niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/adjunct_tort_plot_dp_align.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA = Metadata(
-    id="476f4d1a86214009b6eb0878d5070c11cd6a6a27.boutiques",
+    id="c468ef964fd39278d53eddb2202c1a91c57b8be6.boutiques",
     name="adjunct_tort_plot_dp_align",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA = Metadata(
 
 
 AdjunctTortPlotDpAlignParameters = typing.TypedDict('AdjunctTortPlotDpAlignParameters', {
-    "__STYXTYPE__": typing.Literal["adjunct_tort_plot_dp_align"],
+    "@type": typing.NotRequired[typing.Literal["afni/adjunct_tort_plot_dp_align"]],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "enorm_max": typing.NotRequired[float | None],
+    "enorm_hline": typing.NotRequired[float | None],
+    "no_svg": bool,
+})
+AdjunctTortPlotDpAlignParametersTagged = typing.TypedDict('AdjunctTortPlotDpAlignParametersTagged', {
+    "@type": typing.Literal["afni/adjunct_tort_plot_dp_align"],
     "input_file": InputPathType,
     "output_prefix": str,
     "enorm_max": typing.NotRequired[float | None],
     "enorm_hline": typing.NotRequired[float | None],
     "no_svg": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "adjunct_tort_plot_dp_align": adjunct_tort_plot_dp_align_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 {
-        "adjunct_tort_plot_dp_align": adjunct_tort_plot_dp_align_outputs,
-    }.get(t)
 
 
 class AdjunctTortPlotDpAlignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `adjunct_tort_plot_dp_align(...)`.
+    Output object returned when calling `AdjunctTortPlotDpAlignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +55,7 @@ def adjunct_tort_plot_dp_align_params(
     enorm_max: float | None = None,
     enorm_hline: float | None = None,
     no_svg: bool = False,
-) -> AdjunctTortPlotDpAlignParameters:
+) -> AdjunctTortPlotDpAlignParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +74,7 @@ def adjunct_tort_plot_dp_align_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "adjunct_tort_plot_dp_align",
+        "@type": "afni/adjunct_tort_plot_dp_align",
         "input_file": input_file,
         "output_prefix": output_prefix,
         "no_svg": no_svg,
@@ -127,23 +103,23 @@ def adjunct_tort_plot_dp_align_cargs(
     cargs.append("adjunct_tort_plot_dp_align")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("enorm_max") is not None:
+    if params.get("enorm_max", None) is not None:
         cargs.extend([
             "-enorm_max",
-            str(params.get("enorm_max"))
+            str(params.get("enorm_max", None))
         ])
-    if params.get("enorm_hline") is not None:
+    if params.get("enorm_hline", None) is not None:
         cargs.extend([
             "-enorm_hline",
-            str(params.get("enorm_hline"))
+            str(params.get("enorm_hline", None))
         ])
-    if params.get("no_svg"):
+    if params.get("no_svg", False):
         cargs.append("-no_svg")
     return cargs
 
@@ -163,21 +139,23 @@ def adjunct_tort_plot_dp_align_outputs(
     """
     ret = AdjunctTortPlotDpAlignOutputs(
         root=execution.output_file("."),
-        align_params=execution.output_file(params.get("output_prefix") + "_align.1D"),
-        enorm_file=execution.output_file(params.get("output_prefix") + "_enorm.1D"),
-        plot_jpg=execution.output_file(params.get("output_prefix") + ".jpg"),
-        plot_svg=execution.output_file(params.get("output_prefix") + ".svg"),
+        align_params=execution.output_file(params.get("output_prefix", None) + "_align.1D"),
+        enorm_file=execution.output_file(params.get("output_prefix", None) + "_enorm.1D"),
+        plot_jpg=execution.output_file(params.get("output_prefix", None) + ".jpg"),
+        plot_svg=execution.output_file(params.get("output_prefix", None) + ".svg"),
     )
     return ret
 
 
 def adjunct_tort_plot_dp_align_execute(
     params: AdjunctTortPlotDpAlignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AdjunctTortPlotDpAlignOutputs:
     """
-    Tool to display the rigid-body alignment parameters from TORTOISE's DIFFPREP,
-    useful for analyzing subject motion in DWI data.
+    adjunct_tort_plot_dp_align
+    
+    Tool to display the rigid-body alignment parameters from TORTOISE's
+    DIFFPREP, useful for analyzing subject motion in DWI data.
     
     Author: AFNI Developers
     
@@ -185,10 +163,12 @@ def adjunct_tort_plot_dp_align_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AdjunctTortPlotDpAlignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA)
     params = execution.params(params)
     cargs = adjunct_tort_plot_dp_align_cargs(params, execution)
     ret = adjunct_tort_plot_dp_align_outputs(params, execution)
@@ -205,8 +185,10 @@ def adjunct_tort_plot_dp_align(
     runner: Runner | None = None,
 ) -> AdjunctTortPlotDpAlignOutputs:
     """
-    Tool to display the rigid-body alignment parameters from TORTOISE's DIFFPREP,
-    useful for analyzing subject motion in DWI data.
+    adjunct_tort_plot_dp_align
+    
+    Tool to display the rigid-body alignment parameters from TORTOISE's
+    DIFFPREP, useful for analyzing subject motion in DWI data.
     
     Author: AFNI Developers
     
@@ -227,8 +209,6 @@ def adjunct_tort_plot_dp_align(
     Returns:
         NamedTuple of outputs (described in `AdjunctTortPlotDpAlignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA)
     params = adjunct_tort_plot_dp_align_params(
         input_file=input_file,
         output_prefix=output_prefix,
@@ -236,13 +216,13 @@ def adjunct_tort_plot_dp_align(
         enorm_hline=enorm_hline,
         no_svg=no_svg,
     )
-    return adjunct_tort_plot_dp_align_execute(params, execution)
+    return adjunct_tort_plot_dp_align_execute(params, runner)
 
 
 __all__ = [
     "ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA",
     "AdjunctTortPlotDpAlignOutputs",
-    "AdjunctTortPlotDpAlignParameters",
     "adjunct_tort_plot_dp_align",
+    "adjunct_tort_plot_dp_align_execute",
     "adjunct_tort_plot_dp_align_params",
 ]

niwrap_afni/afni/adwarp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ADWARP_METADATA = Metadata(
-    id="953249962a4c4d7f013a230b770e9eb6de08979f.boutiques",
+    id="413bf38a029233ae4ba1804c69eaac899c1142cf.boutiques",
     name="adwarp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ ADWARP_METADATA = Metadata(
 
 
 AdwarpParameters = typing.TypedDict('AdwarpParameters', {
-    "__STYXTYPE__": typing.Literal["adwarp"],
+    "@type": typing.NotRequired[typing.Literal["afni/adwarp"]],
+    "apar": InputPathType,
+    "dpar": str,
+    "prefix": typing.NotRequired[str | None],
+    "dxyz": typing.NotRequired[float | None],
+    "verbose": bool,
+    "force": bool,
+    "resam": typing.NotRequired[str | None],
+    "thr": typing.NotRequired[str | None],
+    "func": typing.NotRequired[str | None],
+})
+AdwarpParametersTagged = typing.TypedDict('AdwarpParametersTagged', {
+    "@type": typing.Literal["afni/adwarp"],
     "apar": InputPathType,
     "dpar": str,
     "prefix": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ AdwarpParameters = typing.TypedDict('AdwarpParameters', {
     "thr": typing.NotRequired[str | None],
     "func": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "adwarp": adwarp_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 {
-        "adwarp": adwarp_outputs,
-    }.get(t)
 
 
 class AdwarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `adwarp(...)`.
+    Output object returned when calling `AdwarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def adwarp_params(
     resam: str | None = None,
     thr: str | None = None,
     func: str | None = None,
-) -> AdwarpParameters:
+) -> AdwarpParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +88,7 @@ def adwarp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "adwarp",
+        "@type": "afni/adwarp",
         "apar": apar,
         "dpar": dpar,
         "verbose": verbose,
@@ -144,40 +124,40 @@ def adwarp_cargs(
     cargs.append("adwarp")
     cargs.extend([
         "-apar",
-        execution.input_file(params.get("apar"))
+        execution.input_file(params.get("apar", None))
     ])
     cargs.extend([
         "-dpar",
-        params.get("dpar")
+        params.get("dpar", 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("dxyz") is not None:
+    if params.get("dxyz", None) is not None:
         cargs.extend([
             "-dxyz",
-            str(params.get("dxyz"))
+            str(params.get("dxyz", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("resam") is not None:
+    if params.get("resam", None) is not None:
         cargs.extend([
             "-resam",
-            params.get("resam")
+            params.get("resam", None)
         ])
-    if params.get("thr") is not None:
+    if params.get("thr", None) is not None:
         cargs.extend([
             "-thr",
-            params.get("thr")
+            params.get("thr", None)
         ])
-    if params.get("func") is not None:
+    if params.get("func", None) is not None:
         cargs.extend([
             "-func",
-            params.get("func")
+            params.get("func", None)
         ])
     return cargs
 
@@ -197,17 +177,19 @@ def adwarp_outputs(
     """
     ret = AdwarpOutputs(
         root=execution.output_file("."),
-        header_output=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
-        brick_output=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+        header_output=execution.output_file(params.get("prefix", None) + ".HEAD") if (params.get("prefix") is not None) else None,
+        brick_output=execution.output_file(params.get("prefix", None) + ".BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def adwarp_execute(
     params: AdwarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AdwarpOutputs:
     """
+    adwarp
+    
     Resamples a 'data parent' dataset to the grid defined by an 'anat parent'
     dataset.
     
@@ -217,10 +199,12 @@ def adwarp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AdwarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADWARP_METADATA)
     params = execution.params(params)
     cargs = adwarp_cargs(params, execution)
     ret = adwarp_outputs(params, execution)
@@ -241,6 +225,8 @@ def adwarp(
     runner: Runner | None = None,
 ) -> AdwarpOutputs:
     """
+    adwarp
+    
     Resamples a 'data parent' dataset to the grid defined by an 'anat parent'
     dataset.
     
@@ -271,8 +257,6 @@ def adwarp(
     Returns:
         NamedTuple of outputs (described in `AdwarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ADWARP_METADATA)
     params = adwarp_params(
         apar=apar,
         dpar=dpar,
@@ -284,13 +268,13 @@ def adwarp(
         thr=thr,
         func=func,
     )
-    return adwarp_execute(params, execution)
+    return adwarp_execute(params, runner)
 
 
 __all__ = [
     "ADWARP_METADATA",
     "AdwarpOutputs",
-    "AdwarpParameters",
     "adwarp",
+    "adwarp_execute",
     "adwarp_params",
 ]

niwrap_afni/afni/afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFNI_METADATA = Metadata(
-    id="dccace569c978ac9a3bbcaf8f78daf4bc37a4707.boutiques",
+    id="976a6bf171352d9ba286989af93704f8127a9901.boutiques",
     name="afni",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,35 @@ AFNI_METADATA = Metadata(
 
 
 AfniParameters = typing.TypedDict('AfniParameters', {
-    "__STYXTYPE__": typing.Literal["afni"],
+    "@type": typing.NotRequired[typing.Literal["afni/afni"]],
+    "session_directories": typing.NotRequired[str | None],
+    "bysub": typing.NotRequired[list[str] | None],
+    "all_dsets": bool,
+    "purge": bool,
+    "posfunc": bool,
+    "recursive": bool,
+    "no1D": bool,
+    "nocsv": bool,
+    "notsv": bool,
+    "unique": bool,
+    "orient": typing.NotRequired[str | None],
+    "noplugins": bool,
+    "seehidden": bool,
+    "allow_all_plugins": bool,
+    "yesplugouts": bool,
+    "debug_plugouts": bool,
+    "noplugouts": bool,
+    "skip_afnirc": bool,
+    "layout": typing.NotRequired[InputPathType | None],
+    "niml": bool,
+    "np": typing.NotRequired[int | None],
+    "npq": typing.NotRequired[int | None],
+    "npb": typing.NotRequired[int | None],
+    "com": typing.NotRequired[str | None],
+    "comsep": typing.NotRequired[str | None],
+})
+AfniParametersTagged = typing.TypedDict('AfniParametersTagged', {
+    "@type": typing.Literal["afni/afni"],
     "session_directories": typing.NotRequired[str | None],
     "bysub": typing.NotRequired[list[str] | None],
     "all_dsets": bool,
@@ -41,43 +69,11 @@ AfniParameters = typing.TypedDict('AfniParameters', {
     "com": typing.NotRequired[str | None],
     "comsep": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "afni": 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 {
-        "afni": afni_outputs,
-    }.get(t)
 
 
 class AfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `afni_(...)`.
+    Output object returned when calling `AfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -111,7 +107,7 @@ def afni_params(
     npb: int | None = None,
     com: str | None = None,
     comsep: str | None = None,
-) -> AfniParameters:
+) -> AfniParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +142,7 @@ def afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "afni",
+        "@type": "afni/afni",
         "all_dsets": all_dsets,
         "purge": purge,
         "posfunc": posfunc,
@@ -200,79 +196,79 @@ def afni_cargs(
     """
     cargs = []
     cargs.append("afni")
-    if params.get("session_directories") is not None:
-        cargs.append(params.get("session_directories"))
-    if params.get("bysub") is not None:
+    if params.get("session_directories", None) is not None:
+        cargs.append(params.get("session_directories", None))
+    if params.get("bysub", None) is not None:
         cargs.extend([
             "-bysub",
-            *params.get("bysub")
+            *params.get("bysub", None)
         ])
-    if params.get("all_dsets"):
+    if params.get("all_dsets", False):
         cargs.append("-all_dsets")
-    if params.get("purge"):
+    if params.get("purge", False):
         cargs.append("-purge")
-    if params.get("posfunc"):
+    if params.get("posfunc", False):
         cargs.append("-posfunc")
-    if params.get("recursive"):
+    if params.get("recursive", False):
         cargs.append("-R")
-    if params.get("no1D"):
+    if params.get("no1D", False):
         cargs.append("-no1D")
-    if params.get("nocsv"):
+    if params.get("nocsv", False):
         cargs.append("-nocsv")
-    if params.get("notsv"):
+    if params.get("notsv", False):
         cargs.append("-notsv")
-    if params.get("unique"):
+    if params.get("unique", False):
         cargs.append("-unique")
-    if params.get("orient") is not None:
+    if params.get("orient", None) is not None:
         cargs.extend([
             "-orient",
-            params.get("orient")
+            params.get("orient", None)
         ])
-    if params.get("noplugins"):
+    if params.get("noplugins", False):
         cargs.append("-noplugins")
-    if params.get("seehidden"):
+    if params.get("seehidden", False):
         cargs.append("-seehidden")
-    if params.get("allow_all_plugins"):
+    if params.get("allow_all_plugins", False):
         cargs.append("-DAFNI_ALLOW_ALL_PLUGINS=YES")
-    if params.get("yesplugouts"):
+    if params.get("yesplugouts", False):
         cargs.append("-yesplugouts")
-    if params.get("debug_plugouts"):
+    if params.get("debug_plugouts", False):
         cargs.append("-YESplugouts")
-    if params.get("noplugouts"):
+    if params.get("noplugouts", False):
         cargs.append("-noplugouts")
-    if params.get("skip_afnirc"):
+    if params.get("skip_afnirc", False):
         cargs.append("-skip_afnirc")
-    if params.get("layout") is not None:
+    if params.get("layout", None) is not None:
         cargs.extend([
             "-layout",
-            execution.input_file(params.get("layout"))
+            execution.input_file(params.get("layout", None))
         ])
-    if params.get("niml"):
+    if params.get("niml", False):
         cargs.append("-niml")
-    if params.get("np") is not None:
+    if params.get("np", None) is not None:
         cargs.extend([
             "-np",
-            str(params.get("np"))
+            str(params.get("np", None))
         ])
-    if params.get("npq") is not None:
+    if params.get("npq", None) is not None:
         cargs.extend([
             "-npq",
-            str(params.get("npq"))
+            str(params.get("npq", None))
         ])
-    if params.get("npb") is not None:
+    if params.get("npb", None) is not None:
         cargs.extend([
             "-npb",
-            str(params.get("npb"))
+            str(params.get("npb", None))
         ])
-    if params.get("com") is not None:
+    if params.get("com", None) is not None:
         cargs.extend([
             "-com",
-            params.get("com")
+            params.get("com", None)
         ])
-    if params.get("comsep") is not None:
+    if params.get("comsep", None) is not None:
         cargs.extend([
             "-comsep",
-            params.get("comsep")
+            params.get("comsep", None)
         ])
     return cargs
 
@@ -299,9 +295,11 @@ def afni_outputs(
 
 def afni_execute(
     params: AfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AfniOutputs:
     """
+    afni
+    
     Tool for reading in sessions of 3D datasets and visualizing them.
     
     Author: AFNI Developers
@@ -310,10 +308,12 @@ def afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFNI_METADATA)
     params = execution.params(params)
     cargs = afni_cargs(params, execution)
     ret = afni_outputs(params, execution)
@@ -350,6 +350,8 @@ def afni_(
     runner: Runner | None = None,
 ) -> AfniOutputs:
     """
+    afni
+    
     Tool for reading in sessions of 3D datasets and visualizing them.
     
     Author: AFNI Developers
@@ -387,8 +389,6 @@ def afni_(
     Returns:
         NamedTuple of outputs (described in `AfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AFNI_METADATA)
     params = afni_params(
         session_directories=session_directories,
         bysub=bysub,
@@ -416,13 +416,13 @@ def afni_(
         com=com,
         comsep=comsep,
     )
-    return afni_execute(params, execution)
+    return afni_execute(params, runner)
 
 
 __all__ = [
     "AFNI_METADATA",
     "AfniOutputs",
-    "AfniParameters",
     "afni_",
+    "afni_execute",
     "afni_params",
 ]