Modify: PIONE tutorial Advanced5

	modified:   SampleCode/PIONE/Advanced5/Main.pione

diff --git a/SampleCode/PIONE/Advanced5/Main.pione b/SampleCode/PIONE/Advanced5/Main.pione
index 299573c..222831f 100644 (file)
--- a/SampleCode/PIONE/Advanced5/Main.pione
+++ b/SampleCode/PIONE/Advanced5/Main.pione
@@ -1,17 +1,73 @@
 param $task := 2
 param $divide := 2
-param $refine := 5
+param $refine := 5 
+
+# Cluster Name
+param $CLUSTER := "all"
+
+# Pad Parameter
+#  Width(Nx) before shrinking 
+param $PADWIDTH := 32
+#  Height(Ny) before shrinking 
+param $PADHEIGHT := 32
+#  Shrink for Speed Up in clustering
+param $SHRINK := 1
+#  Pad Mode 
+param $PADMODE := 13
+#  LOWPASS
+param $LowPassMode := 4 
+param $LowPassResolution := 0.1
+
+# Clustering
+param $ClusterCorrelationMode := 19
+#
+param $ClusterRotationRangeMin := 0
+param $ClusterRotationRangeMax := 360
+param $ClusterRotationRangePartitionNumber := 72
+param $ClusterRotationIterationNumber := 2
+param $ClusterRotationCorrelationMode := 0
+#
+param $ClusterMode := 2
+
+
+# ClusterShow
+param $TreeRootPositionX := 0
+param $TreeRootPositionY := 400
+param $TreeScaleX := 10
+param $TreeScaleY := 100
+param $TreeOffset := "1e1"
+
+# Sequence with Keys(Makefile.config for 2D Clustering)
+$Config :=     ("CLUSTER":$CLUSTER) |
+                       ("PADWIDTH":$PADWIDTH) |
+                       ("PADHEIGHT":$PADHEIGHT) |
+                       ("SHRINK":$SHRINK) |
+                       ("PADMODE":$PADMODE) |
+                       ("LowPassMode":$LowPassMode) |
+                       ("LowPassResolution":$LowPassResolution) |
+                       ("ClusterCorrelationMode":$ClusterCorrelationMode) |
+                       ("ClusterRotationRangeMin":$ClusterRotationRangeMin) |
+                       ("ClusterRotationRangeMax":$ClusterRotationRangeMax) |
+                       ("ClusterRotationRangePartitionNumber":$ClusterRotationRangePartitionNumber) |
+                       ("ClusterRotationIterationNumber":$ClusterRotationIterationNumber) |
+                       ("ClusterRotationCorrelationMode":$ClusterRotationCorrelationMode) |
+                       ("ClusterMode":$ClusterMode) |
+                       ("TreeRootPositionX":$TreeRootPositionX) |
+                       ("TreeRootPositionY":$TreeRootPositionY) |
+                       ("TreeScaleX":$TreeScaleX) |
+                       ("TreeScaleY":$TreeScaleY) |
+                       ("TreeOffset":$TreeOffset)
 
 Rule Main
        input '*.roi'.all
        input 'Makefile'
-       input 'Makefile.config'
        output '*.avg'.all
        output '*.tiff'.all
        output 'all.logps'
        output 'all.treeinfo'
        output 'all.avgsortlst'
 Flow
+       rule SetParam
        rule Preprocess {filelist:$I[1].all, num:1.upto($task), length:$I[1].length()}
        rule Process
        rule Refinement {num:1.upto($divide)}
@@ -19,6 +75,17 @@ Flow
        rule MontageAverage
 End
 
+Rule SetParam
+       output 'Makefile.config'
+Action
+       key=({$Config.keys})
+       value=({$Config.values})
+       for (( i=0; i<{$Config.length}; i++ ))
+       do
+               echo "${key[${i}]}=${value[${i}]}" >> {$O[1]}
+       done
+End
+
 Rule Preprocess
        input $filelist.nth(((($num-1)*((($length-1)/$task)+1))+1).upto((($num*((($length-1)/$task)+1))|$length).min()))
        input 'Makefile'
@@ -219,5 +286,3 @@ Action
        mrcImageMontageCreate -i {$I[1]} -o {$O[1]}
        mrc2tiff -i {$O[1]} -o {$O[2]}
 End
-
-param $roi := false