From 05be8ac4091470e0513b4eaec95fe80969b0ce1c Mon Sep 17 00:00:00 2001 From: Sorina Pop Date: Thu, 4 Jul 2019 15:03:30 +0200 Subject: [PATCH] added boutiques descriptors --- boutiquesDesc/1D_creaPhase.json | 153 ++++++++++++++++++++++ boutiquesDesc/3wires_creaPhase.json | 153 ++++++++++++++++++++++ boutiquesDesc/circle_creaPhase.json | 188 ++++++++++++++++++++++++++++ 3 files changed, 494 insertions(+) create mode 100644 boutiquesDesc/1D_creaPhase.json create mode 100644 boutiquesDesc/3wires_creaPhase.json create mode 100644 boutiquesDesc/circle_creaPhase.json diff --git a/boutiquesDesc/1D_creaPhase.json b/boutiquesDesc/1D_creaPhase.json new file mode 100644 index 0000000..06f6827 --- /dev/null +++ b/boutiquesDesc/1D_creaPhase.json @@ -0,0 +1,153 @@ +{ + "name": "CreaPhase1D", + "container-image": { + "type": "docker", + "image": "camarasu/creaphase:0.3" + }, + "tool-version": "v0.3", + "schema-version": "0.5", + "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", + "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]", + "description": "x-ray phase-contrast simulator", + "error-codes": [ + { + "code": 1, + "description": "Crashed" + } + ], + "inputs": [ + { + "id": "oversamp", + "name": "Oversampling of the projections : use 2 or 4", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[OVERSAMP]" + }, + { + "id": "basename", + "name": "Basename of the result files", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[BASENAME]" + }, + { + "id": "dist", + "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIST]" + }, + { + "id": "energy", + "name": "Energy of the incoming X-ray beam (in keV)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[ENERGY]" + }, + { + "id": "pixelSize", + "name": "Pixel size of the detector (in um)", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[PIXELSIZE]" + }, + { + "id": "nbProj", + "name": "Number of projections (e.g., 360)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NBPROJ]" + }, + { + "id": "rangeAngle", + "name": "Range of the tomography : 180 or 360 degrees", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[RANGEANGLE]" + }, + { + "id": "modelCtf", + "name": "Use 1 if you want to use the CTF model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELCTF]" + }, + { + "id": "modelFresnel", + "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELFRESNEL]" + }, + { + "id": "attfile", + "name": "Attenuation map file (in cm^-1)", + "optional": false, + "type": "File", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[ATTFILE]" + }, + { + "id": "PHFILE", + "name": "Refrcative index decrement map (delta)", + "optional": false, + "type": "File", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[PHFILE]" + }, + { + "id": "dirOut", + "name": "Output directory name", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIROUT]" + }, + { + "id": "noiseType", + "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NOISETYPE]" + }, + { + "id": "noiseAmount", + "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].", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[NOISEAMOUNT]" + } + ], + "output-files":[ + { + "id" : "resultTarball", + "name" : "resultTarball", + "description" : "archive of the output folder containing execution results, and the output of the command", + "path-template" : "results.tar.gz", + "optional": false, + "value-key" : "[RESULTS]" + } + ] +} \ No newline at end of file diff --git a/boutiquesDesc/3wires_creaPhase.json b/boutiquesDesc/3wires_creaPhase.json new file mode 100644 index 0000000..37c6239 --- /dev/null +++ b/boutiquesDesc/3wires_creaPhase.json @@ -0,0 +1,153 @@ +{ + "name": "CreaPhase3Wires", + "container-image": { + "type": "docker", + "image": "camarasu/creaphase:0.3" + }, + "tool-version": "v0.3", + "schema-version": "0.5", + "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", + "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]", + "description": "x-ray phase-contrast simulator", + "error-codes": [ + { + "code": 1, + "description": "Crashed" + } + ], + "inputs": [ + { + "id": "vers", + "name": "Set it to 'Radon' OR 'Analytical'to calculate projections accordingly", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[VERS]" + }, + { + "id": "oversamp", + "name": "Oversampling of the projections : use 2 or 4", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[OVERSAMP]" + }, + { + "id": "basename", + "name": "Basename of the result files", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[BASENAME]" + }, + { + "id": "dist", + "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIST]" + }, + { + "id": "energy", + "name": "Energy of the incoming X-ray beam (in keV)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[ENERGY]" + }, + { + "id": "pixelSize", + "name": "Pixel size of the detector (in um)", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[PIXELSIZE]" + }, + { + "id": "nbProj", + "name": "Number of projections (e.g., 360)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NBPROJ]" + }, + { + "id": "rangeAngle", + "name": "Range of the tomography : 180 or 360 degrees", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[RANGEANGLE]" + }, + { + "id": "modelCtf", + "name": "Use 1 if you want to use the CTF model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELCTF]" + }, + { + "id": "modelFresnel", + "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELFRESNEL]" + }, + { + "id": "height", + "name": "height of the object. If height == 1, the simulation is computed in 1D. If height >=2 , the simulation turns into 2D.", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[HEIGHT]" + }, + { + "id": "dirOut", + "name": "Output directory name", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIROUT]" + }, + { + "id": "noiseType", + "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NOISETYPE]" + }, + { + "id": "noiseAmount", + "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].", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[NOISEAMOUNT]" + } + ], + "output-files":[ + { + "id" : "resultTarball", + "name" : "resultTarball", + "description" : "archive of the output folder containing execution results, and the output of the command", + "path-template" : "results.tar.gz", + "optional": false, + "value-key" : "[RESULTS]" + } + ] +} \ No newline at end of file diff --git a/boutiquesDesc/circle_creaPhase.json b/boutiquesDesc/circle_creaPhase.json new file mode 100644 index 0000000..7825a45 --- /dev/null +++ b/boutiquesDesc/circle_creaPhase.json @@ -0,0 +1,188 @@ +{ + "name": "CreaPhaseCircle", + "container-image": { + "type": "docker", + "image": "camarasu/creaphase:0.3" + }, + "tool-version": "v0.3", + "schema-version": "0.5", + "author": "Loriane Weber, Simon Rit, Jean Michel Létang, Françoise Peyrin, Max Langer", + "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]", + "description": "x-ray phase-contrast simulator", + "error-codes": [ + { + "code": 1, + "description": "Crashed" + } + ], + "inputs": [ + { + "id": "vers", + "name": "Set it to 'Radon' OR 'Analytical'to calculate projections accordingly", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[VERS]" + }, + { + "id": "oversamp", + "name": "Oversampling of the projections : use 2 or 4", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[OVERSAMP]" + }, + { + "id": "basename", + "name": "Basename of the result files", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[BASENAME]" + }, + { + "id": "dist", + "name": "Distances of propagation (in m), e.g. 0 0.01 0.1 0.20 0.50", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIST]" + }, + { + "id": "energy", + "name": "Energy of the incoming X-ray beam (in keV)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[ENERGY]" + }, + { + "id": "pixelSize", + "name": "Pixel size of the detector (in um)", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[PIXELSIZE]" + }, + { + "id": "nbProj", + "name": "Number of projections (e.g., 360)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NBPROJ]" + }, + { + "id": "rangeAngle", + "name": "Range of the tomography : 180 or 360 degrees", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[RANGEANGLE]" + }, + { + "id": "modelCtf", + "name": "Use 1 if you want to use the CTF model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELCTF]" + }, + { + "id": "modelFresnel", + "name": "Use 1 if you want to use the Fresnel model, 0 otherwise", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MODELFRESNEL]" + }, + { + "id": "muMat", + "name": "Linear attenuation coefficient of the material of the circle (e.g. 0.89 cm-1 for PET at 19keV)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[MUMAT]" + }, + { + "id": "deltaMat", + "name": "Refractive index decrement of the material of the circle, in 10^-7 (e.g. 8.265 for PET at 19keV)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DELTAMAT]" + }, + { + "id": "Rcircle", + "name": "Radius of the circle (in pixels)", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[RCIRCLE]" + }, + { + "id": "imageSize", + "name": "Size of the image (square; in pixels)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[IMAGESIZE]" + }, + { + "id": "circleCenter", + "name": "2D coordinates of the circle center (in pixels; e.g., 200 250)", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[CIRCLECENTER]" + }, + { + "id": "dirOut", + "name": "Output directory name", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[DIROUT]" + }, + { + "id": "noiseType", + "name": "Use noise='gaussian' (addition of gaussian noise) or noise='poisson' (generation of Poisson noise).", + "optional": false, + "type": "String", + "command-line-flag": "", + "command-line-flag-separator": "", + "value-key": "[NOISETYPE]" + }, + { + "id": "noiseAmount", + "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].", + "optional": false, + "type": "String", + "command-line-flag": "", + "value-key": "[NOISEAMOUNT]" + } + ], + "output-files":[ + { + "id" : "resultTarball", + "name" : "resultTarball", + "description" : "archive of the output folder containing execution results, and the output of the command", + "path-template" : "results.tar.gz", + "optional": false, + "value-key" : "[RESULTS]" + } + ] +} \ No newline at end of file -- 2.44.0