Fixing hardware problems on channel5

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

@@ -46,6 +46,7 @@ import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.Properties;
 import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
@@ -60,6 +61,7 @@ import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
+import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.TileNeibs;
 
 import ij.ImagePlus;
@@ -96,6 +98,11 @@ public class ImagejJp4Tiff {
 	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_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 --
 
@@ -252,7 +259,12 @@ public class ImagejJp4Tiff {
 		int fixed_center =  fix000E6410C435(
 				meta_hash, // Hashtable<String, Object> meta_hash,
 				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
 		
@@ -336,6 +348,9 @@ public class ImagejJp4Tiff {
 		if (fixed_center > 0) {
 			imp.setProperty("FIXED_CHN6", ""+fixed_center);
 		}
+		if (fixed_chn5 > 0) {
+			imp.setProperty("FIXED_CHN5", ""+fixed_chn5);
+		}
 		encodeProperiesToInfo(imp);
 		Location.mapFile(content_fileName, null);
 		return imp;
@@ -530,6 +545,119 @@ public class ImagejJp4Tiff {
 		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
 	public int fix000E6410C435(