Merge pull request orbisgis#7 from SPalominos/master

Rework the typo class and test.
ebocher · Dec 13, 2019 · 73e8b52 · 73e8b52
2 parents 2b27d48 + 45946ea
commit 73e8b52
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Showing 37 changed files with 188 additions and 200 deletions.
diff --git a/geoclimate/pom.xml b/geoclimate/pom.xml
@@ -22,41 +22,17 @@
             <groupId>org.codehaus.groovy</groupId>
             <artifactId>groovy</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.orbisgis.orbisdata.datamanager</groupId>
-            <artifactId>jdbc</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.orbisgis.orbisdata.processmanager</groupId>
-            <artifactId>process</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.orbisgis.orbisprocess.geoclimate</groupId>
             <artifactId>preparedata</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.orbisgis.orbisprocess.geoclimate</groupId>
             <artifactId>geoindicators</artifactId>
-            <version>${project.version}</version>
         </dependency>
         <dependency>
             <groupId>org.orbisgis.orbisprocess.geoclimate</groupId>
             <artifactId>processingchain</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <!-- Test dependencies -->
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-simple</artifactId>
         </dependency>
     </dependencies>
 

diff --git a/geoclimate/src/main/groovy/org/orbisgis/orbisprocess/geoclimate/Geoclimate.groovy b/geoclimate/src/main/groovy/org/orbisgis/orbisprocess/geoclimate/Geoclimate.groovy
@@ -1,25 +1,13 @@
 package org.orbisgis.orbisprocess.geoclimate
 
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.BlockIndicators
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.BuildingIndicators
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.DataUtils
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.GenericIndicators
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.Geoindicators
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.RsuIndicators
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.SpatialUnits
-import org.orbisgis.orbisprocess.geoclimate.geoindicators.TypologyClassification
+import org.orbisgis.orbisprocess.geoclimate.geoindicators.*
 import org.orbisgis.orbisprocess.geoclimate.preparedata.PrepareData
 import org.orbisgis.orbisprocess.geoclimate.preparedata.bdtopo.BDTopoGISLayers
 import org.orbisgis.orbisprocess.geoclimate.preparedata.common.AbstractTablesInitialization
 import org.orbisgis.orbisprocess.geoclimate.preparedata.common.InputDataFormatting
 import org.orbisgis.orbisprocess.geoclimate.preparedata.osm.FormattingForAbstractModel
 import org.orbisgis.orbisprocess.geoclimate.preparedata.osm.OSMGISLayers
-import org.orbisgis.orbisprocess.geoclimate.processingchain.BuildGeoIndicators
-import org.orbisgis.orbisprocess.geoclimate.processingchain.BuildSpatialUnits
-import org.orbisgis.orbisprocess.geoclimate.processingchain.Workflow
-import org.orbisgis.orbisprocess.geoclimate.processingchain.PrepareBDTopo
-import org.orbisgis.orbisprocess.geoclimate.processingchain.PrepareOSM
-import org.orbisgis.orbisprocess.geoclimate.processingchain.ProcessingChain
+import org.orbisgis.orbisprocess.geoclimate.processingchain.*
 
 /**
  * Root access point to the Geoindicators processes.

diff --git a/geoindicators/pom.xml b/geoindicators/pom.xml
@@ -24,14 +24,6 @@
             <groupId>org.codehaus.groovy</groupId>
             <artifactId>groovy</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-engine</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.orbisgis.orbisdata.datamanager</groupId>
             <artifactId>jdbc</artifactId>
@@ -47,24 +39,29 @@
         <dependency>
             <groupId>org.orbisgis</groupId>
             <artifactId>h2gis-network</artifactId>
-            <version>2.0.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>com.github.haifengl</groupId>
             <artifactId>smile-core</artifactId>
-            <version>2.0.0</version>
         </dependency>
         <dependency>
             <groupId>com.thoughtworks.xstream</groupId>
             <artifactId>xstream</artifactId>
-            <version>1.4.11.1</version>
         </dependency>
 
         <!-- Test dependencies -->
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-simple</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/...n/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/TypologyClassification.groovy b/...n/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/TypologyClassification.groovy
@@ -3,18 +3,16 @@ package org.orbisgis.orbisprocess.geoclimate.geoindicators
 import com.thoughtworks.xstream.XStream
 import groovy.transform.BaseScript
 import org.orbisgis.orbisdata.datamanager.api.dataset.ITable
+import org.orbisgis.orbisdata.datamanager.dataframe.DataFrame
 import org.orbisgis.orbisdata.datamanager.jdbc.JdbcDataSource
 import org.orbisgis.orbisdata.processmanager.api.IProcess
-import smile.classification.RandomForest;
-import smile.data.formula.Formula
-import org.orbisgis.orbisdata.datamanager.dataframe.DataFrame
 import smile.base.cart.SplitRule
-import smile.validation.Validation;
+import smile.classification.RandomForest
+import smile.data.formula.Formula
 import smile.validation.Accuracy
+import smile.validation.Validation
 
-import java.util.zip.GZIPOutputStream;
-
-
+import java.util.zip.GZIPOutputStream
 
 @BaseScript Geoindicators geoindicators
 
@@ -42,6 +40,7 @@ import java.util.zip.GZIPOutputStream;
  * the American Meteorological Society 93, no. 12 (2012): 1879-1900.
  *
  * @return A database table name.
+ *
  * @author Jérémy Bernard
  */
 IProcess identifyLczType() {
@@ -265,91 +264,92 @@ IProcess identifyLczType() {
  * @param varToModel String where is saved the name of the field to model
  * @param save Boolean to save the model into a file if needed
  * @param pathAndFileName String of the path and name where the model has to be saved (default "/home/RfModel")
- * @param ntrees the number of trees to build the forest
- * @param mtry the number of input variables to be used to determine the decision
+ * @param ntrees The number of trees to build the forest
+ * @param mtry The number of input variables to be used to determine the decision
  * at a node of the tree. p/3 seems to give generally good performance,
  * where p is the number of variables
  * @param rule Decision tree split rule (The function to measure the quality of a split. Supported rules
  * are “gini” for the Gini impurity and “entropy” for the information gain)
- * @param maxDepth the maximum depth of the tree.
- * @param maxNodes the maximum number of leaf nodes in the tree.
- * @param nodeSize the number of instances in a node below which the tree will
+ * @param maxDepth The maximum depth of the tree.
+ * @param maxNodes The maximum number of leaf nodes in the tree.
+ * @param nodeSize The number of instances in a node below which the tree will
  * not split, setting nodeSize = 5 generally gives good results.
- * @param subsample the sampling rate for training tree. 1.0 means sampling with replacement. < 1.0 means
+ * @param subsample The sampling rate for training tree. 1.0 means sampling with replacement. < 1.0 means
  * sampling without replacement.
  * @param datasource A connection to a database
  *
  * @return RfModel A randomForest model (see smile library for further information about the object)
+ *
  * @author Jérémy Bernard
  */
 IProcess createRandomForestClassif() {
     return create({
         title "Create a Random Forest model"
-        inputs trainingTableName: String, varToModel: String, save: boolean, pathAndFileName: String,
-                ntrees: int, mtry: int, rule: "GINI", maxDepth: int, maxNodes: int, nodeSize: int,
-                subsample: double, datasource: JdbcDataSource
+        inputs trainingTableName: String, varToModel: String, save: boolean, pathAndFileName: String, ntrees: int,
+                mtry: int, rule: "GINI", maxDepth: int, maxNodes: int, nodeSize: int, subsample: double,
+                datasource: JdbcDataSource
         outputs RfModel: RandomForest
-        run { trainingTableName, varToModel, save, pathAndFileName,  ntrees, mtry, rule,
-              maxDepth, maxNodes, nodeSize, subsample, datasource ->
+        run { String trainingTableName, String varToModel, save, pathAndFileName,  ntrees, mtry, rule, maxDepth,
+              maxNodes, nodeSize, subsample, JdbcDataSource datasource ->
 
-            SplitRule splitRule
+            def splitRule
             if(rule){
                 switch(rule.toUpperCase()) {
                     case "GINI":
-                        splitRule = SplitRule.GINI
-                        break
                     case "ENTROPY":
-                        splitRule = SplitRule.ENTROPY
+                        splitRule = SplitRule.valueOf(rule)
                         break
                     default:
-                        error "The rule value ${rule} is not supported. Please use GINI or ENTROPY"
+                        error "The rule value ${rule} is not supported. Please use 'GINI' or 'ENTROPY'"
                         return null;
                 }
             }
             else{
-                error "The rule value cannot be null or empty. Please use GINI or ENTROPY"
+                error "The rule value cannot be null or empty. Please use 'GINI' or 'ENTROPY'"
                 return null;
             }
             info "Create a Random Forest model"
 
             //Check if the column names exists
             def columnTypo = "I_TYPO"
 
-            ITable trainingTable = datasource.getTable(trainingTableName)
+            def trainingTable = datasource.getTable(trainingTableName)
 
-            assert trainingTable.hasColumn(columnTypo, String.class)
+            if(!trainingTable.hasColumn(columnTypo, String.class)){
+                error "The training table should have a String column name 'I_TYPO'"
+                return null
+            }
 
             // Read the training table as a DataFrame
             def df = DataFrame.of(trainingTable)
 
-            Formula formula = Formula.lhs(varToModel)
+            def formula = Formula.lhs(varToModel)
 
             // Convert the variable to model into factors (if string for example) and remove rows containing null values
             df = df.factorize(varToModel).omitNullRows()
 
             // Create the randomForest
-            RandomForest model = RandomForest.fit(formula, df, ntrees, mtry,
-                    splitRule, maxDepth, maxNodes, nodeSize, subsample)
+            def model = RandomForest.fit(formula, df, ntrees, mtry, splitRule, maxDepth, maxNodes, nodeSize, subsample)
 
 
             // Calculate the prediction using the same sample in order to identify what is the
             // data rate that has been well classified
             int[] prediction = Validation.test(model, df)
             int[] truth = df.apply(varToModel).toIntArray()
-            double accuracy = Accuracy.of(truth, prediction)
+            def accuracy = Accuracy.of(truth, prediction)
             logger.info "The percentage of the data that have been well classified is : ${accuracy*100}%"
 
             try {
                 if (save) {
-                    def zOut =
-                            new GZIPOutputStream(new FileOutputStream(pathAndFileName));
-                    XStream xs = new XStream()
+                    def zOut = new GZIPOutputStream(new FileOutputStream(pathAndFileName));
+                    def xs = new XStream()
                     xs.toXML(model, zOut)
                     zOut.close()
                 }
             }
             catch (Exception e){
                 logger.error("Cannot save the model", e)
+                return null
             }
 
             [RfModel: model]

diff --git a/.../groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/BuildingIndicatorsTests.groovy b/.../groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/BuildingIndicatorsTests.groovy
@@ -2,10 +2,11 @@ package org.orbisgis.orbisprocess.geoclimate.geoindicators
 
 import org.junit.jupiter.api.BeforeAll
 import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
 import org.orbisgis.orbisdata.datamanager.jdbc.h2gis.H2GIS
 
-import static org.junit.jupiter.api.Assertions.*
-import org.junit.jupiter.api.Test
+import static org.junit.jupiter.api.Assertions.assertEquals
+import static org.junit.jupiter.api.Assertions.assertTrue
 
 class BuildingIndicatorsTests {
 

diff --git a/.../src/test/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/DataUtilsTests.groovy b/.../src/test/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/DataUtilsTests.groovy
@@ -1,10 +1,11 @@
 package org.orbisgis.orbisprocess.geoclimate.geoindicators
 
+import org.junit.jupiter.api.Test
 import org.orbisgis.orbisdata.datamanager.jdbc.h2gis.H2GIS
 import org.orbisgis.orbisdata.processmanager.api.IProcess
 
-import static org.junit.jupiter.api.Assertions.*
-import org.junit.jupiter.api.Test
+import static org.junit.jupiter.api.Assertions.assertEquals
+import static org.junit.jupiter.api.Assertions.assertTrue
 
 class DataUtilsTests {
 

diff --git a/...c/test/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/SpatialUnitsTests.groovy b/...c/test/groovy/org/orbisgis/orbisprocess/geoclimate/geoindicators/SpatialUnitsTests.groovy
@@ -5,9 +5,7 @@ import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.orbisgis.orbisdata.datamanager.jdbc.h2gis.H2GIS
 
-import static org.junit.jupiter.api.Assertions.assertEquals
-import static org.junit.jupiter.api.Assertions.assertNotNull
-import static org.junit.jupiter.api.Assertions.assertTrue
+import static org.junit.jupiter.api.Assertions.*
 
 class SpatialUnitsTests {