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QGIS/python/plugins/processing/algs/r/RAlgorithm.py
Victor Olaya 79757fabee [processing] some fixes in help system
2014-04-24 18:33:56 +02:00

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# -*- coding: utf-8 -*-
"""
***************************************************************************
RAlgorithm.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************
"""
__author__ = 'Victor Olaya'
__date__ = 'August 2012'
__copyright__ = '(C) 2012, Victor Olaya'
# This will get replaced with a git SHA1 when you do a git archive
__revision__ = '$Format:%H$'
import os
import subprocess
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4 import QtGui
from processing.core.GeoAlgorithm import GeoAlgorithm
from processing.core.GeoAlgorithmExecutionException import \
GeoAlgorithmExecutionException
from processing.core.ProcessingLog import ProcessingLog
from processing.gui.Help2Html import getHtmlFromHelpFile
from processing.parameters.ParameterRaster import ParameterRaster
from processing.parameters.ParameterTable import ParameterTable
from processing.parameters.ParameterVector import ParameterVector
from processing.parameters.ParameterMultipleInput import ParameterMultipleInput
from processing.parameters.ParameterString import ParameterString
from processing.parameters.ParameterNumber import ParameterNumber
from processing.parameters.ParameterBoolean import ParameterBoolean
from processing.parameters.ParameterSelection import ParameterSelection
from processing.parameters.ParameterTableField import ParameterTableField
from processing.parameters.ParameterExtent import ParameterExtent
from processing.parameters.ParameterFile import ParameterFile
from processing.outputs.OutputTable import OutputTable
from processing.outputs.OutputVector import OutputVector
from processing.outputs.OutputRaster import OutputRaster
from processing.outputs.OutputHTML import OutputHTML
from processing.outputs.OutputFile import OutputFile
from processing.tools.system import *
from processing.script.WrongScriptException import WrongScriptException
from RUtils import RUtils
class RAlgorithm(GeoAlgorithm):
R_CONSOLE_OUTPUT = 'R_CONSOLE_OUTPUT'
RPLOTS = 'RPLOTS'
def getCopy(self):
newone = RAlgorithm(self.descriptionFile)
newone.provider = self.provider
return newone
def __init__(self, descriptionFile, script=None):
GeoAlgorithm.__init__(self)
self.script = script
self.descriptionFile = descriptionFile
if script is not None:
self.defineCharacteristicsFromScript()
if descriptionFile is not None:
self.defineCharacteristicsFromFile()
def getIcon(self):
return QtGui.QIcon(os.path.dirname(__file__) + '/../../images/r.png')
def defineCharacteristicsFromScript(self):
lines = self.script.split('\n')
self.name = '[Unnamed algorithm]'
self.group = 'User R scripts'
self.parseDescription(iter(lines))
def defineCharacteristicsFromFile(self):
filename = os.path.basename(self.descriptionFile)
self.name = filename[:filename.rfind('.')].replace('_', ' ')
self.group = 'User R scripts'
with open(self.descriptionFile, 'r') as f:
lines = [line.strip() for line in f]
self.parseDescription(iter(lines))
def parseDescription(self, lines):
self.script = ''
self.commands = []
self.showPlots = False
self.showConsoleOutput = False
self.useRasterPackage = True
self.passFileNames = False
self.verboseCommands = []
ender = 0
line = lines.next().strip('\n').strip('\r')
while ender < 10:
if line.startswith('##'):
try:
self.processParameterLine(line)
except Exception:
raise WrongScriptException('Could not load R script:'
+ self.descriptionFile + '.\n Problem with line "'
+ line + '"')
elif line.startswith('>'):
self.commands.append(line[1:])
self.verboseCommands.append(line[1:])
if not self.showConsoleOutput:
self.addOutput(OutputHTML(RAlgorithm.R_CONSOLE_OUTPUT,
'R Console Output'))
self.showConsoleOutput = True
else:
if line == '':
ender += 1
else:
ender = 0
self.commands.append(line)
self.script += line + '\n'
try:
line = lines.next().strip('\n').strip('\r')
except:
break
def getVerboseCommands(self):
return self.verboseCommands
def createDescriptiveName(self, s):
return s.replace('_', ' ')
def processParameterLine(self, line):
param = None
out = None
line = line.replace('#', '')
if line.lower().strip().startswith('showplots'):
self.showPlots = True
self.addOutput(OutputHTML(RAlgorithm.RPLOTS, 'R Plots'))
return
if line.lower().strip().startswith('dontuserasterpackage'):
self.useRasterPackage = False
return
if line.lower().strip().startswith('passfilenames'):
self.passFileNames = True
return
tokens = line.split('=')
desc = self.createDescriptiveName(tokens[0])
if tokens[1].lower().strip() == 'group':
self.group = tokens[0]
return
if tokens[1].lower().strip().startswith('raster'):
param = ParameterRaster(tokens[0], desc, False)
elif tokens[1].lower().strip() == 'vector':
param = ParameterVector(tokens[0], desc,
[ParameterVector.VECTOR_TYPE_ANY])
elif tokens[1].lower().strip() == 'table':
param = ParameterTable(tokens[0], desc, False)
elif tokens[1].lower().strip().startswith('multiple raster'):
param = ParameterMultipleInput(tokens[0], desc,
ParameterMultipleInput.TYPE_RASTER)
param.optional = False
elif tokens[1].lower().strip() == 'multiple vector':
param = ParameterMultipleInput(tokens[0], desc,
ParameterMultipleInput.TYPE_VECTOR_ANY)
param.optional = False
elif tokens[1].lower().strip().startswith('selection'):
options = tokens[1].strip()[len('selection'):].split(';')
param = ParameterSelection(tokens[0], desc, options)
elif tokens[1].lower().strip().startswith('boolean'):
default = tokens[1].strip()[len('boolean') + 1:]
param = ParameterBoolean(tokens[0], desc, default)
elif tokens[1].lower().strip().startswith('number'):
try:
default = float(tokens[1].strip()[len('number') + 1:])
param = ParameterNumber(tokens[0], desc, default=default)
except:
raise WrongScriptException('Could not load R script:'
+ self.descriptionFile + '.\n Problem with line "'
+ line + '"')
elif tokens[1].lower().strip().startswith('field'):
field = tokens[1].strip()[len('field') + 1:]
found = False
for p in self.parameters:
if p.name == field:
found = True
break
if found:
param = ParameterTableField(tokens[0], tokens[0], field)
elif tokens[1].lower().strip() == 'extent':
param = ParameterExtent(tokens[0], desc)
elif tokens[1].lower().strip() == 'file':
param = ParameterFile(tokens[0], desc, False)
elif tokens[1].lower().strip() == 'folder':
param = ParameterFile(tokens[0], desc, True)
elif tokens[1].lower().strip().startswith('string'):
default = tokens[1].strip()[len('string') + 1:]
param = ParameterString(tokens[0], desc, default)
elif tokens[1].lower().strip().startswith('output raster'):
out = OutputRaster()
elif tokens[1].lower().strip().startswith('output vector'):
out = OutputVector()
elif tokens[1].lower().strip().startswith('output table'):
out = OutputTable()
elif tokens[1].lower().strip().startswith('output file'):
out = OutputFile()
if param is not None:
self.addParameter(param)
elif out is not None:
out.name = tokens[0]
out.description = tokens[0]
self.addOutput(out)
else:
raise WrongScriptException('Could not load R script:'
+ self.descriptionFile
+ '.\n Problem with line "' + line + '"'
)
def processAlgorithm(self, progress):
if isWindows():
path = RUtils.RFolder()
if path == '':
raise GeoAlgorithmExecutionException(
'R folder is not configured.\nPlease configure it \
before running R scripts.')
loglines = []
loglines.append('R execution commands')
loglines += self.getFullSetOfRCommands()
for line in loglines:
progress.setCommand(line)
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)
RUtils.executeRAlgorithm(self, progress)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
f = open(htmlfilename, 'w')
f.write('<img src="' + self.plotsFilename + '"/>')
f.close()
if self.showConsoleOutput:
htmlfilename = self.getOutputValue(RAlgorithm.R_CONSOLE_OUTPUT)
f = open(htmlfilename, 'w')
f.write(RUtils.getConsoleOutput())
f.close()
def getFullSetOfRCommands(self):
commands = []
commands += self.getImportCommands()
commands += self.getRCommands()
commands += self.getExportCommands()
return commands
def getExportCommands(self):
commands = []
for out in self.outputs:
if isinstance(out, OutputRaster):
value = out.value
value = value.replace('\\', '/')
if self.useRasterPackage or self.passFileNames:
commands.append('writeRaster(' + out.name + ',"' + value
+ '", overwrite=TRUE)')
else:
if not value.endswith('tif'):
value = value + '.tif'
commands.append('writeGDAL(' + out.name + ',"' + value
+ '")')
if isinstance(out, OutputVector):
value = out.value
if not value.endswith('shp'):
value = value + '.shp'
value = value.replace('\\', '/')
filename = os.path.basename(value)
filename = filename[:-4]
commands.append('writeOGR(' + out.name + ',"' + value + '","'
+ filename + '", driver="ESRI Shapefile")')
if self.showPlots:
commands.append('dev.off()')
return commands
def getImportCommands(self):
commands = []
# Just use main mirror
commands.append('options("repos"="http://cran.at.r-project.org/")')
# Try to install packages if needed
packages = RUtils.getRequiredPackages(self.script)
packages.extend(['rgdal', 'raster'])
for p in packages:
commands.append('tryCatch(find.package("' + p
+ '"), error=function(e) install.packages("' + p
+ '", dependencies=TRUE))')
commands.append('library("raster")')
commands.append('library("rgdal")')
for param in self.parameters:
if isinstance(param, ParameterRaster):
value = param.value
value = value.replace('\\', '/')
if self.passFileNames:
commands.append(param.name + ' = "' + value + '"')
elif self.useRasterPackage:
commands.append(param.name + ' = ' + 'brick("' + value
+ '")')
else:
commands.append(param.name + ' = ' + 'readGDAL("' + value
+ '")')
if isinstance(param, ParameterVector):
value = param.getSafeExportedLayer()
value = value.replace('\\', '/')
filename = os.path.basename(value)
filename = filename[:-4]
folder = os.path.dirname(value)
if self.passFileNames:
commands.append(param.name + ' = "' + value + '"')
else:
commands.append(param.name + ' = readOGR("' + folder
+ '",layer="' + filename + '")')
if isinstance(param, ParameterTable):
value = param.value
if not value.lower().endswith('csv'):
raise GeoAlgorithmExecutionException(
'Unsupported input file format.\n' + value)
if self.passFileNames:
commands.append(param.name + ' = "' + value + '"')
else:
commands.append(param.name + ' <- read.csv("' + value
+ '", head=TRUE, sep=",")')
elif isinstance(param, (ParameterTableField, ParameterString,
ParameterFile)):
commands.append(param.name + '="' + param.value + '"')
elif isinstance(param, (ParameterNumber, ParameterSelection)):
commands.append(param.name + '=' + str(param.value))
elif isinstance(param, ParameterBoolean):
if param.value:
commands.append(param.name + '=TRUE')
else:
commands.append(param.name + '=FALSE')
elif isinstance(param, ParameterMultipleInput):
iLayer = 0
if param.datatype == ParameterMultipleInput.TYPE_RASTER:
layers = param.value.split(';')
for layer in layers:
layer = layer.replace('\\', '/')
if self.passFileNames:
commands.append('tempvar' + str(iLayer) + ' <- "'
+ layer + '"')
elif self.useRasterPackage:
commands.append('tempvar' + str(iLayer) + ' <- '
+ 'brick("' + layer + '")')
else:
commands.append('tempvar' + str(iLayer) + ' <- '
+ 'readGDAL("' + layer + '")')
iLayer += 1
else:
exported = param.getSafeExportedLayers()
layers = exported.split(';')
for layer in layers:
if not layer.lower().endswith('shp') \
and not self.passFileNames:
raise GeoAlgorithmExecutionException(
'Unsupported input file format.\n' + layer)
layer = layer.replace('\\', '/')
filename = os.path.basename(layer)
filename = filename[:-4]
if self.passFileNames:
commands.append('tempvar' + str(iLayer) + ' <- "'
+ layer + '"')
else:
commands.append('tempvar' + str(iLayer) + ' <- '
+ 'readOGR("' + layer + '",layer="'
+ filename + '")')
iLayer += 1
s = ''
s += param.name
s += ' = c('
iLayer = 0
for layer in layers:
if iLayer != 0:
s += ','
s += 'tempvar' + str(iLayer)
iLayer += 1
s += ')\n'
commands.append(s)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
self.plotsFilename = htmlfilename + '.png'
self.plotsFilename = self.plotsFilename.replace('\\', '/')
commands.append('png("' + self.plotsFilename + '")')
return commands
def getRCommands(self):
return self.commands
def help(self):
helpfile = unicode(self.descriptionFile) + '.help'
if os.path.exists(helpfile):
return True, getHtmlFromHelpFile(self, helpfile)
else:
return False, None
def checkBeforeOpeningParametersDialog(self):
msg = RUtils.checkRIsInstalled()
if msg is not None:
html = '<p>This algorithm requires R to be run.Unfortunately, \
it seems that R is not installed in your system, or it \
is not correctly configured to be used from QGIS</p>'
html += '<p><a href= "http://docs.qgis.org/2.0/en/docs/user_manual/processing/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with QGIS</p>'
return html
def getPostProcessingErrorMessage(self, wrongLayers):
html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
msg = RUtils.checkRIsInstalled(True)
html += '<p>This algorithm requires R to be run. A test to check if \
R is correctly installed and configured in your system has \
been performed, with the following result:</p><ul><i>'
if msg is None:
html += 'R seems to be correctly installed and \
configured</i></li></ul>'
html += '<p>The script you have executed needs the following \
packages:</p><ul>'
packages = RUtils.getRequiredPackages(self.script)
for p in packages:
html += '<li>' + p + '</li>'
html += '</ul><p>Make sure they are installed in your R \
environment before trying to execute this script.</p>'
else:
html += msg + '</i></li></ul>'
html += '<p><a href= "http://docs.qgis.org/2.0/en/docs/user_manual/processing/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with QGIS</p>'
return html
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