python/plugins/sextante/__init__.py

@@ -17,9 +17,9 @@
 ***************************************************************************
 """
 
-from sextante.core.Sextante import runalg, runandload, alghelp, alglist, algoptions, load, \
-                                    extent, getObjectFromName, getObjectFromUri, getobject, getfeatures
-
+from sextante.tools.general import runalg, runandload, alghelp, alglist, algoptions, load, extent, getobject
+from sextante.tools.vector import getfeatures, spatialindex, values, uniquevalues
+from sextante.tools.raster import scanraster
 from sextante.tests.TestData import loadTestData
 
 __author__ = 'Victor Olaya'

python/plugins/sextante/algs/FieldPyculator.py

@@ -122,8 +122,8 @@ def processAlgorithm(self, progress):
             bytecode = compile(code, '<string>', 'exec')
         except:
             raise GeoAlgorithmExecutionException("FieldPyculator code execute error\n"+
-                                 "Field code block can't be executed! %s \n %s"
-                                 (unicode(sys.exc_info()[0].__name__), unicode(sys.exc_info()[1])))
+                                 "Field code block can't be executed! %s \n %s",
+                                 unicode(sys.exc_info()[0].__name__), unicode(sys.exc_info()[1]))
 
         #run
         features = QGisLayers.features(layer)
@@ -151,17 +151,7 @@ def processAlgorithm(self, progress):
                 del new_ns[self.RESULT_VAR_NAME]
 
             #exec
-            #try:
             exec bytecode in new_ns
-            #except:
-            #    raise e
-            #===============================================================
-            # GeoAlgorithmExecutionException("FieldPyculator code execute error\n"+
-            #            "Field code block can't be executed for feature %s\n%s\n%s" %
-            #            (unicode(sys.exc_info()[0].__name__),
-            #            unicode(sys.exc_info()[1]),
-            #            unicode(feat_id)))
-            #===============================================================
 
             #check result
             if not new_ns.has_key(self.RESULT_VAR_NAME):

python/plugins/sextante/core/Sextante.py

@@ -346,94 +346,3 @@ def cancel():
 ##==========================================================
 
 
-def alglist(text=None):
-    s=""
-    for provider in Sextante.algs.values():
-        sortedlist = sorted(provider.values(), key= lambda alg: alg.name)
-        for alg in sortedlist:
-            if text == None or text.lower() in alg.name.lower():
-                s+=(alg.name.ljust(50, "-") + "--->" + alg.commandLineName() + "\n")
-    print s
-
-def algoptions(name):
-    alg = Sextante.getAlgorithm(name)
-    if alg != None:
-        s =""
-        for param in alg.parameters:
-            if isinstance(param, ParameterSelection):
-                s+=param.name + "(" + param.description + ")\n"
-                i=0
-                for option in param.options:
-                    s+= "\t" + str(i) + " - " + str(option) + "\n"
-                    i+=1
-        print(s)
-    else:
-        print "Algorithm not found"
-
-def alghelp(name):
-    alg = Sextante.getAlgorithm(name)
-    if alg != None:
-        print(str(alg))
-        algoptions(name)
-    else:
-        print "Algorithm not found"
-
-def runalg(algOrName, *args):
-    alg = Sextante.runAlgorithm(algOrName, None, *args)
-    if alg is not None:
-        return alg.getOutputValuesAsDictionary()
-
-def runandload(name, *args):
-    return Sextante.runAlgorithm(name, SextantePostprocessing.handleAlgorithmResults, *args)
-
-def extent(layers):
-    first = True
-    for layer in layers:
-        if not isinstance(layer, (QgsRasterLayer, QgsVectorLayer)):
-            layer = QGisLayers.getObjectFromUri(layer)
-            if layer is None:
-                continue
-        if first:
-            xmin = layer.extent().xMinimum()
-            xmax = layer.extent().xMaximum()
-            ymin = layer.extent().yMinimum()
-            ymax = layer.extent().yMaximum()
-        else:
-            xmin = min(xmin, layer.extent().xMinimum())
-            xmax = max(xmax, layer.extent().xMaximum())
-            ymin = min(ymin, layer.extent().yMinimum())
-            ymax = max(ymax, layer.extent().yMaximum())
-        first = False
-    if first:
-        return "0,0,0,0"
-    else:
-        return str(xmin) + "," + str(xmax) + "," + str(ymin) + "," + str(ymax)
-
-def getObjectFromName(name):
-    layers = QGisLayers.getAllLayers()
-    for layer in layers:
-        if layer.name() == name:
-            return layer
-
-def getObjectFromUri(uri):
-    return QGisLayers.getObjectFromUri(uri, True)
-
-def getobject(uriorname):
-    ret = getObjectFromName(uriorname)
-    if ret is None:
-        ret = getObjectFromUri(uriorname)
-    return ret
-
-def load(path):
-    '''Loads a layer into QGIS'''
-    return QGisLayers.load(path)
-
-def getfeatures(layer):
-    return QGisLayers.features(layer)
-
-#===============================================================================
-# def loadFromAlg(layersdict):
-#    '''Load all layer resulting from a given algorithm.
-#    Layers are passed as a dictionary, obtained from alg.getOutputValuesAsDictionary()'''
-#    QGisLayers.loadFromDict(layersdict)
-#===============================================================================

python/plugins/sextante/grass/GrassAlgorithm.py

@@ -294,9 +294,14 @@ def processAlgorithm(self, progress):
         uniqueSufix = str(uuid.uuid4()).replace("-","");
         for out in self.outputs:
             if isinstance(out, OutputFile):
-                command+=(" " + out.name + "=\"" + out.value + "\"");
-            elif not isinstance(out, OutputHTML): #html files are not generated by grass, only by sextante to decorate grass output
-                #an output name to make sure it is unique if the session uses this algorithm several times
+                if out.name == 'outputtext':
+                    #the 'outputtext' file is generated by piping output from GRASS, is not an actual grass command
+                    command+= (" > " + out.value)
+                else:
+                    command+=(" " + out.name + "=\"" + out.value + "\"");
+            elif not isinstance(out, OutputHTML):                         
+                #html files are not generated by GRASS, only by SEXTANTE to decorate grass output, so we skip them                
+                #An output name to make sure it is unique if the session uses this algorithm several times
                 uniqueOutputName = out.name + uniqueSufix
                 command += (" " + out.name + "=" + uniqueOutputName)
                 # add output file to exported layers, to indicate that they are present in GRASS

python/plugins/sextante/grass/description/r.quantile.txt

@@ -5,3 +5,4 @@ ParameterRaster|input|Input raster layer|False
 ParameterNumber|quantiles|Number of quantiles|2|None|4
 *ParameterBoolean|-r|Generate recode rules based on quantile-defined intervals|False
 OutputHTML|html|Output report
+OutputFile|outputtext|Output text file

python/plugins/sextante/grass/grass.txt

@@ -76,3 +76,19 @@ to tag a parameter as "advanced", just add "*" before its declaration. For insta
 *ParameterBoolean|-c|-c|True
 
 
+ADVANCED OUTPUT PROCESSING
+-------------------------
+
+In some cases, it might be interesting to take the console otput from GRASS and extract a part of it for saving or formatting.
+
+Two things can be done about this:
+
+-Creating an HTML file with output. Just add an output of type OutputHTML. 
+It's value will not be passed to GRASS, but you can use it later to create the HTML file from the console output. 
+You should create a python file in the grass/ext package, with the same name as the grass module, with dots replaced by low hyphens
+(for instance r_quantile.py for the r.quantile command), and add a postProcessResults(alg) method. It will be called when the 
+execution of the GRASS command is finished.
+-Creating a text file. Do as above, but adding an otput of type OutputFile. Since some GRASS commands might use this type of output, 
+and to make sure that the value of this output is not passed to the GRASS comman when calling it, the output has to be named 'outputtext'
+
+

python/plugins/sextante/script/scripts/Create_tiling_from_vector_layer.py

@@ -28,7 +28,7 @@
 ##numpolygons=number 10
 ##polygons=output vector
 
-input = sextante.getObjectFromUri(input)
+input = sextante.getobject(input)
 centerx = (input.extent().xMinimum() + input.extent().xMaximum()) / 2
 centery = (input.extent().yMinimum() + input.extent().yMaximum()) / 2
 width = (input.extent().xMaximum() - input.extent().xMinimum())

python/plugins/sextante/script/scripts/Hex_grid_from_layer_bounds.py

@@ -29,7 +29,7 @@
 ##grid=output vector
 from sextante.core.QGisLayers import QGisLayers
 
-input = QGisLayers.getObjectFromUri(input)
+input = sextante.getobject(input)
 centerx = (input.extent().xMinimum() + input.extent().xMaximum()) / 2
 centery = (input.extent().yMinimum() + input.extent().yMaximum()) / 2
 width = (input.extent().xMaximum() - input.extent().xMinimum())

python/plugins/sextante/tests/GdalTest.py

@@ -0,0 +1,37 @@
+import sextante
+import unittest
+from sextante.tests.TestData import points, points2, polygons, polygons2, lines, union,\
+    table, polygonsGeoJson, raster
+from sextante.core.QGisLayers import QGisLayers
+import os
+from osgeo import gdal
+from osgeo.gdalconst import GA_ReadOnly
+from sextante.core.SextanteUtils import SextanteUtils
+
+class GdalTest(unittest.TestCase):
+
+    def test_gdalogrsieve(self):
+        outputs=sextante.runalg("gdalogr:sieve",raster(),2,0,None)
+        output=outputs['dst_filename']
+        self.assertTrue(os.path.isfile(output))
+        dataset=gdal.Open(output, GA_ReadOnly)
+        strhash=hash(str(dataset.ReadAsArray(0).tolist()))
+        self.assertEqual(strhash,-1353696889)
+
+    def test_gdalogrsieveWithUnsupportedOutputFormat(self):
+        outputs=sextante.runalg("gdalogr:sieve",raster(),2,0, SextanteUtils.getTempFilename("img"))
+        output=outputs['dst_filename']
+        self.assertTrue(os.path.isfile(output))
+        dataset=gdal.Open(output, GA_ReadOnly)
+        strhash=hash(str(dataset.ReadAsArray(0).tolist()))
+        self.assertEqual(strhash,-1353696889)        
+
+def suite():
+    suite = unittest.makeSuite(GdalTest, 'test')
+    return suite
+
+def runtests():
+    result = unittest.TestResult()
+    testsuite = suite()
+    testsuite.run(result)
+    return result

python/plugins/sextante/tests/ModelerAlgorithmTest.py

@@ -29,14 +29,7 @@ def testRemoveAlgorithm(self):
         model.provider = Providers.providers['model']
         self.assertTrue(2, len(model.algs))
         self.assertFalse(model.removeAlgorithm(0))
-        self.assertTrue(model.removeAlgorithm(len(model.algs) - 1));
-        from threading import settrace
-
-        import sys
-        sys.path.append("D:\eclipse\plugins\org.python.pydev_2.6.0.2012062818\pysrc")
-        from pydevd import *
-        settrace()
-
+        self.assertTrue(model.removeAlgorithm(len(model.algs) - 1));        
         model.execute(None)
         outputs = model.outputs
         self.assertEquals(1, len(outputs))

python/plugins/sextante/tests/SagaTest.py

@@ -85,12 +85,12 @@ def test_SagaVectorAlgorithWithUnsupportedInputAndOutputFormat(self):
         self.assertEqual(wkt, str(feature.geometry().exportToWkt()))
 
     def test_SagaRasterAlgorithmWithUnsupportedOutputFormat(self):
-        outputs=sextante.runalg("saga:convergenceindex",raster(),0,0,None)
+        outputs=sextante.runalg("saga:convergenceindex",raster(),0,0,SextanteUtils.getTempFilename("img"))
         output=outputs['RESULT']
         self.assertTrue(os.path.isfile(output))
         dataset=gdal.Open(output, GA_ReadOnly)
         strhash=hash(str(dataset.ReadAsArray(0).tolist()))
-        self.assertEqual(strhash,-807227462)
+        self.assertEqual(strhash, 485390137)
 
 
 def suite():

python/plugins/sextante/tests/ScriptTest.py

@@ -52,7 +52,9 @@ def test_scripthexgridfromlayerbounds(self):
     def test_scriptascriptthatreturnsanumber(self):
         outputs=sextante.runalg("script:ascriptthatreturnsanumber")
         output=outputs['number']
-        self.assertTrue(10, output.value)
+        self.assertTrue(10, output)
+
+
 
 def suite():
     suite = unittest.makeSuite(ScriptTest, 'test')

python/plugins/sextante/tests/SextanteTests.py

@@ -7,12 +7,14 @@
 from sextante.tests import ScriptTest
 from sextante.tests import SagaTest
 from sextante.tests import GeoAlgorithmTest
+from sextante.tests import GdalTest
 
 def suite():
     suite = unittest.TestSuite()
     suite.addTests(QgisAlgsTest.suite())
     suite.addTests(ModelerAlgorithmTest.suite())
     suite.addTests(SagaTest.suite())
+    suite.addTests(GdalTest.suite())
     suite.addTests(ScriptTest.suite())
     suite.addTests(SextanteToolsTest.suite())    
     #suite.addTests(ParametersTest.suite())

python/plugins/sextante/tests/SextanteToolsTest.py

@@ -3,7 +3,8 @@
 from sextante.tests.TestData import points, points2, polygons, polygons2, lines, union,\
     table, polygonsGeoJson, raster
 from sextante.core import Sextante
-from sextante.tools.vector import getAttributeValues
+from sextante.tools.vector import values
+from sextante.tools.general import getfromname
 
 class SextanteToolsTest(unittest.TestCase):
     '''tests the method imported when doing an "import sextante", and also in sextante.tools. 
@@ -17,7 +18,7 @@ def test_getobject(self):
 
     def test_runandload(self):
         sextante.runandload("qgis:countpointsinpolygon",polygons(),points(),"NUMPOINTS", None)        
-        layer = Sextante.getObjectFromName("Result")
+        layer = getfromname("Result")
         self.assertIsNotNone(layer)  
 
     def test_featuresWithoutSelection(self):
@@ -36,9 +37,9 @@ def test_featuresWithSelection(self):
 
     def test_attributeValues(self):
         layer = sextante.getobject(points()) 
-        values = getAttributeValues(layer, "ID")
+        attributeValues = values(layer, "ID")
         i = 1
-        for value in values['ID']:
+        for value in attributeValues['ID']:
             self.assertEqual(int(i), int(value))
             i+=1            
         self.assertEquals(13,i)

python/plugins/sextante/tools/__init__.py

@@ -23,5 +23,3 @@
 # This will get replaced with a git SHA1 when you do a git archive
 __revision__ = '$Format:%H$'
 
-from sextante.tools.vector import getAttributeValues
-from sextante.tools.raster import scanraster