Hello,
I was working with MSNoise without problems until I decided to change the
*mwcs_wlen* and *mwcs_step*. I ran *s05compute_mwcs.py* and
*s06compute_dtt.py* with the new parameters and then I ran
*s07plot_dtt.py* giving
me the next error message:
*oscar@terminus:~/Doctorado/TI_2/sweet_noise$ py s07plot_dtt.py *
*/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py:1045:
UserWarning: /home/oscar/.python-eggs is writable by group/others and
vulnerable to attack when used with get_resource_filename. Consider a more
secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE
environment variable).*
*Traceback (most recent call last):*
* File "s07plot_dtt.py", line 96, in <module>*
* data = detrend(py1_wmean)*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/statsmodels/tsa/tsatools.py",
line 230, in detrend*
* beta = np.linalg.lstsq(trends, x)[0]*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py",
line 1837, in lstsq*
* nlvl = max( 0, int( math.log( float(min(m, n))/2. ) ) + 1 )*
*ValueError: math domain error*
*oscar@terminus:~/Doctorado/TI_2/sweet_noise$ vi s06compute_dtt.py *
*oscar@terminus:~/Doctorado/TI_2/sweet_noise$ py s07plot_dtt.py *
*/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py:1045:
UserWarning: /home/oscar/.python-eggs is writable by group/others and
vulnerable to attack when used with get_resource_filename. Consider a more
secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE
environment variable).*
*Traceback (most recent call last):*
* File "s07plot_dtt.py", line 96, in <module>*
* data = detrend(py1_wmean)*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/statsmodels/tsa/tsatools.py",
line 230, in detrend*
* beta = np.linalg.lstsq(trends, x)[0]*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py",
line 1837, in lstsq*
* nlvl = max( 0, int( math.log( float(min(m, n))/2. ) ) + 1 )*
*ValueError: math domain error*
Does anyone can help me? Thank you very much in advance!
Oscar
**
Dear Thomas and MSnoise users,
I just completed my first installation and processing on the test case
from AGU 2013 and I had a few observation and comments to improve the
existing documentation for future users.
In the Configurator:
*
I made the mistake to set keep_days as “No”, probably because I
copied the screenshot from the doc. This was, of course, a problem
when I computed the CC. I think it would be worth either to change
the screenshot, or to mention in the doc that this setting could be
problematic.
*
The ref begin and end are set by default in relative, potentially
causing errors if the REF folder is not created by s04stack.
*
I had no filter values by default, I think it would be good to have
suggested values for those who are quickly trying MSnoise.
*
I think it would also be nice to have more advice on the use of
sqlite and mysql. Maybe recommend a sqlite manager, the way it is
done with EasyPHP for mysql.
*
It was already mentioned in the mailing list but it would also be
nice to have suggestions on the best way to reset jobs from “D” to
“T”. It probably won’t be a problem when the toolbox will be ready.
*
I didn’t install wx, so to plot the dt/t I had to disable the line 3
“mpl.use('WxAgg')”. Also the red line didn’t show on the plot, but I
think this is a known problem.
I hope this will be useful for future users.
Cheers,
Raphael De Plaen
PhD Student
University of Luxembourg
**
Using MSNoise 1.24 there are two python scripts that plot; they are
07plot_dtt.py and s07plot_dtt.py. I get errors for either.
Using s07plot_dtt.py yields attachment s07plot_dtt.png. There are two
problems:
1) I entered mov_stack values 1,3,5, and 10 days into the configurator but
the graphical output includes only 1, 3, and 5 days moving window graphs,
and the only graph with any data plotted onto it is the 5 days moving
window.
2) the graph x axes automatically include a much larger time period than
covered by the data plotted. This includes dates back to 2013 and forward
into 2016, while all the data I have is from 2014. I am unsure if this
problem is related to some of my settings in the configurator. My settings
that I can see might be related are: enddate=2100-01-01, ref_begin=-100,
ref_end=0, startdate=2014-05-04.
Using 07plot_dtt.py yields attachment image 07.plot_dtt.png the following:
>>> runfile('/home/devora/MSNoise-master/07.plot_dtt.py',
wdir=r'/home/devora/MSNoise-master')
UMD has deleted: database_tools, msnoise_table_def
loading 1 days
loading 3 days
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/usr/lib/python2.7/site-packages/spyderlib/widgets/externalshell/sitecustomize.py",
line 540, in runfile
execfile(filename, namespace)
File "/home/devora/MSNoise-master/07.plot_dtt.py", line 128, in <module>
plt.fill_between(ALL.index,ALL[dttname]-ALL[errname],ALL[dttname]+ALL[errname],lw=1,color='red',zorder=-1,alpha=0.3)
File "/usr/lib64/python2.7/site-packages/matplotlib/pyplot.py", line 2757,
in fill_between
interpolate=interpolate, **kwargs)
File "/usr/lib64/python2.7/site-packages/matplotlib/axes.py", line 6988, in
fill_between
x = ma.masked_invalid(self.convert_xunits(x))
File "/usr/lib64/python2.7/site-packages/numpy/ma/core.py", line 2239, in
masked_invalid
condition = ~(np.isfinite(a))
TypeError: ufunc 'isfinite' not supported for the input types, and the
inputs could not be safely coerced to any supported types according to the
casting rule ''safe''
>>>
Has anyone else encountered these problems before? Does anyone have any
suggestions for what I might do to overcome them?
Thankyou
Josiah
Dear Thomas, dear MSNoise users,
No problem to fix, just a tip.
For people who are not familiar at all with MySQL (like me), here is how to
reset the correlation computation jobs from 'D'one to 'T'odo between a
certain range of dates. I needed to do that because the disk where I wrote
the correlations get full, but MSNoise kept trying to do the following job
even if the correlation couldn't be written. Actually, maybe there is a way
to let the job set to 'T' if the correlation is not really saved on a
disk...
Anyway, here is the command I used in phpMyAdmin, using the SQL tab, once
you selected your database:
UPDATE `job` SET `flag` = 'T' WHERE `day` BETWEEN 'date1' AND 'date2';
Then press Go button.
Before using it, I would like to have the advice from a MySQL expert: is it
the right way to do it? If yes, it could be worth to have this line in the
documentation somewhere.
Cheers,
Aurelien.
--
aurelien.mordret(a)gmail.com
Mobile: 0033 6 67 51 53 56
Dear all,
When I run Compute_cc the terminal show this message:
File "s03compute_cc.py", line 313, in <module>
X0 = s1.X
AttributeError: 'NoneType' object has no attribute 'X'
?In which way can I fix it?? The attribute X, Y and also Z exits in the table and I also populate it. So I don't understand this type of error. thank you very much. I hope to receive some answer..
cheers,
Carmelo
The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.
Hi,
I have just updated to 1.2.5 and tried to run *s07plot_dtt.py *(again on
both PCs) and I got this error message:
oscar@terminus:~/msnoise_sismo$ py s07plot_dtt.py
Traceback (most recent call last):
File "s07plot_dtt.py", line 13, in <module>
import matplotlib.pyplot as plt
File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py",
line 98, in <module>
_backend_mod, new_figure_manager, draw_if_interactive, _show =
pylab_setup()
File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
line 28, in pylab_setup
globals(),locals(),[backend_name],0)
File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_wxagg.py",
line 6, in <module>
import backend_wx # already uses wxversion.ensureMinimal('2.8')
File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_wx.py",
line 53, in <module>
raise ImportError(missingwxversion)
ImportError: Matplotlib backend_wx and backend_wxagg require wxversion,
which was not found.
Please help!!!!!
Oscar
Hi Achmad,
1/ Did you follow the steps of the workflow ?
2/ What is your archive folder structure / format ?
3/ for the filter problem, consider reading this thread of the ML :
http://news.gmane.org/gmane.science.geophysics.msnoise --> "Problem with
the filters tab"
Thomas
ps: your message was not forwarded to the ML because of attached images,
I have to find a way to fix this.
Le 09/10/2014 05:56, achmad gunar saadi a écrit :
> Good morning,
> I am Achmad Gunar Saadi, Gephisics student in Universitas Gadjah Mada.
> I wanna ask about menu in the configurator, why in the Filters and
> Networks tab doesn't appear any option?. And also about setting
> data_structure, How to fix this problems?. I have watched your video
> tutorial "Msnoise first install", but I still get those problems.
> Herewith I sent also the screenshot.
> Thank you very much.
>
> Yours sincerely,
>
> Achmad Gunar Saadi
> Universitas Gadjah Mada
> Inline image 1Inline image 2
Hello,
I am using MSNoise on two different PC's (Ubuntu 12.04 [AMD A6] and Ubuntu
14.04 [Intel i7]), each computer has the same version of MSNoise (1.2.4)
but differents sets of data. I compute all the steps without a problem but
when I try to compute *07.plot_dtt.py <http://07.plot_dtt.py>* the routine
fails. I got two different error messages:
Ubuntu 12.04:
*oscar@bayta:~/sweet_noise$ py 07.plot_dtt.py <http://07.plot_dtt.py> *
*/home/oscar/anaconda/lib/python2.7/site-packages/numpy/oldnumeric/__init__.py:11:
ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy
1.9*
* warnings.warn(_msg, ModuleDeprecationWarning)*
*/home/oscar/anaconda/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg/pkg_resources.py:991:
UserWarning: /home/oscar/.python-eggs is writable by group/others and
vulnerable to attack when used with get_resource_filename. Consider a more
secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE
environment variable).*
*loading 1 days*
*Traceback (most recent call last):*
* File "07.plot_dtt.py <http://07.plot_dtt.py>", line 115, in <module>*
* py1_wmean, py1_wstd = get_wavgwstd(allbut)*
* File "07.plot_dtt.py <http://07.plot_dtt.py>", line 59, in get_wavgwstd*
* h = grouped.apply(wstd)*
* File
"/home/oscar/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py",
line 424, in apply*
* return self._python_apply_general(f)*
* File
"/home/oscar/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py",
line 427, in _python_apply_general*
* keys, values, mutated = self.grouper.apply(f, self.obj, self.axis)*
* File
"/home/oscar/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py",
line 883, in apply*
* res = f(group)*
* File
"/home/oscar/anaconda/lib/python2.7/site-packages/pandas/core/groupby.py",
line 422, in f*
* return func(g, *args, **kwargs)*
* File "07.plot_dtt.py <http://07.plot_dtt.py>", line 52, in wstd*
* wstd = np.sqrt(np.sum(w * (d - wavg) ** 2) / ((N - 1) * np.sum(w) /
N))*
*ZeroDivisionError: float division by zero*
Ubuntu 14.04:
*oscar@terminus:~/msnoise_sismo$ py 07.plot_dtt.py <http://07.plot_dtt.py>*
*/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/setuptools-3.6-py2.7.egg/pkg_resources.py:1045:
UserWarning: /home/oscar/.python-eggs is writable by group/others and
vulnerable to attack when used with get_resource_filename. Consider a more
secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE
environment variable).*
*loading 1 days*
*Traceback (most recent call last):*
* File "07.plot_dtt.py <http://07.plot_dtt.py>", line 128, in <module>*
*
plt.fill_between(ALL.index,ALL[dttname]-ALL[errname],ALL[dttname]+ALL[errname],lw=1,color='red',zorder=-1,alpha=0.3)*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py",
line 2757, in fill_between*
* interpolate=interpolate, **kwargs)*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/matplotlib/axes.py",
line 6988, in fill_between*
* x = ma.masked_invalid(self.convert_xunits(x))*
* File
"/home/oscar/bin/python/anaconda/lib/python2.7/site-packages/numpy/ma/core.py",
line 2239, in masked_invalid*
* condition = ~(np.isfinite(a))*
*TypeError: ufunc 'isfinite' not supported for the input types, and the
inputs could not be safely coerced to any supported types according to the
casting rule ''safe''*
I am not a python expert and I haven't could solve these problems. If
anyone knows how to solve it please help me!
Thanks in advance!
Oscar
Hi Carmelo,
Tom suggested the issue may be linux related, and proposed some hard-coding
of the filters, but I have not had any problems on two linux installs (both
fedora and ubuntu) defining the filters. They are defined in the
configurator:
http://msnoise.org/doc/workflow.html#module-MSNoise.s001configurator
Do you see the filter tab on the left? This should open up boxes in the gui
where you can set the filters according to your desires. If your system
behaves differently, please describe in detail.
Cheers,
Kasper
On 4 October 2014 10:05, Sammarco, Carmelo <carmelosammarco(a)abdn.ac.uk>
wrote:
> Dear Thomas, Aurelien and MsNoise users,
>
> When I run s03compute_cc.py the terminal shows: 'NO FILTERS DEFINED,
> exiting'. If I go in the configurator and in the filter Tab the section is
> blank. In which way can I populate the filter tab?? Someone could explain
> me in which way can I fix the problem?? I am using linux and Mysql. Can I
> add the filters information on the database with phpmyadmin? And if yes in
> which way? I am a PhD student of the university of Aberdeen and I need to
> fix this problem as soon as possible. Please someone help me please. I need
> to do a lot of job so I can't rerun like Aurelien says:
>
> "IF you rerun s03compute_cc.py after this error, it will jump to the next
> job. It's a dirty quick fix and it does not help if the error happens every
> two days of data..."
>
>
> Thank you very much for the info!! Better than nothing.. I appreciate a
> lot but I am looking if possible for a permanent solution.
>
> I hope to recieve your replay.
>
> Cheers,
>
> Carmelo
>
>
>
>
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
> SC013683.
> _______________________________________________
> MSNoise mailing list
> MSNoise(a)mailman-as.oma.be
> http://mailman-as.oma.be/mailman/listinfo/msnoise
>
