pione 0.4.2 → 0.5.0.alpha.1

data/example/SingleParticlesWithRef/Package.pione

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+#
+# 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

data/example/SingleParticlesWithRef/SingleParticlesWithRef.action.md

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+# Actions for SingleParticlesWithRef package
+
+## ConvertRoiToPad
+
+```
+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
+```
+
+## ConvertPadToCorinfo
+
+```
+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
+```
+
+## ConvertCorinfoTo3dinfo
+
+```
+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
+```
+
+## Create3dlst
+
+```
+cat {$I[1].as_string.join(" ")} | sort > {$TARGET}.3dlst
+```
+
+## Create3d
+
+```
+mrc2Dto3D -I {$TARGET}.3dlst -o {$TARGET}.3d -InterpolationMode 2 -Double -DoubleCounter {$TARGET}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
+```

data/example/SingleParticlesWithRef/SingleParticlesWithRef.pnml

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+<?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">
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+        <graphics>
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+      </name>
+      <graphics>
+        <position x="550" y="260"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p6">
+      <name>
+        <text>'{$*}.fit'</text>
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+        </graphics>
+      </name>
+      <graphics>
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+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p4">
+      <name>
+        <text>'*.roi'</text>
+        <graphics>
+          <offset x="390" y="220"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="390" y="180"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p3">
+      <name>
+        <text>&lt;'{$TARGET}.ref2d'</text>
+        <graphics>
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+        </graphics>
+      </name>
+      <graphics>
+        <position x="390" y="260"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <initialMarking>
+        <text>1</text>
+      </initialMarking>
+    </place>
+    <place id="p1">
+      <name>
+        <text>&lt;'*.roi'.all</text>
+        <graphics>
+          <offset x="230" y="220"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="230" y="180"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <initialMarking>
+        <text>1</text>
+      </initialMarking>
+    </place>
+    <place id="p10">
+      <name>
+        <text>'{$TARGET}.3dlst'</text>
+        <graphics>
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+        </graphics>
+      </name>
+      <graphics>
+        <position x="870" y="260"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p9">
+      <name>
+        <text>'*.fit'.all</text>
+        <graphics>
+          <offset x="870" y="220"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="870" y="180"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p8">
+      <name>
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+        </graphics>
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+      <graphics>
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+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p11">
+      <name>
+        <text>>'{$TARGET}.3d'</text>
+        <graphics>
+          <offset x="1030" y="260"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="1030" y="220"/>
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+      </graphics>
+    </place>
+    <transition id="t3">
+      <name>
+        <text/>
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+      <graphics>
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+      <graphics>
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+        <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>extern Create3dinfo</text>
+        <graphics>
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+        </graphics>
+      </name>
+      <graphics>
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+      </toolspecific>
+    </transition>
+    <transition id="t4">
+      <name>
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+        <graphics>
+          <offset x="790" y="300"/>
+        </graphics>
+      </name>
+      <graphics>
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+        </graphics>
+      </name>
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+      <simulations/>
+      <partnerLinks/>
+      <variables/>
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