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

niwrap_mrtrix/mrtrix/sh2peaks.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SH2PEAKS_METADATA = Metadata(
-    id="fa5c5976ef9cd75e8ab67b278ed530d08b43702c.boutiques",
+    id="1cf460ab2a2a452d9f75103cade5ef23706312a1.boutiques",
     name="sh2peaks",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,21 +14,51 @@ SH2PEAKS_METADATA = Metadata(
 
 
 Sh2peaksDirectionParameters = typing.TypedDict('Sh2peaksDirectionParameters', {
-    "__STYXTYPE__": typing.Literal["direction"],
+    "@type": typing.NotRequired[typing.Literal["direction"]],
+    "phi": float,
+    "theta": float,
+})
+Sh2peaksDirectionParametersTagged = typing.TypedDict('Sh2peaksDirectionParametersTagged', {
+    "@type": typing.Literal["direction"],
     "phi": float,
     "theta": float,
 })
 
 
 Sh2peaksConfigParameters = typing.TypedDict('Sh2peaksConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Sh2peaksConfigParametersTagged = typing.TypedDict('Sh2peaksConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Sh2peaksParameters = typing.TypedDict('Sh2peaksParameters', {
-    "__STYXTYPE__": typing.Literal["sh2peaks"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/sh2peaks"]],
+    "num": typing.NotRequired[int | None],
+    "direction": typing.NotRequired[list[Sh2peaksDirectionParameters] | None],
+    "peaks": typing.NotRequired[InputPathType | None],
+    "threshold": typing.NotRequired[float | None],
+    "seeds": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "fast": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2peaksConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "output": str,
+})
+Sh2peaksParametersTagged = typing.TypedDict('Sh2peaksParametersTagged', {
+    "@type": typing.Literal["mrtrix/sh2peaks"],
     "num": typing.NotRequired[int | None],
     "direction": typing.NotRequired[list[Sh2peaksDirectionParameters] | None],
     "peaks": typing.NotRequired[InputPathType | None],
@@ -47,46 +77,12 @@ Sh2peaksParameters = typing.TypedDict('Sh2peaksParameters', {
     "SH": InputPathType,
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "sh2peaks": sh2peaks_cargs,
-        "direction": sh2peaks_direction_cargs,
-        "config": sh2peaks_config_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 {
-        "sh2peaks": sh2peaks_outputs,
-    }.get(t)
 
 
 def sh2peaks_direction_params(
     phi: float,
     theta: float,
-) -> Sh2peaksDirectionParameters:
+) -> Sh2peaksDirectionParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +96,7 @@ def sh2peaks_direction_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "direction",
+        "@type": "direction",
         "phi": phi,
         "theta": theta,
     }
@@ -122,15 +118,15 @@ def sh2peaks_direction_cargs(
     """
     cargs = []
     cargs.append("-direction")
-    cargs.append(str(params.get("phi")))
-    cargs.append(str(params.get("theta")))
+    cargs.append(str(params.get("phi", None)))
+    cargs.append(str(params.get("theta", None)))
     return cargs
 
 
 def sh2peaks_config_params(
     key: str,
     value: str,
-) -> Sh2peaksConfigParameters:
+) -> Sh2peaksConfigParametersTagged:
     """
     Build parameters.
     
@@ -141,7 +137,7 @@ def sh2peaks_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -163,14 +159,14 @@ def sh2peaks_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class Sh2peaksOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sh2peaks(...)`.
+    Output object returned when calling `Sh2peaksParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -197,7 +193,7 @@ def sh2peaks_params(
     config: list[Sh2peaksConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Sh2peaksParameters:
+) -> Sh2peaksParametersTagged:
     """
     Build parameters.
     
@@ -236,7 +232,7 @@ def sh2peaks_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sh2peaks",
+        "@type": "mrtrix/sh2peaks",
         "fast": fast,
         "info": info,
         "quiet": quiet,
@@ -281,56 +277,56 @@ def sh2peaks_cargs(
     """
     cargs = []
     cargs.append("sh2peaks")
-    if params.get("num") is not None:
+    if params.get("num", None) is not None:
         cargs.extend([
             "-num",
-            str(params.get("num"))
+            str(params.get("num", None))
         ])
-    if params.get("direction") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("direction")] for a in c])
-    if params.get("peaks") is not None:
+    if params.get("direction", None) is not None:
+        cargs.extend([a for c in [sh2peaks_direction_cargs(s, execution) for s in params.get("direction", None)] for a in c])
+    if params.get("peaks", None) is not None:
         cargs.extend([
             "-peaks",
-            execution.input_file(params.get("peaks"))
+            execution.input_file(params.get("peaks", None))
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("seeds") is not None:
+    if params.get("seeds", None) is not None:
         cargs.extend([
             "-seeds",
-            execution.input_file(params.get("seeds"))
+            execution.input_file(params.get("seeds", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("fast"):
+    if params.get("fast", False):
         cargs.append("-fast")
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [sh2peaks_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("SH")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("SH", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -349,16 +345,18 @@ def sh2peaks_outputs(
     """
     ret = Sh2peaksOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def sh2peaks_execute(
     params: Sh2peaksParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Sh2peaksOutputs:
     """
+    sh2peaks
+    
     Extract the peaks of a spherical harmonic function in each voxel.
     
     Peaks of the spherical harmonic function in each voxel are located by
@@ -381,10 +379,12 @@ def sh2peaks_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Sh2peaksOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2PEAKS_METADATA)
     params = execution.params(params)
     cargs = sh2peaks_cargs(params, execution)
     ret = sh2peaks_outputs(params, execution)
@@ -413,6 +413,8 @@ def sh2peaks(
     runner: Runner | None = None,
 ) -> Sh2peaksOutputs:
     """
+    sh2peaks
+    
     Extract the peaks of a spherical harmonic function in each voxel.
     
     Peaks of the spherical harmonic function in each voxel are located by
@@ -468,8 +470,6 @@ def sh2peaks(
     Returns:
         NamedTuple of outputs (described in `Sh2peaksOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SH2PEAKS_METADATA)
     params = sh2peaks_params(
         num=num,
         direction=direction,
@@ -489,17 +489,15 @@ def sh2peaks(
         sh=sh,
         output=output,
     )
-    return sh2peaks_execute(params, execution)
+    return sh2peaks_execute(params, runner)
 
 
 __all__ = [
     "SH2PEAKS_METADATA",
-    "Sh2peaksConfigParameters",
-    "Sh2peaksDirectionParameters",
     "Sh2peaksOutputs",
-    "Sh2peaksParameters",
     "sh2peaks",
     "sh2peaks_config_params",
     "sh2peaks_direction_params",
+    "sh2peaks_execute",
     "sh2peaks_params",
 ]

niwrap_mrtrix/mrtrix/sh2power.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SH2POWER_METADATA = Metadata(
-    id="51541fdc4332f8deff6104a920269e275945d304.boutiques",
+    id="a770bfd27441085e1e72ab3538cb5be866f4dd4f.boutiques",
     name="sh2power",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ SH2POWER_METADATA = Metadata(
 
 
 Sh2powerConfigParameters = typing.TypedDict('Sh2powerConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Sh2powerConfigParametersTagged = typing.TypedDict('Sh2powerConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Sh2powerParameters = typing.TypedDict('Sh2powerParameters', {
-    "__STYXTYPE__": typing.Literal["sh2power"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/sh2power"]],
+    "spectrum": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Sh2powerConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "SH": InputPathType,
+    "power": str,
+})
+Sh2powerParametersTagged = typing.TypedDict('Sh2powerParametersTagged', {
+    "@type": typing.Literal["mrtrix/sh2power"],
     "spectrum": bool,
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ Sh2powerParameters = typing.TypedDict('Sh2powerParameters', {
     "SH": InputPathType,
     "power": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "sh2power": sh2power_cargs,
-        "config": sh2power_config_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 {
-        "sh2power": sh2power_outputs,
-    }.get(t)
 
 
 def sh2power_config_params(
     key: str,
     value: str,
-) -> Sh2powerConfigParameters:
+) -> Sh2powerConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def sh2power_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def sh2power_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class Sh2powerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sh2power(...)`.
+    Output object returned when calling `Sh2powerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def sh2power_params(
     config: list[Sh2powerConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Sh2powerParameters:
+) -> Sh2powerParametersTagged:
     """
     Build parameters.
     
@@ -157,7 +143,7 @@ def sh2power_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sh2power",
+        "@type": "mrtrix/sh2power",
         "spectrum": spectrum,
         "info": info,
         "quiet": quiet,
@@ -190,29 +176,29 @@ def sh2power_cargs(
     """
     cargs = []
     cargs.append("sh2power")
-    if params.get("spectrum"):
+    if params.get("spectrum", False):
         cargs.append("-spectrum")
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [sh2power_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("SH")))
-    cargs.append(params.get("power"))
+    cargs.append(execution.input_file(params.get("SH", None)))
+    cargs.append(params.get("power", None))
     return cargs
 
 
@@ -231,16 +217,18 @@ def sh2power_outputs(
     """
     ret = Sh2powerOutputs(
         root=execution.output_file("."),
-        power=execution.output_file(params.get("power")),
+        power=execution.output_file(params.get("power", None)),
     )
     return ret
 
 
 def sh2power_execute(
     params: Sh2powerParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Sh2powerOutputs:
     """
+    sh2power
+    
     Compute the total power of a spherical harmonics image.
     
     This command computes the sum of squared SH coefficients, which equals the
@@ -260,10 +248,12 @@ def sh2power_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Sh2powerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SH2POWER_METADATA)
     params = execution.params(params)
     cargs = sh2power_cargs(params, execution)
     ret = sh2power_outputs(params, execution)
@@ -286,6 +276,8 @@ def sh2power(
     runner: Runner | None = None,
 ) -> Sh2powerOutputs:
     """
+    sh2power
+    
     Compute the total power of a spherical harmonics image.
     
     This command computes the sum of squared SH coefficients, which equals the
@@ -324,8 +316,6 @@ def sh2power(
     Returns:
         NamedTuple of outputs (described in `Sh2powerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SH2POWER_METADATA)
     params = sh2power_params(
         spectrum=spectrum,
         info=info,
@@ -339,15 +329,14 @@ def sh2power(
         sh=sh,
         power=power,
     )
-    return sh2power_execute(params, execution)
+    return sh2power_execute(params, runner)
 
 
 __all__ = [
     "SH2POWER_METADATA",
-    "Sh2powerConfigParameters",
     "Sh2powerOutputs",
-    "Sh2powerParameters",
     "sh2power",
     "sh2power_config_params",
+    "sh2power_execute",
     "sh2power_params",
 ]