cleaned up some comments

added more tests, mockito

Author: bryantChhun

README.md

@@ -1,21 +1,21 @@
 <!--[![Build Status](https://travis-ci.org/java-native-access/jna.svg?branch=master)](https://travis-ci.org/java-native-access/jna)-->
 
-# mm2python
+# org.mm2python
 micro-manager 2.0 plugin that enables python control using Py4j remote procedure calls and IPC data transfer using memory mapped files
 
 # dependencies
-mm2python is a plugin for the open-source microscopy control project Micro-Manager (https://micro-manager.org/) (https://github.com/micro-manager/micro-manager)
+org.mm2python is a plugin for the open-source microscopy control project Micro-Manager (https://micro-manager.org/) (https://github.com/micro-manager/micro-manager)
 Please download and install version 2.0 from that site.
 
-mm2python depends on the Py4j project (https://www.py4j.org/).  It is included as a dependency in the gradle build
+org.mm2python depends on the Py4j project (https://www.py4j.org/).  It is included as a dependency in the gradle build
 
 # getting started
 For micro-manager users:
-> copy the mm2python .jar file from build/libs folder to your micro-manager plugin directory.
+> copy the org.mm2python .jar file from build/libs folder to your micro-manager plugin directory.
 > The next time you start micro-manager, it should be selectable from the menu.
 
 For developers:
-> mm2python uses the gradle build system to manage tests, dependencies and build.
+> org.mm2python uses the gradle build system to manage tests, dependencies and build.
 >
 > Additionally, it was developed in IntelliJ and includes .idea files to help manage debugging configurations.
 > The package .jar can be built by running the "Jar" configuration.  Then that .jar can be copied to your micro-manager directory by running "copyCoreToMM" configuration.
@@ -25,7 +25,7 @@ For developers:
 >
 
 # how to use
-mm2python has a simple UI with three tabs:
+org.mm2python has a simple UI with three tabs:
 > 1) Main Pane:  Contains a console to display events.  Initiate the bridge to python (using py4j) by clicking the "create python bridge" button.  Initiate the event monitor to track data generation by clicking the "START monitor" button
 
 > 2) Configuration:  Currently, there is only one implemented messenger interface: Py4j.  You can select one of two temp-file management systems: fixed or dynamic.
@@ -48,7 +48,7 @@ For most users, you will simply use default values.  Then the only need is to cl
 > gate = gateway.entry_point
 > ```
 >
-> 3 - to access data using mm2python (method 1):
+> 3 - to access data using org.mm2python (method 1):
 > ``` buildoutcfg
 > # if you want the newest data
 > meta = gate.getLastMeta()
@@ -63,7 +63,7 @@ For most users, you will simply use default values.  Then the only need is to cl
 > ```
 > "dat" is an ndarray-like object that can be used interchangeably with numpy arrays.
 >
-> 4 - to access data using mm2python (method 2):
+> 4 - to access data using org.mm2python (method 2):
 > ``` buildoutcfg
 > # to retrieve any data based on coordinates, or subset of coordinates, use the builder
 > paramBuilder = gate.getParameterBuilder()
@@ -107,8 +107,8 @@ For most users, you will simply use default values.  Then the only need is to cl
 > Be careful to use appropriate types when passing values.  Most micro-manager methods require float.
 
 # about
-> clicking "START monitor" causes mm2python to register for some global and datastore events (https://micro-manager.org/wiki/Version_2.0_API_Events).
-> Every time a "New Image Event" occurs, mm2python pulls a new thread to:
+> clicking "START monitor" causes org.mm2python to register for some global and datastore events (https://micro-manager.org/wiki/Version_2.0_API_Events).
+> Every time a "New Image Event" occurs, org.mm2python pulls a new thread to:
 > 1) create a MetaDataStore object that contains coordinate and additional information.
 > 2) write a memory mapped file, representing this data's location in system memory, to disk.
 > 3) write the MetaDataStore object in 1 to a concurrent hashmap and to a concurrent linked deque

build.gradle

@@ -81,27 +81,35 @@ dependencies {
     // This dependency is used internally, and not exposed to consumers on their own compile classpath.
     implementation 'com.google.guava:guava:23.0'
 
+    testImplementation 'org.mockito:mockito-inline:2.13.0'
+
     // JUnit 5
     compile group: 'org.junit.platform', name: 'junit-platform-commons', version: '1.2.0'
     compile group: 'org.junit.jupiter', name: 'junit-jupiter-api', version: '5.2.0'
     compile group: 'org.junit.vintage', name: 'junit-vintage-engine', version: '5.2.0'
 
+    // Mockito
+    compile group: 'org.mockito', name: 'mockito-core', version: '3.0.0'
+//    compile group: 'org.mockito', name: 'mockito-junit-jupiter', version: '3.0.0'
+
+    // PowerMock
+//    compile group: 'org.powermock', name: 'powermock-api-mockito', version: '1.7.4'
+//    compile group: 'org.powermock', name: 'powermock-module-junit4', version: '2.0.2'
+
+
     // Micromanager core jars
     // somehow, micro-manager depends critically on this distributed scijava .jar
     compile fileTree(include: ['MMCoreJ.jar', 'MMJ_.jar', 'scijava-common-2.46.0.jar'], exclude: 'mm2Python.jar', dir: core_plugin_path)
+    compile fileTree(include: ['ij.jar'], dir: app_path)
 
     //zeroMQ
-    // compile group: 'org.zeromq', name: 'jzmq', version: '2.1.0'
-
-    //scijava-common
-//    compile group: 'org.scijava', name: 'scijava-common', version: '2.46.0'
-//    core_libs group: 'org.scijava', name: 'scijava-common', version: '2.46.0'
+    // compile group: 'org.zeromq', name: 'jeromq', version: '0.5.1'
 
     //Py4J
     compile group: 'net.sf.py4j', name: 'py4j', version: '0.10.8.1'
     core_libs group: 'net.sf.py4j', name: 'py4j', version: '0.10.8.1'
 
-    // IntelliJ mm2python.UI Designer
+    // IntelliJ org.mm2python.UI Designer
     compile group: 'com.intellij', name: 'forms_rt', version: '7.0.3'
     core_libs group: 'com.intellij', name: 'forms_rt', version: '7.0.3'
 
@@ -127,11 +135,11 @@ jar {
 
 task copyCoreToMM(type: Copy) {
     if(OperatingSystem.current().isMacOsX()) {
-        from 'build/libs/mm2Python.jar'
+        from 'build/libs/mm2python.jar'
         into app_path + "/plugins/Micro-Manager"
     }
     else if(OperatingSystem.current().isWindows()) {
-        from 'build/libs/mm2Python.jar'
+        from 'build/libs/mm2python.jar'
         into app_path + "\\plugins\\Micro-Manager"
     } else {
         println "unsupported OS"
@@ -142,7 +150,7 @@ task copyCoreToMM(type: Copy) {
 // PUBLISHING
 
 archivesBaseName = 'mm2python'
-group = 'org.bryantchhun'
+group = 'bryantchhun'
 version = '0.0.1'
 description = 'desc. for mm2python'
 
@@ -158,6 +166,7 @@ publishing {
 }
 
 bintray {
+    // DO NOT PUT YOUR KEY HERE.  Set your computer's system environment variable instead.
     user = System.getenv('BINTRAY_USER')
     key = System.getenv('BINTRAY_KEY')
     publications = ['MyPublication']

build/libs/mm2python.jar

@@ -4,7 +4,7 @@
 from py4j.java_gateway import JavaGateway, GatewayParameters
 import numpy as np
 
-# connect to mm2python
+# connect to org.mm2python
 gateway = JavaGateway(gateway_parameters=GatewayParameters(auto_field=True))
 
 # link to class
@@ -41,7 +41,7 @@
 
 
 # ===========================================
-# ===== access mm2python MetaDataStores =====
+# ===== access org.mm2python MetaDataStores =====
 # ===========================================
 
 # retrieve MetaData object for the most recent image

examples/python_basic.py

@@ -86,15 +86,15 @@ private static void createDynamicMemMapStore() {
     }
 
     // if called before getCurrentBuffer and positionQueue is empty, will fail.
-    public static int getCurrentPosition() {
+    public int getCurrentPosition() {
         return positions.remove();
     }
 
-    public static boolean isEmpty() {
+    public boolean isEmpty() {
         return positions.isEmpty();
     }
 
-    public static MappedByteBuffer getCurrentBuffer() {
+    public MappedByteBuffer getCurrentBuffer() {
         if(isEmpty()) {
             createDynamicMemMapStore();
             return current_buf;
@@ -103,11 +103,11 @@ public static MappedByteBuffer getCurrentBuffer() {
         }
     }
 
-    public static int getCurrentByteLength() {
+    public int getCurrentByteLength() {
         return bytelength;
     }
 
-    public static String getCurrentFileName() {
+    public String getCurrentFileName() {
         return dynamicMapname;
     }
 

src/main/java/org/mm2python/DataStructures/Queues/DynamicMemMapReferenceQueue.java

@@ -23,7 +23,7 @@ public class FixedMemMapReferenceQueue {
 
     private static Queue<MappedByteBuffer> mmap_buffer_queue = new ConcurrentLinkedDeque<>();
 
-    public static void resetQueue() {
+    public static void resetQueues() {
         mmap_filename_queue.clear();
         mmap_buffer_queue.clear();
     }
@@ -42,17 +42,15 @@ public static void createFileNames(int num) throws FileNotFoundException {
         }
 
         // create num amount of blank mmaps
-
         if (Constants.getFixedMemMap()) {
             for (int i = 0; i < num; i++) {
                 String fixedMapName = Constants.tempFilePath + "/mmap_fixed_" + i+".dat";
 
                 // write filename
-//                writeBlankToMemMap(fixedMapName, bytelength);
-                putMemMapQueue(fixedMapName);
+                mmap_filename_queue.add(fixedMapName);
 
                 MappedByteBuffer buf = initializeMemMapBuffers(fixedMapName, bytelength);
-                putMemMapBufferQueue(buf);
+                mmap_buffer_queue.add(buf);
 
             }
         }
@@ -64,7 +62,7 @@ public static void createFileNames(int num) throws FileNotFoundException {
      * check if is empty.  Should never be empty
      * @return : boolean
      */
-    public static boolean nextFileNameExists() {
+    public boolean nextFileNameExists() {
         return !mmap_filename_queue.isEmpty();
     }
 
@@ -73,7 +71,7 @@ public static boolean nextFileNameExists() {
      * for FILENAME
      * @return : String, head value
      */
-    public static String getNextFileName() {
+    public String getNextFileName() {
         String next = mmap_filename_queue.poll();
         mmap_filename_queue.offer(next);
         return next;
@@ -84,23 +82,12 @@ public static String getNextFileName() {
      * for MAPPED BYTE BUFFER
      * @return : MappedByteBuffer
      */
-    public static MappedByteBuffer getNextBuffer() {
+    public MappedByteBuffer getNextBuffer() {
         MappedByteBuffer buf = mmap_buffer_queue.poll();
         mmap_buffer_queue.offer(buf);
         return buf;
     }
 
-    // =================== SETTERS for filename, buffer ===============
-
-
-    private static void putMemMapQueue(String mmap) {
-        mmap_filename_queue.add(mmap);
-    }
-
-    private static void putMemMapBufferQueue(MappedByteBuffer buf) {
-        mmap_buffer_queue.add(buf);
-    }
-
     // =============== WRITE TO FILE METHODS ==================
 
     /**

src/main/java/org/mm2python/DataStructures/Queues/FixedMemMapReferenceQueue.java

@@ -42,11 +42,13 @@ public static boolean isQueueEmpty() {
 
     public MetaDataStore getFirstMDS() {
         // should we use takeFirst()?  This will wait till mds available, while poll returns null
+        // poll takes and removes
         return mdsQueue.pollFirst();
     }
 
     public MetaDataStore getLastMDS() {
         // should we use takeLast()?  This will wait till mds available, while poll returns null
+        // poll takes and removes
         return mdsQueue.pollLast();
     }
 

src/main/java/org/mm2python/DataStructures/Queues/MDSQueue.java

@@ -22,20 +22,20 @@ public class Py4J implements messengerInterface {
     private static Studio mm;
     private static GatewayServer gatewayServer;
 
+    /**
+     * Constructor sets classloading strategy.
+     * micro-manager plugin system has its own classloading strategy, which interferes with py4j
+     * @param mm_ : Studio
+     */
     public Py4J(Studio mm_) {
         mm = mm_;
         RootClassLoadingStrategy rmmClassLoader = new RootClassLoadingStrategy();
         ReflectionUtil.setClassLoadingStrategy(rmmClassLoader);
     }
 
-    @Override
-    public void startConnection(int port) {
-        gatewayServer = new GatewayServer(new Py4JEntryPoint(mm), port);
-        gatewayServer.start();
-
-        reporter.set_report_area(true, true, true,"Gateway Started at IP:port = "+gatewayServer.getAddress()+":"+gatewayServer.getPort());
-    }
-    
+    /**
+     * Open ports using py4j for python process
+     */
     @Override
     public void startConnection() {
         gatewayServer = new GatewayServer(new Py4JEntryPoint(mm));
@@ -44,19 +44,24 @@ public void startConnection() {
         Constants.ports.add(port);
         reporter.set_report_area(true, true, true,"Gateway Started at IP:port = "+gatewayServer.getAddress()+":"+gatewayServer.getPort());
     }
-    
+
+    /**
+     * close default port
+     */
     @Override
-    public void stopConnection(int port) {
+    public void stopConnection() {
         gatewayServer.shutdown();
-        reporter.set_report_area(true, true, true, String.format("Gateway at port %04d shut down", port));
+        reporter.set_report_area(true, true, true, "Gateway at default port shut down");
     }
-    
-    @Override
-    public void stopConnection() {
-        Constants.ports.stream().forEach((port) -> {
-            gatewayServer.shutdown();
-            reporter.set_report_area(true, true, true, String.format("Gateway at port %04d shut down", port));
-        });
 
-    }
+//    /**
+//     * close ports for
+//     * @param port
+//     */
+//    @Override
+//    public void stopConnection(int port) {
+//        gatewayServer.shutdown();
+//        reporter.set_report_area(true, true, true, String.format("Gateway at port %04d shut down", port));
+//    }
+
 }