improved r and saga behaviour, specially on linux; changed some grass…

… descriptions git-svn-id: http://sextante.googlecode.com/svn/trunk/soft/bindings/qgis-plugin@54 881b9c09-3ef8-f3c2-ec3d-21d735c97f4d
qgis · Mar 27, 2012 · 4dbb90e · 4dbb90e
1 parent 9dbfabc
commit 4dbb90e
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Showing 208 changed files with 2,207 additions and 1,912 deletions.
diff --git a/build.xml b/build.xml
@@ -2,14 +2,11 @@
     <description>
         SEXTANTE
     </description>
-    <property name="version.number" value="0.1"/>
-
+    <property name="version.number" value="1.0"/>
   <target name="copy"
     description="copy files">
-
     <copy todir="C:/Users/volaya/.qgis/python/plugins/sextante">
         <fileset dir="src/sextante" includes="**"/>
     </copy>
-
   </target>
 </project>
diff --git a/license.txt b/license.txt
diff --git a/src/sextante/about/about.htm b/src/sextante/about/about.htm
@@ -1,13 +1,14 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head>
-<title>SEXTANTE Spatial Data Analysis Library</title>
+<title>SEXTANTE</title>
 </head>
 <body>
 <img src="sextante_logo.png" />
 <h2>SEXTANTE for QGIS</h2>
 <p>SEXTANTE, a geoprocessing platform for QGIS</p>
-<p>A development by Victor Olaya (volayaf@gmail.com)</p>
+<p>A development by Victor Olaya (volayaf@gmail.com). Portions of this software by Michael Nimm and Carson Farmer</p>
 <p>You are currently using SEXTANTE v1.0</p>
+<p>This software is distributed under the terms of the GNU GPL License v2.
 <p>For more information, please visit our website at <a href="http://sextantegis.com">http://sextantegis.com</a></p>
 </body>
 </html>
diff --git a/src/sextante/core/AlgorithmProvider.py b/src/sextante/core/AlgorithmProvider.py
@@ -22,7 +22,9 @@ def loadAlgorithms(self):
     #methods to be overridden.
     #==============================
 
-    #Algorithm loading should take place here
+    #Algorithm loading should take place here, filling sefl.algs
+    #Since algorithms should have a reference to the provider they come
+    #from, this is also the place to set the 'provider' variable of each algorithm
     def _loadAlgorithms(self):
         pass
 

diff --git a/src/sextante/core/GeoAlgorithm.py b/src/sextante/core/GeoAlgorithm.py
@@ -11,24 +11,30 @@
 class GeoAlgorithm:
 
     def __init__(self):
+        #parameters needed by the algorithm
         self.parameters = list()
+        #outputs generated by the algorithm
         self.outputs = list()
         self.name = ""
         self.group = ""
         self.defineCharacteristics()
-        self.providerName = ""
+        #the crs taken from input layers (if possible), and used when loading output layers
         self.crs = None
-        self.helpfile = None
 
     #methods to overwrite when creating a custom geoalgorithm
     #=========================================================
     def getIcon(self):
         return QtGui.QIcon(os.path.dirname(__file__) + "/../images/alg.png")
 
+    def helpFile(self):
+        return None
+
     def processAlgorithm(self):
+        '''here goes the algorithm itself'''
         pass
 
     def defineCharacteristics(self):
+        '''here is where the parameters and outputs should be filled'''
         pass
 
     #=========================================================
@@ -39,6 +45,7 @@ def execute(self, progress):
         self.processAlgorithm(progress)
 
     def resolveTemporaryOutputs(self):
+        '''sets temporary outputs (output.value = None) with a temporary file instead)'''
         for out in self.outputs:
             if out.value == None:
                 SextanteUtils.setTempOutput(out, self)
@@ -77,21 +84,28 @@ def setOutputValue(self, outputName, value):
             if out.name == outputName:
                 out.value = value
 
+    def getVisibleOutputsCount(self):
+        '''returns the number of non-hidden outputs'''
+        i = 0;
+        for out in self.outputs:
+            if not out.hidden:
+                i+=1
+        return i;
+
     def getOutputValuesAsDictionary(self):
         d = {}
         for out in self.outputs:
             d[out.name] = out.value
         return d
 
-    def canBeExecuted(self, layersCount):
-        return True
 
     def __str__(self):
         s = "ALGORITHM: " + self.name + "\n"
         for param in self.parameters:
             s+=("\t" + str(param) + "\n")
         for out in self.outputs:
-            s+=("\t" + str(out) + "\n")
+            if not out.hidden:
+                s+=("\t" + str(out) + "\n")
         s+=("\n")
         return s
 
@@ -113,13 +127,6 @@ def getParameterFromName(self, name):
     def getParameterValue(self, name):
         for param in self.parameters:
             if param.name == name:
-                #===============================================================
-                # if isinstance(param, ParameterNumber):
-                #    return float(param.value)
-                # elif isinstance(param, ParameterBoolean):
-                #    return param.value == str(True)
-                # else:
-                #===============================================================
                 return param.value
         return None
 
@@ -131,6 +138,7 @@ def getOutputValue(self, name):
 
 
     def getAsCommand(self):
+        '''Returns the command that would run this same algorithm from the console'''
         s="Sextante.runalg(\"" + self.commandLineName() + "\","
         for param in self.parameters:
             s+=param.getValueAsCommandLineParameter() + ","

diff --git a/src/sextante/core/QGisLayers.py b/src/sextante/core/QGisLayers.py
@@ -7,6 +7,8 @@
 import os.path
 
 class QGisLayers:
+    '''This class contains method to communicate SEXTANTE with the QGIS interface,
+    mostly for retrieving layers and adding new ones to the QGIS canvas'''
 
     ALL_TYPES = -1
     iface = None;

diff --git a/src/sextante/core/Sextante.py b/src/sextante/core/Sextante.py
@@ -23,7 +23,7 @@ class Sextante:
     iface = None
     providers = [SagaAlgorithmProvider(), ScriptAlgorithmProvider(),
                  MMQGISAlgorithmProvider(), FToolsAlgorithmProvider(),
-                 RAlgorithmProvider()]##, GrassAlgorithmProvider()]
+                 RAlgorithmProvider()]#, GrassAlgorithmProvider()]
     algs = {}
     actions = {}
     contextMenuActions = []
@@ -134,8 +134,10 @@ def getAlgorithm(name):
                 return provider[name]
         return None
 
+
     ##This methods are here to be used from the python console,
     ##making it easy to use SEXTANTE from there
+    ##==========================================================
 
     @staticmethod
     def alglist(text=None):
@@ -179,7 +181,7 @@ def runalg(name, *args):
         if alg == None:
             print("Error: Algorithm not found\n")
             return
-        if len(args) != len(alg.parameters) + len(alg.outputs):
+        if len(args) != len(alg.parameters) + len(alg.getVisibleOutputsCount()):
             print ("Error: Wrong number of parameters")
             Sextante.alghelp(name)
             return
@@ -193,10 +195,11 @@ def runalg(name, *args):
             i = i +1
 
         for output in alg.outputs:
-            if not output.setValue(args[i]):
-                print ("Error: Wrong output value: " + args[i])
-                return
-            i = i +1
+            if not output.hidden:
+                if not output.setValue(args[i]):
+                    print ("Error: Wrong output value: " + args[i])
+                    return
+                i = i +1
 
         SextanteLog.addToLog(SextanteLog.LOG_ALGORITHM, alg.getAsCommand())
 
@@ -211,15 +214,19 @@ def runalg(name, *args):
 
     @staticmethod
     def load(layer):
+        '''loads a layer into QGIS'''
         QGisLayers.load(layer)
 
     @staticmethod
     def loadFromAlg(layersdict):
+        '''load all layer resulting from a given algorithm.
+        Layers are passed as a dictionary, obtained from alg.getOutputValuesAsDictionary()'''
         QGisLayers.loadFromDict(layersdict)
 
     @staticmethod
-    def getObject(string):
-        QGisLayers.getObjectFromUri(string)
+    def getObject(uri):
+        '''Returns the QGIS object identified the given URI'''
+        QGisLayers.getObjectFromUri(uri)
 
     @staticmethod
     def runandload(name, *args):
@@ -229,7 +236,7 @@ def runandload(name, *args):
             #in theory, this could not happen. Maybe we should show a message box?
             QMessageBox.critical(None,"Error", "Error: Algorithm not found\n")
             return
-        if len(args) != len(alg.parameters) + len(alg.outputs):
+        if len(args) != len(alg.parameters) + len(alg.getVisibleOutputsCount()):
             QMessageBox.critical(None,"Error", "Error: Wrong number of parameters")
             Sextante.alghelp(name)
             return
@@ -243,10 +250,11 @@ def runandload(name, *args):
             i = i +1
 
         for output in alg.outputs:
-            if not output.setValue(args[i]):
-                QMessageBox.critical(None, "Error", "Error: Wrong output value: " + args[i])
-                return
-            i = i +1
+            if not output.hidden:
+                if not output.setValue(args[i]):
+                    QMessageBox.critical(None, "Error", "Error: Wrong output value: " + args[i])
+                    return
+                i = i +1
 
         try:
             QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))

diff --git a/src/sextante/ftools/copyright.txt b/src/sextante/ftools/copyright.txt
@@ -1,7 +1,7 @@
 Copyright notice
 -------------------
 
-Algorithms in this folder have been adapted from the original ftools QGis plugin
+Algorithms in this folder have been adapted from the original fTools QGis plugin
 source code, by Carson Farmer, licensed under the terms of GNU GPL 2
 
 For more info, please check http://www.ftools.ca/fTools.html

diff --git a/src/sextante/grass/GrassAlgorithm.py b/src/sextante/grass/GrassAlgorithm.py
@@ -28,7 +28,10 @@ def __init__(self, descriptionfile):
         self.descriptionFile = descriptionfile
         self.defineCharacteristicsFromFile()
         self.numExportedLayers = 0
-        self.needsregion = False
+        #=======================================================================
+        # #true if the algorithms uses a region
+        # self.needsregion = False
+        #=======================================================================
 
     def __deepcopy__(self,memo):
         newone = GrassAlgorithm(self.descriptionFile)
@@ -38,6 +41,12 @@ def __deepcopy__(self,memo):
     def getIcon(self):
         return  QIcon(os.path.dirname(__file__) + "/../images/grass.png")
 
+    def helpFile(self):
+        folder = SextanteConfig.getSetting(GrassUtils.GRASS_HELP_FOLDER)
+        if str(folder).strip() != "":
+            helpfile = str(folder) + os.sep + self.name + ".html"
+            return helpfile
+        return None
     def defineCharacteristicsFromFile(self):
         lines = open(self.descriptionFile)
         line = lines.readline().strip("\n").strip()
@@ -49,8 +58,10 @@ def defineCharacteristicsFromFile(self):
                 line = line.strip("\n").strip()
                 if line.startswith("Parameter"):
                     self.addParameter(ParameterFactory.getFromString(line))
-                elif line.startswith("Region"):
-                    self.needsregion = True
+                #===============================================================
+                # elif line.startswith("Region"):
+                #    self.needsregion = True
+                #===============================================================
                 else:
                     self.addOutput(OutputFactory.getFromString(line))
                 line = lines.readline().strip("\n").strip()
@@ -64,8 +75,8 @@ def calculateResamplingExtent(self):
         if auto:
             first = True;
             for param in self.parameters:
-                if isinstance(param, ParameterRaster):
-                    if isinstance(param.value, QgsRasterLayer):
+                if isinstance(param, (ParameterRaster, ParameterVector)):
+                    if isinstance(param.value, (QgsRasterLayer, QgsVectorLayer)):
                         value = param.value
                     else:
                         value = QGisLayers.getObjectFromUri(param.value)
@@ -83,35 +94,34 @@ def calculateResamplingExtent(self):
                         self.ymax = max(self.ymax, value.extent().yMaximum())
                         self.cellsize = max(self.cellsize, (value.extent().xMaximum() - value.extent().xMinimum())/value.getRasterXDim())
         else:
-            self.xmin = SextanteConfig.getSetting(SagaUtils.SAGA_RESAMPLING_REGION_XMIN)
-            self.xmax = SextanteConfig.getSetting(SagaUtils.SAGA_RESAMPLING_REGION_XMAX)
-            self.ymin = SextanteConfig.getSetting(SagaUtils.SAGA_RESAMPLING_REGION_YMIN)
-            self.ymax = SextanteConfig.getSetting(SagaUtils.SAGA_RESAMPLING_REGION_YMAX)
-            self.cellsize = SextanteConfig.getSetting(SagaUtils.SAGA_RESAMPLING_REGION_CELLSIZE)
+            self.xmin = SextanteConfig.getSetting(GrassUtils.GRASS_REGION_XMIN)
+            self.xmax = SextanteConfig.getSetting(GrassUtils.GRASS_REGION_XMAX)
+            self.ymin = SextanteConfig.getSetting(GrassUtils.GRASS_REGION_YMIN)
+            self.ymax = SextanteConfig.getSetting(GrassUtils.GRASS_REGION_YMAX)
+            self.cellsize = SextanteConfig.getSetting(GrassUtils.GRASS_REGION_CELLSIZE)
 
 
     def processAlgorithm(self, progress):
         path = GrassUtils.grassPath()
         if path == "":
             raise GeoAlgorithmExecutionException("GRASS folder is not configured.\nPlease configure it before running GRASS algorithms.")
-        useSelection = SextanteConfig.getSetting(SagaUtils.SAGA_USE_SELECTED)
 
         commands = []
         self.exportedLayers = {}
         self.numExportedLayers = 0;
 
-        if self.needsregion:
-            self.calculateResamplingExtent()
+        ##if self.needsregion:
+        self.calculateResamplingExtent()
         GrassUtils.createTempMapset();
 
-        if self.needsregion:
-            command = "g.region"
-            command += " n=" + str(self.ymax)
-            command +=" s=" + str(self.ymin)
-            command +=" e=" + str(self.xmax)
-            command +=" w=" + str(self.xmin)
-            command +=" res=" + str(self.cellsize);
-            commands.append(command)
+        ##if self.needsregion:
+        command = "g.region"
+        command += " n=" + str(self.ymax)
+        command +=" s=" + str(self.ymin)
+        command +=" e=" + str(self.xmax)
+        command +=" w=" + str(self.xmin)
+        command +=" res=" + str(self.cellsize);
+        commands.append(command)
 
         #1: Export layer to grass mapset
         for param in self.parameters:
@@ -138,8 +148,7 @@ def processAlgorithm(self, progress):
                         commands.append(self.exportRasterLayer(layer))
                 elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY:
                     for layer in layers:
-                        if (not value.endswith("shp")) or useSelection:
-                            commands.append(self.exportRasterLayer(layer))
+                        commands.append(self.exportVectorLayer(layer))
 
         #2: set parameters and outputs
         command = self.name