[GRASS-dev] how to sample a series at one location?

Fri Feb 22 11:53:35 PST 2013

Thanks Doug,

I knew I could do it with a script and v.what.rast.

What I was hoping was that there is a shortcut already usable in GRASS modules. Looks like the new temporal GIS tools may be able to do it.

Michael
______________________________
C. Michael Barton
Director, Center for Social Dynamics & Complexity
Professor of Anthropology, School of Human Evolution & Social Change
Arizona State University
Tempe, AZ  85287-2402
USA

voice:  480-965-6262 (SHESC), 480-727-9746 (CSDC)
fax:          480-965-7671(SHESC), 480-727-0709 (CSDC)
www:  http://csdc.asu.edu, http://shesc.asu.edu
http://www.public.asu.edu/~cmbarton

On Feb 22, 2013, at 12:31 PM, "Newcomb, Doug" <doug_newcomb at fws.gov<mailto:doug_newcomb at fws.gov>>
 wrote:

Michael,
You could use v.what.rast  in a python script , iterating the raster layers with an sqlite database back end.  I think that would go up to 2000 columns for each point you have.

Alternatively, you could use a bit of python with gdal.  I was trying to do something similar in GRASS, to change the Z value of each point in a text LiDAR file, from absolute above sea level to relative the elevation of the ground.  For 25.5 billion text points and a Statewide 20 ft elevation grid (6.5 ? billion cells) , it was a bit slow using r.what.  So I converted the LiDAR data to (7)  3.3 billion point  LAS format files and exported the GRASS layer to an Erdas imagine format file and wrote the following ugly python script:

#!/usr/bin/python
import os,string,glob,re,gdal
from liblas import file
from liblas import header
from liblas import point
from gdalconst import *
h=header.Header()
#enter the LAS point file name
infile=raw_input("Enter the input lidar data points file: ")
#Hardcoded edras imagine file, you will have to use an array for the different data layer names
imgfile="/gisdata2/raster/allnc_20ft_el.img"
#print "suggest /gisdata2/raster for output dir\n"
inarr=infile.split('.')
#This sets the LAS output file, substitute your output text file instead
outfil=inarr[0]+"_norm.las"
#outfil=raw_input("Enter output text file name: ")
#This part reads the LAS file, if you
l=file.File(infile,mode='r')
#Outputs the LAS file
lout=file.File(outfil,mode='w',header=h)
# register all of the drivers, hopefully your gdal speaks GRASS
gdal.AllRegister()
#opening and closing the image layers might take some time if you are reading thousands of images
ds=gdal.Open(imgfile,GA_ReadOnly)
if ds is None:
    print 'Could not open image'
    sys.exit(1)
# get image size
rows = ds.RasterYSize
cols = ds.RasterXSize
bands = ds.RasterCount
# get georeference info, not sure how this would work for GRASS data layers
transform = ds.GetGeoTransform()
xOrigin = transform[0]
yOrigin = transformAsArray(xOffset, yOffset, 1, 1)
pixelWidth = transform[1]
pixelHeight = transform[5]
for p in l:
    x=float(p.x)
    y=float(p.y)
    z=float(p.z)
    # compute pixel offset
    xOffset = int((x - xOrigin) / pixelWidth)
    yOffset = int((y - yOrigin) / pixelHeight)
    band = ds.GetRasterBand(1) # 1-based index 0? 1?
    data = band.Readr(value) :continue
    value = data[0,0]
    #print value,"11","\n"
    if "nan" in st[3]
    znorm = z-value
    #print znorm,"\n"
    pt=point.Point()
    pt.x=p.x
    pt.y=p.y
    pt.z=znorm
    lout.write(pt)

l.close()
lout.close()
#25561312019 points in allreturns

This managed to process everything over a weekend( in 7 parallel threads), which was fast enough for me at the time.  Approaching your problem , if your data layers are all n GRASS and your version of gdal can read GRASS data layers,  I would grab the list of GRASS layers via glob and iterate the layers , writing the name of the raster layer and the value of the raster layer at the point coordinates out to a text file as you state below.

Hope this helps,
Doug

On Fri, Feb 22, 2013 at 1:23 PM, Michael Barton <Michael.Barton at asu.edu<mailto:Michael.Barton at asu.edu>> wrote:
But I want to do it with a time series of hundreds or thousands of maps.

Michael
______________________________
C. Michael Barton
Director, Center for Social Dynamics & Complexity
Professor of Anthropology, School of Human Evolution & Social Change
Arizona State University
Tempe, AZ  85287-2402
USA

voice:  480-965-6262 (SHESC), 480-727-9746 (CSDC)
fax:          480-965-7671(SHESC), 480-727-0709 (CSDC)
www:    http://csdc.asu.edu<http://csdc.asu.edu/>, http://shesc.asu.edu<http://shesc.asu.edu/>
                http://www.public.asu.edu/~cmbarton

On Feb 22, 2013, at 10:53 AM, Markus Neteler <neteler at osgeo.org<mailto:neteler at osgeo.org>>
 wrote:

> On Fri, Feb 22, 2013 at 6:41 PM, Michael Barton <Michael.Barton at asu.edu<mailto:Michael.Barton at asu.edu>> wrote:
>> Is there tool somewhere, including in the new temporal GIS modules, to
>> sample the value of a raster series at one cell location? I'd like to get
>> text something like this for a cell that I specify with xy coordinates or a
>> cat:
>>
>> map1, value 1
>> map2, value 2
>> map3, value 3
>> map4, value 4
>> map5, value 5
>> …
>>
>
> I do such queries with r.what which accepts multiple input:
>
> http://grass.osgeo.org/grass64/manuals/r.what.html
>
> Markus

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--
Doug Newcomb
USFWS
Raleigh, NC
919-856-4520 ext. 14 doug_newcomb at fws.gov<mailto:doug_newcomb at fws.gov>
---------------------------------------------------------------------------------------------------------
The opinions I express are my own and are not representative of the official policy of the U.S.Fish and Wildlife Service or Dept. of the Interior.   Life is too short for undocumented, proprietary data formats.

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