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

niwrap_freesurfer/freesurfer/mmppsp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MMPPSP_METADATA = Metadata(
-    id="ed33242168bcb8e40435e7c590174310c28760c1.boutiques",
+    id="a458598bfb10337a371df949596a84de46846b3b.boutiques",
     name="mmppsp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MMPPSP_METADATA = Metadata(
 
 
 MmppspParameters = typing.TypedDict('MmppspParameters', {
-    "__STYXTYPE__": typing.Literal["mmppsp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mmppsp"]],
+    "samseg_dir": str,
+    "outdir": str,
+    "lh_flag": bool,
+    "rh_flag": bool,
+    "likelihood_flag": bool,
+    "posterior_flag": bool,
+    "force_update_flag": bool,
+    "threads": typing.NotRequired[float | None],
+    "no_initsphreg_flag": bool,
+    "stop_after": typing.NotRequired[str | None],
+    "wexpanddist": typing.NotRequired[float | None],
+})
+MmppspParametersTagged = typing.TypedDict('MmppspParametersTagged', {
+    "@type": typing.Literal["freesurfer/mmppsp"],
     "samseg_dir": str,
     "outdir": str,
     "lh_flag": bool,
@@ -27,43 +41,11 @@ MmppspParameters = typing.TypedDict('MmppspParameters', {
     "stop_after": typing.NotRequired[str | None],
     "wexpanddist": typing.NotRequired[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 {
-        "mmppsp": mmppsp_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 {
-        "mmppsp": mmppsp_outputs,
-    }.get(t)
 
 
 class MmppspOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mmppsp(...)`.
+    Output object returned when calling `MmppspParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def mmppsp_params(
     no_initsphreg_flag: bool = False,
     stop_after: str | None = None,
     wexpanddist: float | None = None,
-) -> MmppspParameters:
+) -> MmppspParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +87,7 @@ def mmppsp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mmppsp",
+        "@type": "freesurfer/mmppsp",
         "samseg_dir": samseg_dir,
         "outdir": outdir,
         "lh_flag": lh_flag,
@@ -141,38 +123,38 @@ def mmppsp_cargs(
     cargs.append("mmppsp")
     cargs.extend([
         "--samseg",
-        params.get("samseg_dir")
+        params.get("samseg_dir", None)
     ])
     cargs.extend([
         "--o",
-        params.get("outdir")
+        params.get("outdir", None)
     ])
-    if params.get("lh_flag"):
+    if params.get("lh_flag", False):
         cargs.append("--lh")
-    if params.get("rh_flag"):
+    if params.get("rh_flag", False):
         cargs.append("--rh")
-    if params.get("likelihood_flag"):
+    if params.get("likelihood_flag", False):
         cargs.append("--likelihood")
-    if params.get("posterior_flag"):
+    if params.get("posterior_flag", False):
         cargs.append("--posterior")
-    if params.get("force_update_flag"):
+    if params.get("force_update_flag", False):
         cargs.append("--force-update")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("no_initsphreg_flag"):
+    if params.get("no_initsphreg_flag", False):
         cargs.append("--no-initsphreg")
-    if params.get("stop_after") is not None:
+    if params.get("stop_after", None) is not None:
         cargs.extend([
             "--stop-after",
-            params.get("stop_after")
+            params.get("stop_after", None)
         ])
-    if params.get("wexpanddist") is not None:
+    if params.get("wexpanddist", None) is not None:
         cargs.extend([
             "--wexpanddist",
-            str(params.get("wexpanddist"))
+            str(params.get("wexpanddist", None))
         ])
     return cargs
 
@@ -192,16 +174,18 @@ def mmppsp_outputs(
     """
     ret = MmppspOutputs(
         root=execution.output_file("."),
-        output_surface=execution.output_file(params.get("outdir") + "/surf"),
+        output_surface=execution.output_file(params.get("outdir", None) + "/surf"),
     )
     return ret
 
 
 def mmppsp_execute(
     params: MmppspParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MmppspOutputs:
     """
+    mmppsp
+    
     MultiModal Posterior Probability Surface Placement.
     
     Author: FreeSurfer Developers
@@ -210,10 +194,12 @@ def mmppsp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MmppspOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MMPPSP_METADATA)
     params = execution.params(params)
     cargs = mmppsp_cargs(params, execution)
     ret = mmppsp_outputs(params, execution)
@@ -236,6 +222,8 @@ def mmppsp(
     runner: Runner | None = None,
 ) -> MmppspOutputs:
     """
+    mmppsp
+    
     MultiModal Posterior Probability Surface Placement.
     
     Author: FreeSurfer Developers
@@ -260,8 +248,6 @@ def mmppsp(
     Returns:
         NamedTuple of outputs (described in `MmppspOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MMPPSP_METADATA)
     params = mmppsp_params(
         samseg_dir=samseg_dir,
         outdir=outdir,
@@ -275,13 +261,13 @@ def mmppsp(
         stop_after=stop_after,
         wexpanddist=wexpanddist,
     )
-    return mmppsp_execute(params, execution)
+    return mmppsp_execute(params, runner)
 
 
 __all__ = [
     "MMPPSP_METADATA",
     "MmppspOutputs",
-    "MmppspParameters",
     "mmppsp",
+    "mmppsp_execute",
     "mmppsp_params",
 ]

niwrap_freesurfer/freesurfer/mni152reg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MNI152REG_METADATA = Metadata(
-    id="dfc37620e722a922c216aae5f87bf785a7f52f00.boutiques",
+    id="e38838d20584eef2c81916aa92999b19e8822af6.boutiques",
     name="mni152reg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MNI152REG_METADATA = Metadata(
 
 
 Mni152regParameters = typing.TypedDict('Mni152regParameters', {
-    "__STYXTYPE__": typing.Literal["mni152reg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mni152reg"]],
+    "subject": str,
+    "register_1mm": bool,
+    "output": typing.NotRequired[str | None],
+    "symmetric": bool,
+    "save_volume": bool,
+})
+Mni152regParametersTagged = typing.TypedDict('Mni152regParametersTagged', {
+    "@type": typing.Literal["freesurfer/mni152reg"],
     "subject": str,
     "register_1mm": bool,
     "output": typing.NotRequired[str | None],
     "symmetric": bool,
     "save_volume": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mni152reg": mni152reg_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 {
-        "mni152reg": mni152reg_outputs,
-    }.get(t)
 
 
 class Mni152regOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mni152reg(...)`.
+    Output object returned when calling `Mni152regParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def mni152reg_params(
     output: str | None = None,
     symmetric: bool = False,
     save_volume: bool = False,
-) -> Mni152regParameters:
+) -> Mni152regParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def mni152reg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mni152reg",
+        "@type": "freesurfer/mni152reg",
         "subject": subject,
         "register_1mm": register_1mm,
         "symmetric": symmetric,
@@ -115,18 +91,18 @@ def mni152reg_cargs(
     cargs.append("mni152reg")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("register_1mm"):
+    if params.get("register_1mm", False):
         cargs.append("--1")
-    if params.get("output") is not None:
+    if params.get("output", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output")
+            params.get("output", None)
         ])
-    if params.get("symmetric"):
+    if params.get("symmetric", False):
         cargs.append("--sym")
-    if params.get("save_volume"):
+    if params.get("save_volume", False):
         cargs.append("--save-vol")
     return cargs
 
@@ -146,17 +122,19 @@ def mni152reg_outputs(
     """
     ret = Mni152regOutputs(
         root=execution.output_file("."),
-        reg_matrix_2mm=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/transforms/reg.mni152.2mm.dat"),
-        reg_matrix_1mm=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/transforms/reg.mni152.1mm.dat"),
+        reg_matrix_2mm=execution.output_file("$SUBJECTS_DIR/" + params.get("subject", None) + "/mri/transforms/reg.mni152.2mm.dat"),
+        reg_matrix_1mm=execution.output_file("$SUBJECTS_DIR/" + params.get("subject", None) + "/mri/transforms/reg.mni152.1mm.dat"),
     )
     return ret
 
 
 def mni152reg_execute(
     params: Mni152regParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Mni152regOutputs:
     """
+    mni152reg
+    
     Registers the FreeSurfer subject to the FSL MNI 152 brain to create a
     tkregister-style registration matrix.
     
@@ -166,10 +144,12 @@ def mni152reg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Mni152regOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MNI152REG_METADATA)
     params = execution.params(params)
     cargs = mni152reg_cargs(params, execution)
     ret = mni152reg_outputs(params, execution)
@@ -186,6 +166,8 @@ def mni152reg(
     runner: Runner | None = None,
 ) -> Mni152regOutputs:
     """
+    mni152reg
+    
     Registers the FreeSurfer subject to the FSL MNI 152 brain to create a
     tkregister-style registration matrix.
     
@@ -203,8 +185,6 @@ def mni152reg(
     Returns:
         NamedTuple of outputs (described in `Mni152regOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MNI152REG_METADATA)
     params = mni152reg_params(
         subject=subject,
         register_1mm=register_1mm,
@@ -212,13 +192,13 @@ def mni152reg(
         symmetric=symmetric,
         save_volume=save_volume,
     )
-    return mni152reg_execute(params, execution)
+    return mni152reg_execute(params, runner)
 
 
 __all__ = [
     "MNI152REG_METADATA",
     "Mni152regOutputs",
-    "Mni152regParameters",
     "mni152reg",
+    "mni152reg_execute",
     "mni152reg_params",
 ]

niwrap_freesurfer/freesurfer/morph_only_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_ONLY_SUBJECT_METADATA = Metadata(
-    id="bff2c0f8f21164dcde88d76e1c6a7e662e454b4a.boutiques",
+    id="72b3c75846433fc7ab32ea849f4e2739a5324249.boutiques",
     name="morph_only_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_ONLY_SUBJECT_METADATA = Metadata(
 
 
 MorphOnlySubjectParameters = typing.TypedDict('MorphOnlySubjectParameters', {
-    "__STYXTYPE__": typing.Literal["morph_only_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_only_subject"]],
+    "placeholder_input": typing.NotRequired[str | None],
+})
+MorphOnlySubjectParametersTagged = typing.TypedDict('MorphOnlySubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_only_subject"],
     "placeholder_input": 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 {
-        "morph_only_subject": morph_only_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 MorphOnlySubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_only_subject(...)`.
+    Output object returned when calling `MorphOnlySubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphOnlySubjectOutputs(typing.NamedTuple):
 
 def morph_only_subject_params(
     placeholder_input: str | None = None,
-) -> MorphOnlySubjectParameters:
+) -> MorphOnlySubjectParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def morph_only_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_only_subject",
+        "@type": "freesurfer/morph_only_subject",
     }
     if placeholder_input is not None:
         params["placeholder_input"] = placeholder_input
@@ -93,8 +66,8 @@ def morph_only_subject_cargs(
     """
     cargs = []
     cargs.append("morph_only_subject")
-    if params.get("placeholder_input") is not None:
-        cargs.append(params.get("placeholder_input"))
+    if params.get("placeholder_input", None) is not None:
+        cargs.append(params.get("placeholder_input", None))
     return cargs
 
 
@@ -119,9 +92,11 @@ def morph_only_subject_outputs(
 
 def morph_only_subject_execute(
     params: MorphOnlySubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphOnlySubjectOutputs:
     """
+    morph_only_subject
+    
     A placeholder descriptor for morph_only_subject tool as help content is
     unavailable.
     
@@ -131,10 +106,12 @@ def morph_only_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_ONLY_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = morph_only_subject_cargs(params, execution)
     ret = morph_only_subject_outputs(params, execution)
@@ -147,6 +124,8 @@ def morph_only_subject(
     runner: Runner | None = None,
 ) -> MorphOnlySubjectOutputs:
     """
+    morph_only_subject
+    
     A placeholder descriptor for morph_only_subject tool as help content is
     unavailable.
     
@@ -161,18 +140,16 @@ def morph_only_subject(
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_ONLY_SUBJECT_METADATA)
     params = morph_only_subject_params(
         placeholder_input=placeholder_input,
     )
-    return morph_only_subject_execute(params, execution)
+    return morph_only_subject_execute(params, runner)
 
 
 __all__ = [
     "MORPH_ONLY_SUBJECT_METADATA",
     "MorphOnlySubjectOutputs",
-    "MorphOnlySubjectParameters",
     "morph_only_subject",
+    "morph_only_subject_execute",
     "morph_only_subject_params",
 ]

niwrap_freesurfer/freesurfer/morph_only_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_ONLY_SUBJECT_LH_METADATA = Metadata(
-    id="8e5603f71227f3739180dffce6a4cb9e0e78be9d.boutiques",
+    id="67acdc0e273b394588661257155f3da478009855.boutiques",
     name="morph_only_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ MORPH_ONLY_SUBJECT_LH_METADATA = Metadata(
 
 
 MorphOnlySubjectLhParameters = typing.TypedDict('MorphOnlySubjectLhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_only_subject-lh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_only_subject-lh"]],
+    "subject_dir": str,
+})
+MorphOnlySubjectLhParametersTagged = typing.TypedDict('MorphOnlySubjectLhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_only_subject-lh"],
     "subject_dir": 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_only_subject-lh": morph_only_subject_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 {
-        "morph_only_subject-lh": morph_only_subject_lh_outputs,
-    }.get(t)
 
 
 class MorphOnlySubjectLhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_only_subject_lh(...)`.
+    Output object returned when calling `MorphOnlySubjectLhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class MorphOnlySubjectLhOutputs(typing.NamedTuple):
 
 def morph_only_subject_lh_params(
     subject_dir: str,
-) -> MorphOnlySubjectLhParameters:
+) -> MorphOnlySubjectLhParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def morph_only_subject_lh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_only_subject-lh",
+        "@type": "freesurfer/morph_only_subject-lh",
         "subject_dir": subject_dir,
     }
     return params
@@ -96,7 +68,7 @@ def morph_only_subject_lh_cargs(
     cargs.append("morph_only_subject-lh")
     cargs.extend([
         "-lh",
-        params.get("subject_dir")
+        params.get("subject_dir", None)
     ])
     return cargs
 
@@ -116,16 +88,18 @@ def morph_only_subject_lh_outputs(
     """
     ret = MorphOnlySubjectLhOutputs(
         root=execution.output_file("."),
-        morph_results=execution.output_file(params.get("subject_dir") + "/morph_results"),
+        morph_results=execution.output_file(params.get("subject_dir", None) + "/morph_results"),
     )
     return ret
 
 
 def morph_only_subject_lh_execute(
     params: MorphOnlySubjectLhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphOnlySubjectLhOutputs:
     """
+    morph_only_subject-lh
+    
     A tool for morphological processing for the left hemisphere.
     
     Author: FreeSurfer Developers
@@ -134,10 +108,12 @@ def morph_only_subject_lh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectLhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_ONLY_SUBJECT_LH_METADATA)
     params = execution.params(params)
     cargs = morph_only_subject_lh_cargs(params, execution)
     ret = morph_only_subject_lh_outputs(params, execution)
@@ -150,6 +126,8 @@ def morph_only_subject_lh(
     runner: Runner | None = None,
 ) -> MorphOnlySubjectLhOutputs:
     """
+    morph_only_subject-lh
+    
     A tool for morphological processing for the left hemisphere.
     
     Author: FreeSurfer Developers
@@ -162,18 +140,16 @@ def morph_only_subject_lh(
     Returns:
         NamedTuple of outputs (described in `MorphOnlySubjectLhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_ONLY_SUBJECT_LH_METADATA)
     params = morph_only_subject_lh_params(
         subject_dir=subject_dir,
     )
-    return morph_only_subject_lh_execute(params, execution)
+    return morph_only_subject_lh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_ONLY_SUBJECT_LH_METADATA",
     "MorphOnlySubjectLhOutputs",
-    "MorphOnlySubjectLhParameters",
     "morph_only_subject_lh",
+    "morph_only_subject_lh_execute",
     "morph_only_subject_lh_params",
 ]