workflow/1D_CreaPhase.gwendia

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <workflow name="1D_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="oversamp" type="string">
  12       <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
  13       </source-comment>
  14     </source>
  15     <source name="basename" type="string">
  16       <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 files
  17       </source-comment>
  18     </source>
  19     <source name="dist" type="string">
  20       <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
  21       </source-comment>
  22     </source>
  23     <source name="energy" type="string">
  24       <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)
  25       </source-comment>
  26     </source>
  27     <source name="pixelSize" type="string">
  28       <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)
  29       </source-comment>
  30     </source>
  31     <source name="nbProj" type="string">
  32       <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)
  33       </source-comment>
  34     </source>
  35     <source name="rangeAngle" type="string">
  36       <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
  37       </source-comment>
  38     </source>
  39     <source name="modelCtf" type="string">
  40       <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
  41       </source-comment>
  42     </source>
  43     <source name="modelFresnel" type="string">
  44       <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
  45       </source-comment>
  46     </source>
  47     <source name="muMatLfn" type="uri">
  48       <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;):  Attenuation map file (in cm^-1)
  49       </source-comment>
  50     </source>
  51     <source name="deltaMatLfn" type="uri">
  52       <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;): Refractive index decrement map file (delta)
  53       </source-comment>
  54     </source>
  55     <source name="noiseType" type="string">
  56       <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).
  57       </source-comment>
  58     </source>
  59     <source name="noiseAmount" type="string">
  60       <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). If 'poisson', please specify a scaling factor ranging in [0:1].
  61       </source-comment>
  62     </source>
  63     <constant name="dirOut" type="string" value="dirOut" cardinality="scalar" />
  64     <sink name="resultTarball" type="uri" />
  65   </interface>
  66
  67   <processors>
  68     <processor name="append-date" >
  69       <in name="dir" type="uri" depth="0" />
  70       <out name="result" type="string" depth="0" />
  71       <beanshell>/*----------Beginning of Beanshell------------*/
  72                         import java.text.DateFormat;
  73                         import java.text.SimpleDateFormat;
  74                         import java.util.Date;
  75
  76 DateFormat dateFormat = new SimpleDateFormat("dd-MM-yyyy_HH:mm:ss");
  77 String result = dir.toString()+"/"+(dateFormat.format(System.currentTimeMillis()));
  78 /*------------End of Beanshell------------*/
  79       </beanshell>
  80     </processor>
  81     <processor name="CreaPhase" >
  82       <in name="dirOut" type="string" depth="0" />
  83       <in name="dist" type="string" depth="0" />
  84       <in name="pixelSize" type="string" depth="0" />
  85       <in name="muMat" type="string" depth="0" />
  86       <in name="deltaMat" type="string" depth="0" />
  87       <in name="modelFresnel" type="string" depth="0" />
  88       <in name="rangeAngle" type="string" depth="0" />
  89       <in name="nbProj" type="string" depth="0" />
  90       <in name="oversamp" type="string" depth="0" />
  91       <in name="basename" type="string" depth="0" />
  92       <in name="modelCtf" type="string" depth="0" />
  93       <in name="noiseAmount" type="string" depth="0" />
  94       <in name="noiseType" type="string" depth="0" />
  95       <in name="muLfn" type="uri" depth="0" />
  96       <in name="deltaLfn" type="uri" depth="0" />
  97       <in name="results-directory" type="string" depth="0" />
  98       <in name="energy" type="string" depth="0" />
  99       <out name="resultTarball" type="uri" depth="0" />
 100       <iterationstrategy>
 101         <cross>
 102           <port name="results-directory" />
 103           <port name="oversamp" />
 104           <port name="basename" />
 105           <port name="dist" />
 106           <port name="energy" />
 107           <port name="pixelSize" />
 108           <port name="nbProj" />
 109           <port name="rangeAngle" />
 110           <port name="modelCtf" />
 111           <port name="modelFresnel" />
 112           <port name="muMat" />
 113           <port name="deltaMat" />
 114           <port name="dirOut" />
 115           <port name="noiseType" />
 116           <port name="noiseAmount" />
 117           <port name="muLfn" />
 118           <port name="deltaLfn" />
 119         </cross>
 120       </iterationstrategy>
 121       <gasw descriptor="[GASW_DIR]/1D_CreaPhase.xml"/>
 122     </processor>
 123     <processor name="append-brackets" >
 124       <in name="inputString" type="string" depth="0" />
 125       <out name="out" type="string" depth="0" />
 126       <beanshell>/*----------Beginning of Beanshell------------*/
 127 //String toAppend="\\\"";
 128 out="["+inputString+"]";
 129       </beanshell>
 130     </processor>
 131     <processor name="append-simple-quotes_2" >
 132       <in name="inputString" type="string" depth="0" />
 133       <out name="out" type="string" depth="0" />
 134       <beanshell>/*----------Beginning of Beanshell------------*/
 135 String toAppend="'";
 136 out=toAppend+inputString+toAppend;
 137       </beanshell>
 138     </processor>
 139     <processor name="append-simple-quotes_3" >
 140       <in name="inputString" type="string" depth="0" />
 141       <out name="out" type="string" depth="0" />
 142       <beanshell>/*----------Beginning of Beanshell------------*/
 143 String toAppend="'";
 144 out=toAppend+inputString+toAppend;
 145       </beanshell>
 146     </processor>
 147     <processor name="append-simple-quotes_4" >
 148       <in name="inputString" type="string" depth="0" />
 149       <out name="out" type="string" depth="0" />
 150       <beanshell>/*----------Beginning of Beanshell------------*/
 151 String toAppend="'";
 152 out=toAppend+inputString+toAppend;
 153       </beanshell>
 154     </processor>
 155     <processor name="getFileName_1" >
 156       <in name="lfn" type="uri" depth="0" />
 157       <out name="fileName" type="string" depth="0" />
 158       <beanshell>/*----------Beginning of Beanshell------------*/
 159 String[] bits = lfn.toString().split("/");
 160 String lastOne = bits[bits.length-1];
 161 String toAppend="'";
 162 fileName=toAppend+lastOne+toAppend;
 163       </beanshell>
 164     </processor>
 165     <processor name="getFileName_2" >
 166       <in name="lfn" type="uri" depth="0" />
 167       <out name="fileName" type="string" depth="0" />
 168       <beanshell>/*----------Beginning of Beanshell------------*/
 169 String[] bits = lfn.toString().split("/");
 170 String lastOne = bits[bits.length-1];
 171 String toAppend="'";
 172 fileName=toAppend+lastOne+toAppend;
 173       </beanshell>
 174     </processor>
 175   </processors>
 176
 177   <links>
 178       <link from="results-directory" to="append-date:dir" />
 179       <link from="append-date:result" to="CreaPhase:results-directory" />
 180       <link from="oversamp" to="CreaPhase:oversamp" />
 181       <link from="energy" to="CreaPhase:energy" />
 182       <link from="pixelSize" to="CreaPhase:pixelSize" />
 183       <link from="nbProj" to="CreaPhase:nbProj" />
 184       <link from="rangeAngle" to="CreaPhase:rangeAngle" />
 185       <link from="modelCtf" to="CreaPhase:modelCtf" />
 186       <link from="modelFresnel" to="CreaPhase:modelFresnel" />
 187       <link from="noiseAmount" to="CreaPhase:noiseAmount" />
 188       <link from="CreaPhase:resultTarball" to="resultTarball" />
 189       <link from="dist" to="append-brackets:inputString" />
 190       <link from="append-brackets:out" to="CreaPhase:dist" />
 191       <link from="basename" to="append-simple-quotes_2:inputString" />
 192       <link from="append-simple-quotes_2:out" to="CreaPhase:basename" />
 193       <link from="append-simple-quotes_3:out" to="CreaPhase:dirOut" />
 194       <link from="noiseType" to="append-simple-quotes_4:inputString" />
 195       <link from="append-simple-quotes_4:out" to="CreaPhase:noiseType" />
 196       <link from="dirOut" to="append-simple-quotes_3:inputString" />
 197       <link from="deltaMatLfn" to="CreaPhase:deltaLfn" />
 198       <link from="muMatLfn" to="CreaPhase:muLfn" />
 199       <link from="deltaMatLfn" to="getFileName_2:lfn" />
 200       <link from="getFileName_2:fileName" to="CreaPhase:deltaMat" />
 201       <link from="muMatLfn" to="getFileName_1:lfn" />
 202       <link from="getFileName_1:fileName" to="CreaPhase:muMat" />
 203   </links>
 204
 205 </workflow>