niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__suma_fsvol_to_brik.py

@@ -0,0 +1,189 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_FSVOL_TO_BRIK_METADATA = Metadata(
+    id="34a251de0c81f7f2fc2da3a56752e5c868f22a46.boutiques",
+    name="@SUMA_FSvolToBRIK",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaFsvolToBrikParameters = typing.TypedDict('VSumaFsvolToBrikParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_FSvolToBRIK"],
+    "fs_vol_data": InputPathType,
+    "prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_FSvolToBRIK": v__suma_fsvol_to_brik_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 {
+        "@SUMA_FSvolToBRIK": v__suma_fsvol_to_brik_outputs,
+    }.get(t)
+
+
+class VSumaFsvolToBrikOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_fsvol_to_brik(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_brik: OutputPathType
+    """Output BRIK volume converted from FreeSurfer data"""
+    out_head: OutputPathType
+    """Header file for the output BRIK volume"""
+
+
+def v__suma_fsvol_to_brik_params(
+    fs_vol_data: InputPathType,
+    prefix: str,
+) -> VSumaFsvolToBrikParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fs_vol_data: Input FreeSurfer volume data (e.g. COR- images or .mgz\
+            volume).
+        prefix: Prefix for output BRIK volume.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_FSvolToBRIK",
+        "fs_vol_data": fs_vol_data,
+        "prefix": prefix,
+    }
+    return params
+
+
+def v__suma_fsvol_to_brik_cargs(
+    params: VSumaFsvolToBrikParameters,
+    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("@SUMA_FSvolToBRIK")
+    cargs.append(execution.input_file(params.get("fs_vol_data")))
+    cargs.append(params.get("prefix"))
+    return cargs
+
+
+def v__suma_fsvol_to_brik_outputs(
+    params: VSumaFsvolToBrikParameters,
+    execution: Execution,
+) -> VSumaFsvolToBrikOutputs:
+    """
+    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 = VSumaFsvolToBrikOutputs(
+        root=execution.output_file("."),
+        out_brik=execution.output_file(params.get("prefix") + ".BRIK"),
+        out_head=execution.output_file(params.get("prefix") + ".HEAD"),
+    )
+    return ret
+
+
+def v__suma_fsvol_to_brik_execute(
+    params: VSumaFsvolToBrikParameters,
+    execution: Execution,
+) -> VSumaFsvolToBrikOutputs:
+    """
+    A script to convert COR- or .mgz files from FreeSurfer to BRIK format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaFsvolToBrikOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_fsvol_to_brik_cargs(params, execution)
+    ret = v__suma_fsvol_to_brik_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_fsvol_to_brik(
+    fs_vol_data: InputPathType,
+    prefix: str,
+    runner: Runner | None = None,
+) -> VSumaFsvolToBrikOutputs:
+    """
+    A script to convert COR- or .mgz files from FreeSurfer to BRIK format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        fs_vol_data: Input FreeSurfer volume data (e.g. COR- images or .mgz\
+            volume).
+        prefix: Prefix for output BRIK volume.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaFsvolToBrikOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_FSVOL_TO_BRIK_METADATA)
+    params = v__suma_fsvol_to_brik_params(
+        fs_vol_data=fs_vol_data,
+        prefix=prefix,
+    )
+    return v__suma_fsvol_to_brik_execute(params, execution)
+
+
+__all__ = [
+    "VSumaFsvolToBrikOutputs",
+    "VSumaFsvolToBrikParameters",
+    "V__SUMA_FSVOL_TO_BRIK_METADATA",
+    "v__suma_fsvol_to_brik",
+    "v__suma_fsvol_to_brik_params",
+]

niwrap_afni/afni/v__suma_make_spec_caret.py

@@ -0,0 +1,183 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SUMA_MAKE_SPEC_CARET_METADATA = Metadata(
+    id="950a20d0f240b4840873e5b78497c9b7e5e19277.boutiques",
+    name="@SUMA_Make_Spec_Caret",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaMakeSpecCaretParameters = typing.TypedDict('VSumaMakeSpecCaretParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_Make_Spec_Caret"],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_Make_Spec_Caret": v__suma_make_spec_caret_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 {
+        "@SUMA_Make_Spec_Caret": v__suma_make_spec_caret_outputs,
+    }.get(t)
+
+
+class VSumaMakeSpecCaretOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_make_spec_caret(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    left_hemisphere_spec: OutputPathType
+    """Output spec file for the left hemisphere"""
+    right_hemisphere_spec: OutputPathType
+    """Output spec file for the right hemisphere"""
+
+
+def v__suma_make_spec_caret_params(
+    subject_id: str,
+) -> VSumaMakeSpecCaretParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Subject ID for file naming.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_Make_Spec_Caret",
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def v__suma_make_spec_caret_cargs(
+    params: VSumaMakeSpecCaretParameters,
+    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("@SUMA_Make_Spec_Caret")
+    cargs.append("[OPTIONS]")
+    cargs.extend([
+        "-sid",
+        params.get("subject_id")
+    ])
+    return cargs
+
+
+def v__suma_make_spec_caret_outputs(
+    params: VSumaMakeSpecCaretParameters,
+    execution: Execution,
+) -> VSumaMakeSpecCaretOutputs:
+    """
+    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 = VSumaMakeSpecCaretOutputs(
+        root=execution.output_file("."),
+        left_hemisphere_spec=execution.output_file(params.get("subject_id") + "_lh.spec"),
+        right_hemisphere_spec=execution.output_file(params.get("subject_id") + "_rh.spec"),
+    )
+    return ret
+
+
+def v__suma_make_spec_caret_execute(
+    params: VSumaMakeSpecCaretParameters,
+    execution: Execution,
+) -> VSumaMakeSpecCaretOutputs:
+    """
+    Prepare surfaces for viewing in SUMA, tested with Caret-5.2 surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecCaretOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_make_spec_caret_cargs(params, execution)
+    ret = v__suma_make_spec_caret_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_make_spec_caret(
+    subject_id: str,
+    runner: Runner | None = None,
+) -> VSumaMakeSpecCaretOutputs:
+    """
+    Prepare surfaces for viewing in SUMA, tested with Caret-5.2 surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        subject_id: Subject ID for file naming.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecCaretOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_CARET_METADATA)
+    params = v__suma_make_spec_caret_params(
+        subject_id=subject_id,
+    )
+    return v__suma_make_spec_caret_execute(params, execution)
+
+
+__all__ = [
+    "VSumaMakeSpecCaretOutputs",
+    "VSumaMakeSpecCaretParameters",
+    "V__SUMA_MAKE_SPEC_CARET_METADATA",
+    "v__suma_make_spec_caret",
+    "v__suma_make_spec_caret_params",
+]

niwrap_afni/afni/v__suma_make_spec_fs.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__SUMA_MAKE_SPEC_FS_METADATA = Metadata(
+    id="35abec1cbcc0a7c9a8b395b5a4855788850c3f95.boutiques",
+    name="@SUMA_Make_Spec_FS",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSumaMakeSpecFsParameters = typing.TypedDict('VSumaMakeSpecFsParameters', {
+    "__STYX_TYPE__": typing.Literal["@SUMA_Make_Spec_FS"],
+    "subject_id": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SUMA_Make_Spec_FS": v__suma_make_spec_fs_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 {
+        "@SUMA_Make_Spec_FS": v__suma_make_spec_fs_outputs,
+    }.get(t)
+
+
+class VSumaMakeSpecFsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__suma_make_spec_fs(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    suma_output: OutputPathType
+    """All created files are stored in a new SUMA directory"""
+
+
+def v__suma_make_spec_fs_params(
+    subject_id: str,
+) -> VSumaMakeSpecFsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        subject_id: Required subject ID for file naming.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SUMA_Make_Spec_FS",
+        "subject_id": subject_id,
+    }
+    return params
+
+
+def v__suma_make_spec_fs_cargs(
+    params: VSumaMakeSpecFsParameters,
+    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("@SUMA_Make_Spec_FS")
+    cargs.append("[OPTIONS]")
+    cargs.extend([
+        "-sid",
+        params.get("subject_id")
+    ])
+    return cargs
+
+
+def v__suma_make_spec_fs_outputs(
+    params: VSumaMakeSpecFsParameters,
+    execution: Execution,
+) -> VSumaMakeSpecFsOutputs:
+    """
+    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 = VSumaMakeSpecFsOutputs(
+        root=execution.output_file("."),
+        suma_output=execution.output_file("SUMA/*"),
+    )
+    return ret
+
+
+def v__suma_make_spec_fs_execute(
+    params: VSumaMakeSpecFsParameters,
+    execution: Execution,
+) -> VSumaMakeSpecFsOutputs:
+    """
+    Prepare for surface viewing in SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecFsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__suma_make_spec_fs_cargs(params, execution)
+    ret = v__suma_make_spec_fs_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__suma_make_spec_fs(
+    subject_id: str,
+    runner: Runner | None = None,
+) -> VSumaMakeSpecFsOutputs:
+    """
+    Prepare for surface viewing in SUMA.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        subject_id: Required subject ID for file naming.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSumaMakeSpecFsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_FS_METADATA)
+    params = v__suma_make_spec_fs_params(
+        subject_id=subject_id,
+    )
+    return v__suma_make_spec_fs_execute(params, execution)
+
+
+__all__ = [
+    "VSumaMakeSpecFsOutputs",
+    "VSumaMakeSpecFsParameters",
+    "V__SUMA_MAKE_SPEC_FS_METADATA",
+    "v__suma_make_spec_fs",
+    "v__suma_make_spec_fs_params",
+]