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

niwrap_freesurfer/freesurfer/mri_concatenate_lta.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CONCATENATE_LTA_METADATA = Metadata(
-    id="954e185b276c52b9e741616fe3781dbd26c9152a.boutiques",
+    id="38907d5d0cdc2fb65560e3c353ab51490258ebd2.boutiques",
     name="mri_concatenate_lta",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_CONCATENATE_LTA_METADATA = Metadata(
 
 
 MriConcatenateLtaParameters = typing.TypedDict('MriConcatenateLtaParameters', {
-    "__STYXTYPE__": typing.Literal["mri_concatenate_lta"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_concatenate_lta"]],
+    "lta_1": InputPathType,
+    "lta_2": InputPathType,
+    "lta_final": str,
+    "tal_src": typing.NotRequired[InputPathType | None],
+    "tal_template": typing.NotRequired[InputPathType | None],
+    "invert1": bool,
+    "invert2": bool,
+    "invertout": bool,
+    "out_type": typing.NotRequired[float | None],
+    "subject": typing.NotRequired[str | None],
+    "rmsdiff_radius": typing.NotRequired[float | None],
+    "rmsdiff_outputfile": typing.NotRequired[str | None],
+})
+MriConcatenateLtaParametersTagged = typing.TypedDict('MriConcatenateLtaParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_concatenate_lta"],
     "lta_1": InputPathType,
     "lta_2": InputPathType,
     "lta_final": str,
@@ -28,42 +43,11 @@ MriConcatenateLtaParameters = typing.TypedDict('MriConcatenateLtaParameters', {
     "rmsdiff_radius": typing.NotRequired[float | None],
     "rmsdiff_outputfile": 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_concatenate_lta": mri_concatenate_lta_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 MriConcatenateLtaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_concatenate_lta(...)`.
+    Output object returned when calling `MriConcatenateLtaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +66,7 @@ def mri_concatenate_lta_params(
     subject: str | None = None,
     rmsdiff_radius: float | None = None,
     rmsdiff_outputfile: str | None = None,
-) -> MriConcatenateLtaParameters:
+) -> MriConcatenateLtaParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +88,7 @@ def mri_concatenate_lta_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_concatenate_lta",
+        "@type": "freesurfer/mri_concatenate_lta",
         "lta_1": lta_1,
         "lta_2": lta_2,
         "lta_final": lta_final,
@@ -142,39 +126,39 @@ def mri_concatenate_lta_cargs(
     """
     cargs = []
     cargs.append("mri_concatenate_lta")
-    cargs.append(execution.input_file(params.get("lta_1")))
-    cargs.append(execution.input_file(params.get("lta_2")))
-    cargs.append(params.get("lta_final"))
-    if params.get("tal_src") is not None:
+    cargs.append(execution.input_file(params.get("lta_1", None)))
+    cargs.append(execution.input_file(params.get("lta_2", None)))
+    cargs.append(params.get("lta_final", None))
+    if params.get("tal_src", None) is not None:
         cargs.extend([
             "-tal",
-            execution.input_file(params.get("tal_src"))
+            execution.input_file(params.get("tal_src", None))
         ])
-    if params.get("tal_template") is not None:
-        cargs.append(execution.input_file(params.get("tal_template")))
-    if params.get("invert1"):
+    if params.get("tal_template", None) is not None:
+        cargs.append(execution.input_file(params.get("tal_template", None)))
+    if params.get("invert1", False):
         cargs.append("-invert1")
-    if params.get("invert2"):
+    if params.get("invert2", False):
         cargs.append("-invert2")
-    if params.get("invertout"):
+    if params.get("invertout", False):
         cargs.append("-invertout")
-    if params.get("out_type") is not None:
+    if params.get("out_type", None) is not None:
         cargs.extend([
             "-out_type",
-            str(params.get("out_type"))
+            str(params.get("out_type", None))
         ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "-subject",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("rmsdiff_radius") is not None:
+    if params.get("rmsdiff_radius", None) is not None:
         cargs.extend([
             "-rmsdiff",
-            str(params.get("rmsdiff_radius"))
+            str(params.get("rmsdiff_radius", None))
         ])
-    if params.get("rmsdiff_outputfile") is not None:
-        cargs.append(params.get("rmsdiff_outputfile"))
+    if params.get("rmsdiff_outputfile", None) is not None:
+        cargs.append(params.get("rmsdiff_outputfile", None))
     return cargs
 
 
@@ -199,9 +183,11 @@ def mri_concatenate_lta_outputs(
 
 def mri_concatenate_lta_execute(
     params: MriConcatenateLtaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriConcatenateLtaOutputs:
     """
+    mri_concatenate_lta
+    
     Concatenates two consecutive LTA transformations into one overall
     transformation, Out = LTA2*LTA1.
     
@@ -211,10 +197,12 @@ def mri_concatenate_lta_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriConcatenateLtaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CONCATENATE_LTA_METADATA)
     params = execution.params(params)
     cargs = mri_concatenate_lta_cargs(params, execution)
     ret = mri_concatenate_lta_outputs(params, execution)
@@ -238,6 +226,8 @@ def mri_concatenate_lta(
     runner: Runner | None = None,
 ) -> MriConcatenateLtaOutputs:
     """
+    mri_concatenate_lta
+    
     Concatenates two consecutive LTA transformations into one overall
     transformation, Out = LTA2*LTA1.
     
@@ -263,8 +253,6 @@ def mri_concatenate_lta(
     Returns:
         NamedTuple of outputs (described in `MriConcatenateLtaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CONCATENATE_LTA_METADATA)
     params = mri_concatenate_lta_params(
         lta_1=lta_1,
         lta_2=lta_2,
@@ -279,13 +267,13 @@ def mri_concatenate_lta(
         rmsdiff_radius=rmsdiff_radius,
         rmsdiff_outputfile=rmsdiff_outputfile,
     )
-    return mri_concatenate_lta_execute(params, execution)
+    return mri_concatenate_lta_execute(params, runner)
 
 
 __all__ = [
     "MRI_CONCATENATE_LTA_METADATA",
     "MriConcatenateLtaOutputs",
-    "MriConcatenateLtaParameters",
     "mri_concatenate_lta",
+    "mri_concatenate_lta_execute",
     "mri_concatenate_lta_params",
 ]

niwrap_freesurfer/freesurfer/mri_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CONVERT_METADATA = Metadata(
-    id="1c59f2dc0abd2a457f5c93c0eac8edb5b8b4b77d.boutiques",
+    id="9406949087be72683c99241b992dfb378a7af3d7.boutiques",
     name="mri_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ MRI_CONVERT_METADATA = Metadata(
 
 
 MriConvertParameters = typing.TypedDict('MriConvertParameters', {
-    "__STYXTYPE__": typing.Literal["mri_convert"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_convert"]],
+    "inp_volume": InputPathType,
+    "out_volume": str,
+    "read_only": bool,
+    "no_write": bool,
+    "in_info": bool,
+    "out_info": bool,
+    "in_stats": bool,
+    "out_stats": bool,
+    "upsample": typing.NotRequired[float | None],
+    "force_ras_good": bool,
+    "apply_transform": typing.NotRequired[InputPathType | None],
+    "apply_inverse_transform": typing.NotRequired[InputPathType | None],
+    "in_type": typing.NotRequired[str | None],
+    "out_type": typing.NotRequired[str | None],
+    "in_orientation": typing.NotRequired[str | None],
+    "out_orientation": typing.NotRequired[str | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "bfile_little_endian": bool,
+    "sphinx": bool,
+})
+MriConvertParametersTagged = typing.TypedDict('MriConvertParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_convert"],
     "inp_volume": InputPathType,
     "out_volume": str,
     "read_only": bool,
@@ -35,43 +57,11 @@ MriConvertParameters = typing.TypedDict('MriConvertParameters', {
     "bfile_little_endian": bool,
     "sphinx": 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_convert": mri_convert_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_convert": mri_convert_outputs,
-    }.get(t)
 
 
 class MriConvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_convert(...)`.
+    Output object returned when calling `MriConvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +89,7 @@ def mri_convert_params(
     scale_factor: float | None = None,
     bfile_little_endian: bool = False,
     sphinx: bool = False,
-) -> MriConvertParameters:
+) -> MriConvertParametersTagged:
     """
     Build parameters.
     
@@ -128,7 +118,7 @@ def mri_convert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_convert",
+        "@type": "freesurfer/mri_convert",
         "inp_volume": inp_volume,
         "out_volume": out_volume,
         "read_only": read_only,
@@ -175,65 +165,65 @@ def mri_convert_cargs(
     """
     cargs = []
     cargs.append("mri_convert")
-    cargs.append(execution.input_file(params.get("inp_volume")))
-    cargs.append(params.get("out_volume"))
-    if params.get("read_only"):
+    cargs.append(execution.input_file(params.get("inp_volume", None)))
+    cargs.append(params.get("out_volume", None))
+    if params.get("read_only", False):
         cargs.append("-ro")
-    if params.get("no_write"):
+    if params.get("no_write", False):
         cargs.append("-nw")
-    if params.get("in_info"):
+    if params.get("in_info", False):
         cargs.append("-ii")
-    if params.get("out_info"):
+    if params.get("out_info", False):
         cargs.append("-oi")
-    if params.get("in_stats"):
+    if params.get("in_stats", False):
         cargs.append("-is")
-    if params.get("out_stats"):
+    if params.get("out_stats", False):
         cargs.append("-os")
-    if params.get("upsample") is not None:
+    if params.get("upsample", None) is not None:
         cargs.extend([
             "--upsample",
-            str(params.get("upsample"))
+            str(params.get("upsample", None))
         ])
-    if params.get("force_ras_good"):
+    if params.get("force_ras_good", False):
         cargs.append("--force_ras_good")
-    if params.get("apply_transform") is not None:
+    if params.get("apply_transform", None) is not None:
         cargs.extend([
             "--apply_transform",
-            execution.input_file(params.get("apply_transform"))
+            execution.input_file(params.get("apply_transform", None))
         ])
-    if params.get("apply_inverse_transform") is not None:
+    if params.get("apply_inverse_transform", None) is not None:
         cargs.extend([
             "--apply_inverse_transform",
-            execution.input_file(params.get("apply_inverse_transform"))
+            execution.input_file(params.get("apply_inverse_transform", None))
         ])
-    if params.get("in_type") is not None:
+    if params.get("in_type", None) is not None:
         cargs.extend([
             "--in_type",
-            params.get("in_type")
+            params.get("in_type", None)
         ])
-    if params.get("out_type") is not None:
+    if params.get("out_type", None) is not None:
         cargs.extend([
             "--out_type",
-            params.get("out_type")
+            params.get("out_type", None)
         ])
-    if params.get("in_orientation") is not None:
+    if params.get("in_orientation", None) is not None:
         cargs.extend([
             "--in_orientation",
-            params.get("in_orientation")
+            params.get("in_orientation", None)
         ])
-    if params.get("out_orientation") is not None:
+    if params.get("out_orientation", None) is not None:
         cargs.extend([
             "--out_orientation",
-            params.get("out_orientation")
+            params.get("out_orientation", None)
         ])
-    if params.get("scale_factor") is not None:
+    if params.get("scale_factor", None) is not None:
         cargs.extend([
             "--scale",
-            str(params.get("scale_factor"))
+            str(params.get("scale_factor", None))
         ])
-    if params.get("bfile_little_endian"):
+    if params.get("bfile_little_endian", False):
         cargs.append("--bfile-little-endian")
-    if params.get("sphinx"):
+    if params.get("sphinx", False):
         cargs.append("--sphinx")
     return cargs
 
@@ -253,16 +243,18 @@ def mri_convert_outputs(
     """
     ret = MriConvertOutputs(
         root=execution.output_file("."),
-        converted_volume=execution.output_file(params.get("out_volume")),
+        converted_volume=execution.output_file(params.get("out_volume", None)),
     )
     return ret
 
 
 def mri_convert_execute(
     params: MriConvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriConvertOutputs:
     """
+    mri_convert
+    
     A general purpose utility for converting between different file formats
     supported by FreeSurfer.
     
@@ -272,10 +264,12 @@ def mri_convert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriConvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CONVERT_METADATA)
     params = execution.params(params)
     cargs = mri_convert_cargs(params, execution)
     ret = mri_convert_outputs(params, execution)
@@ -306,6 +300,8 @@ def mri_convert(
     runner: Runner | None = None,
 ) -> MriConvertOutputs:
     """
+    mri_convert
+    
     A general purpose utility for converting between different file formats
     supported by FreeSurfer.
     
@@ -338,8 +334,6 @@ def mri_convert(
     Returns:
         NamedTuple of outputs (described in `MriConvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CONVERT_METADATA)
     params = mri_convert_params(
         inp_volume=inp_volume,
         out_volume=out_volume,
@@ -361,13 +355,13 @@ def mri_convert(
         bfile_little_endian=bfile_little_endian,
         sphinx=sphinx,
     )
-    return mri_convert_execute(params, execution)
+    return mri_convert_execute(params, runner)
 
 
 __all__ = [
     "MRI_CONVERT_METADATA",
     "MriConvertOutputs",
-    "MriConvertParameters",
     "mri_convert",
+    "mri_convert_execute",
     "mri_convert_params",
 ]

niwrap_freesurfer/freesurfer/mri_copy_params.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_COPY_PARAMS_METADATA = Metadata(
-    id="6b84fe06a3127af4a89a68072867303d2f8a2771.boutiques",
+    id="6dfca8512036b7264f42b971565bc4fd7c5253b5.boutiques",
     name="mri_copy_params",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_COPY_PARAMS_METADATA = Metadata(
 
 
 MriCopyParamsParameters = typing.TypedDict('MriCopyParamsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_copy_params"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_copy_params"]],
+    "in_vol": InputPathType,
+    "template_vol": InputPathType,
+    "out_vol": str,
+    "size_flag": bool,
+})
+MriCopyParamsParametersTagged = typing.TypedDict('MriCopyParamsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_copy_params"],
     "in_vol": InputPathType,
     "template_vol": InputPathType,
     "out_vol": str,
     "size_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 {
-        "mri_copy_params": mri_copy_params_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_copy_params": mri_copy_params_outputs,
-    }.get(t)
 
 
 class MriCopyParamsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_copy_params(...)`.
+    Output object returned when calling `MriCopyParamsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_copy_params_params(
     template_vol: InputPathType,
     out_vol: str,
     size_flag: bool = False,
-) -> MriCopyParamsParameters:
+) -> MriCopyParamsParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mri_copy_params_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_copy_params",
+        "@type": "freesurfer/mri_copy_params",
         "in_vol": in_vol,
         "template_vol": template_vol,
         "out_vol": out_vol,
@@ -106,10 +81,10 @@ def mri_copy_params_cargs(
     """
     cargs = []
     cargs.append("mri_copy_params")
-    cargs.append(execution.input_file(params.get("in_vol")))
-    cargs.append(execution.input_file(params.get("template_vol")))
-    cargs.append(params.get("out_vol"))
-    if params.get("size_flag"):
+    cargs.append(execution.input_file(params.get("in_vol", None)))
+    cargs.append(execution.input_file(params.get("template_vol", None)))
+    cargs.append(params.get("out_vol", None))
+    if params.get("size_flag", False):
         cargs.append("--size")
     return cargs
 
@@ -129,16 +104,18 @@ def mri_copy_params_outputs(
     """
     ret = MriCopyParamsOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("out_vol")),
+        output_volume=execution.output_file(params.get("out_vol", None)),
     )
     return ret
 
 
 def mri_copy_params_execute(
     params: MriCopyParamsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCopyParamsOutputs:
     """
+    mri_copy_params
+    
     A tool to replace the volume parameters of an input volume with those of a
     template volume.
     
@@ -148,10 +125,12 @@ def mri_copy_params_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCopyParamsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_COPY_PARAMS_METADATA)
     params = execution.params(params)
     cargs = mri_copy_params_cargs(params, execution)
     ret = mri_copy_params_outputs(params, execution)
@@ -167,6 +146,8 @@ def mri_copy_params(
     runner: Runner | None = None,
 ) -> MriCopyParamsOutputs:
     """
+    mri_copy_params
+    
     A tool to replace the volume parameters of an input volume with those of a
     template volume.
     
@@ -183,21 +164,19 @@ def mri_copy_params(
     Returns:
         NamedTuple of outputs (described in `MriCopyParamsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_COPY_PARAMS_METADATA)
     params = mri_copy_params_params(
         in_vol=in_vol,
         template_vol=template_vol,
         out_vol=out_vol,
         size_flag=size_flag,
     )
-    return mri_copy_params_execute(params, execution)
+    return mri_copy_params_execute(params, runner)
 
 
 __all__ = [
     "MRI_COPY_PARAMS_METADATA",
     "MriCopyParamsOutputs",
-    "MriCopyParamsParameters",
     "mri_copy_params",
+    "mri_copy_params_execute",
     "mri_copy_params_params",
 ]