--- /dev/null
+{\r
+ "name": "CreaPhase1D", \r
+ "container-image": {\r
+ "type": "docker",\r
+ "image": "camarasu/creaphase:0.3"\r
+ },\r
+ "tool-version": "v0.3", \r
+ "schema-version": "0.5", \r
+ "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", \r
+ "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]", \r
+ "description": "x-ray phase-contrast simulator", \r
+ "error-codes": [\r
+ {\r
+ "code": 1, \r
+ "description": "Crashed"\r
+ }\r
+ ], \r
+ "inputs": [\r
+ {\r
+ "id": "oversamp", \r
+ "name": "Oversampling of the projections : use 2 or 4", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[OVERSAMP]"\r
+ }, \r
+ {\r
+ "id": "basename", \r
+ "name": "Basename of the result files", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[BASENAME]"\r
+ }, \r
+ {\r
+ "id": "dist", \r
+ "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIST]"\r
+ }, \r
+ {\r
+ "id": "energy", \r
+ "name": "Energy of the incoming X-ray beam (in keV)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[ENERGY]"\r
+ }, \r
+ {\r
+ "id": "pixelSize", \r
+ "name": "Pixel size of the detector (in um)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[PIXELSIZE]"\r
+ },\r
+ {\r
+ "id": "nbProj", \r
+ "name": "Number of projections (e.g., 360)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NBPROJ]"\r
+ },\r
+ {\r
+ "id": "rangeAngle", \r
+ "name": "Range of the tomography : 180 or 360 degrees", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[RANGEANGLE]"\r
+ },\r
+ {\r
+ "id": "modelCtf", \r
+ "name": "Use 1 if you want to use the CTF model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELCTF]"\r
+ }, \r
+ {\r
+ "id": "modelFresnel", \r
+ "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELFRESNEL]"\r
+ }, \r
+ {\r
+ "id": "attfile", \r
+ "name": "Attenuation map file (in cm^-1)", \r
+ "optional": false, \r
+ "type": "File", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[ATTFILE]"\r
+ }, \r
+ {\r
+ "id": "PHFILE", \r
+ "name": "Refrcative index decrement map (delta)", \r
+ "optional": false, \r
+ "type": "File", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[PHFILE]"\r
+ }, \r
+ {\r
+ "id": "dirOut", \r
+ "name": "Output directory name", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIROUT]"\r
+ }, \r
+ {\r
+ "id": "noiseType", \r
+ "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NOISETYPE]"\r
+ }, \r
+ {\r
+ "id": "noiseAmount", \r
+ "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
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[NOISEAMOUNT]"\r
+ }\r
+ ], \r
+ "output-files":[\r
+ {\r
+ "id" : "resultTarball",\r
+ "name" : "resultTarball",\r
+ "description" : "archive of the output folder containing execution results, and the output of the command",\r
+ "path-template" : "results.tar.gz",\r
+ "optional": false, \r
+ "value-key" : "[RESULTS]"\r
+ }\r
+ ]\r
+}
\ No newline at end of file
--- /dev/null
+{\r
+ "name": "CreaPhase3Wires", \r
+ "container-image": {\r
+ "type": "docker",\r
+ "image": "camarasu/creaphase:0.3"\r
+ },\r
+ "tool-version": "v0.3", \r
+ "schema-version": "0.5", \r
+ "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", \r
+ "command-line": "MYDIR=$PWD; cd /CreaPhase; mkdir [DIROUT]; octave --silent --eval \"SimuPBI_3WiresPhant_func('[VERS]', [OVERSAMP], '[BASENAME]', [[DIST]], [ENERGY], [PIXELSIZE], [NBPROJ], [RANGEANGLE], [MODELCTF], [MODELFRESNEL], [HEIGHT], '[DIROUT]', '[NOISETYPE]', [NOISEAMOUNT])\"; tar czf $MYDIR/[RESULTS] [DIROUT]", \r
+ "description": "x-ray phase-contrast simulator", \r
+ "error-codes": [\r
+ {\r
+ "code": 1, \r
+ "description": "Crashed"\r
+ }\r
+ ], \r
+ "inputs": [\r
+ {\r
+ "id": "vers", \r
+ "name": "Set it to 'Radon' OR 'Analytical'to calculate projections accordingly", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[VERS]"\r
+ },\r
+ {\r
+ "id": "oversamp", \r
+ "name": "Oversampling of the projections : use 2 or 4", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[OVERSAMP]"\r
+ }, \r
+ {\r
+ "id": "basename", \r
+ "name": "Basename of the result files", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[BASENAME]"\r
+ }, \r
+ {\r
+ "id": "dist", \r
+ "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIST]"\r
+ }, \r
+ {\r
+ "id": "energy", \r
+ "name": "Energy of the incoming X-ray beam (in keV)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[ENERGY]"\r
+ }, \r
+ {\r
+ "id": "pixelSize", \r
+ "name": "Pixel size of the detector (in um)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[PIXELSIZE]"\r
+ },\r
+ {\r
+ "id": "nbProj", \r
+ "name": "Number of projections (e.g., 360)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NBPROJ]"\r
+ },\r
+ {\r
+ "id": "rangeAngle", \r
+ "name": "Range of the tomography : 180 or 360 degrees", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[RANGEANGLE]"\r
+ },\r
+ {\r
+ "id": "modelCtf", \r
+ "name": "Use 1 if you want to use the CTF model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELCTF]"\r
+ }, \r
+ {\r
+ "id": "modelFresnel", \r
+ "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELFRESNEL]"\r
+ }, \r
+ {\r
+ "id": "height", \r
+ "name": "height of the object. If height == 1, the simulation is computed in 1D. If height >=2 , the simulation turns into 2D.", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[HEIGHT]"\r
+ }, \r
+ {\r
+ "id": "dirOut", \r
+ "name": "Output directory name", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIROUT]"\r
+ }, \r
+ {\r
+ "id": "noiseType", \r
+ "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NOISETYPE]"\r
+ }, \r
+ {\r
+ "id": "noiseAmount", \r
+ "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
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[NOISEAMOUNT]"\r
+ }\r
+ ], \r
+ "output-files":[\r
+ {\r
+ "id" : "resultTarball",\r
+ "name" : "resultTarball",\r
+ "description" : "archive of the output folder containing execution results, and the output of the command",\r
+ "path-template" : "results.tar.gz",\r
+ "optional": false, \r
+ "value-key" : "[RESULTS]"\r
+ }\r
+ ]\r
+}
\ No newline at end of file
--- /dev/null
+{\r
+ "name": "CreaPhaseCircle", \r
+ "container-image": {\r
+ "type": "docker",\r
+ "image": "camarasu/creaphase:0.3"\r
+ },\r
+ "tool-version": "v0.3", \r
+ "schema-version": "0.5", \r
+ "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", \r
+ "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
+ "description": "x-ray phase-contrast simulator", \r
+ "error-codes": [\r
+ {\r
+ "code": 1, \r
+ "description": "Crashed"\r
+ }\r
+ ], \r
+ "inputs": [\r
+ {\r
+ "id": "vers", \r
+ "name": "Set it to 'Radon' OR 'Analytical'to calculate projections accordingly", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[VERS]"\r
+ },\r
+ {\r
+ "id": "oversamp", \r
+ "name": "Oversampling of the projections : use 2 or 4", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[OVERSAMP]"\r
+ }, \r
+ {\r
+ "id": "basename", \r
+ "name": "Basename of the result files", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[BASENAME]"\r
+ }, \r
+ {\r
+ "id": "dist", \r
+ "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIST]"\r
+ }, \r
+ {\r
+ "id": "energy", \r
+ "name": "Energy of the incoming X-ray beam (in keV)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[ENERGY]"\r
+ }, \r
+ {\r
+ "id": "pixelSize", \r
+ "name": "Pixel size of the detector (in um)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[PIXELSIZE]"\r
+ },\r
+ {\r
+ "id": "nbProj", \r
+ "name": "Number of projections (e.g., 360)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NBPROJ]"\r
+ },\r
+ {\r
+ "id": "rangeAngle", \r
+ "name": "Range of the tomography : 180 or 360 degrees", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[RANGEANGLE]"\r
+ },\r
+ {\r
+ "id": "modelCtf", \r
+ "name": "Use 1 if you want to use the CTF model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELCTF]"\r
+ }, \r
+ {\r
+ "id": "modelFresnel", \r
+ "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MODELFRESNEL]"\r
+ }, \r
+ {\r
+ "id": "muMat", \r
+ "name": "Linear attenuation coefficient of the material of the circle (e.g. 0.89 cm-1 for PET at 19keV)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[MUMAT]"\r
+ }, \r
+ {\r
+ "id": "deltaMat", \r
+ "name": "Refractive index decrement of the material of the circle, in 10^-7 (e.g. 8.265 for PET at 19keV)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DELTAMAT]"\r
+ }, \r
+ {\r
+ "id": "Rcircle", \r
+ "name": "Radius of the circle (in pixels)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[RCIRCLE]"\r
+ },\r
+ {\r
+ "id": "imageSize", \r
+ "name": "Size of the image (square; in pixels)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[IMAGESIZE]"\r
+ }, \r
+ {\r
+ "id": "circleCenter", \r
+ "name": "2D coordinates of the circle center (in pixels; e.g., 200 250)", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[CIRCLECENTER]"\r
+ }, \r
+ {\r
+ "id": "dirOut", \r
+ "name": "Output directory name", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[DIROUT]"\r
+ }, \r
+ {\r
+ "id": "noiseType", \r
+ "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", \r
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "command-line-flag-separator": "",\r
+ "value-key": "[NOISETYPE]"\r
+ }, \r
+ {\r
+ "id": "noiseAmount", \r
+ "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
+ "optional": false, \r
+ "type": "String", \r
+ "command-line-flag": "",\r
+ "value-key": "[NOISEAMOUNT]"\r
+ }\r
+ ], \r
+ "output-files":[\r
+ {\r
+ "id" : "resultTarball",\r
+ "name" : "resultTarball",\r
+ "description" : "archive of the output folder containing execution results, and the output of the command",\r
+ "path-template" : "results.tar.gz",\r
+ "optional": false, \r
+ "value-key" : "[RESULTS]"\r
+ }\r
+ ]\r
+}
\ No newline at end of file