This repository is for tutorials of Eos.
Revisión | 34c3378beb409e2d86fd188e798a5b5660974b28 (tree) |
---|---|
Tiempo | 2014-11-04 15:28:18 |
Autor | kinoshita-eos <kinoshita@yasu...> |
Commiter | kinoshita-eos |
Add: tutorial for PIONE-PNML
new file: SampleCode/PIONE-PNML/Basic1/HelloWorld.md
new file: SampleCode/PIONE-PNML/Basic1/HelloWorld.pnml
new file: SampleCode/PIONE-PNML/Basic2/Serial2.md
new file: SampleCode/PIONE-PNML/Basic2/Serial2.pnml
new file: SampleCode/PIONE-PNML/Basic2/SerialInput/test1.in
new file: SampleCode/PIONE-PNML/Basic2/SerialInput/test2.in
new file: SampleCode/PIONE-PNML/Basic2/SerialInput/test3.in
new file: SampleCode/PIONE-PNML/Basic2/SerialInput/test4.in
new file: SampleCode/PIONE-PNML/Basic2/SerialInput/test5.in
Add: tutorial for PIONE
new file: SampleCode/PIONE/Advanced1/CenterGet.pione
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1 | +# HelloWorld.pione ## Hello Here, you can write Comment. ``` echo "Hello PIONE world !" > {$O[1]} ``` | |
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1 | +<?xml version="1.0" encoding="UTF-8"?> | |
2 | +<!--PLEASE DO NOT EDIT THIS FILE | |
3 | +Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)--> | |
4 | +<pnml> | |
5 | + <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID"> | |
6 | + <place id="p3"> | |
7 | + <name> | |
8 | + <text>>'message.txt'</text> | |
9 | + <graphics> | |
10 | + <offset x="400" y="90"/> | |
11 | + </graphics> | |
12 | + </name> | |
13 | + <graphics> | |
14 | + <position x="420" y="50"/> | |
15 | + <dimension x="40" y="40"/> | |
16 | + </graphics> | |
17 | + </place> | |
18 | + <transition id="t2"> | |
19 | + <name> | |
20 | + <text>Hello</text> | |
21 | + <graphics> | |
22 | + <offset x="270" y="90"/> | |
23 | + </graphics> | |
24 | + </name> | |
25 | + <graphics> | |
26 | + <position x="270" y="50"/> | |
27 | + <dimension x="40" y="40"/> | |
28 | + </graphics> | |
29 | + <toolspecific tool="WoPeD" version="1.0"> | |
30 | + <time>0</time> | |
31 | + <timeUnit>1</timeUnit> | |
32 | + <orientation>1</orientation> | |
33 | + </toolspecific> | |
34 | + </transition> | |
35 | + <arc id="a3" source="t2" target="p3"> | |
36 | + <inscription> | |
37 | + <text>1</text> | |
38 | + </inscription> | |
39 | + <graphics/> | |
40 | + <toolspecific tool="WoPeD" version="1.0"> | |
41 | + <probability>1.0</probability> | |
42 | + <displayProbabilityOn>false</displayProbabilityOn> | |
43 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
44 | + </toolspecific> | |
45 | + </arc> | |
46 | + <toolspecific tool="WoPeD" version="1.0"> | |
47 | + <bounds> | |
48 | + <position x="11" y="33"/> | |
49 | + <dimension x="755" y="474"/> | |
50 | + </bounds> | |
51 | + <scale>100</scale> | |
52 | + <treeWidthRight>597</treeWidthRight> | |
53 | + <overviewPanelVisible>true</overviewPanelVisible> | |
54 | + <treeHeightOverview>100</treeHeightOverview> | |
55 | + <treePanelVisible>true</treePanelVisible> | |
56 | + <verticalLayout>false</verticalLayout> | |
57 | + <resources/> | |
58 | + <simulations/> | |
59 | + <partnerLinks/> | |
60 | + <variables/> | |
61 | + </toolspecific> | |
62 | + </net> | |
63 | +</pnml> | |
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1 | +# Serial2.pione | |
2 | + | |
3 | +## First | |
4 | +Multiply 2 to all input data. | |
5 | + | |
6 | +``` | |
7 | +awk '{print $1*2}' {$I[1]} > {$O[1]} | |
8 | +``` | |
9 | + | |
10 | +## Second | |
11 | +Add 1 to all input data. | |
12 | + | |
13 | +``` | |
14 | +awk '{print $1+1}' {$I[1]} > {$O[1]} | |
15 | +``` |
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1 | +<?xml version="1.0" encoding="UTF-8"?> | |
2 | +<!--PLEASE DO NOT EDIT THIS FILE | |
3 | +Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)--> | |
4 | +<pnml> | |
5 | + <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID"> | |
6 | + <place id="p1"> | |
7 | + <name> | |
8 | + <text><'*.in'</text> | |
9 | + <graphics> | |
10 | + <offset x="10" y="60"/> | |
11 | + </graphics> | |
12 | + </name> | |
13 | + <graphics> | |
14 | + <position x="10" y="20"/> | |
15 | + <dimension x="40" y="40"/> | |
16 | + </graphics> | |
17 | + </place> | |
18 | + <place id="p3"> | |
19 | + <name> | |
20 | + <text>'{$*}.out'</text> | |
21 | + <graphics> | |
22 | + <offset x="410" y="60"/> | |
23 | + </graphics> | |
24 | + </name> | |
25 | + <graphics> | |
26 | + <position x="410" y="20"/> | |
27 | + <dimension x="40" y="40"/> | |
28 | + </graphics> | |
29 | + </place> | |
30 | + <place id="p4"> | |
31 | + <name> | |
32 | + <text>'*.route'</text> | |
33 | + <graphics> | |
34 | + <offset x="260" y="60"/> | |
35 | + </graphics> | |
36 | + </name> | |
37 | + <graphics> | |
38 | + <position x="270" y="20"/> | |
39 | + <dimension x="40" y="40"/> | |
40 | + </graphics> | |
41 | + </place> | |
42 | + <place id="p5"> | |
43 | + <name> | |
44 | + <text>'{$*}.route'</text> | |
45 | + <graphics> | |
46 | + <offset x="130" y="60"/> | |
47 | + </graphics> | |
48 | + </name> | |
49 | + <graphics> | |
50 | + <position x="140" y="20"/> | |
51 | + <dimension x="40" y="40"/> | |
52 | + </graphics> | |
53 | + </place> | |
54 | + <place id="p6"> | |
55 | + <name> | |
56 | + <text>>'*.out'</text> | |
57 | + <graphics> | |
58 | + <offset x="530" y="60"/> | |
59 | + </graphics> | |
60 | + </name> | |
61 | + <graphics> | |
62 | + <position x="530" y="20"/> | |
63 | + <dimension x="40" y="40"/> | |
64 | + </graphics> | |
65 | + </place> | |
66 | + <transition id="t6"> | |
67 | + <name> | |
68 | + <text/> | |
69 | + <graphics> | |
70 | + <offset x="200" y="60"/> | |
71 | + </graphics> | |
72 | + </name> | |
73 | + <graphics> | |
74 | + <position x="200" y="20"/> | |
75 | + <dimension x="40" y="40"/> | |
76 | + </graphics> | |
77 | + <toolspecific tool="WoPeD" version="1.0"> | |
78 | + <time>0</time> | |
79 | + <timeUnit>1</timeUnit> | |
80 | + <orientation>1</orientation> | |
81 | + </toolspecific> | |
82 | + </transition> | |
83 | + <transition id="t7"> | |
84 | + <name> | |
85 | + <text/> | |
86 | + <graphics> | |
87 | + <offset x="470" y="60"/> | |
88 | + </graphics> | |
89 | + </name> | |
90 | + <graphics> | |
91 | + <position x="470" y="20"/> | |
92 | + <dimension x="40" y="40"/> | |
93 | + </graphics> | |
94 | + <toolspecific tool="WoPeD" version="1.0"> | |
95 | + <time>0</time> | |
96 | + <timeUnit>1</timeUnit> | |
97 | + <orientation>1</orientation> | |
98 | + </toolspecific> | |
99 | + </transition> | |
100 | + <transition id="t1"> | |
101 | + <name> | |
102 | + <text>First</text> | |
103 | + <graphics> | |
104 | + <offset x="80" y="60"/> | |
105 | + </graphics> | |
106 | + </name> | |
107 | + <graphics> | |
108 | + <position x="80" y="20"/> | |
109 | + <dimension x="40" y="40"/> | |
110 | + </graphics> | |
111 | + <toolspecific tool="WoPeD" version="1.0"> | |
112 | + <time>0</time> | |
113 | + <timeUnit>1</timeUnit> | |
114 | + <orientation>1</orientation> | |
115 | + </toolspecific> | |
116 | + </transition> | |
117 | + <transition id="t2"> | |
118 | + <name> | |
119 | + <text>Second</text> | |
120 | + <graphics> | |
121 | + <offset x="340" y="60"/> | |
122 | + </graphics> | |
123 | + </name> | |
124 | + <graphics> | |
125 | + <position x="340" y="20"/> | |
126 | + <dimension x="40" y="40"/> | |
127 | + </graphics> | |
128 | + <toolspecific tool="WoPeD" version="1.0"> | |
129 | + <time>0</time> | |
130 | + <timeUnit>1</timeUnit> | |
131 | + <orientation>1</orientation> | |
132 | + </toolspecific> | |
133 | + </transition> | |
134 | + <arc id="a1" source="p1" target="t1"> | |
135 | + <inscription> | |
136 | + <text>1</text> | |
137 | + </inscription> | |
138 | + <graphics/> | |
139 | + <toolspecific tool="WoPeD" version="1.0"> | |
140 | + <probability>1.0</probability> | |
141 | + <displayProbabilityOn>false</displayProbabilityOn> | |
142 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
143 | + </toolspecific> | |
144 | + </arc> | |
145 | + <arc id="a11" source="t6" target="p4"> | |
146 | + <inscription> | |
147 | + <text>1</text> | |
148 | + </inscription> | |
149 | + <graphics/> | |
150 | + <toolspecific tool="WoPeD" version="1.0"> | |
151 | + <probability>1.0</probability> | |
152 | + <displayProbabilityOn>false</displayProbabilityOn> | |
153 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
154 | + </toolspecific> | |
155 | + </arc> | |
156 | + <arc id="a10" source="p5" target="t6"> | |
157 | + <inscription> | |
158 | + <text>1</text> | |
159 | + </inscription> | |
160 | + <graphics/> | |
161 | + <toolspecific tool="WoPeD" version="1.0"> | |
162 | + <probability>1.0</probability> | |
163 | + <displayProbabilityOn>false</displayProbabilityOn> | |
164 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
165 | + </toolspecific> | |
166 | + </arc> | |
167 | + <arc id="a3" source="t2" target="p3"> | |
168 | + <inscription> | |
169 | + <text>1</text> | |
170 | + </inscription> | |
171 | + <graphics/> | |
172 | + <toolspecific tool="WoPeD" version="1.0"> | |
173 | + <probability>1.0</probability> | |
174 | + <displayProbabilityOn>false</displayProbabilityOn> | |
175 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
176 | + </toolspecific> | |
177 | + </arc> | |
178 | + <arc id="a13" source="t7" target="p6"> | |
179 | + <inscription> | |
180 | + <text>1</text> | |
181 | + </inscription> | |
182 | + <graphics/> | |
183 | + <toolspecific tool="WoPeD" version="1.0"> | |
184 | + <probability>1.0</probability> | |
185 | + <displayProbabilityOn>false</displayProbabilityOn> | |
186 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
187 | + </toolspecific> | |
188 | + </arc> | |
189 | + <arc id="a12" source="p3" target="t7"> | |
190 | + <inscription> | |
191 | + <text>1</text> | |
192 | + </inscription> | |
193 | + <graphics/> | |
194 | + <toolspecific tool="WoPeD" version="1.0"> | |
195 | + <probability>1.0</probability> | |
196 | + <displayProbabilityOn>false</displayProbabilityOn> | |
197 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
198 | + </toolspecific> | |
199 | + </arc> | |
200 | + <arc id="a6" source="p4" target="t2"> | |
201 | + <inscription> | |
202 | + <text>1</text> | |
203 | + </inscription> | |
204 | + <graphics/> | |
205 | + <toolspecific tool="WoPeD" version="1.0"> | |
206 | + <probability>1.0</probability> | |
207 | + <displayProbabilityOn>false</displayProbabilityOn> | |
208 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
209 | + </toolspecific> | |
210 | + </arc> | |
211 | + <arc id="a9" source="t1" target="p5"> | |
212 | + <inscription> | |
213 | + <text>1</text> | |
214 | + </inscription> | |
215 | + <graphics/> | |
216 | + <toolspecific tool="WoPeD" version="1.0"> | |
217 | + <probability>1.0</probability> | |
218 | + <displayProbabilityOn>false</displayProbabilityOn> | |
219 | + <displayProbabilityPosition x="500.0" y="0.0"/> | |
220 | + </toolspecific> | |
221 | + </arc> | |
222 | + <toolspecific tool="WoPeD" version="1.0"> | |
223 | + <bounds> | |
224 | + <position x="11" y="33"/> | |
225 | + <dimension x="755" y="474"/> | |
226 | + </bounds> | |
227 | + <scale>100</scale> | |
228 | + <treeWidthRight>597</treeWidthRight> | |
229 | + <overviewPanelVisible>true</overviewPanelVisible> | |
230 | + <treeHeightOverview>100</treeHeightOverview> | |
231 | + <treePanelVisible>true</treePanelVisible> | |
232 | + <verticalLayout>false</verticalLayout> | |
233 | + <resources/> | |
234 | + <simulations/> | |
235 | + <partnerLinks/> | |
236 | + <variables/> | |
237 | + </toolspecific> | |
238 | + </net> | |
239 | +</pnml> | |
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1 | +1 | |
2 | +2 | |
3 | +3 | |
4 | +4 | |
5 | +5 | |
6 | +6 | |
7 | +7 | |
8 | +8 | |
9 | +9 |
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1 | +Rule Main | |
2 | + input '*.mrc'.all | |
3 | + input '*.parameters'.all | |
4 | + output '*.roi'.all | |
5 | + output '*.tiff'.all | |
6 | +Flow | |
7 | +# rule Initial | |
8 | + rule First | |
9 | + rule Second | |
10 | + rule Final | |
11 | +End | |
12 | + | |
13 | +Rule Initial | |
14 | + input '${EOS_HOME}/tutorial/SampleData/1VOM.mrc' | |
15 | + input '${EOS_HOME}/tutorial/SampleData/1VOM-N.mrc' | |
16 | + output '1VOM.mrc' | |
17 | + output '1VOM-N.mrc' | |
18 | +Action | |
19 | + ln -s {$I[1]} {$O[1]} | |
20 | + ln -s {$I[2]} {$O[2]} | |
21 | +End | |
22 | + | |
23 | +Rule First | |
24 | + input '*.mrc' | |
25 | + output '{$I[1]}.info' | |
26 | +Action | |
27 | + mrcImageInfo -I -i {$I[1]} \ | |
28 | + | head -2 | tail -1 \ | |
29 | + | awk '{printf("%s %s %s", $3, $4, $5)}' \ | |
30 | + | tr -c '[0-9]' ' ' \ | |
31 | + > {$O[1]} | |
32 | +End | |
33 | + | |
34 | +Rule Second | |
35 | + input '*.mrc' | |
36 | + input '*.info' | |
37 | + input '{$I[1][1]}.parameters' | |
38 | + output '{$I[1][1]}.roi' | |
39 | +Action | |
40 | + Center_x=$(awk '{printf("%s\n", $1)}' {$I[2]}) | |
41 | + Center_y=$(awk '{printf("%s\n", $2)}' {$I[2]}) | |
42 | + Center_z=$(awk '{printf("%s\n", $3)}' {$I[2]}) | |
43 | + N_x=$(awk '{printf("%s\n", $1)}' {$I[3]}) | |
44 | + N_y=$(awk '{printf("%s\n", $2)}' {$I[3]}) | |
45 | + N_z=$(awk '{printf("%s\n", $3)}' {$I[3]}) | |
46 | + mrcImageCenterGet -i {$I[1]} -o {$O[1]} \ | |
47 | + -Cx $Center_x -Cy $Center_y -Cz $Center_z \ | |
48 | + -Nx $N_x -Ny $N_y -Nz $N_z | |
49 | +End | |
50 | + | |
51 | +Rule Final | |
52 | + input '*.mrc' | |
53 | + input '*.roi' | |
54 | + output '{$I[1]}-1.tiff' | |
55 | + output '{$I[2]}-1.tiff' | |
56 | + output '{$I[1]}-2.tiff' | |
57 | + output '{$I[2]}-2.tiff' | |
58 | +Action | |
59 | + mrcImageProjection -i {$I[1]} -o {$I[1]}.2d | |
60 | + mrc2tiff -i {$I[1]}.2d -o {$O[1]} | |
61 | + mrcImageProjection -i {$I[1]} -o {$I[1]}.2d1 -m 1 | |
62 | + mrc2tiff -i {$I[1]}.2d1 -o {$O[3]} | |
63 | + mrcImageProjection -i {$I[2]} -o {$I[2]}.2d | |
64 | + mrc2tiff -i {$I[2]}.2d -o {$O[2]} | |
65 | + mrcImageProjection -i {$I[2]} -o {$I[2]}.2d1 -m 1 | |
66 | + mrc2tiff -i {$I[2]}.2d1 -o {$O[4]} | |
67 | +End |