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mnive93/BloodScanner.java

Created March 31, 2017 14:45
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BloodScanner.java
package com.sigtuple.aadi.autoscan.blood;
import android.app.Activity;
import android.content.Context;
import android.content.Intent;
import android.graphics.Bitmap;
import android.os.AsyncTask;
import android.os.Handler;
import android.widget.Toast;
import com.sigtuple.aadi.asynctasks.SaveToFile;
import com.sigtuple.aadi.autoscan.ASConstants;
import com.sigtuple.aadi.autoscan.BaseScanner;
import com.sigtuple.aadi.bluetooth.BLECommand;
import com.sigtuple.aadi.bluetooth.BLEConstants;
import com.sigtuple.aadi.bluetooth.BluetoothLeService;
import com.sigtuple.aadi.bluetooth.BluetoothLeServiceAdapter;
import com.sigtuple.aadi.events.OnBLETaskCompleted;
import com.sigtuple.aadi.events.RequestImageCapture;
import com.sigtuple.aadi.events.RequestNextScan;
import com.sigtuple.aadi.interfaces.ScannerController;
import com.sigtuple.aadi.models.QIFactors;
import com.sigtuple.aadi.models.Slide;
import com.sigtuple.aadi.processing.image.ImageUtils;
import com.sigtuple.aadi.utils.LogWrapper;
import com.sigtuple.aadi.utils.SharedPrefUtils;
import com.sigtuple.aadi.utils.URLUtils;
import com.sigtuple.aadi.views.CustomAlertDialog;
import org.greenrobot.eventbus.EventBus;
import org.greenrobot.eventbus.Subscribe;
import org.greenrobot.eventbus.ThreadMode;
import org.json.JSONException;
import org.json.JSONObject;
import org.opencv.core.CvType;
import org.opencv.core.Mat;
import java.util.HashMap;
/**
* Created by prateek on 12/8/16.
*/
public class BloodScanner extends BaseScanner {
private BloodScanPlan mPlan;
private HashMap<Integer, JSONObject> sequenceObjects;
private ScannerController controller;
public static final String ACTION_TAKE_PICTURE = "action_picture";
public static final String ACTION_AUTO_SCAN = "action_auto_scan";
int autoScanState;
int prevAutoScanState;
int autoScanStateArg;
int vertical = 0;
int horizontal = 0;
int numImages;
Mat autoScanStateObj;
Bitmap bitmap;
boolean isScanning = false;
int x;
int y;
Slide slide;
Handler mhandler = new Handler();
Context context;
public static final String TAG = "BloodScanner";
public BloodScanner(BluetoothLeServiceAdapter adapter) {
super(adapter);
mPlan = new BloodScanPlan();
x = 0;
y = 0;
sequenceObjects = new HashMap<>();
}
@Override
public void start(Context context) {
mPlan = new BloodScanPlan();
// prepareNextCommand(new RequestNextScan());
this.context = context;
autoScan();
}
@Override
public void subscribe(ScannerController controller) {
this.controller = controller;
}
public void ackReceivedFromBluetooth(Intent intent) {
if (!ASConstants.AUTO_SCAN)
return;
String status = intent.getStringExtra("status");
int seqId = intent.getIntExtra("seq", 0);
JSONObject seqObj = getJsonForSeq(seqId);
String opType = "";
try {
if (seqObj != null) {
opType = seqObj.getString("optype");
setCoordinates(seqObj.getString("opcode").charAt(0), seqObj.getInt("oparg"));
}
} catch (Exception e) {
e.printStackTrace();
}
if (status != null && !status.equals(URLUtils.STATUS_OK)) {
if (autoScanState == BLEConstants.AUTOSCAN_STATE_CONN_RETRY || bleAdapter.isConnected()) {
//handle error
CustomAlertDialog alertDialog = new CustomAlertDialog(context, "BLE Communication Error", "Stopping Auto Scan");
alertDialog.showAlertDialog();
return;
} else {
//try reconnecting
bleAdapter.reconnect();
prevAutoScanState = autoScanState;
autoScanState = BLEConstants.AUTOSCAN_STATE_CONN_RETRY;
}
} else if (autoScanState == BLEConstants.AUTOSCAN_STATE_CONN_RETRY) {
autoScanState = prevAutoScanState;
}
int origState = autoScanState;
switch (autoScanState) {
case BLEConstants.AUTOSCAN_STATE_START:
autoScanState = BLEConstants.AUTOSCAN_STATE_SET_SPEED;
autoScanStateArg = 0;
setSpeed(ASConstants.AUTO_SCAN_SPEED, true);
break;
case BLEConstants.AUTOSCAN_STATE_SET_SPEED:
autoScanState = BLEConstants.AUTOSCAN_STATE_HOME_X;
autoScanStateArg = 0;
homeX(true);
break;
case BLEConstants.AUTOSCAN_STATE_HOME_X:
autoScanState = BLEConstants.AUTOSCAN_STATE_HOME_Y;
autoScanStateArg = 0;
homeY(true);
break;
case BLEConstants.AUTOSCAN_STATE_HOME_Y:
autoScanState = BLEConstants.AUTOSCAN_STATE_HOME_OFFSET_X;
autoScanStateArg = 0;
if (ASConstants.AUTOSCAN_HOME_OFFSET_X > 0) {
if (ASConstants.AUTOSCAN_HOME_OFFSET_X > ASConstants.AUTOSCAN_MAX_SINGLE_STEP) {
autoScanStateArg += ASConstants.AUTOSCAN_MAX_SINGLE_STEP;
}
moveX(Math.min(ASConstants.AUTOSCAN_HOME_OFFSET_X, ASConstants.AUTOSCAN_MAX_SINGLE_STEP), true);
break;
}
case BLEConstants.AUTOSCAN_STATE_HOME_OFFSET_X:
if (ASConstants.AUTOSCAN_HOME_OFFSET_X > ASConstants.AUTOSCAN_MAX_SINGLE_STEP &&
autoScanStateArg < ASConstants.AUTOSCAN_HOME_OFFSET_X) {
LogWrapper.e(TAG, "Inside move x");
int toMove = Math.min(ASConstants.AUTOSCAN_MAX_SINGLE_STEP, (ASConstants.AUTOSCAN_HOME_OFFSET_X - autoScanStateArg));
autoScanStateArg += toMove;
moveX(toMove, true);
break;
} else {
LogWrapper.e(TAG, "Inside else move y");
autoScanState = BLEConstants.AUTOSCAN_STATE_HOME_OFFSET_Y;
autoScanStateArg = 0;
LogWrapper.e(TAG, "Home offset Y : " + ASConstants.AUTOSCAN_HOME_OFFSET_Y + "Max single step is : " + ASConstants.AUTOSCAN_MAX_SINGLE_STEP);
if (ASConstants.AUTOSCAN_HOME_OFFSET_Y > 0) {
if (ASConstants.AUTOSCAN_HOME_OFFSET_Y > ASConstants.AUTOSCAN_MAX_SINGLE_STEP) {
autoScanStateArg += ASConstants.AUTOSCAN_MAX_SINGLE_STEP;
}
LogWrapper.e(TAG, "Moving Y now");
moveY(Math.min(ASConstants.AUTOSCAN_MAX_SINGLE_STEP, ASConstants.AUTOSCAN_HOME_OFFSET_Y), true);
break;
}
}
case BLEConstants.AUTOSCAN_STATE_HOME_OFFSET_Y:
if (ASConstants.AUTOSCAN_HOME_OFFSET_Y > ASConstants.AUTOSCAN_MAX_SINGLE_STEP &&
autoScanStateArg < ASConstants.AUTOSCAN_HOME_OFFSET_Y) {
int toMove = Math.min(ASConstants.AUTOSCAN_MAX_SINGLE_STEP, (ASConstants.AUTOSCAN_HOME_OFFSET_Y - autoScanStateArg));
autoScanStateArg += toMove;
moveY(toMove, true);
break;
} else {
LogWrapper.e(TAG, "State is now find state smear");
autoScanState = BLEConstants.AUTOSCAN_STATE_FIND_SMEAR;
ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS = 0;
}
case BLEConstants.AUTOSCAN_STATE_FIND_SMEAR:
if (ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS == -1) {
LogWrapper.e(TAG, "start scanning");
//start scanning
autoScanState = BLEConstants.AUTOSCAN_STATE_SCAN;
ASConstants.reset();
//set vertical count since we will be starting at AUTOSCAN_HOME_OFFSET_X
vertical = Math.abs((ASConstants.AUTOSCAN_HOME_OFFSET_X - ASConstants.AUTOSCAN_HOME_SLIDE_START_X)) / Math.abs(ASConstants.AUTOSCAN_STEP_X);
autoScan();
//broadcast(ACTION_AUTO_SCAN);
} else {
int findAttempts = ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS;
if (findAttempts >= (ASConstants.AUTOSCAN_SLIDE_LENGTH / Math.abs(ASConstants.AUTOSCAN_STEP_Y))) {
//TODO: end autoscan
// stopScan();
} else if (findAttempts == 0) {
ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS = findAttempts + 1;
moveY(ASConstants.AUTOSCAN_STEP_Y, true);
} else if (opType.equals("move")) {
// Todo
LogWrapper.e(TAG, "Resetting focus here");
ASConstants.reset();
controller.takePicture();
//broadcast(ACTION_TAKE_PICTURE);
} else {
if (ASConstants.FOCUS_ATTEMPTS >= 0) {
LogWrapper.e(TAG, "Taking picture now");
controller.takePicture();
//broadcast(ACTION_TAKE_PICTURE);
} else {
LogWrapper.e(TAG, "Moving now");
ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS = findAttempts + 1;
moveY(ASConstants.AUTOSCAN_STEP_Y, true);
}
}
}
break;
case BLEConstants.AUTOSCAN_STATE_SCAN:
if (opType.equals("move")) {
// try {
//Thread.sleep(ASConstants.AUTOSCAN_CAPTURE_DELAY);
controller.takePicture();
// broadcast(ACTION_TAKE_PICTURE);
} else if (opType.equals("home") ||
opType.equals("speed") ||
opType.equals("reconn")) {
autoScan();
// broadcast(ACTION_AUTO_SCAN);
} else {
//default and focus have the same handler
//[NSThread sleepForTimeInterval:1];
if (ASConstants.FOCUS_ATTEMPTS >= 0) {
controller.takePicture();
// broadcast(ACTION_TAKE_PICTURE);
} else {
autoScan();
// broadcast(ACTION_AUTO_SCAN);
}
}
break;
default:
break;
}
if (autoScanState != origState) {
LogWrapper.e(TAG, "Auto scan state has been changed");
}
}
public void setContext(Context context){
this.context = context;
}
public void initiateScan() {
Intent intent = new Intent(BluetoothLeService.BLUETOOTH_INFO);
intent.putExtra("status", URLUtils.STATUS_OK);
ackReceivedFromBluetooth(intent);
}
public void initiateReconnection() {
Intent intent = new Intent(BluetoothLeService.BLUETOOTH_INFO);
intent.putExtra("status", URLUtils.STATUS_ERR);
ackReceivedFromBluetooth(intent);
}
public void autoScan() {
if (!ASConstants.AUTO_SCAN) {
vertical = 0;
horizontal = 0;
if (!bleAdapter.isConnected()) {
CustomAlertDialog alertDialog = new CustomAlertDialog(context, "BLE Not Found", "Unable to connect to the BLE Device. Please try again after some time");
alertDialog.showAlertDialog();
return;
}
autoScanState = BLEConstants.AUTOSCAN_STATE_START;
autoScanStateArg = 0;
ASConstants.AUTO_SCAN = true;
ASConstants.AUTO_SCAN_IMAGE_COUNT = 0;
initiateScan();
return;
}
if (horizontal >= (ASConstants.AUTOSCAN_SLIDE_LENGTH / Math.abs(ASConstants.AUTOSCAN_STEP_Y)) || ASConstants.AUTO_SCAN_IMAGE_COUNT >= ASConstants.AUTOSCAN_NUM_IMAGES) {
// stop scan
LogWrapper.e(TAG, "Stopping scan.");
stopScan();
}
if (vertical > (ASConstants.AUTOSCAN_SLIDE_WIDTH / Math.abs(ASConstants.AUTOSCAN_STEP_X))) {
vertical = 0;
horizontal++;
moveY(ASConstants.AUTOSCAN_STEP_Y, true);
return;
}
//move
if (horizontal % 2 == 0) {
moveX(ASConstants.AUTOSCAN_STEP_X, true);
vertical++;
} else {
moveX((-1 * ASConstants.AUTOSCAN_STEP_X), true);
vertical++;
}
}
public void setCoordinates(char opcode, int oparg) {
if (opcode == 'h' && oparg == 1) {
x = 0;
} else if (opcode == 'h' && oparg == 2) {
y = 0;
} else if (opcode == 'h' && oparg == 3) {
x = 0;
y = 0;
} else if (opcode == 'x') {
x += oparg;
} else if (opcode == 'y') {
y += oparg;
}
}
public void stopScan() {
LogWrapper.e(TAG, "Stopping scan now");
ASConstants.AUTO_SCAN = false;
ASConstants.AUTO_SCAN_IMAGE_COUNT = 0;
ASConstants.reset();
numImages = 0;
bleAdapter.disconnect();
((Activity)context).runOnUiThread(new Runnable() {
@Override
public void run() {
CustomAlertDialog dialog = new CustomAlertDialog(context, "Scan Stopped", "Stopped Auto scan");
dialog.showAlertDialog();
}
});
}
@Subscribe
public void onBLETaskDone(OnBLETaskCompleted event) {
// capture image and fire next command
LogWrapper.i(EventBus.TAG, "Handle OnBLETaskCompleted event");
EventBus.getDefault().post(new RequestImageCapture());
}
public void moveX(int offset, boolean withAsync) {
byte[] message = BLECommand.prepareMessage(BLECommand.MOVE_X, offset);
addSequenceInfo(message, "x", offset);
bleAdapter.sendMessage(message);
}
public void moveY(int offset, boolean withAsync) {
byte[] message = BLECommand.prepareMessage(BLECommand.MOVE_Y, offset);
addSequenceInfo(message, "y", offset);
bleAdapter.sendMessage(message);
}
public void homeX(boolean withAsync) {
byte[] message = BLECommand.prepareMessage(BLECommand.HOME, 1);
addSequenceInfo(message, "h", 1);
bleAdapter.sendMessage(message);
}
public void homeY(boolean withAsync) {
byte[] message = BLECommand.prepareMessage(BLECommand.HOME, 2);
addSequenceInfo(message, "h", 2);
bleAdapter.sendMessage(message);
}
public void setSpeed(int speed, boolean withAsync) {
byte[] message = BLECommand.prepareMessage(BLECommand.SETSPEED, speed);
addSequenceInfo(message, "s", speed);
bleAdapter.sendMessage(message);
}
public void focus(int offset, boolean withAsync) {
LogWrapper.e(TAG, "Focus offset is : " + offset);
byte[] message = BLECommand.prepareMessage(BLECommand.FOCUS, offset);
addSequenceInfo(message, "f", offset);
bleAdapter.sendMessage(message);
}
public void addSequenceInfo(byte[] data, String opCode, int oparg) {
int seqID = data[BLECommand.SEQ_NUMBER];
LogWrapper.e(TAG, "opcode is : " + opCode);
String opType = BLECommand.getOpType(opCode);
JSONObject seqObj = new JSONObject();
try {
seqObj.put("opcode", opCode);
seqObj.put("optype", opType);
seqObj.put("seq", seqID);
seqObj.put("oparg", oparg);
sequenceObjects.put(seqID, seqObj);
} catch (JSONException e) {
e.printStackTrace();
}
}
public boolean isGoodImage(final QIFactors factors) {
double sharpnessThreshold = ASConstants.IMAGE_BLUR_THRESHOLD;
//Add normalised sharpness threshoold
double cappedDensity = 0.0;
if(factors.density>=ASConstants.IMAGE_NORM_CAPPED_DENSITY_THRESHOLD){
cappedDensity = ASConstants.IMAGE_NORM_CAPPED_DENSITY_THRESHOLD;
}
else{
cappedDensity = factors.density;
}
double normalisedSharpness = factors.sharpness * (1 - cappedDensity);
double normalisedCount = factors.cell_count / (factors.density + 0.001);
factors.setNormalised_count(normalisedCount);
factors.setNormalised_sharpness(normalisedSharpness);
LogWrapper.e(TAG, "Cell count : " + factors.cell_count + ", sharpness : " + factors.sharpness + ", Density is : " + factors.density);
if (autoScanState == BLEConstants.AUTOSCAN_STATE_FIND_SMEAR) {
sharpnessThreshold = 0.8 * sharpnessThreshold;
} else {
// Unused code
if (factors.density >= 2.5 * ASConstants.SCAN_DENSITY_MIN_THRESHOLD) {
sharpnessThreshold = 1.1 * ASConstants.IMAGE_BLUR_THRESHOLD;
}
}
if (factors.density >= ASConstants.IMAGE_DENSITY_MIN_THRESHOLD && factors.density <= ASConstants.IMAGE_DENSITY_MAX_THRESHOLD &&
factors.cell_count >= ASConstants.SCAN_CELL_COUNT_THRESHOLD
) {
if (autoScanState == BLEConstants.AUTOSCAN_STATE_FIND_SMEAR && factors.sharpness >= sharpnessThreshold) {
//
// showToast("It's a good image");
LogWrapper.e(TAG, "Checking for good image");
((Activity) context).runOnUiThread(new Runnable() {
@Override
public void run() {
Toast.makeText(context, "It is a good image", Toast.LENGTH_SHORT).show();
}
});
return true;
} else if (autoScanState != BLEConstants.AUTOSCAN_STATE_FIND_SMEAR && factors.sharpness >= ASConstants.IMAGE_BLUR_THRESHOLD) /**&&
factors.normalised_sharpness >= ASConstants.IMAGE_NORM_SHARPNESS_THRESHOLD &&
factors.normalised_count >= ASConstants.IMAGE_NORM_CELL_COUNT_THRESHOLD)**/ {
// showToast("It's a good image");
((Activity) context).runOnUiThread(new Runnable() {
@Override
public void run() {
Toast.makeText(context, "It is a good image", Toast.LENGTH_SHORT).show();
}
});
return true;
}
}
final double finalSharpnessThreshold = sharpnessThreshold;
((Activity) context).runOnUiThread(new Runnable() {
@Override
public void run() {
LogWrapper.e(TAG, "Not a good image . Cell count : " + factors.cell_count + ", sharpness : " + factors.sharpness + ", Density is : " + factors.density + ", Sharpness threshold is : " + finalSharpnessThreshold + ", brightness_index") ;
Toast.makeText(context, "It is not a good image", Toast.LENGTH_SHORT).show();
}
});
return false;
}
public void checkForRefocus(QIFactors factors, int bestDirection, Mat matrix, int fstep, int focusBestOffset) {
LogWrapper.e(TAG, "Checking for refocus here");
LogWrapper.e(TAG, "Best sharpness is : " + ASConstants.FOCUS_BEST_SHARPNESS + "sharpness is : " + factors.sharpness);
int prevDirection = ASConstants.FOCUS_PREV_DIRECTION;
int focusStep = fstep;
int focusOffset = ASConstants.FOCUS_OFFSET;
float roundedSharpness = (float)(Math.round(factors.sharpness * 100.0) / 100.0);
float roundedBestSharpness = (float)Math.round(ASConstants.FOCUS_BEST_SHARPNESS);
LogWrapper.e(TAG, "Cell count : " + factors.cell_count + ", sharpness : " + factors.sharpness + ", Density is : " + factors.density);
if (roundedSharpness > roundedBestSharpness && factors.density > 0
) {
ASConstants.FOCUS_BEST_OFFSET = (-1 * focusStep * prevDirection);
ASConstants.FOCUS_OFFSET += (-1 * focusStep * prevDirection);
ASConstants.FOCUS_DIRECTION_STEPS += 1;
ASConstants.setFocusQIFactors(factors);
if (bestDirection != prevDirection)
ASConstants.FOCUS_BEST_DIRECTION = prevDirection;
if (autoScanStateObj != null) {
autoScanStateObj.release();
}
autoScanStateObj = new Mat(matrix.rows(), matrix.cols(), CvType.CV_8UC4);
if(autoScanStateObj != null)
matrix.copyTo(autoScanStateObj);
focus(prevDirection * focusStep, true);
return;
} else {
tuneInDifferentDirection(focusBestOffset);
}
}
public void tuneInDifferentDirection(int focusBestOffset) {
LogWrapper.e(TAG, "Tuning in different direction");
// LogWrapper.e(TAG, "Size of autoscan obj is : " + autoScanStateObj.size());
if (ASConstants.FOCUS_DIRECTION_CHANGES > 0 || (ASConstants.FOCUS_DIRECTION_STEPS > 1 && autoScanStateObj != null)) {
ASConstants.reset();
doImageQualityCheck(focusBestOffset);
} else {
int prevDirection = ASConstants.FOCUS_PREV_DIRECTION;
int focusOffset = ASConstants.FOCUS_OFFSET;
double initialStep = ASConstants.FOCUS_INITIAL_STEP;
ASConstants.FOCUS_PREV_DIRECTION = (-1 * prevDirection);
ASConstants.FOCUS_DIRECTION_CHANGES++;
ASConstants.FOCUS_DIRECTION_STEPS = 1;
ASConstants.FOCUS_BEST_OFFSET += (int) (-1 * focusOffset + prevDirection * initialStep);
ASConstants.FOCUS_OFFSET = (int) (prevDirection * initialStep);
LogWrapper.i(TAG, "Tuning in different direction FocusOffset : " + focusOffset + ", PrevDirection :" + prevDirection + ", Initial Step : " + initialStep);
focus((int) (focusOffset - 1 * prevDirection * initialStep), true);
}
}
public void doImageQualityCheck(int bestOffset) {
// autoScanStateObj = new Mat();
// Utils.bitmapToMat(bitmap, autoScanStateObj);
float imageQualitySharpness = ImageUtils.calculateSharpness(autoScanStateObj, ASConstants.IMAGE_QUALITY_PATCH_SIZE);
QIFactors bestfactors = ImageUtils.calculateImageProperties(autoScanStateObj, ASConstants.IMAGE_QUALITY_PATCH_SIZE, ASConstants.SCAN_CELL_COUNT_MIN_AREA, ASConstants.SCAN_CELL_COUNT_MAX_AREA);
if (bestfactors == null)
return;
bestfactors.setSharpness(imageQualitySharpness);
LogWrapper.e(TAG, "brightness : " + bestfactors.brightness_index + "cell_count : " + bestfactors.cell_count);
if (isGoodImage(bestfactors)) {
if (autoScanState == BLEConstants.AUTOSCAN_STATE_FIND_SMEAR) {
ASConstants.AUTO_SCAN_FIND_SMEAR_ATTEMPTS = -1;
LogWrapper.e(TAG, "Focus best offset is : " + ASConstants.FOCUS_BEST_OFFSET);
focus(bestOffset, true);
autoScanStateObj.release();
autoScanStateObj = null;
} else {
bestfactors.setCoord_x(x);
bestfactors.setCoord_y(y);
bitmap = ImageUtils.convertBGRToBitmap(bitmap, autoScanStateObj);
SaveToFile saveToFile = new SaveToFile(slide, bestfactors, bitmap);
saveToFile.executeOnExecutor(AsyncTask.THREAD_POOL_EXECUTOR);
controller.incrementPictureCount();
ASConstants.AUTO_SCAN_IMAGE_COUNT = ++numImages;
focus(bestOffset, true);
autoScanStateObj.release();
autoScanStateObj = null;
}
} else {
LogWrapper.e(TAG, "Focusing now again");
focus(bestOffset, true);
autoScanStateObj.release();
autoScanStateObj = null;
}
autoScanStateObj = null;
}
public JSONObject getJsonForSeq(int seqId) {
return sequenceObjects.get(seqId);
}
@Override
@Subscribe(threadMode = ThreadMode.BACKGROUND)
public void prepareNextCommand(RequestNextScan event) {
if (mPlan.hasNext()) {
// ask plan object to prepare the command
// and internally revise the next step
mPlan.count++;
byte[] message = BLECommand.prepareMessage(BLECommand.MOVE_X, 20);
bleAdapter.sendMessage(message);
}
}
@Override
public void analyseImage(Mat matrix) {
int patchSize = ASConstants.SCAN_QUALITY_PATCH_SIZE;
int minArea = ASConstants.SCAN_CELL_COUNT_MIN_AREA;
int maxArea = ASConstants.SCAN_CELL_COUNT_MAX_AREA;
QIFactors factors = ImageUtils.calculateImageProperties(matrix, patchSize, minArea, maxArea);
float sharpness = ImageUtils.calculateSharpness(matrix, patchSize);
double imageNormDensityThreshold = ASConstants.IMAGE_NORM_CAPPED_DENSITY_THRESHOLD;
double cappedDensity = 0.0;
if (factors.density >= imageNormDensityThreshold) {
cappedDensity = imageNormDensityThreshold;
} else {
cappedDensity = factors.density;
}
factors.setSharpness(sharpness);
final double normalisedSharpness = factors.sharpness * (1 - cappedDensity);
double normalisedCount = factors
.cell_count / (factors.density + 0.001);
factors.setNormalised_count(normalisedCount);
factors.setNormalised_sharpness(normalisedSharpness);
LogWrapper.e(TAG, "Cell count : " + factors.cell_count + ", sharpness : " + factors.sharpness + ", Density is : " + factors.density);
LogWrapper.e(TAG, "Focus attempts is : " + ASConstants.FOCUS_ATTEMPTS);
int focusStep = Integer.valueOf(SharedPrefUtils.getValueForKey(ASConstants.AUTOSCANFOCUSSTEP));
int bestDirection = ASConstants.FOCUS_BEST_DIRECTION;
if (bestDirection == 0) {
bestDirection = -1;
}
LogWrapper.e(TAG, "Best direction is : " + bestDirection);
LogWrapper.e(TAG, "Focus step is : " + focusStep);
if ((sharpness <= 0.125 * ASConstants.SCAN_BLUR_THRESHOLD || (factors.density < 0.125 * ASConstants.SCAN_DENSITY_MIN_THRESHOLD)) ) {
focusStep *= 4;
} else if ((sharpness <= 0.25 * ASConstants.SCAN_BLUR_THRESHOLD || (factors.density < 0.5 * ASConstants.SCAN_DENSITY_MIN_THRESHOLD)) ) {
focusStep *= 2;
} else if (sharpness >= 0.85 * ASConstants.SCAN_BLUR_THRESHOLD && factors.density >= ASConstants.SCAN_DENSITY_MIN_THRESHOLD) {
focusStep *= 0.25;
} else if (sharpness >= 0.75 * ASConstants.SCAN_BLUR_THRESHOLD && factors.density >= ASConstants.SCAN_DENSITY_MIN_THRESHOLD) {
focusStep *= 0.5;
}
ASConstants.FOCUS_STEP = focusStep;
if (ASConstants.FOCUS_ATTEMPTS == -1) {
if (factors.density < ASConstants.SCAN_DENSITY_MIN_THRESHOLD / 8 && autoScanState == BLEConstants.AUTOSCAN_STATE_FIND_SMEAR) {
ASConstants.reset();
matrix.release();
focus(0, true);
return;
}
ASConstants.intialise(focusStep, bestDirection, factors.sharpness, factors.density, factors.cell_count, factors.brightness_index, factors.color_index);
autoScanStateObj = new Mat(matrix.rows(), matrix.cols(), CvType.CV_8UC4);
matrix.copyTo(autoScanStateObj);
focus((bestDirection * focusStep), true);
return;
} else {
// Check for focus attempt value and if it's within the range
int focusBestOffset = ASConstants.FOCUS_BEST_OFFSET;
if (ASConstants.FOCUS_ATTEMPTS < ASConstants.AUTOSCAN_MAX_FOCUS_ATTEMPTS) {
ASConstants.FOCUS_ATTEMPTS += 1;
LogWrapper.e(TAG, "Focus attempts is : " + ASConstants.FOCUS_ATTEMPTS);
checkForRefocus(factors, bestDirection, matrix, focusStep, focusBestOffset);
} else {
ASConstants.reset();
doImageQualityCheck(focusBestOffset);
}
}
}
public void broadcast(String action){
Intent intent = new Intent(action);
context.sendBroadcast(intent);
}
@Override
public void onSlideLoaded(Slide slide) {
this.slide = slide;
}
public void register() {
EventBus.getDefault().register(this);
}
public void unregister() {
EventBus.getDefault().unregister(this);
}
}
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