MSNoise

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349 discussions

by Josiah Ensing

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

10 years, 11 months

Re-setting jobs from 'D'one to 'T'odo

by Aurélien Mordret

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

11 years

compatibility at Windows 8.1?

by Kohtaro R. Araragi

Hi MSNoise users, Does anyone attempt to use MSNoise by windows 8.1? I am trying to use via Anaconda, but matplotlib or obspy seems not to work properly from some reasons... I dowonload pandas, matplotlibs, and scikits.sa,plerate from http://www.lfd.uci.edu <http://www.lfd.uci.edu/%7Egohlke/pythonlibs/#scikits.samplerate>, but obspy or other things does not work zell and I cannot run s000installer.py. I appreciate if any of you tell me how you overcome this issue if you had in the past. Thanks in advance; Run (Kohtaro Araragi) C:\Research\MSNoise-master>python s000installer.py Traceback (most recent call last): File "s000installer.py", line 33, in <module> from database_tools import create_database_inifile File "C:\Research\MSNoise-master\database_tools.py", line 16, in <module> from obspy.signal import cosTaper File "C:\Anaconda\lib\site-packages\obspy-0.9.2-py2.7-win-amd64.egg\obspy\sign al\__init__.py", line 203, in <module> from spectral_estimation import psd, PPSD File "C:\Anaconda\lib\site-packages\obspy-0.9.2-py2.7-win-amd64.egg\obspy\sign al\spectral_estimation.py", line 34, in <module> MATPLOTLIB_VERSION = getMatplotlibVersion() File "C:\Anaconda\lib\site-packages\obspy-0.9.2-py2.7-win-amd64.egg\obspy\core \util\base.py", line 293, in getMatplotlibVersion import matplotlib File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 1048, in <mo dule> rcParams = rc_params() File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 897, in rc_p arams fname = matplotlib_fname() File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 759, in matp lotlib_fname configdir = _get_configdir() File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 630, in _get _configdir return _get_config_or_cache_dir(_get_xdg_config_dir()) File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 555, in _get _xdg_config_dir path = get_home() File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 323, in wrap per ret = func(*args, **kwargs) File "C:\Anaconda\lib\site-packages\matplotlib\__init__.py", line 509, in _get _home path = os.path.expanduser("~") File "C:\Anaconda\lib\ntpath.py", line 310, in expanduser return userhome + path[i:] UnicodeDecodeError: 'ascii' codec can't decode byte 0x8d in position 9: ordinal not in range(128) C:\Research\MSNoise-master>python bugreport.py -a ************* Computer Report ************* ----------------+SYSTEM+------------------- Windows Earthsea 8 6.2.9200 AMD64 Intel64 Family 6 Model 58 Stepping 9, GenuineIntel ----------------+PYTHON+------------------- Python: 2.7.8 |Anaconda 2.1.0 (64-bit)| (default, Jul 2 2014, 15:12:11) [MSC v. 1500 64 bit (AMD64)] ---------------+MODULES+------------------- Required: [X] numpy: 1.9.0 [X] scipy: 0.14.0 [ ] pandas: not found [ ] matplotlib: not found [X] statsmodels: 0.5.0 [X] sqlalchemy: 0.9.7 [X] traitsui: 4.4.0 [X] traits: 4.4.0 [X] enable: 4.3.0 [X] scikits.samplerate: present (no version) [X] obspy: 0.9.2 [X] sphinx: 1.2.3 [X] jinja2: 2.7.3 [X] flask: 0.10.1 [X] flask.ext.admin: 0.10.1 [X] wtforms: 2.0.1 [X] json: 2.0.9 [X] psutil: 2.1.1 Backends: (at least one is required) [ ] wx: not found [X] PyQt4: present (no version) [ ] PySide: not found Not required, just checking: [X] setuptools: 5.8 [ ] reportlab: not found [X] configobj: 5.0.6 [X] pkg_resources: present (no version) [ ] paramiko: not found [X] ctypes: 1.1.0 [X] pyparsing: 2.0.1 [X] distutils: 2.7.8 [X] IPython: 2.2.0 [ ] vtk: not found ------------------+ENV+-------------------- TMP [X] C:\Users\幸太郎\AppData\Local\Temp COMPUTERNAME [ ] EARTHSEA USERDOMAIN [ ] EARTHSEA PSMODULEPATH [X] C:\WINDOWS\system32\WindowsPowerShell\v1.0\Modules\ COMMONPROGRAMFILES [X] C:\Program Files\Common Files PROCESSOR_IDENTIFIER [ ] Intel64 Family 6 Model 58 Stepping 9, GenuineIntel PROGRAMFILES [X] C:\Program Files PROCESSOR_REVISION [ ] 3a09 PATH [X] C:\Anaconda\lib\site-packages\PyQt4 [X] C:\Anaconda\lib\site-packages\numpy\core [X] C:\Program Files (x86)\EasyPHP-DevServer-14.1VC11\binaries\php\php_running version [X] C:\Program Files (x86)\Intel\iCLS Client\ [X] C:\Program Files\Intel\iCLS Client\ [X] C:\WINDOWS\system32 [X] C:\WINDOWS [X] C:\WINDOWS\System32\Wbem [X] C:\WINDOWS\System32\WindowsPowerShell\v1.0\ [X] C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x86 [X] C:\Program Files (x86)\Intel\OpenCL SDK\2.0\bin\x64 [X] C:\Program Files\Intel\Intel(R) Management Engine Components\DAL [X] C:\Program Files\Intel\Intel(R) Management Engine Components\IPT [X] C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL [X] C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT [X] C:\Program Files (x86)\Windows Live\Shared [X] C:\MinGW\bin [X] C:\Program Files (x86)\QuickTime\QTSystem\ [X] C:\Program Files (x86)\GnuWin32\bin [X] C:\Anaconda [X] C:\Anaconda\Scripts [X] C:\Users\幸太郎\Anaconda [ ] C:\Users\幸太郎\Anaconda\Scripts SYSTEMROOT [X] C:\WINDOWS PROGRAMFILES(X86) [X] C:\Program Files (x86) TEMP [X] C:\Users\幸太郎\AppData\Local\Temp COMMONPROGRAMFILES(X86) [X] C:\Program Files (x86)\Common Files PROCESSOR_ARCHITECTURE [ ] AMD64 ALLUSERSPROFILE [X] C:\ProgramData LOCALAPPDATA [X] C:\Users\幸太郎\AppData\Local HOMEPATH [X] \Users\幸太郎 USERDOMAIN_ROAMINGPROFILE [ ] EARTHSEA PROGRAMW6432 [X] C:\Program Files USERNAME [ ] 幸太郎 LOGONSERVER [ ] \\MicrosoftAccount PROMPT [ ] $P$G COMSPEC [X] C:\WINDOWS\system32\cmd.exe PROGRAMDATA [X] C:\ProgramData GPSFISH_HOME [X] C:\Program Files\gpsfish SESSIONNAME [ ] Console PATHEXT [ ] .COM [ ] .EXE [ ] .BAT [ ] .CMD [ ] .VBS [ ] .VBE [ ] .JS [ ] .JSE [ ] .WSF [ ] .WSH [ ] .MSC ASL.LOG [ ] Destination=file OSL_HOME [X] C:\Program Files (x86)\gpsshogi FP_NO_HOST_CHECK [ ] NO WINDIR [X] C:\WINDOWS APPDATA [X] C:\Users\幸太郎\AppData\Roaming HOMEDRIVE [X] C: SYSTEMDRIVE [X] C: NUMBER_OF_PROCESSORS [ ] 4 PROCESSOR_LEVEL [ ] 6 COMMONPROGRAMW6432 [X] C:\Program Files\Common Files OS [ ] Windows_NT PUBLIC [X] C:\Users\Public USERPROFILE [X] C:\Users\幸太郎

11 years

Error to run compute_cc

by Sammarco, Carmelo

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.

11 years

Problem with s07plot_dtt.py

by Oscar Alberto Castro Artola

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

11 years

Re: [MSNoise] [input data]

by Thomas Lecocq

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

11 years

Problem with 07.plot_dtt.py

by Oscar Alberto Castro Artola

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

11 years

Re: [MSNoise] Problem with the s03compute_cc.py

by Kasper van Wijk

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 >

11 years

Re: [MSNoise] Some little things and one question about data from more than one network.

by Kasper van Wijk

Tom, as you suggested, the problem may be bigger than file names/ networks. Here's the output after changing to the NZ network name of our extra station to match that of the rest of the stations. Both are mseed data types: 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/Test/s03compute_cc.py", line 214, in <module> stream.merge(fill_value=0) File "/usr/lib64/python2.7/site-packages/obspy/core/stream.py", line 1715, in merge self._mergeChecks() File "/usr/lib64/python2.7/site-packages/obspy/core/stream.py", line 1660, in _mergeChecks raise Exception(msg) Exception: Can't merge traces with same ids but differing data types! On 3 October 2014 20:27, Thomas Lecocq <thomas.lecocq(a)oma.be> wrote: > Dear Kasper, > > Le 02/10/2014 23:38, Kasper van Wijk a écrit : > > Dear Tom et al., > > > > I am working with a student to replicate the install of MSNOISE for the > > Auckland Volcanic Field. Below are a few things we have ran into: > > > > 1. http://msnoise.org/doc/workflow.html#module-MSNoise.s001configurator > > misses the explicit call to start the configurator: python > > s001configurator.py > > > > (this is obvious to anyone who has used MSNOISE before, but stumped the > > aforementioned new student) > I've updated the documentation, thanks ! > > > > 2. On CENTOS linux, I have an issue with sqlalchemy. The "fix" is as ugly > > as it is mysterious: > > > > > http://stackoverflow.com/questions/14600530/cant-import-from-sqlalchemy-ext… > Well, this looks strange indeed, but good to know, I'll make a new > "Troobleshooting" section in the doc ! > > > > 3. We have a font problem (which I don't know how to fix), but starting > the > > configurator, we get the attached warning. Just a warning, though. > Never seen this before... probably somehow specific to paranoid-CentOS > ... :) > > > > 4. Is it correct that sqlite can only work on one thread? > > > > [devora@localhost MSNoise-master]$ python s01scan_archive.py --init -t 2 > > 2014-08-22 10:14:13,724 [INFO] *** Starting: Scan Archive *** > > 2014-08-22 10:14:13,727 [INFO] Initializing (should be run only once) > > 2014-08-22 10:14:13,727 [INFO] You can not work on 2 threads because > SQLite > > only supports 1 connection at a time > > 2014-08-22 10:14:13,727 [INFO] Will work on 1 threads > > Well, in "theory", it could work on more than one thread, but there is a > very big risk of problems, because SQLite can only accept one > transaction at a time, so if two process try to insert, update (...) in > the DB at the same time, you'll get a "Cannot insert, database locked" > and the data will be lost... > > > > > 5. And this is where are currently: we imported a station into our NZ > > network with a different network name. This resulted in errors when > pairing > > the AK station with an NZ station. What should we do? After getting an > > error, we tried renaming the AK data to NZ to be consistent, but we are > > unable to cleanly perge the AK info in the database. Alternatively, can > we > > set up two networks in the configurator? > > Are you trying to run a second "project", independent of the AVF ? Or > using a NZ station for the AVF monitoring ? I don't get this. > > Renaming station files is usually not enough, if you don't rename > metadata within the files + update the database... I'd say it's usually > not worth the effort, MSNoise should be able to process data from > different networks... What is the error you get ? > > Best regards and thanks for using MSNoise :) > > Tom > > > > Cheers, > > kasper > > > > > > _______________________________________________ > > MSNoise mailing list > > MSNoise(a)mailman-as.oma.be > > http://mailman-as.oma.be/mailman/listinfo/msnoise > > _______________________________________________ > MSNoise mailing list > MSNoise(a)mailman-as.oma.be > http://mailman-as.oma.be/mailman/listinfo/msnoise >

11 years

Problem with the filters tab

by Sammarco, Carmelo

Dear all, Someone can explain me in which way I can populate in the configurator the filters tab?? When I try to start cross correlation give me this error message: 'NO FILTERS DEFINED, exiting'. what it means? thank you very much and I hope to find a solution as soon as possible. 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.

11 years

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