pione 0.1.0 → 0.1.1

data/History.txt

@@ -0,0 +1,13 @@
+# History
+
+## 0.1.1
+
+* Improved performance
+* Added the concept of document parameter
+* Added --list-params option
+* Fixed bugs of features handling
+* Improved comment parser
+
+## 0.1.0
+
+* First gem release

data/Rakefile

@@ -3,13 +3,13 @@ require "bundler/gem_tasks"
 $stand_alone = "bin/pione-client --stand-aline"
 
 desc 'generate HTML API documentation'
-task :html do
-  sh "yard doc -o html --hide-void-return --no-api --private"
+task 'html' do
+  sh 'bundle exec yard doc -o html --hide-void-return --no-api --private'
 end
 
 desc 'Show undocumented function list'
 task 'html:undoc' do
-  sh 'yard stats --list-undoc --no-api --private'
+  sh 'bundle exec yard stats --list-undoc --no-api --private'
 end
 
 desc 'count characters in input direcotry'

data/example/DeferredChoice/DeferredChoice.pione

@@ -0,0 +1,50 @@
+Rule Main
+  output 'result.txt'
+  param $DIALOG := "zenity"
+Flow
+  rule UserSelect.params({DIALOG: $DIALOG})
+  rule A
+  rule B
+  rule C
+End
+
+Rule UserSelect
+  output 'a.txt:b.txt:c.txt'
+  param $DIALOG
+  feature +Interactive
+Action
+  if [ "{$DIALOG}" = "zenity" ]
+  then
+    zenity --list --title "select action" --column rule "rule A" "rule B" "rule C" > rule.txt
+  else
+    xmessage -print -center -buttons "rule A,rule B,rule C" "select action" > rule.txt
+  fi
+  RULE=`cat rule.txt`
+  case "$RULE" in
+    "rule A") touch a.txt ;;
+    "rule B") touch b.txt ;;
+    "rule C") touch c.txt ;;
+  esac
+End
+
+Rule A
+  input 'a.txt'
+  output 'result.txt'
+Action
+  echo 'You selected rule A' > {$O[1]}
+End
+
+Rule B
+  input 'b.txt'
+  output 'result.txt'
+Action
+  echo 'You selected rule B' > {$O[1]}
+End
+
+Rule C
+  input 'c.txt'
+  output 'result.txt'
+Action
+  echo 'You selected rule C' > {$O[1]}
+End
+

data/example/Fib/Fib.pione

@@ -1,9 +1,10 @@
+param $NUM := 3
+
 Rule Main
   output 'result.txt'
-  param $NUM := 3
 Flow
-  rule Fib
-  rule Result
+  rule Fib.params({N: $NUM})
+  rule Result.params({N: $NUM})
 End
 
 Rule Fib0
@@ -19,38 +20,38 @@ Action
 End
 
 Rule Fib
-  output 'fib{$NUM}.txt'
-  param $NUM
+  output 'fib{$N}.txt'
+  param $N
 Flow
-  case $NUM
+  case $N
   when 0
     rule Fib0
   when 1
     rule Fib1
   else
-    $P1 := $NUM - 2
-    $P2 := $NUM - 1
-    rule Fib.params({NUM: $P1})
-    rule Fib.params({NUM: $P2})
-    rule Calc.params({NUM: $NUM, P1: $P1, P2: $P2})
+    $P1 := $N - 2
+    $P2 := $N - 1
+    rule Fib.params({N: $P1})
+    rule Fib.params({N: $P2})
+    rule Calc.params({N: $N, P1: $P1, P2: $P2})
   end
 End
 
 Rule Calc
   input 'fib{$P1}.txt'
   input 'fib{$P2}.txt'
-  output 'fib{$NUM}.txt'
-  param $NUM
+  output 'fib{$N}.txt'
+  param $N
   param $P1
   param $P2
 Action
-  expr `cat {$I[1]}` + `cat {$I[2]}` > {$O[1]}
+  echo "`cat {$I[1]}` + `cat {$I[2]}`" | bc > {$O[1]}
 End
 
 Rule Result
-  input 'fib{$NUM}.txt'
+  input 'fib{$N}.txt'
   output 'result.txt'
-  param $NUM
+  param $N
 Action
   cat {$I[1]} > {$O[1]}
 End

data/example/SingleParticlesWithRef/SingleParticlesWithRef.Display2.pione

@@ -0,0 +1,128 @@
+#
+# Eos for 3D reconstrucion from 2D rois using 3D initail reference
+#
+
+#
+# Variables
+#
+
+# Target structure name
+$TARGET := "all"
+
+#
+# Search Area for 3D
+#
+
+# Rot1
+$ROT1MIN := 0
+$ROT1MAX := 359
+$ROT1D   := 30
+$nRot1   := 12
+
+# Rot2
+$ROT2MIN := 0
+$ROT2MAX := 359
+$ROT2D   := 30
+$nRot2   := 12
+
+# Rot3
+$ROT3MIN := 0
+$ROT3MAX := 0
+$ROT3D   := 30
+$nRot3   := 1
+
+# For 2D
+$STEP   := 12
+$ROTMIN := 0
+$ROTMAX := 359
+$nROT   := 360 / $STEP
+
+# Pad size for 2D
+$PAD_W := 64
+$PAD_H := 64
+
+#
+# Rules
+#
+
+Rule Main
+  input '*.roi'.all
+  input '{$TARGET}.ref3d'
+  input '{$TARGET}.ref2d'
+  output '{$TARGET}.3d'
+  output 'checked'
+Flow
+  rule Create3dinfo
+  rule Create3dlst
+  rule Create3d
+  rule ShowResult
+End
+
+Rule Create3dinfo
+  input '*.roi'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+  output '{$*}.3dinfo'
+Flow
+  rule ConvertRoiToPad
+  rule ConvertPadToCorinfo
+  rule ConvertCorinfoTo3dinfo
+End
+
+# .roi.pad
+Rule ConvertRoiToPad
+  input '*.roi'
+  output '{$*}.pad'
+Action
+  mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
+  mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
+  mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
+End
+
+# .pad.corinfo
+Rule ConvertPadToCorinfo
+  input '*.pad'
+  input '{$TARGET}.ref2d'
+  output '{$*}.corinfo'
+  output '{$*}.fit'
+Action
+  mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
+End
+
+# .corinfo.3dinfo
+Rule ConvertCorinfoTo3dinfo
+  input '*.corinfo'
+  output '{$*}.3dinfo'
+Action
+  awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
+  head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
+End
+
+# .3dinfo.3dlst
+Rule Create3dlst
+  input '*.3dinfo'.all
+  output '{$TARGET}.3dlst'
+Action
+  cat {$I[1].join(" ")} | sort > {$TARGET}.3dlst
+End
+
+# .3dlst.3d
+Rule Create3d
+  input '{$TARGET}.3dlst'
+  input '*.fit'.all
+  output '{$TARGET}.3d'
+Action
+  mrc2Dto3D -I {$TARGET}.3dlst -o {$TARGET}.3d -InterpolationMode 2 -Double -DoubleCounter {$TARGET}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
+End
+
+# show result by Display2
+Rule ShowResult
+  input '{$TARGET}.3d'
+  output 'checked'
+  feature +Interactive
+Action
+  Display2 -i '{$TARGET}.3d'
+  echo "I checked the result." > checked
+End
+

data/lib/pione.rb

@@ -29,6 +29,7 @@ require 'ostruct'
 require 'net/ftp'
 require 'highline'
 require 'dropbox_sdk'
+require 'naming'
 
 #
 # load pione

data/lib/pione/agent/broker.rb

@@ -106,7 +106,7 @@ module Pione
 
         # Return excess number of workers belongs to this broker.
         def excess_task_workers
-          @task_worker_resource - @task_workers.size
+          @task_worker_resource - @task_workers.size - @spawnings
         end
 
         # Return task wainting workers.
@@ -128,7 +128,14 @@ module Pione
         def create_task_worker(tuple_space_server)
           connection_id = Util.generate_uuid
           @assignment_table[connection_id] = tuple_space_server
-          Agent[:task_worker].spawn(Global.front, connection_id)
+          Thread.new do
+            begin
+              @spawnings += 1
+              Agent[:task_worker].spawn(Global.front, connection_id, @features)
+            ensure
+              @spawnings -= 1
+            end
+          end
         end
 
         # Deletes unavilable tuple space servers.
@@ -197,8 +204,11 @@ module Pione
       attr_reader :tuple_space_servers
       attr_reader :task_worker_resource
 
+      # current spawning task worker number
+      attr_reader :spawnings
+
       # @api private
-      def initialize(data={})
+      def initialize(features, data={})
         super()
         @task_workers = []
         @tuple_space_servers = []
@@ -206,6 +216,8 @@ module Pione
         @sleeping_time = data[:sleeping_time] || 1
         @assignment_table = {}
         @tuple_space_server_lock = Mutex.new
+        @spawnings = 0
+        @features = features
 
         # balancer
         @balancer = EasyBalancer.new(self)
@@ -265,7 +277,9 @@ module Pione
 
       # Transits to the state +sleeping+.
       def transit_to_sleeping
-        sleep 1
+        if @tuple_space_servers.size == 0 or excess_task_workers == 0
+          sleep 1
+        end
       end
     end
 

data/lib/pione/agent/task-worker.rb

@@ -25,28 +25,26 @@ module Pione
       # @return [Thread]
       #   worker monitor thread
       def self.spawn(front, connection_id, features=nil)
-        @mutex.synchronize do
-          args = [
-            "pione-task-worker",
-            "--parent-front", Global.front.uri,
-            "--connection-id", connection_id
-          ]
-          args << "--debug" if Pione.debug_mode?
-          args << "--show-communication" if Global.show_communication
-          args << "--features" << features if features
-          pid = Process.spawn(*args)
-          thread = Process.detach(pid)
-          # connection check
-          while thread.alive?
-            break if front.task_worker_front_connection_id.include?(connection_id)
-            sleep 0.1
-          end
-          # error check
-          unless thread.alive?
-            Process.abort("You cannot run pione-task-worker.")
-          end
-          return thread
+        args = [
+          "pione-task-worker",
+          "--parent-front", Global.front.uri,
+          "--connection-id", connection_id
+        ]
+        args << "--debug" if Pione.debug_mode?
+        args << "--show-communication" if Global.show_communication
+        args << "--features" << features if features
+        pid = Process.spawn(*args)
+        thread = Process.detach(pid)
+        # connection check
+        while thread.alive?
+          break if front.task_worker_front_connection_id.include?(connection_id)
+          sleep 0.1
+        end
+        # error check
+        unless thread.alive?
+          Process.abort("You cannot run pione-task-worker.")
         end
+        return thread
       end
 
       define_state :task_waiting

data/lib/pione/command-option/task-worker-owner-option.rb

@@ -9,7 +9,7 @@ module Pione
       end
 
       # --features
-      define_option('--features="FEATURES"', 'set features') do |features|
+      define_option('--features=FEATURES', 'set features') do |features|
         @features = features
       end
     end

data/lib/pione/command/basic-command.rb

@@ -25,13 +25,18 @@ module Pione
     end
 
     module InstanceInterface
-      # Returns program name.
-      # @return [String]
-      #   program name
-      def program_name
-        name, b = self.class.program_name
-        tail = self.instance_exec(&b)
-        "%s %s" % [name, tail]
+      # Setup program name. If the setup process is failed, program name is not
+      # changed.
+      #
+      # @return [void]
+      def setup_program_name
+        begin
+          name, b = self.class.program_name
+          tail = self.instance_exec(&b)
+          $PROGRAM_NAME = "%s %s" % [name, tail]
+        rescue Exception
+          nil
+        end
       end
 
       # Returns program message.
@@ -65,7 +70,7 @@ module Pione
         parse_options
         validate_options
         prepare
-        $PROGRAM_NAME = program_name
+        setup_program_name
         start
       end
 

data/lib/pione/command/front-owner-command.rb

@@ -11,7 +11,7 @@ module Pione
         validate_options
         setup_front
         prepare
-        $PROGRAM_NAME = program_name
+        setup_program_name
         start
       end
 

data/lib/pione/command/pione-broker.rb

@@ -16,6 +16,7 @@ TXT
 
       def initialize
         @task_worker = [Util.core_number - 1, 1].max
+        @features = nil
       end
 
       def create_front
@@ -30,7 +31,7 @@ TXT
 
       def prepare
         super
-        @broker = Pione::Agent[:broker].new(task_worker_resource: @task_worker)
+        @broker = Pione::Agent[:broker].new(@features, task_worker_resource: @task_worker)
         @tuple_space_receiver = Pione::TupleSpaceReceiver.instance
       end