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

niwrap_freesurfer/freesurfer/dmri_violin_plots.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_VIOLIN_PLOTS_METADATA = Metadata(
-    id="a193f3c5d1fcce153b59c31f2df32aafdf44cb45.boutiques",
+    id="bfd3395e98f397268b14fd38e421efd6a400a506.boutiques",
     name="dmri_violinPlots",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ DMRI_VIOLIN_PLOTS_METADATA = Metadata(
 
 
 DmriViolinPlotsParameters = typing.TypedDict('DmriViolinPlotsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_violinPlots"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_violinPlots"]],
+    "input_directory": str,
+    "labels": InputPathType,
+    "structure": str,
+})
+DmriViolinPlotsParametersTagged = typing.TypedDict('DmriViolinPlotsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_violinPlots"],
     "input_directory": str,
     "labels": InputPathType,
     "structure": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_violinPlots": dmri_violin_plots_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 DmriViolinPlotsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_violin_plots(...)`.
+    Output object returned when calling `DmriViolinPlotsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def dmri_violin_plots_params(
     input_directory: str,
     labels: InputPathType,
     structure: str,
-) -> DmriViolinPlotsParameters:
+) -> DmriViolinPlotsParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def dmri_violin_plots_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_violinPlots",
+        "@type": "freesurfer/dmri_violinPlots",
         "input_directory": input_directory,
         "labels": labels,
         "structure": structure,
@@ -101,15 +76,15 @@ def dmri_violin_plots_cargs(
     cargs.append("dmri_violinPlots")
     cargs.extend([
         "-i",
-        params.get("input_directory")
+        params.get("input_directory", None)
     ])
     cargs.extend([
         "-l",
-        execution.input_file(params.get("labels"))
+        execution.input_file(params.get("labels", None))
     ])
     cargs.extend([
         "-s",
-        params.get("structure")
+        params.get("structure", None)
     ])
     return cargs
 
@@ -135,9 +110,11 @@ def dmri_violin_plots_outputs(
 
 def dmri_violin_plots_execute(
     params: DmriViolinPlotsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriViolinPlotsOutputs:
     """
+    dmri_violinPlots
+    
     Generate violin plots for dMRI data.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def dmri_violin_plots_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriViolinPlotsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_VIOLIN_PLOTS_METADATA)
     params = execution.params(params)
     cargs = dmri_violin_plots_cargs(params, execution)
     ret = dmri_violin_plots_outputs(params, execution)
@@ -164,6 +143,8 @@ def dmri_violin_plots(
     runner: Runner | None = None,
 ) -> DmriViolinPlotsOutputs:
     """
+    dmri_violinPlots
+    
     Generate violin plots for dMRI data.
     
     Author: FreeSurfer Developers
@@ -178,20 +159,18 @@ def dmri_violin_plots(
     Returns:
         NamedTuple of outputs (described in `DmriViolinPlotsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_VIOLIN_PLOTS_METADATA)
     params = dmri_violin_plots_params(
         input_directory=input_directory,
         labels=labels,
         structure=structure,
     )
-    return dmri_violin_plots_execute(params, execution)
+    return dmri_violin_plots_execute(params, runner)
 
 
 __all__ = [
     "DMRI_VIOLIN_PLOTS_METADATA",
     "DmriViolinPlotsOutputs",
-    "DmriViolinPlotsParameters",
     "dmri_violin_plots",
+    "dmri_violin_plots_execute",
     "dmri_violin_plots_params",
 ]

niwrap_freesurfer/freesurfer/dmri_vox2vox.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_VOX2VOX_METADATA = Metadata(
-    id="a9c7d072c67909100e5d0cc0f852b4f198351ffb.boutiques",
+    id="e98d1aa0dd9e6a6212d4ed9294022ac34a2aae3a.boutiques",
     name="dmri_vox2vox",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ DMRI_VOX2VOX_METADATA = Metadata(
 
 
 DmriVox2voxParameters = typing.TypedDict('DmriVox2voxParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_vox2vox"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_vox2vox"]],
+    "input_files": list[InputPathType],
+    "input_directory": typing.NotRequired[str | None],
+    "output_files": list[str],
+    "output_directory": typing.NotRequired[str | None],
+    "input_reference": InputPathType,
+    "output_reference": InputPathType,
+    "affine_registration": InputPathType,
+    "nonlinear_registration": InputPathType,
+    "inverse_nonlinear": bool,
+    "debug": bool,
+    "check_options": bool,
+    "help": bool,
+    "version": bool,
+})
+DmriVox2voxParametersTagged = typing.TypedDict('DmriVox2voxParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_vox2vox"],
     "input_files": list[InputPathType],
     "input_directory": typing.NotRequired[str | None],
     "output_files": list[str],
@@ -29,42 +45,11 @@ DmriVox2voxParameters = typing.TypedDict('DmriVox2voxParameters', {
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_vox2vox": dmri_vox2vox_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 DmriVox2voxOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_vox2vox(...)`.
+    Output object returned when calling `DmriVox2voxParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def dmri_vox2vox_params(
     check_options: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> DmriVox2voxParameters:
+) -> DmriVox2voxParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +95,7 @@ def dmri_vox2vox_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_vox2vox",
+        "@type": "freesurfer/dmri_vox2vox",
         "input_files": input_files,
         "output_files": output_files,
         "input_reference": input_reference,
@@ -147,47 +132,47 @@ def dmri_vox2vox_cargs(
     cargs.append("dmri_vox2vox")
     cargs.extend([
         "--in",
-        *[execution.input_file(f) for f in params.get("input_files")]
+        *[execution.input_file(f) for f in params.get("input_files", None)]
     ])
-    if params.get("input_directory") is not None:
+    if params.get("input_directory", None) is not None:
         cargs.extend([
             "--indir",
-            params.get("input_directory")
+            params.get("input_directory", None)
         ])
     cargs.extend([
         "--out",
-        *params.get("output_files")
+        *params.get("output_files", None)
     ])
-    if params.get("output_directory") is not None:
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "--outdir",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
     cargs.extend([
         "--inref",
-        execution.input_file(params.get("input_reference"))
+        execution.input_file(params.get("input_reference", None))
     ])
     cargs.extend([
         "--outref",
-        execution.input_file(params.get("output_reference"))
+        execution.input_file(params.get("output_reference", None))
     ])
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("affine_registration"))
+        execution.input_file(params.get("affine_registration", None))
     ])
     cargs.extend([
         "--regnl",
-        execution.input_file(params.get("nonlinear_registration"))
+        execution.input_file(params.get("nonlinear_registration", None))
     ])
-    if params.get("inverse_nonlinear"):
+    if params.get("inverse_nonlinear", False):
         cargs.append("--invnl")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("check_options"):
+    if params.get("check_options", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -213,9 +198,11 @@ def dmri_vox2vox_outputs(
 
 def dmri_vox2vox_execute(
     params: DmriVox2voxParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriVox2voxOutputs:
     """
+    dmri_vox2vox
+    
     Tool for voxel-to-voxel transformations in diffusion MRI data processing.
     
     Author: FreeSurfer Developers
@@ -224,10 +211,12 @@ def dmri_vox2vox_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriVox2voxOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_VOX2VOX_METADATA)
     params = execution.params(params)
     cargs = dmri_vox2vox_cargs(params, execution)
     ret = dmri_vox2vox_outputs(params, execution)
@@ -252,6 +241,8 @@ def dmri_vox2vox(
     runner: Runner | None = None,
 ) -> DmriVox2voxOutputs:
     """
+    dmri_vox2vox
+    
     Tool for voxel-to-voxel transformations in diffusion MRI data processing.
     
     Author: FreeSurfer Developers
@@ -280,8 +271,6 @@ def dmri_vox2vox(
     Returns:
         NamedTuple of outputs (described in `DmriVox2voxOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_VOX2VOX_METADATA)
     params = dmri_vox2vox_params(
         input_files=input_files,
         input_directory=input_directory,
@@ -297,13 +286,13 @@ def dmri_vox2vox(
         help_=help_,
         version=version,
     )
-    return dmri_vox2vox_execute(params, execution)
+    return dmri_vox2vox_execute(params, runner)
 
 
 __all__ = [
     "DMRI_VOX2VOX_METADATA",
     "DmriVox2voxOutputs",
-    "DmriVox2voxParameters",
     "dmri_vox2vox",
+    "dmri_vox2vox_execute",
     "dmri_vox2vox_params",
 ]

niwrap_freesurfer/freesurfer/dt_recon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DT_RECON_METADATA = Metadata(
-    id="e2e2bdcf7e463218626ecd3b7295c2fc21a1670a.boutiques",
+    id="0e86e8ca45a5e3376c51be3517688e8262426cd3.boutiques",
     name="dt_recon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ DT_RECON_METADATA = Metadata(
 
 
 DtReconParameters = typing.TypedDict('DtReconParameters', {
-    "__STYXTYPE__": typing.Literal["dt_recon"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dt_recon"]],
+    "input_volume": InputPathType,
+    "bvals_bvecs": typing.NotRequired[str | None],
+    "subject_id": str,
+    "output_dir": str,
+    "info_dump": typing.NotRequired[InputPathType | None],
+    "ec_reference": typing.NotRequired[float | None],
+    "no_ec_flag": bool,
+    "no_reg_flag": bool,
+    "register_file": typing.NotRequired[InputPathType | None],
+    "no_tal_flag": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+    "save_ec_residuals_flag": bool,
+    "pca_analysis_flag": bool,
+    "mask_prune_threshold": typing.NotRequired[float | None],
+    "init_spm_flag": bool,
+    "init_fsl_flag": bool,
+    "debug_flag": bool,
+    "version_flag": bool,
+})
+DtReconParametersTagged = typing.TypedDict('DtReconParametersTagged', {
+    "@type": typing.Literal["freesurfer/dt_recon"],
     "input_volume": InputPathType,
     "bvals_bvecs": typing.NotRequired[str | None],
     "subject_id": str,
@@ -34,43 +55,11 @@ DtReconParameters = typing.TypedDict('DtReconParameters', {
     "debug_flag": bool,
     "version_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dt_recon": dt_recon_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 {
-        "dt_recon": dt_recon_outputs,
-    }.get(t)
 
 
 class DtReconOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dt_recon(...)`.
+    Output object returned when calling `DtReconParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -109,7 +98,7 @@ def dt_recon_params(
     init_fsl_flag: bool = False,
     debug_flag: bool = False,
     version_flag: bool = False,
-) -> DtReconParameters:
+) -> DtReconParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +128,7 @@ def dt_recon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dt_recon",
+        "@type": "freesurfer/dt_recon",
         "input_volume": input_volume,
         "subject_id": subject_id,
         "output_dir": output_dir,
@@ -185,63 +174,63 @@ def dt_recon_cargs(
     cargs.append("dt_recon")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
-    if params.get("bvals_bvecs") is not None:
+    if params.get("bvals_bvecs", None) is not None:
         cargs.extend([
             "--b",
-            params.get("bvals_bvecs")
+            params.get("bvals_bvecs", None)
         ])
     cargs.extend([
         "--s",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     cargs.extend([
         "--o",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
-    if params.get("info_dump") is not None:
+    if params.get("info_dump", None) is not None:
         cargs.extend([
             "--info-dump",
-            execution.input_file(params.get("info_dump"))
+            execution.input_file(params.get("info_dump", None))
         ])
-    if params.get("ec_reference") is not None:
+    if params.get("ec_reference", None) is not None:
         cargs.extend([
             "--ecref",
-            str(params.get("ec_reference"))
+            str(params.get("ec_reference", None))
         ])
-    if params.get("no_ec_flag"):
+    if params.get("no_ec_flag", False):
         cargs.append("--no-ec")
-    if params.get("no_reg_flag"):
+    if params.get("no_reg_flag", False):
         cargs.append("--no-reg")
-    if params.get("register_file") is not None:
+    if params.get("register_file", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("register_file"))
+            execution.input_file(params.get("register_file", None))
         ])
-    if params.get("no_tal_flag"):
+    if params.get("no_tal_flag", False):
         cargs.append("--no-tal")
-    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("save_ec_residuals_flag"):
+    if params.get("save_ec_residuals_flag", False):
         cargs.append("--eres-save")
-    if params.get("pca_analysis_flag"):
+    if params.get("pca_analysis_flag", False):
         cargs.append("--pca")
-    if params.get("mask_prune_threshold") is not None:
+    if params.get("mask_prune_threshold", None) is not None:
         cargs.extend([
             "--prune_thr",
-            str(params.get("mask_prune_threshold"))
+            str(params.get("mask_prune_threshold", None))
         ])
-    if params.get("init_spm_flag"):
+    if params.get("init_spm_flag", False):
         cargs.append("--init-spm")
-    if params.get("init_fsl_flag"):
+    if params.get("init_fsl_flag", False):
         cargs.append("--init-fsl")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -261,22 +250,24 @@ def dt_recon_outputs(
     """
     ret = DtReconOutputs(
         root=execution.output_file("."),
-        dwi_nifti=execution.output_file(params.get("output_dir") + "/dwi.nii.gz"),
-        dwi_eddy_corrected=execution.output_file(params.get("output_dir") + "/dwi-ec.nii.gz"),
-        tensor_map=execution.output_file(params.get("output_dir") + "/tensor.nii.gz"),
-        fa_map=execution.output_file(params.get("output_dir") + "/fa.nii.gz"),
-        fa_tal_map=execution.output_file(params.get("output_dir") + "/fa-tal.nii.gz"),
-        register_file_output=execution.output_file(params.get("output_dir") + "/register.lta"),
-        mask_file=execution.output_file(params.get("output_dir") + "/mask.nii.gz"),
+        dwi_nifti=execution.output_file(params.get("output_dir", None) + "/dwi.nii.gz"),
+        dwi_eddy_corrected=execution.output_file(params.get("output_dir", None) + "/dwi-ec.nii.gz"),
+        tensor_map=execution.output_file(params.get("output_dir", None) + "/tensor.nii.gz"),
+        fa_map=execution.output_file(params.get("output_dir", None) + "/fa.nii.gz"),
+        fa_tal_map=execution.output_file(params.get("output_dir", None) + "/fa-tal.nii.gz"),
+        register_file_output=execution.output_file(params.get("output_dir", None) + "/register.lta"),
+        mask_file=execution.output_file(params.get("output_dir", None) + "/mask.nii.gz"),
     )
     return ret
 
 
 def dt_recon_execute(
     params: DtReconParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DtReconOutputs:
     """
+    dt_recon
+    
     Performs DTI reconstruction from the raw DWI input files.
     
     Author: FreeSurfer Developers
@@ -285,10 +276,12 @@ def dt_recon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DtReconOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DT_RECON_METADATA)
     params = execution.params(params)
     cargs = dt_recon_cargs(params, execution)
     ret = dt_recon_outputs(params, execution)
@@ -318,6 +311,8 @@ def dt_recon(
     runner: Runner | None = None,
 ) -> DtReconOutputs:
     """
+    dt_recon
+    
     Performs DTI reconstruction from the raw DWI input files.
     
     Author: FreeSurfer Developers
@@ -350,8 +345,6 @@ def dt_recon(
     Returns:
         NamedTuple of outputs (described in `DtReconOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DT_RECON_METADATA)
     params = dt_recon_params(
         input_volume=input_volume,
         bvals_bvecs=bvals_bvecs,
@@ -372,13 +365,13 @@ def dt_recon(
         debug_flag=debug_flag,
         version_flag=version_flag,
     )
-    return dt_recon_execute(params, execution)
+    return dt_recon_execute(params, runner)
 
 
 __all__ = [
     "DT_RECON_METADATA",
     "DtReconOutputs",
-    "DtReconParameters",
     "dt_recon",
+    "dt_recon_execute",
     "dt_recon_params",
 ]