boutiquesDesc/circle_creaPhase.json

   1 {\r
   2     "name": "CreaPhaseCircle", \r
   3         "container-image": {\r
   4                 "type": "docker",\r
   5                 "image": "camarasu/creaphase:0.3"\r
   6         },\r
   7     "tool-version": "v0.3",   \r
   8         "schema-version": "0.5", \r
   9     "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer",  \r
  10     "command-line": "MYDIR=$PWD; cd /CreaPhase; mkdir [DIROUT]; octave --silent --eval \"SimuPBI_circle_func('[VERS]', [OVERSAMP], '[BASENAME]', [[DIST]], [ENERGY], [PIXELSIZE], [NBPROJ], [RANGEANGLE], [MODELCTF], [MODELFRESNEL], [MUMAT], [DELTAMAT], [RCIRCLE], [IMAGESIZE], [[CIRCLECENTER]], '[DIROUT]', '[NOISETYPE]', [NOISEAMOUNT])\";  tar czf $MYDIR/[RESULTS] [DIROUT]", \r
  11     "description": "x-ray phase-contrast simulator", \r
  12     "error-codes": [\r
  13         {\r
  14             "code": 1, \r
  15             "description": "Crashed"\r
  16         }\r
  17     ], \r
  18     "inputs": [\r
  19         {\r
  20             "id": "vers", \r
  21             "name": "Set it to 'Radon' OR 'Analytical'to calculate projections accordingly", \r
  22             "optional": false, \r
  23             "type": "String", \r
  24                         "command-line-flag": "",\r
  25                         "command-line-flag-separator": "",\r
  26             "value-key": "[VERS]"\r
  27         },\r
  28                 {\r
  29             "id": "oversamp", \r
  30             "name": "Oversampling of the projections : use 2 or 4", \r
  31             "optional": false, \r
  32             "type": "String", \r
  33                         "command-line-flag": "",\r
  34                         "command-line-flag-separator": "",\r
  35             "value-key": "[OVERSAMP]"\r
  36         }, \r
  37         {\r
  38             "id": "basename", \r
  39             "name": "Basename of the result files", \r
  40             "optional": false, \r
  41             "type": "String", \r
  42                         "command-line-flag": "",\r
  43                         "command-line-flag-separator": "",\r
  44             "value-key": "[BASENAME]"\r
  45         }, \r
  46         {\r
  47             "id": "dist", \r
  48             "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", \r
  49             "optional": false, \r
  50             "type": "String", \r
  51                         "command-line-flag": "",\r
  52                         "command-line-flag-separator": "",\r
  53             "value-key": "[DIST]"\r
  54         }, \r
  55         {\r
  56             "id": "energy", \r
  57             "name": "Energy of the incoming X-ray beam (in keV)", \r
  58             "optional": false, \r
  59             "type": "String", \r
  60                         "command-line-flag": "",\r
  61                         "command-line-flag-separator": "",\r
  62             "value-key": "[ENERGY]"\r
  63         }, \r
  64         {\r
  65             "id": "pixelSize", \r
  66             "name": "Pixel size of the detector (in um)", \r
  67             "optional": false, \r
  68             "type": "String", \r
  69                         "command-line-flag": "",\r
  70             "value-key": "[PIXELSIZE]"\r
  71         },\r
  72                         {\r
  73             "id": "nbProj", \r
  74             "name": "Number of projections (e.g., 360)", \r
  75             "optional": false, \r
  76             "type": "String", \r
  77                         "command-line-flag": "",\r
  78                         "command-line-flag-separator": "",\r
  79             "value-key": "[NBPROJ]"\r
  80         },\r
  81         {\r
  82             "id": "rangeAngle", \r
  83             "name": "Range of the tomography : 180 or 360 degrees", \r
  84             "optional": false, \r
  85             "type": "String", \r
  86                         "command-line-flag": "",\r
  87             "value-key": "[RANGEANGLE]"\r
  88         },\r
  89                 {\r
  90             "id": "modelCtf", \r
  91             "name": "Use 1 if you want to use the CTF model, 0 otherwise", \r
  92             "optional": false, \r
  93             "type": "String", \r
  94                         "command-line-flag": "",\r
  95                         "command-line-flag-separator": "",\r
  96             "value-key": "[MODELCTF]"\r
  97         }, \r
  98         {\r
  99             "id": "modelFresnel", \r
 100             "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", \r
 101             "optional": false, \r
 102             "type": "String", \r
 103                         "command-line-flag": "",\r
 104                         "command-line-flag-separator": "",\r
 105             "value-key": "[MODELFRESNEL]"\r
 106         }, \r
 107         {\r
 108             "id": "muMat", \r
 109             "name": "Linear attenuation coefficient of the material of the circle (e.g. 0.89 cm-1 for PET at 19keV)", \r
 110             "optional": false, \r
 111             "type": "String", \r
 112                         "command-line-flag": "",\r
 113                         "command-line-flag-separator": "",\r
 114             "value-key": "[MUMAT]"\r
 115         }, \r
 116         {\r
 117             "id": "deltaMat", \r
 118             "name": "Refractive index decrement of the material of the circle, in 10^-7 (e.g. 8.265 for PET at 19keV)", \r
 119             "optional": false, \r
 120             "type": "String", \r
 121                         "command-line-flag": "",\r
 122                         "command-line-flag-separator": "",\r
 123             "value-key": "[DELTAMAT]"\r
 124         }, \r
 125         {\r
 126             "id": "Rcircle", \r
 127             "name": "Radius of the circle (in pixels)", \r
 128             "optional": false, \r
 129             "type": "String", \r
 130                         "command-line-flag": "",\r
 131             "value-key": "[RCIRCLE]"\r
 132         },\r
 133                 {\r
 134             "id": "imageSize", \r
 135             "name": "Size of the image (square; in pixels)", \r
 136             "optional": false, \r
 137             "type": "String", \r
 138                         "command-line-flag": "",\r
 139                         "command-line-flag-separator": "",\r
 140             "value-key": "[IMAGESIZE]"\r
 141         }, \r
 142         {\r
 143             "id": "circleCenter", \r
 144             "name": "2D coordinates of the circle center (in pixels; e.g., 200 250)", \r
 145             "optional": false, \r
 146             "type": "String", \r
 147                         "command-line-flag": "",\r
 148                         "command-line-flag-separator": "",\r
 149             "value-key": "[CIRCLECENTER]"\r
 150         }, \r
 151         {\r
 152             "id": "dirOut", \r
 153             "name": "Output directory name", \r
 154             "optional": false, \r
 155             "type": "String", \r
 156                         "command-line-flag": "",\r
 157                         "command-line-flag-separator": "",\r
 158             "value-key": "[DIROUT]"\r
 159         }, \r
 160         {\r
 161             "id": "noiseType", \r
 162             "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", \r
 163             "optional": false, \r
 164             "type": "String", \r
 165                         "command-line-flag": "",\r
 166                         "command-line-flag-separator": "",\r
 167             "value-key": "[NOISETYPE]"\r
 168         }, \r
 169         {\r
 170             "id": "noiseAmount", \r
 171             "name": "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].", \r
 172             "optional": false, \r
 173             "type": "String", \r
 174                         "command-line-flag": "",\r
 175             "value-key": "[NOISEAMOUNT]"\r
 176         }\r
 177     ], \r
 178         "output-files":[\r
 179                 {\r
 180                         "id" : "resultTarball",\r
 181                         "name" : "resultTarball",\r
 182                         "description" : "archive of the output folder containing execution results, and the output of the command",\r
 183                         "path-template" : "results.tar.gz",\r
 184                         "optional": false, \r
 185                         "value-key" : "[RESULTS]"\r
 186                 }\r
 187         ]\r
 188 }