From 1beec28112be4c9ed8075268209444196809cdc7 Mon Sep 17 00:00:00 2001
From: d2fong <d2fong@uwaterloo.ca>
Date: Wed, 2 Oct 2019 15:26:31 -0400
Subject: [PATCH] more precise java imports, remove unused variables

---
 LEGACY_COMMENTS.txt                    |   6 +-
 README.md                              |   4 +-
 TrackStim_.jar                         | Bin 22530 -> 22530 bytes
 TrackStim_04.java => TrackStim_05.java |  99 +++++++++++++++++--------
 4 files changed, 74 insertions(+), 35 deletions(-)
 rename TrackStim_04.java => TrackStim_05.java (97%)

diff --git a/LEGACY_COMMENTS.txt b/LEGACY_COMMENTS.txt
index 4f0c1c3..9d461f6 100644
--- a/LEGACY_COMMENTS.txt
+++ b/LEGACY_COMMENTS.txt
@@ -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.
@@ -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]
diff --git a/README.md b/README.md
index f7d82db..f4ff80e 100644
--- a/README.md
+++ b/README.md
@@ -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
 ```
 
 
diff --git a/TrackStim_.jar b/TrackStim_.jar
index 2df067a999ffb80c0b455dd7b743e53856d586e5..4ef877742a9d7461b34b56886e61975e11028da6 100755
GIT binary patch
delta 44
xcmZqLz}U2bkte{LnMH(wgM)*?yLuvzHIsMsM$eouAT@b=m?e<f{3%R;5da3d4A=kw

delta 44
xcmZqLz}U2bkte{LnMH(wgM))1zkDK(HB)~1M$eouAT@b=m?e<f{3%R;5daTr4OjpG

diff --git a/TrackStim_04.java b/TrackStim_05.java
similarity index 97%
rename from TrackStim_04.java
rename to TrackStim_05.java
index 7226a7f..d6021f2 100755
--- a/TrackStim_04.java
+++ b/TrackStim_05.java
@@ -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{
 
@@ -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.
@@ -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) {
@@ -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();
@@ -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;
@@ -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
@@ -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")) {
@@ -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;
@@ -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_;
@@ -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;
@@ -2025,7 +2064,7 @@ class SignalSender01 implements Runnable {
     int[] changetimepoints;
     int[] changevalues;
 
-    SignalSender01(TrackStim_04 ts_) {
+    SignalSender02(TrackStim_05 ts_) {
         ts = ts_;
     }
 
@@ -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;
@@ -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());
         }
     }