[GRASS-user] Read/Write numpy array

GRASS GRASS user
1

Hello,

I try to do a mapcalculation with scipy (do to limited functionality of
usual mapcalc functions.

Therefore I want to read a map into numpy-array, do the calculation on it and write it back to a GRASS-map. I tried to follow the instructions in the wiki (http://grass.osgeo.org/wiki/GRASS_and_Python#Interfacing_with_NumPy) but I got stucked when it comes to the writing-process.
Thats my code so far:

    x = garray.array()
    x.read("distance_raster")
    Density = garray.array()
    Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
    Density.write("Density")

The stats.norm.pdf is from the stats-scipy module. I get following error when I try to process the script:

   Density.write("Density")
AttributeError: 'numpy.ndarray' object has no attribute
'write'

I don't know excactly what how I have to use the write command. I am working on 6.5 and I read there were some problems with numpy-arrays. Are the solved now?

/johannes
--
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gratis Handy-Flat! http://portal.gmx.net/de/go/dsl

2

Johannes Radinger wrote:

I try to do a mapcalculation with scipy (do to limited functionality of
usual mapcalc functions.

Therefore I want to read a map into numpy-array, do the calculation
on it and write it back to a GRASS-map. I tried to follow the
instructions in the wiki
(http://grass.osgeo.org/wiki/GRASS_and_Python#Interfacing_with_NumPy)
but I got stucked when it comes to the writing-process.
Thats my code so far:

    x = garray.array()
    x.read("distance_raster")
    Density = garray.array()
    Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
    Density.write("Density")

The stats.norm.pdf is from the stats-scipy module. I get following
error when I try to process the script:

   Density.write("Density")
AttributeError: 'numpy.ndarray' object has no attribute
'write'

I don't know excactly what how I have to use the write command.

The write() method is part of garray.array, which is a subclass of
numpy.array (specifically, of numpy.memmap).

This line:

    Density = garray.array()

creates an instance of garray.array and associates the name "Density"
with it.

This line:

     Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

creates a normal numpy.array and associates the name "Density" with
it, replacing the original association. Consequently, Density.write()
fails because Density now refers to a numpy.array and not a
garray.array().

Rather than making the name Density refer to the resulting
numpy.array, you have to assign the resulting numpy.array *into* the
existing garray.array to which the name Density already refers, i.e.:

     Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

Note that the "..." (ellipsis) is literal. The above is equivalent to:

     Density[:,:] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

I am working on 6.5 and I read there were some problems with
numpy-arrays. Are the solved now?

I believe that the issue with grass.script.array requiring the 7.0
version of r.{in,out}.bin has been solved by backporting the changes
into 6.5.

--
Glynn Clements <glynn@gclements.plus.com>

3

Hello Glynn,
Hello Josef,

Thank you for your answer but I still get an error, although I changed the code
which is now:
    x = garray.array()
    x.read("distance_raster")
    Density = garray.array()
    Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
    Density.write("Density")

the error says:
   Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) +
(1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
  File "/Library/Frameworks/Python.framework/Versions/2.6/li
b/python2.6/site-packages/scipy/stats/distributions.py",
line 1104, in pdf
    x = arr((x-loc)*1.0/scale)
TypeError: unsupported operand type(s) for /:
'numpy.ndarray' and 'numpy.ndarray'

Propably it has something to do with the stats-norm function of scipy which is working
with numpy array (maybe not with the garray)..or what does that error mean?

PS: @ You once helped me with this scipy equation I now want to use within a python-GRASS-GIS script.
Transforming a raster-map into an array and apply the scipy-function on it and transform it back to a raster.
Maybe you have some ideas what is the problem...

Am 05.04.2011 um 19:43 schrieb Glynn Clements:

Johannes Radinger wrote:

I try to do a mapcalculation with scipy (do to limited functionality of
usual mapcalc functions.

Therefore I want to read a map into numpy-array, do the calculation
on it and write it back to a GRASS-map. I tried to follow the
instructions in the wiki
(http://grass.osgeo.org/wiki/GRASS_and_Python#Interfacing_with_NumPy)
but I got stucked when it comes to the writing-process.
Thats my code so far:

   x = garray.array()
   x.read("distance_raster")
   Density = garray.array()
   Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
   Density.write("Density")

The stats.norm.pdf is from the stats-scipy module. I get following
error when I try to process the script:

  Density.write("Density")
AttributeError: 'numpy.ndarray' object has no attribute
'write'

I don't know excactly what how I have to use the write command.

The write() method is part of garray.array, which is a subclass of
numpy.array (specifically, of numpy.memmap).

This line:

   Density = garray.array()

creates an instance of garray.array and associates the name "Density"
with it.

This line:

    Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

creates a normal numpy.array and associates the name "Density" with
it, replacing the original association. Consequently, Density.write()
fails because Density now refers to a numpy.array and not a
garray.array().

Rather than making the name Density refer to the resulting
numpy.array, you have to assign the resulting numpy.array *into* the
existing garray.array to which the name Density already refers, i.e.:

    Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

Note that the "..." (ellipsis) is literal. The above is equivalent to:

    Density[:,:] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

I am working on 6.5 and I read there were some problems with
numpy-arrays. Are the solved now?

I believe that the issue with grass.script.array requiring the 7.0
version of r.{in,out}.bin has been solved by backporting the changes
into 6.5.

--
Glynn Clements <glynn@gclements.plus.com>
_______________________________________________
grass-user mailing list
grass-user@lists.osgeo.org
http://lists.osgeo.org/mailman/listinfo/grass-user

4

Johannes Radinger wrote:

Thank you for your answer but I still get an error, although I changed the code
which is now:
    x = garray.array()
    x.read("distance_raster")
    Density = garray.array()
    Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
    Density.write("Density")

the error says:
   Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) +
(1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
  File "/Library/Frameworks/Python.framework/Versions/2.6/li
b/python2.6/site-packages/scipy/stats/distributions.py",
line 1104, in pdf
    x = arr((x-loc)*1.0/scale)
TypeError: unsupported operand type(s) for /:
'numpy.ndarray' and 'numpy.ndarray'

Propably it has something to do with the stats-norm function of scipy which is working
with numpy array (maybe not with the garray)..or what does that error mean?

garray.array is a subclass of numpy.memmap which itself is a subclass
of numpy.ndarray. You should be able to use a garray.array anywhere
you can use a numpy array.

But I don't think that has anything to do with the error message,
which suggests that both arguments are plain numpy arrays.

I can't even import scipy.stats here; possibly because SciPy is out of
date with respect to my Python version. I'll have another look when
I've updated SciPy.

--
Glynn Clements <glynn@gclements.plus.com>

5

Hello,

Am 06.04.2011 um 17:36 schrieb josef.pktd@gmail.com:

On Wed, Apr 6, 2011 at 10:58 AM, Johannes Radinger <JRadinger@gmx.at> wrote:

Hello Glynn,
Hello Josef,

Thank you for your answer but I still get an error, although I changed the code
which is now:
   x = garray.array()
   x.read("distance_raster")
   Density = garray.array()
   Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
   Density.write("Density")

the error says:
  Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) +
(1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
File "/Library/Frameworks/Python.framework/Versions/2.6/li
b/python2.6/site-packages/scipy/stats/distributions.py",
line 1104, in pdf
   x = arr((x-loc)*1.0/scale)
TypeError: unsupported operand type(s) for /:
'numpy.ndarray' and 'numpy.ndarray'

Propably it has something to do with the stats-norm function of scipy which is working
with numpy array (maybe not with the garray)..or what does that error mean?

I guess is that one of your variables doesn't have a type that is
numpy compatible (or defines division).
My guess is that the exception shows up too late in the code, I would
think there should be an asarray earlier in the
scipy.stats.distributions code. (If it's not then that might be a
bug.)

you could try np.asarray on all your variables and check which one has
not have been converted yet

O thank you for that, I didn't realize that the variables K and s weren't converted
into a float, they were still a string... so stupid from me that I didn't check that
before, I was only thinking about the input array(x)...It is now working!

anyway just some questions about the handling of NULL values. Like in that example:

   x = garray.array()
   x.read("distance_raster")
   Density = garray.array()
   Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
   Density.write("Density")

The distance_raster contains a lot of NULL-values. It seems that they are somehow transformed
into a real value (I don't now to which one exactly) because after the Scipy-calculation (Density[...] =)
and the rewrite process I a value of 0.00101776158703459 in every cell which was a NULL-cell before.

Two questions:

1) is it possible to exclude NULL values from calculation (to speed up the process)
2) What do I've to set that NULL cells remain NULL cells also after the processing?

/johannes

stats.norm.pdf(np.asarray(x), loc=np.asarray(m), scale=np.asarray(s1*K))

I don't know what methods garray.array() inherits or has, so I don't
know any specific answer.

Cheers,

Josef

PS: @ You once helped me with this scipy equation I now want to use within a python-GRASS-GIS script.
Transforming a raster-map into an array and apply the scipy-function on it and transform it back to a raster.
Maybe you have some ideas what is the problem...

Am 05.04.2011 um 19:43 schrieb Glynn Clements:

Johannes Radinger wrote:

I try to do a mapcalculation with scipy (do to limited functionality of
usual mapcalc functions.

Therefore I want to read a map into numpy-array, do the calculation
on it and write it back to a GRASS-map. I tried to follow the
instructions in the wiki
(http://grass.osgeo.org/wiki/GRASS_and_Python#Interfacing_with_NumPy)
but I got stucked when it comes to the writing-process.
Thats my code so far:

   x = garray.array()
   x.read("distance_raster")
   Density = garray.array()
   Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)
   Density.write("Density")

The stats.norm.pdf is from the stats-scipy module. I get following
error when I try to process the script:

  Density.write("Density")
AttributeError: 'numpy.ndarray' object has no attribute
'write'

I don't know excactly what how I have to use the write command.

The write() method is part of garray.array, which is a subclass of
numpy.array (specifically, of numpy.memmap).

This line:

   Density = garray.array()

creates an instance of garray.array and associates the name "Density"
with it.

This line:

    Density = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

creates a normal numpy.array and associates the name "Density" with
it, replacing the original association. Consequently, Density.write()
fails because Density now refers to a numpy.array and not a
garray.array().

Rather than making the name Density refer to the resulting
numpy.array, you have to assign the resulting numpy.array *into* the
existing garray.array to which the name Density already refers, i.e.:

    Density[...] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

Note that the "..." (ellipsis) is literal. The above is equivalent to:

    Density[:,:] = p * stats.norm.pdf(x,loc=m, scale=s1*K) + (1-p) * stats.norm.pdf(x, loc=m, scale=s2*K)

I am working on 6.5 and I read there were some problems with
numpy-arrays. Are the solved now?

I believe that the issue with grass.script.array requiring the 7.0
version of r.{in,out}.bin has been solved by backporting the changes
into 6.5.

--
Glynn Clements <glynn@gclements.plus.com>
_______________________________________________
grass-user mailing list
grass-user@lists.osgeo.org
http://lists.osgeo.org/mailman/listinfo/grass-user