Merge pull request #60 from TheD2Lab/testing

Analysis DGM tests and more

src/main/java/com/github/thed2lab/analysis/Analysis.java

@@ -187,9 +187,9 @@ private static List<List<String>> generateResultsHelper(DataEntry allGaze, DataE
         resultsMap.putAll(Angles.analyze(validAreaFixations));
         resultsMap.putAll(ConvexHull.analyze(validAreaFixations));
         resultsMap.putAll(GazeEntropy.analyze(validAreaFixations));
-        resultsMap.putAll(Blinks.analyze(areaGaze));
+        resultsMap.putAll(Blinks.analyze(areaGaze));    // unfiltered
         resultsMap.putAll(Gaze.analyze(validAreaGaze));
-        resultsMap.putAll(Event.analyze(validAreaGaze));
+        resultsMap.putAll(Event.analyze(areaGaze)); // unfiltered
 
         var resultsList = new ArrayList<List<String>>(2);
         resultsList.add(new ArrayList<>(resultsMap.keySet()));

src/main/java/com/github/thed2lab/analysis/AreaOfInterests.java

@@ -3,8 +3,6 @@
 import static com.github.thed2lab.analysis.Constants.AOI_LABEL;
 import static com.github.thed2lab.analysis.Constants.FIXATION_DURATION;
 import static com.github.thed2lab.analysis.Constants.FIXATION_ID;
-import static com.github.thed2lab.analysis.Constants.SCREEN_HEIGHT;
-import static com.github.thed2lab.analysis.Constants.SCREEN_WIDTH;
 
 import java.util.ArrayList;
 import java.util.Arrays;

src/main/java/com/github/thed2lab/analysis/ConvexHull.java

@@ -158,7 +158,7 @@ protected static Point2D.Double getLowestPoint(List<Point2D.Double> points) {
     /**
      * Returns a sorted set of points from the list <code>points</code>. The
      * set of points are sorted in increasing order of the angle they and the
-     * lowest point <tt>P</tt> make with the x-axis. If tow (or more) points
+     * lowest point <tt>P</tt> make with the x-axis. If two (or more) points
      * form the same angle towards <tt>P</tt>, the one closest to <tt>P</tt>
      * comes first.
      *

src/main/java/com/github/thed2lab/analysis/DataEntry.java

@@ -1,7 +1,7 @@
 package com.github.thed2lab.analysis;
 
-import java.util.*;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 

src/main/java/com/github/thed2lab/analysis/GazeEntropy.java

@@ -1,6 +1,7 @@
 package com.github.thed2lab.analysis;
 
 import static com.github.thed2lab.analysis.Constants.AOI_LABEL;
+import static com.github.thed2lab.analysis.Constants.FIXATION_ID;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -22,20 +23,23 @@ static public LinkedHashMap<String,String> analyze(DataEntry fixations) {
         var transitionProbability = new HashMap<String, Map<String, Double>>();
         var aoiSequence = new ArrayList<String>();
         String lastAoi = null;
+        int lastId = -1; // arbitrary number that will never be the ID
 
         int fixationCount = fixations.rowCount();
 
         for (int row = 0; row < fixations.rowCount(); row++) {
             String aoi = fixations.getValue(AOI_LABEL, row);
+            int curId = Integer.valueOf(fixations.getValue(FIXATION_ID, row));
             aoiSequence.add(aoi);
             aoiProbability.put(aoi, aoiProbability.getOrDefault(aoi, 0.0) + 1);
-            if (lastAoi != null) {  // skips the first loop
+            if (lastAoi != null && curId == lastId + 1) {  // skips the first loop and non-consecutive fixations
                 Map<String, Double> relationMatrix = transitionProbability.getOrDefault(lastAoi, new HashMap<String,Double>());
                 double count = relationMatrix.getOrDefault(aoi, 0.0);
                 relationMatrix.put(aoi, count + 1);
                 transitionProbability.put(lastAoi, relationMatrix);
             }
             lastAoi = aoi;
+            lastId = curId;
         }
 
         for (Map.Entry<String, Double> entry : aoiProbability.entrySet()) {

src/main/java/com/github/thed2lab/analysis/Windows.java

@@ -257,6 +257,11 @@ static void outputWindowFiles(List<DataEntry> windows, double time0, String outp
             headers.add("window_duration");
             headers.add("initial_seconds_elapsed_since_start");
             headers.add("final_seconds_elapsed_since_start");
+
+            // In the combined window folder, add headers if there are none
+            if (allWindowDGMs.size() == 0) {
+                allWindowDGMs.add(headers);
+            }
 
             List<String> dgms = results.get(1);
             dgms.add(String.valueOf(time1));
@@ -265,11 +270,6 @@ static void outputWindowFiles(List<DataEntry> windows, double time0, String outp
             dgms.add(String.valueOf(initialDuration));
             dgms.add(String.valueOf(finalDuration));
             allWindowDGMs.add(dgms);
-
-            // In the combined window folder, add headers if there are none
-            if (allWindowDGMs.size() == 0) {
-                allWindowDGMs.add(headers);
-            }
 
             FileHandler.writeToCSV(results, windowDirectory, fileName + "_DGMs");
             AreaOfInterests.generateAOIs(windowGaze, windowFixations, windowDirectory, fileName);

src/test/java/com/github/thed2lab/analysis/AnalysisTest.java

@@ -0,0 +1,65 @@
+package com.github.thed2lab.analysis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+import java.io.FileReader;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.junit.Test;
+
+import com.opencsv.CSVReader;
+
+public class AnalysisTest {
+
+   private final double PRECISION = 0.000000001; // allowable floating point error
+   private final String ALL_GAZE_PATH = "./src/test/resources/test_all_gaze.csv";
+   private final DataEntry ALL_GAZE = FileHandler.buildDataEntry(new File(ALL_GAZE_PATH));
+   private final String ALL_FIXATION_PATH = "./src/test/resources/filtered_by_fixation.csv";
+   private final DataEntry ALL_FIXATION = FileHandler.buildDataEntry(new File(ALL_FIXATION_PATH));
+
+   @Test
+   public void testGenerateResults_wholeScreenData() {
+      List<String[]> expected = new LinkedList<>();
+      try (
+         FileReader fileReader = new FileReader("./src/test/resources/test_DGMs.csv");
+         CSVReader csvReader = new CSVReader(fileReader);
+      ) {
+         expected.add(csvReader.readNext());
+         expected.add(csvReader.readNext());
+      } catch (Exception e) {
+         fail("Could not read file");
+      }
+
+      List<List<String>> actual = Analysis.generateResults(ALL_GAZE, ALL_FIXATION);
+      assertEquals(2, actual.size()); // headers and 1 row of data
+
+      // check headers
+      Iterator<String> actualIter = actual.get(0).iterator();
+      for (String expValue : expected.get(0)) {
+         assertEquals(expValue.trim(), actualIter.next());
+      }
+
+      // check values
+      actualIter = actual.get(1).iterator();
+      for (String expValue : expected.get(1)) {
+         var bloop = actualIter.next();
+         if (!isEqual(expValue, bloop)) {
+            fail();
+         }
+      }
+   }
+
+   /**
+    * Checks if two numbers saved as strings are equal, within an allowable amount of floating point error.
+    * @param double1 first number to compare
+    * @param double2 second number to compare
+    * @return if the two numbers are equal
+    */
+   private boolean isEqual(String double1, String double2) {
+      return Math.abs(Double.parseDouble(double1) - Double.parseDouble(double2)) < PRECISION;
+   }
+}

src/test/java/com/github/thed2lab/analysis/GazeEntropyTest.java

@@ -16,11 +16,11 @@ public class GazeEntropyTest {
    public void testGazeEntropyAnalyze_singleAoi_0entropy() {
       final double EXPECTED_STATIONARY = 0.0;
       final double EXPECTED_TRANSITION = 0.0;
-      DataEntry data = new DataEntry(Arrays.asList("AOI")) {{
-         process(Arrays.asList("A"));
-         process(Arrays.asList("A"));
-         process(Arrays.asList("A"));
-         process(Arrays.asList("A"));
+      DataEntry data = new DataEntry(Arrays.asList("FPOGID","AOI")) {{
+         process(Arrays.asList("0", "A"));
+         process(Arrays.asList("1", "A"));
+         process(Arrays.asList("1", "A"));
+         process(Arrays.asList("1", "A"));
       }};
       var results = GazeEntropy.analyze(data);
       assertEquals(
@@ -40,15 +40,15 @@ public void testGazeEntropyAnalyze_singleAoi_0entropy() {
    public void testGazeEntropyAnalyze_threeAoi() {
       final double EXPECTED_STATIONARY = 0.4699915470362;
       final double EXPECTED_TRANSITION = 0.282583442123752;
-      DataEntry data = new DataEntry(Arrays.asList("AOI")) {{
-         process(Arrays.asList("A"));
-         process(Arrays.asList("B"));
-         process(Arrays.asList("B"));
-         process(Arrays.asList("A"));
-         process(Arrays.asList("A"));
-         process(Arrays.asList("B"));
-         process(Arrays.asList("C"));
-         process(Arrays.asList("C"));
+      DataEntry data = new DataEntry(Arrays.asList("FPOGID", "AOI")) {{
+         process(Arrays.asList("1", "A"));
+         process(Arrays.asList("2", "B"));
+         process(Arrays.asList("3", "B"));
+         process(Arrays.asList("4", "A"));
+         process(Arrays.asList("5", "A"));
+         process(Arrays.asList("6", "B"));
+         process(Arrays.asList("7", "C"));
+         process(Arrays.asList("8", "C"));
       }};
       var results = GazeEntropy.analyze(data);
       assertEquals(
@@ -68,13 +68,39 @@ public void testGazeEntropyAnalyze_threeAoi() {
    public void testGazeEntropyAnalyze_undefinedAoi() {
       final double EXPECTED_STATIONARY = 0.301029995663981;
       final double EXPECTED_TRANSITION = 0.288732293303828;
-      DataEntry data = new DataEntry(Arrays.asList("AOI")) {{
-         process(Arrays.asList("A"));
-         process(Arrays.asList(""));
-         process(Arrays.asList(""));
-         process(Arrays.asList("A"));
-         process(Arrays.asList("A"));
-         process(Arrays.asList(""));
+      DataEntry data = new DataEntry(Arrays.asList("FPOGID", "AOI")) {{
+         process(Arrays.asList("0", "A"));
+         process(Arrays.asList("1", ""));
+         process(Arrays.asList("2", ""));
+         process(Arrays.asList("3", "A"));
+         process(Arrays.asList("4", "A"));
+         process(Arrays.asList("5", ""));
+      }};
+      var results = GazeEntropy.analyze(data);
+      assertEquals(
+         "Unexpected stationary entropy.",
+         EXPECTED_STATIONARY,
+         Double.parseDouble(results.get(STATIONARY_ENTROPY)),
+         PRECISION
+      );
+      assertEquals(
+         "Unexpected transition entropy.",
+         EXPECTED_TRANSITION, Double.parseDouble(results.get(TRANSITION_ENTROPY)),
+         PRECISION
+      );
+   }
+
+   @Test
+   public void testGazeEntropyAnalyze_nonConsecutiveFixations() {
+      final double EXPECTED_STATIONARY = 0.301029995663981;
+      final double EXPECTED_TRANSITION = 0.138217295471837;
+      DataEntry data = new DataEntry(Arrays.asList("FPOGID", "AOI")) {{
+         process(Arrays.asList("0", "A"));
+         process(Arrays.asList("1", ""));
+         process(Arrays.asList("2", ""));
+         process(Arrays.asList("4", "A"));
+         process(Arrays.asList("5", "A"));
+         process(Arrays.asList("6", ""));
       }};
       var results = GazeEntropy.analyze(data);
       assertEquals(

src/test/resources/test_DGMs.csv

@@ -0,0 +1,2 @@
+total_number_of_fixations,sum_of_all_fixation_duration_s,mean_fixation_duration_s,median_fixation_duration_s,stdev_of_fixation_durations_s,min_fixation_duration_s,max_fixation_duration_s,total_number_of_saccades,sum_of_all_saccade_lengths,mean_saccade_length,median_saccade_length,stdev_of_saccade_lengths,min_saccade_length,max_saccade_length,sum_of_all_saccade_durations,mean_saccade_duration,median_saccade_duration,stdev_of_saccade_durations,min_saccade_duration,max_saccade_duration,scanpath_duration,fixation_to_saccade_ratio,average_peak_saccade_velocity,sum_of_all_absolute_degrees,mean_absolute_degree,median_absolute_degree,stdev_of_absolute_degrees,min_absolute_degree,max_absolute_degree,sum_of_all_relative_degrees,mean_relative_degree,median_relative_degree,stdev_of_relative_degrees,min_relative_degree,max_relative_degree,convex_hull_area,stationary_entropy,transition_entropy,total_number_of_blinks,average_blink_rate_per_minute,total_number_of_valid_recordings,average_pupil_size_of_left_eye,average_pupil_size_of_right_eye,average_pupil_size_of_both_eyes,total_number_of_l_mouse_clicks
+20,4.76282,0.238141,0.16748,0.152435548482145,0.08044,0.66125,16,2530.86608142828,158.179130089267,119.346748844631,106.3517507880460,20.7083517064975,349.414837212159,0.19091,0.011931875,0.00671,0.0094964149156,0.00598,0.03028,4.95373,24.9479859619718,179.969192732729,395.580356733446,24.7237722958404,15.4757613889113,22.7925364835493,2.9677710724739,81.4803527675405,1618.85106640278,124.527005107906,123.297847178851,26.0218488445123,79.5855258680609,163.151086040417,168928.54539264,0.3482253728572,0.2295311788752,3,27.5902238640109,822,4.5235607299270,4.3886963746959,4.4561285523114,2