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Re: [Matplotlib-users] memory error - netcdf plots
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From: questions a. <que...@gm...> - 2011-10-19 02:56:05
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Thanks Jeff, that certainly speeds it up! But when I take them out of the
loop and place them elsewhere they are no longer added to the map.
Is there someway I can call them in the loop but still get it to run
quickly?
Thanks
On Fri, Oct 14, 2011 at 10:54 PM, Jeff Whitaker <js...@fa...> wrote:
> On 10/12/11 8:20 PM, questions anon wrote:
>
> Hi All,
> I keep receiving a memory error when processing many netcdf files. I
> assumed it had something to do with how I loop things and maybe needed to
> close things off properly but I recently received an error that made me
> think it might be because of matplotlib.
>
> In the code below I am looping through a bunch of netcdf files (each file
> is hourly data for one month) and within each netcdf file I am outputting a
> *png file every three hours. This works for one netcdf file (therefore one
> month) but when it begins to process the next netcdf file I receive a memory
> error (see below). Since I have tidied some of my code up it seems to
> process partly into the second file but then I still receive the memory
> error.
> I have tried a few suggestions such as:
> -Combining the dataset using MFDataset (using NETCDF4) is not an option
> because the files do not have unlimited dimension.
> - gc.collect() but that just results in a *GEOS_ERROR: bad allocation
> error*.
> -only open LAT and LON once (which worked)
>
> System Details:
> Python 2.7.2 |EPD 7.1-2 (32-bit)| (default, Jul 3 2011, 15:13:59) [MSC
> v.1500 32 bit (Intel)] on win32
>
> Any feedback will be greatly appreciated as I seem to keep ending up with
> memory errors when working with netcdf files this even happens if I am using
> a much better computer.
>
> *Most recent error: *
> Traceback (most recent call last):
> File "C:\plot_netcdf_merc_multiplot_across_multifolders_TSFC.py", line
> 78, in <module>
> plt.savefig((os.path.join(outputfolder, 'TSFC'+date_string+'UTC.png')))
> File "C:\Python27\lib\site-packages\matplotlib\pyplot.py", line 363, in
> savefig
> return fig.savefig(*args, **kwargs)
> File "C:\Python27\lib\site-packages\matplotlib\figure.py", line 1084, in
> savefig
> self.canvas.print_figure(*args, **kwargs)
> File
> "C:\Python27\lib\site-packages\matplotlib\backends\backend_wxagg.py", line
> 100, in print_figure
> FigureCanvasAgg.print_figure(self, filename, *args, **kwargs)
> File "C:\Python27\lib\site-packages\matplotlib\backend_bases.py", line
> 1923, in print_figure
> **kwargs)
> File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 438, in print_png
> FigureCanvasAgg.draw(self)
> File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 393, in draw
> self.renderer = self.get_renderer()
> File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 404, in get_renderer
> self.renderer = RendererAgg(w, h, self.figure.dpi)
> File "C:\Python27\lib\site-packages\matplotlib\backends\backend_agg.py",
> line 59, in __init__
> self._renderer = _RendererAgg(int(width), int(height), dpi,
> debug=False)
> RuntimeError: Could not allocate memory for image
>
> *Error when I added gc.collect()*
> GEOS_ERROR: bad allocation
>
> *Old error (before adding gc.collect() )*
> *Traceback (most recent call last):
> File "d:/plot_netcdf_merc_multiplot_across_multifolders__memoryerror.py",
> line 44, in <module>
> TSFC=ncfile.variables['T_SFC'][1::3]
> File "netCDF4.pyx", line 2473, in netCDF4.Variable.__getitem__
> (netCDF4.c:23094)
> MemoryError*
>
>
>
> from netCDF4 import Dataset
> import numpy as N
> import matplotlib.pyplot as plt
> from mpl_toolkits.basemap import Basemap
> from netcdftime import utime
> from datetime import datetime
> import os
> import gc
>
>
> shapefile1="E:/
>>
>> griddeddatasamples/GIS/DSE_REGIONS"
>> MainFolder=r"E:/griddeddatasamples/GriddedData/InputsforValidation/T_SFC/"
>> OutputFolder=r"E:/griddeddatasamples/GriddedData/OutputsforValidation"
>> fileforlatlon=Dataset("E:/griddeddatasamples/GriddedData/InputsforValidation/T_SFC/TSFC_1974_01/IDZ00026_VIC_ADFD_T_SFC.nc",
>> 'r+', 'NETCDF4')
>> LAT=fileforlatlon.variables['latitude'][:]
>> LON=fileforlatlon.variables['longitude'][:]
>>
>> for (path, dirs, files) in os.walk(MainFolder):
>> for dir in dirs:
>> print dir
>> path=path+'/'
>> for ncfile in files:
>> if ncfile[-3:]=='.nc':
>> print "dealing with ncfiles:", ncfile
>> ncfile=os.path.join(path,ncfile)
>> ncfile=Dataset(ncfile, 'r+', 'NETCDF4')
>> TSFC=ncfile.variables['T_SFC'][1::3]
>> TIME=ncfile.variables['time'][1::3]
>> ncfile.close()
>> gc.collect()
>>
>> for TSFC, TIME in zip((TSFC[:]),(TIME[:])):
>> cdftime=utime('seconds since 1970-01-01 00:00:00')
>> ncfiletime=cdftime.num2date(TIME)
>> print ncfiletime
>> timestr=str(ncfiletime)
>> d = datetime.strptime(timestr, '%Y-%m-%d %H:%M:%S')
>> date_string = d.strftime('%Y%m%d_%H%M')
>>
>> map =
>> Basemap(projection='merc',llcrnrlat=-40,urcrnrlat=-33,
>>
>> llcrnrlon=139.0,urcrnrlon=151.0,lat_ts=0,resolution='i')
>> x,y=map(*N.meshgrid(LON,LAT))
>> map.drawcoastlines(linewidth=0.5)
>> map.readshapefile(shapefile1, 'DSE_REGIONS')
>> map.drawstates()
>>
>> plt.title('Surface temperature at %s UTC'%ncfiletime)
>> ticks=[-5,0,5,10,15,20,25,30,35,40,45,50]
>> CS = map.contourf(x,y,TSFC, ticks, cmap=plt.cm.jet)
>> l,b,w,h =0.1,0.1,0.8,0.8
>> cax = plt.axes([l+w+0.025, b, 0.025, h], )
>> cbar=plt.colorbar(CS, cax=cax, drawedges=True)
>>
>> plt.savefig((os.path.join(OutputFolder,
>> 'TSFC'+date_string+'UTC.png')))
>> plt.close()
>> gc.collect()
>>
>>
> Try moving these lines
>
>
> map =
> Basemap(projection='merc',llcrnrlat=-40,urcrnrlat=-33,
>
> llcrnrlon=139.0,urcrnrlon=151.0,lat_ts=0,resolution='i')
> x,y=map(*N.meshgrid(LON,LAT))
> map.drawcoastlines(linewidth=0.5)
> map.readshapefile(shapefile1, 'DSE_REGIONS')
> map.drawstates()
>
> out of the loop.
>
> -Jeff
>
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