added boutiques descriptors

diff --git a/boutiquesDesc/1D_creaPhase.json b/boutiquesDesc/1D_creaPhase.json
new file mode 100644 (file)
index 0000000..06f6827
--- /dev/null
+++ b/boutiquesDesc/1D_creaPhase.json
@@ -0,0 +1,153 @@
+{\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

diff --git a/boutiquesDesc/3wires_creaPhase.json b/boutiquesDesc/3wires_creaPhase.json
new file mode 100644 (file)
index 0000000..37c6239
--- /dev/null
+++ b/boutiquesDesc/3wires_creaPhase.json
@@ -0,0 +1,153 @@
+{\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

diff --git a/boutiquesDesc/circle_creaPhase.json b/boutiquesDesc/circle_creaPhase.json
new file mode 100644 (file)
index 0000000..7825a45
--- /dev/null
+++ b/boutiquesDesc/circle_creaPhase.json
@@ -0,0 +1,188 @@
+{\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