Add: pione-pnml tutorial for Advanced1.(using mrc3Dto2D)

	new file:   SampleCode/PIONE-PNML/Advanced1/Initial.md
	new file:   SampleCode/PIONE-PNML/Advanced1/Initial.pione
	new file:   SampleCode/PIONE-PNML/Advanced1/Initial.pnml
	new file:   SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.md
	new file:   SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pione
	new file:   SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pnml
	new file:   SampleCode/PIONE-PNML/Advanced1/Ref3Dto2D.md
	new file:   SampleCode/PIONE-PNML/Advanced1/Ref3Dto2D.pnml

diff --git a/SampleCode/PIONE-PNML/Advanced1/Initial.md b/SampleCode/PIONE-PNML/Advanced1/Initial.md
new file mode 100644 (file)
index 0000000..e114231
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Initial.md
@@ -0,0 +1,23 @@
+# Initial.pione
+
+## Initial
+It brings ref3d files as Input.
+
+```
+       cp {$I[1]} {$O[1]};
+```
+
+## Angle
+It creates angle files.
+
+```
+for (( rot1 = 0; rot1 < 360; rot1 += 30 )) ; \
+do \
+       for (( rot2 = 0; rot2 < 360; rot2 += 30 )) ; \
+       do \
+               rot22=`expr $rot2 + 15`; \
+               echo "YOYS $rot1 $rot2 0" >> {$O[1]}; \
+               echo "YOYS $rot1 $rot22 0" >> {$O[2]}; \
+       done; \
+done;
+```
\ No newline at end of file

diff --git a/SampleCode/PIONE-PNML/Advanced1/Initial.pione b/SampleCode/PIONE-PNML/Advanced1/Initial.pione
new file mode 100644 (file)
index 0000000..e95fa98
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Initial.pione
@@ -0,0 +1,32 @@
+
+Rule Main
+  input '1VOM.mrc'
+  input '1VOM-N.mrc'
+  output '*.ref3d'
+  output '*.refangle'
+Flow
+  rule Angle
+  rule Initial
+End
+
+Rule Angle
+  output 'Angle2.refangle'
+  output 'Angle1.refangle'
+Action
+  for (( rot1 = 0; rot1 < 360; rot1 += 30 )) ; \
+  do \
+       for (( rot2 = 0; rot2 < 360; rot2 += 30 )) ; \
+       do \
+               rot22=`expr $rot2 + 15`; \
+               echo "YOYS $rot1 $rot2 0" >> {$O[1]}; \
+               echo "YOYS $rot1 $rot22 0" >> {$O[2]}; \
+       done; \
+  done;
+End
+
+Rule Initial
+  input '*.mrc'
+  output '{$*}.ref3d'
+Action
+       cp {$I[1]} {$O[1]};
+End

diff --git a/SampleCode/PIONE-PNML/Advanced1/Initial.pnml b/SampleCode/PIONE-PNML/Advanced1/Initial.pnml
new file mode 100644 (file)
index 0000000..4874223
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Initial.pnml
@@ -0,0 +1,370 @@
+<?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="p1">
+      <name>
+        <text>&lt;'1VOM.mrc'</text>
+        <graphics>
+          <offset x="20" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="20" y="20"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p2">
+      <name>
+        <text>'{$*}.ref3d'</text>
+        <graphics>
+          <offset x="290" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="290" y="20"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p3">
+      <name>
+        <text>&lt;'1VOM-N.mrc'</text>
+        <graphics>
+          <offset x="20" y="120"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="20" y="80"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p4">
+      <name>
+        <text>>'*.ref3d'</text>
+        <graphics>
+          <offset x="410" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="410" y="20"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p5">
+      <name>
+        <text>'*.mrc'</text>
+        <graphics>
+          <offset x="170" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="170" y="20"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p6">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="120" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="120" y="100"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p7">
+      <name>
+        <text>'Angle1.refangle'</text>
+        <graphics>
+          <offset x="300" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="300" y="100"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p8">
+      <name>
+        <text>'Angle2.refangle'</text>
+        <graphics>
+          <offset x="300" y="230"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="300" y="190"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p9">
+      <name>
+        <text>>'*.refangle'</text>
+        <graphics>
+          <offset x="450" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="450" y="100"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <transition id="t4">
+      <name>
+        <text>Angle</text>
+        <graphics>
+          <offset x="230" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="230" y="100"/>
+        <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="t5">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="390" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="390" y="100"/>
+        <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="t1">
+      <name>
+        <text>Initial</text>
+        <graphics>
+          <offset x="220" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="220" y="20"/>
+        <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="120" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="120" y="20"/>
+        <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="t3">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="350" y="60"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="350" y="20"/>
+        <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="a11" source="t4" target="p8">
+      <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="a10" source="p5" 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="a13" source="p8" target="t5">
+      <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="a12" source="p7" target="t5">
+      <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="a14" source="t5" target="p9">
+      <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="a1" source="t2" target="p6">
+      <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>
+    <arc id="a3" source="p6" target="t4">
+      <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="a4" source="t4" target="p7">
+      <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="a5" source="p1" target="t2">
+      <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="a6" source="p2" target="t3">
+      <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="a7" source="t3" target="p4">
+      <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="a8" source="p3" target="t2">
+      <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="a9" source="t2" target="p5">
+      <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="11" y="33"/>
+        <dimension x="755" y="474"/>
+      </bounds>
+      <scale>100</scale>
+      <treeWidthRight>561</treeWidthRight>
+      <overviewPanelVisible>true</overviewPanelVisible>
+      <treeHeightOverview>100</treeHeightOverview>
+      <treePanelVisible>true</treePanelVisible>
+      <verticalLayout>false</verticalLayout>
+      <resources/>
+      <simulations/>
+      <partnerLinks/>
+      <variables/>
+    </toolspecific>
+  </net>
+</pnml>
\ No newline at end of file

diff --git a/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.md b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.md
new file mode 100644 (file)
index 0000000..cafa050
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.md
@@ -0,0 +1,8 @@
+# Ref2DtoTiff.pione
+
+## Ref2DtoTiff
+Convert mrc 2D to tiff.
+
+```
+       mrc2tiff -i {$I[1]} -o {$O[1]};
+```

diff --git a/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pione b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pione
new file mode 100644 (file)
index 0000000..122d861
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pione
@@ -0,0 +1,14 @@
+
+Rule Main
+  input '*.ref2d'.all
+  output '*.tiff'
+Flow
+  rule Ref2DtoTiff
+End
+
+Rule Ref2DtoTiff
+  input '*.ref2d'
+  output '{$*}.tiff'
+Action
+       mrc2tiff -i {$I[1]} -o {$O[1]};
+End

diff --git a/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pnml b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pnml
new file mode 100644 (file)
index 0000000..0c01020
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Ref2DtoTiff.pnml
@@ -0,0 +1,188 @@
+<?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="p1">
+      <name>
+        <text>&lt;'*.ref2d'.all</text>
+        <graphics>
+          <offset x="30" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="30" y="70"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p2">
+      <name>
+        <text>'{$*}.tiff'</text>
+        <graphics>
+          <offset x="290" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="290" y="70"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p3">
+      <name>
+        <text>'*.ref2d'</text>
+        <graphics>
+          <offset x="150" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="160" y="70"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p4">
+      <name>
+        <text>>'*.tiff'</text>
+        <graphics>
+          <offset x="410" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="410" y="70"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <transition id="t1">
+      <name>
+        <text>Ref2DtoTiff</text>
+        <graphics>
+          <offset x="220" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="220" y="70"/>
+        <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="100" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="100" y="70"/>
+        <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="t3">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="350" y="110"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="350" y="70"/>
+        <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="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>
+    <arc id="a3" source="p1" target="t2">
+      <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="a4" source="t2" target="p3">
+      <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="a5" source="p3" 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="a6" source="p2" target="t3">
+      <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="a7" source="t3" target="p4">
+      <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="11" y="33"/>
+        <dimension x="755" y="474"/>
+      </bounds>
+      <scale>100</scale>
+      <treeWidthRight>561</treeWidthRight>
+      <overviewPanelVisible>true</overviewPanelVisible>
+      <treeHeightOverview>100</treeHeightOverview>
+      <treePanelVisible>true</treePanelVisible>
+      <verticalLayout>false</verticalLayout>
+      <resources/>
+      <simulations/>
+      <partnerLinks/>
+      <variables/>
+    </toolspecific>
+  </net>
+</pnml>
\ No newline at end of file

diff --git a/SampleCode/PIONE-PNML/Advanced1/Ref3Dto2D.md b/SampleCode/PIONE-PNML/Advanced1/Ref3Dto2D.md
new file mode 100644 (file)
index 0000000..8088c48
--- /dev/null
+++ b/SampleCode/PIONE-PNML/Advanced1/Ref3Dto2D.md
@@ -0,0 +1,26 @@
+# Ref3Dto2D.pione
+
+## Ref3Dto2D
+Projection 3D to 2D depending on an angle.
+
+```
+num=1;
+while [ "$line" != "$(tail -1 {$I[1]})" ] ; \
+do \
+       line=$(head -$num {$I[1]} | tail -1); \
+       EA=$(echo $line | awk '{printf("%s", $1)}'); \
+       ROT1=$(echo $line | awk '{printf("%s", $2)}'); \
+       ROT2=$(echo $line | awk '{printf("%s", $3)}'); \
+       ROT3=$(echo $line | awk '{printf("%s", $4)}'); \
+       mrc3Dto2D -i {$I[2]} \
+                               -o "{$I[2][1]}-{$I[1][1]}-$num.ref2d" \
+                               -EulerMode $EA \
+                               -Rot1 $ROT1 $ROT1 1 \
+                               -Rot2 $ROT2 $ROT2 1 \
+                               -Rot3 $ROT3 $ROT3 1; \
+       if [ -z "$line" ] ; then \
+               break; \
+       fi; \
+       num=`expr $num + 1`; \
+done;
+```

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