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

niwrap_freesurfer/freesurfer/mri_entowm_seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_ENTOWM_SEG_METADATA = Metadata(
-    id="ddf086c5e432c411bc2194c0bac1a7f6b35bb81f.boutiques",
+    id="97b977eaf3884ebf2d162e0264ea73d091e86320.boutiques",
     name="mri_entowm_seg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,35 @@ MRI_ENTOWM_SEG_METADATA = Metadata(
 
 
 MriEntowmSegParameters = typing.TypedDict('MriEntowmSegParameters', {
-    "__STYXTYPE__": typing.Literal["mri_entowm_seg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_entowm_seg"]],
+    "input_image": typing.NotRequired[InputPathType | None],
+    "output_segmentation": typing.NotRequired[str | None],
+    "recon_subjects": typing.NotRequired[list[str] | None],
+    "subjects_directory": typing.NotRequired[str | None],
+    "conform": bool,
+    "etiv": bool,
+    "tal": typing.NotRequired[str | None],
+    "write_posteriors": bool,
+    "write_volumes": bool,
+    "write_qa_stats": bool,
+    "exclude_labels": typing.NotRequired[list[str] | None],
+    "keep_ac": bool,
+    "vox_count_volumes": bool,
+    "model_weights": typing.NotRequired[str | None],
+    "color_table": typing.NotRequired[str | None],
+    "population_stats": typing.NotRequired[str | None],
+    "debug": bool,
+    "vmp": bool,
+    "threads": typing.NotRequired[float | None],
+    "seven_tesla": bool,
+    "percentile": typing.NotRequired[float | None],
+    "cuda_device": typing.NotRequired[str | None],
+    "output_base": typing.NotRequired[str | None],
+    "no_cite_sclimbic": bool,
+    "nchannels": typing.NotRequired[float | None],
+})
+MriEntowmSegParametersTagged = typing.TypedDict('MriEntowmSegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_entowm_seg"],
     "input_image": typing.NotRequired[InputPathType | None],
     "output_segmentation": typing.NotRequired[str | None],
     "recon_subjects": typing.NotRequired[list[str] | None],
@@ -41,43 +69,11 @@ MriEntowmSegParameters = typing.TypedDict('MriEntowmSegParameters', {
     "no_cite_sclimbic": bool,
     "nchannels": 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 {
-        "mri_entowm_seg": mri_entowm_seg_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_entowm_seg": mri_entowm_seg_outputs,
-    }.get(t)
 
 
 class MriEntowmSegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_entowm_seg(...)`.
+    Output object returned when calling `MriEntowmSegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -117,7 +113,7 @@ def mri_entowm_seg_params(
     output_base: str | None = None,
     no_cite_sclimbic: bool = False,
     nchannels: float | None = None,
-) -> MriEntowmSegParameters:
+) -> MriEntowmSegParametersTagged:
     """
     Build parameters.
     
@@ -160,7 +156,7 @@ def mri_entowm_seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_entowm_seg",
+        "@type": "freesurfer/mri_entowm_seg",
         "conform": conform,
         "etiv": etiv,
         "write_posteriors": write_posteriors,
@@ -219,97 +215,97 @@ def mri_entowm_seg_cargs(
     """
     cargs = []
     cargs.append("mri_entowm_seg")
-    if params.get("input_image") is not None:
+    if params.get("input_image", None) is not None:
         cargs.extend([
             "-i",
-            execution.input_file(params.get("input_image"))
+            execution.input_file(params.get("input_image", None))
         ])
-    if params.get("output_segmentation") is not None:
+    if params.get("output_segmentation", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_segmentation")
+            params.get("output_segmentation", None)
         ])
-    if params.get("recon_subjects") is not None:
+    if params.get("recon_subjects", None) is not None:
         cargs.extend([
             "-s",
-            *params.get("recon_subjects")
+            *params.get("recon_subjects", None)
         ])
-    if params.get("subjects_directory") is not None:
+    if params.get("subjects_directory", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_directory")
+            params.get("subjects_directory", None)
         ])
-    if params.get("conform"):
+    if params.get("conform", False):
         cargs.append("--conform")
-    if params.get("etiv"):
+    if params.get("etiv", False):
         cargs.append("--etiv")
-    if params.get("tal") is not None:
+    if params.get("tal", None) is not None:
         cargs.extend([
             "--tal",
-            params.get("tal")
+            params.get("tal", None)
         ])
-    if params.get("write_posteriors"):
+    if params.get("write_posteriors", False):
         cargs.append("--write_posteriors")
-    if params.get("write_volumes"):
+    if params.get("write_volumes", False):
         cargs.append("--write_volumes")
-    if params.get("write_qa_stats"):
+    if params.get("write_qa_stats", False):
         cargs.append("--write_qa_stats")
-    if params.get("exclude_labels") is not None:
+    if params.get("exclude_labels", None) is not None:
         cargs.extend([
             "--exclude",
-            *params.get("exclude_labels")
+            *params.get("exclude_labels", None)
         ])
-    if params.get("keep_ac"):
+    if params.get("keep_ac", False):
         cargs.append("--keep_ac")
-    if params.get("vox_count_volumes"):
+    if params.get("vox_count_volumes", False):
         cargs.append("--vox-count-volumes")
-    if params.get("model_weights") is not None:
+    if params.get("model_weights", None) is not None:
         cargs.extend([
             "--model",
-            params.get("model_weights")
+            params.get("model_weights", None)
         ])
-    if params.get("color_table") is not None:
+    if params.get("color_table", None) is not None:
         cargs.extend([
             "--ctab",
-            params.get("color_table")
+            params.get("color_table", None)
         ])
-    if params.get("population_stats") is not None:
+    if params.get("population_stats", None) is not None:
         cargs.extend([
             "--population-stats",
-            params.get("population_stats")
+            params.get("population_stats", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("vmp"):
+    if params.get("vmp", False):
         cargs.append("--vmp")
-    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("seven_tesla"):
+    if params.get("seven_tesla", False):
         cargs.append("--7T")
-    if params.get("percentile") is not None:
+    if params.get("percentile", None) is not None:
         cargs.extend([
             "--percentile",
-            str(params.get("percentile"))
+            str(params.get("percentile", None))
         ])
-    if params.get("cuda_device") is not None:
+    if params.get("cuda_device", None) is not None:
         cargs.extend([
             "--cuda-device",
-            params.get("cuda_device")
+            params.get("cuda_device", None)
         ])
-    if params.get("output_base") is not None:
+    if params.get("output_base", None) is not None:
         cargs.extend([
             "--output-base",
-            params.get("output_base")
+            params.get("output_base", None)
         ])
-    if params.get("no_cite_sclimbic"):
+    if params.get("no_cite_sclimbic", False):
         cargs.append("--no-cite-sclimbic")
-    if params.get("nchannels") is not None:
+    if params.get("nchannels", None) is not None:
         cargs.extend([
             "--nchannels",
-            str(params.get("nchannels"))
+            str(params.get("nchannels", None))
         ])
     return cargs
 
@@ -329,21 +325,23 @@ def mri_entowm_seg_outputs(
     """
     ret = MriEntowmSegOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_segmentation")) if (params.get("output_segmentation") is not None) else None,
-        label_posteriors=execution.output_file(params.get("output_base") + "_posterior.mgz") if (params.get("output_base") is not None) else None,
-        volume_stats=execution.output_file(params.get("output_base") + "_volumes.txt") if (params.get("output_base") is not None) else None,
-        qa_stats=execution.output_file(params.get("output_base") + "_qa_stats.txt") if (params.get("output_base") is not None) else None,
+        output_file=execution.output_file(params.get("output_segmentation", None)) if (params.get("output_segmentation") is not None) else None,
+        label_posteriors=execution.output_file(params.get("output_base", None) + "_posterior.mgz") if (params.get("output_base") is not None) else None,
+        volume_stats=execution.output_file(params.get("output_base", None) + "_volumes.txt") if (params.get("output_base") is not None) else None,
+        qa_stats=execution.output_file(params.get("output_base", None) + "_qa_stats.txt") if (params.get("output_base") is not None) else None,
     )
     return ret
 
 
 def mri_entowm_seg_execute(
     params: MriEntowmSegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriEntowmSegOutputs:
     """
-    Segment white matter near gyrus ambiens entorhinal cortex using a deep learning
-    model.
+    mri_entowm_seg
+    
+    Segment white matter near gyrus ambiens entorhinal cortex using a deep
+    learning model.
     
     Author: FreeSurfer Developers
     
@@ -351,10 +349,12 @@ def mri_entowm_seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriEntowmSegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_ENTOWM_SEG_METADATA)
     params = execution.params(params)
     cargs = mri_entowm_seg_cargs(params, execution)
     ret = mri_entowm_seg_outputs(params, execution)
@@ -391,8 +391,10 @@ def mri_entowm_seg(
     runner: Runner | None = None,
 ) -> MriEntowmSegOutputs:
     """
-    Segment white matter near gyrus ambiens entorhinal cortex using a deep learning
-    model.
+    mri_entowm_seg
+    
+    Segment white matter near gyrus ambiens entorhinal cortex using a deep
+    learning model.
     
     Author: FreeSurfer Developers
     
@@ -437,8 +439,6 @@ def mri_entowm_seg(
     Returns:
         NamedTuple of outputs (described in `MriEntowmSegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_ENTOWM_SEG_METADATA)
     params = mri_entowm_seg_params(
         input_image=input_image,
         output_segmentation=output_segmentation,
@@ -466,13 +466,13 @@ def mri_entowm_seg(
         no_cite_sclimbic=no_cite_sclimbic,
         nchannels=nchannels,
     )
-    return mri_entowm_seg_execute(params, execution)
+    return mri_entowm_seg_execute(params, runner)
 
 
 __all__ = [
     "MRI_ENTOWM_SEG_METADATA",
     "MriEntowmSegOutputs",
-    "MriEntowmSegParameters",
     "mri_entowm_seg",
+    "mri_entowm_seg_execute",
     "mri_entowm_seg_params",
 ]

niwrap_freesurfer/freesurfer/mri_evaluate_morph.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EVALUATE_MORPH_METADATA = Metadata(
-    id="8b5379065ffffdf5c07e98cd80b8cf2450d1c4d8.boutiques",
+    id="91435da5bb49d12fbadeee3ef5601bd8b0c830c3.boutiques",
     name="mri_evaluate_morph",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_EVALUATE_MORPH_METADATA = Metadata(
 
 
 MriEvaluateMorphParameters = typing.TypedDict('MriEvaluateMorphParameters', {
-    "__STYXTYPE__": typing.Literal["mri_evaluate_morph"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_evaluate_morph"]],
+    "xform_name": InputPathType,
+    "segmentation_files": list[InputPathType],
+    "output_file": str,
+})
+MriEvaluateMorphParametersTagged = typing.TypedDict('MriEvaluateMorphParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_evaluate_morph"],
     "xform_name": InputPathType,
     "segmentation_files": list[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 {
-        "mri_evaluate_morph": mri_evaluate_morph_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_evaluate_morph": mri_evaluate_morph_outputs,
-    }.get(t)
 
 
 class MriEvaluateMorphOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_evaluate_morph(...)`.
+    Output object returned when calling `MriEvaluateMorphParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_evaluate_morph_params(
     xform_name: InputPathType,
     segmentation_files: list[InputPathType],
     output_file: str,
-) -> MriEvaluateMorphParameters:
+) -> MriEvaluateMorphParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_evaluate_morph_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_evaluate_morph",
+        "@type": "freesurfer/mri_evaluate_morph",
         "xform_name": xform_name,
         "segmentation_files": segmentation_files,
         "output_file": output_file,
@@ -102,9 +76,9 @@ def mri_evaluate_morph_cargs(
     """
     cargs = []
     cargs.append("mri_evaluate_morph")
-    cargs.append(execution.input_file(params.get("xform_name")))
-    cargs.extend([execution.input_file(f) for f in params.get("segmentation_files")])
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("xform_name", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("segmentation_files", None)])
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -123,18 +97,20 @@ def mri_evaluate_morph_outputs(
     """
     ret = MriEvaluateMorphOutputs(
         root=execution.output_file("."),
-        output_overlap_file=execution.output_file(params.get("output_file")),
+        output_overlap_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_evaluate_morph_execute(
     params: MriEvaluateMorphParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriEvaluateMorphOutputs:
     """
-    This program computes the overlap of a set of segmentations for a given morph
-    using an xform file.
+    mri_evaluate_morph
+    
+    This program computes the overlap of a set of segmentations for a given
+    morph using an xform file.
     
     Author: FreeSurfer Developers
     
@@ -142,10 +118,12 @@ def mri_evaluate_morph_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriEvaluateMorphOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EVALUATE_MORPH_METADATA)
     params = execution.params(params)
     cargs = mri_evaluate_morph_cargs(params, execution)
     ret = mri_evaluate_morph_outputs(params, execution)
@@ -160,8 +138,10 @@ def mri_evaluate_morph(
     runner: Runner | None = None,
 ) -> MriEvaluateMorphOutputs:
     """
-    This program computes the overlap of a set of segmentations for a given morph
-    using an xform file.
+    mri_evaluate_morph
+    
+    This program computes the overlap of a set of segmentations for a given
+    morph using an xform file.
     
     Author: FreeSurfer Developers
     
@@ -175,20 +155,18 @@ def mri_evaluate_morph(
     Returns:
         NamedTuple of outputs (described in `MriEvaluateMorphOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EVALUATE_MORPH_METADATA)
     params = mri_evaluate_morph_params(
         xform_name=xform_name,
         segmentation_files=segmentation_files,
         output_file=output_file,
     )
-    return mri_evaluate_morph_execute(params, execution)
+    return mri_evaluate_morph_execute(params, runner)
 
 
 __all__ = [
     "MRI_EVALUATE_MORPH_METADATA",
     "MriEvaluateMorphOutputs",
-    "MriEvaluateMorphParameters",
     "mri_evaluate_morph",
+    "mri_evaluate_morph_execute",
     "mri_evaluate_morph_params",
 ]

niwrap_freesurfer/freesurfer/mri_extract.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXTRACT_METADATA = Metadata(
-    id="bb9185c31bdade906f8b697ecaec1eac1188e514.boutiques",
+    id="e000b6af5ec93608d4809e5e4ae8dad354b9be33.boutiques",
     name="mri_extract",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_EXTRACT_METADATA = Metadata(
 
 
 MriExtractParameters = typing.TypedDict('MriExtractParameters', {
-    "__STYXTYPE__": typing.Literal["mri_extract"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_extract"]],
+    "like_template": typing.NotRequired[InputPathType | None],
+    "src_volume": InputPathType,
+    "dst_volume": InputPathType,
+    "coordinates": typing.NotRequired[list[float] | None],
+})
+MriExtractParametersTagged = typing.TypedDict('MriExtractParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_extract"],
     "like_template": typing.NotRequired[InputPathType | None],
     "src_volume": InputPathType,
     "dst_volume": InputPathType,
     "coordinates": typing.NotRequired[list[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 {
-        "mri_extract": mri_extract_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_extract": mri_extract_outputs,
-    }.get(t)
 
 
 class MriExtractOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_extract(...)`.
+    Output object returned when calling `MriExtractParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_extract_params(
     dst_volume: InputPathType,
     like_template: InputPathType | None = None,
     coordinates: list[float] | None = None,
-) -> MriExtractParameters:
+) -> MriExtractParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def mri_extract_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_extract",
+        "@type": "freesurfer/mri_extract",
         "src_volume": src_volume,
         "dst_volume": dst_volume,
     }
@@ -110,15 +85,15 @@ def mri_extract_cargs(
     """
     cargs = []
     cargs.append("mri_extract")
-    if params.get("like_template") is not None:
+    if params.get("like_template", None) is not None:
         cargs.extend([
             "-like",
-            execution.input_file(params.get("like_template"))
+            execution.input_file(params.get("like_template", None))
         ])
-    cargs.append(execution.input_file(params.get("src_volume")))
-    cargs.append(execution.input_file(params.get("dst_volume")))
-    if params.get("coordinates") is not None:
-        cargs.extend(map(str, params.get("coordinates")))
+    cargs.append(execution.input_file(params.get("src_volume", None)))
+    cargs.append(execution.input_file(params.get("dst_volume", None)))
+    if params.get("coordinates", None) is not None:
+        cargs.extend(map(str, params.get("coordinates", None)))
     return cargs
 
 
@@ -137,16 +112,18 @@ def mri_extract_outputs(
     """
     ret = MriExtractOutputs(
         root=execution.output_file("."),
-        output_extracted_volume=execution.output_file(pathlib.Path(params.get("dst_volume")).name),
+        output_extracted_volume=execution.output_file(pathlib.Path(params.get("dst_volume", None)).name),
     )
     return ret
 
 
 def mri_extract_execute(
     params: MriExtractParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExtractOutputs:
     """
+    mri_extract
+    
     MRI data extraction tool for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -155,10 +132,12 @@ def mri_extract_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExtractOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXTRACT_METADATA)
     params = execution.params(params)
     cargs = mri_extract_cargs(params, execution)
     ret = mri_extract_outputs(params, execution)
@@ -174,6 +153,8 @@ def mri_extract(
     runner: Runner | None = None,
 ) -> MriExtractOutputs:
     """
+    mri_extract
+    
     MRI data extraction tool for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -191,21 +172,19 @@ def mri_extract(
     Returns:
         NamedTuple of outputs (described in `MriExtractOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXTRACT_METADATA)
     params = mri_extract_params(
         like_template=like_template,
         src_volume=src_volume,
         dst_volume=dst_volume,
         coordinates=coordinates,
     )
-    return mri_extract_execute(params, execution)
+    return mri_extract_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXTRACT_METADATA",
     "MriExtractOutputs",
-    "MriExtractParameters",
     "mri_extract",
+    "mri_extract_execute",
     "mri_extract_params",
 ]