Updating Maars

.gitignore

@@ -10,3 +10,7 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+
+*.LOG
+
+*~

README.md

@@ -1,2 +1,2 @@
-# Objects detection and robust tracking for cell biology
+# Set of Fiji and Micro-manager plugin for biology analysis
 

maars_config.txt

@@ -0,0 +1 @@
+{"SEGMENTATION_PARAMETERS":{"CHANNEL":"BF","NEW_MAX_WIDTH_FOR_CHANGE_SCALE":1500,"NEW_MAX_HEIGTH_FOR_CHANGE_SCALE":1500,"FRAME_NUMBER":1,"RANGE_SIZE_FOR_MOVIE":9.0,"STEP":0.3,"MEAN_GREY_VALUE":-177660.0,"SOLIDITY":0.84,"FILTER_MEAN_GREY_VALUE":true,"FILTER_SOLIDITY":true,"MINIMUM_CELL_AREA":9.0,"CELL_SIZE":3.0,"MAXIMUM_CELL_AREA":400.0},"EXPLORATION_PARAMETERS":{"X_FIELD_NUMBER":2,"Y_FIELD_NUMBER":3},"FLUO_ANALYSIS_PARAMETERS":{"FRAME_NUMBER":1,"RANGE_SIZE_FOR_MOVIE":7.0,"STEP":0.3,"SPOT_RADIUS":0.15,"FIND_BEST_MITOSIS_IN_FIELD":true,"SAVE_FLUORESCENT_MOVIES":true,"MAXIMUM_NUMBER_OF_SPOT":2,"CHANNEL":"CFP"},"MITOSIS_MOVIE_PARAMETERS":{"END_MOVIE_CONDITIONS":{"CONDITIONS":{"RELATIVE_SPINDLE_ANGLE":false,"TIME_LIMIT":true,"ABSOLUTE_MAXIMUM_SPINDLE_SIZE":false,"RELATIVE_MAXIMUM_SPINDLE_SIZE":true,"GROWING_SPINDLE":false},"VALUES":{"ABSOLUTE_MAXIMUM_SPINDLE_SIZE":10,"RELATIVE_SPINDLE_ANGLE":0,"TIME_LIMIT":20.0,"GROWING_SPINDLE":0.0010,"RELATIVE_MAXIMUM_SPINDLE_SIZE":2.0}},"START_MOVIE_CONDITIONS":{"CONDITIONS":{"ABSOLUTE_MINIMUM_SPINDLE_SIZE":true,"ABSOLUTE_MAXIMUM_SPINDLE_SIZE":true,"RELATIVE_SPINDLE_ANGLE":false},"VALUES":{"RELATIVE_SPINDLE_ANGLE":90,"ABSOLUTE_MAXIMUM_SPINDLE_SIZE":5.0,"ABSOLUTE_MINIMUM_SPINDLE_SIZE":0.5}},"FRAME_NUMBER":1000,"MARGIN_AROUD_CELL":5,"TIME_INTERVAL":10000.0,"RANGE_SIZE_FOR_MOVIE":4.0,"CHANNEL":["GFP","CFP"],"STEP":0.3,"SAVING_PATH":"D:/Data/Marie/mutant57/test1/"},"GENERAL_ACQUISITION_PARAMETERS":{"CHANNEL_GROUP":"Illumination","DEFAULT_CHANNEL_PARAMATERS":{"BF":{"COLOR":"WHITE","EXPOSURE":30,"SHUTTER":"TIDiaLamp"},"GFP":{"COLOR":"GREEN","EXPOSURE":200,"SHUTTER":"Spectra"},"CFP":{"COLOR":"CYAN","EXPOSURE":200,"SHUTTER":"Spectra"},"DAPI":{"COLOR":"BLUE","EXPOSURE":100,"SHUTTER":"Spectra"},"TxRed":{"COLOR":"RED","EXPOSURE":200,"SHUTTER":"Spectra"}}}}

testMaarsLib.bsh

@@ -0,0 +1,139 @@
+//addClassPath("/home/marie/workspace/MaarsLib/MaarsLib.jar");
+addClassPath("C:/Program Files/Micro-Manager-1.4/jars/MaarsLib.jar");
+import MaarsLib.*;
+import MaarsLib.MaarsMainDialog;
+import MaarsLib.AllMaarsParameters;
+import MaarsLib.ExplorationXYPositions;
+import mmcorej.*;
+import org.micromanager.api.*;
+import ij.*;
+import java.io.IOException;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+
+double calibration = gui.getMMCore().getPixelSizeUm();
+mmc.setAutoShutter(false);
+mmc.waitForDevice(mmc.getShutterDevice());
+
+gui.message("Create main window");
+MaarsMainDialog md = null;
+try {
+	//md = new MaarsMainDialog(gui, mmc, "/home/marie/workspace/MaarsLib/");
+	md = new MaarsMainDialog(gui, mmc, "D:/Data/marie/");
+} catch (IOException e) {
+	gui.message("Error");
+}
+
+gui.message("Show main window");
+
+md.show();
+
+while(md.isVisible()) {
+	gui.sleep(1000);
+}
+start = System.currentTimeMillis();
+gui.message("start "+start);
+if(md.isOkClicked()) {
+
+	AllMaarsParameters param = null;
+	autofocus = gui.getAutofocus();
+	param = md.getParameters();
+	mmc.setOriginXY(mmc.getXYStageDevice());
+	int nbXField = param
+						.getParametersAsJsonObject()
+						.get(AllMaarsParameters.EXPLORATION_PARAMETERS)
+						.getAsJsonObject()
+						.get(AllMaarsParameters.X_FIELD_NUMBER)
+						.getAsInt();
+	int nbYField = param
+						.getParametersAsJsonObject()
+						.get(AllMaarsParameters.EXPLORATION_PARAMETERS)
+						.getAsJsonObject()
+						.get(AllMaarsParameters.Y_FIELD_NUMBER)
+						.getAsInt();
+
+	gui.message("nb x field "+nbXField+" nb y field "+nbYField);
+
+
+	ExplorationXYPositions explo = new ExplorationXYPositions(nbXField,
+													nbYField,
+													(double) mmc.getImageWidth()*calibration,
+													(double) mmc.getImageHeight()*calibration);
+
+	for (int i = 0; i < explo.length(); i++) {
+		gui.message("x : "+explo.getX(i)+" y : "+explo.getY(i));
+
+		gui.setXYStagePosition(explo.getX(i),explo.getY(i));
+
+		MaarsAcquisitionForSegmentation mas = new MaarsAcquisitionForSegmentation(md,
+				explo.getX(i),
+				explo.getY(i));
+
+		mas.setupParameters();
+
+		mmc.waitForDevice(mmc.getXYStageDevice());
+
+		autofocus.fullFocus();
+
+		mas.acquire(false);
+
+		MaarsSegmentation ms = new MaarsSegmentation(param, mas.getPathToMovie()+"\\MMStack.ome.tif");
+		ms.segmentation();
+		while(ms.isAnalysing()) {
+			gui.sleep(3000);
+		}
+
+		MaarsFluoAnalysis mfa = new MaarsFluoAnalysis(param, ms.getSegmentationObject());
+		MaarsAcquisitionMitosis mmad = new MaarsAcquisitionMitosis(md, mfa, explo.getX(i), explo.getY(i));
+
+
+		mfa.getSetOfCells().shuffle();
+
+		MaarsAcquisitionForFluoAnalysis mafa = new MaarsAcquisitionForFluoAnalysis(md,
+														explo.getX(i),
+														explo.getY(i),
+														mfa.getSetOfCells());
+		if(param
+				.getParametersAsJsonObject()
+				.get(AllMaarsParameters.FLUO_ANALYSIS_PARAMETERS)
+				.getAsJsonObject()
+				.get(AllMaarsParameters.FIND_BEST_MITOSIS_IN_FIELD)
+				.getAsBoolean()) {
+
+			String acqNameFluo = "movie_X"
+				+Math.round(explo.getX(i))
+				+"_Y"+Math.round(explo.getY(i))
+				+"FLUO";
+
+			ImagePlus fluoImage = mafa.acquire(false, acqNameFluo);
+			int cellNumber = mfa.analyzeEntireField(fluoImage, mas.getPathToMovie());
+			if (cellNumber != -1) {
+				mmad.acquire(false, cellNumber, true, true);
+			}
+		}
+		else {
+			int j = 0;
+			boolean mitosis = false;
+			while(j <  mfa.getSetOfCells().length() && !mitosis) {
+				ImagePlus fluoImage = mafa.acquire(false, j);
+				fluoImage.show();
+				if (mfa.checkStartConditions(mfa.getSpindle(fluoImage, j))) {
+					gui.message("mitosis");
+					mmad.acquire(true, j, false); //don't crop image because it is already cropped
+					mitosis = true;
+				}
+				j++;
+			}
+		}
+		// close roi manager
+		mfa.getSetOfCells().closeRoiManager();
+		mas.setupParameters();
+	}
+}
+
+mmc.setAutoShutter(true);
+mmc.waitForDevice(mmc.getShutterDevice());
+gui.message("end "+System.currentTimeMillis());
+gui.message("it took "+(System.currentTimeMillis()-start));
+gui.message("DONE");
+gui.message("DONE.");