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more precise java imports, remove unused variables
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@d2fong
d2fong committed Oct 2, 2019
1 parent d5fb0c0 commit 1beec28
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6 changes: 3 additions & 3 deletions LEGACY_COMMENTS.txt
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Expand Up @@ -16,8 +16,8 @@
//fluorescent object detection and tracking plugin. need motorized stage
//works with stack
//compiled with
//javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.3nb/ij.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim_04.java
//jar cvf TrackStim_.jar TrackStim_04.class TrackingThread11.class SignalSender01.class
//javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.3nb/ij.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim_05.java
//jar cvf TrackStim_.jar TrackStim_05.class TrackingThread12.class SignalSender02.class
//ver3 initiall release
//ver4 avarage thresholding. also can choose thresholding method.
// ver5 implement change roi function by clicking image.
Expand All @@ -34,6 +34,6 @@
//121203 adding manual trackig option

//cd /Applications/Micro-Manager1.4/plugins/
//javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.4/ij.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim_04.java
//javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.4/ij.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.4/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim_05.java

//[Serial, /dev/tty.SLAB_USBtoUART, /dev/tty.SLAB_USBtoUART, /dev/tty.SLAB_USBtoUART, Serial, /dev/tty.usbmodem3d21]
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -16,14 +16,14 @@ In this repository is a file called TrackStim.java
You must use this command to take TrackStim.java and other packages that TrackStim.java depends on to build the plugin (macOSX specific):

```sh
javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.3/ij.jar:/Applications/Micro-Manager1.3/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.3/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim.java
javac -source 1.5 -target 1.5 -classpath /Applications/Micro-Manager1.3/ij.jar:/Applications/Micro-Manager1.3/plugins/Micro-Manager/MMCoreJ.jar:/Applications/Micro-Manager1.3/plugins/Micro-Manager/MMJ_.jar -Xlint:unchecked TrackStim_05.java

```

Then, run the following command:

```sh
jar cvf TrackStim_.jar TrackStim_04.class TrackingThread11.class SignalSender01.class
jar cvf TrackStim_.jar TrackStim_05.class TrackingThread12.class SignalSender02.class
```


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99 changes: 69 additions & 30 deletions TrackStim_04.java → TrackStim_05.java
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@@ -1,26 +1,67 @@
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.prefs.Preferences;
import java.util.concurrent.*;
import java.io.*;
import java.awt.*;
import java.awt.event.*;

import ij.*;
import ij.io.*;
import ij.process.*;
import ij.gui.*;
import ij.plugin.*;
import ij.plugin.filter.*;

import java.util.concurrent.ScheduledFuture;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;

import java.io.File;
import java.io.OutputStream;
import java.io.FileOutputStream;

import java.awt.TextField;
import java.awt.Label;
import java.awt.GridBagConstraints;
import java.awt.Dimension;
import java.awt.Checkbox;
import java.awt.Rectangle;
import java.awt.Point;
import java.awt.Button;
import java.awt.Choice;
import java.awt.GridBagLayout;

import java.awt.event.ActionListener;
import java.awt.event.MouseListener;
import java.awt.event.MouseEvent;
import java.awt.event.ItemListener;
import java.awt.event.KeyEvent;
import java.awt.event.ActionEvent;
import java.awt.event.ItemEvent;

import ij.ImageListener;
import ij.ImagePlus;
import ij.IJ;
import ij.WindowManager;
import ij.ImageStack;

import ij.io.DirectoryChooser;
import ij.io.FileInfo;
import ij.io.TiffEncoder;

import ij.process.ImageProcessor;
import ij.process.ImageStatistics;

import ij.gui.Roi;
import ij.gui.Wand;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.PolygonRoi;

import ij.plugin.*; // not sure if needed
import ij.plugin.filter.*; // not sure if needed

import ij.plugin.frame.PlugInFrame;

import mmcorej.CMMCore;
import mmcorej.MMCoreJ;
import mmcorej.StrVector;
import org.micromanager.*;
import mmcorej.Configuration;
import mmcorej.PropertySetting;

public class TrackStim_04 extends PlugInFrame implements ActionListener, ImageListener, MouseListener, ItemListener {
public class TrackStim_05 extends PlugInFrame implements ActionListener, ImageListener, MouseListener, ItemListener {
// public class RealTimeTracker_09 extends PlugInFrame implements
// ActionListener,ImageListener{

Expand All @@ -30,7 +71,7 @@ public class TrackStim_04 extends PlugInFrame implements ActionListener, ImageLi
TextField skiptext;
// TextField intervaltext;
// TrackingThread(RealTimeTracker_01 tpf);
TrackingThread11 tt = null;
TrackingThread12 tt = null;

// filed used in TrackingThread
java.awt.Checkbox closest;// target definition method.
Expand Down Expand Up @@ -73,7 +114,7 @@ public class TrackStim_04 extends PlugInFrame implements ActionListener, ImageLi
int frame = 1200;// String defaultframestring;
boolean ready;

public TrackStim_04() {
public TrackStim_05() {
super("TrackerwithStimulater");
// First, check if there is mmc.
if (mmc_ == null) {
Expand All @@ -87,8 +128,6 @@ public TrackStim_04() {
}
IJ.log("TrackStim Constructor: MMCore initialized");

MMStudioMainFrame mmcmf = MMStudioPlugin.frame_;

prefs = Preferences.userNodeForPackage(this.getClass());// make instance?
imp = WindowManager.getCurrentImage();
ImageWindow iw = imp.getWindow();
Expand Down Expand Up @@ -604,7 +643,7 @@ void prepSignals(int channel) {
// mili sec, and 0-63
// helper function for prepSignals
void setSender(int channel, int timepoint, int signalstrength) {
SignalSender01 sd = new SignalSender01(this);
SignalSender02 sd = new SignalSender02(this);
sd.setChannel(channel);
sd.setSignalStrength(signalstrength);
ScheduledExecutorService ses;
Expand Down Expand Up @@ -754,7 +793,7 @@ public void actionPerformed(ActionEvent e) {
// ready button pushed
if (lable.equals("Ready")) {
ready = true;
tt = new TrackingThread11(this);
tt = new TrackingThread12(this);
tt.start();

// go button pressed
Expand Down Expand Up @@ -817,7 +856,7 @@ public void actionPerformed(ActionEvent e) {
prepSignals(0);
}

tt = new TrackingThread11(this);
tt = new TrackingThread12(this);
tt.start();
}
} else if (lable.equals("Stop")) {
Expand Down Expand Up @@ -894,9 +933,9 @@ public void mouseReleased(MouseEvent e) {
////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////
// To watch the process during data collection, use different thread.
class TrackingThread11 extends Thread {
class TrackingThread12 extends Thread {
// vaiables recieve from RealTimeTracker
TrackStim_04 tpf;
TrackStim_05 tpf;
CMMCore mmc_;
ImagePlus imp;
ImageCanvas ic;
Expand Down Expand Up @@ -935,7 +974,7 @@ class TrackingThread11 extends Thread {
// allowance distance change
static double mindistancechange = 0.3;

TrackingThread11(TrackStim_04 tpf) {
TrackingThread12(TrackStim_05 tpf) {
IJ.log("TrackingThread constructor");
this.tpf = tpf;
mmc_ = tpf.mmc_;
Expand Down Expand Up @@ -2014,8 +2053,8 @@ public void startAcq(String arg) {
}// class TrackingThread9 extends Thread { end

/// for stimulation using arduino DA converter
class SignalSender01 implements Runnable {
TrackStim_04 ts;
class SignalSender02 implements Runnable {
TrackStim_05 ts;
int channel;
int strength;
int sendingdata;
Expand All @@ -2025,7 +2064,7 @@ class SignalSender01 implements Runnable {
int[] changetimepoints;
int[] changevalues;

SignalSender01(TrackStim_04 ts_) {
SignalSender02(TrackStim_05 ts_) {
ts = ts_;
}

Expand All @@ -2039,8 +2078,8 @@ void setSignalStrength(int strength_) {
}

public void run() {
IJ.log("SignalSender01: system time is " + String.valueOf(System.nanoTime() / 1000000));
IJ.log("SignalSender01: strength is " + String.valueOf(strength));
IJ.log("SignalSender02: system time is " + String.valueOf(System.nanoTime() / 1000000));
IJ.log("SignalSender02: strength is " + String.valueOf(strength));

// testing sending vale
sendingdata = channel << 7 | strength;
Expand All @@ -2050,7 +2089,7 @@ public void run() {
try {
ts.mmc_.writeToSerialPort(ts.adportsname, sendingchrvec);
} catch (java.lang.Exception e) {
IJ.log("SignalSender01: error trying to write data " + String.valueOf(sendingdata) + " to the serial port " + ts.adportsname);
IJ.log("SignalSender02: error trying to write data " + String.valueOf(sendingdata) + " to the serial port " + ts.adportsname);
IJ.log(e.getMessage());
}
}
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