Adopt universal label scheme z.id-rgn^z.id-rgn

00_DOC/HowTo_Montage.txt

@@ -159,7 +159,7 @@ Inspect results
 
 Each layer's montaging work is done within a folder 'temp0/z/montage' where z is a layer index.
 
-Each montage job gets a master log file called 'temp0/z/montage/lsq.txt' as well as other reports in the montage folder listing suspicious results.
+Each montage job gets a master log file called 'temp0/z/montage/lsqw_0.txt' as well as other reports in the montage folder listing suspicious results.
 
 A quick summary report over all layers is obtained at the temp0 level using:
 
@@ -174,12 +174,9 @@ This creates 'MonSumy.txt' which shows for each layer's montage:
 Fetch results
 ===============
 
-Within each montage folder (temp0/z/montage) find key output files:
-- MultLayAff.xml	# TrakEM2 for this layer
-- TAffineTable.txt	# Table of affines labeled by {z,tile-id,rgn-id}.
+Within each montage folder (temp0/z/montage) find key output folder:
+- X_A_BIN	# binary table of transforms and flags
 
-To get an expanded version of TAffineTable.txt that links these data to other meta-data from the idb, you can cp/edit/run the script found at ???/Alignment_Projects/2_TFormTableEx/tformtableex.sht.
-
-Currently this operates on one layer at a time.
+This can be converted to text tables with tool ???/Alignment_Projects/1_XView/xvgo.sht.
 
 

0_GEN/Agenda.h

@@ -23,7 +23,7 @@ what's the interior.
 matchparams, so one param file drives pipeline.
 
 - MOS needs better name handling (that is, ween off of string labels
-and onto idb z.id:rgn labels).
+and onto idb z.id-rgn labels).
 
 LSQ maybes:
 - LSQ weight CPOINT by Q,R?
@@ -69,7 +69,7 @@ Saalfeld Notes:
 recover correct connectivity in the cut zone by adding corr.
 point pairs into the mix wherein the (x,y) coords are the same
 for A::B, as are the {z,id} labels, but the rgn numbers differ.
-For example: CPOINT2 z.id:1 x0 y0 z.id:2 x0 y0. Essentially, this
+For example: CPOINT2 z.id-1 x0 y0 z.id-2 x0 y0. Essentially, this
 describes a single point labelled two ways.
 
 - In dmesh, when finding corr points across layers, use even more

0_GEN/CThmScan.cpp

@@ -441,7 +441,7 @@ void CThmScan::DebugAngs(
 {
 	char	file[256];
 
-	sprintf( file, "angs_%d_%d_@_%d_%d.log", alyr, atil, blyr, btil );
+	sprintf( file, "angs_%d.%d^%d.%d.log", alyr, atil, blyr, btil );
 	FILE	*f = fopen( file, "w" );
 
 	fprintf( f, "Deg\tR\tX\tY\n" );

0_GEN/CTileSet.cpp

@@ -133,7 +133,7 @@ static TiXmlElement* XMLGetTiles(
 			int	rgn, col, row, cam;
 
 			if( 6 == sscanf( ptch->Attribute( "title" ),
-				"%d.%d:%d_%d.%d.%d",
+				"%d.%d-%d_%d.%d.%d",
 				&z, &til.id, &rgn,
 				&col, &row, &cam ) ) {
 
@@ -1052,11 +1052,11 @@ void CTileSet::WriteTrakEM2Layer(
 
 		if( U.col != -999 ) {
 
-			sprintf( title, "%d.%d:1_%d.%d.%d",
+			sprintf( title, "%d.%d-1_%d.%d.%d",
 				U.z, U.id, U.col, U.row, U.cam );
 		}
 		else
-			sprintf( title, "%d.%d:1", U.z, U.id );
+			sprintf( title, "%d.%d-1", U.z, U.id );
 
 		fprintf( f,
 		"\t\t\t<t2_patch\n"

0_GEN/PipeFiles.cpp

@@ -33,7 +33,7 @@ void OpenPairLog( int alr, int atl, int blr, int btl )
 {
 	char	slog[256];
 
-	sprintf( slog, "pair_%d_%d_@_%d_%d.log",
+	sprintf( slog, "pair_%d.%d^%d.%d.log",
 		alr, atl, blr, btl );
 
 	freopen( slog, "a", stdout );
@@ -1006,7 +1006,7 @@ bool ReadThmPair(
 
 	if( M.Get( name ) ) {
 
-		sprintf( name, "ThmPair_%d_@_%d.txt", alr, blr );
+		sprintf( name, "ThmPair_%d^%d.txt", alr, blr );
 		f = fopen( name, "r" );
 
 		if( f ) {
@@ -1026,7 +1026,7 @@ bool ReadThmPair(
 				"%d\t%d\t%d\t%d\t%d"
 				"\t%lf\t%lf"
 				"\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
-				&tpr.atl, &tpr.btl, &tpr.acr, &tpr.bcr, &tpr.err,
+				&tpr.atl, &tpr.acr, &tpr.btl, &tpr.bcr, &tpr.err,
 				&tpr.A, &tpr.R,
 				&tpr.T.t[0], &tpr.T.t[1], &tpr.T.t[2],
 				&tpr.T.t[3], &tpr.T.t[4], &tpr.T.t[5] );
@@ -1048,8 +1048,8 @@ bool ReadThmPair(
 			}
 
 			fprintf( flog,
-			"ReadThmPair: No entry for %d_%d@%d_%d; cr:%d-%d\n",
-			alr, atl, blr, btl, acr, bcr );
+			"ReadThmPair: No entry for %d.%d-%d^%d.%d-%d\n",
+			alr, atl, acr, blr, btl, bcr );
 		}
 		else
 			fprintf( flog, "ReadThmPair: Can't open [%s].\n", name );
@@ -1088,7 +1088,7 @@ bool ReadAllThmPair(
 
 	if( M.Get( name ) ) {
 
-		sprintf( name, "ThmPair_%d_@_%d.txt", alr, blr );
+		sprintf( name, "ThmPair_%d^%d.txt", alr, blr );
 		f = fopen( name, "r" );
 
 		if( f ) {
@@ -1110,7 +1110,7 @@ bool ReadAllThmPair(
 				"%d\t%d\t%d\t%d\t%d"
 				"\t%lf\t%lf"
 				"\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
-				&P.atl, &P.btl, &P.acr, &P.bcr, &P.err,
+				&P.atl, &P.acr, &P.btl, &P.bcr, &P.err,
 				&P.A, &P.R,
 				&P.T.t[0], &P.T.t[1], &P.T.t[2],
 				&P.T.t[3], &P.T.t[4], &P.T.t[5] );
@@ -1140,7 +1140,7 @@ bool ReadAllThmPair(
 void WriteThmPairHdr( FILE *f )
 {
 	fprintf( f,
-	"Atl\tBtl\tAcr\tBcr\tErr\tDeg\tR"
+	"Atl\tAcr\tBtl\tBcr\tErr\tDeg\tR"
 	"\tT0\tT1\tX\tT3\tT4\tY\n" );
 }
 
@@ -1166,7 +1166,7 @@ void CreateJobsDir(
 
 // Create ThmPair file
 	if( zb >= 0 ) {
-		sprintf( name + len, "/ThmPair_%d_@_%d.txt", za, zb );
+		sprintf( name + len, "/ThmPair_%d^%d.txt", za, zb );
 		FILE	*f = FileOpenOrDie( name, "w", flog );
 		WriteThmPairHdr( f );
 		fclose( f );
@@ -1193,15 +1193,15 @@ void WriteThmPair(
 
 	if( M.Get( name ) ) {
 
-		sprintf( name, "ThmPair_%d_@_%d.txt", alr, blr );
+		sprintf( name, "ThmPair_%d^%d.txt", alr, blr );
 		FILE *f = fopen( name, "a" );
 
 		if( f ) {
 			fprintf( f,
 				"%d\t%d\t%d\t%d\t%d"
 				"\t%f\t%f"
 				"\t%f\t%f\t%f\t%f\t%f\t%f\n",
-				atl, btl, acr, bcr, tpr.err,
+				atl, acr, btl, bcr, tpr.err,
 				tpr.A, tpr.R,
 				tpr.T.t[0], tpr.T.t[1], tpr.T.t[2],
 				tpr.T.t[3], tpr.T.t[4], tpr.T.t[5] );

0_GEN/PipeFiles.h

@@ -100,8 +100,8 @@ typedef struct {
 // entry: ThmPair.txt
 	TAffine	T;
 	double	A, R;
-	int		atl, btl,
-			acr, bcr,
+	int		atl, acr,
+			btl, bcr,
 			err;
 } ThmPair;
 

1_Clean_ThmPairs/cleanthmpair.cpp

@@ -1,5 +1,5 @@
 //
-// Reset all ThmPair_N_@_M.txt files to headers-only state
+// Reset all ThmPair_N^M.txt files to headers-only state
 // in given range [zmin,zmax]. Current dir must be 'temp'
 // at execution time.
 //
@@ -109,11 +109,11 @@ static void WriteOne( int a, int b )
 	char	name[256];
 	FILE	*f;
 
-	sprintf( name, "%d/ThmPair_%d_@_%d.txt", a, a, b );
+	sprintf( name, "%d/ThmPair_%d^%d.txt", a, a, b );
 
 	f = FileOpenOrDie( name, "w", flog );
 
-	fprintf( f, "Atl\tBtl\tAcr\tBcr\tErr\tDeg\tQ\tR"
+	fprintf( f, "Atl\tAcr\tBtl\tBcr\tErr\tDeg\tQ\tR"
 	"\tT0\tT1\tX\tT3\tT4\tY\n" );
 
 	fclose( f );

1_Cross_CarveBlocks/cross_carveblocks.cpp

@@ -196,8 +196,8 @@ static void WriteTestblockFile()
 	fprintf( f, "# -blkmincorr=0.45\t;required min corr for alignment\n" );
 	fprintf( f, "# -blknomcorr=0.50\t;nominal corr for alignment\n" );
 	fprintf( f, "# -xyconf=0.75\t\t;search radius = (1-xyconf)*blkwide\n" );
-	fprintf( f, "# -abdbg\t\t\t;make diagnostic images and exit (Z@Z-1)\n" );
-	fprintf( f, "# -abdbg=k\t\t\t;make diagnostic images and exit (Z@k)\n" );
+	fprintf( f, "# -abdbg\t\t\t;make diagnostic images and exit (Z^Z-1)\n" );
+	fprintf( f, "# -abdbg=k\t\t\t;make diagnostic images and exit (Z^k)\n" );
 	fprintf( f, "# -abctr=0\t\t\t;debug at this a-to-b angle\n" );
 	fprintf( f, "\n" );
 	fprintf( f, "\n" );
@@ -242,8 +242,8 @@ static void WriteSubblocksFile()
 	fprintf( f, "# -blkmincorr=0.45\t;required min corr for alignment\n" );
 	fprintf( f, "# -blknomcorr=0.50\t;nominal corr for alignment\n" );
 	fprintf( f, "# -xyconf=0.75\t\t;search radius = (1-xyconf)*blkwide\n" );
-	fprintf( f, "# -abdbg\t\t\t;make diagnostic images and exit (Z@Z-1)\n" );
-	fprintf( f, "# -abdbg=k\t\t\t;make diagnostic images and exit (Z@k)\n" );
+	fprintf( f, "# -abdbg\t\t\t;make diagnostic images and exit (Z^Z-1)\n" );
+	fprintf( f, "# -abdbg=k\t\t\t;make diagnostic images and exit (Z^k)\n" );
 	fprintf( f, "# -abctr=0\t\t\t;debug at this a-to-b angle\n" );
 	fprintf( f, "\n" );
 	fprintf( f, "\n" );

1_Cross_ThisBlock/cross_thisblock.cpp

@@ -880,7 +880,7 @@ static void WriteMakeFile(
 			T.FromAToB( T, b.T );
 
 			fprintf( f,
-			"\tptest %d/%d@%d/%d"
+			"\tptest %d.%d^%d.%d"
 			" -Tab=%f,%f,%f,%f,%f,%f%s ${EXTRA}\n\n",
 			a.z, a.id, b.z, b.id,
 			T.t[0], T.t[1], T.t[2], T.t[3], T.t[4], T.t[5],
@@ -905,7 +905,7 @@ static void WriteThumbFiles( const vector<BlkZ> &vZ )
 			continue;
 
 		char	name[128];
-		sprintf( name, "ThmPair_%d_@_%d.txt", gDat.za, vZ[iz].Z );
+		sprintf( name, "ThmPair_%d^%d.txt", gDat.za, vZ[iz].Z );
 		FILE	*f = FileOpenOrDie( name, "w", flog );
 		WriteThmPairHdr( f );
 		fclose( f );

1_Cross_ThisBlock/subblocks.sht

@@ -15,8 +15,8 @@
 # -blkmincorr=0.45	;required min corr for alignment
 # -blknomcorr=0.50	;nominal corr for alignment
 # -xyconf=0.75		;search radius = (1-xyconf)*blkwide
-# -abdbg			;make diagnostic images and exit (Z@Z-1)
-# -abdbg=k			;make diagnostic images and exit (Z@k)
+# -abdbg			;make diagnostic images and exit (Z^Z-1)
+# -abdbg=k			;make diagnostic images and exit (Z^k)
 # -abctr=0			;debug at this a-to-b angle
 
 

1_Cross_ThisBlock/testblock.sht

@@ -11,8 +11,8 @@
 # -blkmincorr=0.45	;required min corr for alignment
 # -blknomcorr=0.50	;nominal corr for alignment
 # -xyconf=0.75		;search radius = (1-xyconf)*blkwide
-# -abdbg			;make diagnostic images and exit (Z@Z-1)
-# -abdbg=k			;make diagnostic images and exit (Z@k)
+# -abdbg			;make diagnostic images and exit (Z^Z-1)
+# -abdbg=k			;make diagnostic images and exit (Z^k)
 # -abctr=0			;debug at this a-to-b angle
 
 

1_DMesh/ApproximateMatch.cpp

@@ -106,7 +106,7 @@
 //
 // Return true and add one entry to guesses if successful.
 //
-// Also, output an entry in the ThmPair_lyrA_@_lyrB.txt file.
+// Also, output an entry in the ThmPair_lyrA^lyrB.txt file.
 //
 // Discussion
 // ----------

1_DMesh/ApproximateMatch_NoCR.cpp

@@ -16,7 +16,7 @@
 //
 // Return true and add one entry to guesses if successful.
 //
-// Also, output an entry in the ThmPair_lyrA_@_lyrB.txt file.
+// Also, output an entry in the ThmPair_lyrA^lyrB.txt file.
 //
 // Discussion
 // ----------

1_DMesh/CGBL_dmesh.cpp

@@ -166,11 +166,11 @@ bool CGBL_dmesh::SetCmdLine( int argc, char* argv[] )
 // Decode labels in key
 
 	if( !key ||
-		(4 != sscanf( key, "%d/%d@%d/%d",
+		(4 != sscanf( key, "%d.%d^%d.%d",
 				&A.z, &A.id,
 				&B.z, &B.id )) ) {
 
-		printf( "main: Usage: ptest <za/ia@zb/ib>.\n" );
+		printf( "main: Usage: ptest <za.ia^zb.ib>.\n" );
 		return false;
 	}
 

1_DMesh/CThmUtil.cpp

@@ -728,7 +728,7 @@ void CThmUtil::RecordSumSqDif( const TAffine &T )
 
 	if( M.Get( name ) ) {
 
-		sprintf( name, "SmSqDf_%d_@_%d.log", A.z, B.z );
+		sprintf( name, "SmSqDf_%d^%d.log", A.z, B.z );
 
 		FILE *f;
 		int  is;

1_DMesh/dmesh.cpp

@@ -217,7 +217,7 @@ static void FitAffine(
 
 				fprintf( f,
 				"AFFINE"
-				" %d.%d:%d %d.%d:%d"
+				" %d.%d-%d %d.%d-%d"
 				" %f %f %f %f %f %f\n",
 				GBL.A.z, GBL.A.id, argn,
 				GBL.B.z, GBL.B.id, brgn,
@@ -342,7 +342,7 @@ static void FitHmgphy(
 
 				fprintf( f,
 				"HMGPHY"
-				" %d.%d:%d %d.%d:%d"
+				" %d.%d-%d %d.%d-%d"
 				" %f %f %f %f %f %f %.12g %.12g\n",
 				GBL.A.z, GBL.A.id, argn,
 				GBL.B.z, GBL.B.id, brgn,
@@ -530,8 +530,8 @@ static void WritePOINTEntries(
 
 					fprintf( f,
 					"CPOINT2"
-					" %d.%d:%d %f %f"
-					" %d.%d:%d %f %f\n",
+					" %d.%d-%d %f %f"
+					" %d.%d-%d %f %f\n",
 					GBL.A.z, GBL.A.id, ma, pa.x, pa.y,
 					GBL.B.z, GBL.B.id, mb, pb.x, pb.y );
 

1_LSQi/lsq_Layers.cpp

@@ -43,7 +43,7 @@ static int ThmPair( const struct dirent* E )
 
 		int	za, zb;
 
-		if( 2 == sscanf( E->d_name, "ThmPair_%d_@_%d", &za, &zb )
+		if( 2 == sscanf( E->d_name, "ThmPair_%d^%d", &za, &zb )
 			&& za == _L->z ) {
 
 			_L->zdown.insert( zb );

1_LSQw/lsq_Dropout.cpp

@@ -66,19 +66,19 @@ void* _Scan( void* ithr )
 				RealZIDR( z, i, r, iz, ir );
 
 				if( FLAG_ISREAD( R.flag[ir] ) ) {
-					fprintf( q, "R %d.%d:%d\n", z, i, r );
+					fprintf( q, "R %d.%d-%d\n", z, i, r );
 					++D.read;
 				}
 				else if( FLAG_ISPNTS( R.flag[ir] ) ) {
-					fprintf( q, "P %d.%d:%d\n", z, i, r );
+					fprintf( q, "P %d.%d-%d\n", z, i, r );
 					++D.pnts;
 				}
 				else if( FLAG_ISKILL( R.flag[ir] ) ) {
-					fprintf( q, "K %d.%d:%d\n", z, i, r );
+					fprintf( q, "K %d.%d-%d\n", z, i, r );
 					++D.kill;
 				}
 				else if( FLAG_ISCUTD( R.flag[ir] ) ) {
-					fprintf( q, "C %d.%d:%d\n", z, i, r );
+					fprintf( q, "C %d.%d-%d\n", z, i, r );
 					++D.cutd;
 				}
 			}

1_LSQw/lsq_Error.cpp

@@ -370,7 +370,7 @@ void Stat::Topn( FILE *f, int SorD ) const
 			RealZIDR( z1, i1, r1, C.z1, C.i1 );
 			RealZIDR( z2, i2, r2, C.z2, C.i2 );
 
-			fprintf( f, "\t%d.%d:%d^%d.%d:%d",
+			fprintf( f, "\t%d.%d-%d^%d.%d-%d",
 				z1, i1, r1, z2, i2, r2 );
 		}
 	}
@@ -517,7 +517,7 @@ void StatG::Topn( FILE *f, int SorD ) const
 
 			const EG&	G = veg[i];
 
-			fprintf( f, "\t%d.%d:%d^%d.%d:%d",
+			fprintf( f, "\t%d.%d-%d^%d.%d-%d",
 				G.z1, G.i1, G.r1, G.z2, G.i2, G.r2 );
 		}
 	}

1_LSQw/lsq_Magnitude.cpp

@@ -276,7 +276,7 @@ void Stat::Topn( FILE *f, int SorB ) const
 
 			int	z, i, r;
 			RealZIDR( z, i, r, vei[ie].iz, vei[ie].i );
-			fprintf( f, "\t%d.%d:%d", z, i, r );
+			fprintf( f, "\t%d.%d-%d", z, i, r );
 		}
 	}
 	else
@@ -383,7 +383,7 @@ void StatG::Topn( FILE *f, int SorB ) const
 
 			const EG&	G = veg[i];
 
-			fprintf( f, "\t%d.%d:%d", G.z, G.i, G.r );
+			fprintf( f, "\t%d.%d-%d", G.z, G.i, G.r );
 		}
 	}
 	else