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imagej-elphel
Commit 446646b6 authored by Andrey Filippov's avatar Andrey Filippov
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Started refactoring to get rid of default package

parent 6f3a4fba
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Showing with 269 additions and 38 deletions
src/main/java/BiQuadParameters.java
View file @ 446646b6
......@@ -24,6 +24,8 @@
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
public class BiQuadParameters {
public boolean rig_mode_debug = true;
public boolean no_int_x0 = true; // do not offset window to integer maximum for the rig - used when averaging low textures to avoid "jumps" for very wide maximums
......@@ -1223,8 +1225,8 @@ public class BiQuadParameters {
if (properties.getProperty(prefix+"lt_replace_lone")!=null) this.lt_replace_lone=Boolean.parseBoolean(properties.getProperty(prefix+"lt_replace_lone"));
if (properties.getProperty(prefix+"lt_extend_dist")!=null) this.lt_extend_dist=Integer.parseInt(properties.getProperty(prefix+"lt_extend_dist"));
if (properties.getProperty(prefix+"lt_wsigma")!=null) this.lt_wsigma=Double.parseDouble(properties.getProperty(prefix+"lt_wsigma"));
if (properties.getProperty(prefix+"lt_max_asigma")!=null) this.lt_max_asigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_sigma"));
if (properties.getProperty(prefix+"lt_max_rsigma")!=null) this.lt_max_rsigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_sigma"));
if (properties.getProperty(prefix+"lt_max_asigma")!=null) this.lt_max_asigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_asigma"));
if (properties.getProperty(prefix+"lt_max_rsigma")!=null) this.lt_max_rsigma=Double.parseDouble(properties.getProperty(prefix+"lt_max_rsigma"));
if (properties.getProperty(prefix+"lt_repeat")!=null) this.lt_repeat=Integer.parseInt(properties.getProperty(prefix+"lt_repeat"));
if (properties.getProperty(prefix+"lt_min_new")!=null) this.lt_min_new=Integer.parseInt(properties.getProperty(prefix+"lt_min_new"));
......
src/main/java/CorrectionColorProc.java
View file @ 446646b6
......@@ -28,6 +28,8 @@
import java.util.Properties;
import java.util.concurrent.atomic.AtomicInteger;
import com.elphel.imagej.common.GenericJTabbedDialog;
import ij.ImageStack;
import ij.gui.GenericDialog;
......
src/main/java/EyesisCorrectionParameters.java
View file @ 446646b6
......@@ -33,6 +33,8 @@ import java.util.HashMap;
import java.util.Properties;
import java.util.Set;
import com.elphel.imagej.common.GenericJTabbedDialog;
import ij.IJ;
import ij.Prefs;
import ij.gui.GenericDialog;
......
src/main/java/Eyesis_Correction.java
View file @ 446646b6
......@@ -70,6 +70,7 @@ import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
import com.elphel.imagej.common.GenericJTabbedDialog;
import com.elphel.imagej.lwir.LwirReader;
import ij.CompositeImage;
......@@ -159,6 +160,7 @@ private Panel panel1,
public static QuadCLT QUAD_CLT_AUX = null;
public static TwoQuadCLT TWO_QUAD_CLT = null;
public static GPUTileProcessor GPU_TILE_PROCESSOR = null;
public static LwirReader LWIR_READER = null;
public static EyesisCorrectionParameters.DebayerParameters DEBAYER_PARAMETERS = new EyesisCorrectionParameters.DebayerParameters(
64, // size //128;
......@@ -4805,9 +4807,12 @@ private Panel panel1,
/* ======================================================================== */
} else if (label.equals("LWIR_ACQUIRE")) {
DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
loci.common.DebugTools.enableLogging("ERROR"); // INFO"); // ERROR");
LwirReader lwirReader = new LwirReader();
ImagePlus [][] imps = lwirReader.readAllMultiple(
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();
}
ImagePlus [][] imps = LWIR_READER.readAllMultiple(
10, // final int num_frames,
true, // final boolean show,
false); // true); // final boolean scale)
......@@ -4816,15 +4821,14 @@ private Panel panel1,
}
System.out.println("LWIR_ACQUIRE: got "+imps.length+" image sets");
ImagePlus [][] imps_sync = lwirReader.matchSets(imps, 0.001, 3); // double max_mismatch)
ImagePlus [][] imps_sync = LWIR_READER.matchSets(imps, 0.001, 3); // double max_mismatch)
if (imps_sync != null) {
ImagePlus [] imps_avg = lwirReader.averageMultiFrames(imps_sync);
ImagePlus [] imps_avg = LWIR_READER.averageMultiFrames(imps_sync);
for (ImagePlus imp: imps_avg) {
imp.show();
}
}
//JTabbedTest
// End of buttons code
}
......
src/main/java/GeometryCorrection.java
View file @ 446646b6
import java.util.ArrayList;
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
import Jama.Matrix;
import ij.IJ;
......
src/main/java/ImageDttParameters.java
View file @ 446646b6
......@@ -24,6 +24,8 @@
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
public class ImageDttParameters {
public boolean corr_mode_debug = true;
public boolean mix_corr_poly = true;
......
src/main/java/PoleProcessorParameters.java
View file @ 446646b6
import java.util.Properties;
import com.elphel.imagej.common.GenericJTabbedDialog;
/**
**
** PoleProcessorParameters - parameters for PoleProcessor class that identifies
......
src/main/java/TwoQuadCLT.java
View file @ 446646b6
......@@ -39,6 +39,8 @@ import java.util.ArrayList;
import java.util.Properties;
import java.util.Random;
import com.elphel.imagej.common.GenericJTabbedDialog;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
......
src/main/java/GenericJTabbedDialog.java → src/main/java/com/elphel/imagej/common/GenericJTabbedDialog.java
View file @ 446646b6
package com.elphel.imagej.common;
/*
* TabbedPaneDemo.java requires one additional file:
* images/middle.gif.
......
src/main/java/com/elphel/imagej/common/package-info.java 0 → 100644
View file @ 446646b6
/**
*
*/
/**
* @author Andrey Filippov
*
*/
package com.elphel.imagej.common;
\ No newline at end of file
src/main/java/com/elphel/imagej/lwir/LwirReader.java
View file @ 446646b6
......@@ -32,7 +32,6 @@ import java.util.Properties;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.elphel.imagej.readers.ElphelTiffReader;
import com.elphel.imagej.readers.ImagejJp4TiffMulti;
import ij.ImagePlus;
......@@ -51,10 +50,6 @@ public class LwirReader {
"http://192.168.0.38:2325/bchn4",
"http://192.168.0.38:2326/bchn4",
};
// public static String IMAGE_URL_FIRST="/towp/wait/img/next/save";
// public static String IMAGE_URL_NEXT= "/torp/wait/img/next/save";
// public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
// public static String IMAGE_URL_NEXT= "/torp/wait/img/save"; // same image name, same image number/time
public static String IMAGE_URL_FIRST="/towp/wait/img/save"; // next image name, same image number/time
public static String IMAGE_URL_NEXT= "/torp/next/wait/img/save"; // same image name, same image number/time
......@@ -64,10 +59,14 @@ public class LwirReader {
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(ElphelTiffReader.class);
LoggerFactory.getLogger(LwirReader.class);
private ImagejJp4TiffMulti imagejJp4TiffMulti;
public LwirReader() {
imagejJp4TiffMulti = null;
}
......@@ -103,7 +102,7 @@ public class LwirReader {
} catch (FormatException e) {
LOGGER.error("readAllMultiple0:FormatException, priming");
}
LOGGER.error("priming..."+(i+1));
LOGGER.info("priming..."+(i+1));
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
......@@ -113,7 +112,7 @@ public class LwirReader {
}
}
for (int n = 0; n < num_frames; n++) {
LOGGER.error("---- Acquiring frame set "+n);
LOGGER.info("---- Acquiring frame set "+n);
try {
imagejJp4TiffMulti.getMultiImages( (n==0)? urls0:urls1, imps[n], scale, std);
} catch (IOException e) {
......@@ -141,7 +140,7 @@ public class LwirReader {
img_numbers[n][i] = -1;
}
img_names[n][i] = (String) imps[n][i].getProperty("CONTENT_FILENAME");
LOGGER.error("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
LOGGER.info("Seconds for" + n+":"+i+" - "+img_seconds[n][i]+", number"+img_numbers[n][i]+", name "+img_names[n][i]);
}
}
......@@ -251,7 +250,7 @@ public class LwirReader {
}
for (int i = 0; i < num_channels; i++) {
// change to info later:
LOGGER.error("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
LOGGER.info("Channel "+ i+" frame offset="+frame_offsets[i]+ ", time offset = "+time_offsets[i]+" sec");
}
ImagePlus [][] imps_synced = new ImagePlus [num_frames - fr_max + fr_min][num_channels];
for (int n = 0; n < imps_synced.length; n++) {
......
src/main/java/com/elphel/imagej/readers/services.properties.forelphel 0 → 100644
View file @ 446646b6
###
# #%L
# Common package for I/O and related utilities
# %%
# Copyright (C) 2005 - 2016 Open Microscopy Environment:
# - Board of Regents of the University of Wisconsin-Madison
# - Glencoe Software, Inc.
# - University of Dundee
# %%
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
# #L%
###
#
# NOTE: All service classes must be fully qualified
#
## ClassNotFoundException: loci.formats.services.JPEGXRService
## ClassNotFoundException: loci.formats.services.JHDFService
# OME-XML service (interface and implementation in bio-formats component)
loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
# POI service (interface and implementation in bio-formats component)
###loci.formats.services.POIService=loci.formats.services.POIServiceImpl
# NetCDF service (interface and implementation in bio-formats component)
###loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
# JHDF service (interface and implementation in bio-formats component)
## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
# MDB Tools service (interface and implementation in bio-formats component)
###loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
# JAI Image I/O service (interface and implementation in bio-formats component)
###loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
# LuraWave decoder service (interface and implementation in bio-formats
# component; depends on stubs.jar for compilation)
###loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
# Metakit reader service (interface and implementation in bio-formats component;
# depends upon metakit.jar for compilation)
###loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
# libjpeg-turbo service
###loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
# Woolz service (interface and implementation in bio-formats)
###loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
# Minio S3 client service
###loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
# OME Codecs JAI Image I/O service
###ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
###ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl
src/main/resources/services.properties 0 → 100644
View file @ 446646b6
###
# #%L
# Common package for I/O and related utilities
# %%
# Copyright (C) 2005 - 2016 Open Microscopy Environment:
# - Board of Regents of the University of Wisconsin-Madison
# - Glencoe Software, Inc.
# - University of Dundee
# %%
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
# #L%
###
#
# NOTE: All service classes must be fully qualified
#
## ClassNotFoundException: loci.formats.services.JPEGXRService
## ClassNotFoundException: loci.formats.services.JHDFService
# OME-XML service (interface and implementation in bio-formats component)
loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
# POI service (interface and implementation in bio-formats component)
loci.formats.services.POIService=loci.formats.services.POIServiceImpl
# NetCDF service (interface and implementation in bio-formats component)
loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
# JHDF service (interface and implementation in bio-formats component)
## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
# MDB Tools service (interface and implementation in bio-formats component)
loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
# JAI Image I/O service (interface and implementation in bio-formats component)
loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
# LuraWave decoder service (interface and implementation in bio-formats
# component; depends on stubs.jar for compilation)
loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
# Metakit reader service (interface and implementation in bio-formats component;
# depends upon metakit.jar for compilation)
loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
# libjpeg-turbo service
loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
# Woolz service (interface and implementation in bio-formats)
loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
# Minio S3 client service
loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
# OME Codecs JAI Image I/O service
ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl
src/main/resources/services.properties.forelphel 0 → 100644
View file @ 446646b6
###
# #%L
# Common package for I/O and related utilities
# %%
# Copyright (C) 2005 - 2016 Open Microscopy Environment:
# - Board of Regents of the University of Wisconsin-Madison
# - Glencoe Software, Inc.
# - University of Dundee
# %%
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
# #L%
###
#
# NOTE: All service classes must be fully qualified
#
## ClassNotFoundException: loci.formats.services.JPEGXRService
## ClassNotFoundException: loci.formats.services.JHDFService
# OME-XML service (interface and implementation in bio-formats component)
loci.formats.services.OMEXMLService=loci.formats.services.OMEXMLServiceImpl
# POI service (interface and implementation in bio-formats component)
###loci.formats.services.POIService=loci.formats.services.POIServiceImpl
# NetCDF service (interface and implementation in bio-formats component)
###loci.formats.services.NetCDFService=loci.formats.services.NetCDFServiceImpl
# JHDF service (interface and implementation in bio-formats component)
## loci.formats.services.JHDFService=loci.formats.services.JHDFServiceImpl # ClassNotFoundException
# MDB Tools service (interface and implementation in bio-formats component)
###loci.formats.services.MDBService=loci.formats.services.MDBServiceImpl
# JAI Image I/O service (interface and implementation in bio-formats component)
###loci.formats.services.JAIIIOService=loci.formats.services.JAIIIOServiceImpl
# LuraWave decoder service (interface and implementation in bio-formats
# component; depends on stubs.jar for compilation)
###loci.formats.services.LuraWaveService=loci.formats.services.LuraWaveServiceImpl
# Metakit reader service (interface and implementation in bio-formats component;
# depends upon metakit.jar for compilation)
###loci.formats.services.MetakitService=loci.formats.services.MetakitServiceImpl
# libjpeg-turbo service
###loci.formats.services.JPEGTurboService=loci.formats.services.JPEGTurboServiceImpl
# Woolz service (interface and implementation in bio-formats)
###loci.formats.services.WlzService=loci.formats.services.WlzServiceImpl
loci.formats.services.EXIFService=loci.formats.services.EXIFServiceImpl
## loci.formats.services.JPEGXRService=loci.formats.services.JPEGXRServiceImpl # ClassNotFoundException
# Minio S3 client service
###loci.common.services.S3ClientService=loci.common.services.S3ClientServiceImpl
# OME Codecs JAI Image I/O service
###ome.codecs.services.JAIIIOService=ome.codecs.services.JAIIIOServiceImpl
# OME Codecs LuraWave decoder service (depends on stubs.jar for compilation)
###ome.codecs.services.LuraWaveService=ome.codecs.services.LuraWaveServiceImpl
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