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

niwrap_freesurfer/freesurfer/sfa2fieldsign.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SFA2FIELDSIGN_METADATA = Metadata(
-    id="7f94ee11352613b06c9c4748c7eadb754e7722c8.boutiques",
+    id="a31f34e180604d273b75695a96957bbe9c820533.boutiques",
     name="sfa2fieldsign",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ SFA2FIELDSIGN_METADATA = Metadata(
 
 
 Sfa2fieldsignParameters = typing.TypedDict('Sfa2fieldsignParameters', {
-    "__STYXTYPE__": typing.Literal["sfa2fieldsign"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/sfa2fieldsign"]],
+    "sfadir": str,
+    "register_dat": str,
+    "threshold": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "proj_frac": typing.NotRequired[float | None],
+    "occip": bool,
+    "patch": typing.NotRequired[str | None],
+    "osd": typing.NotRequired[str | None],
+    "lh": bool,
+    "rh": bool,
+})
+Sfa2fieldsignParametersTagged = typing.TypedDict('Sfa2fieldsignParametersTagged', {
+    "@type": typing.Literal["freesurfer/sfa2fieldsign"],
     "sfadir": str,
     "register_dat": str,
     "threshold": typing.NotRequired[float | None],
@@ -26,72 +39,46 @@ Sfa2fieldsignParameters = typing.TypedDict('Sfa2fieldsignParameters', {
     "lh": bool,
     "rh": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "sfa2fieldsign": sfa2fieldsign_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 {
-        "sfa2fieldsign": sfa2fieldsign_outputs,
-    }.get(t)
 
 
 class Sfa2fieldsignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sfa2fieldsign(...)`.
+    Output object returned when calling `Sfa2fieldsignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    fsig_bin: OutputPathType
+    fsig_bin: OutputPathType | None
     """Intersection of polar and eccentricity thresholded fieldsigns"""
-    eccen_masked: OutputPathType
+    eccen_masked: OutputPathType | None
     """Eccentricity angle (rad) volume masked by fieldsign bin"""
-    polar_masked: OutputPathType
+    polar_masked: OutputPathType | None
     """Polar angle (rad) volume masked by fieldsign bin"""
-    eccen_masked_mgh: OutputPathType
-    """Masked eccentricity angle sampled on the hemisphere surface"""
-    polar_masked_mgh: OutputPathType
-    """Masked polar angle sampled on the hemisphere surface"""
-    fieldsign_masked_mgh: OutputPathType
-    """Masked fieldsign map"""
+    left_eccen_masked_mgh: OutputPathType | None
+    """Masked eccentricity angle sampled on the left hemisphere surface"""
+    left_polar_masked_mgh: OutputPathType | None
+    """Masked polar angle sampled on the left hemisphere surface"""
+    left_fieldsign_masked_mgh: OutputPathType | None
+    """Masked fieldsign map on left hemispehre"""
+    right_eccen_masked_mgh: OutputPathType | None
+    """Masked eccentricity angle sampled on the right hemisphere surface"""
+    right_polar_masked_mgh: OutputPathType | None
+    """Masked polar angle sampled on the right hemisphere surface"""
+    right_fieldsign_masked_mgh: OutputPathType | None
+    """Masked fieldsign map on the right hemisphere"""
 
 
 def sfa2fieldsign_params(
     sfadir: str,
     register_dat: str,
-    threshold: float | None = 2,
-    fwhm: float | None = 10,
-    proj_frac: float | None = 0.5,
+    threshold: float | None = None,
+    fwhm: float | None = None,
+    proj_frac: float | None = None,
     occip: bool = False,
     patch: str | None = None,
     osd: str | None = None,
     lh: bool = False,
     rh: bool = False,
-) -> Sfa2fieldsignParameters:
+) -> Sfa2fieldsignParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +88,7 @@ def sfa2fieldsign_params(
         threshold: Sigthresh threshold (Default: 2).
         fwhm: Full width at half maximum (FWHM) (Default: 10mm).
         proj_frac: Projection fraction (Default: 0.5).
-        occip: Use ?h.occip.patch.flat.
+        occip: Use rh.occip.patch.flat.
         patch: Use specific patch (?)h.patch.
         osd: Directory under SFA to put output (Default: fieldsign).
         lh: Process left hemisphere only.
@@ -110,7 +97,7 @@ def sfa2fieldsign_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sfa2fieldsign",
+        "@type": "freesurfer/sfa2fieldsign",
         "sfadir": sfadir,
         "register_dat": register_dat,
         "occip": occip,
@@ -147,42 +134,42 @@ def sfa2fieldsign_cargs(
     cargs.append("sfa2fieldsign")
     cargs.extend([
         "--sfa",
-        params.get("sfadir")
+        params.get("sfadir", None)
     ])
     cargs.extend([
         "--reg",
-        params.get("register_dat")
+        params.get("register_dat", None)
     ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "--fwhm",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("proj_frac") is not None:
+    if params.get("proj_frac", None) is not None:
         cargs.extend([
             "--proj-frac",
-            str(params.get("proj_frac"))
+            str(params.get("proj_frac", None))
         ])
-    if params.get("occip"):
+    if params.get("occip", False):
         cargs.append("--occip")
-    if params.get("patch") is not None:
+    if params.get("patch", None) is not None:
         cargs.extend([
             "--patch",
-            params.get("patch")
+            params.get("patch", None)
         ])
-    if params.get("osd") is not None:
+    if params.get("osd", None) is not None:
         cargs.extend([
             "--osd",
-            params.get("osd")
+            params.get("osd", None)
         ])
-    if params.get("lh"):
+    if params.get("lh", False):
         cargs.append("--lh")
-    if params.get("rh"):
+    if params.get("rh", False):
         cargs.append("--rh")
     return cargs
 
@@ -202,23 +189,28 @@ def sfa2fieldsign_outputs(
     """
     ret = Sfa2fieldsignOutputs(
         root=execution.output_file("."),
-        fsig_bin=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/fsig.bin.nii"),
-        eccen_masked=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/eccen.masked.nii"),
-        polar_masked=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/polar.masked.nii"),
-        eccen_masked_mgh=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/?h.eccen.masked.mgh"),
-        polar_masked_mgh=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/?h.polar.masked.mgh"),
-        fieldsign_masked_mgh=execution.output_file(params.get("sfadir") + "/[OSD or fieldsign]/?h.fieldsign.masked.mgh"),
+        fsig_bin=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/fsig.bin.nii") if (params.get("osd") is not None) else None,
+        eccen_masked=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/eccen.masked.nii") if (params.get("osd") is not None) else None,
+        polar_masked=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/polar.masked.nii") if (params.get("osd") is not None) else None,
+        left_eccen_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/lh.eccen.masked.mgh") if (params.get("osd") is not None) else None,
+        left_polar_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/lh.polar.masked.mgh") if (params.get("osd") is not None) else None,
+        left_fieldsign_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/lh.fieldsign.masked.mgh") if (params.get("osd") is not None) else None,
+        right_eccen_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/rh.eccen.masked.mgh") if (params.get("osd") is not None) else None,
+        right_polar_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/rh.polar.masked.mgh") if (params.get("osd") is not None) else None,
+        right_fieldsign_masked_mgh=execution.output_file(params.get("sfadir", None) + "/" + params.get("osd", None) + "/rh.fieldsign.masked.mgh") if (params.get("osd") is not None) else None,
     )
     return ret
 
 
 def sfa2fieldsign_execute(
     params: Sfa2fieldsignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Sfa2fieldsignOutputs:
     """
-    Computes fieldsign map from sfa-sess output. Masks the angle volumes and samples
-    them to the surface.
+    sfa2fieldsign
+    
+    Computes fieldsign map from sfa-sess output. Masks the angle volumes and
+    samples them to the surface.
     
     Author: FreeSurfer Developers
     
@@ -226,10 +218,12 @@ def sfa2fieldsign_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Sfa2fieldsignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SFA2FIELDSIGN_METADATA)
     params = execution.params(params)
     cargs = sfa2fieldsign_cargs(params, execution)
     ret = sfa2fieldsign_outputs(params, execution)
@@ -240,9 +234,9 @@ def sfa2fieldsign_execute(
 def sfa2fieldsign(
     sfadir: str,
     register_dat: str,
-    threshold: float | None = 2,
-    fwhm: float | None = 10,
-    proj_frac: float | None = 0.5,
+    threshold: float | None = None,
+    fwhm: float | None = None,
+    proj_frac: float | None = None,
     occip: bool = False,
     patch: str | None = None,
     osd: str | None = None,
@@ -251,8 +245,10 @@ def sfa2fieldsign(
     runner: Runner | None = None,
 ) -> Sfa2fieldsignOutputs:
     """
-    Computes fieldsign map from sfa-sess output. Masks the angle volumes and samples
-    them to the surface.
+    sfa2fieldsign
+    
+    Computes fieldsign map from sfa-sess output. Masks the angle volumes and
+    samples them to the surface.
     
     Author: FreeSurfer Developers
     
@@ -264,7 +260,7 @@ def sfa2fieldsign(
         threshold: Sigthresh threshold (Default: 2).
         fwhm: Full width at half maximum (FWHM) (Default: 10mm).
         proj_frac: Projection fraction (Default: 0.5).
-        occip: Use ?h.occip.patch.flat.
+        occip: Use rh.occip.patch.flat.
         patch: Use specific patch (?)h.patch.
         osd: Directory under SFA to put output (Default: fieldsign).
         lh: Process left hemisphere only.
@@ -273,8 +269,6 @@ def sfa2fieldsign(
     Returns:
         NamedTuple of outputs (described in `Sfa2fieldsignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SFA2FIELDSIGN_METADATA)
     params = sfa2fieldsign_params(
         sfadir=sfadir,
         register_dat=register_dat,
@@ -287,13 +281,13 @@ def sfa2fieldsign(
         lh=lh,
         rh=rh,
     )
-    return sfa2fieldsign_execute(params, execution)
+    return sfa2fieldsign_execute(params, runner)
 
 
 __all__ = [
     "SFA2FIELDSIGN_METADATA",
     "Sfa2fieldsignOutputs",
-    "Sfa2fieldsignParameters",
     "sfa2fieldsign",
+    "sfa2fieldsign_execute",
     "sfa2fieldsign_params",
 ]

niwrap_freesurfer/freesurfer/slicedelay.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SLICEDELAY_METADATA = Metadata(
-    id="fefd12c00942108f1db83dac38baac8c6a806f9e.boutiques",
+    id="f6f4fe4c58eddbc76a9cd5aa81640e121ea9f052.boutiques",
     name="slicedelay",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ SLICEDELAY_METADATA = Metadata(
 
 
 SlicedelayParameters = typing.TypedDict('SlicedelayParameters', {
-    "__STYXTYPE__": typing.Literal["slicedelay"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/slicedelay"]],
+    "slicedelayfile": str,
+    "nslices": float,
+    "order": typing.Literal["up", "down", "odd", "even", "siemens"],
+    "ngroups": float,
+})
+SlicedelayParametersTagged = typing.TypedDict('SlicedelayParametersTagged', {
+    "@type": typing.Literal["freesurfer/slicedelay"],
     "slicedelayfile": str,
     "nslices": float,
     "order": typing.Literal["up", "down", "odd", "even", "siemens"],
     "ngroups": float,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "slicedelay": slicedelay_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 {
-        "slicedelay": slicedelay_outputs,
-    }.get(t)
 
 
 class SlicedelayOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `slicedelay(...)`.
+    Output object returned when calling `SlicedelayParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def slicedelay_params(
     nslices: float,
     order: typing.Literal["up", "down", "odd", "even", "siemens"],
     ngroups: float,
-) -> SlicedelayParameters:
+) -> SlicedelayParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def slicedelay_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "slicedelay",
+        "@type": "freesurfer/slicedelay",
         "slicedelayfile": slicedelayfile,
         "nslices": nslices,
         "order": order,
@@ -108,19 +83,19 @@ def slicedelay_cargs(
     cargs.append("slicedelay")
     cargs.extend([
         "--o",
-        params.get("slicedelayfile")
+        params.get("slicedelayfile", None)
     ])
     cargs.extend([
         "--nslices",
-        str(params.get("nslices"))
+        str(params.get("nslices", None))
     ])
     cargs.extend([
         "--order",
-        params.get("order")
+        params.get("order", None)
     ])
     cargs.extend([
         "--ngroups",
-        str(params.get("ngroups"))
+        str(params.get("ngroups", None))
     ])
     return cargs
 
@@ -140,18 +115,20 @@ def slicedelay_outputs(
     """
     ret = SlicedelayOutputs(
         root=execution.output_file("."),
-        slicedelayfile=execution.output_file(params.get("slicedelayfile")),
+        slicedelayfile=execution.output_file(params.get("slicedelayfile", None)),
     )
     return ret
 
 
 def slicedelay_execute(
     params: SlicedelayParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SlicedelayOutputs:
     """
-    Creates an FSL custom slice delay file for use with slicetimer for slice-time
-    correction of fMRI.
+    slicedelay
+    
+    Creates an FSL custom slice delay file for use with slicetimer for
+    slice-time correction of fMRI.
     
     Author: FreeSurfer Developers
     
@@ -159,10 +136,12 @@ def slicedelay_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SlicedelayOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SLICEDELAY_METADATA)
     params = execution.params(params)
     cargs = slicedelay_cargs(params, execution)
     ret = slicedelay_outputs(params, execution)
@@ -178,8 +157,10 @@ def slicedelay(
     runner: Runner | None = None,
 ) -> SlicedelayOutputs:
     """
-    Creates an FSL custom slice delay file for use with slicetimer for slice-time
-    correction of fMRI.
+    slicedelay
+    
+    Creates an FSL custom slice delay file for use with slicetimer for
+    slice-time correction of fMRI.
     
     Author: FreeSurfer Developers
     
@@ -194,21 +175,19 @@ def slicedelay(
     Returns:
         NamedTuple of outputs (described in `SlicedelayOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SLICEDELAY_METADATA)
     params = slicedelay_params(
         slicedelayfile=slicedelayfile,
         nslices=nslices,
         order=order,
         ngroups=ngroups,
     )
-    return slicedelay_execute(params, execution)
+    return slicedelay_execute(params, runner)
 
 
 __all__ = [
     "SLICEDELAY_METADATA",
     "SlicedelayOutputs",
-    "SlicedelayParameters",
     "slicedelay",
+    "slicedelay_execute",
     "slicedelay_params",
 ]

niwrap_freesurfer/freesurfer/sphere_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPHERE_SUBJECT_METADATA = Metadata(
-    id="e4907d9aa35e3f0d55ae261149fe778f0b917dfd.boutiques",
+    id="bd69d54e1894c7c9176c25b17eac17fd1b114a79.boutiques",
     name="sphere_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ SPHERE_SUBJECT_METADATA = Metadata(
 
 
 SphereSubjectParameters = typing.TypedDict('SphereSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["sphere_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/sphere_subject"]],
+    "input_dir": str,
+    "output_file": str,
+    "license_file": typing.NotRequired[str | None],
+})
+SphereSubjectParametersTagged = typing.TypedDict('SphereSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/sphere_subject"],
     "input_dir": str,
     "output_file": str,
     "license_file": 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 {
-        "sphere_subject": sphere_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 {
-        "sphere_subject": sphere_subject_outputs,
-    }.get(t)
 
 
 class SphereSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sphere_subject(...)`.
+    Output object returned when calling `SphereSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,8 +40,8 @@ class SphereSubjectOutputs(typing.NamedTuple):
 def sphere_subject_params(
     input_dir: str,
     output_file: str,
-    license_file: str | None = "/usr/local/freesurfer/.license",
-) -> SphereSubjectParameters:
+    license_file: str | None = None,
+) -> SphereSubjectParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def sphere_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sphere_subject",
+        "@type": "freesurfer/sphere_subject",
         "input_dir": input_dir,
         "output_file": output_file,
     }
@@ -103,10 +77,10 @@ def sphere_subject_cargs(
     """
     cargs = []
     cargs.append("sphere_subject")
-    cargs.append(params.get("input_dir"))
-    cargs.append(params.get("output_file"))
-    if params.get("license_file") is not None:
-        cargs.append(params.get("license_file"))
+    cargs.append(params.get("input_dir", None))
+    cargs.append(params.get("output_file", None))
+    if params.get("license_file", None) is not None:
+        cargs.append(params.get("license_file", None))
     return cargs
 
 
@@ -125,16 +99,18 @@ def sphere_subject_outputs(
     """
     ret = SphereSubjectOutputs(
         root=execution.output_file("."),
-        output_result=execution.output_file(params.get("output_file")),
+        output_result=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def sphere_subject_execute(
     params: SphereSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SphereSubjectOutputs:
     """
+    sphere_subject
+    
     A FreeSurfer tool for processing subject data.
     
     Author: FreeSurfer Developers
@@ -143,10 +119,12 @@ def sphere_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SphereSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPHERE_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = sphere_subject_cargs(params, execution)
     ret = sphere_subject_outputs(params, execution)
@@ -157,10 +135,12 @@ def sphere_subject_execute(
 def sphere_subject(
     input_dir: str,
     output_file: str,
-    license_file: str | None = "/usr/local/freesurfer/.license",
+    license_file: str | None = None,
     runner: Runner | None = None,
 ) -> SphereSubjectOutputs:
     """
+    sphere_subject
+    
     A FreeSurfer tool for processing subject data.
     
     Author: FreeSurfer Developers
@@ -175,20 +155,18 @@ def sphere_subject(
     Returns:
         NamedTuple of outputs (described in `SphereSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SPHERE_SUBJECT_METADATA)
     params = sphere_subject_params(
         input_dir=input_dir,
         output_file=output_file,
         license_file=license_file,
     )
-    return sphere_subject_execute(params, execution)
+    return sphere_subject_execute(params, runner)
 
 
 __all__ = [
     "SPHERE_SUBJECT_METADATA",
     "SphereSubjectOutputs",
-    "SphereSubjectParameters",
     "sphere_subject",
+    "sphere_subject_execute",
     "sphere_subject_params",
 ]