niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mvm.py

@@ -0,0 +1,359 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MVM_METADATA = Metadata(
+    id="f66a98f269fed22500c7f8aa62cd43c5d51fda61.boutiques",
+    name="3dMVM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMvmParameters = typing.TypedDict('V3dMvmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMVM"],
+    "dbgArgs": typing.NotRequired[str | None],
+    "prefix": str,
+    "jobs": typing.NotRequired[int | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bsVars": str,
+    "wsVars": typing.NotRequired[str | None],
+    "qVars": typing.NotRequired[str | None],
+    "qVarCenters": typing.NotRequired[str | None],
+    "num_glt": typing.NotRequired[int | None],
+    "gltLabel": typing.NotRequired[str | None],
+    "gltCode": typing.NotRequired[str | None],
+    "num_glf": typing.NotRequired[int | None],
+    "glfLabel": typing.NotRequired[str | None],
+    "glfCode": typing.NotRequired[str | None],
+    "dataTable": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMVM": v_3d_mvm_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 {
+        "3dMVM": v_3d_mvm_outputs,
+    }.get(t)
+
+
+class V3dMvmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mvm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile_head: OutputPathType
+    """Output HEAD file in AFNI format"""
+    outfile_brik: OutputPathType
+    """Output BRIK file in AFNI format"""
+
+
+def v_3d_mvm_params(
+    prefix: str,
+    bs_vars: str,
+    data_table: str,
+    dbg_args: str | None = None,
+    jobs: int | None = None,
+    mask: InputPathType | None = None,
+    ws_vars: str | None = None,
+    q_vars: str | None = None,
+    q_var_centers: str | None = None,
+    num_glt: int | None = None,
+    glt_label: str | None = None,
+    glt_code: str | None = None,
+    num_glf: int | None = None,
+    glf_label: str | None = None,
+    glf_code: str | None = None,
+) -> V3dMvmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file name prefix.
+        bs_vars: Formula for between-subjects variables.
+        data_table: Data table for analysis.
+        dbg_args: Enable R to save parameters in a file for debugging.
+        jobs: Number of jobs for parallel processing.
+        mask: Only process voxels inside this mask.
+        ws_vars: Formula for within-subjects variables.
+        q_vars: Comma-separated list of quantitative variables (covariates).
+        q_var_centers: Comma-separated centering values for quantitative\
+            variables.
+        num_glt: Number of general linear t-tests (GLTs).
+        glt_label: Label for each general linear t-test (GLT).
+        glt_code: Coding for each general linear t-test (GLT).
+        num_glf: Number of general linear F-tests (GLFs).
+        glf_label: Label for each general linear F-test (GLF).
+        glf_code: Coding for each general linear F-test (GLF).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMVM",
+        "prefix": prefix,
+        "bsVars": bs_vars,
+        "dataTable": data_table,
+    }
+    if dbg_args is not None:
+        params["dbgArgs"] = dbg_args
+    if jobs is not None:
+        params["jobs"] = jobs
+    if mask is not None:
+        params["mask"] = mask
+    if ws_vars is not None:
+        params["wsVars"] = ws_vars
+    if q_vars is not None:
+        params["qVars"] = q_vars
+    if q_var_centers is not None:
+        params["qVarCenters"] = q_var_centers
+    if num_glt is not None:
+        params["num_glt"] = num_glt
+    if glt_label is not None:
+        params["gltLabel"] = glt_label
+    if glt_code is not None:
+        params["gltCode"] = glt_code
+    if num_glf is not None:
+        params["num_glf"] = num_glf
+    if glf_label is not None:
+        params["glfLabel"] = glf_label
+    if glf_code is not None:
+        params["glfCode"] = glf_code
+    return params
+
+
+def v_3d_mvm_cargs(
+    params: V3dMvmParameters,
+    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("3dMVM")
+    if params.get("dbgArgs") is not None:
+        cargs.append(params.get("dbgArgs"))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.extend([
+        "-bsVars",
+        params.get("bsVars")
+    ])
+    if params.get("wsVars") is not None:
+        cargs.extend([
+            "-wsVars",
+            params.get("wsVars")
+        ])
+    if params.get("qVars") is not None:
+        cargs.extend([
+            "-qVars",
+            params.get("qVars")
+        ])
+    if params.get("qVarCenters") is not None:
+        cargs.extend([
+            "-qVarCenters",
+            params.get("qVarCenters")
+        ])
+    if params.get("num_glt") is not None:
+        cargs.extend([
+            "-num_glt",
+            str(params.get("num_glt"))
+        ])
+    if params.get("gltLabel") is not None:
+        cargs.extend([
+            "-gltLabel",
+            params.get("gltLabel")
+        ])
+    if params.get("gltCode") is not None:
+        cargs.extend([
+            "-gltCode",
+            params.get("gltCode")
+        ])
+    if params.get("num_glf") is not None:
+        cargs.extend([
+            "-num_glf",
+            str(params.get("num_glf"))
+        ])
+    if params.get("glfLabel") is not None:
+        cargs.extend([
+            "-glfLabel",
+            params.get("glfLabel")
+        ])
+    if params.get("glfCode") is not None:
+        cargs.extend([
+            "-glfCode",
+            params.get("glfCode")
+        ])
+    cargs.extend([
+        "-dataTable",
+        params.get("dataTable")
+    ])
+    return cargs
+
+
+def v_3d_mvm_outputs(
+    params: V3dMvmParameters,
+    execution: Execution,
+) -> V3dMvmOutputs:
+    """
+    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 = V3dMvmOutputs(
+        root=execution.output_file("."),
+        outfile_head=execution.output_file(params.get("prefix") + "+tlrc.HEAD"),
+        outfile_brik=execution.output_file(params.get("prefix") + "+tlrc.BRIK"),
+    )
+    return ret
+
+
+def v_3d_mvm_execute(
+    params: V3dMvmParameters,
+    execution: Execution,
+) -> V3dMvmOutputs:
+    """
+    AFNI Group Analysis Program with Multi-Variate Modeling Approach.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMvmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mvm_cargs(params, execution)
+    ret = v_3d_mvm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mvm(
+    prefix: str,
+    bs_vars: str,
+    data_table: str,
+    dbg_args: str | None = None,
+    jobs: int | None = None,
+    mask: InputPathType | None = None,
+    ws_vars: str | None = None,
+    q_vars: str | None = None,
+    q_var_centers: str | None = None,
+    num_glt: int | None = None,
+    glt_label: str | None = None,
+    glt_code: str | None = None,
+    num_glf: int | None = None,
+    glf_label: str | None = None,
+    glf_code: str | None = None,
+    runner: Runner | None = None,
+) -> V3dMvmOutputs:
+    """
+    AFNI Group Analysis Program with Multi-Variate Modeling Approach.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file name prefix.
+        bs_vars: Formula for between-subjects variables.
+        data_table: Data table for analysis.
+        dbg_args: Enable R to save parameters in a file for debugging.
+        jobs: Number of jobs for parallel processing.
+        mask: Only process voxels inside this mask.
+        ws_vars: Formula for within-subjects variables.
+        q_vars: Comma-separated list of quantitative variables (covariates).
+        q_var_centers: Comma-separated centering values for quantitative\
+            variables.
+        num_glt: Number of general linear t-tests (GLTs).
+        glt_label: Label for each general linear t-test (GLT).
+        glt_code: Coding for each general linear t-test (GLT).
+        num_glf: Number of general linear F-tests (GLFs).
+        glf_label: Label for each general linear F-test (GLF).
+        glf_code: Coding for each general linear F-test (GLF).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMvmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MVM_METADATA)
+    params = v_3d_mvm_params(
+        dbg_args=dbg_args,
+        prefix=prefix,
+        jobs=jobs,
+        mask=mask,
+        bs_vars=bs_vars,
+        ws_vars=ws_vars,
+        q_vars=q_vars,
+        q_var_centers=q_var_centers,
+        num_glt=num_glt,
+        glt_label=glt_label,
+        glt_code=glt_code,
+        num_glf=num_glf,
+        glf_label=glf_label,
+        glf_code=glf_code,
+        data_table=data_table,
+    )
+    return v_3d_mvm_execute(params, execution)
+
+
+__all__ = [
+    "V3dMvmOutputs",
+    "V3dMvmParameters",
+    "V_3D_MVM_METADATA",
+    "v_3d_mvm",
+    "v_3d_mvm_params",
+]

niwrap_afni/afni/v_3d_mvm_validator.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MVM_VALIDATOR_METADATA = Metadata(
+    id="922fe2d0a794693ed3858b8e880aa7f811995c48.boutiques",
+    name="3dMVM_validator",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMvmValidatorParameters = typing.TypedDict('V3dMvmValidatorParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMVM_validator"],
+    "datatable": InputPathType,
+    "shinyfolder": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMVM_validator": v_3d_mvm_validator_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 {
+        "3dMVM_validator": v_3d_mvm_validator_outputs,
+    }.get(t)
+
+
+class V3dMvmValidatorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mvm_validator(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    temp_folder: OutputPathType
+    """Temporary folder created during the shiny app session."""
+
+
+def v_3d_mvm_validator_params(
+    datatable: InputPathType,
+    shinyfolder: str | None = None,
+) -> V3dMvmValidatorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datatable: A file containing a data table formatted like the 3dMVM\
+            "-dataTable".
+        shinyfolder: Use a custom shiny folder (for testing purposes).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMVM_validator",
+        "datatable": datatable,
+    }
+    if shinyfolder is not None:
+        params["shinyfolder"] = shinyfolder
+    return params
+
+
+def v_3d_mvm_validator_cargs(
+    params: V3dMvmValidatorParameters,
+    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("3dMVM_validator")
+    cargs.append(execution.input_file(params.get("datatable")))
+    if params.get("shinyfolder") is not None:
+        cargs.extend([
+            "-ShinyFolder",
+            params.get("shinyfolder")
+        ])
+    return cargs
+
+
+def v_3d_mvm_validator_outputs(
+    params: V3dMvmValidatorParameters,
+    execution: Execution,
+) -> V3dMvmValidatorOutputs:
+    """
+    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 = V3dMvmValidatorOutputs(
+        root=execution.output_file("."),
+        temp_folder=execution.output_file("__*_3dMVM_validator_temp_delete"),
+    )
+    return ret
+
+
+def v_3d_mvm_validator_execute(
+    params: V3dMvmValidatorParameters,
+    execution: Execution,
+) -> V3dMvmValidatorOutputs:
+    """
+    Launch the 3dMVM model validation shiny app in a web browser.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMvmValidatorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mvm_validator_cargs(params, execution)
+    ret = v_3d_mvm_validator_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mvm_validator(
+    datatable: InputPathType,
+    shinyfolder: str | None = None,
+    runner: Runner | None = None,
+) -> V3dMvmValidatorOutputs:
+    """
+    Launch the 3dMVM model validation shiny app in a web browser.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datatable: A file containing a data table formatted like the 3dMVM\
+            "-dataTable".
+        shinyfolder: Use a custom shiny folder (for testing purposes).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMvmValidatorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MVM_VALIDATOR_METADATA)
+    params = v_3d_mvm_validator_params(
+        datatable=datatable,
+        shinyfolder=shinyfolder,
+    )
+    return v_3d_mvm_validator_execute(params, execution)
+
+
+__all__ = [
+    "V3dMvmValidatorOutputs",
+    "V3dMvmValidatorParameters",
+    "V_3D_MVM_VALIDATOR_METADATA",
+    "v_3d_mvm_validator",
+    "v_3d_mvm_validator_params",
+]