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

niwrap_mrtrix/mrtrix/dirsplit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DIRSPLIT_METADATA = Metadata(
-    id="6943dfd21fe636f218d9d7ac572829fa9eeb0c9b.boutiques",
+    id="7c55878e57655ef50ae5568918ecc61af1b94ca1.boutiques",
     name="dirsplit",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,34 @@ DIRSPLIT_METADATA = Metadata(
 
 
 DirsplitConfigParameters = typing.TypedDict('DirsplitConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+DirsplitConfigParametersTagged = typing.TypedDict('DirsplitConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 DirsplitParameters = typing.TypedDict('DirsplitParameters', {
-    "__STYXTYPE__": typing.Literal["dirsplit"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/dirsplit"]],
+    "permutations": typing.NotRequired[int | None],
+    "cartesian": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirsplitConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "dirs": InputPathType,
+    "out": str,
+})
+DirsplitParametersTagged = typing.TypedDict('DirsplitParametersTagged', {
+    "@type": typing.Literal["mrtrix/dirsplit"],
     "permutations": typing.NotRequired[int | None],
     "cartesian": bool,
     "info": bool,
@@ -35,45 +55,12 @@ DirsplitParameters = typing.TypedDict('DirsplitParameters', {
     "dirs": InputPathType,
     "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 {
-        "dirsplit": dirsplit_cargs,
-        "config": dirsplit_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 {
-        "dirsplit": dirsplit_outputs,
-    }.get(t)
 
 
 def dirsplit_config_params(
     key: str,
     value: str,
-) -> DirsplitConfigParameters:
+) -> DirsplitConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +71,7 @@ def dirsplit_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +93,14 @@ def dirsplit_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 DirsplitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dirsplit(...)`.
+    Output object returned when calling `DirsplitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -134,7 +121,7 @@ def dirsplit_params(
     config: list[DirsplitConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> DirsplitParameters:
+) -> DirsplitParametersTagged:
     """
     Build parameters.
     
@@ -160,7 +147,7 @@ def dirsplit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dirsplit",
+        "@type": "mrtrix/dirsplit",
         "cartesian": cartesian,
         "info": info,
         "quiet": quiet,
@@ -195,34 +182,34 @@ def dirsplit_cargs(
     """
     cargs = []
     cargs.append("dirsplit")
-    if params.get("permutations") is not None:
+    if params.get("permutations", None) is not None:
         cargs.extend([
             "-permutations",
-            str(params.get("permutations"))
+            str(params.get("permutations", None))
         ])
-    if params.get("cartesian"):
+    if params.get("cartesian", False):
         cargs.append("-cartesian")
-    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 [dirsplit_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("dirs")))
-    cargs.append(params.get("out"))
+    cargs.append(execution.input_file(params.get("dirs", None)))
+    cargs.append(params.get("out", None))
     return cargs
 
 
@@ -241,16 +228,18 @@ def dirsplit_outputs(
     """
     ret = DirsplitOutputs(
         root=execution.output_file("."),
-        out=execution.output_file(params.get("out")),
+        out=execution.output_file(params.get("out", None)),
     )
     return ret
 
 
 def dirsplit_execute(
     params: DirsplitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DirsplitOutputs:
     """
+    dirsplit
+    
     Split a set of evenly distributed directions (as generated by dirgen) into
     approximately uniformly distributed subsets.
     
@@ -266,10 +255,12 @@ def dirsplit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DirsplitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRSPLIT_METADATA)
     params = execution.params(params)
     cargs = dirsplit_cargs(params, execution)
     ret = dirsplit_outputs(params, execution)
@@ -293,6 +284,8 @@ def dirsplit(
     runner: Runner | None = None,
 ) -> DirsplitOutputs:
     """
+    dirsplit
+    
     Split a set of evenly distributed directions (as generated by dirgen) into
     approximately uniformly distributed subsets.
     
@@ -328,8 +321,6 @@ def dirsplit(
     Returns:
         NamedTuple of outputs (described in `DirsplitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DIRSPLIT_METADATA)
     params = dirsplit_params(
         permutations=permutations,
         cartesian=cartesian,
@@ -344,15 +335,14 @@ def dirsplit(
         dirs=dirs,
         out=out,
     )
-    return dirsplit_execute(params, execution)
+    return dirsplit_execute(params, runner)
 
 
 __all__ = [
     "DIRSPLIT_METADATA",
-    "DirsplitConfigParameters",
     "DirsplitOutputs",
-    "DirsplitParameters",
     "dirsplit",
     "dirsplit_config_params",
+    "dirsplit_execute",
     "dirsplit_params",
 ]

niwrap_mrtrix/mrtrix/dirstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DIRSTAT_METADATA = Metadata(
-    id="54c92c56f5ceb3968ec6cf9bb9929c2227e1f7a2.boutiques",
+    id="369098dbdbd016bf94682e0106a2f2e1711f2a5b.boutiques",
     name="dirstat",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,21 +14,47 @@ DIRSTAT_METADATA = Metadata(
 
 
 DirstatFslgradParameters = typing.TypedDict('DirstatFslgradParameters', {
-    "__STYXTYPE__": typing.Literal["fslgrad"],
+    "@type": typing.NotRequired[typing.Literal["fslgrad"]],
+    "bvecs": InputPathType,
+    "bvals": InputPathType,
+})
+DirstatFslgradParametersTagged = typing.TypedDict('DirstatFslgradParametersTagged', {
+    "@type": typing.Literal["fslgrad"],
     "bvecs": InputPathType,
     "bvals": InputPathType,
 })
 
 
 DirstatConfigParameters = typing.TypedDict('DirstatConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+DirstatConfigParametersTagged = typing.TypedDict('DirstatConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 DirstatParameters = typing.TypedDict('DirstatParameters', {
-    "__STYXTYPE__": typing.Literal["dirstat"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/dirstat"]],
+    "output": typing.NotRequired[str | None],
+    "shells": typing.NotRequired[list[float] | None],
+    "grad": typing.NotRequired[InputPathType | None],
+    "fslgrad": typing.NotRequired[DirstatFslgradParameters | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DirstatConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "dirs": InputPathType,
+})
+DirstatParametersTagged = typing.TypedDict('DirstatParametersTagged', {
+    "@type": typing.Literal["mrtrix/dirstat"],
     "output": typing.NotRequired[str | None],
     "shells": typing.NotRequired[list[float] | None],
     "grad": typing.NotRequired[InputPathType | None],
@@ -43,45 +69,12 @@ DirstatParameters = typing.TypedDict('DirstatParameters', {
     "version": bool,
     "dirs": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dirstat": dirstat_cargs,
-        "fslgrad": dirstat_fslgrad_cargs,
-        "config": dirstat_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 {
-    }.get(t)
 
 
 def dirstat_fslgrad_params(
     bvecs: InputPathType,
     bvals: InputPathType,
-) -> DirstatFslgradParameters:
+) -> DirstatFslgradParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +91,7 @@ def dirstat_fslgrad_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fslgrad",
+        "@type": "fslgrad",
         "bvecs": bvecs,
         "bvals": bvals,
     }
@@ -120,15 +113,15 @@ def dirstat_fslgrad_cargs(
     """
     cargs = []
     cargs.append("-fslgrad")
-    cargs.append(execution.input_file(params.get("bvecs")))
-    cargs.append(execution.input_file(params.get("bvals")))
+    cargs.append(execution.input_file(params.get("bvecs", None)))
+    cargs.append(execution.input_file(params.get("bvals", None)))
     return cargs
 
 
 def dirstat_config_params(
     key: str,
     value: str,
-) -> DirstatConfigParameters:
+) -> DirstatConfigParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +132,7 @@ def dirstat_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -161,14 +154,14 @@ def dirstat_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 DirstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dirstat(...)`.
+    Output object returned when calling `DirstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -188,7 +181,7 @@ def dirstat_params(
     config: list[DirstatConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> DirstatParameters:
+) -> DirstatParametersTagged:
     """
     Build parameters.
     
@@ -233,7 +226,7 @@ def dirstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dirstat",
+        "@type": "mrtrix/dirstat",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -272,43 +265,43 @@ def dirstat_cargs(
     """
     cargs = []
     cargs.append("dirstat")
-    if params.get("output") is not None:
+    if params.get("output", None) is not None:
         cargs.extend([
             "-output",
-            params.get("output")
+            params.get("output", None)
         ])
-    if params.get("shells") is not None:
+    if params.get("shells", None) is not None:
         cargs.extend([
             "-shells",
-            ",".join(map(str, params.get("shells")))
+            ",".join(map(str, params.get("shells", None)))
         ])
-    if params.get("grad") is not None:
+    if params.get("grad", None) is not None:
         cargs.extend([
             "-grad",
-            execution.input_file(params.get("grad"))
+            execution.input_file(params.get("grad", None))
         ])
-    if params.get("fslgrad") is not None:
-        cargs.extend(dyn_cargs(params.get("fslgrad")["__STYXTYPE__"])(params.get("fslgrad"), execution))
-    if params.get("info"):
+    if params.get("fslgrad", None) is not None:
+        cargs.extend(dirstat_fslgrad_cargs(params.get("fslgrad", None), execution))
+    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 [dirstat_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("dirs")))
+    cargs.append(execution.input_file(params.get("dirs", None)))
     return cargs
 
 
@@ -333,9 +326,11 @@ def dirstat_outputs(
 
 def dirstat_execute(
     params: DirstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DirstatOutputs:
     """
+    dirstat
+    
     Report statistics on a direction set.
     
     This command will accept as inputs:
@@ -383,10 +378,12 @@ def dirstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DirstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIRSTAT_METADATA)
     params = execution.params(params)
     cargs = dirstat_cargs(params, execution)
     ret = dirstat_outputs(params, execution)
@@ -411,6 +408,8 @@ def dirstat(
     runner: Runner | None = None,
 ) -> DirstatOutputs:
     """
+    dirstat
+    
     Report statistics on a direction set.
     
     This command will accept as inputs:
@@ -497,8 +496,6 @@ def dirstat(
     Returns:
         NamedTuple of outputs (described in `DirstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DIRSTAT_METADATA)
     params = dirstat_params(
         output=output,
         shells=shells,
@@ -514,17 +511,15 @@ def dirstat(
         version=version,
         dirs=dirs,
     )
-    return dirstat_execute(params, execution)
+    return dirstat_execute(params, runner)
 
 
 __all__ = [
     "DIRSTAT_METADATA",
-    "DirstatConfigParameters",
-    "DirstatFslgradParameters",
     "DirstatOutputs",
-    "DirstatParameters",
     "dirstat",
     "dirstat_config_params",
+    "dirstat_execute",
     "dirstat_fslgrad_params",
     "dirstat_params",
 ]