Commit f760790f authored by Andrey Filippov's avatar Andrey Filippov
Browse files

Fixing hardware problems on channel5

parent 1cf71ddd

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

+130 −2
Original line number Original line Diff line number Diff line
@@ -46,6 +46,7 @@ import java.util.Hashtable; 
import java.util.Iterator;

import java.util.Iterator;

import java.util.Properties;

import java.util.Properties;

import java.util.Set;

import java.util.Set;

import java.util.concurrent.atomic.AtomicInteger;





import javax.xml.parsers.DocumentBuilder;

import javax.xml.parsers.DocumentBuilder;

import javax.xml.parsers.DocumentBuilderFactory;

import javax.xml.parsers.DocumentBuilderFactory;
@@ -60,6 +61,7 @@ import org.xml.sax.InputSource; 
import org.xml.sax.SAXException;

import org.xml.sax.SAXException;





import com.elphel.imagej.common.ShowDoubleFloatArrays;

import com.elphel.imagej.common.ShowDoubleFloatArrays;

import com.elphel.imagej.tileprocessor.ImageDtt;

import com.elphel.imagej.tileprocessor.TileNeibs;

import com.elphel.imagej.tileprocessor.TileNeibs;





import ij.ImagePlus;

import ij.ImagePlus;
@@ -96,6 +98,11 @@ public class ImagejJp4Tiff { 
	private static final int    FIXCH6_EXPECTED  = 21319; // expected value 

	private static final int    FIXCH6_EXPECTED  = 21319; // expected value 

	private static final String FIXCH6_EARLIEST = "2021-12-01 00:00:00.000";

	private static final String FIXCH6_EARLIEST = "2021-12-01 00:00:00.000";

	private static final String FIXCH6_LATEST =   "2024-12-01 00:00:00.000";

	private static final String FIXCH6_LATEST =   "2024-12-01 00:00:00.000";

	private static final String FIXCH5_SERIAL =   "00:0E:64:10:C4:35";

//	private static final String FIXCH5_EARLIEST = "2023-11-02 00:00:00.000";

	private static final String FIXCH5_EARLIEST = "2023-10-01 00:00:00.000";

	private static final String FIXCH5_LATEST =   "2024-12-01 00:00:00.000";

	private static final int    FIXCH5_CHANNEL =  1;

	

	

	// -- Fields --

	// -- Fields --
@@ -252,7 +259,12 @@ public class ImagejJp4Tiff { 
		int fixed_center =  fix000E6410C435(

		int fixed_center =  fix000E6410C435(

				meta_hash, // Hashtable<String, Object> meta_hash,

				meta_hash, // Hashtable<String, Object> meta_hash,

				pixels); // short [] pixels)

				pixels); // short [] pixels)

		

		int fixed_chn5=0;

		if (fixed_center < 0) {

			fixed_chn5 =  fix000E6410C435_ch5(

					meta_hash, // Hashtable<String, Object> meta_hash,

					pixels); // short [] pixels)

		}

		

		

		boolean degamma = bytes_per_pixel < 2; // both JP4 and 8-bit tiff

		boolean degamma = bytes_per_pixel < 2; // both JP4 and 8-bit tiff
@@ -336,6 +348,9 @@ public class ImagejJp4Tiff { 
		if (fixed_center > 0) {

		if (fixed_center > 0) {

			imp.setProperty("FIXED_CHN6", ""+fixed_center);

			imp.setProperty("FIXED_CHN6", ""+fixed_center);

		}

		}

		if (fixed_chn5 > 0) {

			imp.setProperty("FIXED_CHN5", ""+fixed_chn5);

		}

		encodeProperiesToInfo(imp);

		encodeProperiesToInfo(imp);

		Location.mapFile(content_fileName, null);

		Location.mapFile(content_fileName, null);

		return imp;

		return imp;
@@ -530,6 +545,119 @@ public class ImagejJp4Tiff { 
		return true;

		return true;

	}

	}





	public static boolean needsFix000E6410C435_ch5(ImagePlus imp) {

		String prefix = "STD_";

		String serial = (String) imp.getProperty(prefix+"Serial_Number");

		if ((serial == null) || !serial.equals(FIXCH5_SERIAL)) {

			return false; // wrong camera 

		}

		String schannel = ((String) imp.getProperty(prefix+"PageNumber")).substring(0,1);

		if ((schannel == null) || (Integer.parseInt(schannel) != FIXCH5_CHANNEL)) {

			return false; // wrong channel

		}		

		String sfdate = (String) imp.getProperty(prefix+"DateTime");

		sfdate = sfdate.replaceFirst(":", "-");

		sfdate = sfdate.replaceFirst(":", "-")+".000";

		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss.SSS");

		try {

			Date startDate = dateFormat.parse(FIXCH5_EARLIEST);

			Date endDate =   dateFormat.parse(FIXCH5_LATEST);

			Date fileDate =  dateFormat.parse(sfdate);

			if (fileDate.before(startDate) || fileDate.after(endDate)) {

				return false; // too early or too late 

			}

		} catch (ParseException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		return true;

	}

	public int fix000E6410C435_ch5(

			Hashtable<String, Object> meta_hash,

			final float [] pixels)

	{

		final float [] pixels_in = pixels.clone();

		final int width =  reader.getSizeX();

		final int height = reader.getSizeY();

		final int dbg_pix = -(190+189*width);

		String serial = (String) meta_hash.get("Serial_Number");

		if ((serial == null) || !serial.equals(FIXCH5_SERIAL)) {

			return -1; // wrong camera 

		}

		String schannel = ((String) meta_hash.get("PageNumber")).substring(0,1);

		if ((schannel == null) || (Integer.parseInt(schannel) != FIXCH5_CHANNEL)) {

			return -2; // wrong channel

		}		

		

		String sfdate = (String) meta_hash.get("DateTime");

		sfdate = sfdate.replaceFirst(":", "-");

		sfdate = sfdate.replaceFirst(":", "-")+".000";

		SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd hh:mm:ss.SSS");

		try {

			Date startDate = dateFormat.parse(FIXCH5_EARLIEST);

			Date endDate =   dateFormat.parse(FIXCH5_LATEST);

			Date fileDate =  dateFormat.parse(sfdate);

			if (fileDate.before(startDate) || fileDate.after(endDate)) {

				return -3; // too early or too late 

			}

		} catch (ParseException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		final int [] patts = {0x060, 0x0e0};

//		final int [] masks = {0x7e0, 0x7c0};

		final int [] masks = {0x7c0, 0x780};

		final int [] offs =  {0x080, 0x100}; 

		final TileNeibs tn = new TileNeibs(width,height);

//		int [] clusters = new int [width*height];

		final Thread[] threads = ImageDtt.newThreadArray(ImageDtt.THREADS_MAX);

		final AtomicInteger ai = new AtomicInteger(0);

		final AtomicInteger ancorr = new AtomicInteger(0);

		for (int ithread = 0; ithread < threads.length; ithread++) {

			threads[ithread] = new Thread() {

				public void run() {

					for (int ipix = ai.getAndIncrement(); ipix < pixels_in.length; ipix = ai.getAndIncrement()) {

						if (ipix == dbg_pix) {

							System.out.println("ipix==dbg_pix=="+ipix);

						}

						double dd = pixels_in[ipix];

						int id = (int) dd;

						int mode = -1;

						for (int i = 0; i < patts.length; i++) {

							if (((id ^ patts[i]) & masks[i]) == 0) {

								mode = i;

								break;

							}

						}

						if (mode >= 0) {

//							int px = ipix % width;

//							int py = ipix / width;

							int npix = 0;

							double sd = 0;

							for (int dir = 0; dir < TileNeibs.DIRS; dir++) {

								int ipix1 = tn.getNeibIndex(ipix, dir);

								if (ipix1 >= 0) {

									sd+= pixels_in[ipix1];

									npix++;

								}

							}

							if (npix > 0) { // always

								sd /= npix;

								if ((sd - dd) > (offs[mode]/2)) {

									pixels[ipix] += offs[mode];

									ancorr.getAndIncrement();

								}

							}

							

						}

						

					}

				}

			};

		}		      

		ImageDtt.startAndJoin(threads);

		return ancorr.get(); // number of corrected pixels

	}

	

	

	// fixing "00:0E:64:10:C4:35" camera

	// fixing "00:0E:64:10:C4:35" camera

	public int fix000E6410C435(

	public int fix000E6410C435(