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

niwrap_mrtrix/mrtrix/fod2fixel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FOD2FIXEL_METADATA = Metadata(
-    id="a00904c7bdbccc20a322e2bbb4456d2ea946b6a4.boutiques",
+    id="789d8f209b3fdf4c5f81cd43bcf2cd1ab6e4addc.boutiques",
     name="fod2fixel",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,43 @@ FOD2FIXEL_METADATA = Metadata(
 
 
 Fod2fixelConfigParameters = typing.TypedDict('Fod2fixelConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Fod2fixelConfigParametersTagged = typing.TypedDict('Fod2fixelConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Fod2fixelParameters = typing.TypedDict('Fod2fixelParameters', {
-    "__STYXTYPE__": typing.Literal["fod2fixel"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fod2fixel"]],
+    "afd": typing.NotRequired[str | None],
+    "peak_amp": typing.NotRequired[str | None],
+    "disp": typing.NotRequired[str | None],
+    "fmls_integral": typing.NotRequired[float | None],
+    "fmls_peak_value": typing.NotRequired[float | None],
+    "fmls_no_thresholds": bool,
+    "fmls_lobe_merge_ratio": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "maxnum": typing.NotRequired[int | None],
+    "nii": bool,
+    "dirpeak": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Fod2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fod": InputPathType,
+    "fixel_directory": str,
+})
+Fod2fixelParametersTagged = typing.TypedDict('Fod2fixelParametersTagged', {
+    "@type": typing.Literal["mrtrix/fod2fixel"],
     "afd": typing.NotRequired[str | None],
     "peak_amp": typing.NotRequired[str | None],
     "disp": typing.NotRequired[str | None],
@@ -44,45 +73,12 @@ Fod2fixelParameters = typing.TypedDict('Fod2fixelParameters', {
     "fod": InputPathType,
     "fixel_directory": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fod2fixel": fod2fixel_cargs,
-        "config": fod2fixel_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 {
-        "fod2fixel": fod2fixel_outputs,
-    }.get(t)
 
 
 def fod2fixel_config_params(
     key: str,
     value: str,
-) -> Fod2fixelConfigParameters:
+) -> Fod2fixelConfigParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +89,7 @@ def fod2fixel_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -115,14 +111,14 @@ def fod2fixel_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 Fod2fixelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fod2fixel(...)`.
+    Output object returned when calling `Fod2fixelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -160,7 +156,7 @@ def fod2fixel_params(
     config: list[Fod2fixelConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Fod2fixelParameters:
+) -> Fod2fixelParametersTagged:
     """
     Build parameters.
     
@@ -212,7 +208,7 @@ def fod2fixel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fod2fixel",
+        "@type": "mrtrix/fod2fixel",
         "fmls_no_thresholds": fmls_no_thresholds,
         "nii": nii,
         "dirpeak": dirpeak,
@@ -263,73 +259,73 @@ def fod2fixel_cargs(
     """
     cargs = []
     cargs.append("fod2fixel")
-    if params.get("afd") is not None:
+    if params.get("afd", None) is not None:
         cargs.extend([
             "-afd",
-            params.get("afd")
+            params.get("afd", None)
         ])
-    if params.get("peak_amp") is not None:
+    if params.get("peak_amp", None) is not None:
         cargs.extend([
             "-peak_amp",
-            params.get("peak_amp")
+            params.get("peak_amp", None)
         ])
-    if params.get("disp") is not None:
+    if params.get("disp", None) is not None:
         cargs.extend([
             "-disp",
-            params.get("disp")
+            params.get("disp", None)
         ])
-    if params.get("fmls_integral") is not None:
+    if params.get("fmls_integral", None) is not None:
         cargs.extend([
             "-fmls_integral",
-            str(params.get("fmls_integral"))
+            str(params.get("fmls_integral", None))
         ])
-    if params.get("fmls_peak_value") is not None:
+    if params.get("fmls_peak_value", None) is not None:
         cargs.extend([
             "-fmls_peak_value",
-            str(params.get("fmls_peak_value"))
+            str(params.get("fmls_peak_value", None))
         ])
-    if params.get("fmls_no_thresholds"):
+    if params.get("fmls_no_thresholds", False):
         cargs.append("-fmls_no_thresholds")
-    if params.get("fmls_lobe_merge_ratio") is not None:
+    if params.get("fmls_lobe_merge_ratio", None) is not None:
         cargs.extend([
             "-fmls_lobe_merge_ratio",
-            str(params.get("fmls_lobe_merge_ratio"))
+            str(params.get("fmls_lobe_merge_ratio", 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("maxnum") is not None:
+    if params.get("maxnum", None) is not None:
         cargs.extend([
             "-maxnum",
-            str(params.get("maxnum"))
+            str(params.get("maxnum", None))
         ])
-    if params.get("nii"):
+    if params.get("nii", False):
         cargs.append("-nii")
-    if params.get("dirpeak"):
+    if params.get("dirpeak", False):
         cargs.append("-dirpeak")
-    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 [fod2fixel_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("fod")))
-    cargs.append(params.get("fixel_directory"))
+    cargs.append(execution.input_file(params.get("fod", None)))
+    cargs.append(params.get("fixel_directory", None))
     return cargs
 
 
@@ -348,19 +344,21 @@ def fod2fixel_outputs(
     """
     ret = Fod2fixelOutputs(
         root=execution.output_file("."),
-        fixel_directory=execution.output_file(params.get("fixel_directory")),
-        afd=execution.output_file(params.get("afd")) if (params.get("afd") is not None) else None,
-        peak_amp=execution.output_file(params.get("peak_amp")) if (params.get("peak_amp") is not None) else None,
-        disp=execution.output_file(params.get("disp")) if (params.get("disp") is not None) else None,
+        fixel_directory=execution.output_file(params.get("fixel_directory", None)),
+        afd=execution.output_file(params.get("afd", None)) if (params.get("afd") is not None) else None,
+        peak_amp=execution.output_file(params.get("peak_amp", None)) if (params.get("peak_amp") is not None) else None,
+        disp=execution.output_file(params.get("disp", None)) if (params.get("disp") is not None) else None,
     )
     return ret
 
 
 def fod2fixel_execute(
     params: Fod2fixelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fod2fixelOutputs:
     """
+    fod2fixel
+    
     Perform segmentation of continuous Fibre Orientation Distributions (FODs) to
     produce discrete fixels.
     
@@ -385,10 +383,12 @@ def fod2fixel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fod2fixelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FOD2FIXEL_METADATA)
     params = execution.params(params)
     cargs = fod2fixel_cargs(params, execution)
     ret = fod2fixel_outputs(params, execution)
@@ -421,6 +421,8 @@ def fod2fixel(
     runner: Runner | None = None,
 ) -> Fod2fixelOutputs:
     """
+    fod2fixel
+    
     Perform segmentation of continuous Fibre Orientation Distributions (FODs) to
     produce discrete fixels.
     
@@ -491,8 +493,6 @@ def fod2fixel(
     Returns:
         NamedTuple of outputs (described in `Fod2fixelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FOD2FIXEL_METADATA)
     params = fod2fixel_params(
         afd=afd,
         peak_amp=peak_amp,
@@ -516,15 +516,14 @@ def fod2fixel(
         fod=fod,
         fixel_directory=fixel_directory,
     )
-    return fod2fixel_execute(params, execution)
+    return fod2fixel_execute(params, runner)
 
 
 __all__ = [
     "FOD2FIXEL_METADATA",
-    "Fod2fixelConfigParameters",
     "Fod2fixelOutputs",
-    "Fod2fixelParameters",
     "fod2fixel",
     "fod2fixel_config_params",
+    "fod2fixel_execute",
     "fod2fixel_params",
 ]

niwrap_mrtrix/mrtrix/label2colour.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL2COLOUR_METADATA = Metadata(
-    id="b27f3ed9ad207fb471639dd9e4b52130d8a534ac.boutiques",
+    id="9c64d87e6b80097d51226570fbf47cc009d84140.boutiques",
     name="label2colour",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ LABEL2COLOUR_METADATA = Metadata(
 
 
 Label2colourConfigParameters = typing.TypedDict('Label2colourConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Label2colourConfigParametersTagged = typing.TypedDict('Label2colourConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Label2colourParameters = typing.TypedDict('Label2colourParameters', {
-    "__STYXTYPE__": typing.Literal["label2colour"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/label2colour"]],
+    "lut": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Label2colourConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "nodes_in": InputPathType,
+    "colour_out": str,
+})
+Label2colourParametersTagged = typing.TypedDict('Label2colourParametersTagged', {
+    "@type": typing.Literal["mrtrix/label2colour"],
     "lut": typing.NotRequired[InputPathType | None],
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ Label2colourParameters = typing.TypedDict('Label2colourParameters', {
     "nodes_in": InputPathType,
     "colour_out": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "label2colour": label2colour_cargs,
-        "config": label2colour_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 {
-        "label2colour": label2colour_outputs,
-    }.get(t)
 
 
 def label2colour_config_params(
     key: str,
     value: str,
-) -> Label2colourConfigParameters:
+) -> Label2colourConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def label2colour_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def label2colour_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 Label2colourOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label2colour(...)`.
+    Output object returned when calling `Label2colourParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def label2colour_params(
     config: list[Label2colourConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Label2colourParameters:
+) -> Label2colourParametersTagged:
     """
     Build parameters.
     
@@ -157,7 +143,7 @@ def label2colour_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label2colour",
+        "@type": "mrtrix/label2colour",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -191,32 +177,32 @@ def label2colour_cargs(
     """
     cargs = []
     cargs.append("label2colour")
-    if params.get("lut") is not None:
+    if params.get("lut", None) is not None:
         cargs.extend([
             "-lut",
-            execution.input_file(params.get("lut"))
+            execution.input_file(params.get("lut", None))
         ])
-    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 [label2colour_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("nodes_in")))
-    cargs.append(params.get("colour_out"))
+    cargs.append(execution.input_file(params.get("nodes_in", None)))
+    cargs.append(params.get("colour_out", None))
     return cargs
 
 
@@ -235,17 +221,20 @@ def label2colour_outputs(
     """
     ret = Label2colourOutputs(
         root=execution.output_file("."),
-        colour_out=execution.output_file(params.get("colour_out")),
+        colour_out=execution.output_file(params.get("colour_out", None)),
     )
     return ret
 
 
 def label2colour_execute(
     params: Label2colourParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Label2colourOutputs:
     """
-    Convert a parcellated image (where values are node indices) into a colour image.
+    label2colour
+    
+    Convert a parcellated image (where values are node indices) into a colour
+    image.
     
     Many software packages handle this colouring internally within their viewer
     program; this binary explicitly converts a parcellation image into a colour
@@ -261,10 +250,12 @@ def label2colour_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Label2colourOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL2COLOUR_METADATA)
     params = execution.params(params)
     cargs = label2colour_cargs(params, execution)
     ret = label2colour_outputs(params, execution)
@@ -287,7 +278,10 @@ def label2colour(
     runner: Runner | None = None,
 ) -> Label2colourOutputs:
     """
-    Convert a parcellated image (where values are node indices) into a colour image.
+    label2colour
+    
+    Convert a parcellated image (where values are node indices) into a colour
+    image.
     
     Many software packages handle this colouring internally within their viewer
     program; this binary explicitly converts a parcellation image into a colour
@@ -322,8 +316,6 @@ def label2colour(
     Returns:
         NamedTuple of outputs (described in `Label2colourOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL2COLOUR_METADATA)
     params = label2colour_params(
         lut=lut,
         info=info,
@@ -337,15 +329,14 @@ def label2colour(
         nodes_in=nodes_in,
         colour_out=colour_out,
     )
-    return label2colour_execute(params, execution)
+    return label2colour_execute(params, runner)
 
 
 __all__ = [
     "LABEL2COLOUR_METADATA",
-    "Label2colourConfigParameters",
     "Label2colourOutputs",
-    "Label2colourParameters",
     "label2colour",
     "label2colour_config_params",
+    "label2colour_execute",
     "label2colour_params",
 ]