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Camtrap DP export standard conformance
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@swoellauer
swoellauer committed Oct 4, 2024
1 parent 877f039 commit c5a7717
Showing 1 changed file with 195 additions and 28 deletions.
223 changes: 195 additions & 28 deletions src/photo/task/Task_photo_export_Camtrap_DP.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,10 @@
import java.nio.file.Path;
import java.nio.file.Paths;
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.time.ZonedDateTime;
import java.time.format.DateTimeFormatter;
import java.util.HashMap;
import java.util.HashSet;

import org.json.JSONWriter;
Expand All @@ -20,11 +24,50 @@
import task.Role;
import task.Tag;
import task.Task;
import util.yaml.YamlMap;

@Tag("photo")
@Description("Export photo meta data to CSV files in structure of Camtrap DP.")
@Role("admin")
public class Task_photo_export_Camtrap_DP extends Task {

private static final DateTimeFormatter CAMTRAP_DP_DATETIME_FORMATTER = DateTimeFormatter.ofPattern("YYYY-MM-dd'T'HH:mm:ssXXX");
private final ZoneId TIMEZONE = ZoneId.systemDefault();

private static final LocalDateTime MAX_DATE = LocalDateTime.parse("3000-12-31T23:59:59");
private static final LocalDateTime MIN_DATE = LocalDateTime.parse("1000-01-01T00:00:00");

private String localDateTimeToString(LocalDateTime localDateTime) {
//return localDateTime.toString()+"Z";
//return ZonedDateTime.of(localDateTime, ZoneId.systemDefault()).toString();
return CAMTRAP_DP_DATETIME_FORMATTER.format(ZonedDateTime.of(localDateTime, TIMEZONE));
}

public static String classificatorToClassificationMethod(String classificator) {
if(classificator == null) {
return "";
}
if(classificator.isBlank()) {
return "";
}
switch(classificator) {
case "expert":
return "human";
default:
return "machine";
}
}

public String getClassifiedBy(YamlMap cmap) {
String pre = "";
if(cmap.contains("classificator")) {
String c = cmap.getString("classificator");
if(!c.equals("expert")) {
pre = c;
}
}
return pre + " " + (cmap.contains("identity") ? cmap.getString("identity") : "");
}

private static final CsvWriterBuilder CSV_BUILDER = CsvWriter.builder()
.fieldSeparator(',')
Expand All @@ -45,28 +88,46 @@ public void run() {
}

HashSet<String> scientificNameSet = new HashSet<String>();
LocalDateTime[] deplMin = new LocalDateTime[] {MAX_DATE};
LocalDateTime[] deplMax = new LocalDateTime[] {MIN_DATE};
HashMap<String, LocalDateTime[]> rangeMap = new HashMap<String, LocalDateTime[]>();

try (
CsvWriter mediaCSV = CSV_BUILDER.build(output_folder_path.resolve("media" + ".csv"));
CsvWriter observationsCSV = CSV_BUILDER.build(output_folder_path.resolve("observations" + ".csv"));
) {
mediaCSV.writeRecord(
"mediaID",
"deploymentID",
"deploymentID",
"captureMethod",
"timestamp",
"filePath",
"filePublic",
"fileMediatype"
"filePublic",
"fileName",
"fileMediatype",
"exifData",
"favorite",
"mediaComments"
);
observationsCSV.writeRecord(
"observationID",
"deploymentID",
"mediaID",
"eventID",
"eventStart",
"eventEnd",
"observationLevel",
"observationType",
"cameraSetupType",
"scientificName",
"count",
"lifeStage",
"sex",
"behavior",
"individualID",
"individualPositionRadius",
"individualPositionAngle",
"individualSpeed",
"bboxX",
"bboxY",
"bboxWidth",
Expand All @@ -75,38 +136,70 @@ public void run() {
"classifiedBy",
"classificationTimestamp",
"classificationProbability",
"observationTags",
"observationComments"
);

ctx.broker.photodb2().foreachIdNotLocked(photo_id -> {
Photo2 photo = ctx.broker.photodb2().getPhoto2(photo_id, true);
if(photo != null) {
Logger.info(photo.id);
String mediaID = photo.id;
String deploymentID = photo.location;
String timestamp = photo.date.toString();
String captureMethod = ""; // optional
String timestamp = localDateTimeToString(photo.date);
String filePath = photo.imagePath.toString();
String filePublic = false ? "true" : "false";
String fileName = ""; // optional
String fileMediatype = "image/jpeg";
String observationComments = "comment"; // TODO
String exifData = ""; // optional
String favorite = ""; // optional
String mediaComments = ""; // optional

if(deplMin[0].isAfter(photo.date)) {
deplMin[0] = photo.date;
}
if(deplMax[0].isBefore(photo.date)) {
deplMax[0] = photo.date;
}

LocalDateTime[] range = rangeMap.get(photo.location);
if(range == null) {
range = new LocalDateTime[] {MAX_DATE, MIN_DATE};
rangeMap.put(photo.location, range);
}
if(range[0].isAfter(photo.date)) {
range[0] = photo.date;
}
if(range[1].isBefore(photo.date)) {
range[1] = photo.date;
}

mediaCSV.writeRecord(
mediaID,
deploymentID,
captureMethod,
timestamp,
filePath,
filePublic,
fileMediatype
fileName,
fileMediatype,
exifData,
favorite,
mediaComments
);


int[] obsCnt = new int[]{0};
String eventStart = timestamp;
String eventEnd = eventStart;
String observationLevel = "media";
photo.foreachDetection(map -> {

String bboxX = "";
String bboxY = "";
String bboxWidth = "";
String bboxHeight = "";
String bboxX = ""; // optional
String bboxY = ""; // optional
String bboxWidth = ""; // optional
String bboxHeight = ""; // optional

if(map.contains("bbox")) {
float[] bbox = map.getList("bbox").asFloatArray();
Expand All @@ -126,22 +219,44 @@ public void run() {
map.optList("classifications").asMaps().forEach(cmap -> {

String observationID = mediaID + "__" + obsCnt[0]++;
String observationType = "unknown"; // TODO
String scientificName = cmap.contains("classification") ? cmap.getString("classification") : "";
String classificationMethod = cmap.contains("classificator") ? cmap.getString("classificator") : "";
String classifiedBy = cmap.contains("identity") ? cmap.getString("identity") : "";
String classificationTimestamp = cmap.contains("date") ? cmap.getLocalDateTime("date").toString() : "";
String classificationProbability = cmap.contains("conf") ? cmap.getString("conf") : "";
String eventID = ""; // optional
String observationType = "unknown"; // TODO
String cameraSetupType = ""; // optional
String scientificName = cmap.contains("classification") ? cmap.getString("classification") : ""; // optional
String count = ""; // optional
String lifeStage = ""; // optional
String sex = ""; // optional
String behavior = ""; // optional
String individualID = ""; // optional
String individualPositionRadius = ""; // optional
String individualPositionAngle = ""; // optional
String individualSpeed = ""; // optional
String classificationMethod = cmap.contains("classificator") ? classificatorToClassificationMethod(cmap.getString("classificator")) : ""; // optional
String classifiedBy = getClassifiedBy(cmap); // optional
String classificationTimestamp = cmap.contains("date") ? localDateTimeToString(cmap.getLocalDateTime("date")) : ""; // optional
String classificationProbability = cmap.contains("conf") ? cmap.getString("conf") : ""; // optional
String observationTags = ""; // optional
String observationComments = ""; // optional

observationsCSV.writeRecord(
observationID,
deploymentID,
mediaID,
mediaID, // optional
eventID,
eventStart,
eventEnd,
observationLevel,
observationType,
cameraSetupType,
scientificName,
count,
lifeStage,
sex,
behavior,
individualID,
individualPositionRadius,
individualPositionAngle,
individualSpeed,
_bboxX,
_bboxY,
_bboxWidth,
Expand All @@ -150,9 +265,10 @@ public void run() {
classifiedBy,
classificationTimestamp,
classificationProbability,
observationTags,
observationComments
);

scientificNameSet.add(scientificName);
});

Expand All @@ -166,8 +282,8 @@ public void run() {
} catch (IOException e) {
Logger.warn(e);
}


try (
CsvWriter deploymentsCSV = CSV_BUILDER.build(output_folder_path.resolve("deployments" + ".csv"));
) {
Expand All @@ -177,26 +293,77 @@ public void run() {
"locationName",
"latitude",
"longitude",
"coordinateUncertainty",
"deploymentStart",
"deploymentEnd"
"deploymentEnd",
"setupBy",
"cameraID",
"cameraModel",
"cameraDelay",
"cameraHeight",
"cameraDepth",
"cameraTilt",
"cameraHeading",
"detectionDistance",
"timestampIssues",
"baitUse",
"featureType",
"habitat",
"deploymentGroups",
"deploymentTags",
"deploymentComments"
);
ctx.broker.photodb2().foreachProject(projectConfig -> {
ctx.broker.photodb2().foreachLocation(projectConfig.project, location -> {
String deploymentID = location;
String locationID = location;
String locationName = location;
String locationID = location; // optional
String locationName = location; // optional
String latitude = Double.toString(0);
String longitude = Double.toString(0);
String deploymentStart = "2000-01-01T00:00:00Z"; // TODO
String deploymentEnd = "2000-01-01T00:00:00Z"; // TODO
String coordinateUncertainty = Integer.toString(1); // optional
String deploymentStart = localDateTimeToString(rangeMap.get(location)[0]);
String deploymentEnd = localDateTimeToString(rangeMap.get(location)[1]);
String setupBy = ""; // optional
String cameraID = ""; // optional
String cameraModel = ""; // optional
String cameraDelay = ""; // optional
String cameraHeight = ""; // optional
String cameraDepth = ""; // optional
String cameraTilt = ""; // optional
String cameraHeading = ""; // optional
String detectionDistance = ""; // optional
String timestampIssues = ""; // optional
String baitUse = ""; // optional
String featureType = ""; // optional
String habitat = ""; // optional
String deploymentGroups = ""; // optional
String deploymentTags = ""; // optional
String deploymentComments = ""; // optional
deploymentsCSV.writeRecord(
deploymentID,
locationID,
locationName,
latitude,
longitude,
coordinateUncertainty,
deploymentStart,
deploymentEnd
deploymentEnd,
setupBy,
cameraID,
cameraModel,
cameraDelay,
cameraHeight,
cameraDepth,
cameraTilt,
cameraHeading,
detectionDistance,
timestampIssues,
baitUse,
featureType,
habitat,
deploymentGroups,
deploymentTags,
deploymentComments
);
});
});
Expand Down Expand Up @@ -302,9 +469,9 @@ public void run() {
json.key("temporal");
json.object();
json.key("start");
json.value("2000-01-01"); // TODO
json.value(localDateTimeToString(deplMin[0]));
json.key("end");
json.value("2000-01-01"); // TODO
json.value(localDateTimeToString(deplMax[0]));
json.endObject();
json.key("taxonomic");
json.array();
Expand Down

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