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

niwrap_freesurfer/freesurfer/morph_only_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_ONLY_SUBJECT_RH_METADATA = Metadata(
-    id="892fafe85c02e372400e532043654263ee16d857.boutiques",
+    id="39f3ef5dc6626de5e13541d5392f7fa0a5dab6f1.boutiques",
     name="morph_only_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ MORPH_ONLY_SUBJECT_RH_METADATA = Metadata(
 
 
 MorphOnlySubjectRhParameters = typing.TypedDict('MorphOnlySubjectRhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_only_subject-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_only_subject-rh"]],
+    "subject_dir": InputPathType,
+})
+MorphOnlySubjectRhParametersTagged = typing.TypedDict('MorphOnlySubjectRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_only_subject-rh"],
     "subject_dir": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_only_subject-rh": morph_only_subject_rh_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 {
-        "morph_only_subject-rh": morph_only_subject_rh_outputs,
-    }.get(t)
 
 
 class MorphOnlySubjectRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_only_subject_rh(...)`.
+    Output object returned when calling `MorphOnlySubjectRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +36,7 @@ class MorphOnlySubjectRhOutputs(typing.NamedTuple):
 
 def morph_only_subject_rh_params(
     subject_dir: InputPathType,
-) -> MorphOnlySubjectRhParameters:
+) -> MorphOnlySubjectRhParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +47,7 @@ def morph_only_subject_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_only_subject-rh",
+        "@type": "freesurfer/morph_only_subject-rh",
         "subject_dir": subject_dir,
     }
     return params
@@ -98,7 +70,7 @@ def morph_only_subject_rh_cargs(
     cargs.append("morph_only_subject-rh")
     cargs.extend([
         "-rh",
-        execution.input_file(params.get("subject_dir"))
+        execution.input_file(params.get("subject_dir", None))
     ])
     return cargs
 
@@ -118,18 +90,20 @@ def morph_only_subject_rh_outputs(
     """
     ret = MorphOnlySubjectRhOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file("/usr/local/freesurfer/subjects/" + pathlib.Path(params.get("subject_dir")).name + "/rh.morph"),
+        output_files=execution.output_file("/usr/local/freesurfer/subjects/" + pathlib.Path(params.get("subject_dir", None)).name + "/rh.morph"),
     )
     return ret
 
 
 def morph_only_subject_rh_execute(
     params: MorphOnlySubjectRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphOnlySubjectRhOutputs:
     """
-    This tool processes morph-specific operations for the right hemisphere of the
-    brain using Freesurfer.
+    morph_only_subject-rh
+    
+    This tool processes morph-specific operations for the right hemisphere of
+    the brain using Freesurfer.
     
     Author: FreeSurfer Developers
     
@@ -137,10 +111,12 @@ def morph_only_subject_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_ONLY_SUBJECT_RH_METADATA)
     params = execution.params(params)
     cargs = morph_only_subject_rh_cargs(params, execution)
     ret = morph_only_subject_rh_outputs(params, execution)
@@ -153,8 +129,10 @@ def morph_only_subject_rh(
     runner: Runner | None = None,
 ) -> MorphOnlySubjectRhOutputs:
     """
-    This tool processes morph-specific operations for the right hemisphere of the
-    brain using Freesurfer.
+    morph_only_subject-rh
+    
+    This tool processes morph-specific operations for the right hemisphere of
+    the brain using Freesurfer.
     
     Author: FreeSurfer Developers
     
@@ -167,18 +145,16 @@ def morph_only_subject_rh(
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_ONLY_SUBJECT_RH_METADATA)
     params = morph_only_subject_rh_params(
         subject_dir=subject_dir,
     )
-    return morph_only_subject_rh_execute(params, execution)
+    return morph_only_subject_rh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_ONLY_SUBJECT_RH_METADATA",
     "MorphOnlySubjectRhOutputs",
-    "MorphOnlySubjectRhParameters",
     "morph_only_subject_rh",
+    "morph_only_subject_rh_execute",
     "morph_only_subject_rh_params",
 ]

niwrap_freesurfer/freesurfer/morph_rgb_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_RGB_LH_METADATA = Metadata(
-    id="044963f7616c001fb9f232b33ff6dda1d55eaf4f.boutiques",
+    id="081232cef0c878dce79f09cb329a498db61fc850.boutiques",
     name="morph_rgb-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_RGB_LH_METADATA = Metadata(
 
 
 MorphRgbLhParameters = typing.TypedDict('MorphRgbLhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_rgb-lh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_rgb-lh"]],
+    "subject_id": str,
+})
+MorphRgbLhParametersTagged = typing.TypedDict('MorphRgbLhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_rgb-lh"],
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_rgb-lh": morph_rgb_lh_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 MorphRgbLhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_rgb_lh(...)`.
+    Output object returned when calling `MorphRgbLhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphRgbLhOutputs(typing.NamedTuple):
 
 def morph_rgb_lh_params(
     subject_id: str,
-) -> MorphRgbLhParameters:
+) -> MorphRgbLhParametersTagged:
     """
     Build parameters.
     
@@ -72,7 +45,7 @@ def morph_rgb_lh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_rgb-lh",
+        "@type": "freesurfer/morph_rgb-lh",
         "subject_id": subject_id,
     }
     return params
@@ -95,7 +68,7 @@ def morph_rgb_lh_cargs(
     cargs.append("morph_rgb-lh")
     cargs.extend([
         "-lh",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -121,9 +94,11 @@ def morph_rgb_lh_outputs(
 
 def morph_rgb_lh_execute(
     params: MorphRgbLhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphRgbLhOutputs:
     """
+    morph_rgb-lh
+    
     Tool for working with and generating RGB images of morphometric data for the
     left hemisphere in FreeSurfer.
     
@@ -133,10 +108,12 @@ def morph_rgb_lh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphRgbLhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_RGB_LH_METADATA)
     params = execution.params(params)
     cargs = morph_rgb_lh_cargs(params, execution)
     ret = morph_rgb_lh_outputs(params, execution)
@@ -149,6 +126,8 @@ def morph_rgb_lh(
     runner: Runner | None = None,
 ) -> MorphRgbLhOutputs:
     """
+    morph_rgb-lh
+    
     Tool for working with and generating RGB images of morphometric data for the
     left hemisphere in FreeSurfer.
     
@@ -164,18 +143,16 @@ def morph_rgb_lh(
     Returns:
         NamedTuple of outputs (described in `MorphRgbLhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_RGB_LH_METADATA)
     params = morph_rgb_lh_params(
         subject_id=subject_id,
     )
-    return morph_rgb_lh_execute(params, execution)
+    return morph_rgb_lh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_RGB_LH_METADATA",
     "MorphRgbLhOutputs",
-    "MorphRgbLhParameters",
     "morph_rgb_lh",
+    "morph_rgb_lh_execute",
     "morph_rgb_lh_params",
 ]

niwrap_freesurfer/freesurfer/morph_rgb_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_RGB_RH_METADATA = Metadata(
-    id="a6a24e50abf67ab8cf1bf35fab1d30fde98e108c.boutiques",
+    id="6459d87713d1d9ce11c249695188f2e420e4a55e.boutiques",
     name="morph_rgb-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_RGB_RH_METADATA = Metadata(
 
 
 MorphRgbRhParameters = typing.TypedDict('MorphRgbRhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_rgb-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_rgb-rh"]],
+    "subject_id": str,
+})
+MorphRgbRhParametersTagged = typing.TypedDict('MorphRgbRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_rgb-rh"],
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_rgb-rh": morph_rgb_rh_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 MorphRgbRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_rgb_rh(...)`.
+    Output object returned when calling `MorphRgbRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphRgbRhOutputs(typing.NamedTuple):
 
 def morph_rgb_rh_params(
     subject_id: str,
-) -> MorphRgbRhParameters:
+) -> MorphRgbRhParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def morph_rgb_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_rgb-rh",
+        "@type": "freesurfer/morph_rgb-rh",
         "subject_id": subject_id,
     }
     return params
@@ -93,7 +66,7 @@ def morph_rgb_rh_cargs(
     cargs.append("morph_rgb-rh")
     cargs.extend([
         "-rh",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def morph_rgb_rh_outputs(
 
 def morph_rgb_rh_execute(
     params: MorphRgbRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphRgbRhOutputs:
     """
+    morph_rgb-rh
+    
     Morphs RGB values onto a FreeSurfer right hemisphere surface.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def morph_rgb_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphRgbRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_RGB_RH_METADATA)
     params = execution.params(params)
     cargs = morph_rgb_rh_cargs(params, execution)
     ret = morph_rgb_rh_outputs(params, execution)
@@ -146,6 +123,8 @@ def morph_rgb_rh(
     runner: Runner | None = None,
 ) -> MorphRgbRhOutputs:
     """
+    morph_rgb-rh
+    
     Morphs RGB values onto a FreeSurfer right hemisphere surface.
     
     Author: FreeSurfer Developers
@@ -158,18 +137,16 @@ def morph_rgb_rh(
     Returns:
         NamedTuple of outputs (described in `MorphRgbRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_RGB_RH_METADATA)
     params = morph_rgb_rh_params(
         subject_id=subject_id,
     )
-    return morph_rgb_rh_execute(params, execution)
+    return morph_rgb_rh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_RGB_RH_METADATA",
     "MorphRgbRhOutputs",
-    "MorphRgbRhParameters",
     "morph_rgb_rh",
+    "morph_rgb_rh_execute",
     "morph_rgb_rh_params",
 ]

niwrap_freesurfer/freesurfer/morph_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_SUBJECT_METADATA = Metadata(
-    id="685f97530d830d12a67cb8468c38864b69d1e65c.boutiques",
+    id="dab11133f0d14ca55b5d68228d09dee883987b8a.boutiques",
     name="morph_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_SUBJECT_METADATA = Metadata(
 
 
 MorphSubjectParameters = typing.TypedDict('MorphSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["morph_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_subject"]],
+    "subjid": str,
+})
+MorphSubjectParametersTagged = typing.TypedDict('MorphSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_subject"],
     "subjid": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_subject": morph_subject_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 MorphSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_subject(...)`.
+    Output object returned when calling `MorphSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphSubjectOutputs(typing.NamedTuple):
 
 def morph_subject_params(
     subjid: str,
-) -> MorphSubjectParameters:
+) -> MorphSubjectParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def morph_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_subject",
+        "@type": "freesurfer/morph_subject",
         "subjid": subjid,
     }
     return params
@@ -91,7 +64,7 @@ def morph_subject_cargs(
     """
     cargs = []
     cargs.append("morph_subject")
-    cargs.append(params.get("subjid"))
+    cargs.append(params.get("subjid", None))
     return cargs
 
 
@@ -116,11 +89,13 @@ def morph_subject_outputs(
 
 def morph_subject_execute(
     params: MorphSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphSubjectOutputs:
     """
-    A morphological processing tool for Freesurfer subjects. The specific operations
-    and options are not documented in the available help text.
+    morph_subject
+    
+    A morphological processing tool for Freesurfer subjects. The specific
+    operations and options are not documented in the available help text.
     
     Author: FreeSurfer Developers
     
@@ -128,10 +103,12 @@ def morph_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = morph_subject_cargs(params, execution)
     ret = morph_subject_outputs(params, execution)
@@ -144,8 +121,10 @@ def morph_subject(
     runner: Runner | None = None,
 ) -> MorphSubjectOutputs:
     """
-    A morphological processing tool for Freesurfer subjects. The specific operations
-    and options are not documented in the available help text.
+    morph_subject
+    
+    A morphological processing tool for Freesurfer subjects. The specific
+    operations and options are not documented in the available help text.
     
     Author: FreeSurfer Developers
     
@@ -157,18 +136,16 @@ def morph_subject(
     Returns:
         NamedTuple of outputs (described in `MorphSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_SUBJECT_METADATA)
     params = morph_subject_params(
         subjid=subjid,
     )
-    return morph_subject_execute(params, execution)
+    return morph_subject_execute(params, runner)
 
 
 __all__ = [
     "MORPH_SUBJECT_METADATA",
     "MorphSubjectOutputs",
-    "MorphSubjectParameters",
     "morph_subject",
+    "morph_subject_execute",
     "morph_subject_params",
 ]