# -*- 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. *
* *
***************************************************************************
"""
from future import standard_library
standard_library.install_aliases()
from builtins import str
__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 json
from qgis.PyQt.QtGui import QIcon
from qgis.core import QgsApplication
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.core.parameters import ParameterRaster
from processing.core.parameters import ParameterTable
from processing.core.parameters import ParameterVector
from processing.core.parameters import ParameterMultipleInput
from processing.core.parameters import ParameterString
from processing.core.parameters import ParameterNumber
from processing.core.parameters import ParameterBoolean
from processing.core.parameters import ParameterSelection
from processing.core.parameters import ParameterTableField
from processing.core.parameters import ParameterExtent
from processing.core.parameters import ParameterCrs
from processing.core.parameters import ParameterFile
from processing.core.parameters import ParameterPoint
from processing.core.outputs import OutputTable
from processing.core.outputs import OutputVector
from processing.core.outputs import OutputRaster
from processing.core.outputs import OutputHTML
from processing.core.outputs import OutputFile
from processing.core.parameters import getParameterFromString
from processing.core.outputs import getOutputFromString
from processing.tools import dataobjects
from processing.tools.system import isWindows
from processing.script.WrongScriptException import WrongScriptException
from .RUtils import RUtils
pluginPath = os.path.normpath(os.path.join(
os.path.split(os.path.dirname(__file__))[0], os.pardir))
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()
self._icon = None
def getIcon(self):
if self._icon is None:
self._icon = QgsApplication.getThemeIcon("/providerR.svg")
return self._icon
def defineCharacteristicsFromScript(self):
lines = self.script.split('\n')
self.name, self.i18n_name = self.trAlgorithm('[Unnamed algorithm]')
self.group, self.i18n_group = self.trAlgorithm('User R scripts')
self.parseDescription(iter(lines))
def defineCharacteristicsFromFile(self):
filename = os.path.basename(self.descriptionFile)
self.name = filename[:filename.rfind('.')].replace('_', ' ')
self.group, self.i18n_group = self.trAlgorithm('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(
self.tr('Could not load R script: %s.\n Problem with line %s' % (self.descriptionFile, 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,
self.tr('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
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 = self.i18n_group = tokens[0]
return
if tokens[1].lower().strip() == 'name':
self.name = self.i18n_name = tokens[0]
return
out = getOutputFromString(line)
if out is None:
param = getParameterFromString(line)
if param is not None:
self.addParameter(param)
elif out is not None:
out.name = tokens[0]
out.description = desc
self.addOutput(out)
else:
raise WrongScriptException(
self.tr('Could not load script: %s.\n'
'Problem with line "%s"', 'ScriptAlgorithm') % (self.descriptionFile or '', line))
raise WrongScriptException(
self.tr('Could not load R script: %s.\n Problem with line %s' % (self.descriptionFile, line)))
def processAlgorithm(self, feedback):
if isWindows():
path = RUtils.RFolder()
if path == '':
raise GeoAlgorithmExecutionException(
self.tr('R folder is not configured.\nPlease configure it '
'before running R scripts.'))
loglines = []
loglines.append(self.tr('R execution commands'))
loglines += self.getFullSetOfRCommands()
for line in loglines:
feedback.pushCommandInfo(line)
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)
RUtils.executeRAlgorithm(self, feedback)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
with open(htmlfilename, 'w') as f:
f.write('<html><img src="' + self.plotsFilename + '"/></html>')
if self.showConsoleOutput:
htmlfilename = self.getOutputValue(RAlgorithm.R_CONSOLE_OUTPUT)
with open(htmlfilename, 'w') as f:
f.write(RUtils.getConsoleOutput())
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
+ '")')
elif 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")')
elif isinstance(out, OutputTable):
value = out.value
value = value.replace('\\', '/')
commands.append('write.csv(' + out.name + ',"' + value + '")')
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
if isWindows():
commands.append('.libPaths(\"' + str(RUtils.RLibs()).replace('\\', '/') + '\")')
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):
if param.value is None:
commands.append(param.name + '= NULL')
else:
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
+ '")')
elif isinstance(param, ParameterVector):
if param.value is None:
commands.append(param.name + '= NULL')
else:
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 + '")')
elif isinstance(param, ParameterTable):
if param.value is None:
commands.append(param.name + '= NULL')
else:
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, ParameterExtent):
if param.value:
tokens = str(param.value).split(',')
# Extent from raster package is "xmin, xmax, ymin, ymax" like in Processing
# http://www.inside-r.org/packages/cran/raster/docs/Extent
commands.append(param.name + ' = extent(' + tokens[0] + ',' + tokens[1] + ',' + tokens[2] + ',' + tokens[3] + ')')
else:
commands.append(param.name + ' = NULL')
elif isinstance(param, ParameterCrs):
if param.value is None:
commands.append(param.name + '= NULL')
else:
commands.append(param.name + ' = "' + param.value + '"')
elif isinstance(param, (ParameterTableField, ParameterString, ParameterFile)):
if param.value is None:
commands.append(param.name + '= NULL')
else:
commands.append(param.name + '="' + param.value + '"')
elif isinstance(param, (ParameterNumber, ParameterSelection)):
if param.value is None:
commands.append(param.name + '= NULL')
else:
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 == dataobjects.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 = str(self.descriptionFile) + '.help'
if os.path.exists(helpfile):
return True, getHtmlFromHelpFile(self, helpfile)
else:
return False, None
def shortHelp(self):
if self.descriptionFile is None:
return None
helpFile = str(self.descriptionFile) + '.help'
if os.path.exists(helpFile):
with open(helpFile) as f:
try:
descriptions = json.load(f)
if 'ALG_DESC' in descriptions:
return self._formatHelp(str(descriptions['ALG_DESC']))
except:
return None
return None
def getParameterDescriptions(self):
descs = {}
if self.descriptionFile is None:
return descs
helpFile = str(self.descriptionFile) + '.help'
if os.path.exists(helpFile):
with open(helpFile) as f:
try:
descriptions = json.load(f)
for param in self.parameters:
if param.name in descriptions:
descs[param.name] = str(descriptions[param.name])
except:
return descs
return descs
def checkBeforeOpeningParametersDialog(self):
msg = RUtils.checkRIsInstalled()
if msg is not None:
html = self.tr(
'<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>'
'<p><a href="http://docs.qgis.org/testing/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