Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-30 Thread A Short
Thanks Eric and Kio - ive been trying for a couple of days and i just cant
seem to get my head around the interpolation or masked arrays. Would it be
possible for anyone to give me a few pointers on where to start editing the
script.

Ive tried digesting these tutorials the first one seems to be relevant to
what im trying to achieve by using a Laplace filter but im still having
trouble installing all the modules to be able to play with it more 

http://www.trondkristiansen.com/?page_id=846
http://www.trondkristiansen.com/?page_id=846  

http://www.geophysique.be/2010/05/05/matplotlib-basemap-tutorial-part-03-masked-arrays-zoom/
http://www.geophysique.be/2010/05/05/matplotlib-basemap-tutorial-part-03-masked-arrays-zoom/
  

And reading all of the toolkit docseveral times!

Thanks again



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-29 Thread Ian Thomas
On 29 January 2014 03:21, Eric Firing efir...@hawaii.edu wrote:

 On 2014/01/28 10:01 AM, A Short wrote:
  Hi - Ive now improved my code and confirmed the use of the right grib
 file
  but i cant for the life of me figure out the missing data near the
  coastline..? Could anyone help?

 The present contouring algorithm works with rectangular blocks, and if
 any corner has missing data, nothing is filled for that block.


This will improve shortly, cutting off the corners of some of those empty
blocks. I am currently testing the new algorithm for this prior to
submitting it for others' approval.

Ian
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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-29 Thread A Short
Is there any work around so it looks like the below image?

Could anyone confirm that this would be the correct grib file for The North
Atlantic..? 
ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/wave/prod/wave.20140129/nww3.t06z.grib.grib2

Thanks for all the help

http://matplotlib.1069221.n5.nabble.com/file/n42798/figure_1.png 





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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-29 Thread Eric Firing
On 2014/01/28 11:40 PM, Ian Thomas wrote:
 On 29 January 2014 03:21, Eric Firing efir...@hawaii.edu
 mailto:efir...@hawaii.edu wrote:

 On 2014/01/28 10:01 AM, A Short wrote:
   Hi - Ive now improved my code and confirmed the use of the right
 grib file
   but i cant for the life of me figure out the missing data near the
   coastline..? Could anyone help?

 The present contouring algorithm works with rectangular blocks, and if
 any corner has missing data, nothing is filled for that block.


 This will improve shortly, cutting off the corners of some of those
 empty blocks. I am currently testing the new algorithm for this prior to
 submitting it for others' approval.

Ian,

I'm glad to hear that!  One possibility would be to use a temporary 
rcParam (temporary in that it might be phased out after a couple 
releases) to allow switching between the two algorithms.  This would 
make it much easier to test, and it would also allow a transition during 
which people could reproduce results obtained with earlier mpl.  It 
would also be a safety measure, in case someone hits a corner case which 
the new algorithm doesn't handle but the old one does--not that I'm 
expecting such cases to arise.

Eric


 Ian


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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-29 Thread Eric Firing
On 2014/01/29 5:41 AM, A Short wrote:
 Is there any work around so it looks like the below image?

It looks like with any reasonable contouring algorithm, this would 
require interpolating into land regions, contouring, and then plotting 
the land on top.  The key is the interpolation, not the plotting.  The 
example you show might have been interpolated to a finer grid 
everywhere, not just in the missing value regions.

I can't comment on the file itself.

Eric


 Could anyone confirm that this would be the correct grib file for The North
 Atlantic..?
 ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/wave/prod/wave.20140129/nww3.t06z.grib.grib2

 Thanks for all the help

 http://matplotlib.1069221.n5.nabble.com/file/n42798/figure_1.png





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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-29 Thread klo uo
IMHO that's the most straightforward approach.
He can use masked array for empty blocks (if contour data doesn't
already contain the holes as masked array) and apply inpainting, then
draw the land.
For more details about inpainting: http://stackoverflow.com/a/17125125/992005


On Wed, Jan 29, 2014 at 6:22 PM, Eric Firing efir...@hawaii.edu wrote:
 On 2014/01/29 5:41 AM, A Short wrote:
 Is there any work around so it looks like the below image?

 It looks like with any reasonable contouring algorithm, this would
 require interpolating into land regions, contouring, and then plotting
 the land on top.  The key is the interpolation, not the plotting.  The
 example you show might have been interpolated to a finer grid
 everywhere, not just in the missing value regions.

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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-28 Thread A Short
Hi - Ive now improved my code and confirmed the use of the right grib file
but i cant for the life of me figure out the missing data near the
coastline..? Could anyone help?

`import Nio
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np

f = Nio.open_file('nww3.t12z.grib(2).grib2')
lons = f.variables['lon_0'][:]
lats = f.variables['lat_0'][::-1] # flip latitudes so data goes S--N
times = f.variables['forecast_time0'][:]
ntime = 5
data = f.variables['HTSGW_P0_L1_GLL0'][ntime,::-1]

fig = plt.figure(figsize=(16,16))
m = Basemap(llcrnrlon=-35.,llcrnrlat=42.,urcrnrlon=5.,urcrnrlat=65.,
projection='lcc',lat_1=10.,lat_2=15.,lon_0=10.,
resolution ='h',area_thresh=1000.)

x, y = m(*np.meshgrid(lons, lats))
m.fillcontinents(color='#477519')
m.drawcoastlines(linewidth=0.5, color='k', antialiased=1, ax=None,
zorder=None )

m.contourf(x, y, data, np.arange(0,9.9,0.1))
plt.show() `

Resulting plot is here 
http://matplotlib.1069221.n5.nabble.com/file/n42790/figure_7.png 



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-28 Thread Eric Firing
On 2014/01/28 10:01 AM, A Short wrote:
 Hi - Ive now improved my code and confirmed the use of the right grib file
 but i cant for the life of me figure out the missing data near the
 coastline..? Could anyone help?

The present contouring algorithm works with rectangular blocks, and if 
any corner has missing data, nothing is filled for that block.

Eric


 `import Nio
 from mpl_toolkits.basemap import Basemap
 import matplotlib.pyplot as plt
 import numpy as np

 f = Nio.open_file('nww3.t12z.grib(2).grib2')
 lons = f.variables['lon_0'][:]
 lats = f.variables['lat_0'][::-1] # flip latitudes so data goes S--N
 times = f.variables['forecast_time0'][:]
 ntime = 5
 data = f.variables['HTSGW_P0_L1_GLL0'][ntime,::-1]

 fig = plt.figure(figsize=(16,16))
 m = Basemap(llcrnrlon=-35.,llcrnrlat=42.,urcrnrlon=5.,urcrnrlat=65.,
  projection='lcc',lat_1=10.,lat_2=15.,lon_0=10.,
  resolution ='h',area_thresh=1000.)

 x, y = m(*np.meshgrid(lons, lats))
 m.fillcontinents(color='#477519')
 m.drawcoastlines(linewidth=0.5, color='k', antialiased=1, ax=None,
 zorder=None )

 m.contourf(x, y, data, np.arange(0,9.9,0.1))
 plt.show() `

 Resulting plot is here
 http://matplotlib.1069221.n5.nabble.com/file/n42790/figure_7.png



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[Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Rolling Six
Hi im new to Python and basemap i am trying to follow the script below that
was posted in another thread  here
http://matplotlib.1069221.n5.nabble.com/Plotting-NOAA-data-td19588.html  
but im getting this error

alec@alec-imedia-S2870:~$ python Desktop/test.py
/usr/lib/pymodules/python2.7/mpl_toolkits/__init__.py:2: UserWarning: Module
dap was already imported from None, but /usr/lib/python2.7/dist-packages is
being added to sys.path
  __import__('pkg_resources').declare_namespace(__name__)
a
fatal: environment variable not set
b
['VGRD_P0_L1_GLL0', 'WVDIR_P0_L1_GLL0', 'lon_0', 'PERSW_P0_L1_GLL0',
'WIND_P0_L1_GLL0', 'PERPW_P0_L1_GLL0', 'WDIR_P0_L1_GLL0', 'forecast_time0',
'DIRPW_P0_L1_GLL0', 'WVPER_P0_L1_GLL0', 'DIRSW_P0_L1_GLL0',
'HTSGW_P0_L1_GLL0', 'UGRD_P0_L1_GLL0', 'lat_0']
Traceback (most recent call last):
  File Desktop/test.py, line 14, in module
datavar = f.variables['WWSWHGT_P0_L1_GLL0']
KeyError: 'WWSWHGT_P0_L1_GLL0'

The script im trying to run below

import Nio
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
f = Nio.open_file('akw.t00z.grib.grib2')
print f.variables.keys()
lons = f.variables['lon_0'][:]
# flip latitudes so data goes S--N
lats = f.variables['lat_0'][::-1]
times = f.variables['forecast_time0'][:]
datavar = f.variables['WWSWHGT_P0_L1_GLL0']
ntime = 10
data = datavar[ntime,::-1]
print f.variables['WWSWHGT_P0_L1_GLL0']
print data.min(), data.max()
m = Basemap(projection='cyl',llcrnrlat=lats[0],llcrnrlon=lons[0],\
urcrnrlat=lats[-1],urcrnrlon=lons[-1],resolution='l')
x, y = m(*np.meshgrid(lons, lats))
levels = np.arange(0,9.1,0.5)
m.contourf(x,y,data,levels)
m.drawcoastlines()
m.fillcontinents()
m.drawparallels(np.arange(40,81,10),labels=[1,0,0,0])
m.drawmeridians(np.arange(150,241,10),labels=[0,0,0,1])
m.drawparallels(np.arange(40,81,10),labels=[1,0,0,0])
m.drawmeridians(np.arange(150,241,10),labels=[0,0,0,1])
plt.title(datavar.long_name+' %s hr fcst'%(times[ntime]),fontsize=12)
plt.colorbar(orientation='horizontal',shrink=0.9,format=%g)
plt.show() 







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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Paul Hobson
As the error message says, the problem is on Line 14:

print f.variables['WWSWHGT_P0_L1_GLL0']

a KeyError means that you tried to access an element that is not in a
dictionary. In this case f.variables is the dictionary and '
WWSWHGT_P0_L1_GLL0' is the element.

Did your data and script come of the same place? You can't just throw any
basemap script at any grid file.


On Thu, Jan 9, 2014 at 4:52 AM, Rolling Six surfersh...@hotmail.com wrote:

 Hi im new to Python and basemap i am trying to follow the script below that
 was posted in another thread  here
 http://matplotlib.1069221.n5.nabble.com/Plotting-NOAA-data-td19588.html
 but im getting this error

 alec@alec-imedia-S2870:~$ python Desktop/test.py
 /usr/lib/pymodules/python2.7/mpl_toolkits/__init__.py:2: UserWarning:
 Module
 dap was already imported from None, but /usr/lib/python2.7/dist-packages is
 being added to sys.path
   __import__('pkg_resources').declare_namespace(__name__)
 a
 fatal: environment variable not set
 b
 ['VGRD_P0_L1_GLL0', 'WVDIR_P0_L1_GLL0', 'lon_0', 'PERSW_P0_L1_GLL0',
 'WIND_P0_L1_GLL0', 'PERPW_P0_L1_GLL0', 'WDIR_P0_L1_GLL0', 'forecast_time0',
 'DIRPW_P0_L1_GLL0', 'WVPER_P0_L1_GLL0', 'DIRSW_P0_L1_GLL0',
 'HTSGW_P0_L1_GLL0', 'UGRD_P0_L1_GLL0', 'lat_0']
 Traceback (most recent call last):
   File Desktop/test.py, line 14, in module
 datavar = f.variables['WWSWHGT_P0_L1_GLL0']
 KeyError: 'WWSWHGT_P0_L1_GLL0'

 The script im trying to run below

 import Nio
 from mpl_toolkits.basemap import Basemap
 import matplotlib.pyplot as plt
 import numpy as np
 f = Nio.open_file('akw.t00z.grib.grib2')
 print f.variables.keys()
 lons = f.variables['lon_0'][:]
 # flip latitudes so data goes S--N
 lats = f.variables['lat_0'][::-1]
 times = f.variables['forecast_time0'][:]
 datavar = f.variables['WWSWHGT_P0_L1_GLL0']
 ntime = 10
 data = datavar[ntime,::-1]
 print f.variables['WWSWHGT_P0_L1_GLL0']
 print data.min(), data.max()
 m = Basemap(projection='cyl',llcrnrlat=lats[0],llcrnrlon=lons[0],\
 urcrnrlat=lats[-1],urcrnrlon=lons[-1],resolution='l')
 x, y = m(*np.meshgrid(lons, lats))
 levels = np.arange(0,9.1,0.5)
 m.contourf(x,y,data,levels)
 m.drawcoastlines()
 m.fillcontinents()
 m.drawparallels(np.arange(40,81,10),labels=[1,0,0,0])
 m.drawmeridians(np.arange(150,241,10),labels=[0,0,0,1])
 m.drawparallels(np.arange(40,81,10),labels=[1,0,0,0])
 m.drawmeridians(np.arange(150,241,10),labels=[0,0,0,1])
 plt.title(datavar.long_name+' %s hr fcst'%(times[ntime]),fontsize=12)
 plt.colorbar(orientation='horizontal',shrink=0.9,format=%g)
 plt.show()







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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread A Short
Hi Paul,

Thanks for your reply, I managed to fix it after I realised the mistake I
was making.

I've currently got a new problem. If you look at the image below, there's a
lot of white showing up around the coasts which ideally I'd like to remove.
The map is drawn using basemap, is there a function/feature that will fill
this in. Or is it a probem with the grib files that I'm using?

http://matplotlib.1069221.n5.nabble.com/file/n42701/figure_1.png 

If possible, I'd like it to look like the image below. If it is a problem
with our data, is there a way that we can draw a layer of colour on the
bottom to get rid of the white?

http://matplotlib.1069221.n5.nabble.com/file/n42701/figure_1.png 



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Paul Hobson
I think you posted the same image in both cases. Without seeing the
problematic image, I can only guess that it's caused by the resolution of
your data.


On Thu, Jan 9, 2014 at 7:58 AM, A Short surfersh...@hotmail.com wrote:

 Hi Paul,

 Thanks for your reply, I managed to fix it after I realised the mistake I
 was making.

 I've currently got a new problem. If you look at the image below, there's a
 lot of white showing up around the coasts which ideally I'd like to remove.
 The map is drawn using basemap, is there a function/feature that will fill
 this in. Or is it a probem with the grib files that I'm using?

 http://matplotlib.1069221.n5.nabble.com/file/n42701/figure_1.png

 If possible, I'd like it to look like the image below. If it is a problem
 with our data, is there a way that we can draw a layer of colour on the
 bottom to get rid of the white?

 http://matplotlib.1069221.n5.nabble.com/file/n42701/figure_1.png



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread A Short
ok the file im using is this multi_2.glo_30m.t06z.grib2 from  here
ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/wave/prod/wave.20140109/   im
not sure its the right file to get wave heights of the North East Atlantic
so im trying different ones.

as you can see above in the top image there is some data missing (white
boxes) near the coast im wondering if its possible to either zoom into the
map slightly so the data runs underneath the land..?

Thanks
Alec



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Paul Hobson
What I'm saying is that your top image and bottom image are identical and I
don't see any white boxes in either. What is the resolution of the grid?

-paul


On Thu, Jan 9, 2014 at 11:59 AM, A Short surfersh...@hotmail.com wrote:

 ok the file im using is this multi_2.glo_30m.t06z.grib2 from  here
 ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/wave/prod/wave.20140109/
 im
 not sure its the right file to get wave heights of the North East Atlantic
 so im trying different ones.

 as you can see above in the top image there is some data missing (white
 boxes) near the coast im wondering if its possible to either zoom into the
 map slightly so the data runs underneath the land..?

 Thanks
 Alec



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread A Short
Thats strange they look different on this browser. Hopefully the one below
youll see what i mean

Thanks

http://matplotlib.1069221.n5.nabble.com/file/n42708/figure_1.png 



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Paul Hobson
How does it look if you remove the calls to `m.drawcoastlines()` and `
m.fillcontinents()`?


On Thu, Jan 9, 2014 at 1:05 PM, A Short surfersh...@hotmail.com wrote:

 Thats strange they look different on this browser. Hopefully the one below
 youll see what i mean

 Thanks

 http://matplotlib.1069221.n5.nabble.com/file/n42708/figure_1.png



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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread A Short
Ive also changed the grib file from multi_2.glo_30m.t06z.grib2 to
nww3.t12z.grib.grib2 i still cant figure out which is the right file for the
North East Atlantic neither...i wonder if my data source is wrong..?

http://matplotlib.1069221.n5.nabble.com/file/n42710/figure_2.png 





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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread Paul Hobson
Looks like it's just a coarse resolution to me. Try showing the data as an
image with no iterpolation.


On Thu, Jan 9, 2014 at 3:26 PM, A Short surfersh...@hotmail.com wrote:

 Ive also changed the grib file from multi_2.glo_30m.t06z.grib2 to
 nww3.t12z.grib.grib2 i still cant figure out which is the right file for
 the
 North East Atlantic neither...i wonder if my data source is wrong..?

 http://matplotlib.1069221.n5.nabble.com/file/n42710/figure_2.png





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Re: [Matplotlib-users] Plotting NOAA grib2 data in basemap

2014-01-09 Thread A Short
Thanks Paul i added m.imshow(data, origin='lower', interpolation='none')

Its made a little improvement but something still seems to be not right

http://matplotlib.1069221.n5.nabble.com/file/n42712/figure_3.png 





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