Pretty scripts

00_ENV/getsharedbins.sht

@@ -9,4 +9,3 @@
 cp /groups/apig/share/ClusterSupport/bins/SuperLUSymSolve /groups/apig/tomo/lou_stuff/binaries
 cp /groups/apig/share/ClusterSupport/bins/SuperLUSymSolveMPI /groups/apig/tomo/lou_stuff/binaries
 
-

1_Ptestx/findsame.sht

@@ -3,4 +3,3 @@
 grep -e "ptest 30/30021022@30/30022023" S*/make.same
 
 
-

2_GraRan1Lyr/gr1go.sht

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Purpose:
+# Write entry in outfile GRScales.txt having scale min,max for this layer.
+#
+# > GraRan1Lyr <xml-file> -z=i <-chn=chn> <-pct-pct> [options].
+#
+# Required:
+# -chn=0			;for example, scale channel 0
+# -pct=85.0			;for example, use 85% of forground range.
+#
+# Options:
+# -lrbt=0,0,-1,-1	;calculate average intensity in this ROI
+
+
+GraRan1Lyr layer0_48_grn_sim_montage.xml -z=2 -chn=0 -pct=50.0
+

2_GrayRanger/GrayRanger.cpp

@@ -187,7 +187,8 @@ static void WriteScript( vector<int> &zlist )
 
 	int		nz = zlist.size();
 
-	fprintf( f, "#!/bin/sh\n\n" );
+	fprintf( f, "#!/bin/sh\n" );
+	fprintf( f, "\n" );
 
 	for( int iz = 0; iz < nz; ++iz ) {
 
@@ -200,10 +201,7 @@ static void WriteScript( vector<int> &zlist )
 	fprintf( f, "\n" );
 
 	fclose( f );
-
-// make executable
-
-	chmod( "make.scales.sht", S_IRWXU | S_IRWXG | S_IRWXO );
+	FileScriptPerms( "make.scales.sht" );
 }
 
 /* --------------------------------------------------------------- */

2_GrayRanger/grgo.sht

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Purpose:
+# Create script 'make.scales.sht' to submit GraRan1Lyr jobs.
+#
+# > GrayRanger <xml-file> -zmin=i -zmax=j <-chn=chn> <-pct-pct> [options].
+#
+# Required:
+# -chn=0			;for example, scale channel 0
+# -pct=85.0			;for example, use 85% of forground range.
+#
+# Options:
+# -lrbt=0,0,-1,-1	;calculate average intensity in this ROI
+
+
+GrayRanger layer0_48_grn_sim_montage.xml -zmin=2 -zmax=2 -chn=0 -pct=50.0
+

2_HEQLayers/HEQLayers.cpp

@@ -186,7 +186,8 @@ static void WriteScript( vector<int> &zlist )
 
 	int		nz = zlist.size();
 
-	fprintf( f, "#!/bin/sh\n\n" );
+	fprintf( f, "#!/bin/sh\n" );
+	fprintf( f, "\n" );
 
 	for( int iz = 0; iz < nz; ++iz ) {
 
@@ -199,10 +200,7 @@ static void WriteScript( vector<int> &zlist )
 	fprintf( f, "\n" );
 
 	fclose( f );
-
-// make executable
-
-	chmod( "make.heq.sht", S_IRWXU | S_IRWXG | S_IRWXO );
+	FileScriptPerms( "make.heq.sht" );
 }
 
 /* --------------------------------------------------------------- */

2_HEQLayers/heqlayersgo.sht

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Purpose:
+# Create script 'make.heq.sht' to submit HEQ1Lyr jobs.
+#
+# > HEQLayers <xml-file> <tag> -zmin=i -zmax=j <-pct=pct> [options].
+#
+# Required:
+# tag				;text string like HEQ that labels output folder and tifs.
+# -pct=85.0			;for example, use 85% of forground range.
+#
+# Options:
+# -lrbt=0,0,-1,-1	;calculate average intensity in this ROI
+
+
+HEQLayers layer0_48_grn_sim_montage.xml HEQ -zmin=0 -zmax=48 -pct=99.5
+

2_HEQVFY/heqvfygo.sht

@@ -0,0 +1,21 @@
+#!/bin/sh
+
+# Purpose:
+# List missing HEQ files.
+#
+# The input XML file can have either native or tag-modified file-paths.
+# In either case, we call DskExists for each image. We do not check
+# correctness of the XML file itself.
+#
+# > HEQVFY <xml-file> <tag> [options]
+#
+# Required:
+# tag				;text string like HEQ that labels output folder and tifs.
+#
+# Options:
+# -p=_N_			;pattern describes context around tile ID 'N' in img name
+# -zmin=i -zmax=j	;restricts layer range
+
+
+HEQVFY Z7-119.txt HEQ -zmin=7 -zmax=119
+

2_HEQXML/heqxmlgo.sht

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Purpose:
+# Using same tag and Z-range as for HEQLayers, update corresponding XML
+# to point to the new images.
+#
+# > HEQXML <xml-file> <tag> [options]
+#
+# Required:
+# tag				;text string like HEQ that labels output folder and tifs.
+#
+# Options:
+# -zmin=i -zmax=j	;restricts layer range
+
+
+HEQXML Z7-119.txt HEQ -zmin=7 -zmax=119
+

2_Hist1/Hist1.cpp

@@ -70,7 +70,7 @@ void CArgs_hist1::SetCmdLine( int argc, char* argv[] )
 // parse command line args
 
 	if( argc < 3 ) {
-		printf( "Usage: Hist1 <img-file> <hst_file> [options].\n" );
+		printf( "Usage: Hist1 <img-file> <hst_file>.\n" );
 		exit( 42 );
 	}
 

2_Hist1/driver.sht → 2_Hist1/hst1go.sht

@@ -1,5 +1,14 @@
 #!/bin/sh
 
+# Purpose:
+# Write binary histogram file for one 16-bit image.
+#
+# > Hist1 <img-file> <hst-file>.
+#
+# Options:
+# none
+
+
 mkdir HST
 cd HST
 

2_HistAll/HistAll.cpp

@@ -92,7 +92,7 @@ void CArgs_hsta::SetCmdLine( int argc, char* argv[] )
 // parse command line args
 
 	if( argc < 3 ) {
-		printf( "Usage: HistAll <xml-file> -chan=,, [options].\n" );
+		printf( "Usage: HistAll <xml-file> -chan=,,.\n" );
 		exit( 42 );
 	}
 
@@ -212,7 +212,8 @@ static void WriteScript( const vector<Picture> &vp )
 	int		np = vp.size(),
 			nc = gArgs.chn.size();
 
-	fprintf( f, "#!/bin/sh\n\n" );
+	fprintf( f, "#!/bin/sh\n" );
+	fprintf( f, "\n" );
 
 	for( int ip = 0; ip < np; ++ip ) {
 
@@ -233,10 +234,7 @@ static void WriteScript( const vector<Picture> &vp )
 	fprintf( f, "\n" );
 
 	fclose( f );
-
-// make executable
-
-	chmod( "HST/make.hst.sht", S_IRWXU | S_IRWXG | S_IRWXO );
+	FileScriptPerms( "HST/make.hst.sht" );
 }
 
 /* --------------------------------------------------------------- */

2_HistAll/hstgo.sht

@@ -0,0 +1,16 @@
+#!/bin/sh
+
+# Purpose:
+# Create 'HST' directory and script 'HST/make.hst.sht' to submit Hist1 jobs.
+#
+# > HistAll <xml-file> -zmin=i -zmax=j <-chan=,,>.
+#
+# Required:
+# -chan=1,3			;e.g., write histogram files for channels 1 and 3.
+#
+# Options:
+# none
+
+
+HistAll layer0_48_grn_sim_montage.xml -zmin=2 -zmax=2 -chan=1,2
+

2_RGBM1Lyr/rgb1go.sht

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+# Purpose:
+# For one layer, create new folder TIF_tag and create scaled images there.
+#
+# > RGBM1Lyr <xml-file> <tag> -z=i <-[R,G,B]=i,pct> [options].
+#
+# Required:
+# tag				;text string like RGB that labels output folder and tifs.
+# -R=0,85.0			;for example, color channel-0 red using 85% of forground range.
+#
+# Options:
+# -spanRGB=LLL		;three-char string like LTT specifies scaling by {L=whole layer, T=ea. tile}
+# -lrbt=0,0,-1,-1	;calculate average intensity in this ROI
+
+
+RGBM1Lyr layer0_48_grn_sim_montage.xml RGB -z=0 -R=1,99.5 -G=0,99.5 -B=2,99.5
+

2_RGBMerge/RGBMerge.cpp

@@ -244,7 +244,8 @@ static void WriteScript( vector<int> &zlist )
 
 	int		nz = zlist.size();
 
-	fprintf( f, "#!/bin/sh\n\n" );
+	fprintf( f, "#!/bin/sh\n" );
+	fprintf( f, "\n" );
 
 	for( int iz = 0; iz < nz; ++iz ) {
 
@@ -257,10 +258,7 @@ static void WriteScript( vector<int> &zlist )
 	fprintf( f, "\n" );
 
 	fclose( f );
-
-// make executable
-
-	chmod( "make.merge.sht", S_IRWXU | S_IRWXG | S_IRWXO );
+	FileScriptPerms( "make.merge.sht" );
 }
 
 /* --------------------------------------------------------------- */

2_RGBMerge/rgbgo.sht

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+# Purpose:
+# Create script 'make.merge.sht' to submit RGB1Lyr jobs.
+#
+# > RGBMerge <xml-file> <tag> -zmin=i -zmax=j <-[R,G,B]=i,pct> [options].
+#
+# Required:
+# tag				;text string like RGB that labels output folder and tifs.
+# -R=0,85.0			;for example, color channel-0 red using 85% of forground range.
+#
+# Options:
+# -spanRGB=LLL		;three-char string like LTT specifies scaling by {L=whole layer, T=ea. tile}
+# -lrbt=0,0,-1,-1	;calculate average intensity in this ROI
+
+
+RGBMerge layer0_48_grn_sim_montage.xml RGB -zmin=0 -zmax=48 -R=1,99.5 -G=0,99.5 -B=2,99.5
+

macros/CLEAN.sht

@@ -3,6 +3,7 @@
 # Clean work files from older Lou-style temp structure
 #
 
+
 rm lou-*
 rm *.log
 rm *.tif
@@ -14,4 +15,3 @@ rm qual.*
 rm ./*/*map*
 rm ./*/*tf*
 
-

macros/JuanLayout.sht

@@ -2,6 +2,7 @@
 
 # Build rick file for juan
 
+
 rm layout.txt
 
 for i in $(seq 0 99)
@@ -13,4 +14,3 @@ done
 
 rm temp.txt
 
-

macros/ReplaceAll.sht

@@ -1,5 +1,6 @@
 #!/bin/sh
 
+
 searchterm="Plate1_0/fixed_images"
 replaceterm="Plate1_0/TIF"
 inwhich="*.xml"

macros/catlayout.sht

@@ -3,6 +3,7 @@
 # Concatenate Rick files for individual dirs into one big file
 #
 
+
 dir=/groups/bock/bocklab/eric/forbill/cutout1
 
 for i in $(seq 0 60)
@@ -14,4 +15,3 @@ do
 	fi
 done
 
-

macros/catlyr.sht

@@ -3,6 +3,7 @@
 # Concatenate Rick files for individual dirs into one big file
 #
 
+
 dir=/groups/bock/bocklab/people/eric/scratch/32stack-clahe/
 
 for z in $(seq 7 119)
@@ -11,4 +12,3 @@ do
 	cat $dir$N".txt" >> Z7-119.txt
 done
 
-

macros/edit_filepath.sht

@@ -1,6 +1,5 @@
 #!/bin/sh
 
-
 # This script edits the file_path tags in TrakEM2 xml files.
 # It does simple substitutions at the start of the paths.
 #
@@ -64,4 +63,3 @@ fi
 # Do substitutions on all lines
 sed 's|file_path="'$old'|file_path="'$new'|' < $1 > $v2
 
-

macros/edit_title.sht

@@ -1,6 +1,5 @@
 #!/bin/sh
 
-
 # This script edits the title tags in TrakEM2 xml files,
 # to change from one channel specifier to another. The
 # image names are expected to look like B7_15_channel,
@@ -43,4 +42,3 @@ fi
 # Do substitutions on all lines
 sed 's|title="\(.*_[0-9]\{1,\}_\)'$old'|title="\1'$new'|' < $1 > $v2
 
-