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

niwrap_freesurfer/freesurfer/parc_atlas_jackknife_test.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PARC_ATLAS_JACKKNIFE_TEST_METADATA = Metadata(
-    id="73521a0dbbff55000eb66ba615a4c090cafe9838.boutiques",
+    id="f32e0caa24c7fb5cc656fa8604f60ca73245c93d.boutiques",
     name="parc_atlas_jackknife_test",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ PARC_ATLAS_JACKKNIFE_TEST_METADATA = Metadata(
 
 
 ParcAtlasJackknifeTestParameters = typing.TypedDict('ParcAtlasJackknifeTestParameters', {
-    "__STYXTYPE__": typing.Literal["parc_atlas_jackknife_test"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/parc_atlas_jackknife_test"]],
+    "register": bool,
+    "reg_dist": typing.NotRequired[str | None],
+    "reg_append": typing.NotRequired[str | None],
+    "reg_copy": typing.NotRequired[str | None],
+    "train": bool,
+    "classify": bool,
+    "test": bool,
+    "all": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "freesurfer_home": typing.NotRequired[str | None],
+    "binaries_path": typing.NotRequired[str | None],
+    "dontrun": bool,
+})
+ParcAtlasJackknifeTestParametersTagged = typing.TypedDict('ParcAtlasJackknifeTestParametersTagged', {
+    "@type": typing.Literal["freesurfer/parc_atlas_jackknife_test"],
     "register": bool,
     "reg_dist": typing.NotRequired[str | None],
     "reg_append": typing.NotRequired[str | None],
@@ -28,48 +43,16 @@ ParcAtlasJackknifeTestParameters = typing.TypedDict('ParcAtlasJackknifeTestParam
     "binaries_path": typing.NotRequired[str | None],
     "dontrun": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "parc_atlas_jackknife_test": parc_atlas_jackknife_test_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 {
-        "parc_atlas_jackknife_test": parc_atlas_jackknife_test_outputs,
-    }.get(t)
 
 
 class ParcAtlasJackknifeTestOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `parc_atlas_jackknife_test(...)`.
+    Output object returned when calling `ParcAtlasJackknifeTestParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
     jackknife_output: OutputPathType
-    """Output files written to the directory named 'jackknife'."""
+    """Directory named 'jackknife' containing output files"""
 
 
 def parc_atlas_jackknife_test_params(
@@ -85,7 +68,7 @@ def parc_atlas_jackknife_test_params(
     freesurfer_home: str | None = None,
     binaries_path: str | None = None,
     dontrun: bool = False,
-) -> ParcAtlasJackknifeTestParameters:
+) -> ParcAtlasJackknifeTestParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def parc_atlas_jackknife_test_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "parc_atlas_jackknife_test",
+        "@type": "freesurfer/parc_atlas_jackknife_test",
         "register": register,
         "train": train,
         "classify": classify,
@@ -144,47 +127,47 @@ def parc_atlas_jackknife_test_cargs(
     """
     cargs = []
     cargs.append("parc_atlas_jackknife_test")
-    if params.get("register"):
+    if params.get("register", False):
         cargs.append("-register")
-    if params.get("reg_dist") is not None:
+    if params.get("reg_dist", None) is not None:
         cargs.extend([
             "-reg_dist",
-            params.get("reg_dist")
+            params.get("reg_dist", None)
         ])
-    if params.get("reg_append") is not None:
+    if params.get("reg_append", None) is not None:
         cargs.extend([
             "-reg_append",
-            params.get("reg_append")
+            params.get("reg_append", None)
         ])
-    if params.get("reg_copy") is not None:
+    if params.get("reg_copy", None) is not None:
         cargs.extend([
             "-reg_copy",
-            params.get("reg_copy")
+            params.get("reg_copy", None)
         ])
-    if params.get("train"):
+    if params.get("train", False):
         cargs.append("-train")
-    if params.get("classify"):
+    if params.get("classify", False):
         cargs.append("-classify")
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
-    if params.get("all"):
+    if params.get("all", False):
         cargs.append("-all")
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("freesurfer_home") is not None:
+    if params.get("freesurfer_home", None) is not None:
         cargs.extend([
             "-fshome",
-            params.get("freesurfer_home")
+            params.get("freesurfer_home", None)
         ])
-    if params.get("binaries_path") is not None:
+    if params.get("binaries_path", None) is not None:
         cargs.extend([
             "-binhome",
-            params.get("binaries_path")
+            params.get("binaries_path", None)
         ])
-    if params.get("dontrun"):
+    if params.get("dontrun", False):
         cargs.append("-dontrun")
     return cargs
 
@@ -204,16 +187,18 @@ def parc_atlas_jackknife_test_outputs(
     """
     ret = ParcAtlasJackknifeTestOutputs(
         root=execution.output_file("."),
-        jackknife_output=execution.output_file("jackknife/*"),
+        jackknife_output=execution.output_file("jackknife"),
     )
     return ret
 
 
 def parc_atlas_jackknife_test_execute(
     params: ParcAtlasJackknifeTestParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ParcAtlasJackknifeTestOutputs:
     """
+    parc_atlas_jackknife_test
+    
     Tool for conducting a jackknife accuracy test using FreeSurfer atlases.
     
     Author: FreeSurfer Developers
@@ -222,10 +207,12 @@ def parc_atlas_jackknife_test_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ParcAtlasJackknifeTestOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PARC_ATLAS_JACKKNIFE_TEST_METADATA)
     params = execution.params(params)
     cargs = parc_atlas_jackknife_test_cargs(params, execution)
     ret = parc_atlas_jackknife_test_outputs(params, execution)
@@ -249,6 +236,8 @@ def parc_atlas_jackknife_test(
     runner: Runner | None = None,
 ) -> ParcAtlasJackknifeTestOutputs:
     """
+    parc_atlas_jackknife_test
+    
     Tool for conducting a jackknife accuracy test using FreeSurfer atlases.
     
     Author: FreeSurfer Developers
@@ -272,8 +261,6 @@ def parc_atlas_jackknife_test(
     Returns:
         NamedTuple of outputs (described in `ParcAtlasJackknifeTestOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PARC_ATLAS_JACKKNIFE_TEST_METADATA)
     params = parc_atlas_jackknife_test_params(
         register=register,
         reg_dist=reg_dist,
@@ -288,13 +275,13 @@ def parc_atlas_jackknife_test(
         binaries_path=binaries_path,
         dontrun=dontrun,
     )
-    return parc_atlas_jackknife_test_execute(params, execution)
+    return parc_atlas_jackknife_test_execute(params, runner)
 
 
 __all__ = [
     "PARC_ATLAS_JACKKNIFE_TEST_METADATA",
     "ParcAtlasJackknifeTestOutputs",
-    "ParcAtlasJackknifeTestParameters",
     "parc_atlas_jackknife_test",
+    "parc_atlas_jackknife_test_execute",
     "parc_atlas_jackknife_test_params",
 ]

niwrap_freesurfer/freesurfer/pctsurfcon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PCTSURFCON_METADATA = Metadata(
-    id="41f4f72ed55be4072d0d15d9f6300820448d5489.boutiques",
+    id="bc20b6316dfee9817f866a81eff8ba3e5882f17b.boutiques",
     name="pctsurfcon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ PCTSURFCON_METADATA = Metadata(
 
 
 PctsurfconParameters = typing.TypedDict('PctsurfconParameters', {
-    "__STYXTYPE__": typing.Literal["pctsurfcon"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/pctsurfcon"]],
+    "subject": str,
+    "fsvol": typing.NotRequired[str | None],
+    "outbase": typing.NotRequired[str | None],
+    "lh_only": bool,
+    "rh_only": bool,
+    "gm_proj_frac": typing.NotRequired[float | None],
+    "gm_proj_abs": typing.NotRequired[float | None],
+    "wm_proj_abs": typing.NotRequired[float | None],
+    "neg": bool,
+    "no_mask": bool,
+    "pial": bool,
+    "tmp": typing.NotRequired[str | None],
+    "nocleanup": bool,
+})
+PctsurfconParametersTagged = typing.TypedDict('PctsurfconParametersTagged', {
+    "@type": typing.Literal["freesurfer/pctsurfcon"],
     "subject": str,
     "fsvol": typing.NotRequired[str | None],
     "outbase": typing.NotRequired[str | None],
@@ -29,42 +45,11 @@ PctsurfconParameters = typing.TypedDict('PctsurfconParameters', {
     "tmp": typing.NotRequired[str | None],
     "nocleanup": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "pctsurfcon": pctsurfcon_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 PctsurfconOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `pctsurfcon(...)`.
+    Output object returned when calling `PctsurfconParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def pctsurfcon_params(
     pial: bool = False,
     tmp: str | None = None,
     nocleanup: bool = False,
-) -> PctsurfconParameters:
+) -> PctsurfconParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +91,7 @@ def pctsurfcon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "pctsurfcon",
+        "@type": "freesurfer/pctsurfcon",
         "subject": subject,
         "lh_only": lh_only,
         "rh_only": rh_only,
@@ -147,49 +132,49 @@ def pctsurfcon_cargs(
     cargs.append("pctsurfcon")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("fsvol") is not None:
+    if params.get("fsvol", None) is not None:
         cargs.extend([
             "--fsvol",
-            params.get("fsvol")
+            params.get("fsvol", None)
         ])
-    if params.get("outbase") is not None:
+    if params.get("outbase", None) is not None:
         cargs.extend([
             "--b",
-            params.get("outbase")
+            params.get("outbase", None)
         ])
-    if params.get("lh_only"):
+    if params.get("lh_only", False):
         cargs.append("--lh-only")
-    if params.get("rh_only"):
+    if params.get("rh_only", False):
         cargs.append("--rh-only")
-    if params.get("gm_proj_frac") is not None:
+    if params.get("gm_proj_frac", None) is not None:
         cargs.extend([
             "--gm-proj-frac",
-            str(params.get("gm_proj_frac"))
+            str(params.get("gm_proj_frac", None))
         ])
-    if params.get("gm_proj_abs") is not None:
+    if params.get("gm_proj_abs", None) is not None:
         cargs.extend([
             "--gm-proj-abs",
-            str(params.get("gm_proj_abs"))
+            str(params.get("gm_proj_abs", None))
         ])
-    if params.get("wm_proj_abs") is not None:
+    if params.get("wm_proj_abs", None) is not None:
         cargs.extend([
             "--wm-proj-abs",
-            str(params.get("wm_proj_abs"))
+            str(params.get("wm_proj_abs", None))
         ])
-    if params.get("neg"):
+    if params.get("neg", False):
         cargs.append("--neg")
-    if params.get("no_mask"):
+    if params.get("no_mask", False):
         cargs.append("--no-mask")
-    if params.get("pial"):
+    if params.get("pial", False):
         cargs.append("--pial")
-    if params.get("tmp") is not None:
+    if params.get("tmp", None) is not None:
         cargs.extend([
             "--tmp",
-            params.get("tmp")
+            params.get("tmp", None)
         ])
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("--nocleanup")
     return cargs
 
@@ -215,9 +200,11 @@ def pctsurfcon_outputs(
 
 def pctsurfcon_execute(
     params: PctsurfconParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PctsurfconOutputs:
     """
+    pctsurfcon
+    
     Compute surface-wise gray/white matter contrast.
     
     Author: FreeSurfer Developers
@@ -226,10 +213,12 @@ def pctsurfcon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PctsurfconOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PCTSURFCON_METADATA)
     params = execution.params(params)
     cargs = pctsurfcon_cargs(params, execution)
     ret = pctsurfcon_outputs(params, execution)
@@ -254,6 +243,8 @@ def pctsurfcon(
     runner: Runner | None = None,
 ) -> PctsurfconOutputs:
     """
+    pctsurfcon
+    
     Compute surface-wise gray/white matter contrast.
     
     Author: FreeSurfer Developers
@@ -278,8 +269,6 @@ def pctsurfcon(
     Returns:
         NamedTuple of outputs (described in `PctsurfconOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PCTSURFCON_METADATA)
     params = pctsurfcon_params(
         subject=subject,
         fsvol=fsvol,
@@ -295,13 +284,13 @@ def pctsurfcon(
         tmp=tmp,
         nocleanup=nocleanup,
     )
-    return pctsurfcon_execute(params, execution)
+    return pctsurfcon_execute(params, runner)
 
 
 __all__ = [
     "PCTSURFCON_METADATA",
     "PctsurfconOutputs",
-    "PctsurfconParameters",
     "pctsurfcon",
+    "pctsurfcon_execute",
     "pctsurfcon_params",
 ]

niwrap_freesurfer/freesurfer/plot_structure_stats_tcl.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PLOT_STRUCTURE_STATS_TCL_METADATA = Metadata(
-    id="3de0e97c01ce61e97ae009f4560aa157a2bcc2c6.boutiques",
+    id="60fce4021e28a4ededdb51863b8fa98cde23f6df.boutiques",
     name="plot_structure_stats.tcl",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ PLOT_STRUCTURE_STATS_TCL_METADATA = Metadata(
 
 
 PlotStructureStatsTclParameters = typing.TypedDict('PlotStructureStatsTclParameters', {
-    "__STYXTYPE__": typing.Literal["plot_structure_stats.tcl"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/plot_structure_stats.tcl"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+PlotStructureStatsTclParametersTagged = typing.TypedDict('PlotStructureStatsTclParametersTagged', {
+    "@type": typing.Literal["freesurfer/plot_structure_stats.tcl"],
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "plot_structure_stats.tcl": plot_structure_stats_tcl_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 {
-        "plot_structure_stats.tcl": plot_structure_stats_tcl_outputs,
-    }.get(t)
 
 
 class PlotStructureStatsTclOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `plot_structure_stats_tcl(...)`.
+    Output object returned when calling `PlotStructureStatsTclParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class PlotStructureStatsTclOutputs(typing.NamedTuple):
 def plot_structure_stats_tcl_params(
     input_file: InputPathType,
     output_file: str,
-) -> PlotStructureStatsTclParameters:
+) -> PlotStructureStatsTclParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def plot_structure_stats_tcl_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "plot_structure_stats.tcl",
+        "@type": "freesurfer/plot_structure_stats.tcl",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -98,8 +71,8 @@ def plot_structure_stats_tcl_cargs(
     """
     cargs = []
     cargs.append("plot_structure_stats.tcl")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def plot_structure_stats_tcl_outputs(
     """
     ret = PlotStructureStatsTclOutputs(
         root=execution.output_file("."),
-        plot_file=execution.output_file(params.get("output_file") + ".png"),
+        plot_file=execution.output_file(params.get("output_file", None) + ".png"),
     )
     return ret
 
 
 def plot_structure_stats_tcl_execute(
     params: PlotStructureStatsTclParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PlotStructureStatsTclOutputs:
     """
+    plot_structure_stats.tcl
+    
     Script to plot structural statistics.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def plot_structure_stats_tcl_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PlotStructureStatsTclOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PLOT_STRUCTURE_STATS_TCL_METADATA)
     params = execution.params(params)
     cargs = plot_structure_stats_tcl_cargs(params, execution)
     ret = plot_structure_stats_tcl_outputs(params, execution)
@@ -153,6 +130,8 @@ def plot_structure_stats_tcl(
     runner: Runner | None = None,
 ) -> PlotStructureStatsTclOutputs:
     """
+    plot_structure_stats.tcl
+    
     Script to plot structural statistics.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def plot_structure_stats_tcl(
     Returns:
         NamedTuple of outputs (described in `PlotStructureStatsTclOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PLOT_STRUCTURE_STATS_TCL_METADATA)
     params = plot_structure_stats_tcl_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return plot_structure_stats_tcl_execute(params, execution)
+    return plot_structure_stats_tcl_execute(params, runner)
 
 
 __all__ = [
     "PLOT_STRUCTURE_STATS_TCL_METADATA",
     "PlotStructureStatsTclOutputs",
-    "PlotStructureStatsTclParameters",
     "plot_structure_stats_tcl",
+    "plot_structure_stats_tcl_execute",
     "plot_structure_stats_tcl_params",
 ]