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Update the argument type of outputs (#198)
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* Add script to update output args to 'String'

* Update descriptor output args
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kaitj authored Dec 20, 2024
1 parent 8ac6054 commit 409bcf7
Showing 82 changed files with 444 additions and 236 deletions.
4 changes: 2 additions & 2 deletions descriptors/afni/SurfSmooth.json
Original file line number Diff line number Diff line change
@@ -62,7 +62,7 @@
{
"id": "output_file",
"name": "Output File",
"type": "File",
"type": "String",
"description": "Name of output file. Default based on method being used.",
"command-line-flag": "-output",
"optional": true,
@@ -164,4 +164,4 @@
"image": "afni/afni_make_build:AFNI_24.2.06"
},
"url": "https://afni.nimh.nih.gov/"
}
}
4 changes: 2 additions & 2 deletions descriptors/afni/apsearch.json
Original file line number Diff line number Diff line change
@@ -22,7 +22,7 @@
{
"description": "File to save the search results",
"value-key": "[FILE_OUTPUT]",
"type": "File",
"type": "String",
"optional": true,
"id": "file_output",
"name": "File Output"
@@ -47,4 +47,4 @@
"name": "Output File"
}
]
}
}
4 changes: 2 additions & 2 deletions descriptors/afni/imand.json
Original file line number Diff line number Diff line change
@@ -31,7 +31,7 @@
{
"description": "Output image file.",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"optional": false,
"id": "output_image",
"name": "Output Image"
@@ -48,4 +48,4 @@
}
],
"url": "https://afni.nimh.nih.gov/"
}
}
4 changes: 2 additions & 2 deletions descriptors/afni/imrotate.json
Original file line number Diff line number Diff line change
@@ -22,7 +22,7 @@
{
"description": "Output image file",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"optional": false,
"id": "output_image",
"name": "Output Image"
@@ -80,4 +80,4 @@
"name": "Output Image"
}
]
}
}
4 changes: 2 additions & 2 deletions descriptors/afni/qhull.json
Original file line number Diff line number Diff line change
@@ -193,7 +193,7 @@
"command-line-flag": "TO",
"description": "Output results to file.",
"value-key": "[OUTPUT_FILE]",
"type": "File",
"type": "String",
"optional": true,
"id": "output_file",
"name": "Output File"
@@ -208,4 +208,4 @@
"name": "Output Results"
}
]
}
}
4 changes: 2 additions & 2 deletions descriptors/afni/quotize.json
Original file line number Diff line number Diff line change
@@ -24,7 +24,7 @@
{
"description": "Output file which will contain the C array of strings.",
"value-key": "[OUTPUT_FILE]",
"type": "File",
"type": "String",
"optional": false,
"id": "output_file",
"name": "Output file"
@@ -45,4 +45,4 @@
"image": "afni/afni_make_build:AFNI_24.2.06"
},
"url": "https://afni.nimh.nih.gov/"
}
}
22 changes: 17 additions & 5 deletions descriptors/ants/AddNoiseToImage.json
Original file line number Diff line number Diff line change
@@ -18,7 +18,11 @@
"type": "Number",
"integer": true,
"optional": true,
"value-choices": [2, 3, 4],
"value-choices": [
2,
3,
4
],
"command-line-flag": "--image-dimensionality",
"description": "This option forces the image to be treated as a specified-dimensional image. If not specified, the program tries to infer the dimensionality from the input image."
},
@@ -38,14 +42,19 @@
"type": "String",
"optional": false,
"command-line-flag": "--noise-model",
"value-choices": ["AdditiveGaussian", "SaltAndPepper", "Shot", "Speckle"],
"value-choices": [
"AdditiveGaussian",
"SaltAndPepper",
"Shot",
"Speckle"
],
"description": "Use different noise models each with its own (default) parameters."
},
{
"id": "output",
"name": "Output",
"value-key": "[OUTPUT]",
"type": "File",
"type": "String",
"optional": false,
"command-line-flag": "--output",
"description": "The output consists of the noise corrupted version of the input image."
@@ -57,7 +66,10 @@
"type": "Number",
"integer": true,
"optional": true,
"value-choices": [0, 1],
"value-choices": [
0,
1
],
"command-line-flag": "--verbose",
"description": "Verbose output."
}
@@ -70,4 +82,4 @@
"path-template": "[OUTPUT]"
}
]
}
}
4 changes: 2 additions & 2 deletions descriptors/ants/ConvertScalarImageToRGB.json
Original file line number Diff line number Diff line change
@@ -32,7 +32,7 @@
"id": "output_image",
"name": "Output Image",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"optional": false,
"description": "The output RGB image file."
},
@@ -130,4 +130,4 @@
"path-template": "[OUTPUT_IMAGE]"
}
]
}
}
9 changes: 6 additions & 3 deletions descriptors/ants/CreateDisplacementField.json
Original file line number Diff line number Diff line change
@@ -27,7 +27,10 @@
"type": "Number",
"integer": true,
"optional": false,
"value-choices": [0, 1],
"value-choices": [
0,
1
],
"description": "Create zero-valued vectors along the borders when enabled (pass 1), recommended for better displacement field behavior."
},
{
@@ -45,7 +48,7 @@
"id": "output_image",
"name": "Output Image",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"optional": false,
"description": "The output displacement field image with itkVector pixels."
}
@@ -58,4 +61,4 @@
"path-template": "[OUTPUT_IMAGE]"
}
]
}
}
18 changes: 14 additions & 4 deletions descriptors/ants/CreateTiledMosaic.json
Original file line number Diff line number Diff line change
@@ -60,7 +60,7 @@
"id": "output",
"name": "Output Tiled Mosaic Image",
"value-key": "[OUTPUT]",
"type": "File",
"type": "String",
"optional": false,
"command-line-flag": "-o",
"description": "The output is the tiled mosaic image. The format must support the specific data type: floating point images without RGB overlays, Rgb images with intensities scaled to [0,255] if overlays are present."
@@ -82,7 +82,14 @@
"optional": true,
"command-line-flag": "-d",
"description": "Specifies the direction of the slices. Can be based on image storage in memory or aligned physical space. Defaults to z-direction if unspecified.",
"value-choices": ["0", "1", "2", "x", "y", "z"]
"value-choices": [
"0",
"1",
"2",
"x",
"y",
"z"
]
},
{
"id": "pad_or_crop",
@@ -119,7 +126,10 @@
"integer": true,
"optional": true,
"command-line-flag": "-g",
"value-choices": [0, 1],
"value-choices": [
0,
1
],
"description": "Permute (or swap) the axes of the individual slice images."
}
],
@@ -131,4 +141,4 @@
"path-template": "[OUTPUT]"
}
]
}
}
10 changes: 7 additions & 3 deletions descriptors/ants/ImageMath.json
Original file line number Diff line number Diff line change
@@ -18,7 +18,11 @@
"type": "Number",
"integer": true,
"optional": false,
"value-choices": [2, 3, 4],
"value-choices": [
2,
3,
4
],
"description": "The dimensionality of the image. Use 2 or 3 for spatial images, and 4 for 4D images like time-series data."
},
{
@@ -33,7 +37,7 @@
"id": "output_image",
"name": "Output Image",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"optional": false,
"description": "The output image file resulting from the operations."
},
@@ -62,4 +66,4 @@
"path-template": "[OUTPUT_IMAGE]"
}
]
}
}
14 changes: 10 additions & 4 deletions descriptors/ants/MultiplyImages.json
Original file line number Diff line number Diff line change
@@ -19,7 +19,10 @@
"description": "3 or 2. Image dimension (2 or 3).",
"optional": false,
"integer": true,
"value-choices": [3, 2]
"value-choices": [
3,
2
]
},
{
"id": "first_input",
@@ -42,7 +45,7 @@
{
"id": "output_product_image",
"name": "Output product image",
"type": "File",
"type": "String",
"value-key": "[OUTPUT_PRODUCT_IMAGE]",
"description": "Outputfname.nii.gz: the name of the resulting image.",
"optional": false
@@ -77,8 +80,11 @@
{
"id": "second_input_group",
"name": "Second input group",
"members": ["second_input", "second_input_2"],
"members": [
"second_input",
"second_input_2"
],
"mutually-exclusive": true
}
]
}
}
25 changes: 19 additions & 6 deletions descriptors/ants/NonLocalSuperResolution.json
Original file line number Diff line number Diff line change
@@ -14,7 +14,11 @@
"type": "Number",
"integer": true,
"optional": true,
"value-choices": [2, 3, 4],
"value-choices": [
2,
3,
4
],
"description": "This option forces the image to be treated as a specified-dimensional image. If not specified, the program tries to infer the dimensionality from the input image."
},
{
@@ -51,7 +55,10 @@
"value-key": "[PATCH_RADIUS]",
"type": "String",
"optional": true,
"value-choices": ["1", "1x1x1"],
"value-choices": [
"1",
"1x1x1"
],
"description": "Patch radius. Default = 1x1x1."
},
{
@@ -61,7 +68,10 @@
"value-key": "[SEARCH_RADIUS]",
"type": "String",
"optional": true,
"value-choices": ["3", "3x3x3"],
"value-choices": [
"3",
"3x3x3"
],
"description": "Search radius. Default = 3x3x3."
},
{
@@ -118,7 +128,7 @@
"name": "Output",
"command-line-flag": "-o",
"value-key": "[OUTPUT]",
"type": "File",
"type": "String",
"optional": false,
"description": "The output consists of the noise corrected version of the input image. Optionally, one can also output the estimated noise image."
},
@@ -130,7 +140,10 @@
"type": "Number",
"integer": true,
"optional": true,
"value-choices": [0, 1],
"value-choices": [
0,
1
],
"description": "Verbose output."
}
],
@@ -147,4 +160,4 @@
"type": "docker",
"image": "antsx/ants:v2.5.3"
}
}
}
10 changes: 7 additions & 3 deletions descriptors/ants/PasteImageIntoImage.json
Original file line number Diff line number Diff line change
@@ -31,7 +31,7 @@
"id": "output_image",
"name": "Output image",
"value-key": "[OUTPUT_IMAGE]",
"type": "File",
"type": "String",
"description": "The resulting image after pasting."
},
{
@@ -59,7 +59,11 @@
"integer": true,
"optional": true,
"default-value": 0,
"value-choices": [0, 1, 2],
"value-choices": [
0,
1,
2
],
"description": "Defines behavior when the input image voxel is non-background and the corresponding canvas voxel is background: 0 - leave as is, 1 - replace with input voxel value, 2 - replace with conflict label."
},
{
@@ -87,4 +91,4 @@
"type": "docker",
"image": "antsx/ants:v2.5.3"
}
}
}
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