpy.ma as ma
> ImportError: No module named ma
>
> How I can solve the problem? I must warn that I have only marginal
> knowledge of Python.

Seems that there is something wrong between your Matplotlib and Numpy
installation (The error message tells that matplotlib tries to look
something from numpy, and cannot find it). Could you please tell me
which versions of the libraries, exactly, are you using? Also your
operating system and Python version.

Thanks!

m.

[m.s.]

Hi,

Did you manage to solve this? I replied to the group but I've seen no
followup...

Cheers,
M.

[jbiofiz]

Sorry for delay, past weeks were rather busy.
I use Windows XP SP3.
I installed, according to directions on your webpage:
wxPython 2.8.9.2
Numpy 1.0.4
Scipy 0.6.0
Matplotlib 0.98.0
wxMPL 1.2.9

[massimo sandal]

Hi jbiofiz,

thanks for feedback.

2009/4/21 jbiofiz <jbi...@gmail.com>:

>
> Sorry for delay, past weeks were rather busy.
> I use Windows XP SP3.
> I installed, according to directions on your webpage:
> wxPython 2.8.9.2
> Numpy 1.0.4
> Scipy 0.6.0
> Matplotlib 0.98.0
> wxMPL 1.2.9

I would say that your numpy is too old for the matplotlib version you
are using. I would try using numpy 1.2.x . If in doubt, I would look
at this page http://code.google.com/p/hooke/wiki/ListKnownWorkingLibraries
for combinations that are known to work.

Unfortunately this kind of problems does not depend on us but on the
intertwining of dependencies required by Hooke. I will try to put
downloads of known working libraries here on the site, so that people
do not have to become crazy, but there are a number of legal
annoyances that one could hit (e.g. GPL code requires source to be
shipped, etc.)

m.

[massimo sandal]

I also found the documentation was misleading; that probably led to
the problem. Thanks for your feedback, I now hope it is a bit more
clear.

[jbiofiz]

I updated my configuration according to given stable example.
Unfortunately now I get:

Starting Hooke.
Imported plugin fit
Imported plugin procplots
Imported plugin flatfilts
Imported plugin generalclamp
Imported plugin generalvclamp
Imported plugin massanalysis
Imported plugin viewer
Imported plugin macro
Imported plugin autopeak
Imported driver picoforce
Imported driver hemingclamp
Imported driver csvdriver
Imported driver jpk

Traceback (most recent call last):

File "D:\hooke\hooke.py", line 151, in <module>
class CliThread(Thread):
File "D:\hooke\hooke.py", line 160, in CliThread
self.debug=0 #to be used in the future
NameError: name 'self' is not defined

[massimo sandal]

Hi jbiofiz,

> I updated my configuration according to given stable example.
> Unfortunately now I get:
>
> Starting Hooke.
> Imported plugin  fit
> Imported plugin  procplots
> Imported plugin  flatfilts
> Imported plugin  generalclamp
> Imported plugin  generalvclamp
> Imported plugin  massanalysis
> Imported plugin  viewer
> Imported plugin  macro
> Imported plugin  autopeak
> Imported driver  picoforce
> Imported driver  hemingclamp
> Imported driver  csvdriver
> Imported driver  jpk
>
> Traceback (most recent call last):
>  File "D:\hooke\hooke.py", line 151, in <module>
>    class CliThread(Thread):
>  File "D:\hooke\hooke.py", line 160, in CliThread
>    self.debug=0 #to be used in the future
> NameError: name 'self' is not defined

This is extremly puzzling. There is no way I can think for "self" to
be undefined.
I'm sorry you're running into all these problems -but it's the first
time I see this bug!

Would you be so nice to comment (with a #) the apparently offending
line 160 of hooke.py, just to see what happens?

Thanks
m.

[jbiofiz]

Ok, Hooke loaded as soon as I commented out the line. I managed to
read the example titin curves.

However I got some error messages during loading:

Warning: cannot create macros folder.
Probably you do not have permissions in your Hooke folder, use macro
at your own risk.
Loaded 1 curves
Starting at curve 0

Warning (from warnings module):
File "C:\Python25\lib\site-packages\scipy\stats\stats.py", line 1328
ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.std is deprecated; please update your
code to use numpy.std.
Please note that:
- numpy.std axis argument defaults to None, not 0
- numpy.std has a ddof argument to replace bias in a more general
manner.
scipy.stats.std(a, bias=True) can be replaced by numpy.std(x,
axis=0, ddof=0), scipy.stats.std(a, bias=False) by numpy.std(x,
axis=0,
ddof=1).

Warning (from warnings module):
File "C:\Python25\lib\site-packages\scipy\stats\stats.py", line 1304
ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.var is deprecated; please update your
code to use numpy.var.
Please note that:
- numpy.var axis argument defaults to None, not 0
- numpy.var has a ddof argument to replace bias in a more general
manner.
scipy.stats.var(a, bias=True) can be replaced by numpy.var(x,
axis=0, ddof=0), scipy.stats.var(a, bias=False) by var(x,
axis=0,
ddof=1).

Warning (from warnings module):
File "C:\Python25\lib\site-packages\scipy\stats\stats.py", line 420
axis=0, ddof=1).""", DeprecationWarning)
DeprecationWarning: scipy.stats.mean is deprecated; please update your
code to use numpy.mean.
Please note that:
- numpy.mean axis argument defaults to None, not 0
- numpy.mean has a ddof argument to replace bias in a more general
manner.
scipy.stats.mean(a, bias=True) can be replaced by numpy.mean(x,
axis=0, ddof=1).

Thank you very much for your help. Bugs in such complicated are
perfectly normal I guess.