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

niwrap_freesurfer/freesurfer/mri_create_t2combined.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CREATE_T2COMBINED_METADATA = Metadata(
-    id="59237e7a370479a59f7c6f4d5c7258eeec07c44d.boutiques",
+    id="945b3bcb0237a042ad16be5a380e962f8c04a08e.boutiques",
     name="mri_create_t2combined",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_CREATE_T2COMBINED_METADATA = Metadata(
 
 
 MriCreateT2combinedParameters = typing.TypedDict('MriCreateT2combinedParameters', {
-    "__STYXTYPE__": typing.Literal["mri_create_t2combined"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_create_t2combined"]],
+    "subjid": str,
+    "t1wb": InputPathType,
+    "t2upper": InputPathType,
+    "t2middle": typing.NotRequired[InputPathType | None],
+    "t2lower": InputPathType,
+    "t2combined": str,
+    "show": bool,
+})
+MriCreateT2combinedParametersTagged = typing.TypedDict('MriCreateT2combinedParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_create_t2combined"],
     "subjid": str,
     "t1wb": InputPathType,
     "t2upper": InputPathType,
@@ -23,43 +33,11 @@ MriCreateT2combinedParameters = typing.TypedDict('MriCreateT2combinedParameters'
     "t2combined": str,
     "show": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_create_t2combined": mri_create_t2combined_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 {
-        "mri_create_t2combined": mri_create_t2combined_outputs,
-    }.get(t)
 
 
 class MriCreateT2combinedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_create_t2combined(...)`.
+    Output object returned when calling `MriCreateT2combinedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def mri_create_t2combined_params(
     t2combined: str,
     t2middle: InputPathType | None = None,
     show: bool = False,
-) -> MriCreateT2combinedParameters:
+) -> MriCreateT2combinedParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +72,7 @@ def mri_create_t2combined_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_create_t2combined",
+        "@type": "freesurfer/mri_create_t2combined",
         "subjid": subjid,
         "t1wb": t1wb,
         "t2upper": t2upper,
@@ -122,14 +100,14 @@ def mri_create_t2combined_cargs(
     """
     cargs = []
     cargs.append("mri_create_t2combined")
-    cargs.append(params.get("subjid"))
-    cargs.append(execution.input_file(params.get("t1wb")))
-    cargs.append(execution.input_file(params.get("t2upper")))
-    if params.get("t2middle") is not None:
-        cargs.append(execution.input_file(params.get("t2middle")))
-    cargs.append(execution.input_file(params.get("t2lower")))
-    cargs.append(params.get("t2combined"))
-    if params.get("show"):
+    cargs.append(params.get("subjid", None))
+    cargs.append(execution.input_file(params.get("t1wb", None)))
+    cargs.append(execution.input_file(params.get("t2upper", None)))
+    if params.get("t2middle", None) is not None:
+        cargs.append(execution.input_file(params.get("t2middle", None)))
+    cargs.append(execution.input_file(params.get("t2lower", None)))
+    cargs.append(params.get("t2combined", None))
+    if params.get("show", False):
         cargs.append("show")
     return cargs
 
@@ -150,18 +128,20 @@ def mri_create_t2combined_outputs(
     ret = MriCreateT2combinedOutputs(
         root=execution.output_file("."),
         logfile=execution.output_file("/root/mri_create_t2combined.log"),
-        t2combined_output=execution.output_file(params.get("t2combined")),
+        t2combined_output=execution.output_file(params.get("t2combined", None)),
     )
     return ret
 
 
 def mri_create_t2combined_execute(
     params: MriCreateT2combinedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCreateT2combinedOutputs:
     """
-    Utility to combine two or three T2* 7T partial-brain volumes into one volume,
-    retaining resolution and registered to the MPRAGE anatomical.
+    mri_create_t2combined
+    
+    Utility to combine two or three T2* 7T partial-brain volumes into one
+    volume, retaining resolution and registered to the MPRAGE anatomical.
     
     Author: FreeSurfer Developers
     
@@ -169,10 +149,12 @@ def mri_create_t2combined_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCreateT2combinedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CREATE_T2COMBINED_METADATA)
     params = execution.params(params)
     cargs = mri_create_t2combined_cargs(params, execution)
     ret = mri_create_t2combined_outputs(params, execution)
@@ -191,8 +173,10 @@ def mri_create_t2combined(
     runner: Runner | None = None,
 ) -> MriCreateT2combinedOutputs:
     """
-    Utility to combine two or three T2* 7T partial-brain volumes into one volume,
-    retaining resolution and registered to the MPRAGE anatomical.
+    mri_create_t2combined
+    
+    Utility to combine two or three T2* 7T partial-brain volumes into one
+    volume, retaining resolution and registered to the MPRAGE anatomical.
     
     Author: FreeSurfer Developers
     
@@ -211,8 +195,6 @@ def mri_create_t2combined(
     Returns:
         NamedTuple of outputs (described in `MriCreateT2combinedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CREATE_T2COMBINED_METADATA)
     params = mri_create_t2combined_params(
         subjid=subjid,
         t1wb=t1wb,
@@ -222,13 +204,13 @@ def mri_create_t2combined(
         t2combined=t2combined,
         show=show,
     )
-    return mri_create_t2combined_execute(params, execution)
+    return mri_create_t2combined_execute(params, runner)
 
 
 __all__ = [
     "MRI_CREATE_T2COMBINED_METADATA",
     "MriCreateT2combinedOutputs",
-    "MriCreateT2combinedParameters",
     "mri_create_t2combined",
+    "mri_create_t2combined_execute",
     "mri_create_t2combined_params",
 ]

niwrap_freesurfer/freesurfer/mri_create_tests.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CREATE_TESTS_METADATA = Metadata(
-    id="999792ae56910fc6d041db101d550da0a7da203a.boutiques",
+    id="ef9b53b27b38928103e6f01109a7bdb63e3a0cc8.boutiques",
     name="mri_create_tests",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ MRI_CREATE_TESTS_METADATA = Metadata(
 
 
 MriCreateTestsParameters = typing.TypedDict('MriCreateTestsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_create_tests"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_create_tests"]],
+    "input_file": InputPathType,
+    "out_src": str,
+    "out_target": str,
+    "input_target": typing.NotRequired[InputPathType | None],
+    "lta_in": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "noise": typing.NotRequired[float | None],
+    "outlier": typing.NotRequired[float | None],
+    "outlier_box": typing.NotRequired[float | None],
+    "translation_flag": bool,
+    "transdist": typing.NotRequired[float | None],
+    "rotation_flag": bool,
+    "maxdeg": typing.NotRequired[float | None],
+    "intensity_flag": bool,
+    "iscale": typing.NotRequired[float | None],
+    "lta_out": typing.NotRequired[str | None],
+    "lta_outs": typing.NotRequired[str | None],
+    "lta_outt": typing.NotRequired[str | None],
+    "iscale_out": typing.NotRequired[str | None],
+})
+MriCreateTestsParametersTagged = typing.TypedDict('MriCreateTestsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_create_tests"],
     "input_file": InputPathType,
     "out_src": str,
     "out_target": str,
@@ -35,42 +57,11 @@ MriCreateTestsParameters = typing.TypedDict('MriCreateTestsParameters', {
     "lta_outt": typing.NotRequired[str | None],
     "iscale_out": 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 {
-        "mri_create_tests": mri_create_tests_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 MriCreateTestsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_create_tests(...)`.
+    Output object returned when calling `MriCreateTestsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +87,7 @@ def mri_create_tests_params(
     lta_outs: str | None = None,
     lta_outt: str | None = None,
     iscale_out: str | None = None,
-) -> MriCreateTestsParameters:
+) -> MriCreateTestsParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +118,7 @@ def mri_create_tests_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_create_tests",
+        "@type": "freesurfer/mri_create_tests",
         "input_file": input_file,
         "out_src": out_src,
         "out_target": out_target,
@@ -181,86 +172,86 @@ def mri_create_tests_cargs(
     cargs.append("mri_create_tests")
     cargs.extend([
         "--in",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "--outs",
-        params.get("out_src")
+        params.get("out_src", None)
     ])
     cargs.extend([
         "--outt",
-        params.get("out_target")
+        params.get("out_target", None)
     ])
-    if params.get("input_target") is not None:
+    if params.get("input_target", None) is not None:
         cargs.extend([
             "--int",
-            execution.input_file(params.get("input_target"))
+            execution.input_file(params.get("input_target", None))
         ])
-    if params.get("lta_in") is not None:
+    if params.get("lta_in", None) is not None:
         cargs.extend([
             "--lta-in",
-            params.get("lta_in")
+            params.get("lta_in", 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("noise") is not None:
+    if params.get("noise", None) is not None:
         cargs.extend([
             "--noise",
-            str(params.get("noise"))
+            str(params.get("noise", None))
         ])
-    if params.get("outlier") is not None:
+    if params.get("outlier", None) is not None:
         cargs.extend([
             "--outlier",
-            str(params.get("outlier"))
+            str(params.get("outlier", None))
         ])
-    if params.get("outlier_box") is not None:
+    if params.get("outlier_box", None) is not None:
         cargs.extend([
             "--outlier-box",
-            str(params.get("outlier_box"))
+            str(params.get("outlier_box", None))
         ])
-    if params.get("translation_flag"):
+    if params.get("translation_flag", False):
         cargs.append("--translation")
-    if params.get("transdist") is not None:
+    if params.get("transdist", None) is not None:
         cargs.extend([
             "--transdist",
-            str(params.get("transdist"))
+            str(params.get("transdist", None))
         ])
-    if params.get("rotation_flag"):
+    if params.get("rotation_flag", False):
         cargs.append("--rotation")
-    if params.get("maxdeg") is not None:
+    if params.get("maxdeg", None) is not None:
         cargs.extend([
             "--maxdeg",
-            str(params.get("maxdeg"))
+            str(params.get("maxdeg", None))
         ])
-    if params.get("intensity_flag"):
+    if params.get("intensity_flag", False):
         cargs.append("--intensity")
-    if params.get("iscale") is not None:
+    if params.get("iscale", None) is not None:
         cargs.extend([
             "--iscale",
-            str(params.get("iscale"))
+            str(params.get("iscale", None))
         ])
-    if params.get("lta_out") is not None:
+    if params.get("lta_out", None) is not None:
         cargs.extend([
             "--lta-out",
-            params.get("lta_out")
+            params.get("lta_out", None)
         ])
-    if params.get("lta_outs") is not None:
+    if params.get("lta_outs", None) is not None:
         cargs.extend([
             "--lta-outs",
-            params.get("lta_outs")
+            params.get("lta_outs", None)
         ])
-    if params.get("lta_outt") is not None:
+    if params.get("lta_outt", None) is not None:
         cargs.extend([
             "--lta-outt",
-            params.get("lta_outt")
+            params.get("lta_outt", None)
         ])
-    if params.get("iscale_out") is not None:
+    if params.get("iscale_out", None) is not None:
         cargs.extend([
             "--iscale-out",
-            params.get("iscale_out")
+            params.get("iscale_out", None)
         ])
     return cargs
 
@@ -286,11 +277,13 @@ def mri_create_tests_outputs(
 
 def mri_create_tests_execute(
     params: MriCreateTestsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCreateTestsOutputs:
     """
-    Creates test cases for the registration by mapping the input to a source (half
-    way backward) and to a target (half way forward).
+    mri_create_tests
+    
+    Creates test cases for the registration by mapping the input to a source
+    (half way backward) and to a target (half way forward).
     
     Author: FreeSurfer Developers
     
@@ -298,10 +291,12 @@ def mri_create_tests_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCreateTestsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CREATE_TESTS_METADATA)
     params = execution.params(params)
     cargs = mri_create_tests_cargs(params, execution)
     ret = mri_create_tests_outputs(params, execution)
@@ -332,8 +327,10 @@ def mri_create_tests(
     runner: Runner | None = None,
 ) -> MriCreateTestsOutputs:
     """
-    Creates test cases for the registration by mapping the input to a source (half
-    way backward) and to a target (half way forward).
+    mri_create_tests
+    
+    Creates test cases for the registration by mapping the input to a source
+    (half way backward) and to a target (half way forward).
     
     Author: FreeSurfer Developers
     
@@ -366,8 +363,6 @@ def mri_create_tests(
     Returns:
         NamedTuple of outputs (described in `MriCreateTestsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CREATE_TESTS_METADATA)
     params = mri_create_tests_params(
         input_file=input_file,
         out_src=out_src,
@@ -389,13 +384,13 @@ def mri_create_tests(
         lta_outt=lta_outt,
         iscale_out=iscale_out,
     )
-    return mri_create_tests_execute(params, execution)
+    return mri_create_tests_execute(params, runner)
 
 
 __all__ = [
     "MRI_CREATE_TESTS_METADATA",
     "MriCreateTestsOutputs",
-    "MriCreateTestsParameters",
     "mri_create_tests",
+    "mri_create_tests_execute",
     "mri_create_tests_params",
 ]

niwrap_freesurfer/freesurfer/mri_cvs_check.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CVS_CHECK_METADATA = Metadata(
-    id="72ac9d6e08580c333bd915db7bf636a0c1d187a9.boutiques",
+    id="656b052525619a7ac9c0bf4a7c2237b1b92dbad7.boutiques",
     name="mri_cvs_check",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ MRI_CVS_CHECK_METADATA = Metadata(
 
 
 MriCvsCheckParameters = typing.TypedDict('MriCvsCheckParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cvs_check"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cvs_check"]],
+    "mov_subjid": str,
+    "template_subjid": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[typing.Literal["lh", "rh"] | None],
+    "help": bool,
+    "version": bool,
+})
+MriCvsCheckParametersTagged = typing.TypedDict('MriCvsCheckParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cvs_check"],
     "mov_subjid": str,
     "template_subjid": typing.NotRequired[str | None],
     "hemi": typing.NotRequired[typing.Literal["lh", "rh"] | None],
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_cvs_check": mri_cvs_check_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 MriCvsCheckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cvs_check(...)`.
+    Output object returned when calling `MriCvsCheckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def mri_cvs_check_params(
     hemi: typing.Literal["lh", "rh"] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MriCvsCheckParameters:
+) -> MriCvsCheckParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +62,7 @@ def mri_cvs_check_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cvs_check",
+        "@type": "freesurfer/mri_cvs_check",
         "mov_subjid": mov_subjid,
         "help": help_,
         "version": version,
@@ -114,21 +91,21 @@ def mri_cvs_check_cargs(
     cargs.append("mri_cvs_check")
     cargs.extend([
         "--mov",
-        params.get("mov_subjid")
+        params.get("mov_subjid", None)
     ])
-    if params.get("template_subjid") is not None:
+    if params.get("template_subjid", None) is not None:
         cargs.extend([
             "--template",
-            params.get("template_subjid")
+            params.get("template_subjid", None)
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -154,9 +131,11 @@ def mri_cvs_check_outputs(
 
 def mri_cvs_check_execute(
     params: MriCvsCheckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCvsCheckOutputs:
     """
+    mri_cvs_check
+    
     Checks whether the files required for mri_cvs_register all exist.
     
     Author: FreeSurfer Developers
@@ -165,10 +144,12 @@ def mri_cvs_check_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCvsCheckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CVS_CHECK_METADATA)
     params = execution.params(params)
     cargs = mri_cvs_check_cargs(params, execution)
     ret = mri_cvs_check_outputs(params, execution)
@@ -185,6 +166,8 @@ def mri_cvs_check(
     runner: Runner | None = None,
 ) -> MriCvsCheckOutputs:
     """
+    mri_cvs_check
+    
     Checks whether the files required for mri_cvs_register all exist.
     
     Author: FreeSurfer Developers
@@ -204,8 +187,6 @@ def mri_cvs_check(
     Returns:
         NamedTuple of outputs (described in `MriCvsCheckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CVS_CHECK_METADATA)
     params = mri_cvs_check_params(
         mov_subjid=mov_subjid,
         template_subjid=template_subjid,
@@ -213,13 +194,13 @@ def mri_cvs_check(
         help_=help_,
         version=version,
     )
-    return mri_cvs_check_execute(params, execution)
+    return mri_cvs_check_execute(params, runner)
 
 
 __all__ = [
     "MRI_CVS_CHECK_METADATA",
     "MriCvsCheckOutputs",
-    "MriCvsCheckParameters",
     "mri_cvs_check",
+    "mri_cvs_check_execute",
     "mri_cvs_check_params",
 ]