Hi, Thomas
Sorry to reply so late.
I tried to uninstall numpy and use conda to install again, it seems no problem.
But I tried again to run compute_cc command, some error occurs again.
The bug report shows:
Process Process-1:
Traceback (most recent call last):
File "/public/software/anaconda3/lib/python3.5/multiprocessing/process.py", line 249, in _bootstrap
self.run()
File "/public/software/anaconda3/lib/python3.5/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/s03compute_cc.py", line 653, in main
trame2h[i]*cp, Nfft, dt, low, high, plot=False)
File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/whiten.py", line 39, in whiten
freqVec = scipy.fftpack.fftfreq(Nfft,d=delta)[:Nfft/2]
TypeError: slice indices must be integers or None or have an __index__ method
Maybe it's because I set the wrong filter? But I do not know how to correct it.
Best Wishes,
Shuye Huang
> -----原始邮件-----
> 发件人: "Thomas Lecocq" <thomas.lecocq(a)oma.be>
> 发送时间: 2017-03-20 16:08:31 (星期一)
> 收件人: msnoise(a)mailman-as.oma.be
> 抄送:
> 主题: [SPAM] Re: [MSNoise] Error when computing_cc
>
> Hi Shuye,
>
> Never seen this error, it is indeed something wrong with numpy. It looks
> like numpy and its dependencies haven't been installed the same way (or
> installed at all). you could remove numpy (pip uninstall numpy) and,
> assuming you are using anaconda, use "conda install numpy"
>
> Thomas
>
>
> Le 20/03/2017 à 08:17, hsy119(a)mail.ustc.edu.cn a écrit :
> > Hi, Thomas and users
> >
> > I just got an error when I tried to run compute_cc command. It shows:
> >
> > [hsy119@yhjs3 msnoise_my]$ msnoise compute_cc
> > 2017-03-20 15:18:30 [INFO] *** Starting: Compute CC ***
> > 2017-03-20 15:18:30 [INFO] Will compute ZZ RR TT TR RT ZR RZ TZ ZT
> > 2017-03-20 15:18:30 [INFO] New CC Job: 2015-01-10 (3 pairs with 3 stations)
> > 2017-03-20 15:18:31 [DEBUG] G2.XJ16.Z Reading 1 Files
> > 2017-03-20 15:18:31 [DEBUG] Checking sample alignment
> > 2017-03-20 15:18:31 [DEBUG] Checking Gaps
> > Intel MKL FATAL ERROR: Cannot load libmkl_def.so.
> >
> > Is there something wrong with numpy?
> >
> > Best Regards,
> > Shuye Huang
> > _______________________________________________
> > 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
Hi Shuye,
this is a bug in MSNoise running on Python3. It has been reported
(https://github.com/ROBelgium/MSNoise/issues/74) but I haven't corrected
it yet.
Meanwhile, indeed, the --init should work OK (although slower)...
Thomas
Le 17-03-17 à 07:50, caronvossen a écrit :
> Hi Shuye,
> Maybe if you omit "-t 2"? I never use that part, because it gave me a lot of errors at the beginning. However, I am not sure whether it is the same problem as you have right now, because for me it didn't work when I used the --init option either.
> I hope this helps. Otherwise Thomas or someone else will probably have a better idea how to solve your problem :)
> Good luck!
> Best wishes,
> Caron Vossen
> Verzonden vanaf mijn Samsung Galaxy-smartphone.
> -------- Oorspronkelijk bericht --------Van: hsy119(a)mail.ustc.edu.cn Datum: 17-03-17 06:48 (GMT+01:00) Aan: msnoise(a)mailman-as.oma.be Onderwerp: [MSNoise] Scan_archive issue
> Hi, Thomas and users
>
> I meet a bug when I try to do scan_archive.
> First time,I used --init option, and data was added successfully.
> But when I try not to use --init option, there's a bug.
> Here's bug report:
>
> [hsy119@yhjs3 msnoise_my]$ msnoise -t 2 scan_archive
> 2017-03-17 13:22:42 [INFO] *** Starting: Scan Archive ***
> 2017-03-17 13:22:42 [INFO] Will work on 2 threads
> Traceback (most recent call last):
> File "/public/software/anaconda3/bin/msnoise", line 11, in <module>
> sys.exit(run())
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 614, in run
> cli(obj={})
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in __call__
> return self.main(*args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main
> rv = self.invoke(ctx)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
> return _process_result(sub_ctx.command.invoke(sub_ctx))
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke
> return ctx.invoke(self.callback, **ctx.params)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke
> return callback(*args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/decorators.py", line 17, in new_func
> return f(get_current_context(), *args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 262, in scan_archive
> main(init, threads=ctx.obj['MSNOISE_threads'])
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/s01scan_archive.py", line 192, in main
> files = sorted(stdout.replace('\r', '').split('\n'))
> TypeError: a bytes-like object is required, not 'str'
>
>
> So now, every time I want to add some new data, I have to use '--init', not sure whether it would cause new problem
> What shall I do?
>
> Best Regard
> Shuye Huang
> _______________________________________________
> 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
Hi,Caron
Thank you very much for your advice!
Thomas says it's a bug due to Python 3. So, it may be ok to use parallel threading.
Good Luck!
Best Regard
Shuye Huang
> -----原始邮件-----
> 发件人: caronvossen <caronvossen(a)gmail.com>
> 发送时间: 2017-03-17 14:50:21 (星期五)
> 收件人: "Python Package for Monitoring Seismic Velocity Changes using Ambient
> Seismic Noise" <msnoise(a)mailman-as.oma.be>
> 抄送:
> 主题: Re: [MSNoise] Scan_archive issue
>
> Hi Shuye,
> Maybe if you omit "-t 2"? I never use that part, because it gave me a lot of errors at the beginning. However, I am not sure whether it is the same problem as you have right now, because for me it didn't work when I used the --init option either.
> I hope this helps. Otherwise Thomas or someone else will probably have a better idea how to solve your problem :)
> Good luck!
> Best wishes,
> Caron Vossen
> Verzonden vanaf mijn Samsung Galaxy-smartphone.
> -------- Oorspronkelijk bericht --------Van: hsy119(a)mail.ustc.edu.cn Datum: 17-03-17 06:48 (GMT+01:00) Aan: msnoise(a)mailman-as.oma.be Onderwerp: [MSNoise] Scan_archive issue
> Hi, Thomas and users
>
> I meet a bug when I try to do scan_archive.
> First time,I used --init option, and data was added successfully.
> But when I try not to use --init option, there's a bug.
> Here's bug report:
>
> [hsy119@yhjs3 msnoise_my]$ msnoise -t 2 scan_archive
> 2017-03-17 13:22:42 [INFO] *** Starting: Scan Archive ***
> 2017-03-17 13:22:42 [INFO] Will work on 2 threads
> Traceback (most recent call last):
> File "/public/software/anaconda3/bin/msnoise", line 11, in <module>
> sys.exit(run())
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 614, in run
> cli(obj={})
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in __call__
> return self.main(*args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main
> rv = self.invoke(ctx)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
> return _process_result(sub_ctx.command.invoke(sub_ctx))
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke
> return ctx.invoke(self.callback, **ctx.params)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke
> return callback(*args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/click/decorators.py", line 17, in new_func
> return f(get_current_context(), *args, **kwargs)
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 262, in scan_archive
> main(init, threads=ctx.obj['MSNOISE_threads'])
> File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/s01scan_archive.py", line 192, in main
> files = sorted(stdout.replace('\r', '').split('\n'))
> TypeError: a bytes-like object is required, not 'str'
>
>
> So now, every time I want to add some new data, I have to use '--init', not sure whether it would cause new problem
> What shall I do?
>
> Best Regard
> Shuye Huang
> _______________________________________________
> 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
Hi, Thomas and users
I meet a bug when I try to do scan_archive.
First time,I used --init option, and data was added successfully.
But when I try not to use --init option, there's a bug.
Here's bug report:
[hsy119@yhjs3 msnoise_my]$ msnoise -t 2 scan_archive
2017-03-17 13:22:42 [INFO] *** Starting: Scan Archive ***
2017-03-17 13:22:42 [INFO] Will work on 2 threads
Traceback (most recent call last):
File "/public/software/anaconda3/bin/msnoise", line 11, in <module>
sys.exit(run())
File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 614, in run
cli(obj={})
File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 716, in __call__
return self.main(*args, **kwargs)
File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/public/software/anaconda3/lib/python3.5/site-packages/click/core.py", line 534, in invoke
return callback(*args, **kwargs)
File "/public/software/anaconda3/lib/python3.5/site-packages/click/decorators.py", line 17, in new_func
return f(get_current_context(), *args, **kwargs)
File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/scripts/msnoise.py", line 262, in scan_archive
main(init, threads=ctx.obj['MSNOISE_threads'])
File "/public/software/anaconda3/lib/python3.5/site-packages/msnoise/s01scan_archive.py", line 192, in main
files = sorted(stdout.replace('\r', '').split('\n'))
TypeError: a bytes-like object is required, not 'str'
So now, every time I want to add some new data, I have to use '--init', not sure whether it would cause new problem
What shall I do?
Best Regard
Shuye Huang
Hi, Thomas
Thank you for advice.
I'll try MySQL workbench, or maybe just use mysql command line to clear my old database.
Best wishes,
Shuye
> -----原始邮件-----
> 发件人: "Thomas Lecocq" <thomas.lecocq(a)oma.be>
> 发送时间: 2017-03-14 21:19:17 (星期二)
> 收件人: msnoise(a)mailman-as.oma.be
> 抄送:
> 主题: Re: [MSNoise] How to delete old records?
>
> Hi,
>
> Usually, you would create 1 database per "project" and either "delete"
> it or "empty" it at least, so when you run "msnoise install" it'd
> restart from scratch (creating empty tables etc).
>
> If you don't have many data_availability or jobs, you can delete them
> from the admin interface. If you have lots, then you can delete them by
> using MySQL workbench (if you use MySQL) or SQLManager (sqlite) to empty
> the tables manually.
>
> Best regards,
>
> Thomas
>
>
> Le 14/03/2017 à 14:13, hsy119(a)mail.ustc.edu.cn a écrit :
> > Dear everyone,
> >
> > I used to use MSnoise to do some calculation, and the work is done. Now I want to do something new, but meet a problem
> >
> > After using 'msnoise populate' and 'msnoise sacan_archive --init' to import new data, I found the 'data availability' and 'job' record in database(in admin web-interface) still have old records, but I don't need them! And I worry about if old ones wound disturb my new jobs.
> >
> > How can I delete old record in 'data availability' and 'job'? I don't want to do it manually cause it's a realy a lot.
> >
> > Thanks for help！
> >
> > Shuye Huang
> > _______________________________________________
> > 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
Dear everyone,
I used to use MSnoise to do some calculation, and the work is done. Now I want to do something new, but meet a problem
After using 'msnoise populate' and 'msnoise sacan_archive --init' to import new data, I found the 'data availability' and 'job' record in database(in admin web-interface) still have old records, but I don't need them! And I worry about if old ones wound disturb my new jobs.
How can I delete old record in 'data availability' and 'job'? I don't want to do it manually cause it's a realy a lot.
Thanks for help！
Shuye Huang
Hi,Thomas and everyone.
$msnoise test
result in
Ran 29 tests in 33.962s
OK
But $msnoise config also has some problem ,
result in
2017-03-02 23:31:25 [INFO] Could not import traits UI backend 'qt4'
2017-03-02 23:31:25 [ERROR] Cannot import PySide or PyQt4
...
2017-03-02 23:31:25 [INFO] Could not import traits UI backend 'wx'
2017-03-02 23:31:25 [ERROR] No module named wx
...
raise NotImplementedError("No checkbox renderer for backend")
NotImplementedError: No checkbox renderer for backend
As blaž said ,i install the packages using conda.
for pyside
$conda install pyside
it works!
the installer problem has been solved!
many thanks!
Hi,Thomas and everyone.
I'm installing the Msnoise 1.4 version in Ubuntu 16.04 LTS 64bit system with the Quick Start-Linux.
Start process without errors, and now I have this problem after I launch the msnoise 1.4. some package is missing, and wx,Pyside,PyQt4 can not be installed. The error report is described below.
how can I solve this problem? many thanks!
Ubuntu 16.04 LTS 64bit
$ msnoise bugreport -s -m
result in
************* Computer Report *************
----------------+SYSTEM+-------------------
Linux
sj-ThinkPad-L440
4.8.0-36-generic
#36~16.04.1-Ubuntu SMP Sun Feb 5 09:39:57 UTC 2017
x86_64
x86_64
debian - stretch/sid -
----------------+PYTHON+-------------------
Python:2.7.13 |Anaconda 4.3.0 (64-bit)| (default, Dec 20 2016, 23:09:15)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
---------------+MODULES+-------------------
Required:
[X] setuptools: 27.2.0
[X] click: 6.7
[X] numpy: 1.12.0
[X] scipy: 0.18.1
[X] pandas: 0.19.2
[X] matplotlib: 2.0.0
[X] statsmodels: 0.6.1
[X] sqlalchemy: 1.1.5
[X] traitsui: 5.1.0
[X] traits: 4.6.0
[X] scikits.samplerate: present (no version)
[X] obspy: 1.0.2
[X] flask: 0.12
[X] flask.ext.admin: 0.12
[X] flask_admin: 1.4.2
[X] wtforms: 2.1
[X] bokeh: 0.12.4
Only necessary if you plan to build the doc locally:
[X] sphinx: 1.5.1
[X] jinja2: 2.9.5
Graphical Backends: (at least one is required)
[ ] wx: not found (install via None)
[ ] PyQt4: not found (install via None)
[ ] PySide: not found (install via None)
Not required, just checking:
[X] json: 2.0.9
[X] psutil: 5.0.1
[ ] reportlab: not found (install via None)
[X] configobj: 5.0.6
[X] pkg_resources: present (no version)
[ ] paramiko: not found (install via None)
[X] ctypes: 1.1.0
[X] pyparsing: 2.1.4
[X] distutils: 2.7.13
[X] IPython: 5.1.0
[ ] vtk: not found (install via None)
[ ] enable: not found (install via None)
Lack wx ,Pyside,PyQt4
$pip install wx
result in
…
Error running configure
ERROR: failed building wxWidgets
Traceback (most recent call last):
File "build.py", line 1184, in cmd_build_wx
wxbuild.main(wxDir(), build_options)
File "/tmp/pip-build-Gktqot/wx/buildtools/build_wxwidgets.py", line 368, in main
"Error running configure")
File "/tmp/pip-build-Gktqot/wx/buildtools/build_wxwidgets.py", line 85, in exitIfError
raise builder.BuildError(msg)
BuildError
Finished command: build_wx (2.579s)
Finished command: build (2.579s)
Command '"/home/sj/anaconda2/bin/python" -u build.py build' failed with exit code 1.
----------------------------------------
Command "/home/sj/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-Gktqot/wx/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-RY6baU-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-Gktqot/wx/
$pip install PyQt4
result in
Collecting PyQt4
Could not find a version that satisfies the requirement PyQt4 (from versions: )
No matching distribution found for PyQt4
$pip install Pyside
result in
…
Failed building wheel for Pyside
…
Qt QTGUI library not found.
Qt QTXML library not found.
Qt QTCORE library not found.
CMake Error at ApiExtractor/CMakeLists.txt:82 (qt4_add_resources):
Unknown CMake command "qt4_add_resources".
-- Configuring incomplete, errors occurred!
See also "/tmp/pip-build-ZnLx48/Pyside/pyside_build/py2.7-qt5.6.2-64bit-release/shiboken/CMakeFiles/CMakeOutput.log".
error: Error configuring shiboken
----------------------------------------
Command "/home/sj/anaconda2/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-ZnLx48/Pyside/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-WtFOuA-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-ZnLx48/Pyside/
$msnoise config
result in
2017-03-01 22:04:21 [INFO] Could not import traits UI backend 'qt4'
2017-03-01 22:04:21 [ERROR] Cannot import PySide or PyQt4
Traceback (most recent call last):
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/toolkit.py", line 161, in toolkit
_toolkit = _import_toolkit(toolkit_name)
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/toolkit.py", line 83, in _import_toolkit
return __import__( name, globals=globals(), level=1 ).toolkit
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/qt4/__init__.py", line 18, in <module>
import pyface.qt
File "/home/sj/anaconda2/lib/python2.7/site-packages/pyface/qt/__init__.py", line 37, in <module>
raise ImportError('Cannot import PySide or PyQt4')
ImportError: Cannot import PySide or PyQt4
2017-03-01 22:04:21 [INFO] Could not import traits UI backend 'wx'
2017-03-01 22:04:21 [ERROR] No module named wx
Traceback (most recent call last):
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/toolkit.py", line 161, in toolkit
_toolkit = _import_toolkit(toolkit_name)
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/toolkit.py", line 83, in _import_toolkit
return __import__( name, globals=globals(), level=1 ).toolkit
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/wx/__init__.py", line 26, in <module>
import toolkit
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/wx/toolkit.py", line 30, in <module>
import wx
ImportError: No module named wx
Traceback (most recent call last):
File "/home/sj/anaconda2/bin/msnoise", line 11, in <module>
sys.exit(run())
File "/home/sj/anaconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py", line 614, in run
cli(obj={})
File "/home/sj/.local/lib/python2.7/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/sj/.local/lib/python2.7/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/sj/.local/lib/python2.7/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/sj/.local/lib/python2.7/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/sj/.local/lib/python2.7/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/sj/anaconda2/lib/python2.7/site-packages/msnoise/scripts/msnoise.py", line 230, in config
from ..s001configurator import main
File "/home/sj/anaconda2/lib/python2.7/site-packages/msnoise/s001configurator.py", line 38, in <module>
from traitsui.extras.checkbox_column import CheckboxColumn
File "/home/sj/anaconda2/lib/python2.7/site-packages/traitsui/extras/checkbox_column.py", line 36, in <module>
raise NotImplementedError("No checkbox renderer for backend")
NotImplementedError: No checkbox renderer for backend
After all,wx ,PyQt4 or Pyside can not be installed
Hi,Thomas and everyone.
I'm installing the Msnoise 1.4 version in Ubuntu 16.04 LTS system with the Quick Start-Linux.
Start process without errors, and now I have this problem after I launch the msnoise 1.4. some package is missing, and wx,Pyside,PyQt4 can not be installed. The error report is in the attachment.
how can I solve this problem? many thanks!
