matplotlib-users Mailing List for matplotlib (Page 15)

Arthur M. Greene wrote:
> Thanks much for the quick response. I updated both matplotlib and
> basemap (now at 0.99.5) via svn and noticed the new netcdftime.py. 
> First, from within site-packages/mpl_toolkits/basemap,
>
> $ grep date2index *.py
> __init__.py::func:`date2index`: compute a time variable index
> corresponding to a date.
> __init__.py:def date2index(dates, nctime, 
> calendar='proleptic_gregorian'):
> __init__.py:    return netcdftime.date2index(dates, nctime, 
> calendar=None)
> netcdftime.py:def date2index(dates, nctime, calendar=None, 
> select='exact'):
> netcdftime.py:    date2index(dates, nctime, calendar=None, 
> select='exact')
>
> so there seems to be some disagreement between __init__.py and
> netcdftime.py concerning the presence of the "select" argument. When I
> call date2index with the "select" keyword arg I get
>
> In [24]: ix0 = 
> date2index(date0,timedata,timedata.calendar,select='nearest')
> --------------------------------------------------------------------------- 
>
> TypeError                                 Traceback (most recent call 
> last)
>
> /home/amg/work/nhmm/<ipython console> in <module>()
>
> TypeError: date2index() got an unexpected keyword argument 'select'

Arthur:  I forgot to update the wrapper function in __init__.py - that's 
fixed now if you do an svn update.  Concerning your other problems 
below, using your test case exposed a couple of other bugs, but it still 
doesn't work.  The basic problem is that the date2index function was 
designed to work with netCDF4 variable objects 
(http://code.google.com/p/netcdf4-python), and the netcdf file/variable 
objects that are produced by pupynere/pydap (the pure python netcdf /dap 
reader included in basemap) don't quite behave the same way.  Using 
netCDF4, I can get your gfdl_test.nc case to work with

 > cat testdate2index.py

#from mpl_toolkits.basemap import date2index,num2date,NetCDFFile as ncf
from netCDF4 import Dataset as ncf
from netCDF4 import date2index, num2date
from mpl_toolkits import basemap
fname0 = 'http://esgcet.llnl.gov/dap/'
fname1 =\
'ipcc4/20c3m/gfdl_cm2_1/pcmdi.ipcc4.gfdl_cm2_1.20c3m.run1.atm.mo.xml'
fname = fname0+fname1
#fname = 'gfdl_test.nc'
print fname
datobj = ncf(fname)
print datobj.variables['tas'].shape
timedata = datobj.variables['time']
from datetime import datetime as dt
date0 = dt(1951,1,16,12,0,0)
print num2date(timedata[:],timedata.units,calendar=timedata.calendar)
print date0
nt0 = date2index(date0,timedata,select='nearest')
print nt0
print \
timedata[nt0],num2date(timedata[nt0],timedata.units,calendar=timedata.calendar)

 > python testdate2index.py

gfdl_test.nc
(13, 31, 29)
[1950-08-16 12:00:00 1950-09-16 00:00:00 1950-10-16 12:00:00
 1950-11-16 00:00:00 1950-12-16 12:00:00 1951-01-16 12:00:00
 1951-02-15 00:00:00 1951-03-16 12:00:00 1951-04-16 00:00:00
 1951-05-16 12:00:00 1951-06-16 00:00:00 1951-07-16 12:00:00
 1951-08-16 12:00:00]
1951-01-16 12:00:00
5
[ 32865.5] [1951-01-16 12:00:00]


Your original example doesn't work because the URL is not an opendap 
server, it's some kind of CDAT xml file that presumably only CDAT 
understands.

We will see if we can fix the date2index function included in basemap 
(if not I will remove it), but for now I recommend using 
netcdf4-python.  It's really a much more robust and feature-rich 
solution for netcdf reading and writing. 

-Jeff                                                                             




>
> -----------------------
>
> This detail aside, I am still having difficulty with date2index, but
> annoyingly, I seem to get different error messages with different 
> datasets. I'll illustrate two here, starting with the one I initially 
> posted about. (See note below regarding this data.)
>
> In [3]: from mpl_toolkits.basemap import 
> date2index,num2date,NetCDFFile as ncf
> In [10]: from mpl_toolkits import basemap
> In [11]: print basemap.__version__
> 0.99.5
> In [24]: fname0 = 'http://esgcet.llnl.gov/dap/'
> In [25]: fname1 = 
> 'ipcc4/20c3m/gfdl_cm2_1/pcmdi.ipcc4.gfdl_cm2_1.20c3m.run1.atm.mo.xml'
> In [26]: fname = fname0+fname1
> In [28]: datobj = ncf(fname)
> In [33]: datobj.variables['tas'].shape
> Out[33]: (1680, 90, 144)
> In [34]: timedata = datobj.variables['time']
> In [35]: from datetime import datetime as dt
> In [36]: date0 = dt(1951,1,16,12,0,0)
> In [37]: print date0
> 1951-01-16 12:00:00
> In [38]: nt0 = date2index(date0,timedata)
> --------------------------------------------------------------------------- 
>
> ClientError                               Traceback (most recent call 
> last)
>
> /home/amg/work/nhmm/<ipython console> in <module>()
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
> in date2index(dates, nctime, calendar)
>    3931     Returns an index or a sequence of indices.
>    3932     """
> -> 3933     return netcdftime.date2index(dates, nctime, calendar=None)
>    3934
>    3935 def maskoceans(lonsin,latsin,datain,inlands=False):
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
> in date2index(dates, nctime, calendar, select)
>    1006     # If the times do not correspond, then it means that the 
> times
>    1007     # are not increasing uniformly and we try the bisection 
> method.
> -> 1008     if not _check_index(index, dates, nctime, calendar):
>    1009
>    1010         # Use the bisection method. Assumes the dates are 
> ordered.
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
> in _check_index(indices, dates, nctime, calendar)
>     959         return False
>     960
> --> 961     t = nctime[indices]
>     962     return numpy.all( num2date(t, nctime.units, calendar) == 
> dates)
>     963
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdf.pyc 
> in __getitem__(self, index)
>      65
>      66     def __getitem__(self, index):
> ---> 67         datout = squeeze(self._var.__getitem__(index))
>      68         # automatically
>      69         # - remove singleton dimensions
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/dtypes.pyc 
> in __getitem__(self, key)
>     409     def __getitem__(self, key):
>     410         # Return data from the array.
> --> 411         return self.data[key]
>     412
>     413     def __setitem__(self, key, item):
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/proxy.pyc 
> in __getitem__(self, index)
>     112
>     113         # Fetch data.
> --> 114         resp, data = openurl(url, self.cache, self.username, 
> self.password)
>     115
>     116         # First lines are ASCII information that end with 
> 'Data:\n'.
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/util/http.pyc 
> in openurl(url, cache, username, password)
>      19         m = re.search('code = (?P<code>\d+);\s*message = 
> "(?P<msg>.*)"', data, re.DOTALL | re.MULTILINE)
>      20         msg =  'Server error %(code)s: "%(msg)s"' % m.groupdict()
> ---> 21         raise ClientError(msg)
>      22
>      23     return resp, data
>
> ClientError: 'Server error 0: "invalid literal for int(): [1113"'
>
> -----------------------------
>
> Note that this is a different error than previously reported. Also, 
> the correct time index is still 1080:
>
> In [40]: taxvals = datobj.variables['time'][:]
>
> In [41]: num2date(taxvals[1080],timedata.units,timedata.calendar)
> Out[41]: 1951-01-16 12:00:00
>
> -----------------------------
>
> This dataset, generated by one of the IPCC models, is 
> password-protected, but could be a good target for decoding, since it 
> is typical of a large class of climate models, that generate a lot of 
> analytical activity. To get a password (they're free) one must 
> register. Info is here: 
> http://www-pcmdi.llnl.gov/ipcc/info_for_analysts.php. Follow "How to 
> access..." then "Register to download output." Once you get a userid 
> and password they can be inserted in the NetCDFFile call, voila. Note 
> that there is a new iteration of IPCC coming down the pike; new model 
> files to become widely available starting in 2010.
>
> ------------------------------
>
> The underlying data is available via ftp. I fetched it and extracted a 
> small slab, which is available at 
> http://iri.columbia.edu/~amg/test/gfdl_test.nc. The CDAT package can 
> digest this file; first time step is plotted here: 
> http://iri.columbia.edu/~amg/test/gfdl_test_time0.png. The dates can 
> also be read by this package, and run from Aug 1950 to Aug 1951, 
> inclusive (13 mos). So the file does not seem to be garbage.
>
> In [16]: datobj = ncf('gfdl_test.nc')
> In [17]: timedata = datobj.variables['time']
> In [18]: date0 = dt(1951,1,16,12,0,0)
> In [19]: nt0 = date2index(date0,timedata)
> --------------------------------------------------------------------------- 
>
> TypeError                                 Traceback (most recent call 
> last)
>
> /home/amg/work/nhmm/<ipython console> in <module>()
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
> in date2index(dates, nctime, calendar)
>    3931     Returns an index or a sequence of indices.
>    3932     """
> -> 3933     return netcdftime.date2index(dates, nctime, calendar=None)
>    3934
>    3935 def maskoceans(lonsin,latsin,datain,inlands=False):
>
> /home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
> in date2index(dates, nctime, calendar, select)
>    1011         import bisect
>    1012
> -> 1013         index = numpy.array([bisect.bisect_left(nctime, n) for 
> n in num], int)
>    1014
>    1015         nomatch = num2date(nctime[index], nctime.units) != dates
>
> TypeError: object of type 'netcdf_variable' has no len()
>
> Investigating the time axis,
>
> In [20]: taxvals = timedata[:]
>
> In [21]: taxvals
> Out[21]: array([ 32712.5,  32743. ,  32773.5,  32804. ,  32834.5, 
> 32865.5, 32895. ,  32924.5,  32955. ,  32985.5,  33016. ,  33046.5, 
> 33077.5])
>
> In [22]: num2date(taxvals,timedata.units,timedata.calendar)
> Out[22]: array([1950-08-16 12:00:00, 1950-09-16 00:00:00, 1950-10-16 
> 12:00:00,
>        1950-11-16 00:00:00, 1950-12-16 12:00:00, 1951-01-16 12:00:00,
>        1951-02-15 00:00:00, 1951-03-16 12:00:00, 1951-04-16 00:00:00,
>        1951-05-16 12:00:00, 1951-06-16 00:00:00, 1951-07-16 12:00:00,
>        1951-08-16 12:00:00], dtype=object)
>
> Which agrees with what CDAT sees.
>
> -------------------------
>
> I think this is enough for now. I also had problems opening data files 
> whose time units were like "months since xxxx-xx-xx," since the 
> "months" unit does not seem to be supported. ("years since..." could 
> also be useful in some cases.) But maybe one or two things at a time 
> is enough!
>
> Thanks for any assistance/advice!
>
> Best,
>
> Arthur
>
>
> Jeff Whitaker wrote:
>> David Huard wrote:
>>> Arthur,
>>>
>>> I wrote the date2index function and I think what you are seeing is a 
>>> bug that I fixed a couple of months ago. By using the latest version 
>>> of netcdf4-python, not only should this bug disappear, but you'll 
>>> also find that date2index now supports different selection methods: 
>>> 'exact', 'before', 'after', 'nearest', that should help with your 
>>> use case.
>>>
>>> If this does not fix the problem you are seeing, I'd appreciate 
>>> having a copy of the file and code to reproduce the problem and find 
>>> a solution.
>>>
>>> HTH,
>>>
>>> David Huard
>>
>> Arthur:  I've just updated basemap svn with David's latest version of 
>> date2index, so another option is to update basemap from svn.  Or, 
>> even simpler, just drop the attached netcdftime.py file in 
>> lib/mpl_toolkits/basemap (replacing the old one) and run python 
>> setup.py install.
>>
>> -Jeff
>>>
>>>
>>>
>>> On Mon, Sep 7, 2009 at 9:27 AM, Arthur M. Greene 
>>> <am...@ir... <mailto:am...@ir...>> wrote:
>>>
>>>     Hi All,
>>>
>>>     The problem is not with fetching the data slice itself, but
>>>     finding the
>>>     correct indices to specify, particularly with the time 
>>> dimension. The
>>>     below examples refer to a remote dataset that I can open and slice
>>>     using
>>>     indices, as in
>>>
>>>     slice = remoteobj.variables['tas'][:120,20:40,30:50].
>>>
>>>     However, I have problems when trying to use the syntax in
>>>     plotsst.py or
>>>     pnganim.py (from the examples) to find time indices:
>>>
>>>     In [107]: from datetime import datetime as dt
>>>     In [108]: date0 = dt(1951,1,1,0)
>>>     In [110]: print date0
>>>     1951-01-01 00:00:00
>>>
>>>     In [125]: timedata = remoteobj.variables['time']
>>>     In [126]: nt0 = date2index(date0,timedata)
>>>     
>>> --------------------------------------------------------------------------- 
>>>
>>>     AssertionError                            Traceback (most recent
>>>     call last)
>>>
>>>     /home/amg/work/nhmm/<ipython console> in <module>()
>>>
>>>     
>>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
>>>
>>>
>>>     in date2index(dates, nctime, calendar)
>>>        3924     Returns an index or a sequence of indices.
>>>        3925     """
>>>     -> 3926     return netcdftime.date2index(dates, nctime, 
>>> calendar=None)
>>>        3927
>>>        3928 def maskoceans(lonsin,latsin,datain,inlands=False):
>>>
>>>     
>>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
>>>
>>>
>>>     in date2index(dates, nctime, calendar)
>>>         986
>>>         987         # Perform check again.
>>>     --> 988         _check_index(index, dates, nctime, calendar)
>>>         989
>>>         990     # convert numpy scalars or single element arrays to 
>>> python
>>>     ints.
>>>
>>>     
>>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
>>>
>>>
>>>     in _check_index(indices, dates, nctime, calendar)
>>>         941     for n,i in enumerate(indices):
>>>         942         t[n] = nctime[i]
>>>     --> 943     assert numpy.all( num2date(t, nctime.units, calendar)
>>>     == dates)
>>>         944
>>>         945
>>>
>>>     AssertionError:
>>>
>>>     ---------------------------------------------------------
>>>
>>>     It turns out that date0 corresponds best to index 1080:
>>>
>>>     In [139]: remoteobj.variables['time'][1080]
>>>     Out[139]: 32865.5
>>>
>>>     In [141]: num2date(32865.5,timedata.units,timedata.calendar)
>>>     Out[141]: 1951-01-16 12:00:00
>>>
>>>     This isn't the _exact_ date and time I had specified, but
>>>
>>>     In [142]: date0 = dt(1951,01,16,12,00,00)
>>>     In [143]: print date0
>>>     1951-01-16 12:00:00
>>>
>>>     In [144]: date2index(date0,timedata,timedata.calendar)
>>>
>>>     produces the same AssertionError. Where is the problem?
>>>
>>>     What I would _like_ to do is to issue a simple call using 
>>> coordinates
>>>     rather than the indices, of the form:
>>>
>>>     slice = variable[date0:date1,[plev],lat0:lat1,lon0:lon1],
>>>
>>>     or similar, preferably without writing a whole module just to 
>>> find the
>>>     correct indices. I need to fetch similar slices from a group of
>>>     models,
>>>     having time axes that may each be defined slightly differently --
>>>     different calendars, time point set at a different day of the 
>>> month,
>>>     etc. (It's monthly data and I'm specifying only monthly bounds, 
>>> even
>>>     though the calendar may be defined as "days since 1860...") I 
>>> need to
>>>     automate the process so I get back the correct slab regardless.
>>>
>>>     Suggestions appreciated!
>>>
>>>     Thx,
>>>
>>>     Arthur
>>>
>>>
>>>     *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
>>>     Arthur M. Greene, Ph.D.
>>>     The International Research Institute for Climate and Society (IRI)
>>>     The Earth Institute, Columbia University, Lamont Campus
>>>
>>>     amg at iri dot columbia dot edu | http://iri.columbia.edu
>>>     *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
>>>
>>>
>>>     
>>> ------------------------------------------------------------------------------ 
>>>
>>>     Let Crystal Reports handle the reporting - Free Crystal Reports
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>>>     _______________________________________________
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>


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

Thanks much for the quick response. I updated both matplotlib and
basemap (now at 0.99.5) via svn and noticed the new netcdftime.py. 
First, from within site-packages/mpl_toolkits/basemap,

$ grep date2index *.py
__init__.py::func:`date2index`: compute a time variable index
corresponding to a date.
__init__.py:def date2index(dates, nctime, calendar='proleptic_gregorian'):
__init__.py:    return netcdftime.date2index(dates, nctime, calendar=None)
netcdftime.py:def date2index(dates, nctime, calendar=None, select='exact'):
netcdftime.py:    date2index(dates, nctime, calendar=None, select='exact')

so there seems to be some disagreement between __init__.py and
netcdftime.py concerning the presence of the "select" argument. When I
call date2index with the "select" keyword arg I get

In [24]: ix0 = date2index(date0,timedata,timedata.calendar,select='nearest')
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)

/home/amg/work/nhmm/<ipython console> in <module>()

TypeError: date2index() got an unexpected keyword argument 'select'

-----------------------

This detail aside, I am still having difficulty with date2index, but
annoyingly, I seem to get different error messages with different 
datasets. I'll illustrate two here, starting with the one I initially 
posted about. (See note below regarding this data.)

In [3]: from mpl_toolkits.basemap import date2index,num2date,NetCDFFile 
as ncf
In [10]: from mpl_toolkits import basemap
In [11]: print basemap.__version__
0.99.5
In [24]: fname0 = 'http://esgcet.llnl.gov/dap/'
In [25]: fname1 = 
'ipcc4/20c3m/gfdl_cm2_1/pcmdi.ipcc4.gfdl_cm2_1.20c3m.run1.atm.mo.xml'
In [26]: fname = fname0+fname1
In [28]: datobj = ncf(fname)
In [33]: datobj.variables['tas'].shape
Out[33]: (1680, 90, 144)
In [34]: timedata = datobj.variables['time']
In [35]: from datetime import datetime as dt
In [36]: date0 = dt(1951,1,16,12,0,0)
In [37]: print date0
1951-01-16 12:00:00
In [38]: nt0 = date2index(date0,timedata)
---------------------------------------------------------------------------
ClientError                               Traceback (most recent call last)

/home/amg/work/nhmm/<ipython console> in <module>()

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
in date2index(dates, nctime, calendar)
    3931     Returns an index or a sequence of indices.
    3932     """
-> 3933     return netcdftime.date2index(dates, nctime, calendar=None)
    3934
    3935 def maskoceans(lonsin,latsin,datain,inlands=False):

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
in date2index(dates, nctime, calendar, select)
    1006     # If the times do not correspond, then it means that the times
    1007     # are not increasing uniformly and we try the bisection method.
-> 1008     if not _check_index(index, dates, nctime, calendar):
    1009
    1010         # Use the bisection method. Assumes the dates are ordered.

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
in _check_index(indices, dates, nctime, calendar)
     959         return False
     960
--> 961     t = nctime[indices]
     962     return numpy.all( num2date(t, nctime.units, calendar) == dates)
     963

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdf.pyc 
in __getitem__(self, index)
      65
      66     def __getitem__(self, index):
---> 67         datout = squeeze(self._var.__getitem__(index))
      68         # automatically
      69         # - remove singleton dimensions

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/dtypes.pyc 
in __getitem__(self, key)
     409     def __getitem__(self, key):
     410         # Return data from the array.
--> 411         return self.data[key]
     412
     413     def __setitem__(self, key, item):

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/proxy.pyc 
in __getitem__(self, index)
     112
     113         # Fetch data.
--> 114         resp, data = openurl(url, self.cache, self.username, 
self.password)
     115
     116         # First lines are ASCII information that end with 
'Data:\n'.

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/dap/util/http.pyc 
in openurl(url, cache, username, password)
      19         m = re.search('code = (?P<code>\d+);\s*message = 
"(?P<msg>.*)"', data, re.DOTALL | re.MULTILINE)
      20         msg =  'Server error %(code)s: "%(msg)s"' % m.groupdict()
---> 21         raise ClientError(msg)
      22
      23     return resp, data

ClientError: 'Server error 0: "invalid literal for int(): [1113"'

-----------------------------

Note that this is a different error than previously reported. Also, the 
correct time index is still 1080:

In [40]: taxvals = datobj.variables['time'][:]

In [41]: num2date(taxvals[1080],timedata.units,timedata.calendar)
Out[41]: 1951-01-16 12:00:00

-----------------------------

This dataset, generated by one of the IPCC models, is 
password-protected, but could be a good target for decoding, since it is 
typical of a large class of climate models, that generate a lot of 
analytical activity. To get a password (they're free) one must register. 
Info is here: http://www-pcmdi.llnl.gov/ipcc/info_for_analysts.php. 
Follow "How to access..." then "Register to download output." Once you 
get a userid and password they can be inserted in the NetCDFFile call, 
voila. Note that there is a new iteration of IPCC coming down the pike; 
new model files to become widely available starting in 2010.

------------------------------

The underlying data is available via ftp. I fetched it and extracted a 
small slab, which is available at 
http://iri.columbia.edu/~amg/test/gfdl_test.nc. The CDAT package can 
digest this file; first time step is plotted here: 
http://iri.columbia.edu/~amg/test/gfdl_test_time0.png. The dates can 
also be read by this package, and run from Aug 1950 to Aug 1951, 
inclusive (13 mos). So the file does not seem to be garbage.

In [16]: datobj = ncf('gfdl_test.nc')
In [17]: timedata = datobj.variables['time']
In [18]: date0 = dt(1951,1,16,12,0,0)
In [19]: nt0 = date2index(date0,timedata)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)

/home/amg/work/nhmm/<ipython console> in <module>()

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
in date2index(dates, nctime, calendar)
    3931     Returns an index or a sequence of indices.
    3932     """
-> 3933     return netcdftime.date2index(dates, nctime, calendar=None)
    3934
    3935 def maskoceans(lonsin,latsin,datain,inlands=False):

/home/amg/usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
in date2index(dates, nctime, calendar, select)
    1011         import bisect
    1012
-> 1013         index = numpy.array([bisect.bisect_left(nctime, n) for n 
in num], int)
    1014
    1015         nomatch = num2date(nctime[index], nctime.units) != dates

TypeError: object of type 'netcdf_variable' has no len()

Investigating the time axis,

In [20]: taxvals = timedata[:]

In [21]: taxvals
Out[21]: array([ 32712.5,  32743. ,  32773.5,  32804. ,  32834.5, 
32865.5, 32895. ,  32924.5,  32955. ,  32985.5,  33016. ,  33046.5, 
33077.5])

In [22]: num2date(taxvals,timedata.units,timedata.calendar)
Out[22]: array([1950-08-16 12:00:00, 1950-09-16 00:00:00, 1950-10-16 
12:00:00,
        1950-11-16 00:00:00, 1950-12-16 12:00:00, 1951-01-16 12:00:00,
        1951-02-15 00:00:00, 1951-03-16 12:00:00, 1951-04-16 00:00:00,
        1951-05-16 12:00:00, 1951-06-16 00:00:00, 1951-07-16 12:00:00,
        1951-08-16 12:00:00], dtype=object)

Which agrees with what CDAT sees.

-------------------------

I think this is enough for now. I also had problems opening data files 
whose time units were like "months since xxxx-xx-xx," since the "months" 
unit does not seem to be supported. ("years since..." could also be 
useful in some cases.) But maybe one or two things at a time is enough!

Thanks for any assistance/advice!

Best,

Arthur


Jeff Whitaker wrote:
> David Huard wrote:
>> Arthur,
>>
>> I wrote the date2index function and I think what you are seeing is a 
>> bug that I fixed a couple of months ago. By using the latest version 
>> of netcdf4-python, not only should this bug disappear, but you'll also 
>> find that date2index now supports different selection methods: 
>> 'exact', 'before', 'after', 'nearest', that should help with your use 
>> case.
>>
>> If this does not fix the problem you are seeing, I'd appreciate having 
>> a copy of the file and code to reproduce the problem and find a solution.
>>
>> HTH,
>>
>> David Huard
> 
> Arthur:  I've just updated basemap svn with David's latest version of 
> date2index, so another option is to update basemap from svn.  Or, even 
> simpler, just drop the attached netcdftime.py file in 
> lib/mpl_toolkits/basemap (replacing the old one) and run python setup.py 
> install.
> 
> -Jeff
>>
>>
>>
>> On Mon, Sep 7, 2009 at 9:27 AM, Arthur M. Greene <am...@ir... 
>> <mailto:am...@ir...>> wrote:
>>
>>     Hi All,
>>
>>     The problem is not with fetching the data slice itself, but
>>     finding the
>>     correct indices to specify, particularly with the time dimension. The
>>     below examples refer to a remote dataset that I can open and slice
>>     using
>>     indices, as in
>>
>>     slice = remoteobj.variables['tas'][:120,20:40,30:50].
>>
>>     However, I have problems when trying to use the syntax in
>>     plotsst.py or
>>     pnganim.py (from the examples) to find time indices:
>>
>>     In [107]: from datetime import datetime as dt
>>     In [108]: date0 = dt(1951,1,1,0)
>>     In [110]: print date0
>>     1951-01-01 00:00:00
>>
>>     In [125]: timedata = remoteobj.variables['time']
>>     In [126]: nt0 = date2index(date0,timedata)
>>     
>> --------------------------------------------------------------------------- 
>>
>>     AssertionError                            Traceback (most recent
>>     call last)
>>
>>     /home/amg/work/nhmm/<ipython console> in <module>()
>>
>>     
>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc 
>>
>>
>>     in date2index(dates, nctime, calendar)
>>        3924     Returns an index or a sequence of indices.
>>        3925     """
>>     -> 3926     return netcdftime.date2index(dates, nctime, 
>> calendar=None)
>>        3927
>>        3928 def maskoceans(lonsin,latsin,datain,inlands=False):
>>
>>     
>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
>>
>>
>>     in date2index(dates, nctime, calendar)
>>         986
>>         987         # Perform check again.
>>     --> 988         _check_index(index, dates, nctime, calendar)
>>         989
>>         990     # convert numpy scalars or single element arrays to 
>> python
>>     ints.
>>
>>     
>> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc 
>>
>>
>>     in _check_index(indices, dates, nctime, calendar)
>>         941     for n,i in enumerate(indices):
>>         942         t[n] = nctime[i]
>>     --> 943     assert numpy.all( num2date(t, nctime.units, calendar)
>>     == dates)
>>         944
>>         945
>>
>>     AssertionError:
>>
>>     ---------------------------------------------------------
>>
>>     It turns out that date0 corresponds best to index 1080:
>>
>>     In [139]: remoteobj.variables['time'][1080]
>>     Out[139]: 32865.5
>>
>>     In [141]: num2date(32865.5,timedata.units,timedata.calendar)
>>     Out[141]: 1951-01-16 12:00:00
>>
>>     This isn't the _exact_ date and time I had specified, but
>>
>>     In [142]: date0 = dt(1951,01,16,12,00,00)
>>     In [143]: print date0
>>     1951-01-16 12:00:00
>>
>>     In [144]: date2index(date0,timedata,timedata.calendar)
>>
>>     produces the same AssertionError. Where is the problem?
>>
>>     What I would _like_ to do is to issue a simple call using coordinates
>>     rather than the indices, of the form:
>>
>>     slice = variable[date0:date1,[plev],lat0:lat1,lon0:lon1],
>>
>>     or similar, preferably without writing a whole module just to find 
>> the
>>     correct indices. I need to fetch similar slices from a group of
>>     models,
>>     having time axes that may each be defined slightly differently --
>>     different calendars, time point set at a different day of the month,
>>     etc. (It's monthly data and I'm specifying only monthly bounds, even
>>     though the calendar may be defined as "days since 1860...") I need to
>>     automate the process so I get back the correct slab regardless.
>>
>>     Suggestions appreciated!
>>
>>     Thx,
>>
>>     Arthur
>>
>>
>>     *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
>>     Arthur M. Greene, Ph.D.
>>     The International Research Institute for Climate and Society (IRI)
>>     The Earth Institute, Columbia University, Lamont Campus
>>
>>     amg at iri dot columbia dot edu | http://iri.columbia.edu
>>     *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
>>
>>
>>     
>> ------------------------------------------------------------------------------ 
>>
>>     Let Crystal Reports handle the reporting - Free Crystal Reports
>>     2008 30-Day
>>     trial. Simplify your report design, integration and deployment -
>>     and focus on
>>     what you do best, core application coding. Discover what's new with
>>     Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>     _______________________________________________
>>     Matplotlib-users mailing list
>>     Mat...@li...
>>     <mailto:Mat...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------ 
>>
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 
>> 30-Day trial. Simplify your report design, integration and deployment 
>> - and focus on what you do best, core application coding. Discover 
>> what's new with Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> ------------------------------------------------------------------------
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>>   

-- 
*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
Arthur M. Greene, Ph.D.
The International Research Institute for Climate and Society (IRI)
The Earth Institute, Columbia University, Lamont Campus
Monell Building, 61 Route 9W, Palisades, NY  10964-8000 USA
Tel: 845-680-4436      | Fax: 845-680-4865
am...@ir...   | http://iri.columbia.edu
*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*

On Wed, Sep 9, 2009 at 4:30 AM, Yann<ya...@al...> wrote:
> I can not try your revision but I will do it as soon as it is released.
> Nervertheless I try your snippet with an AxesZero. I get the gridlines
> and the axis but the first was over the second. It is not what I expected.

You can rearrange the order of artists by setting the zorder.

> As far as I am concerned, I can wait until matplotlib next release.

Just to clarify, the patch will be included in the 1.0 release, not
the maintenance release of 0.99 version.

Regards,

-JJ


>
> Thanks,
>
> Yann
>
> On 09/08/2009 08:13 PM, Jae-Joon Lee wrote:
>> On Tue, Sep 8, 2009 at 11:51 AM, Yann
>> Goudard<mat...@al...>  wrote:
>>
>>> Hi,
>>>
>>> I have the same behaviour with LocatableAxes. HostAxes, ParasiteAxes and
>>> LocatableAxes depend on 'mpl_toolkits.axes_grid.axislines.Axes'. It must
>>> be the matter origin.
>>>
>> Yes, and this was because I forgot to implement some necessary methods.
>> This is now fixed in the svn trunk. So if you can,please give it a try.
>>
>>
>>> This another example should draw a grid but does not:
>>>
>>> import wx
>>> from wx import Frame
>>> from matplotlib.backends.backend_wxagg import FigureFrameWxAgg,
>>> FigureCanvasWxAgg
>>> from matplotlib.figure import Figure
>>> from mpl_toolkits.axes_grid.axes_divider import LocatableAxes
>>>
>>> fig = Figure((1, 1), 50)
>>> axes = LocatableAxes(fig, [0, 0, 1, 1])
>>> # axes.toggle_axisline(False)
>>> axes.grid(True)
>>> fig.add_axes(axes)
>>>
>>> app = wx.PySimpleApp()
>>> my_viewer = FigureFrameWxAgg(-1, fig)
>>> my_viewer.Show()
>>> app.MainLoop()
>>>
>>> If you uncomment axes.toggle_axisline(False), it works cause it uses
>>> normal 'matplolib.axes.Axes' behaviour. It is not a matter for common
>>> use but if you need 'AxesZero', this trick does not work.
>>>
>> What the toggle_axisline does is simply to make the xaxis and yaxis
>> (which are responsible for drawing ticks, ticklabels, etc  in the
>> mainline mpl) visible again, and make axis["bottom"] and etc
>> invisible.
>> One workaround is to make xaxis and yaxis visible but pnly to draw the
>> gridlines. Something like below.
>>
>> ax.toggle_axisline(True)
>> ax.grid(True)
>> ax.gridlines.set_visible(False) # this is just to make the code not to
>> draw gridlines twice in future release of mpl.
>> ax.xaxis.set_visible(True)
>> ax.yaxis.set_visible(True)
>> for t in ax.xaxis.majorTicks + ax.yaxis.majorTicks:
>>      t.gridOn = True
>>      t.tick1On = False
>>      t.tick2On = False
>>      t.label1On = False
>>      t.label2On = False
>>
>> Let me know if this does not work, or there is a case that this cannot be used.
>> Regards,
>>
>> -JJ
>>
>>
>>
>>> Yann
>>>
>>>
>>> On 09/07/2009 10:37 PM, Andreas Fromm wrote:
>>>
>>>> thanks Sebastian,
>>>>
>>>> you are right, your code works here too. But i don't get it work in my
>>>> multi y-axes plot from the matplotlib examples
>>>> (http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html).
>>>> Even with linear plots, i get no gridlines.
>>>>
>>>> Any idea, whats wrong here?
>>>>
>>>> minimal code example:
>>>> #######################
>>>> import matplotlib.pyplot as plt
>>>> from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
>>>>
>>>> fig = plt.figure(1)
>>>> fig.clf()
>>>> #plt.grid(True)
>>>> host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
>>>> fig.add_axes(host)
>>>>
>>>> host.plot([0, 10, 100], [0, 10, 100], label='host')
>>>>
>>>> host.grid(True)  #?
>>>> host.yaxis.grid(True) #?
>>>>
>>>> host.yaxis.set_scale('log') #?
>>>>
>>>> plt.draw()
>>>> plt.show()
>>>> #######################
>>>>
>>>> Greets,
>>>> Andreas
>>>>
>>>>
>>>> Sebastian Busch schrieb:
>>>>
>>>>
>>>>> from matplotlib.pyplot import *
>>>>>
>>>>> plot([1,10,100],[1,10,100])
>>>>> grid()
>>>>>
>>>>> yscale('log')
>>>>> xscale('log')
>>>>>
>>>>> works here.
>>>>>
>>>>> best,
>>>>> sebastian.
>>>>>
>>>>>
>>>>>
>>>> ------------------------------------------------------------------------------
>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>>>> trial. Simplify your report design, integration and deployment - and focus on
>>>> what you do best, core application coding. Discover what's new with
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>>>> _______________________________________________
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>>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>>
>>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>> trial. Simplify your report design, integration and deployment - and focus on
>>> what you do best, core application coding. Discover what's new with
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>>>
>>>
>
>
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> trial. Simplify your report design, integration and deployment - and focus on
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>

Hi,
I think I found a bug, but I am not sure if it's in the doc or in a method name.
In the doc, there is reference to a method *suptitle* in class
mpl.figure.Figure. The name sounds strange, but the method exists and works. The
example given, though, makes reference to *subtitle*, so either the example or
the method name are wrong. Here's the link to the doc:
http://matplotlib.sourceforge.net/api/figure_api.html?highlight=legend#matplotlib.figure.Figure.suptitle

jorge

"Werner F. Bruhin" <wer...@fr...> writes:

>> I am getting errors "TypeError: unsupported operand type(s) for +=: 
>> 'NoneType' and 'str'" in mlab.pyo after py2exe'd my application.

I think this has been fixed on the trunk for good, by changing all
docstring modifications to use decorators (defined in docstring.py) that
check for nonexistent docstrings. The changes are perhaps too big to
apply on the 0.99 branch.

>> I changed it to:
>> if psd.__doc__ is not None:
>>     psd.__doc__ = psd.__doc__ % kwdocd
>> else:
>>     psd.__doc__ = ""
>>
>> Above is a bit of a hack, if someone can suggest how to correct this in 
>> a way which would get accepted as a patch I would search all modules 
>> correct them.

I think either this or something like

    psd.__doc__ = psd.__doc__ and (psd.__doc__ % kwdocd)

should be acceptable as a bugfix.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Michael Droettboom <md...@st...> writes:

> This change has gone into effect (for me at least on a Liux box).  Can 
> anyone test Windows and Mac and report back?

Using Firefox 3.5.2 on Mac OS X 10.5, the green download link points to
matplotlib-0.99.0-py2.6-macosx10.5.dmg, and when I change my user agent
header to Internet Explorer, to matplotlib-0.99.0.win32-py2.6.exe.

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Werner F. Bruhin wrote:
> I have run into a bit of problem using 0.99 and py2exe.
>
> I am getting errors "TypeError: unsupported operand type(s) for +=: 
> 'NoneType' and 'str'" in mlab.pyo after py2exe'd my application.
>
> This is caused by this type of code, as one normally uses the optimize 
> option with py2exe which means that the docs are stripped from the .pyo 
> files.
> "psd.__doc__ = psd.__doc__ % kwdocd"
>
> I changed it to:
> if psd.__doc__ is not None:
>     psd.__doc__ = psd.__doc__ % kwdocd
> else:
>     psd.__doc__ = ""
>
> Above is a bit of a hack, if someone can suggest how to correct this in 
> a way which would get accepted as a patch I would search all modules 
> correct them.
>   
Maybe a nicer solution would be:
if __debug__:
    psd.__doc__ = psd.__doc__ % kwdocd

Also that would mean that above is not run when running Python as 
"python -O script.py or python -OO script.py where the first solution 
means that with -O the it would still be executed.

Werner

This change has gone into effect (for me at least on a Liux box).  Can 
anyone test Windows and Mac and report back?

Cheers,
Mike

Michael Droettboom wrote:
> I just went in and changed the default file downloads back to correct 
> values, but alas, it appears to have no effect.  There is some hints in 
> the (many) related SF bugs that there may be a delay associated with 
> these settings, so I will check back again at the end of the day.
>
> Mike
>
> On 09/04/2009 05:46 AM, Fabrice Silva wrote:
>   
>> Le jeudi 03 septembre 2009 à 20:16 -0500, John Hunter a écrit :
>>    
>>     
>>> On Thu, Sep 3, 2009 at 8:04 PM, Alan G Isaac<ala...@gm...>  wrote:
>>>      
>>>       
>>>> The default download from the Matplotlib page
>>>> link to http://sourceforge.net/projects/matplotlib/
>>>> which once again highlights basemap.  (I think
>>>> this was fixed at one point.)
>>>>        
>>>>         
>>> I'm not seeng this, nor am I seeing basemap settings in the File
>>> Manager which would trigger this.  Of course, the default download is
>>> platform specific, which may be why I am not seeing this, so please
>>> give us as much info as possible about your platform (mainly the OS)
>>>
>>> When I click on the green download button at
>>> http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
>>> redirected to the mpl 0.99 OSX download::
>>>
>>>    https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx10.5.dmg/download
>>>      
>>>       
>> Strangely, the green button points to
>> http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx-10.3-i386.egg/download
>> when I browse on a linux (debian) machine with epiphany (which uses
>> gecko, the firefox engine). Why macosx ?
>>
>>    
>>     
>
>
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>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

I have run into a bit of problem using 0.99 and py2exe.

I am getting errors "TypeError: unsupported operand type(s) for +=: 
'NoneType' and 'str'" in mlab.pyo after py2exe'd my application.

This is caused by this type of code, as one normally uses the optimize 
option with py2exe which means that the docs are stripped from the .pyo 
files.
"psd.__doc__ = psd.__doc__ % kwdocd"

I changed it to:
if psd.__doc__ is not None:
    psd.__doc__ = psd.__doc__ % kwdocd
else:
    psd.__doc__ = ""

Above is a bit of a hack, if someone can suggest how to correct this in 
a way which would get accepted as a patch I would search all modules 
correct them.

Werner

Hi Giuseppe

you can load your datafile with pylab... see my little function which
i'm using

import pylab as pl

def readXY(filename):

   x,y,z = pl.load(filename, unpack=True)
   return x,y,z

(X, Y, Z) = readXY("datafile.dat")

after that you have your values in the arrays X;Y;Z

kind regards



Giuseppe Aprea wrote:
> Hi list,
> 
> I have some files with data stored in columns:
> 
> x1     y1     z1
> x2     y2     z2
> x3     y3     z3
> x4     y4     z4
> x5     y5     z5
> .......
> 
> and I need to make a contour plot of this data using matplotlib. The
> problem is that contour plot functions usually handle a different kind
> of input:
> 
> X=[[x1,x2,x3,x4,x5,x6],
> [x1,x2,x3,x4,x5,x6],
> [x1,x2,x3,x4,x5,x6],...
> 
> Y=[[y1,y1,y1,y1,y1,y1],
> [y2,y2,y2,y2,y2,y2],
> [y3,y3,y3,y3,y3,y3],.....
> 
> Z=[[z1,z2,z3,z4,z5,z6],
> [z7,z8,zz9,z10,z11,z12],....
> 
> I usually load data using 3 lists: x, y and z; I wonder if there is
> any function which is able to take these 3 lists and return the right
> input for matplotlib functions.
> 
> cheers
> 
> giuseppe
> 
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> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hi list,

I have some files with data stored in columns:

x1     y1     z1
x2     y2     z2
x3     y3     z3
x4     y4     z4
x5     y5     z5
.......

and I need to make a contour plot of this data using matplotlib. The
problem is that contour plot functions usually handle a different kind
of input:

X=[[x1,x2,x3,x4,x5,x6],
[x1,x2,x3,x4,x5,x6],
[x1,x2,x3,x4,x5,x6],...

Y=[[y1,y1,y1,y1,y1,y1],
[y2,y2,y2,y2,y2,y2],
[y3,y3,y3,y3,y3,y3],.....

Z=[[z1,z2,z3,z4,z5,z6],
[z7,z8,zz9,z10,z11,z12],....

I usually load data using 3 lists: x, y and z; I wonder if there is
any function which is able to take these 3 lists and return the right
input for matplotlib functions.

cheers

giuseppe

I can not try your revision but I will do it as soon as it is released.
Nervertheless I try your snippet with an AxesZero. I get the gridlines 
and the axis but the first was over the second. It is not what I expected.
As far as I am concerned, I can wait until matplotlib next release.

Thanks,

Yann

On 09/08/2009 08:13 PM, Jae-Joon Lee wrote:
> On Tue, Sep 8, 2009 at 11:51 AM, Yann
> Goudard<mat...@al...>  wrote:
>    
>> Hi,
>>
>> I have the same behaviour with LocatableAxes. HostAxes, ParasiteAxes and
>> LocatableAxes depend on 'mpl_toolkits.axes_grid.axislines.Axes'. It must
>> be the matter origin.
>>      
> Yes, and this was because I forgot to implement some necessary methods.
> This is now fixed in the svn trunk. So if you can,please give it a try.
>
>    
>> This another example should draw a grid but does not:
>>
>> import wx
>> from wx import Frame
>> from matplotlib.backends.backend_wxagg import FigureFrameWxAgg,
>> FigureCanvasWxAgg
>> from matplotlib.figure import Figure
>> from mpl_toolkits.axes_grid.axes_divider import LocatableAxes
>>
>> fig = Figure((1, 1), 50)
>> axes = LocatableAxes(fig, [0, 0, 1, 1])
>> # axes.toggle_axisline(False)
>> axes.grid(True)
>> fig.add_axes(axes)
>>
>> app = wx.PySimpleApp()
>> my_viewer = FigureFrameWxAgg(-1, fig)
>> my_viewer.Show()
>> app.MainLoop()
>>
>> If you uncomment axes.toggle_axisline(False), it works cause it uses
>> normal 'matplolib.axes.Axes' behaviour. It is not a matter for common
>> use but if you need 'AxesZero', this trick does not work.
>>      
> What the toggle_axisline does is simply to make the xaxis and yaxis
> (which are responsible for drawing ticks, ticklabels, etc  in the
> mainline mpl) visible again, and make axis["bottom"] and etc
> invisible.
> One workaround is to make xaxis and yaxis visible but pnly to draw the
> gridlines. Something like below.
>
> ax.toggle_axisline(True)
> ax.grid(True)
> ax.gridlines.set_visible(False) # this is just to make the code not to
> draw gridlines twice in future release of mpl.
> ax.xaxis.set_visible(True)
> ax.yaxis.set_visible(True)
> for t in ax.xaxis.majorTicks + ax.yaxis.majorTicks:
>      t.gridOn = True
>      t.tick1On = False
>      t.tick2On = False
>      t.label1On = False
>      t.label2On = False
>
> Let me know if this does not work, or there is a case that this cannot be used.
> Regards,
>
> -JJ
>
>
>    
>> Yann
>>
>>
>> On 09/07/2009 10:37 PM, Andreas Fromm wrote:
>>      
>>> thanks Sebastian,
>>>
>>> you are right, your code works here too. But i don't get it work in my
>>> multi y-axes plot from the matplotlib examples
>>> (http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html).
>>> Even with linear plots, i get no gridlines.
>>>
>>> Any idea, whats wrong here?
>>>
>>> minimal code example:
>>> #######################
>>> import matplotlib.pyplot as plt
>>> from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
>>>
>>> fig = plt.figure(1)
>>> fig.clf()
>>> #plt.grid(True)
>>> host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
>>> fig.add_axes(host)
>>>
>>> host.plot([0, 10, 100], [0, 10, 100], label='host')
>>>
>>> host.grid(True)  #?
>>> host.yaxis.grid(True) #?
>>>
>>> host.yaxis.set_scale('log') #?
>>>
>>> plt.draw()
>>> plt.show()
>>> #######################
>>>
>>> Greets,
>>> Andreas
>>>
>>>
>>> Sebastian Busch schrieb:
>>>
>>>        
>>>> from matplotlib.pyplot import *
>>>>
>>>> plot([1,10,100],[1,10,100])
>>>> grid()
>>>>
>>>> yscale('log')
>>>> xscale('log')
>>>>
>>>> works here.
>>>>
>>>> best,
>>>> sebastian.
>>>>
>>>>
>>>>          
>>> ------------------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>>> trial. Simplify your report design, integration and deployment - and focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Matplotlib-users mailing list
>>> Mat...@li...
>>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>        
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>      

On 9/8/2009 1:39 PM, Watson, Nathaniel wrote:
> I am running Windows Vista 64-bit and have installed matplotlib from 
> http://sourceforge.net/projects/matplotlib/ via the "Download Now!". 

What is the name of the file you downloaded?

Alan Isaac

On Tue, Sep 8, 2009 at 11:51 AM, Yann
Goudard<mat...@al...> wrote:
> Hi,
>
> I have the same behaviour with LocatableAxes. HostAxes, ParasiteAxes and
> LocatableAxes depend on 'mpl_toolkits.axes_grid.axislines.Axes'. It must
> be the matter origin.

Yes, and this was because I forgot to implement some necessary methods.
This is now fixed in the svn trunk. So if you can,please give it a try.

> This another example should draw a grid but does not:
>
> import wx
> from wx import Frame
> from matplotlib.backends.backend_wxagg import FigureFrameWxAgg,
> FigureCanvasWxAgg
> from matplotlib.figure import Figure
> from mpl_toolkits.axes_grid.axes_divider import LocatableAxes
>
> fig = Figure((1, 1), 50)
> axes = LocatableAxes(fig, [0, 0, 1, 1])
> # axes.toggle_axisline(False)
> axes.grid(True)
> fig.add_axes(axes)
>
> app = wx.PySimpleApp()
> my_viewer = FigureFrameWxAgg(-1, fig)
> my_viewer.Show()
> app.MainLoop()
>
> If you uncomment axes.toggle_axisline(False), it works cause it uses
> normal 'matplolib.axes.Axes' behaviour. It is not a matter for common
> use but if you need 'AxesZero', this trick does not work.

What the toggle_axisline does is simply to make the xaxis and yaxis
(which are responsible for drawing ticks, ticklabels, etc  in the
mainline mpl) visible again, and make axis["bottom"] and etc
invisible.
One workaround is to make xaxis and yaxis visible but pnly to draw the
gridlines. Something like below.

ax.toggle_axisline(True)
ax.grid(True)
ax.gridlines.set_visible(False) # this is just to make the code not to
draw gridlines twice in future release of mpl.
ax.xaxis.set_visible(True)
ax.yaxis.set_visible(True)
for t in ax.xaxis.majorTicks + ax.yaxis.majorTicks:
    t.gridOn = True
    t.tick1On = False
    t.tick2On = False
    t.label1On = False
    t.label2On = False

Let me know if this does not work, or there is a case that this cannot be used.
Regards,

-JJ


>
> Yann
>
>
> On 09/07/2009 10:37 PM, Andreas Fromm wrote:
>> thanks Sebastian,
>>
>> you are right, your code works here too. But i don't get it work in my
>> multi y-axes plot from the matplotlib examples
>> (http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html).
>> Even with linear plots, i get no gridlines.
>>
>> Any idea, whats wrong here?
>>
>> minimal code example:
>> #######################
>> import matplotlib.pyplot as plt
>> from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
>>
>> fig = plt.figure(1)
>> fig.clf()
>> #plt.grid(True)
>> host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
>> fig.add_axes(host)
>>
>> host.plot([0, 10, 100], [0, 10, 100], label='host')
>>
>> host.grid(True)  #?
>> host.yaxis.grid(True) #?
>>
>> host.yaxis.set_scale('log') #?
>>
>> plt.draw()
>> plt.show()
>> #######################
>>
>> Greets,
>> Andreas
>>
>>
>> Sebastian Busch schrieb:
>>
>>> from matplotlib.pyplot import *
>>>
>>> plot([1,10,100],[1,10,100])
>>> grid()
>>>
>>> yscale('log')
>>> xscale('log')
>>>
>>> works here.
>>>
>>> best,
>>> sebastian.
>>>
>>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

Hi,
 
I am running Windows Vista 64-bit and have installed matplotlib from http://sourceforge.net/projects/matplotlib/ via the "Download Now!".  I currently have Numpy version 1.3.0 installed in the same location as matplotlib (C:\Python26\Lib\site-packages\).  I have tried importing matplotlib, for example     import matplotlib.pyplot    like in the documented examples and unfortunately this does not work for me.  I have searched in site-packages, and elsewhere, for files/directories on my computer named matplotlit or pyplot and found no hits.  I have even reinstalled matplot lib and still have the same problems.  Has anyone else experienced this problem?  
 

 
-Nathan  

Hi,

I have the same behaviour with LocatableAxes. HostAxes, ParasiteAxes and 
LocatableAxes depend on 'mpl_toolkits.axes_grid.axislines.Axes'. It must 
be the matter origin.
This another example should draw a grid but does not:

import wx
from wx import Frame
from matplotlib.backends.backend_wxagg import FigureFrameWxAgg, 
FigureCanvasWxAgg
from matplotlib.figure import Figure
from mpl_toolkits.axes_grid.axes_divider import LocatableAxes

fig = Figure((1, 1), 50)
axes = LocatableAxes(fig, [0, 0, 1, 1])
# axes.toggle_axisline(False)
axes.grid(True)
fig.add_axes(axes)

app = wx.PySimpleApp()
my_viewer = FigureFrameWxAgg(-1, fig)
my_viewer.Show()
app.MainLoop()

If you uncomment axes.toggle_axisline(False), it works cause it uses 
normal 'matplolib.axes.Axes' behaviour. It is not a matter for common 
use but if you need 'AxesZero', this trick does not work.

Yann


On 09/07/2009 10:37 PM, Andreas Fromm wrote:
> thanks Sebastian,
>
> you are right, your code works here too. But i don't get it work in my
> multi y-axes plot from the matplotlib examples
> (http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html).
> Even with linear plots, i get no gridlines.
>
> Any idea, whats wrong here?
>
> minimal code example:
> #######################
> import matplotlib.pyplot as plt
> from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
>
> fig = plt.figure(1)
> fig.clf()
> #plt.grid(True)
> host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
> fig.add_axes(host)
>
> host.plot([0, 10, 100], [0, 10, 100], label='host')
>
> host.grid(True)  #?
> host.yaxis.grid(True) #?
>
> host.yaxis.set_scale('log') #?
>
> plt.draw()
> plt.show()
> #######################
>
> Greets,
> Andreas
>
>
> Sebastian Busch schrieb:
>    
>> from matplotlib.pyplot import *
>>
>> plot([1,10,100],[1,10,100])
>> grid()
>>
>> yscale('log')
>> xscale('log')
>>
>> works here.
>>
>> best,
>> sebastian.
>>
>>      
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>    

Hi list,

I have some files with data stored in columns:

x1     y1     z1
x2     y2     z2
x3     y3     z3
x4     y4     z4
x5     y5     z5
.......

and I need to make a contour plot of this data using matplotlib. The
problem is that contour plot functions usually handle a different kind
of input:

X=[[x1,x2,x3,x4,x5,x6],
[x1,x2,x3,x4,x5,x6],
[x1,x2,x3,x4,x5,x6],...


Y=[[y1,y1,y1,y1,y1,y1],
[y2,y2,y2,y2,y2,y2],
[y3,y3,y3,y3,y3,y3],.....

Z=[[z1,z2,z3,z4,z5,z6],
[z7,z8,zz9,z10,z11,z12],....

I usually load data using 3 lists: x, y and z; I wonder if there is
any function which is able to take these 3 lists and return the right
input for matplotlib functions.

cheers

g

This is a bug in the axes_grid toolkit. As a matter of fact, gridlines
in rectlinear coordinate are not implemented yet.
Unfortunately, I don't see any easy workarounds.

You may use mpl's original axis artists, but some of the functionality
of axes_grid toolkit may be lost.

    host.toggle_axisline(False)
    host.yaxis.set_ticks_position("left")
    host.yaxis.grid()
    host.set_yscale("log")

With new spine support in mpl, I think a similar plot can be drawn
without using axes_grid toolkit.

Regards,

-JJ


On Mon, Sep 7, 2009 at 4:37 PM, Andreas Fromm<an...@gm...> wrote:
> thanks Sebastian,
>
> you are right, your code works here too. But i don't get it work in my
> multi y-axes plot from the matplotlib examples
> (http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html).
> Even with linear plots, i get no gridlines.
>
> Any idea, whats wrong here?
>
> minimal code example:
> #######################
> import matplotlib.pyplot as plt
> from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes
>
> fig = plt.figure(1)
> fig.clf()
> #plt.grid(True)
> host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
> fig.add_axes(host)
>
> host.plot([0, 10, 100], [0, 10, 100], label='host')
>
> host.grid(True)  #?
> host.yaxis.grid(True) #?
>
> host.yaxis.set_scale('log') #?
>
> plt.draw()
> plt.show()
> #######################
>
> Greets,
> Andreas
>
>
> Sebastian Busch schrieb:
>> from matplotlib.pyplot import *
>>
>> plot([1,10,100],[1,10,100])
>> grid()
>>
>> yscale('log')
>> xscale('log')
>>
>> works here.
>>
>> best,
>> sebastian.
>>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

On Tue, Sep 8, 2009 at 7:45 AM, Armando Serrano Lombillo <ars...@gm...
> wrote:

> Hello, I'm finding it a little difficult to make a plot with dates:
>
> I have an array with 2 columns. The first one is seconds since a certain
> date (let's say 8th September, 8:00am). The second one is the variable I
> want to plot. The series spans several months so I want to have the major
> ticks be months (and have the name of the month printed below) and the minor
> ticks be days. I'm sure this is very easy to plot but I don't know how to,
> any help?
>
> Armando.
>


Hello,

You can experiment with the following lines to re-arrange your ticks.

current_axis = gca()
current_axis.xaxis.set_major_formatter()

Similarly set_minor_formatter for x and y axes.

See these links too

http://matplotlib.sourceforge.net/api/dates_api.html
http://matplotlib.sourceforge.net/examples/api/date_index_formatter.html

-- 
Gökhan

I just went in and changed the default file downloads back to correct 
values, but alas, it appears to have no effect.  There is some hints in 
the (many) related SF bugs that there may be a delay associated with 
these settings, so I will check back again at the end of the day.

Mike

On 09/04/2009 05:46 AM, Fabrice Silva wrote:
> Le jeudi 03 septembre 2009 à 20:16 -0500, John Hunter a écrit :
>    
>> On Thu, Sep 3, 2009 at 8:04 PM, Alan G Isaac<ala...@gm...>  wrote:
>>      
>>> The default download from the Matplotlib page
>>> link to http://sourceforge.net/projects/matplotlib/
>>> which once again highlights basemap.  (I think
>>> this was fixed at one point.)
>>>        
>> I'm not seeng this, nor am I seeing basemap settings in the File
>> Manager which would trigger this.  Of course, the default download is
>> platform specific, which may be why I am not seeing this, so please
>> give us as much info as possible about your platform (mainly the OS)
>>
>> When I click on the green download button at
>> http://sourceforge.net/projects/matplotlib using mac OSX 10.5, I get
>> redirected to the mpl 0.99 OSX download::
>>
>>    https://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx10.5.dmg/download
>>      
> Strangely, the green button points to
> http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-0.99/matplotlib-0.99.0-py2.5-macosx-10.3-i386.egg/download
> when I browse on a linux (debian) machine with epiphany (which uses
> gecko, the firefox engine). Why macosx ?
>
>    

Hello, I'm finding it a little difficult to make a plot with dates:

I have an array with 2 columns. The first one is seconds since a certain
date (let's say 8th September, 8:00am). The second one is the variable I
want to plot. The series spans several months so I want to have the major
ticks be months (and have the name of the month printed below) and the minor
ticks be days. I'm sure this is very easy to plot but I don't know how to,
any help?

Armando.

Arthur,

I wrote the date2index function and I think what you are seeing is a bug
that I fixed a couple of months ago. By using the latest version of
netcdf4-python, not only should this bug disappear, but you'll also find
that date2index now supports different selection methods: 'exact', 'before',
'after', 'nearest', that should help with your use case.

If this does not fix the problem you are seeing, I'd appreciate having a
copy of the file and code to reproduce the problem and find a solution.

HTH,

David Huard



On Mon, Sep 7, 2009 at 9:27 AM, Arthur M. Greene <am...@ir...>wrote:

> Hi All,
>
> The problem is not with fetching the data slice itself, but finding the
> correct indices to specify, particularly with the time dimension. The
> below examples refer to a remote dataset that I can open and slice using
> indices, as in
>
> slice = remoteobj.variables['tas'][:120,20:40,30:50].
>
> However, I have problems when trying to use the syntax in plotsst.py or
> pnganim.py (from the examples) to find time indices:
>
> In [107]: from datetime import datetime as dt
> In [108]: date0 = dt(1951,1,1,0)
> In [110]: print date0
> 1951-01-01 00:00:00
>
> In [125]: timedata = remoteobj.variables['time']
> In [126]: nt0 = date2index(date0,timedata)
> ---------------------------------------------------------------------------
> AssertionError                            Traceback (most recent call last)
>
> /home/amg/work/nhmm/<ipython console> in <module>()
>
>
> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/__init__.pyc
>
> in date2index(dates, nctime, calendar)
>    3924     Returns an index or a sequence of indices.
>    3925     """
> -> 3926     return netcdftime.date2index(dates, nctime, calendar=None)
>    3927
>    3928 def maskoceans(lonsin,latsin,datain,inlands=False):
>
>
> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc
>
> in date2index(dates, nctime, calendar)
>     986
>     987         # Perform check again.
> --> 988         _check_index(index, dates, nctime, calendar)
>     989
>     990     # convert numpy scalars or single element arrays to python
> ints.
>
>
> /usr/local/cdat/trunk/lib/python2.5/site-packages/mpl_toolkits/basemap/netcdftime.pyc
>
> in _check_index(indices, dates, nctime, calendar)
>     941     for n,i in enumerate(indices):
>     942         t[n] = nctime[i]
> --> 943     assert numpy.all( num2date(t, nctime.units, calendar) == dates)
>     944
>     945
>
> AssertionError:
>
> ---------------------------------------------------------
>
> It turns out that date0 corresponds best to index 1080:
>
> In [139]: remoteobj.variables['time'][1080]
> Out[139]: 32865.5
>
> In [141]: num2date(32865.5,timedata.units,timedata.calendar)
> Out[141]: 1951-01-16 12:00:00
>
> This isn't the _exact_ date and time I had specified, but
>
> In [142]: date0 = dt(1951,01,16,12,00,00)
> In [143]: print date0
> 1951-01-16 12:00:00
>
> In [144]: date2index(date0,timedata,timedata.calendar)
>
> produces the same AssertionError. Where is the problem?
>
> What I would _like_ to do is to issue a simple call using coordinates
> rather than the indices, of the form:
>
> slice = variable[date0:date1,[plev],lat0:lat1,lon0:lon1],
>
> or similar, preferably without writing a whole module just to find the
> correct indices. I need to fetch similar slices from a group of models,
> having time axes that may each be defined slightly differently --
> different calendars, time point set at a different day of the month,
> etc. (It's monthly data and I'm specifying only monthly bounds, even
> though the calendar may be defined as "days since 1860...") I need to
> automate the process so I get back the correct slab regardless.
>
> Suggestions appreciated!
>
> Thx,
>
> Arthur
>
>
> *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
> Arthur M. Greene, Ph.D.
> The International Research Institute for Climate and Society (IRI)
> The Earth Institute, Columbia University, Lamont Campus
>
> amg at iri dot columbia dot edu | http://iri.columbia.edu
> *^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*^*~*
>
>
>
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>

On Mon, Sep 7, 2009 at 1:02 PM, tva<tv...@br...> wrote:
>
> Problem solved. The backend was set to Qt4Agg. Once set to TkAgg everything
> works.
> I don't get it but it works..........
>
>


I think an explicit call of draw() in the interactive mode (e.g. with
ipython -pylab) should update the figure canvas immediately. And this
is the behavior I currently observe with Gtk and Wx backend. If the
Qt4 backend behaves differently, I guess this is a bug. I don't have
the qt4 backend installed, and I hope other developers take  a look.

-JJ

thanks Sebastian,

you are right, your code works here too. But i don't get it work in my 
multi y-axes plot from the matplotlib examples 
(http://matplotlib.sourceforge.net/examples/axes_grid/demo_parasite_axes.html). 
Even with linear plots, i get no gridlines.

Any idea, whats wrong here?

minimal code example:
#######################
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid.parasite_axes import HostAxes, ParasiteAxes

fig = plt.figure(1)
fig.clf()
#plt.grid(True)
host = HostAxes(fig, [0.15, 0.1, 0.65, 0.8])
fig.add_axes(host)

host.plot([0, 10, 100], [0, 10, 100], label='host')

host.grid(True)  #?
host.yaxis.grid(True) #?

host.yaxis.set_scale('log') #?

plt.draw()
plt.show()
#######################

Greets,
Andreas


Sebastian Busch schrieb:
> from matplotlib.pyplot import *
>
> plot([1,10,100],[1,10,100])
> grid()
>
> yscale('log')
> xscale('log')
>
> works here.
>
> best,
> sebastian.
>   

jihi wrote:
> ... can anybody tell me how to get gridlines in a logarithmic plot? ...
from matplotlib.pyplot import *

plot([1,10,100],[1,10,100])
grid()

yscale('log')
xscale('log')

works here.

best,
sebastian.