niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_2d_im_reg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_2D_IM_REG_METADATA = Metadata(
-    id="d47b19dea6381753231a4f8437ee507f05018c19.boutiques",
+    id="32da490dea2c5596f84ae91dd7499565aaa2b274.boutiques",
     name="2dImReg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_2D_IM_REG_METADATA = Metadata(
 
 
 V2dImRegParameters = typing.TypedDict('V2dImRegParameters', {
-    "__STYXTYPE__": typing.Literal["2dImReg"],
+    "@type": typing.NotRequired[typing.Literal["afni/2dImReg"]],
+    "input_file": InputPathType,
+    "base_file": typing.NotRequired[InputPathType | None],
+    "base": typing.NotRequired[float | None],
+    "nofine": bool,
+    "fine_blur": typing.NotRequired[float | None],
+    "fine_dxy": typing.NotRequired[float | None],
+    "fine_dphi": typing.NotRequired[float | None],
+    "prefix": str,
+    "dprefix": typing.NotRequired[str | None],
+    "dmm": bool,
+    "rprefix": typing.NotRequired[str | None],
+    "debug": bool,
+})
+V2dImRegParametersTagged = typing.TypedDict('V2dImRegParametersTagged', {
+    "@type": typing.Literal["afni/2dImReg"],
     "input_file": InputPathType,
     "base_file": typing.NotRequired[InputPathType | None],
     "base": typing.NotRequired[float | None],
@@ -28,43 +43,11 @@ V2dImRegParameters = typing.TypedDict('V2dImRegParameters', {
     "rprefix": typing.NotRequired[str | None],
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "2dImReg": v_2d_im_reg_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "2dImReg": v_2d_im_reg_outputs,
-    }.get(t)
 
 
 class V2dImRegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_2d_im_reg(...)`.
+    Output object returned when calling `V2dImRegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +78,7 @@ def v_2d_im_reg_params(
     dmm: bool = False,
     rprefix: str | None = None,
     debug: bool = False,
-) -> V2dImRegParameters:
+) -> V2dImRegParametersTagged:
     """
     Build parameters.
     
@@ -123,7 +106,7 @@ def v_2d_im_reg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "2dImReg",
+        "@type": "afni/2dImReg",
         "input_file": input_file,
         "nofine": nofine,
         "prefix": prefix,
@@ -162,27 +145,27 @@ def v_2d_im_reg_cargs(
     """
     cargs = []
     cargs.append("2dImReg")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("base_file") is not None:
-        cargs.append(execution.input_file(params.get("base_file")))
-    if params.get("base") is not None:
-        cargs.append(str(params.get("base")))
-    if params.get("nofine"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("base_file", None) is not None:
+        cargs.append(execution.input_file(params.get("base_file", None)))
+    if params.get("base", None) is not None:
+        cargs.append(str(params.get("base", None)))
+    if params.get("nofine", False):
         cargs.append("-nofine")
-    if params.get("fine_blur") is not None:
-        cargs.append(str(params.get("fine_blur")))
-    if params.get("fine_dxy") is not None:
-        cargs.append(str(params.get("fine_dxy")))
-    if params.get("fine_dphi") is not None:
-        cargs.append(str(params.get("fine_dphi")))
-    cargs.append(params.get("prefix"))
-    if params.get("dprefix") is not None:
-        cargs.append(params.get("dprefix"))
-    if params.get("dmm"):
+    if params.get("fine_blur", None) is not None:
+        cargs.append(str(params.get("fine_blur", None)))
+    if params.get("fine_dxy", None) is not None:
+        cargs.append(str(params.get("fine_dxy", None)))
+    if params.get("fine_dphi", None) is not None:
+        cargs.append(str(params.get("fine_dphi", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("dprefix", None) is not None:
+        cargs.append(params.get("dprefix", None))
+    if params.get("dmm", False):
         cargs.append("-dmm")
-    if params.get("rprefix") is not None:
-        cargs.append(params.get("rprefix"))
-    if params.get("debug"):
+    if params.get("rprefix", None) is not None:
+        cargs.append(params.get("rprefix", None))
+    if params.get("debug", False):
         cargs.append("-debug")
     return cargs
 
@@ -202,21 +185,23 @@ def v_2d_im_reg_outputs(
     """
     ret = V2dImRegOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + ".nii"),
-        dx_file=execution.output_file(params.get("dprefix") + ".dx") if (params.get("dprefix") is not None) else None,
-        dy_file=execution.output_file(params.get("dprefix") + ".dy") if (params.get("dprefix") is not None) else None,
-        psi_file=execution.output_file(params.get("dprefix") + ".psi") if (params.get("dprefix") is not None) else None,
-        oldrms_file=execution.output_file(params.get("rprefix") + ".oldrms") if (params.get("rprefix") is not None) else None,
-        newrms_file=execution.output_file(params.get("rprefix") + ".newrms") if (params.get("rprefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + ".nii"),
+        dx_file=execution.output_file(params.get("dprefix", None) + ".dx") if (params.get("dprefix") is not None) else None,
+        dy_file=execution.output_file(params.get("dprefix", None) + ".dy") if (params.get("dprefix") is not None) else None,
+        psi_file=execution.output_file(params.get("dprefix", None) + ".psi") if (params.get("dprefix") is not None) else None,
+        oldrms_file=execution.output_file(params.get("rprefix", None) + ".oldrms") if (params.get("rprefix") is not None) else None,
+        newrms_file=execution.output_file(params.get("rprefix", None) + ".newrms") if (params.get("rprefix") is not None) else None,
     )
     return ret
 
 
 def v_2d_im_reg_execute(
     params: V2dImRegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V2dImRegOutputs:
     """
+    2dImReg
+    
     2D image registration tool for 3D+time datasets, aligning images on a
     slice-by-slice basis to a specified base image.
     
@@ -226,10 +211,12 @@ def v_2d_im_reg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V2dImRegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_2D_IM_REG_METADATA)
     params = execution.params(params)
     cargs = v_2d_im_reg_cargs(params, execution)
     ret = v_2d_im_reg_outputs(params, execution)
@@ -253,6 +240,8 @@ def v_2d_im_reg(
     runner: Runner | None = None,
 ) -> V2dImRegOutputs:
     """
+    2dImReg
+    
     2D image registration tool for 3D+time datasets, aligning images on a
     slice-by-slice basis to a specified base image.
     
@@ -284,8 +273,6 @@ def v_2d_im_reg(
     Returns:
         NamedTuple of outputs (described in `V2dImRegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_2D_IM_REG_METADATA)
     params = v_2d_im_reg_params(
         input_file=input_file,
         base_file=base_file,
@@ -300,13 +287,13 @@ def v_2d_im_reg(
         rprefix=rprefix,
         debug=debug,
     )
-    return v_2d_im_reg_execute(params, execution)
+    return v_2d_im_reg_execute(params, runner)
 
 
 __all__ = [
     "V2dImRegOutputs",
-    "V2dImRegParameters",
     "V_2D_IM_REG_METADATA",
     "v_2d_im_reg",
+    "v_2d_im_reg_execute",
     "v_2d_im_reg_params",
 ]

niwrap_afni/afni/v_2dcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_2DCAT_METADATA = Metadata(
-    id="1ff7d0dc60f4bf318c5c16752466d2ad9856a898.boutiques",
+    id="03370af5883433df5196ac562f5e8f61af9b2c92.boutiques",
     name="2dcat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,35 @@ V_2DCAT_METADATA = Metadata(
 
 
 V2dcatParameters = typing.TypedDict('V2dcatParameters', {
-    "__STYXTYPE__": typing.Literal["2dcat"],
+    "@type": typing.NotRequired[typing.Literal["afni/2dcat"]],
+    "filenames": list[InputPathType],
+    "scale_image": typing.NotRequired[InputPathType | None],
+    "scale_pixels": typing.NotRequired[InputPathType | None],
+    "scale_intensity": bool,
+    "gscale": typing.NotRequired[float | None],
+    "rgb_out": bool,
+    "res_in": typing.NotRequired[list[float] | None],
+    "respad_in": typing.NotRequired[list[float] | None],
+    "pad_val": typing.NotRequired[float | None],
+    "crop": typing.NotRequired[list[float] | None],
+    "autocrop_ctol": typing.NotRequired[float | None],
+    "autocrop_atol": typing.NotRequired[float | None],
+    "autocrop": bool,
+    "zero_wrap": bool,
+    "white_wrap": bool,
+    "gray_wrap": typing.NotRequired[float | None],
+    "image_wrap": bool,
+    "rand_wrap": bool,
+    "prefix": typing.NotRequired[str | None],
+    "matrix": typing.NotRequired[list[float] | None],
+    "nx": typing.NotRequired[float | None],
+    "ny": typing.NotRequired[float | None],
+    "matrix_from_scale": bool,
+    "gap": typing.NotRequired[float | None],
+    "gap_col": typing.NotRequired[list[float] | None],
+})
+V2dcatParametersTagged = typing.TypedDict('V2dcatParametersTagged', {
+    "@type": typing.Literal["afni/2dcat"],
     "filenames": list[InputPathType],
     "scale_image": typing.NotRequired[InputPathType | None],
     "scale_pixels": typing.NotRequired[InputPathType | None],
@@ -41,43 +69,11 @@ V2dcatParameters = typing.TypedDict('V2dcatParameters', {
     "gap": typing.NotRequired[float | None],
     "gap_col": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "2dcat": v_2dcat_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "2dcat": v_2dcat_outputs,
-    }.get(t)
 
 
 class V2dcatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_2dcat(...)`.
+    Output object returned when calling `V2dcatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -114,7 +110,7 @@ def v_2dcat_params(
     matrix_from_scale: bool = False,
     gap: float | None = None,
     gap_col: list[float] | None = None,
-) -> V2dcatParameters:
+) -> V2dcatParametersTagged:
     """
     Build parameters.
     
@@ -166,7 +162,7 @@ def v_2dcat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "2dcat",
+        "@type": "afni/2dcat",
         "filenames": filenames,
         "scale_intensity": scale_intensity,
         "rgb_out": rgb_out,
@@ -227,102 +223,102 @@ def v_2dcat_cargs(
     """
     cargs = []
     cargs.append("2dcat")
-    cargs.extend([execution.input_file(f) for f in params.get("filenames")])
-    if params.get("scale_image") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("filenames", None)])
+    if params.get("scale_image", None) is not None:
         cargs.extend([
             "-scale_image",
-            execution.input_file(params.get("scale_image"))
+            execution.input_file(params.get("scale_image", None))
         ])
-    if params.get("scale_pixels") is not None:
+    if params.get("scale_pixels", None) is not None:
         cargs.extend([
             "-scale_pixels",
-            execution.input_file(params.get("scale_pixels"))
+            execution.input_file(params.get("scale_pixels", None))
         ])
-    if params.get("scale_intensity"):
+    if params.get("scale_intensity", False):
         cargs.append("-scale_intensity")
-    if params.get("gscale") is not None:
+    if params.get("gscale", None) is not None:
         cargs.extend([
             "-gscale",
-            str(params.get("gscale"))
+            str(params.get("gscale", None))
         ])
-    if params.get("rgb_out"):
+    if params.get("rgb_out", False):
         cargs.append("-rgb_out")
-    if params.get("res_in") is not None:
+    if params.get("res_in", None) is not None:
         cargs.extend([
             "-res_in",
-            *map(str, params.get("res_in"))
+            *map(str, params.get("res_in", None))
         ])
-    if params.get("respad_in") is not None:
+    if params.get("respad_in", None) is not None:
         cargs.extend([
             "-respad_in",
-            *map(str, params.get("respad_in"))
+            *map(str, params.get("respad_in", None))
         ])
-    if params.get("pad_val") is not None:
+    if params.get("pad_val", None) is not None:
         cargs.extend([
             "-pad_val",
-            str(params.get("pad_val"))
+            str(params.get("pad_val", None))
         ])
-    if params.get("crop") is not None:
+    if params.get("crop", None) is not None:
         cargs.extend([
             "-crop",
-            *map(str, params.get("crop"))
+            *map(str, params.get("crop", None))
         ])
-    if params.get("autocrop_ctol") is not None:
+    if params.get("autocrop_ctol", None) is not None:
         cargs.extend([
             "-autocrop_ctol",
-            str(params.get("autocrop_ctol"))
+            str(params.get("autocrop_ctol", None))
         ])
-    if params.get("autocrop_atol") is not None:
+    if params.get("autocrop_atol", None) is not None:
         cargs.extend([
             "-autocrop_atol",
-            str(params.get("autocrop_atol"))
+            str(params.get("autocrop_atol", None))
         ])
-    if params.get("autocrop"):
+    if params.get("autocrop", False):
         cargs.append("-autocrop")
-    if params.get("zero_wrap"):
+    if params.get("zero_wrap", False):
         cargs.append("-zero_wrap")
-    if params.get("white_wrap"):
+    if params.get("white_wrap", False):
         cargs.append("-white_wrap")
-    if params.get("gray_wrap") is not None:
+    if params.get("gray_wrap", None) is not None:
         cargs.extend([
             "-gray_wrap",
-            str(params.get("gray_wrap"))
+            str(params.get("gray_wrap", None))
         ])
-    if params.get("image_wrap"):
+    if params.get("image_wrap", False):
         cargs.append("-image_wrap")
-    if params.get("rand_wrap"):
+    if params.get("rand_wrap", False):
         cargs.append("-rand_wrap")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("matrix") is not None:
+    if params.get("matrix", None) is not None:
         cargs.extend([
             "-matrix",
-            *map(str, params.get("matrix"))
+            *map(str, params.get("matrix", None))
         ])
-    if params.get("nx") is not None:
+    if params.get("nx", None) is not None:
         cargs.extend([
             "-nx",
-            str(params.get("nx"))
+            str(params.get("nx", None))
         ])
-    if params.get("ny") is not None:
+    if params.get("ny", None) is not None:
         cargs.extend([
             "-ny",
-            str(params.get("ny"))
+            str(params.get("ny", None))
         ])
-    if params.get("matrix_from_scale"):
+    if params.get("matrix_from_scale", False):
         cargs.append("-matrix_from_scale")
-    if params.get("gap") is not None:
+    if params.get("gap", None) is not None:
         cargs.extend([
             "-gap",
-            str(params.get("gap"))
+            str(params.get("gap", None))
         ])
-    if params.get("gap_col") is not None:
+    if params.get("gap_col", None) is not None:
         cargs.extend([
             "-gap_col",
-            *map(str, params.get("gap_col"))
+            *map(str, params.get("gap_col", None))
         ])
     return cargs
 
@@ -342,17 +338,19 @@ def v_2dcat_outputs(
     """
     ret = V2dcatOutputs(
         root=execution.output_file("."),
-        output_image=execution.output_file(params.get("prefix") + ".ppm") if (params.get("prefix") is not None) else None,
-        output_1_d=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
+        output_image=execution.output_file(params.get("prefix", None) + ".ppm") if (params.get("prefix") is not None) else None,
+        output_1_d=execution.output_file(params.get("prefix", None) + ".1D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_2dcat_execute(
     params: V2dcatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V2dcatOutputs:
     """
+    2dcat
+    
     Puts a set of images into an image matrix montage of NX by NY images.
     
     Author: AFNI Developers
@@ -361,10 +359,12 @@ def v_2dcat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V2dcatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_2DCAT_METADATA)
     params = execution.params(params)
     cargs = v_2dcat_cargs(params, execution)
     ret = v_2dcat_outputs(params, execution)
@@ -401,6 +401,8 @@ def v_2dcat(
     runner: Runner | None = None,
 ) -> V2dcatOutputs:
     """
+    2dcat
+    
     Puts a set of images into an image matrix montage of NX by NY images.
     
     Author: AFNI Developers
@@ -455,8 +457,6 @@ def v_2dcat(
     Returns:
         NamedTuple of outputs (described in `V2dcatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_2DCAT_METADATA)
     params = v_2dcat_params(
         filenames=filenames,
         scale_image=scale_image,
@@ -484,13 +484,13 @@ def v_2dcat(
         gap=gap,
         gap_col=gap_col,
     )
-    return v_2dcat_execute(params, execution)
+    return v_2dcat_execute(params, runner)
 
 
 __all__ = [
     "V2dcatOutputs",
-    "V2dcatParameters",
     "V_2DCAT_METADATA",
     "v_2dcat",
+    "v_2dcat_execute",
     "v_2dcat_params",
 ]