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Merge pull request #59 from TheD2Lab/testing
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Changed filtering order back and updated some tests
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@ashkjones
ashkjones authored Aug 17, 2024
2 parents 8c96390 + affe6b9 commit c38282f
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Showing 8 changed files with 895 additions and 52 deletions.
18 changes: 9 additions & 9 deletions src/main/java/com/github/thed2lab/analysis/Analysis.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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");
Expand Down Expand Up @@ -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));
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4 changes: 2 additions & 2 deletions src/main/java/com/github/thed2lab/analysis/AreaOfInterests.java
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Expand Up @@ -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
Expand All @@ -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);
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4 changes: 2 additions & 2 deletions src/main/java/com/github/thed2lab/analysis/Windows.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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));
Expand All @@ -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));
Expand Down
22 changes: 11 additions & 11 deletions src/test/java/com/github/thed2lab/analysis/FixationsTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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9 changes: 4 additions & 5 deletions src/test/java/com/github/thed2lab/analysis/SaccadeVelocityTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
}
Expand Down
46 changes: 23 additions & 23 deletions src/test/java/com/github/thed2lab/analysis/SaccadesTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;

Expand Down Expand Up @@ -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)
Expand Down
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