SampleCode/PIONE/Advanced5/Main.pione

   1 param $task := 2
   2 param $divide := 2
   3 param $refine := 5
   4
   5 Rule Main
   6         input '*.roi'.all
   7         input 'Makefile'
   8         input 'Makefile.config'
   9         output '*.avg'.all
  10         output '*.tiff'.all
  11         output 'all.logps'
  12         output 'all.treeinfo'
  13         output 'all.avgsortlst'
  14 Flow
  15         rule Preprocess {filelist:$I[1].all, num:1.upto($task), length:$I[1].length()}
  16         rule Process
  17         rule Refinement {num:1.upto($divide)}
  18         rule RefinementRoot
  19         rule MontageAverage
  20 End
  21
  22 Rule Preprocess
  23         input $filelist.nth(((($num-1)*((($length-1)/$task)+1))+1).upto((($num*((($length-1)/$task)+1))|$length).min()))
  24         input 'Makefile'
  25         input 'Makefile.config'
  26         output '*.pad'.all
  27 Action
  28         for data in {$I[1]}
  29         do
  30                 make $(basename ${data} ".roi").pad
  31         done
  32 End
  33
  34 Rule Process
  35         input '*.pad'.all
  36         input 'Makefile'
  37         input 'Makefile.config'
  38         output 'all.padsortlst'
  39         output 'all.treeinfo'
  40         output 'all.avgsortlst'
  41         output ((1.upto($divide).str())+".lst").d().all()
  42         output ((1.upto($divide).str())+".tree").d().all()
  43         output ("*.pad"+(1.upto($divide).str())).d().all()
  44         output ("*.avg"+(0.upto($divide).str())).d().all()
  45         output '*.avglst'.all
  46         output 'all.padsortmon.tiff'
  47         output 'all.avgsortmon.tiff'
  48         output 'all.logps'
  49 Action
  50         ls -1 *.pad > all.padlst
  51         make Log
  52         make LogPS
  53         mrc2tiff -i all.padsortmon -o all.padsortmon.tiff
  54         mrc2tiff -i all.avgsortmon -o all.avgsortmon.tiff
  55
  56         cp {$O[1]} 1.lst
  57         cp {$O[2]} 1.tree
  58         for (( i=2; i<={$divide}; i++ ))
  59         do
  60                 max=0
  61                 for data in $(ls *.lst)
  62                 do
  63                         num=$(wc -l ${data} | awk '{printf $1}')
  64                         if [ ${num} -gt ${max} ] ; then
  65                                 max=${num}
  66                                 maxlist="${data}"
  67                         fi
  68                 done
  69                 maxtree="$(basename ${maxlist} '.lst').tree"
  70                 root=$(head -1 ${maxtree} | awk '{printf("%d", $1)}')
  71                 rootname=$(basename $(awk -v val=${root} '$2==val {printf("%s", $1)}' ${maxlist}) ".pad")
  72                 cp ${maxlist} ${rootname}.avglst
  73                 cp ${rootname}.pad.avg ${rootname}.pad.avg0
  74                 maxpos=$(awk -v val=${root} '$2==val {printf("%f", $3)}' ${maxlist})
  75                 line=$(awk -v val=${root} '$2==val {print NR}' ${maxlist})
  76                 head -$((${line} - 1)) ${maxlist} > ${i}.lst
  77                 tail -$(($(wc -l ${maxlist} | awk '{print $1}') - ${line} + 1)) ${maxlist} > tmp
  78                 cp tmp ${maxlist}
  79
  80                 max_t=$(wc -l ${maxtree} | awk '{printf $1}')
  81                 max_l=$(wc -l ${maxlist} | awk '{printf $1}')
  82                 line_t=$(awk -v val=${root} '$1==val {print NR}' ${maxtree})
  83                 head -$((${max_l} + ${line_t} - 1)) ${maxtree} | tail -$((${max_l} - 1)) > tmp
  84                 tail -$((${max_t} - ${max_l})) ${maxtree} > ${i}.tree
  85                 cp tmp ${maxtree}
  86         done
  87
  88         for (( i=1; i<={$divide}; i++ ))
  89         do
  90                 for data in $(awk '{print $1}' ${i}.lst)
  91                 do
  92                         cp ${data} ${data}${i}
  93                         cp ${data}.avg ${data}.avg${i}
  94                 done
  95         done
  96 End
  97
  98 Rule Refinement
  99         input '*.pad{$num}'.all
 100         input '*.avg{$num}'.all
 101         input '{$num}.lst'
 102         input '{$num}.tree'
 103         input 'Makefile.config'
 104         output ($I[1][1].str()+".pad.avg").d().all()
 105         output ($I[1][1].str()+".pad.avg.tiff").d().all()
 106         output ($I[1][1].str()+".pad.avg"+$num.str()+".tiff").d().all()
 107 Action
 108         max=$(wc -l {$num}.tree | awk '{printf $1}')
 109         data=$(head -1 {$num}.tree)
 110         i=$(echo ${data} | awk '{print $1}')
 111         name=$(basename $(awk -v i=${i} '$2==i {print $1}' {$num}.lst) ".pad")
 112         cp {$num}.lst ${name}.avglst
 113         cp {$num}.tree ${name}.tree
 114
 115         for (( k=1; k<=max ; k++ ))
 116         do
 117                 i=$(head -${k} {$num}.tree | tail -1 | awk '{print $1}')
 118                 name=$(basename $(awk -v i=${i} '$2==i {print $1}' {$num}.lst) ".pad")
 119
 120                 if [ $(wc -l ${name}.avglst | awk '{print $1}') -gt 2 ] ; then
 121                         tpos=$(awk -v i=${i} '$2==i {print NR}' ${name}.avglst)
 122                         tline=$(wc -l ${name}.avglst | awk '{print $1}')
 123
 124                         head -$((${tline} - ${tpos} + 1)) ${name}.tree | tail -$((${tline} - ${tpos})) > tmp
 125                         i_sub1=$(head -1 tmp | tail -1 | awk '{print $1}')
 126                         name_sub1=$(basename $(awk -v i=${i_sub1} '$2==i {print $1}' ${name}.avglst) ".pad")
 127                         if [ $(wc -l tmp | awk '{print $1}') -ne 0 ] ; then
 128                                 cp tmp ${name_sub1}.tree
 129                                 tail -$((${tline} - ${tpos} + 1)) ${name}.avglst > ${name_sub1}.avglst
 130                         fi
 131
 132                         tail -$((${tpos} - 2)) ${name}.tree > tmp
 133                         i_sub2=$(head -1 tmp | awk '{print $1}')
 134                         name_sub2=$(basename $(awk -v i=${i_sub2} '$2==i {print $1}' ${name}.avglst) ".pad")
 135                         if [ $(wc -l tmp | awk '{print $1}') -ne 0 ] ; then
 136                                 cp tmp ${name_sub2}.tree
 137                                 head -$((${tpos} - 1)) ${name}.avglst > ${name_sub2}.avglst
 138                         fi
 139                 fi
 140         done
 141
 142         cat Makefile.config | sed -e s/'='/' '/ > Makefile.config.tmp
 143         ClusterCorrelationMode=$(awk '$1=="ClusterCorrelationMode" {print $2}' Makefile.config.tmp)
 144         ClusterRotationRangeMin=$(awk '$1=="ClusterRotationRangeMin" {print $2}' Makefile.config.tmp)
 145         ClusterRotationRangeMax=$(awk '$1=="ClusterRotationRangeMax" {print $2}' Makefile.config.tmp)
 146         ClusterRotationRangePartitionNumber=$(awk '$1=="ClusterRotationRangePartitionNumber" {print $2}' Makefile.config.tmp)
 147         ClusterRotationIterationNumber=$(awk '$1=="ClusterRotationIterationNumber" {print $2}' Makefile.config.tmp)
 148         ClusterRotationCorrelationMode=$(awk '$1=="ClusterRotationCorrelationMode" {print $2}' Makefile.config.tmp)
 149
 150         for data in $(ls *.avglst)
 151         do
 152                 name=$(basename ${data} ".avglst")
 153                 awk '{print $1}' ${data} | sed -e s/.pad/.pad.fit/ > ${name}.fitlst
 154                 cp ${name}.pad.avg{$num} ${name}.pad.avg
 155                 for (( i=0; i < {$refine}; i++ ))
 156                 do
 157                         for element in $(awk '{print $1}' ${data})
 158                         do
 159                                 mrcImageAutoRotationCorrelation -i ${element}{$num} -r ${name}.pad.avg -fit ${element}.fit -cor ${element}.cor -O ${element}.corinfo \
 160                                                                                                 -Method ${ClusterRotationCorrelationMode} -m ${ClusterCorrelationMode} -Iter ${ClusterRotationIterationNumber} \
 161                                                                                                 -range ${ClusterRotationRangeMin} ${ClusterRotationRangeMax} -n ${ClusterRotationRangePartitionNumber}
 162                         done
 163
 164                         mrcImageAverage -i ${name}.fitlst -o ${name}.pad.avg
 165                 done
 166                 mrc2tiff -i ${name}.pad.avg -o ${name}.pad.avg.tiff
 167                 mrc2tiff -i ${name}.pad.avg{$num} -o ${name}.pad.avg{$num}.tiff
 168         done
 169 End
 170
 171 Rule RefinementRoot
 172         input '*.pad'.all
 173         input '*.pad.avg0'.all
 174         input ($I[2][1].str()+".avglst").d().all()
 175         input 'Makefile.config'
 176         output ($I[1][1].str()+".pad.avg").d().all()
 177         output ($I[1][1].str()+".pad.avg.tiff").d().all()
 178         output ($I[1][1].str()+".pad.avg0.tiff").d().all()
 179 Action
 180         cat Makefile.config | sed -e s/'='/' '/ > Makefile.config.tmp
 181         ClusterCorrelationMode=$(awk '$1=="ClusterCorrelationMode" {print $2}' Makefile.config.tmp)
 182         ClusterRotationRangeMin=$(awk '$1=="ClusterRotationRangeMin" {print $2}' Makefile.config.tmp)
 183         ClusterRotationRangeMax=$(awk '$1=="ClusterRotationRangeMax" {print $2}' Makefile.config.tmp)
 184         ClusterRotationRangePartitionNumber=$(awk '$1=="ClusterRotationRangePartitionNumber" {print $2}' Makefile.config.tmp)
 185         ClusterRotationIterationNumber=$(awk '$1=="ClusterRotationIterationNumber" {print $2}' Makefile.config.tmp)
 186         ClusterRotationCorrelationMode=$(awk '$1=="ClusterRotationCorrelationMode" {print $2}' Makefile.config.tmp)
 187
 188         for data in $(ls *.avglst)
 189         do
 190                 name=$(basename ${data} ".avglst")
 191                 awk '{print $1}' ${data} | sed -e s/.pad/.pad.fit/ > ${name}.fitlst
 192                 cp ${name}.pad.avg0 ${name}.pad.avg
 193                 for (( i=0; i < {$refine}; i++ ))
 194                 do
 195                         for element in $(awk '{print $1}' ${data})
 196                         do
 197                                 mrcImageAutoRotationCorrelation -i ${element} -r ${name}.pad.avg -fit ${element}.fit -cor ${element}.cor -O ${element}.corinfo \
 198                                                                                                 -Method ${ClusterRotationCorrelationMode} -m ${ClusterCorrelationMode} -Iter ${ClusterRotationIterationNumber} \
 199                                                                                                 -range ${ClusterRotationRangeMin} ${ClusterRotationRangeMax} -n ${ClusterRotationRangePartitionNumber}
 200                         done
 201
 202                         mrcImageAverage -i ${name}.fitlst -o ${name}.pad.avg
 203                 done
 204                 mrc2tiff -i ${name}.pad.avg -o ${name}.pad.avg.tiff
 205                 mrc2tiff -i ${name}.pad.avg0 -o ${name}.pad.avg0.tiff
 206         done
 207 End
 208
 209 Rule MontageAverage
 210         input 'all.avgsortlst'
 211         input 'all.treeinfo'
 212         input '*.pad.avg'.all
 213         output 'all.avgrefinemon'
 214         output 'all.avgrefinemon.tiff'
 215 Action
 216         root=$(head -1 {$I[2]} | awk '{print $1}')
 217         root_file=$(awk -v val=${root} '$2==val {print $1}' {$I[1]})
 218         cp ${root_file} $(head -1 {$I[1]} | awk '{print $1}')
 219         mrcImageMontageCreate -i {$I[1]} -o {$O[1]}
 220         mrc2tiff -i {$O[1]} -o {$O[2]}
 221 End
 222
 223 param $roi := false