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

niwrap_afni/afni/v__grad_flip_test.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__GRAD_FLIP_TEST_METADATA = Metadata(
-    id="f4c7bc4f70165e7a5d15e00cfa90501d609d65ee.boutiques",
+    id="be3d1568dfae8fa36c8177200c0e9f06c516f316.boutiques",
     name="@GradFlipTest",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V__GRAD_FLIP_TEST_METADATA = Metadata(
 
 
 VGradFlipTestParameters = typing.TypedDict('VGradFlipTestParameters', {
-    "__STYXTYPE__": typing.Literal["@GradFlipTest"],
+    "@type": typing.NotRequired[typing.Literal["afni/@GradFlipTest"]],
+    "dwi": InputPathType,
+    "grad_row_vec": typing.NotRequired[InputPathType | None],
+    "grad_col_vec": typing.NotRequired[InputPathType | None],
+    "grad_col_matA": typing.NotRequired[InputPathType | None],
+    "grad_col_matT": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bvals": typing.NotRequired[InputPathType | None],
+    "thresh_fa": typing.NotRequired[float | None],
+    "thresh_len": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "check_abs_min": typing.NotRequired[float | None],
+    "scale_out_1000": bool,
+    "wdir": typing.NotRequired[str | None],
+    "do_clean": bool,
+})
+VGradFlipTestParametersTagged = typing.TypedDict('VGradFlipTestParametersTagged', {
+    "@type": typing.Literal["afni/@GradFlipTest"],
     "dwi": InputPathType,
     "grad_row_vec": typing.NotRequired[InputPathType | None],
     "grad_col_vec": typing.NotRequired[InputPathType | None],
@@ -30,43 +47,11 @@ VGradFlipTestParameters = typing.TypedDict('VGradFlipTestParameters', {
     "wdir": typing.NotRequired[str | None],
     "do_clean": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@GradFlipTest": v__grad_flip_test_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 {
-        "@GradFlipTest": v__grad_flip_test_outputs,
-    }.get(t)
 
 
 class VGradFlipTestOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__grad_flip_test(...)`.
+    Output object returned when calling `VGradFlipTestParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def v__grad_flip_test_params(
     scale_out_1000: bool = False,
     wdir: str | None = None,
     do_clean: bool = False,
-) -> VGradFlipTestParameters:
+) -> VGradFlipTestParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +105,7 @@ def v__grad_flip_test_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@GradFlipTest",
+        "@type": "afni/@GradFlipTest",
         "dwi": dwi,
         "scale_out_1000": scale_out_1000,
         "do_clean": do_clean,
@@ -167,66 +152,66 @@ def v__grad_flip_test_cargs(
     cargs.append("@GradFlipTest")
     cargs.extend([
         "-in_dwi",
-        execution.input_file(params.get("dwi"))
+        execution.input_file(params.get("dwi", None))
     ])
-    if params.get("grad_row_vec") is not None:
+    if params.get("grad_row_vec", None) is not None:
         cargs.extend([
             "-in_row_vec",
-            execution.input_file(params.get("grad_row_vec"))
+            execution.input_file(params.get("grad_row_vec", None))
         ])
-    if params.get("grad_col_vec") is not None:
+    if params.get("grad_col_vec", None) is not None:
         cargs.extend([
             "-in_col_vec",
-            execution.input_file(params.get("grad_col_vec"))
+            execution.input_file(params.get("grad_col_vec", None))
         ])
-    if params.get("grad_col_matA") is not None:
+    if params.get("grad_col_matA", None) is not None:
         cargs.extend([
             "-in_col_matA",
-            execution.input_file(params.get("grad_col_matA"))
+            execution.input_file(params.get("grad_col_matA", None))
         ])
-    if params.get("grad_col_matT") is not None:
+    if params.get("grad_col_matT", None) is not None:
         cargs.extend([
             "-in_col_matT",
-            execution.input_file(params.get("grad_col_matT"))
+            execution.input_file(params.get("grad_col_matT", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("bvals") is not None:
+    if params.get("bvals", None) is not None:
         cargs.extend([
             "-in_bvals",
-            execution.input_file(params.get("bvals"))
+            execution.input_file(params.get("bvals", None))
         ])
-    if params.get("thresh_fa") is not None:
+    if params.get("thresh_fa", None) is not None:
         cargs.extend([
             "-alg_Thresh_FA",
-            str(params.get("thresh_fa"))
+            str(params.get("thresh_fa", None))
         ])
-    if params.get("thresh_len") is not None:
+    if params.get("thresh_len", None) is not None:
         cargs.extend([
             "-alg_Thresh_Len",
-            str(params.get("thresh_len"))
+            str(params.get("thresh_len", None))
         ])
-    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("check_abs_min") is not None:
+    if params.get("check_abs_min", None) is not None:
         cargs.extend([
             "-check_abs_min",
-            str(params.get("check_abs_min"))
+            str(params.get("check_abs_min", None))
         ])
-    if params.get("scale_out_1000"):
+    if params.get("scale_out_1000", False):
         cargs.append("-scale_out_1000")
-    if params.get("wdir") is not None:
+    if params.get("wdir", None) is not None:
         cargs.extend([
             "-wdir",
-            params.get("wdir")
+            params.get("wdir", None)
         ])
-    if params.get("do_clean"):
+    if params.get("do_clean", False):
         cargs.append("-do_clean")
     return cargs
 
@@ -246,7 +231,7 @@ def v__grad_flip_test_outputs(
     """
     ret = VGradFlipTestOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".txt") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".txt") if (params.get("prefix") is not None) else None,
         temp_directory=execution.output_file("_tmp_TESTFLIP"),
     )
     return ret
@@ -254,9 +239,11 @@ def v__grad_flip_test_outputs(
 
 def v__grad_flip_test_execute(
     params: VGradFlipTestParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VGradFlipTestOutputs:
     """
+    @GradFlipTest
+    
     Script to test the correct flip for a data set when using 1dDW_Grad_o_Mat++.
     
     Author: AFNI Developers
@@ -265,10 +252,12 @@ def v__grad_flip_test_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VGradFlipTestOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GRAD_FLIP_TEST_METADATA)
     params = execution.params(params)
     cargs = v__grad_flip_test_cargs(params, execution)
     ret = v__grad_flip_test_outputs(params, execution)
@@ -294,6 +283,8 @@ def v__grad_flip_test(
     runner: Runner | None = None,
 ) -> VGradFlipTestOutputs:
     """
+    @GradFlipTest
+    
     Script to test the correct flip for a data set when using 1dDW_Grad_o_Mat++.
     
     Author: AFNI Developers
@@ -325,8 +316,6 @@ def v__grad_flip_test(
     Returns:
         NamedTuple of outputs (described in `VGradFlipTestOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__GRAD_FLIP_TEST_METADATA)
     params = v__grad_flip_test_params(
         dwi=dwi,
         grad_row_vec=grad_row_vec,
@@ -343,13 +332,13 @@ def v__grad_flip_test(
         wdir=wdir,
         do_clean=do_clean,
     )
-    return v__grad_flip_test_execute(params, execution)
+    return v__grad_flip_test_execute(params, runner)
 
 
 __all__ = [
     "VGradFlipTestOutputs",
-    "VGradFlipTestParameters",
     "V__GRAD_FLIP_TEST_METADATA",
     "v__grad_flip_test",
+    "v__grad_flip_test_execute",
     "v__grad_flip_test_params",
 ]

niwrap_afni/afni/v__grayplot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__GRAYPLOT_METADATA = Metadata(
-    id="958c86831f7afb5a52d51364d6b986bef43d3733.boutiques",
+    id="edf57c96b1687dc03e834d83c0da2408742cbcc5.boutiques",
     name="@grayplot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V__GRAYPLOT_METADATA = Metadata(
 
 
 VGrayplotParameters = typing.TypedDict('VGrayplotParameters', {
-    "__STYXTYPE__": typing.Literal["@grayplot"],
+    "@type": typing.NotRequired[typing.Literal["afni/@grayplot"]],
+    "dirname": str,
+    "pvorder": bool,
+    "peelorder": bool,
+    "ijkorder": bool,
+    "allorder": bool,
+})
+VGrayplotParametersTagged = typing.TypedDict('VGrayplotParametersTagged', {
+    "@type": typing.Literal["afni/@grayplot"],
     "dirname": str,
     "pvorder": bool,
     "peelorder": bool,
     "ijkorder": bool,
     "allorder": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@grayplot": v__grayplot_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 {
-        "@grayplot": v__grayplot_outputs,
-    }.get(t)
 
 
 class VGrayplotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__grayplot(...)`.
+    Output object returned when calling `VGrayplotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def v__grayplot_params(
     peelorder: bool = False,
     ijkorder: bool = False,
     allorder: bool = False,
-) -> VGrayplotParameters:
+) -> VGrayplotParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +64,7 @@ def v__grayplot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@grayplot",
+        "@type": "afni/@grayplot",
         "dirname": dirname,
         "pvorder": pvorder,
         "peelorder": peelorder,
@@ -113,14 +89,14 @@ def v__grayplot_cargs(
     """
     cargs = []
     cargs.append("@grayplot")
-    cargs.append(params.get("dirname"))
-    if params.get("pvorder"):
+    cargs.append(params.get("dirname", None))
+    if params.get("pvorder", False):
         cargs.append("-pvorder")
-    if params.get("peelorder"):
+    if params.get("peelorder", False):
         cargs.append("-peelorder")
-    if params.get("ijkorder"):
+    if params.get("ijkorder", False):
         cargs.append("-ijkorder")
-    if params.get("allorder"):
+    if params.get("allorder", False):
         cargs.append("-ALLorder")
     return cargs
 
@@ -140,19 +116,21 @@ def v__grayplot_outputs(
     """
     ret = VGrayplotOutputs(
         root=execution.output_file("."),
-        grayplot_img=execution.output_file("Grayplot.errts.*.png"),
+        grayplot_img=execution.output_file("Grayplot.errts.png"),
     )
     return ret
 
 
 def v__grayplot_execute(
     params: VGrayplotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VGrayplotOutputs:
     """
+    @grayplot
+    
     Script to read files from an afni_proc.py results directory and produce a
-    grayplot from the errts dataset(s), combined with a motion magnitude indicator
-    graph.
+    grayplot from the errts dataset(s), combined with a motion magnitude
+    indicator graph.
     
     Author: AFNI Developers
     
@@ -160,10 +138,12 @@ def v__grayplot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VGrayplotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GRAYPLOT_METADATA)
     params = execution.params(params)
     cargs = v__grayplot_cargs(params, execution)
     ret = v__grayplot_outputs(params, execution)
@@ -180,9 +160,11 @@ def v__grayplot(
     runner: Runner | None = None,
 ) -> VGrayplotOutputs:
     """
+    @grayplot
+    
     Script to read files from an afni_proc.py results directory and produce a
-    grayplot from the errts dataset(s), combined with a motion magnitude indicator
-    graph.
+    grayplot from the errts dataset(s), combined with a motion magnitude
+    indicator graph.
     
     Author: AFNI Developers
     
@@ -201,8 +183,6 @@ def v__grayplot(
     Returns:
         NamedTuple of outputs (described in `VGrayplotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__GRAYPLOT_METADATA)
     params = v__grayplot_params(
         dirname=dirname,
         pvorder=pvorder,
@@ -210,13 +190,13 @@ def v__grayplot(
         ijkorder=ijkorder,
         allorder=allorder,
     )
-    return v__grayplot_execute(params, execution)
+    return v__grayplot_execute(params, runner)
 
 
 __all__ = [
     "VGrayplotOutputs",
-    "VGrayplotParameters",
     "V__GRAYPLOT_METADATA",
     "v__grayplot",
+    "v__grayplot_execute",
     "v__grayplot_params",
 ]

niwrap_afni/afni/v__help_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__HELP_AFNI_METADATA = Metadata(
-    id="cbdc40aa91ee838c736538ca976d0d8c0c2a19a5.boutiques",
+    id="32090db8a8937db4bee1db92c4aaf17394fb1612.boutiques",
     name="@help.AFNI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__HELP_AFNI_METADATA = Metadata(
 
 
 VHelpAfniParameters = typing.TypedDict('VHelpAfniParameters', {
-    "__STYXTYPE__": typing.Literal["@help.AFNI"],
+    "@type": typing.NotRequired[typing.Literal["afni/@help.AFNI"]],
+    "match": typing.NotRequired[str | None],
+    "lynx": bool,
+    "vi": bool,
+    "less": bool,
+    "nedit": bool,
+    "noview": bool,
+})
+VHelpAfniParametersTagged = typing.TypedDict('VHelpAfniParametersTagged', {
+    "@type": typing.Literal["afni/@help.AFNI"],
     "match": typing.NotRequired[str | None],
     "lynx": bool,
     "vi": bool,
@@ -22,42 +31,11 @@ VHelpAfniParameters = typing.TypedDict('VHelpAfniParameters', {
     "nedit": bool,
     "noview": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@help.AFNI": v__help_afni_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 {
-    }.get(t)
 
 
 class VHelpAfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__help_afni(...)`.
+    Output object returned when calling `VHelpAfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def v__help_afni_params(
     less: bool = False,
     nedit: bool = False,
     noview: bool = False,
-) -> VHelpAfniParameters:
+) -> VHelpAfniParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def v__help_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@help.AFNI",
+        "@type": "afni/@help.AFNI",
         "lynx": lynx,
         "vi": vi,
         "less": less,
@@ -114,20 +92,20 @@ def v__help_afni_cargs(
     """
     cargs = []
     cargs.append("@help.AFNI")
-    if params.get("match") is not None:
+    if params.get("match", None) is not None:
         cargs.extend([
             "-match",
-            params.get("match")
+            params.get("match", None)
         ])
-    if params.get("lynx"):
+    if params.get("lynx", False):
         cargs.append("-lynx")
-    if params.get("vi"):
+    if params.get("vi", False):
         cargs.append("-vi")
-    if params.get("less"):
+    if params.get("less", False):
         cargs.append("-less")
-    if params.get("nedit"):
+    if params.get("nedit", False):
         cargs.append("-nedit")
-    if params.get("noview"):
+    if params.get("noview", False):
         cargs.append("-noview")
     return cargs
 
@@ -153,9 +131,11 @@ def v__help_afni_outputs(
 
 def v__help_afni_execute(
     params: VHelpAfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VHelpAfniOutputs:
     """
+    @help.AFNI
+    
     A script to retrieve and search AFNI's help page for all programs.
     
     Author: AFNI Developers
@@ -164,10 +144,12 @@ def v__help_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VHelpAfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__HELP_AFNI_METADATA)
     params = execution.params(params)
     cargs = v__help_afni_cargs(params, execution)
     ret = v__help_afni_outputs(params, execution)
@@ -185,6 +167,8 @@ def v__help_afni(
     runner: Runner | None = None,
 ) -> VHelpAfniOutputs:
     """
+    @help.AFNI
+    
     A script to retrieve and search AFNI's help page for all programs.
     
     Author: AFNI Developers
@@ -204,8 +188,6 @@ def v__help_afni(
     Returns:
         NamedTuple of outputs (described in `VHelpAfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__HELP_AFNI_METADATA)
     params = v__help_afni_params(
         match=match,
         lynx=lynx,
@@ -214,13 +196,13 @@ def v__help_afni(
         nedit=nedit,
         noview=noview,
     )
-    return v__help_afni_execute(params, execution)
+    return v__help_afni_execute(params, runner)
 
 
 __all__ = [
     "VHelpAfniOutputs",
-    "VHelpAfniParameters",
     "V__HELP_AFNI_METADATA",
     "v__help_afni",
+    "v__help_afni_execute",
     "v__help_afni_params",
 ]