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+#!/usr/bin/env python
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+
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+"""
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+MODULE: v.krige
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+
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+AUTHOR(S): Anne Ghisla <a.ghisla AT gmail.com>
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+
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+PURPOSE: Performs ordinary or block kriging
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+
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+DEPENDS: R 2.x, packages gstat and spgrass6, optional: automap
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+
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+COPYRIGHT: (C) 2009 by the GRASS Development Team
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+
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+This program is free software under the GNU General Public
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+License (>=v2). Read the file COPYING that comes with GRASS
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+for details.
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+"""
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+
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+## g.parser informations
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+
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+#%module
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+#% description: Performs ordinary or block kriging.
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+#% keywords: vector, interpolation, kriging
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+#%end
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+
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+#%option
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+#% key: input
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+#% type: string
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+#% gisprompt: old,vector,vector
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+#% description: Name of point vector map containing sample data
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+#% required: yes
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+#%end
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+#%option
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+#% key: column
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+#% type: string
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+#% gisprompt: old,dbcolumn,dbcolumn
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+#% description: Name of attribute column with numerical value to be interpolated
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+#% required : yes
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+#%end
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+#%option
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+#% key: output
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+#% type: string
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+#% gisprompt: new,cell,raster
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+#% label: Name for output raster map
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+#% description: If omitted, will be <input name>_kriging
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+#% required : no
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+#%end
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+#%option
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+#% key: package
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+#% type: string
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+#% options: gstat
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+#% answer: gstat
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+#% description: R package to use
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+#% required: no
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+#%end
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+#%option
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+#% key: model
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+#% type: string
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+#% options: Exp,Sph,Gau,Mat,Lin
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+#% multiple: yes
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+#% label: Variogram model(s)
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+#% description: Leave empty to test all models (requires automap)
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+#% required: no
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+#%end
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+#%option
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+#% key: block
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+#% type: integer
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+#% multiple: no
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+#% label: Block size (square block)
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+#% description: Block size. Used by block kriging.
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+#% required: no
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+#%end
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+#%option
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+#% key: range
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+#% type: integer
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+#% label: Range value
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+#% description: Automatically fixed if not set
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+#% required : no
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+#%end
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+#%option
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+#% key: nugget
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+#% type: integer
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+#% label: Nugget value
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+#% description: Automatically fixed if not set
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+#% required : no
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+#%end
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+#%option
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+#% key: sill
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+#% type: integer
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+#% label: Sill value
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+#% description: Automatically fixed if not set
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+#% required : no
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+#%end
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+#%option
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+#% key: output_var
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+#% type: string
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+#% gisprompt: new,cell,raster
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+#% label: Name for output variance raster map
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+#% description: If omitted, will be <input name>_kriging_var
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+#% required : no
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+#%end
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+
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+import os, sys
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+from tempfile import gettempdir
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+import time
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+import thread
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+
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+GUIModulesPath = os.path.join(os.getenv("GISBASE"), "etc", "wxpython", "gui_modules")
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+sys.path.append(GUIModulesPath)
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+GUIPath = os.path.join(os.getenv("GISBASE"), "etc", "wxpython")
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+sys.path.append(GUIPath)
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+
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+import globalvar
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+if not os.getenv("GRASS_WXBUNDLED"):
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+ globalvar.CheckForWx()
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+import gselect
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+import goutput
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+import menuform
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+#import help
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+
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+import wx
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+import wx.lib.flatnotebook as FN
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+import wx.lib.plot as plot # for plotting the variogram.
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+
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+### i18N
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+import gettext
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+gettext.install('grasswxpy', os.path.join(os.getenv("GISBASE"), 'locale'), unicode = True)
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+
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+### dependencies to be checked once, as they are quite time-consuming. cfr. grass.parser.
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+# GRASS binding
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+try:
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+ import grass.script as grass
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+except ImportError:
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+ sys.exit(_("No GRASS-python library found."))
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+
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+# move other checks in functions, as R?
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+
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+# globals
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+maxint = 1e6 # instead of sys.maxint, not working with SpinCtrl on 64bit [reported by Bob Moskovitz]
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+Region = grass.region()
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+Command = None
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+InputData = None
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+Variogram = None
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+VariogramFunction = None
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+robjects = None
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+rinterface = None
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+
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+#classes in alphabetical order. methods in logical order :)
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+
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+class Controller():
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+ """ Executes analysis. For the moment, only with gstat functions."""
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+
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+ def ImportMap(self, map, column):
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+ """ Adds x,y columns to the GRASS map and then imports it in R.
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+ Checks for NULL values in the provided column and exits if they are present."""
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+ #@NOTE: it alters original data. Is it correct? Shall I remove those columns
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+ # if they were absent from original data?
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+ cols = grass.vector_columns(map = map, layer = 1)
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+ if not cols.has_key('x') and not cols.has_key('y'):
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+ grass.run_command('v.db.addcolumn', map = map,
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+ columns = 'x double precision, y double precision')
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+ grass.run_command('v.to.db', map = map, option = 'coor', col = 'x,y')
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+ nulls = int(grass.parse_command('v.univar', map = map, column = column, type = 'point', \
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+ parse = (grass.parse_key_val, \
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+ {'sep':': '}))['number of NULL attributes'])
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+ if nulls > 0:
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+ grass.fatal(_("%d NULL value(s) in the selected column - unable to perform kriging.") % nulls)
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+ return robjects.r.readVECT6(map, type = 'point')
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+
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+ def CreateGrid(self, inputdata):
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+ Grid = robjects.r.gmeta2grd()
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+
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+ # addition of coordinates columns into dataframe.
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+ coordinatesDF = robjects.r['as.data.frame'](robjects.r.coordinates(Grid))
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+ data = robjects.r['data.frame'](x = coordinatesDF.r['s1'][0],
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+ y = coordinatesDF.r['s2'][0],
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+ k = robjects.r.rep(1, Region['cols']*Region['rows']))
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+ GridPredicted = robjects.r.SpatialGridDataFrame(Grid,
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+ data,
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+ proj4string = robjects.r.CRS(robjects.r.proj4string(inputdata)))
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+ return GridPredicted
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+
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+ def ComposeFormula(self, column, isblock, inputdata):
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+ if isblock is True:
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+ predictor = 'x+y'
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+ else:
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+ predictor = 1
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+ Formula = robjects.r['as.formula'](robjects.r.paste(column, "~", predictor))
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+ #print Formula
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+ return Formula
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+
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+ def FitVariogram(self, formula, inputdata, sill, nugget, range, model = ''):
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+ """ Fits variogram either automagically either specifying all parameters.
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+ Returns a list containing data and model variograms. """
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+
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+ Variograms = {}
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+
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+ if model is '':
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+ robjects.r.require('automap')
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+ DottedParams = {}
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+ #print (nugget.r_repr(), sill, range)
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+ DottedParams['fix.values'] = robjects.r.c(nugget, range, sill)
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+
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+ VariogramModel = robjects.r.autofitVariogram(formula, inputdata, **DottedParams)
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+ #print robjects.r.warnings()
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+ Variograms['datavariogram'] = VariogramModel.r['exp_var'][0]
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+ Variograms['variogrammodel'] = VariogramModel.r['var_model'][0]
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+ # obtain the model name. *Too* complicated to get the string instead of level, unlike R does.
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+ VariogramAsDF = robjects.r['as.data.frame'](VariogramModel.r['var_model'][0]) # force conversion
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+ ModelDF = VariogramAsDF.r['model'][0]
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+ Variograms['model'] = robjects.r.levels(ModelDF).subset(ModelDF[1])[0]
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+ else:
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+ DataVariogram = robjects.r['variogram'](formula, inputdata)
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+ VariogramModel = robjects.r['fit.variogram'](DataVariogram,
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+ model = robjects.r.vgm(psill = sill,
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+ model = model,
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+ nugget = nugget,
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+ range = range))
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+ Variograms['datavariogram'] = DataVariogram
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+ Variograms['variogrammodel'] = VariogramModel
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+ Variograms['model'] = model
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+ return Variograms
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+
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+ def DoKriging(self, formula, inputdata, grid, model, block):
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+ DottedParams = {'debug.level': -1} # let krige() print percentage status
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+ if block is not '': #@FIXME(anne): but it's a string!! and krige accepts it!!
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+ DottedParams['block'] = block
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+ #print DottedParams
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+ KrigingResult = robjects.r.krige(formula, inputdata, grid, model, **DottedParams)
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+ return KrigingResult
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+
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+ def ExportMap(self, map, column, name, overwrite, command, variograms):
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+ # add kriging parameters to raster map history
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+ robjects.r.writeRAST6(map, vname = name, zcol = column, overwrite = overwrite)
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+ grass.run_command('r.support',
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+ map = name,
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+ title = 'Kriging output',
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+ history = 'Issued from command v.krige ' + command)
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+ if command.find('model') is -1: # if the command has no model option, add automap chosen model
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+ grass.run_command('r.support',
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+ map = name,
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+ history = 'Model chosen by automatic fitting: ' + variograms['model'])
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+
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+ def Run(self, input, column, output, package, sill, nugget, range, logger, \
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+ overwrite, model, block, output_var, command, **kwargs):
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+ """ Wrapper for all functions above. """
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+ logger.message(_("Processing %d cells. Computing time raises exponentially with resolution." % Region['cells']))
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+ logger.message(_("Importing data..."))
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+ if globals()["InputData"] is None:
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+ globals()["InputData"] = self.ImportMap(input, column)
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+ # and from here over, InputData refers to the global variable
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+ #print(robjects.r.slot(InputData, 'data').names)
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+ logger.message(_("Data successfully imported."))
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+
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+ GridPredicted = self.CreateGrid(InputData)
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+
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+ logger.message(_("Fitting variogram..."))
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+ isblock = block is not ''
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+ Formula = self.ComposeFormula(column, isblock, InputData)
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+ if globals()["Variogram"] is None:
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+ globals()["Variogram"] = self.FitVariogram(Formula,
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+ InputData,
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+ model = model,
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+ sill = sill,
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+ nugget = nugget,
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+ range = range)
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+ logger.message(_("Variogram fitted."))
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+
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+ logger.message(_("Kriging..."))
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+ KrigingResult = self.DoKriging(Formula, InputData, GridPredicted, Variogram['variogrammodel'], block) # using global ones
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+ logger.message(_("Kriging performed."))
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+
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+ self.ExportMap(map = KrigingResult,
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+ column='var1.pred',
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+ name = output,
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+ overwrite = overwrite,
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+ command = command,
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+ variograms = Variogram)
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+ if output_var is not '':
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+ self.ExportMap(map = KrigingResult,
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+ column='var1.var',
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+ name = output_var,
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+ overwrite = overwrite,
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+ command = command,
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+ variograms = Variogram)
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+
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+class KrigingPanel(wx.Panel):
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+ """ Main panel. Contains all widgets except Menus and Statusbar. """
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+ def __init__(self, parent, *args, **kwargs):
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+ wx.Panel.__init__(self, parent, *args, **kwargs)
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+
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+ self.parent = parent
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+ self.border = 4
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+
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+ # 1. Input data
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+ InputBoxSizer = wx.StaticBoxSizer(wx.StaticBox(self, id = wx.ID_ANY, label = _("Input Data")),
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+ orient = wx.HORIZONTAL)
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+
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+ flexSizer = wx.FlexGridSizer(cols = 3, hgap = 5, vgap = 5)
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+ flexSizer.AddGrowableCol(1)
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+
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+ flexSizer.Add(item = wx.StaticText(self, id = wx.ID_ANY, label = _("Point dataset:")),
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+ flag = wx.ALIGN_CENTER_VERTICAL)
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+ self.InputDataMap = gselect.VectorSelect(parent = self,
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+ ftype = 'points',
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+ updateOnPopup = False)
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+ self.InputDataMap.SetFocus()
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+ flexSizer.Add(item = self.InputDataMap, flag = wx.ALIGN_CENTER_VERTICAL)
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+
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+ RefreshButton = wx.Button(self, id = wx.ID_REFRESH)
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+ RefreshButton.Bind(wx.EVT_BUTTON, self.OnButtonRefresh)
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+ flexSizer.Add(item = RefreshButton, flag = wx.ALIGN_CENTER_VERTICAL)
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+
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+ flexSizer.Add(item = wx.StaticText(self, id = wx.ID_ANY, label = _("Numeric column:")),
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+ flag = wx.ALIGN_CENTER_VERTICAL)
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+ self.InputDataColumn = gselect.ColumnSelect(self, id = wx.ID_ANY)
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+ self.InputDataColumn.SetSelection(0)
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+ flexSizer.Add(item = self.InputDataColumn)
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+
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+ self.InputDataMap.GetChildren()[0].Bind(wx.EVT_TEXT, self.OnInputDataChanged)
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+
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+ InputBoxSizer.Add(item = flexSizer)
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+
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+ # 2. Kriging. In book pages one for each R package. Includes variogram fit.
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+ KrigingSizer = wx.StaticBoxSizer(wx.StaticBox(self, id = wx.ID_ANY, label = _("Kriging")), wx.HORIZONTAL)
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+
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+ self.RPackagesBook = FN.FlatNotebook(parent = self, id = wx.ID_ANY,
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+ style = FN.FNB_BOTTOM |
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+ FN.FNB_NO_NAV_BUTTONS |
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+ FN.FNB_FANCY_TABS | FN.FNB_NO_X_BUTTON)
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+
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+ for Rpackage in ["gstat"]: # , "geoR"]: #@TODO: enable it if/when it'll be implemented.
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+ self.CreatePage(package = Rpackage)
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+
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+ ## Command output. From menuform module, cmdPanel class
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+ self.goutput = goutput.GMConsole(parent = self, margin = False,
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+ pageid = self.RPackagesBook.GetPageCount(),
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+ notebook = self.RPackagesBook)
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+ self.goutputId = self.RPackagesBook.GetPageCount()
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+ self.outpage = self.RPackagesBook.AddPage(self.goutput, text = _("Command output"))
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+
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+ self.RPackagesBook.SetSelection(0)
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+ KrigingSizer.Add(self.RPackagesBook, proportion = 1, flag = wx.EXPAND)
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+
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+ # 3. Output Parameters.
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+ OutputSizer = wx.StaticBoxSizer(wx.StaticBox(self, id = wx.ID_ANY, label = _("Output")), wx.HORIZONTAL)
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+
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+ OutputParameters = wx.GridBagSizer(hgap = 5, vgap = 5)
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+ OutputParameters.AddGrowableCol(1)
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+ OutputParameters.Add(item = wx.StaticText(self, id = wx.ID_ANY, label = _("Name for the output raster map:")),
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+ flag = wx.ALIGN_CENTER_VERTICAL,
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+ pos = (0, 0))
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+ self.OutputMapName = gselect.Select(parent = self, id = wx.ID_ANY,
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+ type = 'raster',
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+ mapsets = [grass.gisenv()['MAPSET']])
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+ OutputParameters.Add(item = self.OutputMapName, flag = wx.EXPAND | wx.ALL,
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+ pos = (0, 1))
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+ self.VarianceRasterCheckbox = wx.CheckBox(self, id = wx.ID_ANY, label = _("Export variance map as well: "))
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+ self.VarianceRasterCheckbox.SetValue(state = True)
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+ OutputParameters.Add(item = self.VarianceRasterCheckbox,
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+ flag = wx.ALIGN_CENTER_VERTICAL,
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+ pos = (1, 0))
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+ self.OutputVarianceMapName = gselect.Select(parent = self, id = wx.ID_ANY,
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+ type = 'raster',
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+ mapsets = [grass.gisenv()['MAPSET']])
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+ self.VarianceRasterCheckbox.Bind(wx.EVT_CHECKBOX, self.OnVarianceCBChecked)
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+ OutputParameters.Add(item = self.OutputVarianceMapName, flag = wx.EXPAND | wx.ALL,
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+ pos = (1, 1))
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|
+
|
|
|
+ self.OverwriteCheckBox = wx.CheckBox(self, id = wx.ID_ANY,
|
|
|
+ label = _("Allow output files to overwrite existing files"))
|
|
|
+ self.OverwriteCheckBox.SetValue(state = False)
|
|
|
+ OutputParameters.Add(item = self.OverwriteCheckBox,
|
|
|
+ pos = (2, 0), span = (1, 2))
|
|
|
+
|
|
|
+ OutputSizer.Add(OutputParameters, proportion = 0, flag = wx.EXPAND | wx.ALL, border = self.border)
|
|
|
+
|
|
|
+ # 4. Run Button and Quit Button
|
|
|
+ ButtonSizer = wx.BoxSizer(wx.HORIZONTAL)
|
|
|
+ HelpButton = wx.Button(self, id = wx.ID_HELP)
|
|
|
+ HelpButton.Bind(wx.EVT_BUTTON, self.OnHelpButton)
|
|
|
+ QuitButton = wx.Button(self, id = wx.ID_EXIT)
|
|
|
+ QuitButton.Bind(wx.EVT_BUTTON, self.OnCloseWindow)
|
|
|
+ self.RunButton = wx.Button(self, id = wx.ID_ANY, label = _("&Run")) # no stock ID for Run button..
|
|
|
+ self.RunButton.Bind(wx.EVT_BUTTON, self.OnRunButton)
|
|
|
+ self.RunButton.Enable(False) # disable it on loading the interface, as input map is not set
|
|
|
+ ButtonSizer.Add(HelpButton, proportion = 0, flag = wx.ALIGN_LEFT | wx.ALL, border = self.border)
|
|
|
+ ButtonSizer.Add(QuitButton, proportion = 0, flag = wx.ALIGN_RIGHT | wx.ALL, border = self.border)
|
|
|
+ ButtonSizer.Add(self.RunButton, proportion = 0, flag = wx.ALIGN_RIGHT | wx.ALL, border = self.border)
|
|
|
+
|
|
|
+ # Main Sizer. Add each child sizer as soon as it is ready.
|
|
|
+ Sizer = wx.BoxSizer(wx.VERTICAL)
|
|
|
+ Sizer.Add(InputBoxSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = self.border)
|
|
|
+ Sizer.Add(KrigingSizer, proportion = 1, flag = wx.EXPAND | wx.ALL, border = self.border)
|
|
|
+ Sizer.Add(OutputSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = self.border)
|
|
|
+ Sizer.Add(ButtonSizer, proportion = 0, flag = wx.ALIGN_RIGHT | wx.ALL, border = self.border)
|
|
|
+ self.SetSizerAndFit(Sizer)
|
|
|
+
|
|
|
+ # last action of __init__: update imput data list.
|
|
|
+ # it's performed in the few seconds gap while user examines interface before clicking anything.
|
|
|
+ #@TODO: implement a splashcreen IF the maps cause a noticeable lag [markus' suggestion]
|
|
|
+ self.InputDataMap.GetElementList()
|
|
|
+
|
|
|
+ def CreatePage(self, package):
|
|
|
+ """ Creates the three notebook pages, one for each R package """
|
|
|
+ for package in ["gstat"]:
|
|
|
+ classobj = eval("RBook"+package+"Panel")
|
|
|
+ setattr(self, "RBook"+package+"Panel", (classobj(self, id = wx.ID_ANY)))
|
|
|
+ self.RPackagesBook.AddPage(page = getattr(self, "RBook"+package+"Panel"), text = package)
|
|
|
+
|
|
|
+ def OnButtonRefresh(self, event):
|
|
|
+ """ Forces refresh of list of available layers. """
|
|
|
+ self.InputDataMap.GetElementList()
|
|
|
+
|
|
|
+ def OnCloseWindow(self, event):
|
|
|
+ """ Cancel button pressed"""
|
|
|
+ self.parent.Close()
|
|
|
+ event.Skip()
|
|
|
+
|
|
|
+ def OnHelpButton(self, event):
|
|
|
+ # file = os.path.join(os.getenv("GISBASE"), "docs", "html", "v.krige.html")
|
|
|
+ # file = os.path.join(os.path.curdir, "description.html")
|
|
|
+ # @TODO fix HelpWindow
|
|
|
+ # helpFrame = help.HelpWindow(parent=self, id=wx.ID_ANY,
|
|
|
+ # title=_("GRASS - Help page for v.krige"),
|
|
|
+ # size=(640, 480),
|
|
|
+ # file=file)
|
|
|
+ # helpFrame.Show(True)
|
|
|
+
|
|
|
+ grass.run_command('g.manual', entry = 'v.krige')
|
|
|
+
|
|
|
+ event.Skip()
|
|
|
+
|
|
|
+ def OnInputDataChanged(self, event):
|
|
|
+ """ Refreshes list of columns and fills output map name TextCtrl """
|
|
|
+ MapName = event.GetString()
|
|
|
+ self.InputDataColumn.InsertColumns(vector = MapName,
|
|
|
+ layer = 1, excludeKey = True,
|
|
|
+ type = ['integer', 'double precision'])
|
|
|
+ self.InputDataColumn.SetSelection(0)
|
|
|
+ self.RunButton.Enable(self.InputDataColumn.GetSelection() is not -1)
|
|
|
+ self.RBookgstatPanel.PlotButton.Enable(self.InputDataColumn.GetSelection() is not -1)
|
|
|
+
|
|
|
+ if self.InputDataColumn.GetSelection() is not -1:
|
|
|
+ self.OutputMapName.SetValue(MapName.split("@")[0]+"_kriging")
|
|
|
+ self.OutputVarianceMapName.SetValue(MapName.split("@")[0]+"_kriging_var")
|
|
|
+ else:
|
|
|
+ self.OutputMapName.SetValue('')
|
|
|
+ self.OutputVarianceMapName.SetValue('')
|
|
|
+
|
|
|
+ def OnRunButton(self,event):
|
|
|
+ """ Execute R analysis. """
|
|
|
+ #@FIXME: send data to main method instead of running it here.
|
|
|
+
|
|
|
+ #-1: get the selected notebook page. The user shall know that [s]he can modify settings in all
|
|
|
+ # pages, but only the selected one will be executed when Run is pressed.
|
|
|
+ SelectedPanel = self.RPackagesBook.GetCurrentPage()
|
|
|
+
|
|
|
+ if self.RPackagesBook.GetPageText(self.RPackagesBook.GetSelection()) == 'Command output':
|
|
|
+ self.goutput.WriteError("No parameters for running. Please select \"gstat\" tab, check parameters and re-run.")
|
|
|
+ return False # no break invoked by above function
|
|
|
+
|
|
|
+ # mount command string as it would have been written on CLI
|
|
|
+ command = ["v.krige", "input=" + self.InputDataMap.GetValue(),
|
|
|
+ "column=" + self.InputDataColumn.GetValue(),
|
|
|
+ "output=" + self.OutputMapName.GetValue(),
|
|
|
+ "package=" + '%s' % self.RPackagesBook.GetPageText(self.RPackagesBook.GetSelection())]
|
|
|
+
|
|
|
+ if not hasattr(SelectedPanel, 'VariogramCheckBox') or not SelectedPanel.VariogramCheckBox.IsChecked():
|
|
|
+ command.append("model=" + '%s' % SelectedPanel.ModelChoicebox.GetStringSelection().split(" ")[0])
|
|
|
+
|
|
|
+ for i in ['Sill', 'Nugget', 'Range']:
|
|
|
+ if getattr(SelectedPanel, i+"ChextBox").IsChecked():
|
|
|
+ command.append(i.lower() + "=" + '%s' % getattr(SelectedPanel, i+'Ctrl').GetValue())
|
|
|
+
|
|
|
+ if SelectedPanel.KrigingRadioBox.GetStringSelection() == "Block kriging":
|
|
|
+ command.append("block=" + '%s' % SelectedPanel.BlockSpinBox.GetValue())
|
|
|
+ if self.OverwriteCheckBox.IsChecked():
|
|
|
+ command.append("--overwrite")
|
|
|
+ if self.VarianceRasterCheckbox.IsChecked():
|
|
|
+ command.append("output_var=" + self.OutputVarianceMapName.GetValue())
|
|
|
+
|
|
|
+ # give it to the output console
|
|
|
+ #@FIXME: it runs the command as a NEW instance. Reimports data, recalculates variogram fit..
|
|
|
+ #otherwise I can use Controller() and mimic RunCmd behaviour.
|
|
|
+ self.goutput.RunCmd(command, switchPage = True)
|
|
|
+
|
|
|
+ def OnVarianceCBChecked(self, event):
|
|
|
+ self.OutputVarianceMapName.Enable(event.IsChecked())
|
|
|
+
|
|
|
+class KrigingModule(wx.Frame):
|
|
|
+ """ Kriging module for GRASS GIS. Depends on R and its packages gstat and geoR. """
|
|
|
+ def __init__(self, parent, *args, **kwargs):
|
|
|
+ wx.Frame.__init__(self, parent, *args, **kwargs)
|
|
|
+ # setting properties and all widgettery
|
|
|
+ self.SetTitle(_("Kriging Module"))
|
|
|
+ self.SetIcon(wx.Icon(os.path.join(globalvar.ETCICONDIR, 'grass_dialog.ico'), wx.BITMAP_TYPE_ICO))
|
|
|
+ self.log = Log(self)
|
|
|
+ self.CreateStatusBar()
|
|
|
+ self.log.message(_("Ready."))
|
|
|
+
|
|
|
+ self.Panel = KrigingPanel(self)
|
|
|
+ self.SetMinSize(self.GetBestSize())
|
|
|
+ self.SetSize(self.GetBestSize())
|
|
|
+
|
|
|
+class Log:
|
|
|
+ """ The log output is redirected to the status bar of the containing frame. """
|
|
|
+ def __init__(self, parent):
|
|
|
+ self.parent = parent
|
|
|
+
|
|
|
+ def message(self, text_string):
|
|
|
+ """ Updates status bar """
|
|
|
+ self.parent.SetStatusText(text_string.strip())
|
|
|
+
|
|
|
+class RBookPanel(wx.Panel):
|
|
|
+ """ Generic notebook page with shared widgets and empty kriging functions. """
|
|
|
+ def __init__(self, parent, *args, **kwargs):
|
|
|
+ wx.Panel.__init__(self, parent, *args, **kwargs)
|
|
|
+
|
|
|
+ self.parent = parent
|
|
|
+
|
|
|
+ self.VariogramSizer = wx.StaticBoxSizer(wx.StaticBox(self,
|
|
|
+ id = wx.ID_ANY,
|
|
|
+ label = _("Variogram fitting")),
|
|
|
+ wx.HORIZONTAL)
|
|
|
+ self.LeftSizer = wx.BoxSizer(wx.VERTICAL)
|
|
|
+ self.RightSizer = wx.BoxSizer(wx.VERTICAL)
|
|
|
+ self.ParametersSizer = wx.GridBagSizer(vgap = 5, hgap = 5)
|
|
|
+
|
|
|
+ self.VariogramSizer.Add(self.LeftSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+ self.VariogramSizer.Add(self.RightSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+
|
|
|
+ # left side of Variogram fitting. The checkboxes and spinctrls.
|
|
|
+ self.PlotButton = wx.Button(self, id = wx.ID_ANY, label = _("Plot/refresh variogram")) # no stock ID for Run button..
|
|
|
+ self.PlotButton.Bind(wx.EVT_BUTTON, self.OnPlotButton)
|
|
|
+ self.PlotButton.Enable(False) # grey it out until a suitable layer is available
|
|
|
+ self.LeftSizer.Add(self.PlotButton, proportion = 0, flag = wx.ALL, border = parent.border)
|
|
|
+ self.LeftSizer.Add(self.ParametersSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+
|
|
|
+ self.ParametersList = ["Sill", "Nugget", "Range"]
|
|
|
+ MinValues = [0,0,1]
|
|
|
+ for n in self.ParametersList:
|
|
|
+ setattr(self, n+"ChextBox", wx.CheckBox(self,
|
|
|
+ id = self.ParametersList.index(n),
|
|
|
+ label = _(n + ":")))
|
|
|
+ setattr(self, n+"Ctrl", (wx.SpinCtrl(self,
|
|
|
+ id = wx.ID_ANY,
|
|
|
+ min = MinValues[self.ParametersList.index(n)],
|
|
|
+ max = maxint)))
|
|
|
+ getattr(self, n+"ChextBox").Bind(wx.EVT_CHECKBOX,
|
|
|
+ self.UseValue,
|
|
|
+ id = self.ParametersList.index(n))
|
|
|
+ setattr(self, n+"Sizer", (wx.BoxSizer(wx.HORIZONTAL)))
|
|
|
+ self.ParametersSizer.Add(getattr(self, n+"ChextBox"),
|
|
|
+ flag = wx.ALIGN_CENTER_VERTICAL,
|
|
|
+ pos = (self.ParametersList.index(n),0))
|
|
|
+ self.ParametersSizer.Add(getattr(self, n+"Ctrl"),
|
|
|
+ flag = wx.EXPAND | wx.ALIGN_CENTER_VERTICAL,
|
|
|
+ pos = (self.ParametersList.index(n),1))
|
|
|
+
|
|
|
+ # right side of the Variogram fitting. The plot area.
|
|
|
+ #Plot = wx.StaticText(self, id= wx.ID_ANY, label = "Check Plot Variogram to interactively fit model.")
|
|
|
+ #PlotPanel = wx.Panel(self)
|
|
|
+ #self.PlotArea = plot.PlotCanvas(PlotPanel)
|
|
|
+ #self.PlotArea.SetInitialSize(size = (250,250))
|
|
|
+ #self.RightSizer.Add(PlotPanel, proportion=0, flag= wx.EXPAND|wx.ALL, border=parent.border)
|
|
|
+
|
|
|
+ self.KrigingSizer = wx.StaticBoxSizer(wx.StaticBox(self,
|
|
|
+ id = wx.ID_ANY,
|
|
|
+ label = _("Kriging techniques")),
|
|
|
+ wx.VERTICAL)
|
|
|
+
|
|
|
+ KrigingList = ["Ordinary kriging", "Block kriging"]#, "Universal kriging"] #@FIXME: i18n on the list?
|
|
|
+ self.KrigingRadioBox = wx.RadioBox(self,
|
|
|
+ id = wx.ID_ANY,
|
|
|
+ choices = KrigingList,
|
|
|
+ majorDimension = 1,
|
|
|
+ style = wx.RA_SPECIFY_COLS)
|
|
|
+ self.KrigingRadioBox.Bind(wx.EVT_RADIOBOX, self.HideBlockOptions)
|
|
|
+ self.KrigingSizer.Add(self.KrigingRadioBox, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+
|
|
|
+ # block kriging parameters. Size.
|
|
|
+ BlockSizer = wx.BoxSizer(wx.HORIZONTAL)
|
|
|
+ BlockLabel = wx.StaticText(self, id = wx.ID_ANY, label = _("Block size:"))
|
|
|
+ self.BlockSpinBox = wx.SpinCtrl(self, id = wx.ID_ANY, min = 1, max = maxint)
|
|
|
+ self.BlockSpinBox.Enable(False) # default choice is Ordinary kriging so block param is disabled
|
|
|
+ BlockSizer.Add(BlockLabel, flag = wx.ALIGN_CENTER_VERTICAL | wx.ALL, border = parent.border)
|
|
|
+ BlockSizer.Add(self.BlockSpinBox, flag = wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, border = parent.border)
|
|
|
+ self.KrigingSizer.Add(BlockSizer, flag = wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL, border = parent.border)
|
|
|
+
|
|
|
+ self.Sizer = wx.BoxSizer(wx.VERTICAL)
|
|
|
+ self.Sizer.Add(self.VariogramSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+ self.Sizer.Add(self.KrigingSizer, proportion = 0, flag = wx.EXPAND | wx.ALL, border = parent.border)
|
|
|
+
|
|
|
+ def HideBlockOptions(self, event):
|
|
|
+ self.BlockSpinBox.Enable(event.GetInt() == 1)
|
|
|
+
|
|
|
+ def OnPlotButton(self,event):
|
|
|
+ """ Plots variogram with current options. """
|
|
|
+ pass
|
|
|
+
|
|
|
+ def UseValue(self, event):
|
|
|
+ """ Enables/Disables the SpinCtrl in respect of the checkbox. """
|
|
|
+ n = self.ParametersList[event.GetId()]
|
|
|
+ getattr(self, n+"Ctrl").Enable(event.IsChecked())
|
|
|
+
|
|
|
+class RBookgstatPanel(RBookPanel):
|
|
|
+ """ Subclass of RBookPanel, with specific gstat options and kriging functions. """
|
|
|
+ def __init__(self, parent, *args, **kwargs):
|
|
|
+ RBookPanel.__init__(self, parent, *args, **kwargs)
|
|
|
+
|
|
|
+ if robjects.r.require('automap')[0]:
|
|
|
+ self.VariogramCheckBox = wx.CheckBox(self, id = wx.ID_ANY, label = _("Auto-fit variogram"))
|
|
|
+ self.LeftSizer.Insert(0,
|
|
|
+ self.VariogramCheckBox,
|
|
|
+ proportion = 0,
|
|
|
+ flag = wx.EXPAND | wx.ALIGN_CENTER_VERTICAL | wx.ALL,
|
|
|
+ border = 4)
|
|
|
+ self.SetSizerAndFit(self.Sizer)
|
|
|
+ self.VariogramCheckBox.Bind(wx.EVT_CHECKBOX, self.HideOptions)
|
|
|
+ self.VariogramCheckBox.SetValue(state = True) # check it by default
|
|
|
+
|
|
|
+ ModelFactor = robjects.r.vgm().r['long']
|
|
|
+ ModelList = robjects.r.levels(ModelFactor[0])
|
|
|
+ #@FIXME: no other way to let the Python pick it up..
|
|
|
+ # and this is te wrong place where to load this list. should be at the very beginning.
|
|
|
+ self.ModelChoicebox = wx.Choice(self, id = wx.ID_ANY, choices = ModelList)
|
|
|
+
|
|
|
+ # disable model parameters' widgets by default
|
|
|
+ for n in ["Sill", "Nugget", "Range"]:
|
|
|
+ getattr(self, n+"Ctrl").Enable(False)
|
|
|
+ self.ModelChoicebox.Enable(False)
|
|
|
+
|
|
|
+ VariogramSubSizer = wx.BoxSizer(wx.HORIZONTAL)
|
|
|
+ VariogramSubSizer.Add(item = wx.StaticText(self,
|
|
|
+ id = wx.ID_ANY,
|
|
|
+ label = _("Model: ")),
|
|
|
+ flag = wx.ALIGN_CENTER_VERTICAL | wx.ALL,
|
|
|
+ border = 4)
|
|
|
+ VariogramSubSizer.Add(item = self.ModelChoicebox,
|
|
|
+ flag = wx.ALIGN_CENTER_VERTICAL | wx.ALL,
|
|
|
+ border = 4)
|
|
|
+
|
|
|
+ self.LeftSizer.Insert(2, item = VariogramSubSizer)
|
|
|
+
|
|
|
+ self.SetSizerAndFit(self.Sizer)
|
|
|
+
|
|
|
+ def HideOptions(self, event):
|
|
|
+ self.ModelChoicebox.Enable(not event.IsChecked())
|
|
|
+ for n in ["Sill", "Nugget", "Range"]:
|
|
|
+ if not event.IsChecked():
|
|
|
+ getattr(self, n+"Ctrl").Enable(True)
|
|
|
+ getattr(self, n+ "ChextBox").SetValue(True)
|
|
|
+ getattr(self, n+ "ChextBox").Enable(False) # grey it out keeping it checked.. improvable
|
|
|
+ else:
|
|
|
+ getattr(self, n+"Ctrl").Enable(False)
|
|
|
+ getattr(self, n+ "ChextBox").SetValue(False)
|
|
|
+ getattr(self, n+ "ChextBox").Enable(True)
|
|
|
+ #@FIXME: was for n in self.ParametersSizer.GetChildren(): n.Enable(False) but doesn't work
|
|
|
+
|
|
|
+ def OnPlotButton(self,event):
|
|
|
+ """ Plots variogram with current options. """
|
|
|
+ ## BIG WARNING: smell of code duplication. Fix this asap.
|
|
|
+ controller = Controller()
|
|
|
+ map = self.parent.InputDataMap.GetValue()
|
|
|
+ column = self.parent.InputDataColumn.GetValue()
|
|
|
+
|
|
|
+ # import data or pick them up
|
|
|
+ if globals()["InputData"] is None:
|
|
|
+ globals()["InputData"] = controller.ImportMap(map = map,
|
|
|
+ column = column)
|
|
|
+ # fit the variogram or pick it up
|
|
|
+ Formula = controller.ComposeFormula(column = column,
|
|
|
+ isblock = self.KrigingRadioBox.GetStringSelection() == "Block kriging",
|
|
|
+ inputdata = globals()['InputData'])
|
|
|
+ #if globals()["Variogram"] is None:
|
|
|
+ if hasattr(self, 'VariogramCheckBox') and self.VariogramCheckBox.IsChecked():
|
|
|
+ self.model = ''
|
|
|
+ for each in ("Sill","Nugget","Range"):
|
|
|
+ if getattr(self, each+'ChextBox').IsChecked():
|
|
|
+ setattr(self, each.lower(), getattr(self, each+"Ctrl").GetValue())
|
|
|
+ else:
|
|
|
+ setattr(self, each.lower(), robjects.r('''NA'''))
|
|
|
+ else:
|
|
|
+ self.model = self.ModelChoicebox.GetStringSelection().split(" ")[0]
|
|
|
+ for each in ("Sill","Nugget","Range"):
|
|
|
+ if getattr(self, each+'ChextBox').IsChecked(): #@FIXME will be removed when chextboxes will be frozen
|
|
|
+ setattr(self, each.lower(), getattr(self, each+"Ctrl").GetValue())
|
|
|
+
|
|
|
+ globals()["Variogram"] = controller.FitVariogram(Formula,
|
|
|
+ InputData,
|
|
|
+ model = self.model,
|
|
|
+ sill = self.sill,
|
|
|
+ nugget = self.nugget,
|
|
|
+ range = self.range)
|
|
|
+
|
|
|
+ ## A: use wx.plot library. Does not draw lines from f(x), damn.
|
|
|
+ #
|
|
|
+ ## convert R dataframe (data variogram) - points
|
|
|
+ ##print Variogram['datavariogram']
|
|
|
+ #PointList = []
|
|
|
+ #for n in range(len(Variogram['datavariogram'].r['dist'][0])): #@FIXME: so less Pythonic!!
|
|
|
+ # dist = Variogram['datavariogram'].r['dist'][0][n]
|
|
|
+ # gamma = Variogram['datavariogram'].r['gamma'][0][n]
|
|
|
+ # PointList.append((dist,gamma))
|
|
|
+ #DataPoints = plot.PolyMarker(PointList, legend='points', colour='black', marker='circle',size=1)
|
|
|
+ #
|
|
|
+ ## convert R dataframe (model variogram) - line
|
|
|
+ #LineList = []
|
|
|
+ #textplot = robjects.r.plot(Variogram['datavariogram'], Variogram['variogrammodel'])
|
|
|
+ #print textplot
|
|
|
+ ##for n in range(len(Variogram['variogrammodel'].r['dist'][0])): #@FIXME: so less Pythonic!!
|
|
|
+ ## dist = Variogram['datavariogram'].r['dist'][0][n]
|
|
|
+ ## gamma = Variogram['datavariogram'].r['gamma'][0][n]
|
|
|
+ ## LineList.append((dist,gamma))
|
|
|
+ ##
|
|
|
+ ### give them to plot.PolyPoints and plot.PolyLine
|
|
|
+ ## plot it
|
|
|
+ #VariogramPlot = plot.PlotGraphics([DataPoints])#,
|
|
|
+ # #title = "Wa",
|
|
|
+ # #xlabel = "Distance",
|
|
|
+ # #ylabel = "Gamma") #([DataPoints, line], title, xlabel, ylabel)
|
|
|
+ #self.PlotArea.Draw(VariogramPlot)
|
|
|
+
|
|
|
+ # B: use R plot function, in a separate window.
|
|
|
+ thread.start_new_thread(self.plot, ())
|
|
|
+ #self.plot()
|
|
|
+
|
|
|
+ def plot(self):
|
|
|
+ #robjects.r.X11()
|
|
|
+ #robjects.r.png("variogram.png")
|
|
|
+ textplot = robjects.r.plot(Variogram['datavariogram'], Variogram['variogrammodel'])
|
|
|
+ print textplot
|
|
|
+ self.refresh()
|
|
|
+ #robjects.r['dev.off']()
|
|
|
+
|
|
|
+ def refresh(self):
|
|
|
+ while True:
|
|
|
+ rinterface.process_revents()
|
|
|
+ time.sleep(0.1)
|
|
|
+
|
|
|
+class RBookgeoRPanel(RBookPanel):
|
|
|
+ """ Subclass of RBookPanel, with specific geoR options and kriging functions. """
|
|
|
+ def __init__(self, parent, *args, **kwargs):
|
|
|
+ RBookPanel.__init__(self, parent, *args, **kwargs)
|
|
|
+ #@TODO: change these two lines as soon as geoR f(x)s are integrated.
|
|
|
+ for n in self.GetChildren():
|
|
|
+ n.Hide()
|
|
|
+ self.Sizer.Add(wx.StaticText(self, id = wx.ID_ANY, label = _("Work in progress! No functionality provided.")))
|
|
|
+ self.SetSizerAndFit(self.Sizer)
|
|
|
+
|
|
|
+def main(argv = None):
|
|
|
+ #@FIXME: solve this double ifelse. the control should not be done twice.
|
|
|
+
|
|
|
+ if argv is None:
|
|
|
+ importR()
|
|
|
+ argv = sys.argv[1:] #stripping first item, the full name of this script
|
|
|
+ # wxGUI call.
|
|
|
+ app = wx.App()
|
|
|
+ KrigingFrame = KrigingModule(parent = None)
|
|
|
+ KrigingFrame.Centre()
|
|
|
+ KrigingFrame.Show()
|
|
|
+ app.MainLoop()
|
|
|
+
|
|
|
+ else:
|
|
|
+ #CLI
|
|
|
+ options, flags = argv
|
|
|
+ #@TODO: Work on verbosity. Sometimes it's too verbose (R), sometimes not enough.
|
|
|
+ if grass.find_file(options['input'], element = 'vector')['fullname'] is '':
|
|
|
+ grass.fatal(_("option: <input>: Vector map not found."))
|
|
|
+
|
|
|
+ #@TODO: elaborate input string, if contains mapset or not.. thanks again to Bob for testing on 64bit.
|
|
|
+
|
|
|
+ # create output map name, if not specified
|
|
|
+ if options['output'] is '':
|
|
|
+ try: # to strip mapset name from fullname. Ugh.
|
|
|
+ options['input'] = options['input'].split("@")[0]
|
|
|
+ except:
|
|
|
+ pass
|
|
|
+ options['output'] = options['input'] + '_kriging'
|
|
|
+
|
|
|
+ # check for output map with same name. g.parser can't handle this, afaik.
|
|
|
+ if grass.find_file(options['output'], element = 'cell')['fullname'] and os.getenv("GRASS_OVERWRITE") == None:
|
|
|
+ grass.fatal(_("option: <output>: Raster map already exists."))
|
|
|
+ if options['output_var'] is not '' and (grass.find_file(options['output_var'], element = 'cell')['fullname'] and os.getenv("GRASS_OVERWRITE") == None):
|
|
|
+ grass.fatal(_("option: <output>: Variance raster map already exists."))
|
|
|
+
|
|
|
+ importR()
|
|
|
+ if options['model'] is '':
|
|
|
+ try:
|
|
|
+ robjects.r.require("automap")
|
|
|
+ except ImportError, e:
|
|
|
+ grass.fatal(_("R package automap is missing, no variogram autofit available."))
|
|
|
+ else:
|
|
|
+ if options['sill'] is '' or options['nugget'] is '' or options['range'] is '':
|
|
|
+ grass.fatal(_("You have specified model, but forgot at least one of sill, nugget and range."))
|
|
|
+
|
|
|
+ #@TODO: let GRASS remount its commandstring. Until then, keep that 4 lines below.
|
|
|
+ #print grass.write_command(argv)
|
|
|
+ command = ""
|
|
|
+ notnulloptions = {}
|
|
|
+ for k, v in options.items():
|
|
|
+ if v is not '':
|
|
|
+ notnulloptions[k] = v
|
|
|
+ command = command.join("%s=%s " % (k, v) for k, v in notnulloptions.items())
|
|
|
+ #print command
|
|
|
+
|
|
|
+ # re-cast integers from strings, as parser() cast everything to string.
|
|
|
+ for each in ("sill","nugget","range"):
|
|
|
+ if options[each] is not '':
|
|
|
+ options[each] = int(options[each])
|
|
|
+ else:
|
|
|
+ options[each] = robjects.r('''NA''')
|
|
|
+
|
|
|
+ controller = Controller()
|
|
|
+ controller.Run(input = options['input'],
|
|
|
+ column = options['column'],
|
|
|
+ output = options['output'],
|
|
|
+ overwrite = os.getenv("GRASS_OVERWRITE") == 1,
|
|
|
+ package = options['package'],
|
|
|
+ model = options['model'],
|
|
|
+ block = options['block'],
|
|
|
+ sill = options['sill'],
|
|
|
+ nugget = options['nugget'],
|
|
|
+ range = options['range'],
|
|
|
+ output_var = options['output_var'],
|
|
|
+ command = command,
|
|
|
+ logger = grass)
|
|
|
+
|
|
|
+def importR():
|
|
|
+ # R
|
|
|
+ # unuseful since rpy2 will complain adequately.
|
|
|
+ # try:
|
|
|
+ # #@FIXME: in Windows, it launches R terminal
|
|
|
+ # grass.find_program('R')
|
|
|
+ # except:
|
|
|
+ # sys.exit(_("R is not installed. Install it and re-run, or modify environment variables."))
|
|
|
+
|
|
|
+ # rpy2
|
|
|
+ global robjects
|
|
|
+ global rinterface
|
|
|
+ try:
|
|
|
+ import rpy2.robjects as robjects
|
|
|
+ import rpy2.rinterface as rinterface #to speed up kriging? for plots.
|
|
|
+ haveRpy2 = True
|
|
|
+ except ImportError:
|
|
|
+ print >> sys.stderr, "Rpy2 not found. Please install it and re-run." # ok for other OSes?
|
|
|
+ haveRpy2 = False
|
|
|
+ if not haveRpy2:
|
|
|
+ sys.exit(1)
|
|
|
+
|
|
|
+ # R packages check.
|
|
|
+ # @FIXME: it leaves a Rtmpxxxx folder into the make tempfolder and causes make complain. [markus]
|
|
|
+ for each in ["gstat", "spgrass6"]:
|
|
|
+ if not robjects.r.require(each, quietly = True)[0]:
|
|
|
+ sys.exit(_("R package " + each + " is missing. Install it and re-run v.krige."))
|
|
|
+
|
|
|
+if __name__ == '__main__':
|
|
|
+ if len(sys.argv) > 1:
|
|
|
+ sys.exit(main(argv = grass.parser()))
|
|
|
+ else:
|
|
|
+ main()
|
Martin Landa