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

niwrap_freesurfer/freesurfer/recon_all_clinical_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RECON_ALL_CLINICAL_SH_METADATA = Metadata(
-    id="504aa9bce9ae8c5b6244f9955d00b4842b304c48.boutiques",
+    id="93d156b9105b580fcdf9969cf93e0e2914a56d83.boutiques",
     name="recon-all-clinical.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ RECON_ALL_CLINICAL_SH_METADATA = Metadata(
 
 
 ReconAllClinicalShParameters = typing.TypedDict('ReconAllClinicalShParameters', {
-    "__STYXTYPE__": typing.Literal["recon-all-clinical.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/recon-all-clinical.sh"]],
+    "input_scan": InputPathType,
+    "subject_id": str,
+    "threads": int,
+    "subject_dir": typing.NotRequired[str | None],
+})
+ReconAllClinicalShParametersTagged = typing.TypedDict('ReconAllClinicalShParametersTagged', {
+    "@type": typing.Literal["freesurfer/recon-all-clinical.sh"],
     "input_scan": InputPathType,
     "subject_id": str,
     "threads": int,
     "subject_dir": 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 {
-        "recon-all-clinical.sh": recon_all_clinical_sh_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 ReconAllClinicalShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `recon_all_clinical_sh(...)`.
+    Output object returned when calling `ReconAllClinicalShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def recon_all_clinical_sh_params(
     subject_id: str,
     threads: int,
     subject_dir: str | None = None,
-) -> ReconAllClinicalShParameters:
+) -> ReconAllClinicalShParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def recon_all_clinical_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "recon-all-clinical.sh",
+        "@type": "freesurfer/recon-all-clinical.sh",
         "input_scan": input_scan,
         "subject_id": subject_id,
         "threads": threads,
@@ -105,11 +81,11 @@ def recon_all_clinical_sh_cargs(
     """
     cargs = []
     cargs.append("recon-all-clinical.sh")
-    cargs.append(execution.input_file(params.get("input_scan")))
-    cargs.append(params.get("subject_id"))
-    cargs.append(str(params.get("threads")))
-    if params.get("subject_dir") is not None:
-        cargs.append(params.get("subject_dir"))
+    cargs.append(execution.input_file(params.get("input_scan", None)))
+    cargs.append(params.get("subject_id", None))
+    cargs.append(str(params.get("threads", None)))
+    if params.get("subject_dir", None) is not None:
+        cargs.append(params.get("subject_dir", None))
     return cargs
 
 
@@ -134,9 +110,11 @@ def recon_all_clinical_sh_outputs(
 
 def recon_all_clinical_sh_execute(
     params: ReconAllClinicalShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReconAllClinicalShOutputs:
     """
+    recon-all-clinical.sh
+    
     Recon-all-like stream for processing clinical brain MRI scans of arbitrary
     orientation, resolution, and contrast using SynthSeg and SynthSR.
     
@@ -146,10 +124,12 @@ def recon_all_clinical_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReconAllClinicalShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RECON_ALL_CLINICAL_SH_METADATA)
     params = execution.params(params)
     cargs = recon_all_clinical_sh_cargs(params, execution)
     ret = recon_all_clinical_sh_outputs(params, execution)
@@ -165,6 +145,8 @@ def recon_all_clinical_sh(
     runner: Runner | None = None,
 ) -> ReconAllClinicalShOutputs:
     """
+    recon-all-clinical.sh
+    
     Recon-all-like stream for processing clinical brain MRI scans of arbitrary
     orientation, resolution, and contrast using SynthSeg and SynthSR.
     
@@ -182,21 +164,19 @@ def recon_all_clinical_sh(
     Returns:
         NamedTuple of outputs (described in `ReconAllClinicalShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RECON_ALL_CLINICAL_SH_METADATA)
     params = recon_all_clinical_sh_params(
         input_scan=input_scan,
         subject_id=subject_id,
         threads=threads,
         subject_dir=subject_dir,
     )
-    return recon_all_clinical_sh_execute(params, execution)
+    return recon_all_clinical_sh_execute(params, runner)
 
 
 __all__ = [
     "RECON_ALL_CLINICAL_SH_METADATA",
     "ReconAllClinicalShOutputs",
-    "ReconAllClinicalShParameters",
     "recon_all_clinical_sh",
+    "recon_all_clinical_sh_execute",
     "recon_all_clinical_sh_params",
 ]

niwrap_freesurfer/freesurfer/recon_all_exvivo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RECON_ALL_EXVIVO_METADATA = Metadata(
-    id="9f00b252b2f61f947af4a725491db0b3cab46912.boutiques",
+    id="5adc9b2e2c491833707cce4d193fcfb820cf2a1d.boutiques",
     name="recon-all-exvivo",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ RECON_ALL_EXVIVO_METADATA = Metadata(
 
 
 ReconAllExvivoParameters = typing.TypedDict('ReconAllExvivoParameters', {
-    "__STYXTYPE__": typing.Literal["recon-all-exvivo"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/recon-all-exvivo"]],
+    "subject_id": str,
+    "hemisphere": typing.NotRequired[str | None],
+    "nocerebellum": bool,
+})
+ReconAllExvivoParametersTagged = typing.TypedDict('ReconAllExvivoParametersTagged', {
+    "@type": typing.Literal["freesurfer/recon-all-exvivo"],
     "subject_id": str,
     "hemisphere": typing.NotRequired[str | None],
     "nocerebellum": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "recon-all-exvivo": recon_all_exvivo_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 ReconAllExvivoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `recon_all_exvivo(...)`.
+    Output object returned when calling `ReconAllExvivoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def recon_all_exvivo_params(
     subject_id: str,
     hemisphere: str | None = None,
     nocerebellum: bool = False,
-) -> ReconAllExvivoParameters:
+) -> ReconAllExvivoParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def recon_all_exvivo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "recon-all-exvivo",
+        "@type": "freesurfer/recon-all-exvivo",
         "subject_id": subject_id,
         "nocerebellum": nocerebellum,
     }
@@ -102,14 +77,14 @@ def recon_all_exvivo_cargs(
     cargs.append("recon-all-exvivo")
     cargs.extend([
         "-s",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "-[lr]h",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
-    if params.get("nocerebellum"):
+    if params.get("nocerebellum", False):
         cargs.append("-nocerebellum")
     return cargs
 
@@ -135,9 +110,11 @@ def recon_all_exvivo_outputs(
 
 def recon_all_exvivo_execute(
     params: ReconAllExvivoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReconAllExvivoOutputs:
     """
+    recon-all-exvivo
+    
     A script to perform an ex vivo reconstruction with FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def recon_all_exvivo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReconAllExvivoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RECON_ALL_EXVIVO_METADATA)
     params = execution.params(params)
     cargs = recon_all_exvivo_cargs(params, execution)
     ret = recon_all_exvivo_outputs(params, execution)
@@ -164,6 +143,8 @@ def recon_all_exvivo(
     runner: Runner | None = None,
 ) -> ReconAllExvivoOutputs:
     """
+    recon-all-exvivo
+    
     A script to perform an ex vivo reconstruction with FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -178,20 +159,18 @@ def recon_all_exvivo(
     Returns:
         NamedTuple of outputs (described in `ReconAllExvivoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RECON_ALL_EXVIVO_METADATA)
     params = recon_all_exvivo_params(
         subject_id=subject_id,
         hemisphere=hemisphere,
         nocerebellum=nocerebellum,
     )
-    return recon_all_exvivo_execute(params, execution)
+    return recon_all_exvivo_execute(params, runner)
 
 
 __all__ = [
     "RECON_ALL_EXVIVO_METADATA",
     "ReconAllExvivoOutputs",
-    "ReconAllExvivoParameters",
     "recon_all_exvivo",
+    "recon_all_exvivo_execute",
     "recon_all_exvivo_params",
 ]

niwrap_freesurfer/freesurfer/reconbatchjobs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RECONBATCHJOBS_METADATA = Metadata(
-    id="3b88343e632e9bbafdf43ea3df14e2cf0c3f34d1.boutiques",
+    id="ce7e65e0781cc7894875341c56c45af19d18b272.boutiques",
     name="reconbatchjobs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RECONBATCHJOBS_METADATA = Metadata(
 
 
 ReconbatchjobsParameters = typing.TypedDict('ReconbatchjobsParameters', {
-    "__STYXTYPE__": typing.Literal["reconbatchjobs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reconbatchjobs"]],
+    "logfile": str,
+    "cmdfiles": list[str],
+})
+ReconbatchjobsParametersTagged = typing.TypedDict('ReconbatchjobsParametersTagged', {
+    "@type": typing.Literal["freesurfer/reconbatchjobs"],
     "logfile": str,
     "cmdfiles": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reconbatchjobs": reconbatchjobs_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 ReconbatchjobsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reconbatchjobs(...)`.
+    Output object returned when calling `ReconbatchjobsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class ReconbatchjobsOutputs(typing.NamedTuple):
 def reconbatchjobs_params(
     logfile: str,
     cmdfiles: list[str],
-) -> ReconbatchjobsParameters:
+) -> ReconbatchjobsParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def reconbatchjobs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reconbatchjobs",
+        "@type": "freesurfer/reconbatchjobs",
         "logfile": logfile,
         "cmdfiles": cmdfiles,
     }
@@ -95,8 +69,8 @@ def reconbatchjobs_cargs(
     """
     cargs = []
     cargs.append("reconbatchjobs")
-    cargs.append(params.get("logfile"))
-    cargs.extend(params.get("cmdfiles"))
+    cargs.append(params.get("logfile", None))
+    cargs.extend(params.get("cmdfiles", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def reconbatchjobs_outputs(
 
 def reconbatchjobs_execute(
     params: ReconbatchjobsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReconbatchjobsOutputs:
     """
+    reconbatchjobs
+    
     Batch job processor for reconstruction scripts.
     
     Author: FreeSurfer Developers
@@ -132,10 +108,12 @@ def reconbatchjobs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReconbatchjobsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RECONBATCHJOBS_METADATA)
     params = execution.params(params)
     cargs = reconbatchjobs_cargs(params, execution)
     ret = reconbatchjobs_outputs(params, execution)
@@ -149,6 +127,8 @@ def reconbatchjobs(
     runner: Runner | None = None,
 ) -> ReconbatchjobsOutputs:
     """
+    reconbatchjobs
+    
     Batch job processor for reconstruction scripts.
     
     Author: FreeSurfer Developers
@@ -162,19 +142,17 @@ def reconbatchjobs(
     Returns:
         NamedTuple of outputs (described in `ReconbatchjobsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RECONBATCHJOBS_METADATA)
     params = reconbatchjobs_params(
         logfile=logfile,
         cmdfiles=cmdfiles,
     )
-    return reconbatchjobs_execute(params, execution)
+    return reconbatchjobs_execute(params, runner)
 
 
 __all__ = [
     "RECONBATCHJOBS_METADATA",
     "ReconbatchjobsOutputs",
-    "ReconbatchjobsParameters",
     "reconbatchjobs",
+    "reconbatchjobs_execute",
     "reconbatchjobs_params",
 ]

niwrap_freesurfer/freesurfer/reg2subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REG2SUBJECT_METADATA = Metadata(
-    id="bd548e7db5696c14e468b04f1fafbb638585f19c.boutiques",
+    id="cefd2546e44a6b96bd7ddf7a1b9cf638824d614e.boutiques",
     name="reg2subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ REG2SUBJECT_METADATA = Metadata(
 
 
 Reg2subjectParameters = typing.TypedDict('Reg2subjectParameters', {
-    "__STYXTYPE__": typing.Literal["reg2subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reg2subject"]],
+    "regfile": InputPathType,
+})
+Reg2subjectParametersTagged = typing.TypedDict('Reg2subjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/reg2subject"],
     "regfile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reg2subject": reg2subject_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 Reg2subjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reg2subject(...)`.
+    Output object returned when calling `Reg2subjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class Reg2subjectOutputs(typing.NamedTuple):
 
 def reg2subject_params(
     regfile: InputPathType,
-) -> Reg2subjectParameters:
+) -> Reg2subjectParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def reg2subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reg2subject",
+        "@type": "freesurfer/reg2subject",
         "regfile": regfile,
     }
     return params
@@ -93,7 +66,7 @@ def reg2subject_cargs(
     cargs.append("reg2subject")
     cargs.extend([
         "--r",
-        execution.input_file(params.get("regfile"))
+        execution.input_file(params.get("regfile", None))
     ])
     return cargs
 
@@ -119,11 +92,13 @@ def reg2subject_outputs(
 
 def reg2subject_execute(
     params: Reg2subjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Reg2subjectOutputs:
     """
-    Returns the name of the subject in the registration file, whether it is an LTA
-    or register.dat file.
+    reg2subject
+    
+    Returns the name of the subject in the registration file, whether it is an
+    LTA or register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -131,10 +106,12 @@ def reg2subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Reg2subjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REG2SUBJECT_METADATA)
     params = execution.params(params)
     cargs = reg2subject_cargs(params, execution)
     ret = reg2subject_outputs(params, execution)
@@ -147,8 +124,10 @@ def reg2subject(
     runner: Runner | None = None,
 ) -> Reg2subjectOutputs:
     """
-    Returns the name of the subject in the registration file, whether it is an LTA
-    or register.dat file.
+    reg2subject
+    
+    Returns the name of the subject in the registration file, whether it is an
+    LTA or register.dat file.
     
     Author: FreeSurfer Developers
     
@@ -160,18 +139,16 @@ def reg2subject(
     Returns:
         NamedTuple of outputs (described in `Reg2subjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REG2SUBJECT_METADATA)
     params = reg2subject_params(
         regfile=regfile,
     )
-    return reg2subject_execute(params, execution)
+    return reg2subject_execute(params, runner)
 
 
 __all__ = [
     "REG2SUBJECT_METADATA",
     "Reg2subjectOutputs",
-    "Reg2subjectParameters",
     "reg2subject",
+    "reg2subject_execute",
     "reg2subject_params",
 ]