workflow/CreaPhase.gwendia

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <workflow name="CreaPhase" version="0.1">
   3
   4   <description>Propagation-based phase contrast images generation</description>
   5
   6   <interface>
   7     <source name="results-directory" type="uri">
   8       <source-comment>&lt;b&gt;&lt;font color=blue&gt;results-directory&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Directory&lt;/font&gt;&lt;/b&gt;): Directory where the results will be stored.
   9       </source-comment>
  10     </source>
  11     <source name="vers" type="string">
  12       <source-comment>&lt;b&gt;&lt;font color=blue&gt;vers&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): are the projections calculated analytically or using the Radon transform? use the strings 'Radon' OR 'Analytical'
  13       </source-comment>
  14     </source>
  15     <source name="oversamp" type="string">
  16       <source-comment>&lt;b&gt;&lt;font color=blue&gt;oversamp&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Oversampling of the projections : use 2 or 4
  17       </source-comment>
  18     </source>
  19     <source name="basename" type="string">
  20       <source-comment>&lt;b&gt;&lt;font color=blue&gt;basename&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): Basename of the result file
  21       </source-comment>
  22     </source>
  23     <source name="dist" type="string">
  24       <source-comment>&lt;b&gt;&lt;font color=blue&gt;dist&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;):  Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50
  25       </source-comment>
  26     </source>
  27     <source name="energy" type="string">
  28       <source-comment>&lt;b&gt;&lt;font color=blue&gt;energy&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Energy of the incoming X-ray beam (in keV)
  29       </source-comment>
  30     </source>
  31     <source name="pixelSize" type="string">
  32       <source-comment>&lt;b&gt;&lt;font color=blue&gt;pixelSize&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Pixel size of the detector (in um)
  33       </source-comment>
  34     </source>
  35     <source name="nbProj" type="string">
  36       <source-comment>&lt;b&gt;&lt;font color=blue&gt;nbProj&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Number of projections (e.g., 360)
  37       </source-comment>
  38     </source>
  39     <source name="rangeAngle" type="string">
  40       <source-comment>&lt;b&gt;&lt;font color=blue&gt;rangeAngle&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Range of the tomography : 180 or 360 degrees
  41       </source-comment>
  42     </source>
  43     <source name="modelCtf" type="string">
  44       <source-comment>&lt;b&gt;&lt;font color=blue&gt;modelCtf&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;):  Which model do you want to use for the propagation? use 1 or 0
  45       </source-comment>
  46     </source>
  47     <source name="modelFresnel" type="string">
  48       <source-comment>&lt;b&gt;&lt;font color=blue&gt;modelFresnel&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;Number&lt;/font&gt;&lt;/b&gt;): Which model do you want to use for the propagation? use 1 or 0
  49       </source-comment>
  50     </source>
  51     <source name="muMat" type="string">
  52       <source-comment>&lt;b&gt;&lt;font color=blue&gt;muMat&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): Material of the circle (e.g., PET at 19 keV)
  53       </source-comment>
  54     </source>
  55     <source name="deltaMat" type="string">
  56       <source-comment>&lt;b&gt;&lt;font color=blue&gt;deltaMat&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): Material of the circle (e.g., PET at 19 keV)
  57       </source-comment>
  58     </source>
  59     <source name="Rcircle" type="string">
  60       <source-comment>&lt;b&gt;&lt;font color=blue&gt;Rcircle&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): radius of the circle
  61       </source-comment>
  62     </source>
  63     <source name="imageSize" type="string">
  64       <source-comment>&lt;b&gt;&lt;font color=blue&gt;imageSize&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): Size of the image (square)
  65       </source-comment>
  66     </source>
  67     <source name="circleCenter" type="string">
  68       <source-comment>&lt;b&gt;&lt;font color=blue&gt;circleCenter&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): 2D coordinates of the circle center (e.g., 200 250)
  69       </source-comment>
  70     </source>
  71     <source name="noiseType" type="string">
  72       <source-comment>&lt;b&gt;&lt;font color=blue&gt;noiseType&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): Use noise='gaussian' (addition of gaussian noise) or noise='poisson' ( generation of Poisson noise) Put '&lt;b&gt;no&lt;/b&gt;' to ignore this optional input.
  73       </source-comment>
  74     </source>
  75     <source name="noiseAmount" type="string">
  76       <source-comment>&lt;b&gt;&lt;font color=blue&gt;noiseAmount&lt;/font&gt;&lt;/b&gt; (&lt;b&gt;&lt;font color=green&gt;String&lt;/font&gt;&lt;/b&gt;): If 'gaussian' (additive noise), please specify the Peak-to-peak Signe-to-noise ratio (PPSNR, in dB)
  77       </source-comment>
  78     </source>
  79     <constant name="dirOut" type="string" value="dirOut" cardinality="scalar" />
  80     <sink name="resultTarball" type="uri" />
  81   </interface>
  82
  83   <processors>
  84     <processor name="append-date" >
  85       <in name="dir" type="uri" depth="0" />
  86       <out name="result" type="string" depth="0" />
  87       <beanshell>/*----------Beginning of Beanshell------------*/
  88                         import java.text.DateFormat;
  89                         import java.text.SimpleDateFormat;
  90                         import java.util.Date;
  91
  92 DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
  93 String result = dir.toString()+"/"+(dateFormat.format(System.currentTimeMillis()));
  94 /*------------End of Beanshell------------*/
  95       </beanshell>
  96     </processor>
  97     <processor name="CreaPhase" >
  98       <in name="dirOut" type="string" depth="0" />
  99       <in name="vers" type="string" depth="0" />
 100       <in name="dist" type="string" depth="0" />
 101       <in name="Rcircle" type="string" depth="0" />
 102       <in name="pixelSize" type="string" depth="0" />
 103       <in name="muMat" type="string" depth="0" />
 104       <in name="deltaMat" type="string" depth="0" />
 105       <in name="modelFresnel" type="string" depth="0" />
 106       <in name="rangeAngle" type="string" depth="0" />
 107       <in name="nbProj" type="string" depth="0" />
 108       <in name="oversamp" type="string" depth="0" />
 109       <in name="circleCenter" type="string" depth="0" />
 110       <in name="basename" type="string" depth="0" />
 111       <in name="modelCtf" type="string" depth="0" />
 112       <in name="noiseAmount" type="string" depth="0" />
 113       <in name="noiseType" type="string" depth="0" />
 114       <in name="imageSize" type="string" depth="0" />
 115       <in name="results-directory" type="string" depth="0" />
 116       <in name="energy" type="string" depth="0" />
 117       <out name="resultTarball" type="uri" depth="0" />
 118       <iterationstrategy>
 119         <cross>
 120           <port name="results-directory" />
 121           <port name="vers" />
 122           <port name="oversamp" />
 123           <port name="basename" />
 124           <port name="dist" />
 125           <port name="energy" />
 126           <port name="pixelSize" />
 127           <port name="nbProj" />
 128           <port name="rangeAngle" />
 129           <port name="modelCtf" />
 130           <port name="modelFresnel" />
 131           <port name="muMat" />
 132           <port name="deltaMat" />
 133           <port name="Rcircle" />
 134           <port name="imageSize" />
 135           <port name="circleCenter" />
 136           <port name="dirOut" />
 137           <port name="noiseType" />
 138           <port name="noiseAmount" />
 139         </cross>
 140       </iterationstrategy>
 141       <gasw descriptor="[GASW_DIR]/CreaPhase.xml"/>
 142     </processor>
 143     <processor name="append-brackets" >
 144       <in name="inputString" type="string" depth="0" />
 145       <out name="out" type="string" depth="0" />
 146       <beanshell>/*----------Beginning of Beanshell------------*/
 147 //String toAppend="\\\"";
 148 out="["+inputString+"]";
 149       </beanshell>
 150     </processor>
 151     <processor name="append-brackets_2" >
 152       <in name="inputString" type="string" depth="0" />
 153       <out name="out" type="string" depth="0" />
 154       <beanshell>/*----------Beginning of Beanshell------------*/
 155 //String toAppend="\\\"";
 156 out="["+inputString+"]";
 157       </beanshell>
 158     </processor>
 159     <processor name="append-simple-quotes" >
 160       <in name="inputString" type="string" depth="0" />
 161       <out name="out" type="string" depth="0" />
 162       <beanshell>/*----------Beginning of Beanshell------------*/
 163 String toAppend="'";
 164 out=toAppend+inputString+toAppend;
 165       </beanshell>
 166     </processor>
 167     <processor name="append-simple-quotes_2" >
 168       <in name="inputString" type="string" depth="0" />
 169       <out name="out" type="string" depth="0" />
 170       <beanshell>/*----------Beginning of Beanshell------------*/
 171 String toAppend="'";
 172 out=toAppend+inputString+toAppend;
 173       </beanshell>
 174     </processor>
 175     <processor name="append-simple-quotes_3" >
 176       <in name="inputString" type="string" depth="0" />
 177       <out name="out" type="string" depth="0" />
 178       <beanshell>/*----------Beginning of Beanshell------------*/
 179 String toAppend="'";
 180 out=toAppend+inputString+toAppend;
 181       </beanshell>
 182     </processor>
 183     <processor name="append-simple-quotes_4" >
 184       <in name="inputString" type="string" depth="0" />
 185       <out name="out" type="string" depth="0" />
 186       <beanshell>/*----------Beginning of Beanshell------------*/
 187 String toAppend="'";
 188 out=toAppend+inputString+toAppend;
 189       </beanshell>
 190     </processor>
 191   </processors>
 192
 193   <links>
 194       <link from="results-directory" to="append-date:dir" />
 195       <link from="append-date:result" to="CreaPhase:results-directory" />
 196       <link from="oversamp" to="CreaPhase:oversamp" />
 197       <link from="energy" to="CreaPhase:energy" />
 198       <link from="pixelSize" to="CreaPhase:pixelSize" />
 199       <link from="nbProj" to="CreaPhase:nbProj" />
 200       <link from="rangeAngle" to="CreaPhase:rangeAngle" />
 201       <link from="modelCtf" to="CreaPhase:modelCtf" />
 202       <link from="modelFresnel" to="CreaPhase:modelFresnel" />
 203       <link from="muMat" to="CreaPhase:muMat" />
 204       <link from="deltaMat" to="CreaPhase:deltaMat" />
 205       <link from="Rcircle" to="CreaPhase:Rcircle" />
 206       <link from="imageSize" to="CreaPhase:imageSize" />
 207       <link from="noiseAmount" to="CreaPhase:noiseAmount" />
 208       <link from="CreaPhase:resultTarball" to="resultTarball" />
 209       <link from="dist" to="append-brackets:inputString" />
 210       <link from="circleCenter" to="append-brackets_2:inputString" />
 211       <link from="append-brackets_2:out" to="CreaPhase:circleCenter" />
 212       <link from="append-brackets:out" to="CreaPhase:dist" />
 213       <link from="vers" to="append-simple-quotes:inputString" />
 214       <link from="append-simple-quotes:out" to="CreaPhase:vers" />
 215       <link from="basename" to="append-simple-quotes_2:inputString" />
 216       <link from="append-simple-quotes_2:out" to="CreaPhase:basename" />
 217       <link from="append-simple-quotes_3:out" to="CreaPhase:dirOut" />
 218       <link from="noiseType" to="append-simple-quotes_4:inputString" />
 219       <link from="append-simple-quotes_4:out" to="CreaPhase:noiseType" />
 220       <link from="dirOut" to="append-simple-quotes_3:inputString" />
 221   </links>
 222
 223 </workflow>