Switched to bioformats 6.1.0 jar (minimal needed), set logging (a0b7dae3) · Commits · Elphel / imagej-elphel

pom.xml

+28 −26

Original line number	Diff line number	Diff line
		@@ -12,9 +12,11 @@
		<relativePath/>
		</parent>

		<!--
		<properties>
		<imagej.app.directory>/home/foxel/Desktop/Fiji.app</imagej.app.directory>
		</properties>
		-->

		<groupId>com.elphel</groupId>
		<artifactId>imagej-elphel</artifactId>
		@@ -88,8 +90,7 @@
		<dependency>
		<groupId>ome</groupId>
		<artifactId>loci_tools</artifactId>
		<version>6.1.0-SNAPSHOT</version>
		<type>java-source</type>
		<version>6.1.0</version>
		</dependency>
		<dependency>
		<groupId>com.drewnoakes</groupId>
		@@ -97,6 +98,7 @@
		<version>2.11.0</version>
		<type>java-source</type>
		</dependency>

		</dependencies>

		<build>
		@@ -207,7 +209,7 @@
		<format>Build {0,date,yyyy-MM-dd} {0,time,HH:MM:SS} on host {1}</format>
		<items>
		<item>timestamp</item>
		<item>foxel-MRHM7AP</item>
		<!-- <item>foxel-MRHM7AP</item> -->
		</items>
		</configuration>
		</plugin>

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

+16 −4

Original line number	Diff line number	Diff line
		@@ -897,8 +897,22 @@ private Panel panel1,
		if (DEBUG_LEVEL>0) System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
		CLT_PARAMETERS.batch_run = false;
		if (label==null) return;
		System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", MASTER_DEBUG_LEVEL = "+MASTER_DEBUG_LEVEL);
		loci.common.DebugTools.enableLogging((MASTER_DEBUG_LEVEL > 1)?"DEBUG":((MASTER_DEBUG_LEVEL > 0)?"INFO":"ERROR")); // INFO"); // ERROR");
		String LOG_LEVEL;
		switch (MASTER_DEBUG_LEVEL) {
		case -2: LOG_LEVEL = "FATAL"; break;
		case -1: LOG_LEVEL = "ERROR"; break;
		case 0: LOG_LEVEL = "WARN"; break;
		case 1: LOG_LEVEL = "INFO"; break;
		case 2: LOG_LEVEL = "DEBUG"; break;
		default: LOG_LEVEL = "OFF";
		}

		boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
		if (!LOG_LEVEL_SET) { // only first time true
		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
		}
		System.out.println("DEBUG_LEVEL = "+DEBUG_LEVEL+", MASTER_DEBUG_LEVEL = "+MASTER_DEBUG_LEVEL+
		" LOG_LEVEL="+LOG_LEVEL+"LOG_LEVEL_SET="+LOG_LEVEL_SET);

		/* ======================================================================== */
		if (label.equals("Configure spilt")) {
		@@ -4831,7 +4845,6 @@ private Panel panel1,
		/* ======================================================================== */
		} else if (label.equals("LWIR_TEST")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		// loci.common.DebugTools.enableLogging((DEBUG_LEVEL > 1)?"DEBUG":((DEBUG_LEVEL > 0)?"INFO":"ERROR")); // INFO"); // ERROR");
		// public static LwirReader LWIR_READER = null;
		if (LWIR_READER == null) {
		LWIR_READER = new LwirReader(CLT_PARAMETERS.lwir);
		@@ -4856,7 +4869,6 @@ private Panel panel1,
		/* ======================================================================== */
		} else if (label.equals("LWIR_ACQUIRE")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		// loci.common.DebugTools.enableLogging((DEBUG_LEVEL > 1)?"DEBUG":((DEBUG_LEVEL > 0)?"INFO":"ERROR")); // INFO"); // ERROR");
		// public static LwirReader LWIR_READER = null;
		if (LWIR_READER == null) {
		LWIR_READER = new LwirReader(CLT_PARAMETERS.lwir);

src/main/java/com/elphel/imagej/lwir/LwirReader.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -318,6 +318,7 @@ public class LwirReader {
		}

		public boolean calibrate(LwirReaderParameters lrp) {
		// FFC takes 15 frames that are not output (so no need to check operation is over)
		if (lrp.lwir_channels.length == 0) {
		LOGGER.error("calibrate(): No LWIR channels are configured");
		return false;
		@@ -328,7 +329,6 @@ public class LwirReader {
		channels \|= 1 << c;
		}
		String hex_chan = String.format("%x", channels);
		System.out.println("Channels = "+channels+" (0x"+hex_chan);

		String url = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
		"&SENSOR_REGS67=0!"+hex_chan;

src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java

+8 −1

Original line number	Diff line number	Diff line
		@@ -33,12 +33,12 @@ import com.elphel.imagej.common.GenericJTabbedDialog;
		public class LwirReaderParameters {
		private boolean parameters_updated = false;
		protected int avg_number = 4; // number of measurements to average
		protected boolean lwir_ffc = true;
		protected boolean avg_all = true;
		protected String lwir_ip = "192.168.0.36";
		protected String vnir_ip = "192.168.0.38";
		protected int [] lwir_channels = {0, 1, 2 ,3};
		protected int [] vnir_channels = {0, 1, 2 ,3};
		protected boolean lwir_ffc = true;
		protected boolean lwir_telemetry = true;
		protected double vnir_quality = 98.0;
		protected boolean vnir_scale = false; // restore sensor pixel values, undo camera white balancing
		@@ -74,6 +74,7 @@ public class LwirReaderParameters {
		// --- interface methods
		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"avg_number", this.avg_number+"");
		properties.setProperty(prefix+"lwir_ffc", this.lwir_ffc+"");
		properties.setProperty(prefix+"avg_all", this.avg_all+"");
		properties.setProperty(prefix+"lwir_ip", this.lwir_ip+"");
		properties.setProperty(prefix+"vnir_ip", this.vnir_ip+"");
		@@ -99,6 +100,7 @@ public class LwirReaderParameters {

		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"avg_number")!=null) this.avg_number=Integer.parseInt(properties.getProperty(prefix+"avg_number"));
		if (properties.getProperty(prefix+"lwir_ffc")!=null) this.lwir_ffc= Boolean.parseBoolean(properties.getProperty(prefix+"lwir_ffc"));
		if (properties.getProperty(prefix+"avg_all")!=null) this.avg_all= Boolean.parseBoolean(properties.getProperty(prefix+"avg_all"));
		if (properties.getProperty(prefix+"lwir_ip")!=null) this.lwir_ip= properties.getProperty(prefix+"lwir_ip");
		if (properties.getProperty(prefix+"vnir_ip")!=null) this.vnir_ip= properties.getProperty(prefix+"vnir_ip");
		@@ -126,6 +128,7 @@ public class LwirReaderParameters {
		public LwirReaderParameters clone() { // throws CloneNotSupportedException {
		LwirReaderParameters lrp = new LwirReaderParameters();
		lrp.avg_number= this.avg_number;
		lrp.lwir_ffc= this.lwir_ffc;
		lrp.avg_all= this.avg_all;
		lrp.lwir_ip= this.lwir_ip;
		lrp.vnir_ip= this.vnir_ip;
		@@ -160,6 +163,7 @@ public class LwirReaderParameters {
		}
		LwirReaderParameters lrp = (LwirReaderParameters) o;
		return (lrp.avg_number == this.avg_number) &&
		(lrp.lwir_ffc == this.lwir_ffc) &&
		(lrp.avg_all == this.avg_all) &&
		(lrp.lwir_ip.equals(this.lwir_ip)) &&
		(lrp.vnir_ip.equals(this.vnir_ip)) &&
		@@ -188,6 +192,7 @@ public class LwirReaderParameters {
		int prime = 31;
		int result = 1;
		result = prime * result + (new Integer(avg_number)).hashCode();
		result = prime * result + (lwir_ffc?1:0);
		result = prime * result + (avg_all?1:0);
		result = prime * result + lwir_ip.hashCode();
		result = prime * result + vnir_ip.hashCode();
		@@ -215,6 +220,7 @@ public class LwirReaderParameters {

		public void dialogQuestions(GenericJTabbedDialog gd) {
		gd.addNumericField("Number to average",this.avg_number, 0,3,"","Number of acquired consecutive images to average");
		gd.addCheckbox ("Run FFC", this.lwir_ffc, "Perform calibration before each measurements to average (takes ~1.6 sec, 15 frames)");
		gd.addCheckbox ("Average all", this.avg_all, "Average all simultaneously acquired images (unchecked - only requested number to average)");
		gd.addStringField ("LWIR IP", this.lwir_ip, 20, "LWIR camera IP address");
		gd.addStringField ("VNIR IP", this.vnir_ip, 20, "Visible range high resolution camera IP address");
		@@ -240,6 +246,7 @@ public class LwirReaderParameters {

		public void dialogAnswers(GenericJTabbedDialog gd) {
		this.avg_number = (int) gd.getNextNumber();
		this.lwir_ffc = gd.getNextBoolean();
		this.avg_all = gd.getNextBoolean();
		this.lwir_ip = gd.getNextString();
		this.vnir_ip = gd.getNextString();

src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java

+1 −3

Original line number	Diff line number	Diff line
		@@ -91,8 +91,6 @@ public class ImagejJp4Tiff {
		//URL u = this.getClass().getResource(SERVICES_PATH);
		// URL u = this.getClass().getResource("/"+SERVICES_PATH);

		// loci.common.DebugTools.enableLogging("ERROR");

		if (!BYPASS_SERVICES) {
		ServiceFactory factory = null;

		@@ -153,7 +151,7 @@ public class ImagejJp4Tiff {
		}
		//https://stackoverflow.com/questions/39086500/read-http-response-header-and-body-from-one-http-request-in-java
		if (url != null) {
		LOGGER.error("Read "+ path_url +" to memory first");
		LOGGER.info("Read "+ path_url +" to memory first");
		URLConnection connection = url.openConnection();
		// Wrong - waits forever
		String content_disposition = connection.getHeaderField("Content-Disposition"); // reads file

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