Modify: tutorial for PIONE

	new file:   SampleCode/PIONE/Package5/Initial2.pione
	new file:   SampleCode/PIONE/Package6/Annotation3.0.pione
	new file:   SampleCode/PIONE/Package6/Final3.pione

Modify: Add Help Message for lib.
	modified:   Small Tools/Template/Makefile/Makefile

Add: tutorial for mrcImageRandomParticlesImageCreate
	new file:   Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile
	new file:   Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib

diff --git a/SampleCode/PIONE/Package5/Initial2.pione b/SampleCode/PIONE/Package5/Initial2.pione
new file mode 100644 (file)
index 0000000..7c0ea5d
--- /dev/null
+++ b/SampleCode/PIONE/Package5/Initial2.pione
@@ -0,0 +1,12 @@
+Rule Initial
+       input '*.mrc'
+       output '{$I[1][1]}.parameters'
+Action
+       mrcInfo -i {$I[1]} \
+       | head -1 \
+       | awk '{printf("%s %s %s", $4, $5, $6)}' \
+       | tr -c '[0-9]' ' ' \
+       > TMP
+       awk '{printf("%d %d %d", $1*4/5, $2*4/5, $3*4/5)}' TMP \
+       > {$O[1]}
+End

diff --git a/SampleCode/PIONE/Package6/Annotation3.0.pione b/SampleCode/PIONE/Package6/Annotation3.0.pione
new file mode 100644 (file)
index 0000000..e8a73d6
--- /dev/null
+++ b/SampleCode/PIONE/Package6/Annotation3.0.pione
@@ -0,0 +1,4 @@
+.@ PackageName :: "CenterGet"
+.@ Editor              :: "Kinoshita"
+.@ Tag                 :: "v0.3.0"
+.@ Parent              :: &CenterGet.editor("Kinoshita").tag("v0.2.0")

diff --git a/SampleCode/PIONE/Package6/Final3.pione b/SampleCode/PIONE/Package6/Final3.pione
new file mode 100644 (file)
index 0000000..70a1b9e
--- /dev/null
+++ b/SampleCode/PIONE/Package6/Final3.pione
@@ -0,0 +1,13 @@
+Rule Final
+       input '*.mrc'
+       input '{$I[1][1]}.roi'
+       output '*.tiff'.all
+Action
+       for (( num = 0; num <= 2; num++ )) ; \
+       do \
+               mrcImageProjection -i {$I[1]} -o {$I[1]}.2d -m ${num}; \
+               mrc2tiff -i {$I[1]}.2d -o {$I[1]}-${num}.tiff; \
+               mrcImageProjection -i {$I[2]} -o {$I[2]}.2d -m ${num}; \
+               mrc2tiff -i {$I[2]}.2d -o {$I[2]}-${num}.tiff; \
+       done;
+End

diff --git a/Small Tools/Template/Makefile/Makefile b/Small Tools/Template/Makefile/Makefile
index a28bbd9..c3fb1d1 100644 (file)
--- a/Small Tools/Template/Makefile/Makefile
+++ b/Small Tools/Template/Makefile/Makefile
@@ -70,6 +70,9 @@ help_!!Command!!::
        @echo
        @echo "         all:                    Initial -> Exe -> Final."
        @echo
+       @echo "         help:                   Show this help."
+       @echo "         help_XXXX:              Show XXXX help."
+       @echo
        @echo " (Setting Data):"
        @echo "         FILE_NAME:              filename of input"
 

diff --git a/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile
new file mode 100644 (file)
index 0000000..fc19445
--- /dev/null
+++ b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile
@@ -0,0 +1,97 @@
+#
+#      This is Main Makefile for mrcImageRandomParticlesImageCreate.
+#
+#              Created by template v2.0.2p0065
+#
+
+#### Root Makefile ####
+MAKE_ROOT=mrcImageRandomParticlesImageCreate
+TOOLS_CLASS=mrcImage
+TOOLS_COMMAND=$(MAKE_ROOT)
+OBJECTS_GROUP=DataManip
+OBJECTS_CLASS=mrcImage
+OBJECTS_COMMAND=l$(MAKE_ROOT)
+
+#### Input extention ####
+INI=ini
+IN=list
+OUT=mrc
+
+#### Suffixes rule ####
+# Defined at Sub
+
+#### INCLUDE ####
+# Help-include-file must always be put on top.
+-include ${EOS_HOME}/tutorial/TIPS/Help/Makefile/Makefile-lib
+-include ${EOS_HOME}/tutorial/TIPS/Debugger/Makefile/Makefile-lib
+-include Makefile-lib
+
+#### Definition ####
+# Path of Input File
+# Basically, use a linked data from /SampleData.
+INPUT_PATH=${EOS_HOME}/tutorial/SampleData/1VOM.mrc
+
+### FileData
+FILE_NAME=Input
+
+### OPTIONS
+NX=512
+NY=512
+RND_SEED=54321
+
+#### Rules of the list created ####
+# Defined at Sub
+
+##### Commands #####
+# Defined at Sub basically
+# By make Initial, Create input data for this command.
+Initial::
+       make InitialData;
+
+# By make Exe, Execute the sample of this command.
+Exe::
+       if [ ! -z "$(RND_SEED)" ] ; then \
+               OPTION="$${OPTION} -seed $(RND_SEED)"; \
+       fi; \
+       if [ ! -z "$(NX)" -a ! -z "$(NY)" ] ; then \
+               OPTION="$${OPTION} -N $(NX) $(NY)"; \
+       fi; \
+       mrcImageRandomParticlesImageCreate -i $(FILE_NAME).$(IN) -o $(FILE_NAME).$(OUT) $${OPTION};
+
+# By make Final, Make visualize Output for this command.
+Final::
+       mrc2tiff -i $(FILE_NAME).$(OUT) -o $(FILE_NAME).tiff;
+
+# By make all, Initial -> Exe -> Final.
+all::
+       make Initial;
+       make Exe;
+       make Final;
+
+help_mrcImageRandomParticlesImageCreate::
+       @echo
+       @echo "Makefile for mrcImageRandomParticlesImageCreate"
+       @echo "This is Main Makefile for mrcImageRandomParticlesImageCreate."
+       @echo
+       @echo " (Command):"
+       @echo "         Initial:                Create input data for this command."
+       @echo "                 (Setting Data):"
+       @echo "                 INI:            input extention for Initial"
+       @echo
+       @echo "         Exe:                    Execute the sample of this command."
+       @echo "                 (Setting Data):"
+       @echo "                 IN:                     input list extention"
+       @echo "                 OUT:            output extention"
+       @echo "                 NX:                     output size x"
+       @echo "                 NY:                     output size y"
+       @echo "                 RND_SEED:       seed of random number"
+       @echo
+       @echo "         Final:                  Make visualize Output for this command."
+       @echo
+       @echo "         all:                    Initial -> Exe -> Final."
+       @echo
+       @echo " (Setting Data):"
+       @echo "         FILE_NAME:              filename of input"
+
+##### Commands(Input to Output) #####
+# Defined at Sub

diff --git a/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib
new file mode 100644 (file)
index 0000000..76e93de
--- /dev/null
+++ b/Small Tools/mrcImage/mrcImageRandomParticlesImageCreate/Makefile/Makefile-lib
@@ -0,0 +1,31 @@
+#
+#      This is Sub Makefile for mrcImageRandomParticlesImageCreate.
+#
+#              Created by template v2.0.2p0065
+#
+
+#### Input extention ####
+# Defined at Main
+
+#### Suffixes rule ####
+.SUFFIXES: .$(INI)
+
+#### INCLUDE ####
+# Use TIPS File.
+# -include ${EOS_HOME}/tutorial/TIPS/XXXX/Makefile/Makefile-lib
+
+#### Definition ####
+# Defined at Main
+
+#### Rules of the list created ####
+
+
+##### Commands #####
+InitialData::
+       $(RM) $(FILE_NAME).$(INI);
+       $(RM) $(FILE_NAME).$(IN);
+       mrcImageProjection -i $(INPUT_PATH) -o $(FILE_NAME).$(INI);
+       echo "$(FILE_NAME).$(INI)" >> $(FILE_NAME).$(IN);
+
+##### Commands(Input to Output) #####
+