niwrap-mrtrix3tissue 0.5.0__tar.gz

niwrap_mrtrix3tissue-0.5.0/.gitignore

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niwrap_mrtrix3tissue-0.5.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: niwrap_mrtrix3tissue
+Version: 0.5.0
+Summary: NiWrap wrappers for MRTrix3Tissue.
+Author-email: CMI DAIR <dair@childmind.org>
+License-Expression: LGPL-2.1
+Requires-Python: >=3.10
+Requires-Dist: styxdefs~=0.5.0

niwrap_mrtrix3tissue-0.5.0/README.md

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+# NiWrap wrappers for [MRTrix3Tissue](https://3tissue.github.io/)
+
+MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software.
+
+MRTrix3Tissue is made by MRTrix3Tissue Developers.
+
+This package contains wrappers only and has no affiliation with the original authors.

niwrap_mrtrix3tissue-0.5.0/pyproject.toml

@@ -0,0 +1,17 @@
+[project]
+name = "niwrap_mrtrix3tissue"
+version = "0.5.0"
+description = "NiWrap wrappers for MRTrix3Tissue."
+license = "LGPL-2.1"
+authors = [{ name = "CMI DAIR", email = "dair@childmind.org" }]
+requires-python = ">=3.10"
+dependencies = [
+    "styxdefs~=0.5.0"
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/niwrap_mrtrix3tissue"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

niwrap_mrtrix3tissue-0.5.0/src/niwrap_mrtrix3tissue/mrtrix3tissue/__init__.py

@@ -0,0 +1,13 @@
+"""
+MRTrix3Tissue
+
+MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for
+3-Tissue CSD modelling and analysis to a complete version of the MRtrix3
+software.
+
+URL: https://3tissue.github.io/
+"""
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+from .ss3t_csd_beta1 import *

niwrap_mrtrix3tissue-0.5.0/src/niwrap_mrtrix3tissue/mrtrix3tissue/ss3t_csd_beta1.py

@@ -0,0 +1,458 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SS3T_CSD_BETA1_METADATA = Metadata(
+    id="3d7ce53d5c0f3941cd5c3621352793549ea67b37.boutiques",
+    name="ss3t_csd_beta1",
+    package="mrtrix3tissue",
+    container_image_tag="brainlife/3tissue:5.2.8",
+)
+
+
+Ss3tCsdBeta1ConfigParameters = typing.TypedDict('Ss3tCsdBeta1ConfigParameters', {
+    "__STYX_TYPE__": typing.Literal["config"],
+    "key": str,
+    "value": str,
+})
+
+
+Ss3tCsdBeta1ResponseOdfParameters = typing.TypedDict('Ss3tCsdBeta1ResponseOdfParameters', {
+    "__STYX_TYPE__": typing.Literal["response_odf"],
+    "response": InputPathType,
+    "odf": str,
+})
+
+
+Ss3tCsdBeta1Parameters = typing.TypedDict('Ss3tCsdBeta1Parameters', {
+    "__STYX_TYPE__": typing.Literal["ss3t_csd_beta1"],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bzero_pct": typing.NotRequired[float | None],
+    "niter": typing.NotRequired[int | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Ss3tCsdBeta1ConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "dwi": InputPathType,
+    "response_odf": list[Ss3tCsdBeta1ResponseOdfParameters],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "ss3t_csd_beta1": ss3t_csd_beta1_cargs,
+        "config": ss3t_csd_beta1_config_cargs,
+        "response_odf": ss3t_csd_beta1_response_odf_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 {
+        "ss3t_csd_beta1": ss3t_csd_beta1_outputs,
+        "response_odf": ss3t_csd_beta1_response_odf_outputs,
+    }.get(t)
+
+
+def ss3t_csd_beta1_config_params(
+    key: str,
+    value: str,
+) -> Ss3tCsdBeta1ConfigParameters:
+    """
+    Build parameters.
+    
+    Args:
+        key: temporarily set the value of an MRtrix config file entry.
+        value: temporarily set the value of an MRtrix config file entry.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "config",
+        "key": key,
+        "value": value,
+    }
+    return params
+
+
+def ss3t_csd_beta1_config_cargs(
+    params: Ss3tCsdBeta1ConfigParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("-config")
+    cargs.append(params.get("key"))
+    cargs.append(params.get("value"))
+    return cargs
+
+
+class Ss3tCsdBeta1ResponseOdfOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `list[Ss3tCsdBeta1ResponseOdfParameters](...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    odf: OutputPathType
+    """output ODF image"""
+
+
+def ss3t_csd_beta1_response_odf_params(
+    response: InputPathType,
+    odf: str,
+) -> Ss3tCsdBeta1ResponseOdfParameters:
+    """
+    Build parameters.
+    
+    Args:
+        response: input tissue response.
+        odf: output ODF image.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "response_odf",
+        "response": response,
+        "odf": odf,
+    }
+    return params
+
+
+def ss3t_csd_beta1_response_odf_cargs(
+    params: Ss3tCsdBeta1ResponseOdfParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append(execution.input_file(params.get("response")))
+    cargs.append(params.get("odf"))
+    return cargs
+
+
+def ss3t_csd_beta1_response_odf_outputs(
+    params: Ss3tCsdBeta1ResponseOdfParameters,
+    execution: Execution,
+) -> Ss3tCsdBeta1ResponseOdfOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = Ss3tCsdBeta1ResponseOdfOutputs(
+        root=execution.output_file("."),
+        odf=execution.output_file(params.get("odf")),
+    )
+    return ret
+
+
+class Ss3tCsdBeta1Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `ss3t_csd_beta1(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    response_odf: list[Ss3tCsdBeta1ResponseOdfOutputs]
+    """Outputs from `ss3t_csd_beta1_response_odf_outputs`.This is a list of
+    outputs with the same length and order as the inputs."""
+
+
+def ss3t_csd_beta1_params(
+    dwi: InputPathType,
+    response_odf: list[Ss3tCsdBeta1ResponseOdfParameters],
+    mask: InputPathType | None = None,
+    bzero_pct: float | None = None,
+    niter: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Ss3tCsdBeta1ConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+) -> Ss3tCsdBeta1Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        dwi: the input diffusion-weighted image.
+        response_odf: pairs of input tissue response and output ODF images.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        bzero_pct: the threshold below which the amplitude of the FOD is\
+            assumed to be zero, expressed as an absolute amplitude (default = 0).
+        niter: the maximum number of iterations to perform for each voxel\
+            (default = 50). Use '-niter 0' for a linear unconstrained spherical\
+            deconvolution.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "ss3t_csd_beta1",
+        "info": info,
+        "quiet": quiet,
+        "debug": debug,
+        "force": force,
+        "help": help_,
+        "version": version,
+        "dwi": dwi,
+        "response_odf": response_odf,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if bzero_pct is not None:
+        params["bzero_pct"] = bzero_pct
+    if niter is not None:
+        params["niter"] = niter
+    if nthreads is not None:
+        params["nthreads"] = nthreads
+    if config is not None:
+        params["config"] = config
+    return params
+
+
+def ss3t_csd_beta1_cargs(
+    params: Ss3tCsdBeta1Parameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("ss3t_csd_beta1")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bzero_pct") is not None:
+        cargs.extend([
+            "-bzero_pct",
+            str(params.get("bzero_pct"))
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("niter"))
+        ])
+    if params.get("info"):
+        cargs.append("-info")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("nthreads") is not None:
+        cargs.extend([
+            "-nthreads",
+            str(params.get("nthreads"))
+        ])
+    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"):
+        cargs.append("-help")
+    if params.get("version"):
+        cargs.append("-version")
+    cargs.append(execution.input_file(params.get("dwi")))
+    cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("response_odf")] for a in c])
+    return cargs
+
+
+def ss3t_csd_beta1_outputs(
+    params: Ss3tCsdBeta1Parameters,
+    execution: Execution,
+) -> Ss3tCsdBeta1Outputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = Ss3tCsdBeta1Outputs(
+        root=execution.output_file("."),
+        response_odf=[dyn_outputs(i["__STYXTYPE__"])(i, execution) if dyn_outputs(i["__STYXTYPE__"]) else None for i in params.get("response_odf")],
+    )
+    return ret
+
+
+def ss3t_csd_beta1_execute(
+    params: Ss3tCsdBeta1Parameters,
+    execution: Execution,
+) -> Ss3tCsdBeta1Outputs:
+    """
+    SS3T-CSD: beta 1 implementation
+    
+    * Dhollander, T. & Connelly, A. A novel iterative approach to reap the
+    benefits of multi-tissue CSD from just single-shell (+b=0) diffusion MRI
+    data. Proc Intl Soc Mag Reson Med, 2016, 3010.
+    
+    Author: MRTrix3Tissue Developers
+    
+    URL: https://3tissue.github.io/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Ss3tCsdBeta1Outputs`).
+    """
+    params = execution.params(params)
+    cargs = ss3t_csd_beta1_cargs(params, execution)
+    ret = ss3t_csd_beta1_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def ss3t_csd_beta1(
+    dwi: InputPathType,
+    response_odf: list[Ss3tCsdBeta1ResponseOdfParameters],
+    mask: InputPathType | None = None,
+    bzero_pct: float | None = None,
+    niter: int | None = None,
+    info: bool = False,
+    quiet: bool = False,
+    debug: bool = False,
+    force: bool = False,
+    nthreads: int | None = None,
+    config: list[Ss3tCsdBeta1ConfigParameters] | None = None,
+    help_: bool = False,
+    version: bool = False,
+    runner: Runner | None = None,
+) -> Ss3tCsdBeta1Outputs:
+    """
+    SS3T-CSD: beta 1 implementation
+    
+    * Dhollander, T. & Connelly, A. A novel iterative approach to reap the
+    benefits of multi-tissue CSD from just single-shell (+b=0) diffusion MRI
+    data. Proc Intl Soc Mag Reson Med, 2016, 3010.
+    
+    Author: MRTrix3Tissue Developers
+    
+    URL: https://3tissue.github.io/
+    
+    Args:
+        dwi: the input diffusion-weighted image.
+        response_odf: pairs of input tissue response and output ODF images.
+        mask: only perform computation within the specified binary brain mask\
+            image.
+        bzero_pct: the threshold below which the amplitude of the FOD is\
+            assumed to be zero, expressed as an absolute amplitude (default = 0).
+        niter: the maximum number of iterations to perform for each voxel\
+            (default = 50). Use '-niter 0' for a linear unconstrained spherical\
+            deconvolution.
+        info: display information messages.
+        quiet: do not display information messages or progress status;\
+            alternatively, this can be achieved by setting the MRTRIX_QUIET\
+            environment variable to a non-empty string.
+        debug: display debugging messages.
+        force: force overwrite of output files (caution: using the same file as\
+            input and output might cause unexpected behaviour).
+        nthreads: use this number of threads in multi-threaded applications\
+            (set to 0 to disable multi-threading).
+        config: temporarily set the value of an MRtrix config file entry.
+        help_: display this information page and exit.
+        version: display version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Ss3tCsdBeta1Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SS3T_CSD_BETA1_METADATA)
+    params = ss3t_csd_beta1_params(
+        mask=mask,
+        bzero_pct=bzero_pct,
+        niter=niter,
+        info=info,
+        quiet=quiet,
+        debug=debug,
+        force=force,
+        nthreads=nthreads,
+        config=config,
+        help_=help_,
+        version=version,
+        dwi=dwi,
+        response_odf=response_odf,
+    )
+    return ss3t_csd_beta1_execute(params, execution)
+
+
+__all__ = [
+    "SS3T_CSD_BETA1_METADATA",
+    "Ss3tCsdBeta1ConfigParameters",
+    "Ss3tCsdBeta1Outputs",
+    "Ss3tCsdBeta1Parameters",
+    "Ss3tCsdBeta1ResponseOdfOutputs",
+    "Ss3tCsdBeta1ResponseOdfParameters",
+    "ss3t_csd_beta1",
+    "ss3t_csd_beta1_config_params",
+    "ss3t_csd_beta1_params",
+    "ss3t_csd_beta1_response_odf_params",
+]