def exportVectorLayer(self, orgFilename): # TODO: improve this. We are now exporting if it is not a shapefile, # but the functionality of v.in.ogr could be used for this. # We also export if there is a selection if not os.path.exists(orgFilename) or not orgFilename.endswith('shp'): layer = dataobjects.getObjectFromUri(orgFilename, False) if layer: filename = dataobjects.exportVectorLayer(layer) else: layer = dataobjects.getObjectFromUri(orgFilename, False) if layer: useSelection = \ ProcessingConfig.getSetting(ProcessingConfig.USE_SELECTED) if useSelection and layer.selectedFeatureCount() != 0: filename = dataobjects.exportVectorLayer(layer) else: filename = orgFilename else: filename = orgFilename destFilename = self.getTempFilename() self.exportedLayers[orgFilename] = destFilename command = 'v.in.ogr' min_area = self.getParameterValue(self.GRASS_MIN_AREA_PARAMETER) command += ' min_area=' + unicode(min_area) snap = self.getParameterValue(self.GRASS_SNAP_TOLERANCE_PARAMETER) command += ' snap=' + unicode(snap) command += ' input="' + os.path.dirname(filename) + '"' command += ' layer=' + os.path.basename(filename)[:-4] command += ' output=' + destFilename command += ' --overwrite -o' return command
def getSafeExportedLayer(self): """Returns not the value entered by the user, but a string with a filename which contains the data of this layer, but saved in a standard format (currently always a shapefile) so that it can be opened by most external applications. If there is a selection and QGIS is configured to use just the selection, if exports the layer even if it is already in a suitable format. Works only if the layer represented by the parameter value is currently loaded in QGIS. Otherwise, it will not perform any export and return the current value string. If the current value represents a layer in a suitable format, it does not export at all and returns that value. The layer is exported just the first time the method is called. The method can be called several times and it will always return the same file, performing the export only the first time. """ context = dataobjects.createContext() if self.exported: return self.exported layer = QgsProcessingUtils.mapLayerFromString(self.value, context, False) if layer: self.exported = dataobjects.exportVectorLayer(layer) else: self.exported = self.value return self.exported
def getSafeExportedLayers(self): '''Returns not the value entered by the user, but a string with semicolon-separated filenames which contains the data of the selected layers, but saved in a standard format (currently shapefiles for vector layers and GeoTiff for raster) so that they can be opened by most external applications. If there is a selection and QGIS is configured to use just the selection, if exports the layer even if it is already in a suitable format. Works only if the layer represented by the parameter value is currently loaded in QGIS. Otherwise, it will not perform any export and return the current value string. If the current value represents a layer in a suitable format, it does no export at all and returns that value. Currently, it works just for vector layer. In the case of raster layers, it returns the parameter value. The layers are exported just the first time the method is called. The method can be called several times and it will always return the same string, performing the export only the first time.''' if self.exported: return self.exported self.exported = self.value layers = self.value.split(";") if layers == None or len(layers) == 0: return self.value if self.datatype == ParameterMultipleInput.TYPE_RASTER: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportRasterLayer(layer) self.exported = self.exported.replace(layerfile, filename) return self.exported else: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exported = self.exported.replace(layerfile, filename) return self.exported
def processAlgorithm(self, progress): field = self.getParameterValue(self.FIELD) field = field[0:10] # try to handle Shapefile field length limit filename = self.getParameterValue(self.INPUT) layer = dataobjects.getObjectFromUri(filename) filename = dataobjects.exportVectorLayer(layer) contiguity = self.getParameterValue(self.CONTIGUITY) if contiguity == 0: # queen print 'INFO: Moran\'s using queen contiguity' w=pysal.queen_from_shapefile(filename) else: # 1 for rook print 'INFO: Moran\'s using rook contiguity' w=pysal.rook_from_shapefile(filename) f = pysal.open(filename.replace('.shp','.dbf')) y=np.array(f.by_col[str(field)]) m = pysal.Moran(y,w,transformation = "r", permutations = 999) self.setOutputValue(self.I,m.I) print "Moran's I: %f" % (m.I) print "INFO: Moran's I values range from -1 (indicating perfect dispersion) to +1 (perfect correlation). Values close to -1/(n-1) indicate a random spatial pattern." print "p_norm: %f" % (m.p_norm) print "p_rand: %f" % (m.p_rand) print "p_sim: %f" % (m.p_sim) print "INFO: p values smaller than 0.05 indicate spatial autocorrelation that is significant at the 5% level." print "z_norm: %f" % (m.z_norm) print "z_rand: %f" % (m.z_rand) print "z_sim: %f" % (m.z_sim) print "INFO: z values greater than 1.96 or smaller than -1.96 indicate spatial autocorrelation that is significant at the 5% level."
def processAlgorithm(self, progress): commands = self.getConsoleCommands() layers = dataobjects.getVectorLayers() for i, c in enumerate(commands): for layer in layers: if layer.source() in c: c = c.replace(layer.source(), dataobjects.exportVectorLayer(layer)) commands[i] = c GdalUtils.runGdal(commands, progress)
def processAlgorithm(self, progress): commands = self.getConsoleCommands() layers = dataobjects.getVectorLayers() supported = dataobjects.getSupportedOutputVectorLayerExtensions() for i, c in enumerate(commands): for layer in layers: if layer.source() in c: exported = dataobjects.exportVectorLayer(layer, supported) exportedFileName = os.path.splitext(os.path.split(exported)[1])[0] c = c.replace(layer.source(), exported) if os.path.isfile(layer.source()): fileName = os.path.splitext(os.path.split(layer.source())[1])[0] c = c.replace(fileName, exportedFileName) commands[i] = c GdalUtils.runGdal(commands, progress)
def processAlgorithm(self, progress): self.createCatalog() inputFilename = self.getParameterValue(self.INPUT) layer = dataobjects.getObjectFromUri(inputFilename) workspaceName = self.getParameterValue(self.WORKSPACE) filename = dataobjects.exportVectorLayer(layer) basefilename = os.path.basename(filename) basepathname = os.path.dirname(filename) + os.sep + basefilename[:basefilename.find('.')] connection = { 'shp': basepathname + '.shp', 'shx': basepathname + '.shx', 'dbf': basepathname + '.dbf', 'prj': basepathname + '.prj' } workspace = self.catalog.get_workspace(workspaceName) self.catalog.create_featurestore(basefilename, connection, workspace)
def processAlgorithm(self, progress): self.createCatalog() inputFilename = self.getParameterValue(self.INPUT) layer = dataobjects.getObjectFromUri(inputFilename) workspaceName = self.getParameterValue(self.WORKSPACE) filename = dataobjects.exportVectorLayer(layer) basefilename = os.path.basename(filename) basepathname = os.path.dirname(filename) + os.sep + basefilename[: basefilename.find(".")] connection = { "shp": basepathname + ".shp", "shx": basepathname + ".shx", "dbf": basepathname + ".dbf", "prj": basepathname + ".prj", } workspace = self.catalog.get_workspace(workspaceName) self.catalog.create_featurestore(basefilename, connection, workspace)
def processAlgorithm(self, parameters, context, feedback): commands = self.getConsoleCommands(parameters) layers = QgsProcessingUtils.compatibleVectorLayers(QgsProject.instance()) supported = QgsVectorFileWriter.supportedFormatExtensions() for i, c in enumerate(commands): for layer in layers: if layer.source() in c: exported = dataobjects.exportVectorLayer(layer, supported) exportedFileName = os.path.splitext(os.path.split(exported)[1])[0] c = c.replace(layer.source(), exported) if os.path.isfile(layer.source()): fileName = os.path.splitext(os.path.split(layer.source())[1])[0] c = re.sub('[\s]{}[\s]'.format(fileName), ' ' + exportedFileName + ' ', c) c = re.sub('[\s]{}'.format(fileName), ' ' + exportedFileName, c) c = re.sub('["\']{}["\']'.format(fileName), "'" + exportedFileName + "'", c) commands[i] = c GdalUtils.runGdal(commands, feedback)
def processAlgorithm(self, feedback): commands = self.getConsoleCommands() layers = dataobjects.getVectorLayers() supported = dataobjects.getSupportedOutputVectorLayerExtensions() for i, c in enumerate(commands): for layer in layers: if layer.source() in c: exported = dataobjects.exportVectorLayer(layer, supported) exportedFileName = os.path.splitext(os.path.split(exported)[1])[0] c = c.replace(layer.source(), exported) if os.path.isfile(layer.source()): fileName = os.path.splitext(os.path.split(layer.source())[1])[0] c = re.sub('[\s]{}[\s]'.format(fileName), ' ' + exportedFileName + ' ', c) c = re.sub('[\s]{}'.format(fileName), ' ' + exportedFileName, c) c = re.sub('["\']{}["\']'.format(fileName), "'" + exportedFileName + "'", c) commands[i] = c GdalUtils.runGdal(commands, feedback)
def processAlgorithm(self, progress): if isWindows(): path = SagaUtils.sagaPath() if path == "": raise GeoAlgorithmExecutionException("SAGA folder is not configured.\nPlease configure it before running SAGA algorithms.") commands = list() self.exportedLayers = {} self.preProcessInputs() #1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. if self.resample: self.calculateResamplingExtent() for param in self.parameters: if isinstance(param, ParameterRaster): if param.value == None: continue value = param.value if not value.endswith("sgrd"): commands.append(self.exportRasterLayer(value)) if self.resample: commands.append(self.resampleRasterLayer(value)); if isinstance(param, ParameterVector): if param.value == None: continue layer = dataobjects.getObjectFromUri(param.value, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value]=filename elif not param.value.endswith("shp"): raise GeoAlgorithmExecutionException("Unsupported file format") if isinstance(param, ParameterTable): if param.value == None: continue table = dataobjects.getObjectFromUri(param.value, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value]=filename elif not param.value.endswith("shp"): raise GeoAlgorithmExecutionException("Unsupported file format") if isinstance(param, ParameterMultipleInput): if param.value == None: continue layers = param.value.split(";") if layers == None or len(layers) == 0: continue if param.datatype == ParameterMultipleInput.TYPE_RASTER: for layerfile in layers: if not layerfile.endswith("sgrd"): commands.append(self.exportRasterLayer(layerfile)) if self.resample: commands.append(self.resampleRasterLayer(layerfile)); elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile]=filename elif (not layerfile.endswith("shp")): raise GeoAlgorithmExecutionException("Unsupported file format") #2: set parameters and outputs saga208 = ProcessingConfig.getSetting(SagaUtils.SAGA_208) if isWindows() or isMac() or not saga208: command = self.undecoratedGroup + " \"" + self.cmdname + "\"" else: command = "lib" + self.undecoratedGroup + " \"" + self.cmdname + "\"" if self.hardcodedStrings: for s in self.hardcodedStrings: command += " " + s for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in self.exportedLayers.keys(): command += (" -" + param.name + " \"" + self.exportedLayers[value] + "\"") else: command += (" -" + param.name + " \"" + value + "\"") elif isinstance(param, ParameterMultipleInput): s = param.value for layer in self.exportedLayers.keys(): s = s.replace(layer, self.exportedLayers[layer]) command += (" -" + param.name + " \"" + s + "\""); elif isinstance(param, ParameterBoolean): if param.value: command+=(" -" + param.name); elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename("txt") f = open(tempTableFile, "w") f.write('\t'.join([col for col in param.cols]) + "\n") values = param.value.split(",") for i in range(0, len(values), 3): s = values[i] + "\t" + values[i+1] + "\t" + values[i+2] + "\n" f.write(s) f.close() command+=( " -" + param.name + " \"" + tempTableFile + "\"") elif isinstance(param, ParameterExtent): #'we have to substract/add half cell size, since saga is center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(",") for i in range(4): command+=(" -" + self.extentParamNames[i] + " " + str(float(values[i]) + offset[i])); elif isinstance(param, (ParameterNumber, ParameterSelection)): command+=(" -" + param.name + " " + str(param.value)); else: command+=(" -" + param.name + " \"" + str(param.value) + "\""); for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename += ".sgrd" command+=(" -" + out.name + " \"" + filename + "\""); if isinstance(out, OutputVector): filename = out.getCompatibleFileName(self) command+=(" -" + out.name + " \"" + filename + "\""); if isinstance(out, OutputTable): filename = out.getCompatibleFileName(self) command+=(" -" + out.name + " \"" + filename + "\""); commands.append(command) #3:Export resulting raster layers for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + ".sgrd" formatIndex = 1 if saga208 else 4 if isWindows() or isMac() or not saga208: commands.append("io_gdal 1 -GRIDS \"" + filename2 + "\" -FORMAT " + str(formatIndex) +" -TYPE 0 -FILE \"" + filename + "\""); else: commands.append("libio_gdal 1 -GRIDS \"" + filename2 + "\" -FORMAT 1 -TYPE 0 -FILE \"" + filename + "\""); #4 Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append("SAGA execution commands") for line in commands: progress.setCommand(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) SagaUtils.executeSaga(progress);
def processAlgorithm(self, progress): if isWindows(): path = SagaUtils.sagaPath() if path == '': raise GeoAlgorithmExecutionException( 'SAGA folder is not configured.\nPlease configure \ it before running SAGA algorithms.') commands = list() self.exportedLayers = {} self.preProcessInputs() # 1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. if self.resample: self.calculateResamplingExtent() for param in self.parameters: if isinstance(param, ParameterRaster): if param.value is None: continue value = param.value if not value.endswith('sgrd'): exportCommand = self.exportRasterLayer(value) if exportCommand is not None: commands.append(exportCommand) if self.resample: commands.append(self.resampleRasterLayer(value)) if isinstance(param, ParameterVector): if param.value is None: continue layer = dataobjects.getObjectFromUri(param.value, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') if isinstance(param, ParameterTable): if param.value is None: continue table = dataobjects.getObjectFromUri(param.value, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') if isinstance(param, ParameterMultipleInput): if param.value is None: continue layers = param.value.split(';') if layers is None or len(layers) == 0: continue if param.datatype == ParameterMultipleInput.TYPE_RASTER: for layerfile in layers: if not layerfile.endswith('sgrd'): exportCommand = self.exportRasterLayer(layerfile) if exportCommand is not None: commands.append(exportCommand) if self.resample: commands.append( self.resampleRasterLayer(layerfile)) elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile] = filename elif not layerfile.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') # 2: Set parameters and outputs saga208 = ProcessingConfig.getSetting(SagaUtils.SAGA_208) if isWindows() or isMac() or not saga208: command = self.undecoratedGroup + ' "' + self.cmdname + '"' else: command = 'lib' + self.undecoratedGroup + ' "' + self.cmdname + '"' if self.hardcodedStrings: for s in self.hardcodedStrings: command += ' ' + s for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in self.exportedLayers.keys(): command += ' -' + param.name + ' "' \ + self.exportedLayers[value] + '"' else: command += ' -' + param.name + ' "' + value + '"' elif isinstance(param, ParameterMultipleInput): s = param.value for layer in self.exportedLayers.keys(): s = s.replace(layer, self.exportedLayers[layer]) command += ' -' + param.name + ' "' + s + '"' elif isinstance(param, ParameterBoolean): if param.value: command += ' -' + param.name elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename('txt') f = open(tempTableFile, 'w') f.write('\t'.join([col for col in param.cols]) + '\n') values = param.value.split(',') for i in range(0, len(values), 3): s = values[i] + '\t' + values[i + 1] + '\t' + values[i + 2] + '\n' f.write(s) f.close() command += ' -' + param.name + ' "' + tempTableFile + '"' elif isinstance(param, ParameterExtent): # 'We have to substract/add half cell size, since SAGA is # center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(',') for i in range(4): command += ' -' + self.extentParamNames[i] + ' ' \ + str(float(values[i]) + offset[i]) elif isinstance(param, (ParameterNumber, ParameterSelection)): command += ' -' + param.name + ' ' + str(param.value) else: command += ' -' + param.name + ' "' + str(param.value) + '"' for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename += '.sgrd' command += ' -' + out.name + ' "' + filename + '"' if isinstance(out, OutputVector): filename = out.getCompatibleFileName(self) command += ' -' + out.name + ' "' + filename + '"' if isinstance(out, OutputTable): filename = out.getCompatibleFileName(self) command += ' -' + out.name + ' "' + filename + '"' commands.append(command) # 3: Export resulting raster layers optim = ProcessingConfig.getSetting( SagaUtils.SAGA_IMPORT_EXPORT_OPTIMIZATION) for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + '.sgrd' formatIndex = (4 if not saga208 and isWindows() else 1) sessionExportedLayers[filename] = filename2 dontExport = True # Do not export is the output is not a final output # of the model if self.model is not None and optim: for subalg in self.model.algOutputs: if out.name in subalg: if subalg[out.name] is not None: dontExport = False break if dontExport: continue transform = ('' if saga208 else '-TRANSFORM') if isWindows() or isMac() or not saga208: commands.append('io_gdal 1 -GRIDS "' + filename2 + '" -FORMAT ' + str(formatIndex) + ' -TYPE 0 -FILE "' + filename + '"' + transform) else: commands.append('libio_gdal 1 -GRIDS "' + filename2 + '" -FORMAT 1 -TYPE 0 -FILE "' + filename + '"' + transform) # 4: Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append('SAGA execution commands') for line in commands: progress.setCommand(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) SagaUtils.executeSaga(progress)
def processAlgorithm(self, progress): field = self.getParameterValue(self.FIELD) field = field[0:10] # try to handle Shapefile field length limit filename = self.getParameterValue(self.INPUT) layer = dataobjects.getObjectFromUri(filename) filename = dataobjects.exportVectorLayer(layer) provider = layer.dataProvider() fields = provider.fields() fields.append(QgsField('MORANS_P', QVariant.Double)) fields.append(QgsField('MORANS_Z', QVariant.Double)) fields.append(QgsField('MORANS_Q', QVariant.Int)) fields.append(QgsField('MORANS_I', QVariant.Double)) fields.append(QgsField('MORANS_C', QVariant.Double)) writer = self.getOutputFromName(self.OUTPUT).getVectorWriter( fields, provider.geometryType(), layer.crs() ) contiguity = self.getParameterValue(self.CONTIGUITY) if contiguity == 'queen': print 'INFO: Local Moran\'s using queen contiguity' w=pysal.queen_from_shapefile(filename) else: print 'INFO: Local Moran\'s using rook contiguity' w=pysal.rook_from_shapefile(filename) f = pysal.open(filename.replace('.shp','.dbf')) y=np.array(f.by_col[str(field)]) lm = pysal.Moran_Local(y,w,transformation = "r", permutations = 999) # http://pysal.readthedocs.org/en/latest/library/esda/moran.html?highlight=local%20moran#pysal.esda.moran.Moran_Local # values indicate quadrat location 1 HH, 2 LH, 3 LL, 4 HL # http://www.biomedware.com/files/documentation/spacestat/Statistics/LM/Results/Interpreting_univariate_Local_Moran_statistics.htm # category - scatter plot quadrant - autocorrelation - interpretation # high-high - upper right (red) - positive - Cluster - "I'm high and my neighbors are high." # high-low - lower right (pink) - negative - Outlier - "I'm a high outlier among low neighbors." # low-low - lower left (med. blue) - positive - Cluster - "I'm low and my neighbors are low." # low-high - upper left (light blue) - negative - Outlier - "I'm a low outlier among high neighbors." # http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#/What_is_a_z_score_What_is_a_p_value/005p00000006000000/ # z-score (Standard Deviations) | p-value (Probability) | Confidence level # < -1.65 or > +1.65 | < 0.10 | 90% # < -1.96 or > +1.96 | < 0.05 | 95% # < -2.58 or > +2.58 | < 0.01 | 99% self.setOutputValue(self.P_SIM, str(lm.p_sim)) sig_q = lm.q * (lm.p_sim <= 0.01) # could make significance level an option outFeat = QgsFeature() i = 0 for inFeat in processing.features(layer): inGeom = inFeat.geometry() outFeat.setGeometry(inGeom) attrs = inFeat.attributes() attrs.append(float(lm.p_sim[i])) attrs.append(float(lm.z_sim[i])) attrs.append(int(lm.q[i])) attrs.append(float(lm.Is[i])) attrs.append(int(sig_q[i])) outFeat.setAttributes(attrs) writer.addFeature(outFeat) i+=1 del writer
def processAlgorithm(self, progress): commands = list() self.exportedLayers = {} self.preProcessInputs() # 1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. for param in self.parameters: if isinstance(param, ParameterRaster): if param.value is None: continue if param.value.endswith('sdat'): param.value = param.value[:-4] + "sgrd" elif not param.value.endswith('sgrd'): exportCommand = self.exportRasterLayer(param.value) if exportCommand is not None: commands.append(exportCommand) if isinstance(param, ParameterVector): if param.value is None: continue layer = dataobjects.getObjectFromUri(param.value, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) if isinstance(param, ParameterTable): if param.value is None: continue table = dataobjects.getObjectFromUri(param.value, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) if isinstance(param, ParameterMultipleInput): if param.value is None: continue layers = param.value.split(';') if layers is None or len(layers) == 0: continue if param.datatype == ParameterMultipleInput.TYPE_RASTER: for i, layerfile in enumerate(layers): if layerfile.endswith('sdat'): layerfile = param.value[:-4] + "sgrd" layers[i] = layerfile elif not layerfile.endswith('sgrd'): exportCommand = self.exportRasterLayer(layerfile) if exportCommand is not None: commands.append(exportCommand) param.value = ";".join(layers) elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile] = filename elif not layerfile.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) # 2: Set parameters and outputs command = self.undecoratedGroup + ' "' + self.cmdname + '"' if self.hardcodedStrings: for s in self.hardcodedStrings: command += ' ' + s for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in self.exportedLayers.keys(): command += ' -' + param.name + ' "' \ + self.exportedLayers[value] + '"' else: command += ' -' + param.name + ' "' + value + '"' elif isinstance(param, ParameterMultipleInput): s = param.value for layer in self.exportedLayers.keys(): s = s.replace(layer, self.exportedLayers[layer]) command += ' -' + param.name + ' "' + s + '"' elif isinstance(param, ParameterBoolean): if param.value: command += ' -' + param.name elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename('txt') f = open(tempTableFile, 'w') f.write('\t'.join([col for col in param.cols]) + '\n') values = param.value.split(',') for i in range(0, len(values), 3): s = values[i] + '\t' + values[i + 1] + '\t' + values[i + 2] + '\n' f.write(s) f.close() command += ' -' + param.name + ' "' + tempTableFile + '"' elif isinstance(param, ParameterExtent): # 'We have to substract/add half cell size, since SAGA is # center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(',') for i in range(4): command += ' -' + self.extentParamNames[i] + ' ' \ + unicode(float(values[i]) + offset[i]) elif isinstance(param, (ParameterNumber, ParameterSelection)): command += ' -' + param.name + ' ' + unicode(param.value) else: command += ' -' + param.name + ' "' + unicode(param.value) + '"' for out in self.outputs: command += ' -' + out.name + ' "' + out.getCompatibleFileName(self) + '"' commands.append(command) # special treatment for RGB algorithm #TODO: improve this and put this code somewhere else for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + '.sgrd' if self.cmdname == 'RGB Composite': commands.append('io_grid_image 0 -IS_RGB -GRID:"' + filename2 + '" -FILE:"' + filename + '"') # 3: Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append(self.tr('SAGA execution commands')) for line in commands: progress.setCommand(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) SagaUtils.executeSaga(progress) if self.crs is not None: for out in self.outputs: if isinstance(out, (OutputVector, OutputRaster)): prjFile = os.path.splitext(out.getCompatibleFileName(self))[0] + ".prj" with open(prjFile, "w") as f: f.write(self.crs.toWkt())
def processAlgorithm(self, progress): commands = list() self.exportedLayers = {} self.preProcessInputs() # 1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. for param in self.parameters: if isinstance(param, ParameterRaster): if param.value is None: continue value = param.value if not value.endswith("sgrd"): exportCommand = self.exportRasterLayer(value) if exportCommand is not None: commands.append(exportCommand) if isinstance(param, ParameterVector): if param.value is None: continue layer = dataobjects.getObjectFromUri(param.value, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value] = filename elif not param.value.endswith("shp"): raise GeoAlgorithmExecutionException(self.tr("Unsupported file format")) if isinstance(param, ParameterTable): if param.value is None: continue table = dataobjects.getObjectFromUri(param.value, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value] = filename elif not param.value.endswith("shp"): raise GeoAlgorithmExecutionException(self.tr("Unsupported file format")) if isinstance(param, ParameterMultipleInput): if param.value is None: continue layers = param.value.split(";") if layers is None or len(layers) == 0: continue if param.datatype == ParameterMultipleInput.TYPE_RASTER: for layerfile in layers: if not layerfile.endswith("sgrd"): exportCommand = self.exportRasterLayer(layerfile) if exportCommand is not None: commands.append(exportCommand) elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile] = filename elif not layerfile.endswith("shp"): raise GeoAlgorithmExecutionException(self.tr("Unsupported file format")) # 2: Set parameters and outputs command = self.undecoratedGroup + ' "' + self.cmdname + '"' if self.hardcodedStrings: for s in self.hardcodedStrings: command += " " + s for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in self.exportedLayers.keys(): command += " -" + param.name + ' "' + self.exportedLayers[value] + '"' else: command += " -" + param.name + ' "' + value + '"' elif isinstance(param, ParameterMultipleInput): s = param.value for layer in self.exportedLayers.keys(): s = s.replace(layer, self.exportedLayers[layer]) command += " -" + param.name + ' "' + s + '"' elif isinstance(param, ParameterBoolean): if param.value: command += " -" + param.name elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename("txt") f = open(tempTableFile, "w") f.write("\t".join([col for col in param.cols]) + "\n") values = param.value.split(",") for i in range(0, len(values), 3): s = values[i] + "\t" + values[i + 1] + "\t" + values[i + 2] + "\n" f.write(s) f.close() command += " -" + param.name + ' "' + tempTableFile + '"' elif isinstance(param, ParameterExtent): # 'We have to substract/add half cell size, since SAGA is # center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(",") for i in range(4): command += " -" + self.extentParamNames[i] + " " + str(float(values[i]) + offset[i]) elif isinstance(param, (ParameterNumber, ParameterSelection)): command += " -" + param.name + " " + str(param.value) else: command += " -" + param.name + ' "' + str(param.value) + '"' for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename += ".sgrd" command += " -" + out.name + ' "' + filename + '"' if isinstance(out, OutputVector): filename = out.getCompatibleFileName(self) command += " -" + out.name + ' "' + filename + '"' if isinstance(out, OutputTable): filename = out.getCompatibleFileName(self) command += " -" + out.name + ' "' + filename + '"' commands.append(command) # 3: Export resulting raster layers # optim = ProcessingConfig.getSetting(SagaUtils.SAGA_IMPORT_EXPORT_OPTIMIZATION) for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + ".sgrd" formatIndex = 4 if isWindows() else 1 sessionExportedLayers[filename] = filename2 # Do not export is the output is not a final output # of the model # dontExport = True # if self.model is not None and optim: # for subalg in self.model.algOutputs: # if out.name in subalg: # if subalg[out.name] is not None: # dontExport = False # break # if dontExport: # continue if self.cmdname == "RGB Composite": commands.append('io_grid_image 0 -IS_RGB -GRID:"' + filename2 + '" -FILE:"' + filename + '"') else: commands.append( 'io_gdal 1 -GRIDS "' + filename2 + '" -FORMAT ' + str(formatIndex) + ' -TYPE 0 -FILE "' + filename + '"' ) # 4: Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append(self.tr("SAGA execution commands")) for line in commands: progress.setCommand(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) SagaUtils.executeSaga(progress)
def processAlgorithm(self, progress): if isWindows(): path = SagaUtils.sagaPath() if path == '': raise GeoAlgorithmExecutionException( 'SAGA folder is not configured.\nPlease configure \ it before running SAGA algorithms.') commands = list() self.exportedLayers = {} self.preProcessInputs() # 1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. for param in self.parameters: if isinstance(param, ParameterRaster): if param.value is None: continue value = param.value if not value.endswith('sgrd'): exportCommand = self.exportRasterLayer(value) if exportCommand is not None: commands.append(exportCommand) if isinstance(param, ParameterVector): if param.value is None: continue layer = dataobjects.getObjectFromUri(param.value, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') if isinstance(param, ParameterTable): if param.value is None: continue table = dataobjects.getObjectFromUri(param.value, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') if isinstance(param, ParameterMultipleInput): if param.value is None: continue layers = param.value.split(';') if layers is None or len(layers) == 0: continue if param.datatype == ParameterMultipleInput.TYPE_RASTER: for layerfile in layers: if not layerfile.endswith('sgrd'): exportCommand = self.exportRasterLayer(layerfile) if exportCommand is not None: commands.append(exportCommand) elif param.datatype == ParameterMultipleInput.TYPE_VECTOR_ANY: for layerfile in layers: layer = dataobjects.getObjectFromUri(layerfile, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile] = filename elif not layerfile.endswith('shp'): raise GeoAlgorithmExecutionException( 'Unsupported file format') # 2: Set parameters and outputs saga208 = SagaUtils.isSaga208() if isWindows() or isMac() or not saga208: command = self.undecoratedGroup + ' "' + self.cmdname + '"' else: command = 'lib' + self.undecoratedGroup + ' "' + self.cmdname + '"' if self.hardcodedStrings: for s in self.hardcodedStrings: command += ' ' + s for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in self.exportedLayers.keys(): command += ' -' + param.name + ' "' \ + self.exportedLayers[value] + '"' else: command += ' -' + param.name + ' "' + value + '"' elif isinstance(param, ParameterMultipleInput): s = param.value for layer in self.exportedLayers.keys(): s = s.replace(layer, self.exportedLayers[layer]) command += ' -' + param.name + ' "' + s + '"' elif isinstance(param, ParameterBoolean): if param.value: command += ' -' + param.name elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename('txt') f = open(tempTableFile, 'w') f.write('\t'.join([col for col in param.cols]) + '\n') values = param.value.split(',') for i in range(0, len(values), 3): s = values[i] + '\t' + values[i + 1] + '\t' + values[i + 2] + '\n' f.write(s) f.close() command += ' -' + param.name + ' "' + tempTableFile + '"' elif isinstance(param, ParameterExtent): # 'We have to substract/add half cell size, since SAGA is # center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(',') for i in range(4): command += ' -' + self.extentParamNames[i] + ' ' \ + str(float(values[i]) + offset[i]) elif isinstance(param, (ParameterNumber, ParameterSelection)): command += ' -' + param.name + ' ' + str(param.value) else: command += ' -' + param.name + ' "' + str(param.value) + '"' for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename += '.sgrd' command += ' -' + out.name + ' "' + filename + '"' if isinstance(out, OutputVector): filename = out.getCompatibleFileName(self) command += ' -' + out.name + ' "' + filename + '"' if isinstance(out, OutputTable): filename = out.getCompatibleFileName(self) command += ' -' + out.name + ' "' + filename + '"' commands.append(command) # 3: Export resulting raster layers optim = ProcessingConfig.getSetting( SagaUtils.SAGA_IMPORT_EXPORT_OPTIMIZATION) for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + '.sgrd' formatIndex = (4 if not saga208 and isWindows() else 1) sessionExportedLayers[filename] = filename2 dontExport = True # Do not export is the output is not a final output # of the model if self.model is not None and optim: for subalg in self.model.algOutputs: if out.name in subalg: if subalg[out.name] is not None: dontExport = False break if dontExport: continue if self.cmdname == 'RGB Composite': if isWindows() or isMac() or not saga208: commands.append('io_grid_image 0 -IS_RGB -GRID:"' + filename2 + '" -FILE:"' + filename + '"') else: commands.append('libio_grid_image 0 -IS_RGB -GRID:"' + filename2 + '" -FILE:"' + filename + '"') else: if isWindows() or isMac() or not saga208: commands.append('io_gdal 1 -GRIDS "' + filename2 + '" -FORMAT ' + str(formatIndex) + ' -TYPE 0 -FILE "' + filename + '"') else: commands.append('libio_gdal 1 -GRIDS "' + filename2 + '" -FORMAT 1 -TYPE 0 -FILE "' + filename + '"') # 4: Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append('SAGA execution commands') for line in commands: progress.setCommand(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines) SagaUtils.executeSaga(progress)
def processAlgorithm(self, progress): field = self.getParameterValue(self.FIELD) field = field[0:10] # try to handle Shapefile field length limit filename = self.getParameterValue(self.INPUT) layer = dataobjects.getObjectFromUri(filename) filename = dataobjects.exportVectorLayer(layer) provider = layer.dataProvider() fields = provider.fields() fields.append(QgsField('MORANS_P', QVariant.Double)) fields.append(QgsField('MORANS_Z', QVariant.Double)) fields.append(QgsField('MORANS_Q', QVariant.Int)) fields.append(QgsField('MORANS_I', QVariant.Double)) fields.append(QgsField('MORANS_C', QVariant.Double)) writer = self.getOutputFromName(self.OUTPUT).getVectorWriter( fields, provider.geometryType(), layer.crs() ) contiguity = self.getParameterValue(self.CONTIGUITY) if contiguity == 'queen': print 'INFO: Local Moran\'s using queen contiguity' w=pysal.queen_from_shapefile(filename) else: print 'INFO: Local Moran\'s using rook contiguity' w=pysal.rook_from_shapefile(filename) f = pysal.open(pysal.examples.get_path(filename.replace('.shp','.dbf'))) y=np.array(f.by_col[str(field)]) lm = pysal.Moran_Local(y,w,transformation = "r", permutations = 999) # http://pysal.readthedocs.org/en/latest/library/esda/moran.html?highlight=local%20moran#pysal.esda.moran.Moran_Local # values indicate quadrat location 1 HH, 2 LH, 3 LL, 4 HL # http://www.biomedware.com/files/documentation/spacestat/Statistics/LM/Results/Interpreting_univariate_Local_Moran_statistics.htm # category - scatter plot quadrant - autocorrelation - interpretation # high-high - upper right (red) - positive - Cluster - "I'm high and my neighbors are high." # high-low - lower right (pink) - negative - Outlier - "I'm a high outlier among low neighbors." # low-low - lower left (med. blue) - positive - Cluster - "I'm low and my neighbors are low." # low-high - upper left (light blue) - negative - Outlier - "I'm a low outlier among high neighbors." # http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#/What_is_a_z_score_What_is_a_p_value/005p00000006000000/ # z-score (Standard Deviations) | p-value (Probability) | Confidence level # < -1.65 or > +1.65 | < 0.10 | 90% # < -1.96 or > +1.96 | < 0.05 | 95% # < -2.58 or > +2.58 | < 0.01 | 99% self.setOutputValue(self.P_SIM, str(lm.p_sim)) sig_q = lm.q * (lm.p_sim <= 0.01) # could make significance level an option outFeat = QgsFeature() i = 0 for inFeat in processing.features(layer): inGeom = inFeat.geometry() outFeat.setGeometry(inGeom) attrs = inFeat.attributes() attrs.append(float(lm.p_sim[i])) attrs.append(float(lm.z_sim[i])) attrs.append(int(lm.q[i])) attrs.append(float(lm.Is[i])) attrs.append(int(sig_q[i])) outFeat.setAttributes(attrs) writer.addFeature(outFeat) i+=1 del writer
def processAlgorithm(self, context, feedback): commands = list() self.exportedLayers = {} self.preProcessInputs() # 1: Export rasters to sgrd and vectors to shp # Tables must be in dbf format. We check that. for param in self.parameters: if isinstance(param, ParameterRaster): if param.value is None: continue if param.value.endswith('sdat'): param.value = param.value[:-4] + "sgrd" elif not param.value.endswith('sgrd'): exportCommand = self.exportRasterLayer(param.value) if exportCommand is not None: commands.append(exportCommand) if isinstance(param, ParameterVector): if param.value is None: continue layer = QgsProcessingUtils.mapLayerFromString( param.value, context, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) if isinstance(param, ParameterTable): if param.value is None: continue table = QgsProcessingUtils.mapLayerFromString( param.value, context, False) if table: filename = dataobjects.exportTable(table) self.exportedLayers[param.value] = filename elif not param.value.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) if isinstance(param, ParameterMultipleInput): if param.value is None: continue layers = param.value.split(';') if layers is None or len(layers) == 0: continue if param.datatype == dataobjects.TYPE_RASTER: for i, layerfile in enumerate(layers): if layerfile.endswith('sdat'): layerfile = param.value[:-4] + "sgrd" layers[i] = layerfile elif not layerfile.endswith('sgrd'): exportCommand = self.exportRasterLayer(layerfile) if exportCommand is not None: commands.append(exportCommand) param.value = ";".join(layers) elif param.datatype in [ dataobjects.TYPE_VECTOR_ANY, dataobjects.TYPE_VECTOR_LINE, dataobjects.TYPE_VECTOR_POLYGON, dataobjects.TYPE_VECTOR_POINT ]: for layerfile in layers: layer = QgsProcessingUtils.mapLayerFromString( layerfile, context, False) if layer: filename = dataobjects.exportVectorLayer(layer) self.exportedLayers[layerfile] = filename elif not layerfile.endswith('shp'): raise GeoAlgorithmExecutionException( self.tr('Unsupported file format')) # 2: Set parameters and outputs command = self.undecoratedGroup + ' "' + self.cmdname + '"' command += ' ' + ' '.join(self.hardcodedStrings) for param in self.parameters: if param.value is None: continue if isinstance(param, (ParameterRaster, ParameterVector, ParameterTable)): value = param.value if value in list(self.exportedLayers.keys()): command += ' -' + param.name + ' "' \ + self.exportedLayers[value] + '"' else: command += ' -' + param.name + ' "' + value + '"' elif isinstance(param, ParameterMultipleInput): s = param.value for layer in list(self.exportedLayers.keys()): s = s.replace(layer, self.exportedLayers[layer]) command += ' -' + param.name + ' "' + s + '"' elif isinstance(param, ParameterBoolean): if param.value: command += ' -' + param.name.strip() + " true" else: command += ' -' + param.name.strip() + " false" elif isinstance(param, ParameterFixedTable): tempTableFile = getTempFilename('txt') with open(tempTableFile, 'w') as f: f.write('\t'.join([col for col in param.cols]) + '\n') values = param.value.split(',') for i in range(0, len(values), 3): s = values[i] + '\t' + values[i + 1] + '\t' + values[ i + 2] + '\n' f.write(s) command += ' -' + param.name + ' "' + tempTableFile + '"' elif isinstance(param, ParameterExtent): # 'We have to substract/add half cell size, since SAGA is # center based, not corner based halfcell = self.getOutputCellsize() / 2 offset = [halfcell, -halfcell, halfcell, -halfcell] values = param.value.split(',') for i in range(4): command += ' -' + self.extentParamNames[i] + ' ' \ + str(float(values[i]) + offset[i]) elif isinstance(param, (ParameterNumber, ParameterSelection)): command += ' -' + param.name + ' ' + str(param.value) else: command += ' -' + param.name + ' "' + str(param.value) + '"' for out in self.outputs: command += ' -' + out.name + ' "' + out.getCompatibleFileName( self) + '"' commands.append(command) # special treatment for RGB algorithm # TODO: improve this and put this code somewhere else for out in self.outputs: if isinstance(out, OutputRaster): filename = out.getCompatibleFileName(self) filename2 = filename + '.sgrd' if self.cmdname == 'RGB Composite': commands.append('io_grid_image 0 -IS_RGB -GRID:"' + filename2 + '" -FILE:"' + filename + '"') # 3: Run SAGA commands = self.editCommands(commands) SagaUtils.createSagaBatchJobFileFromSagaCommands(commands) loglines = [] loglines.append(self.tr('SAGA execution commands')) for line in commands: feedback.pushCommandInfo(line) loglines.append(line) if ProcessingConfig.getSetting(SagaUtils.SAGA_LOG_COMMANDS): QgsMessageLog.logMessage('\n'.join(loglines), self.tr('Processing'), QgsMessageLog.INFO) SagaUtils.executeSaga(feedback) if self.crs is not None: for out in self.outputs: if isinstance(out, (OutputVector, OutputRaster)): prjFile = os.path.splitext( out.getCompatibleFileName(self))[0] + ".prj" with open(prjFile, "w") as f: f.write(self.crs.toWkt())