pione 0.4.2 → 0.5.0.alpha.1

checksums.yaml

@@ -1,15 +1,15 @@
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data/.travis.yml

@@ -4,7 +4,7 @@ rvm:
 #  - "2.0.0" # pione doesn't work with 2.0
 #  - jruby-19mode
 #  - rbx-19mode # pione doesn't work with 2.0
-script: rake test
+script: rake -I lib test
 
 env:
   global:

data/History.txt

@@ -1,5 +1,11 @@
 # History
 
+## 0.5.0
+
+* Improved PNML compiler.
+* Fixed many bugs.
+* More readable error messages.
+
 ## 0.4.2(2014/9/1)
 
 * Enable to compile PNML with action documents.

data/example/ActionError/ActionError.action.md

@@ -0,0 +1,11 @@
+# Actions for ActionError package
+
+## Error
+
+This action cause an error because of nonexistance of file "hoge.sh" when the
+rule is processed.
+
+```
+sleep 3
+hoge.sh > o1
+```

data/example/ActionError/ActionError.pione

@@ -1,7 +1,10 @@
-.@ PackageName :: "ActionError"
+Rule ActionError
+  output 'o1'
+Flow
+  rule Error
+End
 
-Rule Main
-  input null
+Rule Error
   output 'o1'
 Action
   sleep 3

data/example/ActionError/ActionError.pnml

@@ -0,0 +1,86 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--PLEASE DO NOT EDIT THIS FILE
+Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
+<pnml>
+  <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
+    <place id="p2">
+      <name>
+        <text>>'o1'</text>
+        <graphics>
+          <offset x="320" y="260"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="320" y="220"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p1">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="110" y="260"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="110" y="220"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <transition id="t1">
+      <name>
+        <text>Error</text>
+        <graphics>
+          <offset x="220" y="260"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="220" y="220"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <arc id="a1" source="p1" target="t1">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a2" source="t1" target="p2">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <toolspecific tool="WoPeD" version="1.0">
+      <bounds>
+        <position x="2" y="22"/>
+        <dimension x="1905" y="784"/>
+      </bounds>
+      <scale>100</scale>
+      <treeWidthRight>1551</treeWidthRight>
+      <overviewPanelVisible>true</overviewPanelVisible>
+      <treeHeightOverview>100</treeHeightOverview>
+      <treePanelVisible>true</treePanelVisible>
+      <verticalLayout>false</verticalLayout>
+      <resources/>
+      <simulations/>
+      <partnerLinks/>
+      <variables/>
+    </toolspecific>
+  </net>
+</pnml>

data/example/ActionError/Package.pione

@@ -0,0 +1,2 @@
+.@ PackageName :: "ActionError"
+.@ Entrance :: ActionError

data/example/ActionError/pione-package.json

@@ -4,12 +4,16 @@
 
   ],
   "Documents": [
-    "ActionError.pione"
+    "ActionError.pione",
+    "Package.pione"
   ],
   "Scenarios": [
 
   ],
   "Bins": [
 
+  ],
+  "Etcs": [
+
   ]
 }

data/example/CTFCorrection/CTFCorrection.action.md

@@ -0,0 +1,46 @@
+# Actions for CTFCorrection package
+
+## Tiff2Mrc
+
+```
+tiff2mrc -i {$I[1]} -o {$O[1]}.mrc -r {$RESOLUTION} -m {$TIFF2MRC_m} -Offset {$TIFF2MRC_Offset}
+```
+
+## Mrc2Cen
+
+```
+mrcImageCenterGet -i {$I[1]} -o {$O[1]} -Nx {$MRC_IMAGE_CENTER_Nx} -Ny {$MRC_IMAGE_CENTER_Ny}
+```
+
+## Cen2Nor
+
+```
+mrcImageAbnormalValueRemove -i {$I[1]} -o {$O[1]} -u {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_MAX} {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_HALF} -m {$MRC_IMAGE_ABNORMAL_VALUE_REMOVE_m}
+```
+
+## Nor2Fft
+
+```
+mrcImageFFT -i {$I[1]} -o {$O[1]}
+```
+
+## Fft2Ctfinfo
+
+```
+ctfDetermine -i {$I[1]} -o {$O[1]} -D {$MRC_DETERMINE_D} -m {$MRC_DETERMINE_m} -CutLow {$MRC_DETERMINE_CutLow} -CutHigh {$MRC_DETERMINE_CutHigh} -d {$MRC_DETERMINE_d} -Cc {$CTF_DETERMINE_Cc} -Cs {$CTF_DETERMINE_Cs}
+```
+
+## Ctfinfo2Ctf
+
+### inputs
+
+1. input '*.fft'
+2. input '{$*}.ctfinfo'
+
+### action
+
+```
+mv {$I[2]} {$I[2]}.tmp2
+grep .: {$I[2]}.tmp2 > {$I[2]}
+mrcImageCTFCompensation -i {$I[1]} -info2 {$I[2]} -o {$O[1]} -m {$MRC_IMAGE_CTF_COMPENSATION_m}
+```

data/example/CTFCorrection/CTFCorrection.pione

@@ -1,49 +1,13 @@
-Basic Param
-  $RESOLUTION := 3.80 # tiff2mrc -r
-  $CTF_DETERMINE_Cc := 0.7 # ctfDetermine -Cc
-  $CTF_DETERMINE_Cs := 2.1 # ctfDetermine -Cs
-End
-
-Advanced Param
-  $TIFF2MRC_m := 0
-  $TIFF2MRC_Offset := 0.0
-  $MRC_IMAGE_CENTER_Nx := 1000 # FIXME
-  $MRC_IMAGE_CENTER_Ny := 1000 # FIXME
-  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_MAX := 65535
-  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_HALF := 16384
-  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_m := 1
-  $MRC_DETERMINE_D := 50000
-  $MRC_DETERMINE_m := 128
-  $MRC_DETERMINE_CutLow := 0.025
-  $MRC_DETERMINE_CutHigh := 0.15
-  $MRC_DETERMINE_d := 3
-  $MRC_IMAGE_CTF_COMPENSATION_m := 1
-End
-
-Rule Main
-  input ('*.tif' or '*.mrc').all
+Rule CTFCorrection
+  input '*.tif'.all or '*.mrc'.all
   output '*.ctf'.all
 Flow
-  rule Tiff2Mrc
-  rule Mrc2Cen
   rule Cen2Nor
   rule Nor2Fft
   rule Fft2Ctfinfo
   rule Ctfinfo2Ctf
-End
-
-Rule Tiff2Mrc
-  input '*.tif'
-  output '{$*}.mrc'
-Action
-  tiff2mrc -i {$I[1]} -o {$O[1]}.mrc -r {$RESOLUTION} -m {$TIFF2MRC_m} -Offset {$TIFF2MRC_Offset}
-End
-
-Rule Mrc2Cen
-  input '*.mrc'
-  output '{$*}.cen'
-Action
-  mrcImageCenterGet -i {$I[1]} -o {$O[1]} -Nx {$MRC_IMAGE_CENTER_Nx} -Ny {$MRC_IMAGE_CENTER_Ny}
+  rule Tiff2Mrc
+  rule Mrc2Cen
 End
 
 Rule Cen2Nor
@@ -75,4 +39,18 @@ Action
   mv {$I[2]} {$I[2]}.tmp2
   grep .: {$I[2]}.tmp2 > {$I[2]}
   mrcImageCTFCompensation -i {$I[1]} -info2 {$I[2]} -o {$O[1]} -m {$MRC_IMAGE_CTF_COMPENSATION_m}
-End
+End
+
+Rule Tiff2Mrc
+  input '*.tif'
+  output '{$*}.mrc'
+Action
+  tiff2mrc -i {$I[1]} -o {$O[1]}.mrc -r {$RESOLUTION} -m {$TIFF2MRC_m} -Offset {$TIFF2MRC_Offset}
+End
+
+Rule Mrc2Cen
+  input '*.mrc'
+  output '{$*}.cen'
+Action
+  mrcImageCenterGet -i {$I[1]} -o {$O[1]} -Nx {$MRC_IMAGE_CENTER_Nx} -Ny {$MRC_IMAGE_CENTER_Ny}
+End

data/example/CTFCorrection/CTFCorrection.pnml

@@ -0,0 +1,839 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--PLEASE DO NOT EDIT THIS FILE
+Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
+<pnml>
+  <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
+    <place id="p7">
+      <name>
+        <text>'*.mrc'</text>
+        <graphics>
+          <offset x="690" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="690" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p6">
+      <name>
+        <text>'{$*}.cen'</text>
+        <graphics>
+          <offset x="830" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="830" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p5">
+      <name>
+        <text>'*.tif'</text>
+        <graphics>
+          <offset x="410" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="410" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p4">
+      <name>
+        <text>'{$*}.mrc'</text>
+        <graphics>
+          <offset x="550" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="550" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p3">
+      <name>
+        <text>&lt;'*.tif'.all or '*.mrc'.all</text>
+        <graphics>
+          <offset x="270" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="270" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p2">
+      <name>
+        <text>'*.mrc'</text>
+        <graphics>
+          <offset x="110" y="380"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="110" y="340"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <initialMarking>
+        <text>1</text>
+      </initialMarking>
+    </place>
+    <place id="p1">
+      <name>
+        <text>'*.tif'</text>
+        <graphics>
+          <offset x="110" y="240"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="110" y="200"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p9">
+      <name>
+        <text>'{$*}.nor'</text>
+        <graphics>
+          <offset x="1110" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="1110" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p8">
+      <name>
+        <text>'*.cen'</text>
+        <graphics>
+          <offset x="970" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="970" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p10">
+      <name>
+        <text>'*.nor'</text>
+        <graphics>
+          <offset x="190" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="190" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p18">
+      <name>
+        <text>>'*.ctf'.all</text>
+        <graphics>
+          <offset x="1030" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="1030" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p17">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="610" y="420"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="605" y="378"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p16">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="600" y="480"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="600" y="443"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p15">
+      <name>
+        <text>'{$*}.ctf'</text>
+        <graphics>
+          <offset x="890" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="890" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p13">
+      <name>
+        <text>'{$*}.ctfinfo'</text>
+        <graphics>
+          <offset x="750" y="420"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="750" y="380"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p12">
+      <name>
+        <text>'*.fft'</text>
+        <graphics>
+          <offset x="470" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="470" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p11">
+      <name>
+        <text>'{$*}.fft'</text>
+        <graphics>
+          <offset x="330" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="330" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <transition id="t3">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="190" y="380"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="190" y="340"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t2">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="190" y="240"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="190" y="200"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t10">
+      <name>
+        <text>Cen2Nor</text>
+        <graphics>
+          <offset x="1040" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="1040" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t11">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="110" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="110" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t12">
+      <name>
+        <text>Nor2Fft</text>
+        <graphics>
+          <offset x="260" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="260" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t13">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="400" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="400" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t14">
+      <name>
+        <text>Fft2Ctfinfo</text>
+        <graphics>
+          <offset x="670" y="420"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="670" y="380"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t16">
+      <name>
+        <text>Ctfinfo2Ctf</text>
+        <graphics>
+          <offset x="820" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="820" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t17">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="540" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="540" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t19">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="960" y="460"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="960" y="420"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t4">
+      <name>
+        <text>Tiff2Mrc</text>
+        <graphics>
+          <offset x="480" y="310"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="480" y="270"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
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