2 "name": "CreaPhase1D",
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5 "image": "camarasu/creaphase:0.3"
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7 "tool-version": "v0.3",
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8 "schema-version": "0.5",
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9 "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer",
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10 "command-line": "MYDIR=$PWD; cd /CreaPhase; mkdir [DIROUT]; octave --silent --eval \"SimuPBI_unknown_1D_func('[BASENAME]', [OVERSAMP], [[DIST]], [ENERGY], [PIXELSIZE], [NBPROJ], [RANGEANGLE], [MODELCTF], [MODELFRESNEL], [ATTFILE], [PHFILE], '[DIROUT]', '[NOISETYPE]', [NOISEAMOUNT])\"; tar czf $MYDIR/[RESULTS] [DIROUT]",
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11 "description": "x-ray phase-contrast simulator",
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15 "description": "Crashed"
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21 "name": "Oversampling of the projections : use 2 or 4",
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24 "command-line-flag": "",
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25 "command-line-flag-separator": "",
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26 "value-key": "[OVERSAMP]"
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30 "name": "Basename of the result files",
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33 "command-line-flag": "",
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34 "command-line-flag-separator": "",
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35 "value-key": "[BASENAME]"
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39 "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50",
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42 "command-line-flag": "",
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43 "command-line-flag-separator": "",
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44 "value-key": "[DIST]"
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48 "name": "Energy of the incoming X-ray beam (in keV)",
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51 "command-line-flag": "",
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52 "command-line-flag-separator": "",
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53 "value-key": "[ENERGY]"
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57 "name": "Pixel size of the detector (in um)",
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60 "command-line-flag": "",
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61 "value-key": "[PIXELSIZE]"
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65 "name": "Number of projections (e.g., 360)",
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68 "command-line-flag": "",
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69 "command-line-flag-separator": "",
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70 "value-key": "[NBPROJ]"
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73 "id": "rangeAngle",
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74 "name": "Range of the tomography : 180 or 360 degrees",
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77 "command-line-flag": "",
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78 "value-key": "[RANGEANGLE]"
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82 "name": "Use 1 if you want to use the CTF model, 0 otherwise",
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85 "command-line-flag": "",
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86 "command-line-flag-separator": "",
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87 "value-key": "[MODELCTF]"
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90 "id": "modelFresnel",
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91 "name": "Use 1 if you want to use the Fresnel model, 0 otherwise",
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94 "command-line-flag": "",
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95 "command-line-flag-separator": "",
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96 "value-key": "[MODELFRESNEL]"
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100 "name": "Attenuation map file (in cm^-1)",
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101 "optional": false,
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103 "command-line-flag": "",
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104 "command-line-flag-separator": "",
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105 "value-key": "[ATTFILE]"
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109 "name": "Refrcative index decrement map (delta)",
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110 "optional": false,
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112 "command-line-flag": "",
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113 "command-line-flag-separator": "",
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114 "value-key": "[PHFILE]"
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118 "name": "Output directory name",
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119 "optional": false,
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121 "command-line-flag": "",
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122 "command-line-flag-separator": "",
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123 "value-key": "[DIROUT]"
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126 "id": "noiseType",
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127 "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).",
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128 "optional": false,
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130 "command-line-flag": "",
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131 "command-line-flag-separator": "",
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132 "value-key": "[NOISETYPE]"
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135 "id": "noiseAmount",
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136 "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].",
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137 "optional": false,
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139 "command-line-flag": "",
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140 "value-key": "[NOISEAMOUNT]"
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145 "id" : "resultTarball",
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146 "name" : "resultTarball",
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147 "description" : "archive of the output folder containing execution results, and the output of the command",
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148 "path-template" : "results.tar.gz",
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149 "optional": false,
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150 "value-key" : "[RESULTS]"
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