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

niwrap_freesurfer/freesurfer/surfreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURFREG_METADATA = Metadata(
-    id="d3ce09a4df80f136ffe449469679fe7fc5b7f7ea.boutiques",
+    id="7926379a00df2da00c284be09c4c92596bd13d58.boutiques",
     name="surfreg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ SURFREG_METADATA = Metadata(
 
 
 SurfregParameters = typing.TypedDict('SurfregParameters', {
-    "__STYXTYPE__": typing.Literal["surfreg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/surfreg"]],
+    "subject": str,
+    "target": str,
+    "cross_hemi": bool,
+    "reg_lh": bool,
+    "reg_rh": bool,
+    "reg_both": bool,
+    "no_annot": bool,
+    "annot": typing.NotRequired[str | None],
+    "aparc": bool,
+    "noneg": bool,
+    "init_reg": typing.NotRequired[str | None],
+    "lta": typing.NotRequired[str | None],
+    "init_from_tal": bool,
+    "outsurf": typing.NotRequired[str | None],
+    "no_set_vol_geom": bool,
+    "threads": typing.NotRequired[float | None],
+})
+SurfregParametersTagged = typing.TypedDict('SurfregParametersTagged', {
+    "@type": typing.Literal["freesurfer/surfreg"],
     "subject": str,
     "target": str,
     "cross_hemi": bool,
@@ -32,43 +51,11 @@ SurfregParameters = typing.TypedDict('SurfregParameters', {
     "no_set_vol_geom": bool,
     "threads": 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 {
-        "surfreg": surfreg_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 {
-        "surfreg": surfreg_outputs,
-    }.get(t)
 
 
 class SurfregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surfreg(...)`.
+    Output object returned when calling `SurfregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +80,7 @@ def surfreg_params(
     outsurf: str | None = None,
     no_set_vol_geom: bool = False,
     threads: float | None = None,
-) -> SurfregParameters:
+) -> SurfregParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +105,7 @@ def surfreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "surfreg",
+        "@type": "freesurfer/surfreg",
         "subject": subject,
         "target": target,
         "cross_hemi": cross_hemi,
@@ -161,54 +148,54 @@ def surfreg_cargs(
     cargs.append("surfreg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--t",
-        params.get("target")
+        params.get("target", None)
     ])
-    if params.get("cross_hemi"):
+    if params.get("cross_hemi", False):
         cargs.append("--xhemi")
-    if params.get("reg_lh"):
+    if params.get("reg_lh", False):
         cargs.append("--lh")
-    if params.get("reg_rh"):
+    if params.get("reg_rh", False):
         cargs.append("--rh")
-    if params.get("reg_both"):
+    if params.get("reg_both", False):
         cargs.append("--lhrh")
-    if params.get("no_annot"):
+    if params.get("no_annot", False):
         cargs.append("--no-annot")
-    if params.get("annot") is not None:
+    if params.get("annot", None) is not None:
         cargs.extend([
             "--annot",
-            params.get("annot")
+            params.get("annot", None)
         ])
-    if params.get("aparc"):
+    if params.get("aparc", False):
         cargs.append("--aparc")
-    if params.get("noneg"):
+    if params.get("noneg", False):
         cargs.append("--noneg")
-    if params.get("init_reg") is not None:
+    if params.get("init_reg", None) is not None:
         cargs.extend([
             "--init-reg",
-            params.get("init_reg")
+            params.get("init_reg", None)
         ])
-    if params.get("lta") is not None:
+    if params.get("lta", None) is not None:
         cargs.extend([
             "--lta",
-            params.get("lta")
+            params.get("lta", None)
         ])
-    if params.get("init_from_tal"):
+    if params.get("init_from_tal", False):
         cargs.append("--init-from-tal")
-    if params.get("outsurf") is not None:
+    if params.get("outsurf", None) is not None:
         cargs.extend([
             "--o",
-            params.get("outsurf")
+            params.get("outsurf", None)
         ])
-    if params.get("no_set_vol_geom"):
+    if params.get("no_set_vol_geom", False):
         cargs.append("--no-set-vol-geom")
-    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))
         ])
     return cargs
 
@@ -235,11 +222,14 @@ def surfreg_outputs(
 
 def surfreg_execute(
     params: SurfregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfregOutputs:
     """
+    surfreg
+    
     Performs surface registration (mris_register) between a subject and a target
-    average subject based on the hemi.reg.template.tif atlas in the average subject.
+    average subject based on the hemi.reg.template.tif atlas in the average
+    subject.
     
     Author: FreeSurfer Developers
     
@@ -247,10 +237,12 @@ def surfreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURFREG_METADATA)
     params = execution.params(params)
     cargs = surfreg_cargs(params, execution)
     ret = surfreg_outputs(params, execution)
@@ -278,8 +270,11 @@ def surfreg(
     runner: Runner | None = None,
 ) -> SurfregOutputs:
     """
+    surfreg
+    
     Performs surface registration (mris_register) between a subject and a target
-    average subject based on the hemi.reg.template.tif atlas in the average subject.
+    average subject based on the hemi.reg.template.tif atlas in the average
+    subject.
     
     Author: FreeSurfer Developers
     
@@ -306,8 +301,6 @@ def surfreg(
     Returns:
         NamedTuple of outputs (described in `SurfregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURFREG_METADATA)
     params = surfreg_params(
         subject=subject,
         target=target,
@@ -326,13 +319,13 @@ def surfreg(
         no_set_vol_geom=no_set_vol_geom,
         threads=threads,
     )
-    return surfreg_execute(params, execution)
+    return surfreg_execute(params, runner)
 
 
 __all__ = [
     "SURFREG_METADATA",
     "SurfregOutputs",
-    "SurfregParameters",
     "surfreg",
+    "surfreg_execute",
     "surfreg_params",
 ]

niwrap_freesurfer/freesurfer/swi_preprocess.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SWI_PREPROCESS_METADATA = Metadata(
-    id="a87ddd55dd6e762a7926ab993ca84eb258e4144c.boutiques",
+    id="0a62bba43bd4d353f03ef8edbdd3c20d69162315.boutiques",
     name="swi_preprocess",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ SWI_PREPROCESS_METADATA = Metadata(
 
 
 SwiPreprocessParameters = typing.TypedDict('SwiPreprocessParameters', {
-    "__STYXTYPE__": typing.Literal["swi_preprocess"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/swi_preprocess"]],
+    "scanner": typing.Literal["ge", "siemens", "philips"],
+    "ge_file": typing.NotRequired[InputPathType | None],
+    "philips_file": typing.NotRequired[InputPathType | None],
+    "siemens_magnitude": typing.NotRequired[InputPathType | None],
+    "siemens_phase": typing.NotRequired[InputPathType | None],
+    "out_magnitude": str,
+    "out_phase": str,
+})
+SwiPreprocessParametersTagged = typing.TypedDict('SwiPreprocessParametersTagged', {
+    "@type": typing.Literal["freesurfer/swi_preprocess"],
     "scanner": typing.Literal["ge", "siemens", "philips"],
     "ge_file": typing.NotRequired[InputPathType | None],
     "philips_file": typing.NotRequired[InputPathType | None],
@@ -23,43 +33,11 @@ SwiPreprocessParameters = typing.TypedDict('SwiPreprocessParameters', {
     "out_magnitude": str,
     "out_phase": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "swi_preprocess": swi_preprocess_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 {
-        "swi_preprocess": swi_preprocess_outputs,
-    }.get(t)
 
 
 class SwiPreprocessOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `swi_preprocess(...)`.
+    Output object returned when calling `SwiPreprocessParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def swi_preprocess_params(
     philips_file: InputPathType | None = None,
     siemens_magnitude: InputPathType | None = None,
     siemens_phase: InputPathType | None = None,
-) -> SwiPreprocessParameters:
+) -> SwiPreprocessParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +77,7 @@ def swi_preprocess_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "swi_preprocess",
+        "@type": "freesurfer/swi_preprocess",
         "scanner": scanner,
         "out_magnitude": out_magnitude,
         "out_phase": out_phase,
@@ -132,35 +110,35 @@ def swi_preprocess_cargs(
     cargs.append("swi_preprocess")
     cargs.extend([
         "--scanner",
-        params.get("scanner")
+        params.get("scanner", None)
     ])
-    if params.get("ge_file") is not None:
+    if params.get("ge_file", None) is not None:
         cargs.extend([
             "--ge_file",
-            execution.input_file(params.get("ge_file"))
+            execution.input_file(params.get("ge_file", None))
         ])
-    if params.get("philips_file") is not None:
+    if params.get("philips_file", None) is not None:
         cargs.extend([
             "--philips_file",
-            execution.input_file(params.get("philips_file"))
+            execution.input_file(params.get("philips_file", None))
         ])
-    if params.get("siemens_magnitude") is not None:
+    if params.get("siemens_magnitude", None) is not None:
         cargs.extend([
             "--siemens_mag",
-            execution.input_file(params.get("siemens_magnitude"))
+            execution.input_file(params.get("siemens_magnitude", None))
         ])
-    if params.get("siemens_phase") is not None:
+    if params.get("siemens_phase", None) is not None:
         cargs.extend([
             "--siemens_phase",
-            execution.input_file(params.get("siemens_phase"))
+            execution.input_file(params.get("siemens_phase", None))
         ])
     cargs.extend([
         "--out_magnitude",
-        params.get("out_magnitude")
+        params.get("out_magnitude", None)
     ])
     cargs.extend([
         "--out_phase",
-        params.get("out_phase")
+        params.get("out_phase", None)
     ])
     return cargs
 
@@ -180,17 +158,19 @@ def swi_preprocess_outputs(
     """
     ret = SwiPreprocessOutputs(
         root=execution.output_file("."),
-        output_magnitude_file=execution.output_file(params.get("out_magnitude")),
-        output_phase_file=execution.output_file(params.get("out_phase")),
+        output_magnitude_file=execution.output_file(params.get("out_magnitude", None)),
+        output_phase_file=execution.output_file(params.get("out_phase", None)),
     )
     return ret
 
 
 def swi_preprocess_execute(
     params: SwiPreprocessParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SwiPreprocessOutputs:
     """
+    swi_preprocess
+    
     Pre-process the Susceptibility-weighted images and write out nifti files for
     feeding into PRELUDE (Phase Unwrapping Library of FSL).
     
@@ -200,10 +180,12 @@ def swi_preprocess_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SwiPreprocessOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SWI_PREPROCESS_METADATA)
     params = execution.params(params)
     cargs = swi_preprocess_cargs(params, execution)
     ret = swi_preprocess_outputs(params, execution)
@@ -222,6 +204,8 @@ def swi_preprocess(
     runner: Runner | None = None,
 ) -> SwiPreprocessOutputs:
     """
+    swi_preprocess
+    
     Pre-process the Susceptibility-weighted images and write out nifti files for
     feeding into PRELUDE (Phase Unwrapping Library of FSL).
     
@@ -247,8 +231,6 @@ def swi_preprocess(
     Returns:
         NamedTuple of outputs (described in `SwiPreprocessOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SWI_PREPROCESS_METADATA)
     params = swi_preprocess_params(
         scanner=scanner,
         ge_file=ge_file,
@@ -258,13 +240,13 @@ def swi_preprocess(
         out_magnitude=out_magnitude,
         out_phase=out_phase,
     )
-    return swi_preprocess_execute(params, execution)
+    return swi_preprocess_execute(params, runner)
 
 
 __all__ = [
     "SWI_PREPROCESS_METADATA",
     "SwiPreprocessOutputs",
-    "SwiPreprocessParameters",
     "swi_preprocess",
+    "swi_preprocess_execute",
     "swi_preprocess_params",
 ]

niwrap_freesurfer/freesurfer/swi_process.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SWI_PROCESS_METADATA = Metadata(
-    id="4b331cf7e4a482ca97dcc06c5f065e4fa697e5f1.boutiques",
+    id="738668554ab314e3ebe213ede5cda62840421435.boutiques",
     name="swi_process",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ SWI_PROCESS_METADATA = Metadata(
 
 
 SwiProcessParameters = typing.TypedDict('SwiProcessParameters', {
-    "__STYXTYPE__": typing.Literal["swi_process"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/swi_process"]],
+    "magnitude_image": InputPathType,
+    "phase_image": InputPathType,
+    "swi_output": str,
+    "stddev": typing.NotRequired[float | None],
+    "phase_mask_cutoff": typing.NotRequired[float | None],
+    "phase_mask_right_cutoff": typing.NotRequired[float | None],
+    "sigmoid_a": typing.NotRequired[float | None],
+    "sigmoid_b": typing.NotRequired[float | None],
+    "phase_multiplications": typing.NotRequired[float | None],
+    "mip_level": typing.NotRequired[float | None],
+    "phase_mask_method": typing.NotRequired[str | None],
+})
+SwiProcessParametersTagged = typing.TypedDict('SwiProcessParametersTagged', {
+    "@type": typing.Literal["freesurfer/swi_process"],
     "magnitude_image": InputPathType,
     "phase_image": InputPathType,
     "swi_output": str,
@@ -27,43 +41,11 @@ SwiProcessParameters = typing.TypedDict('SwiProcessParameters', {
     "mip_level": typing.NotRequired[float | None],
     "phase_mask_method": 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 {
-        "swi_process": swi_process_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 {
-        "swi_process": swi_process_outputs,
-    }.get(t)
 
 
 class SwiProcessOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `swi_process(...)`.
+    Output object returned when calling `SwiProcessParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def swi_process_params(
     phase_multiplications: float | None = None,
     mip_level: float | None = None,
     phase_mask_method: str | None = None,
-) -> SwiProcessParameters:
+) -> SwiProcessParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +96,7 @@ def swi_process_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "swi_process",
+        "@type": "freesurfer/swi_process",
         "magnitude_image": magnitude_image,
         "phase_image": phase_image,
         "swi_output": swi_output,
@@ -153,48 +135,48 @@ def swi_process_cargs(
     """
     cargs = []
     cargs.append("swi_process")
-    cargs.append(execution.input_file(params.get("magnitude_image")))
-    cargs.append(execution.input_file(params.get("phase_image")))
-    cargs.append(params.get("swi_output"))
-    if params.get("stddev") is not None:
+    cargs.append(execution.input_file(params.get("magnitude_image", None)))
+    cargs.append(execution.input_file(params.get("phase_image", None)))
+    cargs.append(params.get("swi_output", None))
+    if params.get("stddev", None) is not None:
         cargs.extend([
             "--stddev",
-            str(params.get("stddev"))
+            str(params.get("stddev", None))
         ])
-    if params.get("phase_mask_cutoff") is not None:
+    if params.get("phase_mask_cutoff", None) is not None:
         cargs.extend([
             "--phase_mask_cutoff",
-            str(params.get("phase_mask_cutoff"))
+            str(params.get("phase_mask_cutoff", None))
         ])
-    if params.get("phase_mask_right_cutoff") is not None:
+    if params.get("phase_mask_right_cutoff", None) is not None:
         cargs.extend([
             "--phase_mask_right_cutoff",
-            str(params.get("phase_mask_right_cutoff"))
+            str(params.get("phase_mask_right_cutoff", None))
         ])
-    if params.get("sigmoid_a") is not None:
+    if params.get("sigmoid_a", None) is not None:
         cargs.extend([
             "--sigmoid_a",
-            str(params.get("sigmoid_a"))
+            str(params.get("sigmoid_a", None))
         ])
-    if params.get("sigmoid_b") is not None:
+    if params.get("sigmoid_b", None) is not None:
         cargs.extend([
             "--sigmoid_b",
-            str(params.get("sigmoid_b"))
+            str(params.get("sigmoid_b", None))
         ])
-    if params.get("phase_multiplications") is not None:
+    if params.get("phase_multiplications", None) is not None:
         cargs.extend([
             "--phase_multiplications",
-            str(params.get("phase_multiplications"))
+            str(params.get("phase_multiplications", None))
         ])
-    if params.get("mip_level") is not None:
+    if params.get("mip_level", None) is not None:
         cargs.extend([
             "--mip_level",
-            str(params.get("mip_level"))
+            str(params.get("mip_level", None))
         ])
-    if params.get("phase_mask_method") is not None:
+    if params.get("phase_mask_method", None) is not None:
         cargs.extend([
             "--phase_mask_method",
-            params.get("phase_mask_method")
+            params.get("phase_mask_method", None)
         ])
     return cargs
 
@@ -214,16 +196,18 @@ def swi_process_outputs(
     """
     ret = SwiProcessOutputs(
         root=execution.output_file("."),
-        swi_output_file=execution.output_file(params.get("swi_output")),
+        swi_output_file=execution.output_file(params.get("swi_output", None)),
     )
     return ret
 
 
 def swi_process_execute(
     params: SwiProcessParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SwiProcessOutputs:
     """
+    swi_process
+    
     Process the Susceptibility-weighted images. Ensure the inputs are post-phase
     unwrapping using PRELUDE.
     
@@ -233,10 +217,12 @@ def swi_process_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SwiProcessOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SWI_PROCESS_METADATA)
     params = execution.params(params)
     cargs = swi_process_cargs(params, execution)
     ret = swi_process_outputs(params, execution)
@@ -259,6 +245,8 @@ def swi_process(
     runner: Runner | None = None,
 ) -> SwiProcessOutputs:
     """
+    swi_process
+    
     Process the Susceptibility-weighted images. Ensure the inputs are post-phase
     unwrapping using PRELUDE.
     
@@ -293,8 +281,6 @@ def swi_process(
     Returns:
         NamedTuple of outputs (described in `SwiProcessOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SWI_PROCESS_METADATA)
     params = swi_process_params(
         magnitude_image=magnitude_image,
         phase_image=phase_image,
@@ -308,13 +294,13 @@ def swi_process(
         mip_level=mip_level,
         phase_mask_method=phase_mask_method,
     )
-    return swi_process_execute(params, execution)
+    return swi_process_execute(params, runner)
 
 
 __all__ = [
     "SWI_PROCESS_METADATA",
     "SwiProcessOutputs",
-    "SwiProcessParameters",
     "swi_process",
+    "swi_process_execute",
     "swi_process_params",
 ]