niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__afni_refacer_make_master.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_REFACER_MAKE_MASTER_METADATA = Metadata(
+    id="5d171c695cab39d1411b8652cb05c15ab1caaa20.boutiques",
+    name="@afni_refacer_make_master",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniRefacerMakeMasterParameters = typing.TypedDict('VAfniRefacerMakeMasterParameters', {
+    "__STYX_TYPE__": typing.Literal["@afni_refacer_make_master"],
+    "input_datasets": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@afni_refacer_make_master": v__afni_refacer_make_master_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 {
+        "@afni_refacer_make_master": v__afni_refacer_make_master_outputs,
+    }.get(t)
+
+
+class VAfniRefacerMakeMasterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_refacer_make_master(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_shell_dataset: OutputPathType
+    """Output dataset containing the average 'face' (non-brain tissue)."""
+
+
+def v__afni_refacer_make_master_params(
+    input_datasets: list[InputPathType],
+) -> VAfniRefacerMakeMasterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_datasets: List of T1-weighted datasets that have NOT been\
+            skull-stripped, defaced, or refaced.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@afni_refacer_make_master",
+        "input_datasets": input_datasets,
+    }
+    return params
+
+
+def v__afni_refacer_make_master_cargs(
+    params: VAfniRefacerMakeMasterParameters,
+    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("@afni_refacer_make_master")
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    return cargs
+
+
+def v__afni_refacer_make_master_outputs(
+    params: VAfniRefacerMakeMasterParameters,
+    execution: Execution,
+) -> VAfniRefacerMakeMasterOutputs:
+    """
+    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 = VAfniRefacerMakeMasterOutputs(
+        root=execution.output_file("."),
+        output_shell_dataset=execution.output_file("afni_refacer_shell.nii.gz"),
+    )
+    return ret
+
+
+def v__afni_refacer_make_master_execute(
+    params: VAfniRefacerMakeMasterParameters,
+    execution: Execution,
+) -> VAfniRefacerMakeMasterOutputs:
+    """
+    This script makes a new mask/shell dataset for use with @afni_refacer_run by
+    averaging 'faces' (non-brain tissue) from input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerMakeMasterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_refacer_make_master_cargs(params, execution)
+    ret = v__afni_refacer_make_master_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_refacer_make_master(
+    input_datasets: list[InputPathType],
+    runner: Runner | None = None,
+) -> VAfniRefacerMakeMasterOutputs:
+    """
+    This script makes a new mask/shell dataset for use with @afni_refacer_run by
+    averaging 'faces' (non-brain tissue) from input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_datasets: List of T1-weighted datasets that have NOT been\
+            skull-stripped, defaced, or refaced.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerMakeMasterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_MAKE_MASTER_METADATA)
+    params = v__afni_refacer_make_master_params(
+        input_datasets=input_datasets,
+    )
+    return v__afni_refacer_make_master_execute(params, execution)
+
+
+__all__ = [
+    "VAfniRefacerMakeMasterOutputs",
+    "VAfniRefacerMakeMasterParameters",
+    "V__AFNI_REFACER_MAKE_MASTER_METADATA",
+    "v__afni_refacer_make_master",
+    "v__afni_refacer_make_master_params",
+]

niwrap_afni/afni/v__afni_refacer_make_onebig_a12.py

@@ -0,0 +1,178 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA = Metadata(
+    id="9bef1fa50af4572410be32739de25ad17fe8544e.boutiques",
+    name="@afni_refacer_make_onebigA12",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniRefacerMakeOnebigA12Parameters = typing.TypedDict('VAfniRefacerMakeOnebigA12Parameters', {
+    "__STYX_TYPE__": typing.Literal["@afni_refacer_make_onebigA12"],
+    "t1w_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@afni_refacer_make_onebigA12": v__afni_refacer_make_onebig_a12_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 {
+        "@afni_refacer_make_onebigA12": v__afni_refacer_make_onebig_a12_outputs,
+    }.get(t)
+
+
+class VAfniRefacerMakeOnebigA12Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_refacer_make_onebig_a12(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    aligned_output: OutputPathType
+    """Aligned T1w dataset to MNI template with expanded 'big' grid"""
+
+
+def v__afni_refacer_make_onebig_a12_params(
+    t1w_dataset: InputPathType,
+) -> VAfniRefacerMakeOnebigA12Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1w_dataset: Input T1w dataset name.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@afni_refacer_make_onebigA12",
+        "t1w_dataset": t1w_dataset,
+    }
+    return params
+
+
+def v__afni_refacer_make_onebig_a12_cargs(
+    params: VAfniRefacerMakeOnebigA12Parameters,
+    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("@afni_refacer_make_onebigA12")
+    cargs.append(execution.input_file(params.get("t1w_dataset")))
+    return cargs
+
+
+def v__afni_refacer_make_onebig_a12_outputs(
+    params: VAfniRefacerMakeOnebigA12Parameters,
+    execution: Execution,
+) -> VAfniRefacerMakeOnebigA12Outputs:
+    """
+    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 = VAfniRefacerMakeOnebigA12Outputs(
+        root=execution.output_file("."),
+        aligned_output=execution.output_file(pathlib.Path(params.get("t1w_dataset")).name + "_aligned_to_MNI.nii.gz"),
+    )
+    return ret
+
+
+def v__afni_refacer_make_onebig_a12_execute(
+    params: VAfniRefacerMakeOnebigA12Parameters,
+    execution: Execution,
+) -> VAfniRefacerMakeOnebigA12Outputs:
+    """
+    Script to align a single T1w dataset to the MNI template and expand it to a
+    'big' grid.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerMakeOnebigA12Outputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_refacer_make_onebig_a12_cargs(params, execution)
+    ret = v__afni_refacer_make_onebig_a12_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_refacer_make_onebig_a12(
+    t1w_dataset: InputPathType,
+    runner: Runner | None = None,
+) -> VAfniRefacerMakeOnebigA12Outputs:
+    """
+    Script to align a single T1w dataset to the MNI template and expand it to a
+    'big' grid.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        t1w_dataset: Input T1w dataset name.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerMakeOnebigA12Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA)
+    params = v__afni_refacer_make_onebig_a12_params(
+        t1w_dataset=t1w_dataset,
+    )
+    return v__afni_refacer_make_onebig_a12_execute(params, execution)
+
+
+__all__ = [
+    "VAfniRefacerMakeOnebigA12Outputs",
+    "VAfniRefacerMakeOnebigA12Parameters",
+    "V__AFNI_REFACER_MAKE_ONEBIG_A12_METADATA",
+    "v__afni_refacer_make_onebig_a12",
+    "v__afni_refacer_make_onebig_a12_params",
+]

niwrap_afni/afni/v__afni_refacer_run.py

@@ -0,0 +1,304 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__AFNI_REFACER_RUN_METADATA = Metadata(
+    id="72757fe4907642f44cb063cfa3ee5dc5dda0045b.boutiques",
+    name="@afni_refacer_run",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VAfniRefacerRunParameters = typing.TypedDict('VAfniRefacerRunParameters', {
+    "__STYX_TYPE__": typing.Literal["@afni_refacer_run"],
+    "input_file": InputPathType,
+    "mode_all": bool,
+    "prefix": str,
+    "anonymize_output": bool,
+    "cost_function": typing.NotRequired[str | None],
+    "shell_option": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "no_images": bool,
+    "overwrite": bool,
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@afni_refacer_run": v__afni_refacer_run_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 {
+        "@afni_refacer_run": v__afni_refacer_run_outputs,
+    }.get(t)
+
+
+class VAfniRefacerRunOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__afni_refacer_run(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_deface: OutputPathType
+    """Defaced volume (face+ears replaced with zeros)"""
+    output_reface: OutputPathType
+    """Refaced volume (face+ears replaced with artificial values)"""
+    output_reface_plus: OutputPathType
+    """Reface_plused volume (face+ears+skull replaced with artificial values)"""
+    output_face: OutputPathType
+    """Face+ears used to replace or remove subject data"""
+    output_face_plus: OutputPathType
+    """Face+ears+skull used to replace subject data"""
+
+
+def v__afni_refacer_run_params(
+    input_file: InputPathType,
+    prefix: str,
+    mode_all: bool = False,
+    anonymize_output: bool = False,
+    cost_function: str | None = None,
+    shell_option: str | None = None,
+    no_clean: bool = False,
+    no_images: bool = False,
+    overwrite: bool = False,
+    verbose: bool = False,
+) -> VAfniRefacerRunParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Name of input dataset; can contain path information.
+        prefix: Name of output dataset.
+        mode_all: Output three volumes: one defaced, one refaced and one\
+            reface_plused.
+        anonymize_output: Use 3drefit and nifti_tool to anonymize the output\
+            datasets.
+        cost_function: Specify any cost function that is allowed by 3dAllineate\
+            (default: lpa).
+        shell_option: Specify which shell to use. Options:\
+            afni_refacer_shell_sym_1.0.nii.gz (traditional),\
+            afni_refacer_shell_sym_2.0.nii.gz (more face/neck removal). Default:\
+            afni_refacer_shell_sym_1.0.nii.gz.
+        no_clean: Don't delete temp working directory (default: remove working\
+            directory).
+        no_images: Don't make pretty images to automatically view the results\
+            of re/defacing.
+        overwrite: Final two file outputs will overwrite any existing files of\
+            the same name (default: don't do this). NB: this option does not apply\
+            to the working directory.
+        verbose: Run the 3dAllineate part herein with '-verb' (for verbosity).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@afni_refacer_run",
+        "input_file": input_file,
+        "mode_all": mode_all,
+        "prefix": prefix,
+        "anonymize_output": anonymize_output,
+        "no_clean": no_clean,
+        "no_images": no_images,
+        "overwrite": overwrite,
+        "verbose": verbose,
+    }
+    if cost_function is not None:
+        params["cost_function"] = cost_function
+    if shell_option is not None:
+        params["shell_option"] = shell_option
+    return params
+
+
+def v__afni_refacer_run_cargs(
+    params: VAfniRefacerRunParameters,
+    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("@afni_refacer_run")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("mode_all"):
+        cargs.append("-mode_all")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("anonymize_output"):
+        cargs.append("-anonymize_output")
+    if params.get("cost_function") is not None:
+        cargs.extend([
+            "-cost",
+            params.get("cost_function")
+        ])
+    if params.get("shell_option") is not None:
+        cargs.extend([
+            "-shell",
+            params.get("shell_option")
+        ])
+    if params.get("no_clean"):
+        cargs.append("-no_clean")
+    if params.get("no_images"):
+        cargs.append("-no_images")
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("verbose"):
+        cargs.append("-verb_allin")
+    return cargs
+
+
+def v__afni_refacer_run_outputs(
+    params: VAfniRefacerRunParameters,
+    execution: Execution,
+) -> VAfniRefacerRunOutputs:
+    """
+    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 = VAfniRefacerRunOutputs(
+        root=execution.output_file("."),
+        output_deface=execution.output_file(params.get("prefix") + ".deface.nii.gz"),
+        output_reface=execution.output_file(params.get("prefix") + ".reface.nii.gz"),
+        output_reface_plus=execution.output_file(params.get("prefix") + ".reface_plus.nii.gz"),
+        output_face=execution.output_file(params.get("prefix") + ".face.nii.gz"),
+        output_face_plus=execution.output_file(params.get("prefix") + ".face_plus.nii.gz"),
+    )
+    return ret
+
+
+def v__afni_refacer_run_execute(
+    params: VAfniRefacerRunParameters,
+    execution: Execution,
+) -> VAfniRefacerRunOutputs:
+    """
+    This script re-faces one input dataset, using a master shell dataset to write
+    over the subject's 'face' region.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerRunOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__afni_refacer_run_cargs(params, execution)
+    ret = v__afni_refacer_run_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__afni_refacer_run(
+    input_file: InputPathType,
+    prefix: str,
+    mode_all: bool = False,
+    anonymize_output: bool = False,
+    cost_function: str | None = None,
+    shell_option: str | None = None,
+    no_clean: bool = False,
+    no_images: bool = False,
+    overwrite: bool = False,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> VAfniRefacerRunOutputs:
+    """
+    This script re-faces one input dataset, using a master shell dataset to write
+    over the subject's 'face' region.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Name of input dataset; can contain path information.
+        prefix: Name of output dataset.
+        mode_all: Output three volumes: one defaced, one refaced and one\
+            reface_plused.
+        anonymize_output: Use 3drefit and nifti_tool to anonymize the output\
+            datasets.
+        cost_function: Specify any cost function that is allowed by 3dAllineate\
+            (default: lpa).
+        shell_option: Specify which shell to use. Options:\
+            afni_refacer_shell_sym_1.0.nii.gz (traditional),\
+            afni_refacer_shell_sym_2.0.nii.gz (more face/neck removal). Default:\
+            afni_refacer_shell_sym_1.0.nii.gz.
+        no_clean: Don't delete temp working directory (default: remove working\
+            directory).
+        no_images: Don't make pretty images to automatically view the results\
+            of re/defacing.
+        overwrite: Final two file outputs will overwrite any existing files of\
+            the same name (default: don't do this). NB: this option does not apply\
+            to the working directory.
+        verbose: Run the 3dAllineate part herein with '-verb' (for verbosity).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VAfniRefacerRunOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AFNI_REFACER_RUN_METADATA)
+    params = v__afni_refacer_run_params(
+        input_file=input_file,
+        mode_all=mode_all,
+        prefix=prefix,
+        anonymize_output=anonymize_output,
+        cost_function=cost_function,
+        shell_option=shell_option,
+        no_clean=no_clean,
+        no_images=no_images,
+        overwrite=overwrite,
+        verbose=verbose,
+    )
+    return v__afni_refacer_run_execute(params, execution)
+
+
+__all__ = [
+    "VAfniRefacerRunOutputs",
+    "VAfniRefacerRunParameters",
+    "V__AFNI_REFACER_RUN_METADATA",
+    "v__afni_refacer_run",
+    "v__afni_refacer_run_params",
+]