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imagej-elphel
Commit a0b7dae3 authored by Andrey Filippov's avatar Andrey Filippov
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Switched to bioformats 6.1.0 jar (minimal needed), set logging

parent a17be71e
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Showing with 54 additions and 35 deletions
pom.xml
View file @ a0b7dae3
......@@ -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>
......@@ -73,31 +75,31 @@
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
<!--
<dependency>
<groupId>jama</groupId>
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
-->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>loci_tools</artifactId>
<version>6.1.0-SNAPSHOT</version>
<type>java-source</type>
</dependency>
<dependency>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>2.11.0</version>
<type>java-source</type>
</dependency>
</dependencies>
<!--
<dependency>
<groupId>jama</groupId>
<artifactId>jama</artifactId>
<version>1.0.3</version>
</dependency>
-->
<dependency>
<groupId>commons-lang</groupId>
<artifactId>commons-lang</artifactId>
<version>2.6</version>
</dependency>
<dependency>
<groupId>ome</groupId>
<artifactId>loci_tools</artifactId>
<version>6.1.0</version>
</dependency>
<dependency>
<groupId>com.drewnoakes</groupId>
<artifactId>metadata-extractor</artifactId>
<version>2.11.0</version>
<type>java-source</type>
</dependency>
</dependencies>
<build>
<resources>
......@@ -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
View file @ a0b7dae3
......@@ -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
View file @ a0b7dae3
......@@ -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
View file @ a0b7dae3
......@@ -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
View file @ a0b7dae3
......@@ -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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