Merge branch 'main' of https://github.com/childmindresearch/niwrap

childmindresearch · Nov 15, 2024 · b672311 · b672311
2 parents e43814f + 08b3b87
commit b672311
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Showing 3 changed files with 56 additions and 13 deletions.
diff --git a/descriptors/afni/3dcalc.json b/descriptors/afni/3dcalc.json
@@ -1,6 +1,6 @@
 {
   "name": "3dcalc",
-  "command-line": "3dcalc [EXPR] [IN_FILE_A] [IN_FILE_B] [IN_FILE_C] [OTHER] [OVERWRITE] [SINGLE_IDX] [START_IDX] [STOP_IDX]",
+  "command-line": "3dcalc  [IN_FILE_A] [IN_FILE_B] [IN_FILE_C] [OTHER] [OVERWRITE] [SINGLE_IDX] [START_IDX] [STOP_IDX] [EXPR] [PREFIX]",
   "author": "AFNI Developers",
   "description": "AFNI's calculator program.",
   "url": "https://afni.nimh.nih.gov/",
@@ -11,7 +11,8 @@
       "type": "String",
       "value-key": "[EXPR]",
       "description": "Expr.",
-      "optional": false
+      "optional": false,
+      "command-line-flag": "-expr"
     },
     {
       "id": "in_file_a",
@@ -85,6 +86,15 @@
       "description": "Stop index for in_file_a.",
       "optional": true,
       "requires-inputs": ["start_idx"]
+    },
+    {
+      "id": "prefix",
+      "name": "Prefix",
+      "type": "String",
+      "value-key": "[PREFIX]",
+      "description": "Output image file name.",
+      "optional": true,
+      "command-line-flag": "-prefix"
     }
   ],
   "output-files": [
@@ -93,9 +103,8 @@
       "id": "out_file",
       "optional": true,
       "description": "Output image file name.",
-      "path-template": "[IN_FILE_A]",
-      "value-key": "[OUT_FILE]",
-      "command-line-flag": "-prefix"
+      "path-template": "[PREFIX]",
+      "value-key": "[PREFIX]"
     }
   ],
   "tool-version": "24.2.06",

diff --git a/python/src/niwrap/afni/v_3dcalc.py b/python/src/niwrap/afni/v_3dcalc.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 V_3DCALC_METADATA = Metadata(
-    id="66f28a66a111cc3612e13fb86d7e368e7be0a5a2.boutiques",
+    id="f5920a7aeb8d11c3fc7da3fd2f8b59f05d574b09.boutiques",
     name="3dcalc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -20,20 +20,21 @@ class V3dcalcOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    out_file: OutputPathType
+    out_file: OutputPathType | None
     """Output image file name."""
 
 
 def v_3dcalc(
-    expr: str,
     in_file_a: InputPathType,
+    expr: str,
     in_file_b: InputPathType | None = None,
     in_file_c: InputPathType | None = None,
     other: InputPathType | None = None,
     overwrite: bool = False,
     single_idx: int | None = None,
     start_idx: int | None = None,
     stop_idx: int | None = None,
+    prefix: str | None = None,
     runner: Runner | None = None,
 ) -> V3dcalcOutputs:
     """
@@ -44,15 +45,16 @@ def v_3dcalc(
     URL: https://afni.nimh.nih.gov/
     
     Args:
-        expr: Expr.
         in_file_a: Input file to 3dcalc.
+        expr: Expr.
         in_file_b: Operand file to 3dcalc.
         in_file_c: Operand file to 3dcalc.
         other: Other options.
         overwrite: Overwrite output.
         single_idx: Volume index for in_file_a.
         start_idx: Start index for in_file_a.
         stop_idx: Stop index for in_file_a.
+        prefix: Output image file name.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dcalcOutputs`).
@@ -61,7 +63,6 @@ def v_3dcalc(
     execution = runner.start_execution(V_3DCALC_METADATA)
     cargs = []
     cargs.append("3dcalc")
-    cargs.append(expr)
     cargs.extend([
         "-a",
         execution.input_file(in_file_a)
@@ -86,9 +87,18 @@ def v_3dcalc(
         cargs.append(str(start_idx))
     if stop_idx is not None:
         cargs.append(str(stop_idx))
+    cargs.extend([
+        "-expr",
+        expr
+    ])
+    if prefix is not None:
+        cargs.extend([
+            "-prefix",
+            prefix
+        ])
     ret = V3dcalcOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(in_file_a).name),
+        out_file=execution.output_file(prefix) if (prefix is not None) else None,
     )
     execution.run(cargs)
     return ret

diff --git a/python/src/niwrap/ants/ants_apply_transforms.py b/python/src/niwrap/ants/ants_apply_transforms.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 ANTS_APPLY_TRANSFORMS_METADATA = Metadata(
-    id="84800d70a4619489f4cd962873674d0233d3976b.boutiques",
+    id="51e7058afdec76cc8dda4686e9c908617a912917.boutiques",
     name="antsApplyTransforms",
     package="ants",
     container_image_tag="antsx/ants:v2.5.3",
@@ -227,6 +227,29 @@ def run(
         return cargs
 
 
+@dataclasses.dataclass
+class AntsApplyTransformsMultiLabelnoparams:
+    """
+    Multi label interpolation.
+    """
+
+    def run(
+        self,
+        execution: Execution,
+    ) -> list[str]:
+        """
+        Build command line arguments. This method is called by the main command.
+        
+        Args:
+            execution: The execution object.
+        Returns:
+            Command line arguments
+        """
+        cargs = []
+        cargs.append("MultiLabel")
+        return cargs
+
+
 @dataclasses.dataclass
 class AntsApplyTransformsSigma:
     """
@@ -562,7 +585,7 @@ def ants_apply_transforms(
     output: typing.Union[AntsApplyTransformsWarpedOutput, AntsApplyTransformsCompositeDisplacementFieldOutput, AntsApplyTransformsGenericAffineTransformOutput],
     dimensionality: typing.Literal[2, 3, 4] | None = None,
     input_image_type: typing.Literal[0, 1, 2, 3, 4, 5] | None = None,
-    interpolation: typing.Union[AntsApplyTransformsLinear, AntsApplyTransformsNearestNeighbor, AntsApplyTransformsMultiLabel, AntsApplyTransformsGaussian, AntsApplyTransformsBspline, AntsApplyTransformsCosineWindowedSinc, AntsApplyTransformsWelchWindowedSinc, AntsApplyTransformsHammingWindowedSinc, AntsApplyTransformsLanczosWindowedSinc, AntsApplyTransformsGenericLabel] | None = None,
+    interpolation: typing.Union[AntsApplyTransformsLinear, AntsApplyTransformsNearestNeighbor, AntsApplyTransformsMultiLabelnoparams, AntsApplyTransformsMultiLabel, AntsApplyTransformsGaussian, AntsApplyTransformsBspline, AntsApplyTransformsCosineWindowedSinc, AntsApplyTransformsWelchWindowedSinc, AntsApplyTransformsHammingWindowedSinc, AntsApplyTransformsLanczosWindowedSinc, AntsApplyTransformsGenericLabel] | None = None,
     output_data_type: typing.Literal["char", "uchar", "short", "int", "float", "double", "default"] | None = None,
     transform: list[typing.Union[AntsApplyTransformsTransformFileName, AntsApplyTransformsUseInverse]] | None = None,
     default_value: float | None = None,
@@ -713,6 +736,7 @@ def ants_apply_transforms(
     "AntsApplyTransformsLanczosWindowedSinc",
     "AntsApplyTransformsLinear",
     "AntsApplyTransformsMultiLabel",
+    "AntsApplyTransformsMultiLabelnoparams",
     "AntsApplyTransformsNearestNeighbor",
     "AntsApplyTransformsOutputs",
     "AntsApplyTransformsParam",