[FEATURE] TauDEM provider for SEXTANTE

python/plugins/sextante/CMakeLists.txt

@@ -19,6 +19,7 @@ ADD_SUBDIRECTORY(pymorph)
 ADD_SUBDIRECTORY(r)
 ADD_SUBDIRECTORY(saga)
 ADD_SUBDIRECTORY(script)
+ADD_SUBDIRECTORY(taudem)
 #ADD_SUBDIRECTORY(tests)
 
 FILE(GLOB OTHER_FILES metadata.txt)

python/plugins/sextante/core/Sextante.py

@@ -26,30 +26,37 @@
 
 from PyQt4.QtCore import *
 from PyQt4.QtGui import *
-from sextante.saga.SagaAlgorithmProvider import SagaAlgorithmProvider
-from sextante.script.ScriptAlgorithmProvider import ScriptAlgorithmProvider
+
 from sextante.core.QGisLayers import QGisLayers
-from sextante.gui.AlgorithmExecutor import AlgorithmExecutor
 from sextante.core.SextanteConfig import SextanteConfig
 from sextante.core.GeoAlgorithm import GeoAlgorithm
 from sextante.core.SextanteLog import SextanteLog
-from sextante.modeler.ModelerAlgorithmProvider import ModelerAlgorithmProvider
-from sextante.ftools.FToolsAlgorithmProvider import FToolsAlgorithmProvider
+
+from sextante.gui.AlgorithmExecutor import AlgorithmExecutor
+from sextante.gui.RenderingStyles import RenderingStyles
 from sextante.gui.SextantePostprocessing import SextantePostprocessing
+from sextante.gui.UnthreadedAlgorithmExecutor import UnthreadedAlgorithmExecutor,\
+    SilentProgress
+
 from sextante.modeler.Providers import Providers
-from sextante.r.RAlgorithmProvider import RAlgorithmProvider
-from sextante.parameters.ParameterSelection import ParameterSelection
-from sextante.grass.GrassAlgorithmProvider import GrassAlgorithmProvider
-from sextante.gui.RenderingStyles import RenderingStyles
+from sextante.modeler.ModelerAlgorithmProvider import ModelerAlgorithmProvider
 from sextante.modeler.ModelerOnlyAlgorithmProvider import ModelerOnlyAlgorithmProvider
+
+from sextante.algs.SextanteAlgorithmProvider import SextanteAlgorithmProvider
+
+from sextante.parameters.ParameterSelection import ParameterSelection
+
+from sextante.ftools.FToolsAlgorithmProvider import FToolsAlgorithmProvider
 from sextante.gdal.GdalAlgorithmProvider import GdalAlgorithmProvider
+from sextante.grass.GrassAlgorithmProvider import GrassAlgorithmProvider
+from sextante.lidar.LidarToolsAlgorithmProvider import LidarToolsAlgorithmProvider
+from sextante.mmqgisx.MMQGISXAlgorithmProvider import MMQGISXAlgorithmProvider
 from sextante.otb.OTBAlgorithmProvider import OTBAlgorithmProvider
-from sextante.algs.SextanteAlgorithmProvider import SextanteAlgorithmProvider
 from sextante.pymorph.PymorphAlgorithmProvider import PymorphAlgorithmProvider
-from sextante.mmqgisx.MMQGISXAlgorithmProvider import MMQGISXAlgorithmProvider
-from sextante.lidar.LidarToolsAlgorithmProvider import LidarToolsAlgorithmProvider
-from sextante.gui.UnthreadedAlgorithmExecutor import UnthreadedAlgorithmExecutor,\
-    SilentProgress
+from sextante.r.RAlgorithmProvider import RAlgorithmProvider
+from sextante.saga.SagaAlgorithmProvider import SagaAlgorithmProvider
+from sextante.script.ScriptAlgorithmProvider import ScriptAlgorithmProvider
+from sextante.taudem.TauDEMAlgorithmProvider import TauDEMAlgorithmProvider
 
 class Sextante:
 
@@ -122,6 +129,7 @@ def initialize():
         Sextante.addProvider(SagaAlgorithmProvider())
         Sextante.addProvider(GrassAlgorithmProvider())
         Sextante.addProvider(ScriptAlgorithmProvider())
+        Sextante.addProvider(TauDEMAlgorithmProvider())
         Sextante.modeler.initializeSettings();
         #and initialize
         SextanteLog.startLogging()

python/plugins/sextante/taudem/CMakeLists.txt

@@ -0,0 +1,7 @@
+FILE(GLOB PY_FILES *.py)
+FILE(GLOB DESCR_FILES description/*.txt)
+FILE(GLOB HELP_FILES help/*.html)
+
+INSTALL(FILES ${PY_FILES} DESTINATION ${SEXTANTE_PLUGIN_DIR}/taudem)
+INSTALL(FILES ${DESCR_FILES} DESTINATION ${SEXTANTE_PLUGIN_DIR}/taudem/description)
+INSTALL(FILES ${HELP_FILES} DESTINATION ${SEXTANTE_PLUGIN_DIR}/taudem/help)

python/plugins/sextante/taudem/TauDEMAlgorithm.py

@@ -0,0 +1,131 @@
+# -*- coding: utf-8 -*-
+
+"""
+***************************************************************************
+    TauDEMAlgorithm.py
+    ---------------------
+    Date                 : October 2012
+    Copyright            : (C) 2012 by Alexander Bruy
+    Email                : alexander dot bruy 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__ = 'Alexander Bruy'
+__date__ = 'October 2012'
+__copyright__ = '(C) 2012, Alexander Bruy'
+# This will get replaced with a git SHA1 when you do a git archive
+__revision__ = '$Format:%H$'
+
+import os
+
+from PyQt4.QtCore import *
+from PyQt4.QtGui import *
+
+from qgis.core import *
+
+from sextante.core.GeoAlgorithm import GeoAlgorithm
+from sextante.core.SextanteLog import SextanteLog
+from sextante.core.SextanteUtils import SextanteUtils
+from sextante.core.SextanteConfig import SextanteConfig
+from sextante.core.GeoAlgorithmExecutionException import GeoAlgorithmExecutionException
+
+from sextante.parameters.ParameterFactory import ParameterFactory
+from sextante.parameters.ParameterRaster import ParameterRaster
+from sextante.parameters.ParameterVector import ParameterVector
+from sextante.parameters.ParameterBoolean import ParameterBoolean
+from sextante.parameters.ParameterString import ParameterString
+from sextante.parameters.ParameterNumber import ParameterNumber
+
+from sextante.outputs.OutputFactory import OutputFactory
+from sextante.outputs.OutputRaster import OutputRaster
+from sextante.outputs.OutputVector import OutputVector
+from sextante.outputs.OutputFile import OutputFile
+
+from sextante.taudem.TauDEMUtils import TauDEMUtils
+
+class TauDEMAlgorithm(GeoAlgorithm):
+
+    def __init__(self, descriptionfile):
+        GeoAlgorithm.__init__(self)
+        self.descriptionFile = descriptionfile
+        self.defineCharacteristicsFromFile()
+
+    def getCopy(self):
+        newone = TauDEMAlgorithm(self.descriptionFile)
+        newone.provider = self.provider
+        return newone
+
+    def getIcon(self):
+        return  QIcon(os.path.dirname(__file__) + "/../images/taudem.png")
+
+    def defineCharacteristicsFromFile(self):
+        lines = open(self.descriptionFile)
+        line = lines.readline().strip("\n").strip()
+        self.name = line
+        line = lines.readline().strip("\n").strip()
+        self.cmdName = line
+        line = lines.readline().strip("\n").strip()
+        self.group = line
+        while line != "":
+          try:
+              line = line.strip("\n").strip()
+              if line.startswith("Parameter"):
+                  param = ParameterFactory.getFromString(line)
+                  self.addParameter(param)
+              else:
+                  self.addOutput(OutputFactory.getFromString(line))
+              line = lines.readline().strip("\n").strip()
+          except Exception, e:
+              SextanteLog.addToLog(SextanteLog.LOG_ERROR, "Could not load TauDEM algorithm: " + self.descriptionFile + "\n" + line)
+              raise e
+        lines.close()
+
+    def processAlgorithm(self, progress):
+        commands = []
+        commands.append(os.path.join(TauDEMUtils.mpiexecPath(), "mpiexec"))
+
+        processNum = SextanteConfig.getSetting(TauDEMUtils.MPI_PROCESSES)
+        if processNum <= 0:
+          raise GeoAlgorithmExecutionException("Wrong number of MPI processes used.\nPlease set correct number before running TauDEM algorithms.")
+
+        commands.append("-n")
+        commands.append(str(processNum))
+        commands.append(os.path.join(TauDEMUtils.taudemPath(), self.cmdName))
+
+        for param in self.parameters:
+            if param.value == None or param.value == "":
+                continue
+            if isinstance(param, ParameterNumber):
+                commands.append(param.name)
+                commands.append(str(param.value))
+            if isinstance(param, (ParameterRaster, ParameterVector)):
+                commands.append(param.name)
+                commands.append(param.value)
+            elif isinstance(param, ParameterBoolean):
+                if param.value and str(param.value).lower() == "false":
+                    commands.append(param.name)
+            elif isinstance(param, ParameterString):
+                commands.append(param.name)
+                commands.append(str(param.value))
+
+        for out in self.outputs:
+            commands.append(out.name)
+            commands.append(out.value)
+
+        loglines = []
+        loglines.append("TauDEM execution command")
+        for line in commands:
+            loglines.append(line)
+        SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)
+        TauDEMUtils.executeTauDEM(commands, progress)
+
+    def helpFile(self):
+        return os.path.join(os.path.dirname(__file__), "help", self.cmdName + ".html")

python/plugins/sextante/taudem/TauDEMAlgorithmProvider.py

@@ -0,0 +1,101 @@
+# -*- coding: utf-8 -*-
+
+"""
+***************************************************************************
+    TauDEMAlgorithmProvider.py
+    ---------------------
+    Date                 : October 2012
+    Copyright            : (C) 2012 by Alexander Bruy
+    Email                : alexander dot bruy 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__ = 'Alexander Bruy'
+__date__ = 'October 2012'
+__copyright__ = '(C) 2012, Alexander Bruy'
+# This will get replaced with a git SHA1 when you do a git archive
+__revision__ = '$Format:%H$'
+
+import os
+
+from PyQt4.QtGui import *
+
+from sextante.core.AlgorithmProvider import AlgorithmProvider
+from sextante.core.SextanteConfig import SextanteConfig
+from sextante.core.SextanteConfig import Setting
+from sextante.core.SextanteLog import SextanteLog
+
+from sextante.taudem.TauDEMAlgorithm import TauDEMAlgorithm
+from sextante.taudem.TauDEMUtils import TauDEMUtils
+
+from sextante.taudem.peukerdouglas import PeukerDouglas
+from sextante.taudem.slopearea import SlopeArea
+from sextante.taudem.lengtharea import LengthArea
+from sextante.taudem.dropanalysis import DropAnalysis
+from sextante.taudem.dinfdistdown import DinfDistDown
+from sextante.taudem.dinfdistup import DinfDistUp
+from sextante.taudem.gridnet import GridNet
+from sextante.taudem.dinftranslimaccum import DinfTransLimAccum
+from sextante.taudem.dinftranslimaccum2 import DinfTransLimAccum2
+
+class TauDEMAlgorithmProvider(AlgorithmProvider):
+
+    def __init__(self):
+        AlgorithmProvider.__init__(self)
+        self.createAlgsList()
+
+    def getDescription(self):
+        return "TauDEM (hydrologic analysis)"
+
+    def getName(self):
+        return "taudem"
+
+    def getIcon(self):
+        return QIcon(os.path.dirname(__file__) + "/../images/taudem.png")
+
+    def initializeSettings(self):
+        AlgorithmProvider.initializeSettings(self)
+        SextanteConfig.addSetting(Setting(self.getDescription(), TauDEMUtils.TAUDEM_FOLDER, "TauDEM command line tools folder", TauDEMUtils.taudemPath()))
+        SextanteConfig.addSetting(Setting(self.getDescription(), TauDEMUtils.MPIEXEC_FOLDER, "MPICH2/OpenMPI bin directory", TauDEMUtils.mpiexecPath()))
+        SextanteConfig.addSetting(Setting(self.getDescription(), TauDEMUtils.MPI_PROCESSES, "Number of MPI parallel processes to use", 2))
+
+    def unload(self):
+        AlgorithmProvider.unload(self)
+        SextanteConfig.removeSetting(TauDEMUtils.TAUDEM_FOLDER)
+        SextanteConfig.removeSetting(TauDEMUtils.MPIEXEC_FOLDER)
+        SextanteConfig.removeSetting(TauDEMUtils.MPI_PROCESSES)
+
+    def _loadAlgorithms(self):
+        self.algs = self.preloadedAlgs
+
+    def createAlgsList(self):
+        self.preloadedAlgs = []
+        folder = TauDEMUtils.taudemDescriptionPath()
+        for descriptionFile in os.listdir(folder):
+            if descriptionFile.endswith("txt"):
+                try:
+                    alg = TauDEMAlgorithm(os.path.join(folder, descriptionFile))
+                    if alg.name.strip() != "":
+                        self.preloadedAlgs.append(alg)
+                    else:
+                        SextanteLog.addToLog(SextanteLog.LOG_ERROR, "Could not open TauDEM algorithm: " + descriptionFile)
+                except Exception, e:
+                    SextanteLog.addToLog(SextanteLog.LOG_ERROR, "Could not open TauDEM algorithm: " + descriptionFile)
+
+        self.preloadedAlgs.append(PeukerDouglas())
+        self.preloadedAlgs.append(SlopeArea())
+        self.preloadedAlgs.append(LengthArea())
+        self.preloadedAlgs.append(DropAnalysis())
+        self.preloadedAlgs.append(DinfDistDown())
+        self.preloadedAlgs.append(DinfDistUp())
+        self.preloadedAlgs.append(GridNet())
+        self.preloadedAlgs.append(DinfTransLimAccum())
+        self.preloadedAlgs.append(DinfTransLimAccum2())

python/plugins/sextante/taudem/TauDEMUtils.py

@@ -0,0 +1,68 @@
+# -*- coding: utf-8 -*-
+
+"""
+***************************************************************************
+    TauDEMUtils.py
+    ---------------------
+    Date                 : October 2012
+    Copyright            : (C) 2012 by Alexander Bruy
+    Email                : alexander dot bruy 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__ = 'Alexander Bruy'
+__date__ = 'October 2012'
+__copyright__ = '(C) 2012, Alexander Bruy'
+# This will get replaced with a git SHA1 when you do a git archive
+__revision__ = '$Format:%H$'
+
+import os
+import subprocess
+
+from sextante.core.SextanteConfig import SextanteConfig
+from sextante.core.SextanteLog import SextanteLog
+from sextante.core.SextanteUtils import SextanteUtils
+
+class TauDEMUtils:
+
+    TAUDEM_FOLDER = "TAUDEM_FOLDER"
+    MPIEXEC_FOLDER = "MPIEXEC_FOLDER"
+    MPI_PROCESSES = "MPI_PROCESSES"
+
+    @staticmethod
+    def taudemPath():
+        folder = SextanteConfig.getSetting(TauDEMUtils.TAUDEM_FOLDER)
+        if folder == None:
+            folder = ""
+
+        return folder
+
+    @staticmethod
+    def mpiexecPath():
+        folder = SextanteConfig.getSetting(TauDEMUtils.MPIEXEC_FOLDER)
+        if folder == None:
+            folder = ""
+
+        return folder
+
+    @staticmethod
+    def taudemDescriptionPath():
+        return os.path.normpath(os.path.join(os.path.dirname(__file__), "description"))
+
+    @staticmethod
+    def executeTauDEM(command, progress):
+        loglines = []
+        loglines.append("TauDEM execution console output")
+        fused_command = ''.join(['"%s" ' % c for c in command])
+        proc = subprocess.Popen(fused_command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True).stdout
+        for line in iter(proc.readline, ""):
+            loglines.append(line)
+        SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)

python/plugins/sextante/taudem/description/aread8.txt

@@ -0,0 +1,8 @@
+D8 Contributing Area
+aread8
+Basic Grid Analysis tools
+ParameterRaster|-p|D8 Flow Direction Grid|False
+ParameterVector|-o|Outlets Shapefile|0|True
+ParameterRaster|-wg|Weight Grid|True
+ParameterBoolean|-nc|Check for edge contamination|True
+OutputRaster|-ad8|D8 Contributing Area Grid

python/plugins/sextante/taudem/description/areadinf.txt

@@ -0,0 +1,8 @@
+D-Infinity Contributing Area
+areadinf
+Basic Grid Analysis tools
+ParameterRaster|-ang|D-Infinity Flow Direction Grid|False
+ParameterVector|-o|Outlets Shapefile|0|True
+ParameterRaster|-wg|Weight Grid|True
+ParameterBoolean|-nc|Check for edge contamination|True
+OutputRaster|-sca|D-Infinity Specific Catchment Area Grid