[seek-dev] Re: garp tools

[Chad Berkley]

Hi Ricardo,

could you send me the AVENUE script that you use for 1a?  It's possible 
I can execute arcView from within kepler.  if not, i may rewrite it in 
GRASS or something else.

for 1b, creating the actor is trivial.  would you mind sending me a c++ 
implementation of the vb code?  if you don't have time (I know you're 
out of town), I can probably figure it out, but it would be more 
efficient for you to do it.

thanks,
chad

Pereira, Ricardo Scachetti wrote:
> 	Chad,
> 
> 	Here it is the expansion of "Layer Integration" step that is
> SPECIFIC to GARP nowadays.
> 	I'm assuming you are looking at the file
> /seek/projects/beam/niche-modeling/garp/GarpPipelineNative.jpg on CVS.
> Correct me if I'm wrong.
> 	In your current implementation of GARP pipeline in Kepler, you
> have already implemented the analytical steps (2), (3) and (4). Now you
> will implement A.S. #(1): "Env Layer cliping and resampling".
> 	Here is the procedure, broke down to smaller analytical steps.
> Let me know if you need something else.
> 
> 	
> ==================================================================
> 	1a) Layer clipping and resampling
> 
> 	Description:
> 		In this processing step, a set of environmental layers
> is clipped and resampled so they all have the same extent and cell size.
> 		It is assumed that all layers are stored in the same
> coordinate system.
> 		Currently, this step is executed inside ArcView 3.x
> using an AVENUE script. 
> 		Can be implemented in other GIS, but that will require
> development of other custom scripts that comply to GIS available API.
> 
> 	Inputs: 
> 		- LAYERS: set of environmental layers (files) that will
> be used in the modeling (in a format that your GIS API can read);
> 		- EXT: extent of the area of interest. Defined as 2 pair
> of coordinates, i.e., a (x, y) pair for upper-left corner and another
> for the bottom-right corner of the area of interest;
> 		- CS: cell size to be used in the analysis
> 
> 	Outputs:
> 		- set of layers in ESRI ASCII Raster Grid format, all
> with the same extent (EXT) and cell size (CS). Note: EXT and CS need to
> be exactly the same for all layers, to the last decimal digit!!
> 
> 
> 	Note: This step can probably be broken down to smaller pieces,
> but that will depend on the GIS API you are using.
> 
> 
> 	
> ==================================================================
> 	1b) Scaling of environmental layer values and packaging of GARP
> dataset
> 
> 	Description:
> 		In this step, each ASCII raster grid obtained in step 1a
> is converted to native GARP dataset format. Each layer has its cell
> values scaled to fit a byte. This is a requirement for the original GARP
> algorithm as designed by David Stockwell.
> 		Each layer has its maximum (max) and minimum (min) cell
> value extracted. The following expression is then applied to each of the
> layer cells:
> 
> 			scale_coeficient = (max - min) / 253;
> 			new_scaled_value = (int)( ( (original_value -
> min) / scale_coeficient) + 1);
> 
> 		The reverse operation is (just FYI): 			
> 		
> 			new_original_value = ( ( (double)
> new_scaled_value - 1) * scale_coeficient ) + min
> 
> 		After scaling occurs, the cell values assume values
> between 1 and 254 (0 and 255 are reserved values)
> 		This step is currently implemented in a separate Visual
> Basic application. Below there is the source code (in VB!!) that does
> the processing. I can translate it to C++ when you have the actor and
> the right method signitures (JNI) in place.
> 
> 	Input:
> 		- set of ASCII Raster grids from step 1a
> 
> 	Outputs:
> 		- a directory containing: i) the environmental layer
> scaled values (scaled to fit a byte), one .raw file per layer;
> 		- a GARP dataset file (.dxl) containing the description
> (original values, extent, etc) of each layer in the dataset.
> 
> 	
> ==================================================================
> 
> 
> 
> Visual Basic Code (extract from VB Application source code)
> 
> Dim m_oDS As GARPLib.CoEnvLayerSet  ' VB version of EnvLayerSet cpp
> object 
> Dim m_oLyr As GARPLib.CoEnvLayer    ' VB version of EnvLayer cpp object
> Dim strFile as String               ' ASCII Raster file name (without
> extention .asc)
> 
>     Set m_oLyr = CreateObject("Garp.EnvLayer")
>     m_oLyr.strId = strFile
>     m_oLyr.strTitle = strFile
>     m_oLyr.strFilename = ""
>     m_oLyr.strMatrixFilename = strFile & ".raw"
>     Call m_oLyr.useRawByteMatrixInDisk
>     Call m_oLyr.fromAsciiGrid(strFile * ".asc")
> 
>     If (LCase(strFile) <> "mask") Then
>         Call m_oDS.Add(m_oLyr)
>     Else
>         Call m_oDS.addAsMask(m_oLyr)
>     End If
> 
>     ' check for error: It will raise an error if extents or cell size 
>     ' of this layer is different from the other layers
>     If m_oDS.intLastErrorCode <> 0 Then
>         Call Err.Raise(1, "Ascii Raster Grid Batch Load", _
>                 "Could not add layer to the dataset """ & oFile.Name & _
>                 """ (Garp message: " & m_oDS.strLastErrorMessage & ")")
>     End If
> 
> 
> 
> 
>  
> 
> -----Original Message-----
> From: Chad Berkley [mailto:berkley at nceas.ucsb.edu] 
> Sent: Tuesday, January 20, 2004 12:47 PM
> To: Ricardo Scachetti Pereira
> Cc: seek-dev at ecoinformatics.org
> Subject: garp tools
> 
> Hi Ricardo (and others),
> 
> Now that I think that GARP is working from kepler, matt and I thought it
> would be a good idea to implement the tools necessary to go from raw
> data to the input formats that are in the example data files.  We would
> like to be able to implement a pipeline that goes from a digir (ecogrid)
> query to a garp prediction to rendered output.
> 
> What I need from you (and maybe deana as well) is to know exactly what
> this entails and if any of it is implemented in a way that I could
> harness in kepler or if I need to implement it.  I believe this process
> is what is grouped together under "Layer Integration" in the original
> ppt garp pipeline that came out of BEAM. Could you possibly expand
> "Layer Integration" so I know exactly what the steps are within that
> process?  Are any of these processes implemented in GeoTools or GRASS?
> 
> thanks,
> chad
> 
> 
> --
> -----------------------
> Chad Berkley
> National Center for
> Ecological Analysis
> and Synthesis (NCEAS)
> berkley at nceas.ucsb.edu
> -----------------------
> 


-- 
-----------------------
Chad Berkley
National Center for
Ecological Analysis
and Synthesis (NCEAS)
berkley at nceas.ucsb.edu
-----------------------