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

niwrap_mrtrix/mrtrix/__init__.py

@@ -8,6 +8,8 @@ stability in mind, and is freely available under an open-source license. It is
 developed and maintained by a team of experts in the field, fostering an active
 community of users from diverse backgrounds.
 
+Author: MRTrix3 Developers
+
 URL: https://www.mrtrix.org/
 """
 # This file was auto generated by Styx.
@@ -128,3 +130,134 @@ from .warpconvert import *
 from .warpcorrect import *
 from .warpinit import *
 from .warpinvert import *
+from styxdefs import Runner as _Runner
+
+
+def execute(
+    params: dict,
+    runner: _Runner | None = None,
+) -> None:
+    """
+    Run a command in this package dynamically from a params object.
+    
+    Args:
+        params: The parameters.
+        runner: Command runner.
+    """
+    return {
+        "mrtrix/5tt2gmwmi": v_5tt2gmwmi_execute,
+        "mrtrix/5tt2vis": v_5tt2vis_execute,
+        "mrtrix/5ttcheck": v_5ttcheck_execute,
+        "mrtrix/5ttedit": v_5ttedit_execute,
+        "mrtrix/5ttgen": v_5ttgen_execute,
+        "mrtrix/afdconnectivity": afdconnectivity_execute,
+        "mrtrix/amp2response": amp2response_execute,
+        "mrtrix/amp2sh": amp2sh_execute,
+        "mrtrix/connectome2tck": connectome2tck_execute,
+        "mrtrix/connectomeedit": connectomeedit_execute,
+        "mrtrix/connectomestats": connectomestats_execute,
+        "mrtrix/dcmedit": dcmedit_execute,
+        "mrtrix/dcminfo": dcminfo_execute,
+        "mrtrix/dirflip": dirflip_execute,
+        "mrtrix/dirgen": dirgen_execute,
+        "mrtrix/dirmerge": dirmerge_execute,
+        "mrtrix/dirorder": dirorder_execute,
+        "mrtrix/dirsplit": dirsplit_execute,
+        "mrtrix/dirstat": dirstat_execute,
+        "mrtrix/dwi2adc": dwi2adc_execute,
+        "mrtrix/dwi2fod": dwi2fod_execute,
+        "mrtrix/dwi2mask": dwi2mask_execute,
+        "mrtrix/dwi2response": dwi2response_execute,
+        "mrtrix/dwi2tensor": dwi2tensor_execute,
+        "mrtrix/dwibiascorrect": dwibiascorrect_execute,
+        "mrtrix/dwidenoise": dwidenoise_execute,
+        "mrtrix/dwiextract": dwiextract_execute,
+        "mrtrix/dwigradcheck": dwigradcheck_execute,
+        "mrtrix/fixel2peaks": fixel2peaks_execute,
+        "mrtrix/fixel2sh": fixel2sh_execute,
+        "mrtrix/fixel2tsf": fixel2tsf_execute,
+        "mrtrix/fixel2voxel": fixel2voxel_execute,
+        "mrtrix/fixelcfestats": fixelcfestats_execute,
+        "mrtrix/fixelconnectivity": fixelconnectivity_execute,
+        "mrtrix/fixelconvert": fixelconvert_execute,
+        "mrtrix/fixelcorrespondence": fixelcorrespondence_execute,
+        "mrtrix/fixelcrop": fixelcrop_execute,
+        "mrtrix/fixelfilter": fixelfilter_execute,
+        "mrtrix/fixelreorient": fixelreorient_execute,
+        "mrtrix/fod2dec": fod2dec_execute,
+        "mrtrix/fod2fixel": fod2fixel_execute,
+        "mrtrix/label2colour": label2colour_execute,
+        "mrtrix/label2mesh": label2mesh_execute,
+        "mrtrix/labelconvert": labelconvert_execute,
+        "mrtrix/labelstats": labelstats_execute,
+        "mrtrix/maskdump": maskdump_execute,
+        "mrtrix/maskfilter": maskfilter_execute,
+        "mrtrix/mesh2voxel": mesh2voxel_execute,
+        "mrtrix/meshconvert": meshconvert_execute,
+        "mrtrix/meshfilter": meshfilter_execute,
+        "mrtrix/mraverageheader": mraverageheader_execute,
+        "mrtrix/mrcalc": mrcalc_execute,
+        "mrtrix/mrcat": mrcat_execute,
+        "mrtrix/mrcentroid": mrcentroid_execute,
+        "mrtrix/mrcheckerboardmask": mrcheckerboardmask_execute,
+        "mrtrix/mrclusterstats": mrclusterstats_execute,
+        "mrtrix/mrcolour": mrcolour_execute,
+        "mrtrix/mrconvert": mrconvert_execute,
+        "mrtrix/mrdegibbs": mrdegibbs_execute,
+        "mrtrix/mrdump": mrdump_execute,
+        "mrtrix/mredit": mredit_execute,
+        "mrtrix/mrfilter": mrfilter_execute,
+        "mrtrix/mrgrid": mrgrid_execute,
+        "mrtrix/mrhistmatch": mrhistmatch_execute,
+        "mrtrix/mrhistogram": mrhistogram_execute,
+        "mrtrix/mrinfo": mrinfo_execute,
+        "mrtrix/mrmath": mrmath_execute,
+        "mrtrix/mrmetric": mrmetric_execute,
+        "mrtrix/mrregister": mrregister_execute,
+        "mrtrix/mrstats": mrstats_execute,
+        "mrtrix/mrthreshold": mrthreshold_execute,
+        "mrtrix/mrtransform": mrtransform_execute,
+        "mrtrix/mtnormalise": mtnormalise_execute,
+        "mrtrix/peaks2amp": peaks2amp_execute,
+        "mrtrix/peaks2fixel": peaks2fixel_execute,
+        "mrtrix/responsemean": responsemean_execute,
+        "mrtrix/sh2amp": sh2amp_execute,
+        "mrtrix/sh2peaks": sh2peaks_execute,
+        "mrtrix/sh2power": sh2power_execute,
+        "mrtrix/sh2response": sh2response_execute,
+        "mrtrix/shbasis": shbasis_execute,
+        "mrtrix/shconv": shconv_execute,
+        "mrtrix/tck2connectome": tck2connectome_execute,
+        "mrtrix/tck2fixel": tck2fixel_execute,
+        "mrtrix/tckconvert": tckconvert_execute,
+        "mrtrix/tckdfc": tckdfc_execute,
+        "mrtrix/tckedit": tckedit_execute,
+        "mrtrix/tckgen": tckgen_execute,
+        "mrtrix/tckglobal": tckglobal_execute,
+        "mrtrix/tckinfo": tckinfo_execute,
+        "mrtrix/tckmap": tckmap_execute,
+        "mrtrix/tckresample": tckresample_execute,
+        "mrtrix/tcksample": tcksample_execute,
+        "mrtrix/tcksift": tcksift_execute,
+        "mrtrix/tcksift2": tcksift2_execute,
+        "mrtrix/tckstats": tckstats_execute,
+        "mrtrix/tcktransform": tcktransform_execute,
+        "mrtrix/tensor2metric": tensor2metric_execute,
+        "mrtrix/transformcalc": transformcalc_execute,
+        "mrtrix/transformcompose": transformcompose_execute,
+        "mrtrix/transformconvert": transformconvert_execute,
+        "mrtrix/tsfdivide": tsfdivide_execute,
+        "mrtrix/tsfinfo": tsfinfo_execute,
+        "mrtrix/tsfmult": tsfmult_execute,
+        "mrtrix/tsfsmooth": tsfsmooth_execute,
+        "mrtrix/tsfthreshold": tsfthreshold_execute,
+        "mrtrix/tsfvalidate": tsfvalidate_execute,
+        "mrtrix/vectorstats": vectorstats_execute,
+        "mrtrix/voxel2fixel": voxel2fixel_execute,
+        "mrtrix/voxel2mesh": voxel2mesh_execute,
+        "mrtrix/warp2metric": warp2metric_execute,
+        "mrtrix/warpconvert": warpconvert_execute,
+        "mrtrix/warpcorrect": warpcorrect_execute,
+        "mrtrix/warpinit": warpinit_execute,
+        "mrtrix/warpinvert": warpinvert_execute,
+    }[params["@type"]](params, runner)

niwrap_mrtrix/mrtrix/afdconnectivity.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 AFDCONNECTIVITY_METADATA = Metadata(
-    id="b5133d2715848aa2a01d0deab25470cb3815e66e.boutiques",
+    id="a6fb5580a7faf6e50bbcf57a2c6385623c779645.boutiques",
     name="afdconnectivity",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,35 @@ AFDCONNECTIVITY_METADATA = Metadata(
 
 
 AfdconnectivityConfigParameters = typing.TypedDict('AfdconnectivityConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+AfdconnectivityConfigParametersTagged = typing.TypedDict('AfdconnectivityConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 AfdconnectivityParameters = typing.TypedDict('AfdconnectivityParameters', {
-    "__STYXTYPE__": typing.Literal["afdconnectivity"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/afdconnectivity"]],
+    "wbft": typing.NotRequired[InputPathType | None],
+    "afd_map": typing.NotRequired[str | None],
+    "all_fixels": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[AfdconnectivityConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image": InputPathType,
+    "tracks": InputPathType,
+})
+AfdconnectivityParametersTagged = typing.TypedDict('AfdconnectivityParametersTagged', {
+    "@type": typing.Literal["mrtrix/afdconnectivity"],
     "wbft": typing.NotRequired[InputPathType | None],
     "afd_map": typing.NotRequired[str | None],
     "all_fixels": bool,
@@ -36,45 +57,12 @@ AfdconnectivityParameters = typing.TypedDict('AfdconnectivityParameters', {
     "image": InputPathType,
     "tracks": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "afdconnectivity": afdconnectivity_cargs,
-        "config": afdconnectivity_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 {
-        "afdconnectivity": afdconnectivity_outputs,
-    }.get(t)
 
 
 def afdconnectivity_config_params(
     key: str,
     value: str,
-) -> AfdconnectivityConfigParameters:
+) -> AfdconnectivityConfigParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +73,7 @@ def afdconnectivity_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -107,14 +95,14 @@ def afdconnectivity_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 AfdconnectivityOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `afdconnectivity(...)`.
+    Output object returned when calling `AfdconnectivityParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -136,7 +124,7 @@ def afdconnectivity_params(
     config: list[AfdconnectivityConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> AfdconnectivityParameters:
+) -> AfdconnectivityParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +158,7 @@ def afdconnectivity_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "afdconnectivity",
+        "@type": "mrtrix/afdconnectivity",
         "all_fixels": all_fixels,
         "info": info,
         "quiet": quiet,
@@ -207,39 +195,39 @@ def afdconnectivity_cargs(
     """
     cargs = []
     cargs.append("afdconnectivity")
-    if params.get("wbft") is not None:
+    if params.get("wbft", None) is not None:
         cargs.extend([
             "-wbft",
-            execution.input_file(params.get("wbft"))
+            execution.input_file(params.get("wbft", None))
         ])
-    if params.get("afd_map") is not None:
+    if params.get("afd_map", None) is not None:
         cargs.extend([
             "-afd_map",
-            params.get("afd_map")
+            params.get("afd_map", None)
         ])
-    if params.get("all_fixels"):
+    if params.get("all_fixels", False):
         cargs.append("-all_fixels")
-    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 [afdconnectivity_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("image")))
-    cargs.append(execution.input_file(params.get("tracks")))
+    cargs.append(execution.input_file(params.get("image", None)))
+    cargs.append(execution.input_file(params.get("tracks", None)))
     return cargs
 
 
@@ -258,16 +246,18 @@ def afdconnectivity_outputs(
     """
     ret = AfdconnectivityOutputs(
         root=execution.output_file("."),
-        afd_map=execution.output_file(params.get("afd_map")) if (params.get("afd_map") is not None) else None,
+        afd_map=execution.output_file(params.get("afd_map", None)) if (params.get("afd_map") is not None) else None,
     )
     return ret
 
 
 def afdconnectivity_execute(
     params: AfdconnectivityParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AfdconnectivityOutputs:
     """
+    afdconnectivity
+    
     Obtain an estimate of fibre connectivity between two regions using AFD and
     streamlines tractography.
     
@@ -313,10 +303,12 @@ def afdconnectivity_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AfdconnectivityOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(AFDCONNECTIVITY_METADATA)
     params = execution.params(params)
     cargs = afdconnectivity_cargs(params, execution)
     ret = afdconnectivity_outputs(params, execution)
@@ -341,6 +333,8 @@ def afdconnectivity(
     runner: Runner | None = None,
 ) -> AfdconnectivityOutputs:
     """
+    afdconnectivity
+    
     Obtain an estimate of fibre connectivity between two regions using AFD and
     streamlines tractography.
     
@@ -414,8 +408,6 @@ def afdconnectivity(
     Returns:
         NamedTuple of outputs (described in `AfdconnectivityOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(AFDCONNECTIVITY_METADATA)
     params = afdconnectivity_params(
         wbft=wbft,
         afd_map=afd_map,
@@ -431,15 +423,14 @@ def afdconnectivity(
         image=image,
         tracks=tracks,
     )
-    return afdconnectivity_execute(params, execution)
+    return afdconnectivity_execute(params, runner)
 
 
 __all__ = [
     "AFDCONNECTIVITY_METADATA",
-    "AfdconnectivityConfigParameters",
     "AfdconnectivityOutputs",
-    "AfdconnectivityParameters",
     "afdconnectivity",
     "afdconnectivity_config_params",
+    "afdconnectivity_execute",
     "afdconnectivity_params",
 ]