Changed filtering order back and updated some tests

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

@@ -53,10 +53,10 @@ public boolean run() {
                 System.out.println("Analyzing " + pName);
 
                 // Build DataEntrys
-                DataEntry allGaze = DataFilter.applyScreenSize(FileHandler.buildDataEntry(f), SCREEN_WIDTH, SCREEN_HEIGHT);
-                DataEntry validGaze = DataFilter.filterByValidity(allGaze, SCREEN_WIDTH, SCREEN_HEIGHT);
+                DataEntry allGaze = FileHandler.buildDataEntry(f);
+                DataEntry validGaze = DataFilter.filterByValidity(allGaze);
                 DataEntry fixations = DataFilter.filterByFixations(allGaze);
-                DataEntry validFixations = DataFilter.filterByValidity(fixations, SCREEN_HEIGHT, SCREEN_WIDTH);
+                DataEntry validFixations = DataFilter.filterByValidity(fixations);
 
                 // Write DataEntrys to file
                 validGaze.writeToCSV(pDirectory, pName + "_valid_all_gaze");
@@ -167,18 +167,18 @@ static List<List<String>> generateResults(DataEntry allGaze, DataEntry aoiGaze,
 
     /**
      * Helper methods that generates the descriptive gaze measures.
-     * @param allGaze all gaze data for the whole screen, with screen size applied.
-     * @param areaGaze the gaze data that ocurred within a target portion of screen, i.e., either the whole screen or an AOI, with screen
-     * size applied.
+     * @param allGaze all gaze data for the whole screen.
+     * @param areaGaze the gaze data that ocurred within a target portion of screen, i.e., either the whole screen or an AOI.
      * @param areaFixations the gaze data that ocurred within a target portion of screen, i.e., either the whole screen or an AOI,
      * and filtered by fixation with screen size applied.
      * @return a {@code List<List<String>} where the first inner-list is the measure names, and second inner-list is the calculated values.
      */
     private static List<List<String>> generateResultsHelper(DataEntry allGaze, DataEntry areaGaze, DataEntry areaFixations) {
         // an argument could be made to filter before entering this function; there is a code smell due to blink rate and saccadeV changing
-        DataEntry validAllGaze = DataFilter.filterByValidity(allGaze, SCREEN_WIDTH, SCREEN_HEIGHT); 
-        DataEntry validAreaGaze = DataFilter.filterByValidity(areaGaze, SCREEN_WIDTH, SCREEN_HEIGHT);
-        DataEntry validAreaFixations = DataFilter.filterByValidity(areaFixations, SCREEN_WIDTH, SCREEN_HEIGHT);
+
+        DataEntry validAllGaze = DataFilter.applyScreenSize(DataFilter.filterByValidity(allGaze), SCREEN_WIDTH, SCREEN_HEIGHT); 
+        DataEntry validAreaGaze = DataFilter.applyScreenSize(DataFilter.filterByValidity(areaGaze), SCREEN_WIDTH, SCREEN_HEIGHT);
+        DataEntry validAreaFixations = DataFilter.applyScreenSize(DataFilter.filterByValidity(areaFixations), SCREEN_WIDTH, SCREEN_HEIGHT);
 
         LinkedHashMap<String,String> resultsMap = new LinkedHashMap<String, String>();
         resultsMap.putAll(Fixations.analyze(validAreaFixations));

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

@@ -26,7 +26,7 @@ public static void generateAOIs(DataEntry allGazeData, DataEntry fixationData, S
             return;
         }
 
-        DataEntry filteredFixations = DataFilter.filterByValidity(fixationData, SCREEN_WIDTH, SCREEN_HEIGHT);
+        DataEntry filteredFixations = DataFilter.filterByValidity(fixationData);
         Map<String, DataEntry> aoiFixMap = splitAoiData(filteredFixations);
 
         // For any AOIs not in aoiFixationMetrics, add an empty DataEntry
@@ -39,7 +39,7 @@ public static void generateAOIs(DataEntry allGazeData, DataEntry fixationData, S
 
         for (String aoiKey : aoiGazeMap.keySet()) {
             DataEntry aoiData = aoiGazeMap.get(aoiKey);
-            aoiData.writeToCSV(outputDirectory + "/AOIs", aoiKey + "_all_gaze");
+            aoiData.writeToCSV(outputDirectory + "/AOIs", aoiKey.replace(" ", "_") + "_all_gaze");
         }
 
         List<List<String>> aoiMetrics = getMetrics(allGazeData, filteredFixations, aoiGazeMap, aoiFixMap);

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

@@ -304,7 +304,7 @@ static double getRawEventBaselineValue(DataEntry baselineData, String event) {
         double eventValue = 0;
 
         baselineData = fixationEvents.contains(event) ? DataFilter.filterByFixations(baselineData) : baselineData; // Determine if we need to filter by fixations
-        baselineData = DataFilter.filterByValidity(baselineData, SCREEN_WIDTH, SCREEN_HEIGHT); // Filter by validity
+        baselineData = DataFilter.filterByValidity(baselineData); // Filter by validity
 
         for (int i = 0; i < baselineData.rowCount(); i++) {
             eventValue += Double.parseDouble(baselineData.getValue(event, i));
@@ -317,7 +317,7 @@ static double getRawEventBaselineValue(DataEntry baselineData, String event) {
 
     static double getAveragePupilDilationBaseline(DataEntry baselineData) {
         double eventValue = 0;
-        baselineData = DataFilter.filterByValidity(baselineData, SCREEN_WIDTH, SCREEN_HEIGHT); // Filter by validity
+        baselineData = DataFilter.filterByValidity(baselineData); // Filter by validity
 
         for (int i = 0; i < baselineData.rowCount(); i++) {
             double left = Double.parseDouble(baselineData.getValue(LEFT_PUPIL_DIAMETER, i));

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

@@ -36,24 +36,24 @@ public void testFixationsAnalyze_missingFixationDurationHeader_throwsNullPointer
 
    @Test
    public void testFixationsAnalyze_realData_returnHeadersAndValues() {
-      final String FIXATION_PATH = "./src/test/resources/filtered_by_fixation.csv";
-      Map<String, String> expectedResults = new HashMap<String, String>();
-      expectedResults.put("total_number_of_fixations", "24");
-      expectedResults.put("sum_of_all_fixation_duration_s", "5.63392");
-      expectedResults.put("mean_fixation_duration_s", "0.234746667");
-      expectedResults.put("median_fixation_duration_s", "0.16748");
-      expectedResults.put("stdev_of_fixation_durations_s", "0.154818618");
-      expectedResults.put("min_fixation_duration_s", "0.03382");
-      expectedResults.put("max_fixation_duration_s", "0.66125");
+      final String FIXATION_PATH = "./src/test/resources/valid_fixations.csv";
+      Map<String, Double> expectedResults = new HashMap<String, Double>();
+      expectedResults.put("total_number_of_fixations", 20.);
+      expectedResults.put("sum_of_all_fixation_duration_s", 4.76282);
+      expectedResults.put("mean_fixation_duration_s", 0.238141);
+      expectedResults.put("median_fixation_duration_s", 0.16748);
+      expectedResults.put("stdev_of_fixation_durations_s", 0.152435548482);
+      expectedResults.put("min_fixation_duration_s", 0.08044);
+      expectedResults.put("max_fixation_duration_s", 0.66125);
       DataEntry actual_data = FileHandler.buildDataEntry(new File(FIXATION_PATH));
       Map<String, String> actualResults = Collections.unmodifiableMap(Fixations.analyze(actual_data));
 
       assertEquals("Different number of fixation results", expectedResults.size(), actualResults.size());
 
       for(String key: expectedResults.keySet()) {
-         if(Math.abs(Double.valueOf(expectedResults.get(key)) - Double.valueOf(actualResults.get(key))) > PRECISION) {
+         if(Math.abs(expectedResults.get(key) - Double.valueOf(actualResults.get(key))) > PRECISION) {
             fail(String.format(
-               "Different values for %s\n\tExpected: %s\n\tActual: %s",
+               "Different values for %s\n\tExpected: %f\n\tActual: %s",
                key,
                expectedResults.get(key),
                actualResults.get(key)

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

@@ -56,13 +56,12 @@ public void testGetPeakVelocity_normalUseCase_returnVelocityValue() {
 
    @Test
    public void testSaccadeVelocityAnalyze_nonContinuousWholeScreen() {
-      final String GAZE_PATH = "./src/test/resources/filtered_by_validity.csv";
-      final String FIXATION_PATH = "./src/test/resources/valid_fixations.csv";
+      final String GAZE_PATH = "./src/test/resources/valid_gaze_screenApplied.csv";
+      final String FIXATION_PATH = "./src/test/resources/valid_fixation_screenApplied.csv";
       final double EXPECTED_AVG_PEAK = 179.96919273273;
       final String KEY = "average_peak_saccade_velocity";
-      DataEntry gazeData = DataFilter.applyScreenSize(FileHandler.buildDataEntry(new File(GAZE_PATH)), SCREEN_WIDTH, SCREEN_HEIGHT);
-      DataEntry fixationData = DataFilter.applyScreenSize(FileHandler.buildDataEntry(new File(FIXATION_PATH)), SCREEN_WIDTH, SCREEN_HEIGHT);
-
+      DataEntry gazeData = FileHandler.buildDataEntry(new File(GAZE_PATH));
+      DataEntry fixationData = FileHandler.buildDataEntry(new File(FIXATION_PATH));
       double actualAvgPeak = Double.parseDouble(SaccadeVelocity.analyze(gazeData, fixationData).get(KEY));
       assertEquals(EXPECTED_AVG_PEAK, actualAvgPeak, PRECISION);
    }

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

@@ -6,8 +6,8 @@
 
 import java.io.File;
 import java.util.ArrayList;
-import java.util.HashMap;
 import java.util.Iterator;
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -203,35 +203,35 @@ public void testGetFixationToSaccadeRatio_normalUseCase_returnRatio() {
 
    @Test
    public void testSaccadeAnalyze_validFixations_returnHeadersAndValues() {
-      final String DATA_PATH = "./src/test/resources/valid_fixations.csv";
-      Map<String, String> expectedResults = new HashMap<String, String>();
-      expectedResults.put("total_number_of_saccades", "16");
-
-      expectedResults.put("sum_of_all_saccade_lengths", "1.4804786014");
-      expectedResults.put("mean_saccade_length", "0.0925299126");
-      expectedResults.put("median_saccade_length", "0.0761603796");
-      expectedResults.put("stdev_of_saccade_lengths", "0.0572082421");
-      expectedResults.put("min_saccade_length", "0.0167247123");
-      expectedResults.put("max_saccade_length", "0.2016258416");
-
-      expectedResults.put("sum_of_all_saccade_durations", "0.19091");
-      expectedResults.put("mean_saccade_duration", "0.0119318750");
-      expectedResults.put("median_saccade_duration", "0.0067100000");
-      expectedResults.put("stdev_of_saccade_durations", "0.0094964149");
-      expectedResults.put("min_saccade_duration", "0.0059800000");
-      expectedResults.put("max_saccade_duration", "0.0302800000");
-
-      expectedResults.put("scanpath_duration", "4.95373");
-      expectedResults. put("fixation_to_saccade_ratio", "24.9479859620");
+      final String DATA_PATH = "./src/test/resources/valid_fixation_screenApplied.csv";
+      Map<String, Double> expectedResults = new LinkedHashMap<String, Double>();
+      expectedResults.put("total_number_of_saccades", 16.);
+
+      expectedResults.put("sum_of_all_saccade_lengths", 2530.8660814283);
+      expectedResults.put("mean_saccade_length", 158.1791300893);
+      expectedResults.put("median_saccade_length", 119.3467488446);
+      expectedResults.put("stdev_of_saccade_lengths", 106.3517507880);
+      expectedResults.put("min_saccade_length", 20.7083517065);
+      expectedResults.put("max_saccade_length", 349.4148372122);
+
+      expectedResults.put("sum_of_all_saccade_durations", 0.19091);
+      expectedResults.put("mean_saccade_duration", 0.011931875);
+      expectedResults.put("median_saccade_duration", 0.00671);
+      expectedResults.put("stdev_of_saccade_durations", 0.0094964149);
+      expectedResults.put("min_saccade_duration", 0.00598);
+      expectedResults.put("max_saccade_duration", 0.03028);
+
+      expectedResults.put("scanpath_duration", 4.95373);
+      expectedResults. put("fixation_to_saccade_ratio", 24.9479859620);
 
       DataEntry dEntry = FileHandler.buildDataEntry(new File(DATA_PATH));
       Map<String, String> actualResults = Saccades.analyze(dEntry);
 
       assertEquals("Unexpected output size.", expectedResults.size(), actualResults.size());
 
       for (String key : expectedResults.keySet()) {
-         if (Math.abs(Double.valueOf(expectedResults.get(key)) - Double.valueOf(actualResults.get(key))) > PRECISION) {
-            fail(String.format("Different values for %s\n\tExpected: %s\n\tActual: %s",
+         if (Math.abs(expectedResults.get(key) - Double.valueOf(actualResults.get(key))) > PRECISION) {
+            fail(String.format("Different values for %s\n\tExpected: %f\n\tActual: %s",
                key,
                expectedResults.get(key),
                actualResults.get(key)