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

niwrap_freesurfer/freesurfer/mri_wbc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_WBC_METADATA = Metadata(
-    id="53db1c7b3ddc8b97d52d6c3d88748dff5b0adcfd.boutiques",
+    id="23eaae439e6ac96b243c2e12a8b928ba9fac21f5.boutiques",
     name="mri_wbc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,27 @@ MRI_WBC_METADATA = Metadata(
 
 
 MriWbcParameters = typing.TypedDict('MriWbcParameters', {
-    "__STYXTYPE__": typing.Literal["mri_wbc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_wbc"]],
+    "functional_volume": InputPathType,
+    "volume_mask": typing.NotRequired[InputPathType | None],
+    "lh_functional_surface": InputPathType,
+    "lh_surface": InputPathType,
+    "lh_inflated": typing.NotRequired[InputPathType | None],
+    "lh_mask": typing.NotRequired[InputPathType | None],
+    "lh_label": typing.NotRequired[InputPathType | None],
+    "rh_functional_surface": InputPathType,
+    "rh_surface": InputPathType,
+    "rh_inflated": typing.NotRequired[InputPathType | None],
+    "rh_mask": typing.NotRequired[InputPathType | None],
+    "rh_label": typing.NotRequired[InputPathType | None],
+    "rho_threshold": typing.NotRequired[float | None],
+    "dist_threshold": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+})
+MriWbcParametersTagged = typing.TypedDict('MriWbcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_wbc"],
     "functional_volume": InputPathType,
     "volume_mask": typing.NotRequired[InputPathType | None],
     "lh_functional_surface": InputPathType,
@@ -33,42 +53,11 @@ MriWbcParameters = typing.TypedDict('MriWbcParameters', {
     "debug": bool,
     "checkopts": 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_wbc": mri_wbc_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 MriWbcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_wbc(...)`.
+    Output object returned when calling `MriWbcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -92,7 +81,7 @@ def mri_wbc_params(
     threads: float | None = None,
     debug: bool = False,
     checkopts: bool = False,
-) -> MriWbcParameters:
+) -> MriWbcParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +107,7 @@ def mri_wbc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_wbc",
+        "@type": "freesurfer/mri_wbc",
         "functional_volume": functional_volume,
         "lh_functional_surface": lh_functional_surface,
         "lh_surface": lh_surface,
@@ -167,77 +156,77 @@ def mri_wbc_cargs(
     cargs.append("mri_wbc")
     cargs.extend([
         "--fvol",
-        execution.input_file(params.get("functional_volume"))
+        execution.input_file(params.get("functional_volume", None))
     ])
-    if params.get("volume_mask") is not None:
+    if params.get("volume_mask", None) is not None:
         cargs.extend([
             "--volmask",
-            execution.input_file(params.get("volume_mask"))
+            execution.input_file(params.get("volume_mask", None))
         ])
     cargs.extend([
         "--lh",
-        execution.input_file(params.get("lh_functional_surface"))
+        execution.input_file(params.get("lh_functional_surface", None))
     ])
     cargs.extend([
         "--lh",
-        execution.input_file(params.get("lh_surface"))
+        execution.input_file(params.get("lh_surface", None))
     ])
-    if params.get("lh_inflated") is not None:
+    if params.get("lh_inflated", None) is not None:
         cargs.extend([
             "--lh",
-            execution.input_file(params.get("lh_inflated"))
+            execution.input_file(params.get("lh_inflated", None))
         ])
-    if params.get("lh_mask") is not None:
+    if params.get("lh_mask", None) is not None:
         cargs.extend([
             "--lhmask",
-            execution.input_file(params.get("lh_mask"))
+            execution.input_file(params.get("lh_mask", None))
         ])
-    if params.get("lh_label") is not None:
+    if params.get("lh_label", None) is not None:
         cargs.extend([
             "--lhlabel",
-            execution.input_file(params.get("lh_label"))
+            execution.input_file(params.get("lh_label", None))
         ])
     cargs.extend([
         "--rh",
-        execution.input_file(params.get("rh_functional_surface"))
+        execution.input_file(params.get("rh_functional_surface", None))
     ])
     cargs.extend([
         "--rh",
-        execution.input_file(params.get("rh_surface"))
+        execution.input_file(params.get("rh_surface", None))
     ])
-    if params.get("rh_inflated") is not None:
+    if params.get("rh_inflated", None) is not None:
         cargs.extend([
             "--rh",
-            execution.input_file(params.get("rh_inflated"))
+            execution.input_file(params.get("rh_inflated", None))
         ])
-    if params.get("rh_mask") is not None:
+    if params.get("rh_mask", None) is not None:
         cargs.extend([
             "--rhmask",
-            execution.input_file(params.get("rh_mask"))
+            execution.input_file(params.get("rh_mask", None))
         ])
-    if params.get("rh_label") is not None:
+    if params.get("rh_label", None) is not None:
         cargs.extend([
             "--rhlabel",
-            execution.input_file(params.get("rh_label"))
+            execution.input_file(params.get("rh_label", None))
         ])
-    if params.get("rho_threshold") is not None:
+    if params.get("rho_threshold", None) is not None:
         cargs.extend([
             "--rho",
-            str(params.get("rho_threshold"))
+            str(params.get("rho_threshold", None))
         ])
-    if params.get("dist_threshold") is not None:
+    if params.get("dist_threshold", None) is not None:
         cargs.extend([
             "--dist",
-            str(params.get("dist_threshold"))
+            str(params.get("dist_threshold", None))
         ])
-    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("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -263,10 +252,13 @@ def mri_wbc_outputs(
 
 def mri_wbc_execute(
     params: MriWbcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriWbcOutputs:
     """
-    A tool for working with functional brain imaging data on surfaces and volumes.
+    mri_wbc
+    
+    A tool for working with functional brain imaging data on surfaces and
+    volumes.
     
     Author: FreeSurfer Developers
     
@@ -274,10 +266,12 @@ def mri_wbc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriWbcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_WBC_METADATA)
     params = execution.params(params)
     cargs = mri_wbc_cargs(params, execution)
     ret = mri_wbc_outputs(params, execution)
@@ -306,7 +300,10 @@ def mri_wbc(
     runner: Runner | None = None,
 ) -> MriWbcOutputs:
     """
-    A tool for working with functional brain imaging data on surfaces and volumes.
+    mri_wbc
+    
+    A tool for working with functional brain imaging data on surfaces and
+    volumes.
     
     Author: FreeSurfer Developers
     
@@ -334,8 +331,6 @@ def mri_wbc(
     Returns:
         NamedTuple of outputs (described in `MriWbcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_WBC_METADATA)
     params = mri_wbc_params(
         functional_volume=functional_volume,
         volume_mask=volume_mask,
@@ -355,13 +350,13 @@ def mri_wbc(
         debug=debug,
         checkopts=checkopts,
     )
-    return mri_wbc_execute(params, execution)
+    return mri_wbc_execute(params, runner)
 
 
 __all__ = [
     "MRI_WBC_METADATA",
     "MriWbcOutputs",
-    "MriWbcParameters",
     "mri_wbc",
+    "mri_wbc_execute",
     "mri_wbc_params",
 ]

niwrap_freesurfer/freesurfer/mri_xvolavg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_XVOLAVG_METADATA = Metadata(
-    id="59e2b553a940c4fdb7f3dcfd7c0ee7148a4cce23.boutiques",
+    id="b74f56f50aae77b8cd6b4541c5e9927405e67b6b.boutiques",
     name="mri_xvolavg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_XVOLAVG_METADATA = Metadata(
 
 
 MriXvolavgParameters = typing.TypedDict('MriXvolavgParameters', {
-    "__STYXTYPE__": typing.Literal["mri_xvolavg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_xvolavg"]],
+    "input_volumes": list[InputPathType],
+    "vol_type": str,
+    "output_volume": str,
+    "output_type": typing.NotRequired[str | None],
+})
+MriXvolavgParametersTagged = typing.TypedDict('MriXvolavgParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_xvolavg"],
     "input_volumes": list[InputPathType],
     "vol_type": str,
     "output_volume": str,
     "output_type": 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_xvolavg": mri_xvolavg_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_xvolavg": mri_xvolavg_outputs,
-    }.get(t)
 
 
 class MriXvolavgOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_xvolavg(...)`.
+    Output object returned when calling `MriXvolavgParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_xvolavg_params(
     vol_type: str,
     output_volume: str,
     output_type: str | None = None,
-) -> MriXvolavgParameters:
+) -> MriXvolavgParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def mri_xvolavg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_xvolavg",
+        "@type": "freesurfer/mri_xvolavg",
         "input_volumes": input_volumes,
         "vol_type": vol_type,
         "output_volume": output_volume,
@@ -111,20 +86,20 @@ def mri_xvolavg_cargs(
     cargs.append("mri_xvolavg")
     cargs.extend([
         "--vol",
-        *[execution.input_file(f) for f in params.get("input_volumes")]
+        *[execution.input_file(f) for f in params.get("input_volumes", None)]
     ])
     cargs.extend([
         "--vol_type",
-        params.get("vol_type")
+        params.get("vol_type", None)
     ])
     cargs.extend([
         "--out",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
-    if params.get("output_type") is not None:
+    if params.get("output_type", None) is not None:
         cargs.extend([
             "--out_type",
-            params.get("output_type")
+            params.get("output_type", None)
         ])
     return cargs
 
@@ -144,16 +119,18 @@ def mri_xvolavg_outputs(
     """
     ret = MriXvolavgOutputs(
         root=execution.output_file("."),
-        averaged_output=execution.output_file(params.get("output_volume")),
+        averaged_output=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_xvolavg_execute(
     params: MriXvolavgParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriXvolavgOutputs:
     """
+    mri_xvolavg
+    
     Tool to average multiple volumes together (including 4D volumes).
     
     Author: FreeSurfer Developers
@@ -162,10 +139,12 @@ def mri_xvolavg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriXvolavgOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_XVOLAVG_METADATA)
     params = execution.params(params)
     cargs = mri_xvolavg_cargs(params, execution)
     ret = mri_xvolavg_outputs(params, execution)
@@ -181,6 +160,8 @@ def mri_xvolavg(
     runner: Runner | None = None,
 ) -> MriXvolavgOutputs:
     """
+    mri_xvolavg
+    
     Tool to average multiple volumes together (including 4D volumes).
     
     Author: FreeSurfer Developers
@@ -198,21 +179,19 @@ def mri_xvolavg(
     Returns:
         NamedTuple of outputs (described in `MriXvolavgOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_XVOLAVG_METADATA)
     params = mri_xvolavg_params(
         input_volumes=input_volumes,
         vol_type=vol_type,
         output_volume=output_volume,
         output_type=output_type,
     )
-    return mri_xvolavg_execute(params, execution)
+    return mri_xvolavg_execute(params, runner)
 
 
 __all__ = [
     "MRI_XVOLAVG_METADATA",
     "MriXvolavgOutputs",
-    "MriXvolavgParameters",
     "mri_xvolavg",
+    "mri_xvolavg_execute",
     "mri_xvolavg_params",
 ]

niwrap_freesurfer/freesurfer/mri_z2p.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_Z2P_METADATA = Metadata(
-    id="7987d56daa05e85cf63f7316456ae6a98c40b859.boutiques",
+    id="4a23fadc4e304b9fb71b710792e4e9d45c7b9ebe.boutiques",
     name="mri_z2p",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ MRI_Z2P_METADATA = Metadata(
 
 
 MriZ2pParameters = typing.TypedDict('MriZ2pParameters', {
-    "__STYXTYPE__": typing.Literal["mri_z2p"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_z2p"]],
+    "z_volume": InputPathType,
+    "p_volume": str,
+    "sig_volume": str,
+    "mask_volume": typing.NotRequired[InputPathType | None],
+    "two_sided": bool,
+    "one_sided": bool,
+    "signed": bool,
+    "feat": typing.NotRequired[str | None],
+    "feat_format": typing.NotRequired[str | None],
+    "nii_format": bool,
+    "niigz_format": bool,
+    "mgh_format": bool,
+    "mgz_format": bool,
+    "img_format": bool,
+    "debug": bool,
+    "check_opts": bool,
+})
+MriZ2pParametersTagged = typing.TypedDict('MriZ2pParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_z2p"],
     "z_volume": InputPathType,
     "p_volume": str,
     "sig_volume": str,
@@ -32,43 +51,11 @@ MriZ2pParameters = typing.TypedDict('MriZ2pParameters', {
     "debug": bool,
     "check_opts": 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_z2p": mri_z2p_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_z2p": mri_z2p_outputs,
-    }.get(t)
 
 
 class MriZ2pOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_z2p(...)`.
+    Output object returned when calling `MriZ2pParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +82,7 @@ def mri_z2p_params(
     img_format: bool = False,
     debug: bool = False,
     check_opts: bool = False,
-) -> MriZ2pParameters:
+) -> MriZ2pParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +108,7 @@ def mri_z2p_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_z2p",
+        "@type": "freesurfer/mri_z2p",
         "z_volume": z_volume,
         "p_volume": p_volume,
         "sig_volume": sig_volume,
@@ -162,50 +149,50 @@ def mri_z2p_cargs(
     cargs.append("mri_z2p")
     cargs.extend([
         "--z",
-        execution.input_file(params.get("z_volume"))
+        execution.input_file(params.get("z_volume", None))
     ])
     cargs.extend([
         "--p",
-        params.get("p_volume")
+        params.get("p_volume", None)
     ])
     cargs.extend([
         "--log10p",
-        params.get("sig_volume")
+        params.get("sig_volume", None)
     ])
-    if params.get("mask_volume") is not None:
+    if params.get("mask_volume", None) is not None:
         cargs.extend([
             "--mask",
-            execution.input_file(params.get("mask_volume"))
+            execution.input_file(params.get("mask_volume", None))
         ])
-    if params.get("two_sided"):
+    if params.get("two_sided", False):
         cargs.append("--two-sided")
-    if params.get("one_sided"):
+    if params.get("one_sided", False):
         cargs.append("--one-sided")
-    if params.get("signed"):
+    if params.get("signed", False):
         cargs.append("--signed")
-    if params.get("feat") is not None:
+    if params.get("feat", None) is not None:
         cargs.extend([
             "--feat",
-            params.get("feat")
+            params.get("feat", None)
         ])
-    if params.get("feat_format") is not None:
+    if params.get("feat_format", None) is not None:
         cargs.extend([
             "--featfmt",
-            params.get("feat_format")
+            params.get("feat_format", None)
         ])
-    if params.get("nii_format"):
+    if params.get("nii_format", False):
         cargs.append("--nii")
-    if params.get("niigz_format"):
+    if params.get("niigz_format", False):
         cargs.append("--nii.gz")
-    if params.get("mgh_format"):
+    if params.get("mgh_format", False):
         cargs.append("--mgh")
-    if params.get("mgz_format"):
+    if params.get("mgz_format", False):
         cargs.append("--mgz")
-    if params.get("img_format"):
+    if params.get("img_format", False):
         cargs.append("--img")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("check_opts"):
+    if params.get("check_opts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -225,17 +212,19 @@ def mri_z2p_outputs(
     """
     ret = MriZ2pOutputs(
         root=execution.output_file("."),
-        output_p_volume=execution.output_file(params.get("p_volume")),
-        output_sig_volume=execution.output_file(params.get("sig_volume")),
+        output_p_volume=execution.output_file(params.get("p_volume", None)),
+        output_sig_volume=execution.output_file(params.get("sig_volume", None)),
     )
     return ret
 
 
 def mri_z2p_execute(
     params: MriZ2pParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriZ2pOutputs:
     """
+    mri_z2p
+    
     Converts Z-statistic volumes to P-value volumes.
     
     Author: FreeSurfer Developers
@@ -244,10 +233,12 @@ def mri_z2p_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriZ2pOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_Z2P_METADATA)
     params = execution.params(params)
     cargs = mri_z2p_cargs(params, execution)
     ret = mri_z2p_outputs(params, execution)
@@ -275,6 +266,8 @@ def mri_z2p(
     runner: Runner | None = None,
 ) -> MriZ2pOutputs:
     """
+    mri_z2p
+    
     Converts Z-statistic volumes to P-value volumes.
     
     Author: FreeSurfer Developers
@@ -303,8 +296,6 @@ def mri_z2p(
     Returns:
         NamedTuple of outputs (described in `MriZ2pOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_Z2P_METADATA)
     params = mri_z2p_params(
         z_volume=z_volume,
         p_volume=p_volume,
@@ -323,13 +314,13 @@ def mri_z2p(
         debug=debug,
         check_opts=check_opts,
     )
-    return mri_z2p_execute(params, execution)
+    return mri_z2p_execute(params, runner)
 
 
 __all__ = [
     "MRI_Z2P_METADATA",
     "MriZ2pOutputs",
-    "MriZ2pParameters",
     "mri_z2p",
+    "mri_z2p_execute",
     "mri_z2p_params",
 ]