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imagej-elphel
Commit 681a226e authored by Andrey Filippov's avatar Andrey Filippov
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Improved ML output, testing batch execution

parent 77684393
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Showing with 1663 additions and 703 deletions
src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java
View file @ 681a226e
......@@ -201,7 +201,10 @@ public class EyesisCorrectionParameters {
public String x3dModelVersion="v01";
public String jp4SubDir="jp4"; // FIXME:
public String linkedModels=""; // linked models with reference scenes
public String x3dDirectory="";
public String videoDirectory=""; // combined (with MPEG) from multiple scene sequences video files
public String mlDirectory="ml";
......@@ -308,6 +311,8 @@ public class EyesisCorrectionParameters {
cp.referenceExposure= this.referenceExposure;
cp.relativeExposure= this.relativeExposure;
cp.swapSubchannels01= this.swapSubchannels01;
cp.linkedModels= this.linkedModels;
cp.videoDirectory= this.videoDirectory;
cp.x3dDirectory= this.x3dDirectory;
cp.mlDirectory= this.mlDirectory;
cp.use_x3d_subdirs= this.use_x3d_subdirs;
......@@ -514,6 +519,8 @@ public class EyesisCorrectionParameters {
properties.setProperty(prefix+"cltKernelPrefix", this.cltKernelPrefix);
properties.setProperty(prefix+"cltSuffix", this.cltSuffix);
properties.setProperty(prefix+"linkedModels", this.linkedModels);
properties.setProperty(prefix+"videoDirectory", this.videoDirectory);
properties.setProperty(prefix+"x3dDirectory", this.x3dDirectory);
properties.setProperty(prefix+"use_x3d_subdirs", this.use_x3d_subdirs+"");
......@@ -701,6 +708,8 @@ public class EyesisCorrectionParameters {
if (properties.getProperty(prefix+"cltKernelPrefix")!= null) this.cltKernelPrefix=properties.getProperty(prefix+"cltKernelPrefix");
if (properties.getProperty(prefix+"cltSuffix")!= null) this.cltSuffix=properties.getProperty(prefix+"cltSuffix");
if (properties.getProperty(prefix+"linkedModels")!= null) this.linkedModels=properties.getProperty(prefix+"linkedModels");
if (properties.getProperty(prefix+"videoDirectory")!= null) this.videoDirectory=properties.getProperty(prefix+"videoDirectory");
if (properties.getProperty(prefix+"x3dDirectory")!= null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");
if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean(properties.getProperty(prefix+"use_x3d_subdirs"));
......@@ -870,8 +879,18 @@ public class EyesisCorrectionParameters {
gd.addStringField ("x3d model version", this.x3dModelVersion, 20); // 10a
gd.addStringField ("JP4 source image copy model subdirectory", this.jp4SubDir, 20); // 10b
gd.addStringField ("Linked reference models", this.linkedModels, 60,
"Directory where links to reference models directories will be created.");
gd.addCheckbox ("Select linked reference models directory", false);
gd.addStringField ("Video directory", this.videoDirectory, 60,
"Directory to store combined video files.");
gd.addCheckbox ("Select video directory", false);
gd.addStringField ("x3d output directory", this.x3dDirectory, 60);
gd.addCheckbox ("Select x3d output directory", false);
gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);
gd.addStringField ("x3d subdirectory prefix", this.x3dSubdirPrefix, 10,
......@@ -994,6 +1013,8 @@ public class EyesisCorrectionParameters {
this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true);
this.x3dModelVersion= gd.getNextString(); // 10a
this.jp4SubDir= gd.getNextString(); // 10b
this.linkedModels= gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
this.videoDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);
this.use_x3d_subdirs= gd.getNextBoolean();
......@@ -1065,6 +1086,15 @@ public class EyesisCorrectionParameters {
gd.addStringField ("x3d model version", this.x3dModelVersion, 60); // 10a
gd.addStringField ("jp4 source copy subdirectory", this.jp4SubDir, 60); // 10b
gd.addStringField ("Linked reference models", this.linkedModels, 60,
"Directory where links to reference models directories will be created.");
gd.addCheckbox ("Select linked reference models directory", false);
gd.addStringField ("Video directory", this.videoDirectory, 60,
"Directory to store combined video files.");
gd.addCheckbox ("Select video directory", false);
gd.addStringField ("x3d output directory", this.x3dDirectory, 60); // 8
gd.addCheckbox ("Select x3d output (top model) directory", false); // 9
......@@ -1230,6 +1260,8 @@ public class EyesisCorrectionParameters {
this.x3dModelVersion= gd.getNextString(); // 10a
this.jp4SubDir= gd.getNextString(); // 10b
this.linkedModels= gd.getNextString(); if (gd.getNextBoolean()) selectLinkedModelsDirectory(false, true);
this.videoDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectVideoDirectory(false, true);
this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true); // 9
this.use_x3d_subdirs= gd.getNextBoolean(); // 10
// this.sourcePrefix= gd.getNextString(); // 13
......@@ -2192,6 +2224,31 @@ public class EyesisCorrectionParameters {
return dir;
}
public String selectLinkedModelsDirectory(boolean smart, boolean newAllowed) {
String dir= CalibrationFileManagement.selectDirectory(
smart,
newAllowed, // save
"linked models directory", // title
"Select linked models directory", // button
null, // filter
this.linkedModels); //this.sourceDirectory);
if (dir!=null) this.linkedModels=dir;
return dir;
}
public String selectVideoDirectory(boolean smart, boolean newAllowed) {
String dir= CalibrationFileManagement.selectDirectory(
smart,
newAllowed, // save
"video directory", // title
"Select video directory", // button
null, // filter
this.videoDirectory); //this.sourceDirectory);
if (dir!=null) this.videoDirectory=dir;
return dir;
}
public String selectMlDirectory(String name, boolean smart, boolean newAllowed) {
if ((name != null) && (this.mlDirectory.length()>0) && (!this.mlDirectory.contains(Prefs.getFileSeparator()))) {
// relative to the X3D model version
......@@ -2218,7 +2275,6 @@ public class EyesisCorrectionParameters {
// select qualified (by 'name' - quad timestamp) x3d subdirectory
public String selectX3dDirectory(String name, String version, boolean smart, boolean newAllowed) {
String dir= CalibrationFileManagement.selectDirectory(
smart,
newAllowed, // save
......
src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java
View file @ 681a226e
......@@ -1118,14 +1118,17 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
default:
LOG_LEVEL = "OFF";
}
LOG_LEVEL = "ERROR"; // setting it here to shut up?
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 + ", CLT_PARAMETERS.lwir.getDebugLevel() = "
+ CLT_PARAMETERS.lwir.getDebugLevel() + " LOG_LEVEL=" + LOG_LEVEL + "LOG_LEVEL_SET="
+ CLT_PARAMETERS.lwir.getDebugLevel() + " LOG_LEVEL=" + LOG_LEVEL + " LOG_LEVEL_SET="
+ LOG_LEVEL_SET);
//https://www.javadoc.io/doc/org.openmicroscopy/ome-common/6.0.5/loci/common/DebugTools.html#enableLogging(java.lang.String)
// Temporary overwrite with public static boolean enableIJLogging​(boolean debug)
loci.common.DebugTools.enableIJLogging(false);
}
/* ======================================================================== */
......
src/main/java/com/elphel/imagej/readers/ElphelJp4Reader.java
View file @ 681a226e
......@@ -107,7 +107,7 @@ public class ElphelJp4Reader extends ImageIOReader{
// or these readers are combined with all other readers in readers.txt
suffixNecessary = true; // false
suffixSufficient = true; // false;
LOGGER.debug("ElphelTiffReader(), after super()");
LOGGER.info("ElphelTiffReader(), after super()");
if (REPLACEMENT_TAG_MAP == null) {
REPLACEMENT_TAG_MAP = new HashMap<String,String>();
for (String [] line: REPLACEMENT_TAGS) {
......@@ -156,15 +156,15 @@ public class ElphelJp4Reader extends ImageIOReader{
public void setId(String id) throws FormatException, IOException { // same as for tiff?
image_bytes = null;
// buffered_data = null;
LOGGER.debug("setId("+id+"). before super" );
LOGGER.info("setId("+id+"). before super" );
file_initialized = false;
mapped_externally = false;
if (Location.getIdMap().containsKey(id)) {
LOGGER.debug("id '"+id+"' is already mapped" );
LOGGER.info("id '"+id+"' is already mapped" );
content_fileName = id; // id; // maybe set to null to handle externally?
mapped_externally = true;
LOGGER.debug("Starting initFile() method, read file directly");
LOGGER.info("Starting initFile() method, read file directly");
super.setId(id);
} else {
// If URL, then read to memory, if normal file - use direct access
......@@ -177,7 +177,7 @@ public class ElphelJp4Reader extends ImageIOReader{
// LOGGER.warn("Bad URL1: " + id); // will try direct file, not an error
}
if (url != null) {
LOGGER.debug("Starting initFile() method, read "+ id +" to memory first");
LOGGER.info("Starting initFile() method, read "+ id +" to memory first");
//https://www.rgagnon.com/javadetails/java-0487.html
URLConnection connection = url.openConnection();
......@@ -194,44 +194,44 @@ public class ElphelJp4Reader extends ImageIOReader{
content_fileName = "unknown." + suffix;
}
// currentId = fileName; //???
// LOGGER.debug("Mime type = "+mime);
// LOGGER.info("Mime type = "+mime);
// https://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
//https://stackoverflow.com/questions/2295221/java-net-url-read-stream-to-byte
InputStream is = url.openStream (); //
byte[] inBytes = IOUtils.toByteArray(is);
if (is != null) is.close();
LOGGER.debug("Bytes read: "+ inBytes.length);
LOGGER.info("Bytes read: "+ inBytes.length);
Location.mapFile(content_fileName, new ByteArrayHandle(inBytes));
// HashMap<String,Object> dbg_loc = Location.getIdMap();
super.setId(content_fileName);
} else { // read file normally
content_fileName = id;
LOGGER.debug("read file directly");
LOGGER.info("read file directly");
super.setId(id);
}
}
//getReader
// super.setId(id);
LOGGER.debug("setId("+id+"). after super" );
LOGGER.info("setId("+id+"). after super" );
file_initialized = true;
}
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
LOGGER.debug("initFile("+id+"), currentId="+currentId+", before super" );
LOGGER.info("initFile("+id+"), currentId="+currentId+", before super" );
try {
super.initFile(id); // fails class_not_found
}
catch (IllegalArgumentException e) {
throw new FormatException(e);
}
LOGGER.debug("initFile("+id+"), currentId="+currentId+", after super" );
LOGGER.info("initFile("+id+"), currentId="+currentId+", after super" );
// Below needs to be modified - EXIFService does not work with mapFile
MetadataStore store = makeFilterMetadata();
LOGGER.debug("Parsing JPEG EXIF data");
LOGGER.info("Parsing JPEG EXIF data");
HashMap<String, String> tags = null;
try {
// Reimplementing ExifServiceImpl as original does not have ExifIFD0Directory
......@@ -295,7 +295,7 @@ public class ElphelJp4Reader extends ImageIOReader{
}
catch (ServiceException e) {
LOGGER.debug("Could not parse EXIF data", e);
LOGGER.info("Could not parse EXIF data", e);
}
long [] maker_note = null;
double exposure = Double.NaN;
......@@ -324,14 +324,14 @@ public class ElphelJp4Reader extends ImageIOReader{
int bytes_per_pixel = 1;
Hashtable<String, String> property_table = ElphelMeta.getMeta(
null, maker_note, exposure, date_time, bytes_per_pixel, true );
LOGGER.debug("Created elphelMeta table, size="+property_table.size());
LOGGER.info("Created elphelMeta table, size="+property_table.size());
for (String key:property_table.keySet()) {
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
// Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
// LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
// LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
}
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
}
......@@ -343,9 +343,9 @@ public class ElphelJp4Reader extends ImageIOReader{
// HashMap<String,Object> dbg_loc = Location.getIdMap();
String saveCurrentId = currentId;
currentId = null;
LOGGER.debug("close("+fileOnly+") before super");
LOGGER.info("close("+fileOnly+") before super");
super.close(fileOnly); // curerent_id == null only during actual close?
LOGGER.debug("close("+fileOnly+") after super");
LOGGER.info("close("+fileOnly+") after super");
currentId = saveCurrentId;
// if ((content_fileName != null) && file_initialized){
if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
......@@ -385,7 +385,7 @@ public class ElphelJp4Reader extends ImageIOReader{
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
LOGGER.debug("openBytes() - before super()");
LOGGER.info("openBytes() - before super()");
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (image_bytes == null) {
jp4Decode(no);
......@@ -401,7 +401,7 @@ public class ElphelJp4Reader extends ImageIOReader{
w);
dest += w;
}
LOGGER.debug("openBytes() - after super()");
LOGGER.info("openBytes() - after super()");
return buf;
}
public void jp4Decode(int no) throws FormatException, IOException {
......@@ -436,7 +436,7 @@ public class ElphelJp4Reader extends ImageIOReader{
} else {
image_bytes = ib; // temporary
}
LOGGER.debug("jp4Decode()");
LOGGER.info("jp4Decode()");
}
}
src/main/java/com/elphel/imagej/readers/ElphelTiffReader.java
View file @ 681a226e
......@@ -40,6 +40,8 @@ import org.apache.commons.compress.utils.IOUtils;
import org.joda.time.DateTime;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
///import ch.qos.logback.classic.Level;
///import ch.qos.logback.classic.Logger;
import com.drew.imaging.ImageMetadataReader;
import com.drew.metadata.Metadata;
......@@ -162,10 +164,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
// mergeSubIFDs = true; // false;
// TODO: See if the selection is just between 2 readers (jp4 and tiff - just Elphel cameras),
// or these readers are combined with all other readers in readers.txt
//https://stackoverflow.com/questions/3837801/how-to-change-root-logging-level-programmatically-for-logback
// LOGGER.setLevel(Level.ERROR);
// Logger root = (Logger)LoggerFactory.getLogger(org.slf4j.Logger.ROOT_LOGGER_NAME);
// root.setLevel(Level.ERROR);
suffixNecessary = true; // false
suffixSufficient = true; // false;
/// mergeSubIFDs = true; // false;
LOGGER.debug("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
LOGGER.info("ElphelTiffReader(), after supper(), mergeSubIFDs = true;");
if (REPLACEMENT_TAG_MAP == null) {
REPLACEMENT_TAG_MAP = new HashMap<String,String>();
for (String [] line: REPLACEMENT_TAGS) {
......@@ -211,14 +217,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
@Override
public void setId(String id) throws FormatException, IOException {
LOGGER.debug("setId("+id+"). before super" );
LOGGER.info("setId("+id+"). before super" );
file_initialized = false;
mapped_externally = false;
if (Location.getIdMap().containsKey(id)) {
LOGGER.debug("id '"+id+"' is already mapped" );
LOGGER.info("id '"+id+"' is already mapped" );
content_fileName = id; // id; // maybe set to null to handle externally?
mapped_externally = true;
LOGGER.debug("Starting setId() method, read file directly");
LOGGER.info("Starting setId() method, read file directly");
super.setId(id);
} else {
// If URL, then read to memory, if normal file - use direct access
......@@ -244,7 +250,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
}
if (url != null) {
LOGGER.debug("Starting initFile() method, read "+ id +" to memory first");
LOGGER.info("Starting initFile() method, read "+ id +" to memory first");
//https://www.rgagnon.com/javadetails/java-0487.html
URLConnection connection = url.openConnection();
......@@ -261,27 +267,27 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
content_fileName = "unknown." + suffix;
}
// currentId = fileName; //???
// LOGGER.debug("Mime type = "+mime);
// LOGGER.info("Mime type = "+mime);
// https://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
//https://stackoverflow.com/questions/2295221/java-net-url-read-stream-to-byte
InputStream is = url.openStream (); //
byte[] inBytes = IOUtils.toByteArray(is);
if (is != null) is.close();
LOGGER.debug("Bytes read: "+ inBytes.length);
LOGGER.info("Bytes read: "+ inBytes.length);
Location.mapFile(content_fileName, new ByteArrayHandle(inBytes));
// HashMap<String,Object> dbg_loc = Location.getIdMap();
super.setId(content_fileName);
} else { // read file normally
content_fileName = id;
LOGGER.debug("read file directly");
LOGGER.info("read file directly");
super.setId(id);
}
}
//getReader
// super.setId(id);
LOGGER.debug("setId("+id+"). after super" );
LOGGER.info("setId("+id+"). after super" );
file_initialized = true;
}
......@@ -292,26 +298,26 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
{
// Trying ServiceFactory before it is going to be initialized, so static defaultFactory will be initialized
// with small set of services - only needed for Elphel
LOGGER.debug("Starting initFile() method");
LOGGER.info("Starting initFile() method");
super.initFile(id);
LOGGER.debug("Ending initFile() method");
LOGGER.info("Ending initFile() method");
}
/* @see loci.formats.FormatReader#initFile(String) */
// copied from ElphelJp4Reader
@Override
protected void initFile(String id) throws FormatException, IOException {
LOGGER.debug("initFile("+id+"), currentId="+currentId+", before super" );
LOGGER.info("initFile("+id+"), currentId="+currentId+", before super" );
try {
super.initFile(id); // fails class_not_found
}
catch (IllegalArgumentException e) {
throw new FormatException(e);
}
LOGGER.debug("initFile("+id+"), currentId="+currentId+", after super" );
LOGGER.info("initFile("+id+"), currentId="+currentId+", after super" );
// Below needs to be modified - EXIFService does not work with mapFile
MetadataStore store = makeFilterMetadata();
LOGGER.debug("Parsing TIFF EXIF data");
LOGGER.info("Parsing TIFF EXIF data");
HashMap<String, String> tags = null;
try {
// Reimplementing ExifServiceImpl as original does not have ExifIFD0Directory
......@@ -378,7 +384,7 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
}
catch (ServiceException e) {
LOGGER.debug("Could not parse EXIF data", e);
LOGGER.info("Could not parse EXIF data", e);
}
long [] maker_note = null;
double exposure = Double.NaN;
......@@ -409,14 +415,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
int bytes_per_pixel = (bpp + 7) / 9;
Hashtable<String, String> property_table = ElphelMeta.getMeta(
null, maker_note, exposure, date_time, bytes_per_pixel, true );
LOGGER.debug("Created elphelMeta table, size="+property_table.size());
LOGGER.info("Created elphelMeta table, size="+property_table.size());
for (String key:property_table.keySet()) {
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
// Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
// LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
// LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
}
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
}
......@@ -436,9 +442,9 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
LOGGER.debug("close("+fileOnly+") before super");
LOGGER.info("close("+fileOnly+") before super");
super.close(fileOnly); // curerent_id == null only during actual close?
LOGGER.debug("close("+fileOnly+") after super");
LOGGER.info("close("+fileOnly+") after super");
// if ((content_fileName != null) && file_initialized){
if (!mapped_externally && file_initialized){ // will try to unmap non-mapped file, OK
Location.mapFile(content_fileName, null);
......@@ -463,10 +469,10 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
/* Removed 08/03/2021 to match IP4
@Override
protected void initStandardMetadata() throws FormatException, IOException {
LOGGER.debug("initStandardMetadata() - before super()");
LOGGER.info("initStandardMetadata() - before super()");
super.initStandardMetadata();
String comment = ifds.get(0).getComment(); // IMAGE_DESCRIPTION
LOGGER.debug("initStandardMetadata() - after super()");
LOGGER.info("initStandardMetadata() - after super()");
long[] maker_note = null;
double exposure = Double.NaN;
String date_time = null;
......@@ -505,14 +511,14 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
null, maker_note, exposure, date_time, bytes_per_pixel, true );
LOGGER.debug("Created elphelMeta table, size="+property_table.size());
LOGGER.info("Created elphelMeta table, size="+property_table.size());
for (String key:property_table.keySet()) {
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+key,property_table.get(key));
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
Integer[] tags = ifds.get(0).keySet().toArray(new Integer[0]);
LOGGER.debug("initStandardMetadata() - got "+tags.length+" tags");
LOGGER.info("initStandardMetadata() - got "+tags.length+" tags");
}
addGlobalMeta(ELPHEL_PROPERTY_PREFIX+CONTENT_FILENAME,content_fileName);
// convert MAKER_NOTE to the same text format as in com.drew.metadata
......@@ -549,9 +555,9 @@ public class ElphelTiffReader extends TiffReader{ // BaseTiffReader {
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
LOGGER.debug("openBytes() - before super()");
LOGGER.info("openBytes() - before super()");
super.openBytes(no, buf, x, y, w, h);
LOGGER.debug("openBytes() - after super()");
LOGGER.info("openBytes() - after super()");
return buf;
}
......
src/main/java/com/elphel/imagej/readers/ImagejJp4Tiff.java
View file @ 681a226e
......@@ -645,17 +645,17 @@ public class ImagejJp4Tiff {
}
if (num_diff == 0) {
System.out.println ("No discontinuities remain");
/// System.out.println ("No discontinuities remain");
return center;
}
System.out.println ("Discontinuities remain, will fix by clusters");
/// System.out.println ("Discontinuities remain, will fix by clusters");
boolean OK = fixByClusters(
width,
height,
FIXCH6_BIT, // int bad_bit,
idata, // int [] data)
(dbg_img != null)); // boolean debug)
System.out.println ("FixByClusters -> "+OK);
/// System.out.println ("FixByClusters -> "+OK);
for (int i = 0; i < idata.length; i++) {
pixels[i+640] = idata[i];
}
......
src/main/java/com/elphel/imagej/tileprocessor/GeometryCorrection.java
View file @ 681a226e
......@@ -801,7 +801,7 @@ public class GeometryCorrection {
int [] full_par_index;
public RigOffset () {
System.out.println("created RigOffset");
/// System.out.println("created RigOffset");
par_scales = new double [VECTOR_LENGTH];
par_scales[AUX_AZIMUTH_INDEX] = 1000.0*focalLength/pixelSize;
par_scales[AUX_TILT_INDEX] = 1000.0*focalLength/pixelSize;
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java
View file @ 681a226e
......@@ -2025,16 +2025,16 @@ public class QuadCLT extends QuadCLTCPU {
false, // final boolean updateStatus,
debugLevel); // final int debugLevel);
if (debugLevel >-1) System.out.println("Processing set "+(nSet+1)+" (of "+set_channels.length+") finished at "+
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory1="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
if (eyesisCorrections.stopRequested.get()>0) {
System.out.println("User requested stop");
System.out.println("Processing "+(nSet + 1)+" file sets (of "+set_channels.length+") finished at "+
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory2="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
return;
}
}
System.out.println("processCLTQuadCorrs(): processing "+getTotalFiles(set_channels)+" files ("+set_channels.length+" file sets) finished at "+
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
IJ.d2s(0.000000001*(System.nanoTime()-this.startTime),3)+" sec, --- Free memory3="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
}
public static ImagePlus renderGPUFromDSI(
......
src/main/java/com/elphel/imagej/tileprocessor/TileProcessor.java
View file @ 681a226e
......@@ -37,7 +37,7 @@ import com.elphel.imagej.common.PolynomialApproximation;
import com.elphel.imagej.common.ShowDoubleFloatArrays;
public class TileProcessor {
public boolean run_garbage_collection=false;
public static String [] SCAN_TITLES4 = {
"tile_op", // 0
"final", // 1 - calculated, filtered, combined disparity
......@@ -251,10 +251,11 @@ public class TileProcessor {
rig_pre_poles_sel = null;
rig_post_poles_sel = null;
clt_3d_passes_rig_size = 0;
Runtime runtime = Runtime.getRuntime();
runtime.gc();
System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
if (run_garbage_collection) {
Runtime runtime = Runtime.getRuntime();
runtime.gc();
System.out.println("--- Free memory30="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
}
}
public void saveCLTPasses(boolean rig){
......@@ -309,7 +310,7 @@ public class TileProcessor {
}
Runtime runtime = Runtime.getRuntime();
runtime.gc();
System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
System.out.println("--- Free memory31="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
}
public void removeNonMeasurement(){ // executed during expansion (CLT 3D)
......
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