niwrap-afni 0.5.1__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_afni/afni/v_3d_mema.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEMA_METADATA = Metadata(
-    id="3e49aad2d71d54e4f942b7cc6311a0fe4225ef3f.boutiques",
+    id="706a67099d952759ecce32973deff0aa7728837d.boutiques",
     name="3dMEMA",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,33 @@ V_3D_MEMA_METADATA = Metadata(
 
 V3dMemaParameters = typing.TypedDict('V3dMemaParameters', {
     "__STYX_TYPE__": typing.Literal["3dMEMA"],
+    "prefix": str,
+    "jobs": typing.NotRequired[float | None],
+    "set": list[str],
+    "covariates": typing.NotRequired[InputPathType | None],
+    "covariates_center": typing.NotRequired[str | None],
+    "covariates_model": typing.NotRequired[str | None],
+    "covariates_name": typing.NotRequired[list[str] | None],
+    "groups": typing.NotRequired[list[str] | None],
+    "cio": bool,
+    "HKtest": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "max_zeros": typing.NotRequired[float | None],
+    "missing_data": typing.NotRequired[list[str] | None],
+    "model_outliers": bool,
+    "n_nonzero": typing.NotRequired[float | None],
+    "no_HKtest": bool,
+    "no_model_outliers": bool,
+    "no_residual_Z": bool,
+    "residual_Z": bool,
+    "Rio": bool,
+    "equal_variance": bool,
+    "unequal_variance": bool,
+    "verb": typing.NotRequired[float | None],
+    "dbgArgs": bool,
+    "help": bool,
+    "conditions": typing.NotRequired[list[str] | None],
+    "no_tstat": bool,
 })
 
 
@@ -61,17 +88,112 @@ class V3dMemaOutputs(typing.NamedTuple):
 
 
 def v_3d_mema_params(
+    prefix: str,
+    set_: list[str],
+    jobs: float | None = None,
+    covariates: InputPathType | None = None,
+    covariates_center: str | None = None,
+    covariates_model: str | None = None,
+    covariates_name: list[str] | None = None,
+    groups: list[str] | None = None,
+    cio: bool = False,
+    hktest: bool = False,
+    mask: InputPathType | None = None,
+    max_zeros: float | None = None,
+    missing_data: list[str] | None = None,
+    model_outliers: bool = False,
+    n_nonzero: float | None = None,
+    no_hktest: bool = False,
+    no_model_outliers: bool = False,
+    no_residual_z: bool = False,
+    residual_z: bool = False,
+    rio: bool = False,
+    equal_variance: bool = False,
+    unequal_variance: bool = False,
+    verb: float | None = None,
+    dbg_args: bool = False,
+    help_: bool = False,
+    conditions: list[str] | None = None,
+    no_tstat: bool = False,
 ) -> V3dMemaParameters:
     """
     Build parameters.
     
     Args:
+        prefix: Output prefix (just prefix, no view+suffix needed).
+        set_: Set data for one of the test variables.
+        jobs: Number of jobs for parallel computing.
+        covariates: Specify the name of a text file containing a table for the\
+            covariate(s).
+        covariates_center: Specify the center values for covariates.
+        covariates_model: Specify how covariates should be modeled.
+        covariates_name: Specify the name of each covariate.
+        groups: Label of groups, used for output naming.
+        cio: Use AFNI's C io functions.
+        hktest: Perform Hartung-Knapp adjustment for the output t-statistic.
+        mask: Only process voxels inside the specified mask.
+        max_zeros: Specify how many beta/t-statistics can be zero.
+        missing_data: Specify missing data handling.
+        model_outliers: Model outliers with a Laplace distribution.
+        n_nonzero: Number of non-zero beta values required.
+        no_hktest: Specify not to use Hartung-Knapp adjustment.
+        no_model_outliers: Specify not to model outliers.
+        no_residual_z: Do not output residuals and their Z values.
+        residual_z: Output residuals and their Z values.
+        rio: Use R's io functions.
+        equal_variance: Assume same cross-subjects variability between groups.
+        unequal_variance: Model cross-subject variability difference between\
+            groups.
+        verb: Specify verbosity level.
+        dbg_args: Output missing data debug file.
+        help_: Show help message.
+        conditions: Name of 1 or 2 conditions, tasks, or GLTs.
+        no_tstat: Do not compute t-statistics.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dMEMA",
+        "prefix": prefix,
+        "set": set_,
+        "cio": cio,
+        "HKtest": hktest,
+        "model_outliers": model_outliers,
+        "no_HKtest": no_hktest,
+        "no_model_outliers": no_model_outliers,
+        "no_residual_Z": no_residual_z,
+        "residual_Z": residual_z,
+        "Rio": rio,
+        "equal_variance": equal_variance,
+        "unequal_variance": unequal_variance,
+        "dbgArgs": dbg_args,
+        "help": help_,
+        "no_tstat": no_tstat,
     }
+    if jobs is not None:
+        params["jobs"] = jobs
+    if covariates is not None:
+        params["covariates"] = covariates
+    if covariates_center is not None:
+        params["covariates_center"] = covariates_center
+    if covariates_model is not None:
+        params["covariates_model"] = covariates_model
+    if covariates_name is not None:
+        params["covariates_name"] = covariates_name
+    if groups is not None:
+        params["groups"] = groups
+    if mask is not None:
+        params["mask"] = mask
+    if max_zeros is not None:
+        params["max_zeros"] = max_zeros
+    if missing_data is not None:
+        params["missing_data"] = missing_data
+    if n_nonzero is not None:
+        params["n_nonzero"] = n_nonzero
+    if verb is not None:
+        params["verb"] = verb
+    if conditions is not None:
+        params["conditions"] = conditions
     return params
 
 
@@ -90,7 +212,100 @@ def v_3d_mema_cargs(
     """
     cargs = []
     cargs.append("3dMEMA")
-    cargs.append("[OPTIONS]")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    cargs.extend([
+        "-set",
+        *params.get("set")
+    ])
+    if params.get("covariates") is not None:
+        cargs.extend([
+            "-covariates",
+            execution.input_file(params.get("covariates"))
+        ])
+    if params.get("covariates_center") is not None:
+        cargs.extend([
+            "-covariates_center",
+            params.get("covariates_center")
+        ])
+    if params.get("covariates_model") is not None:
+        cargs.extend([
+            "-covariates_model",
+            params.get("covariates_model")
+        ])
+    if params.get("covariates_name") is not None:
+        cargs.extend([
+            "-covariates_name",
+            *params.get("covariates_name")
+        ])
+    if params.get("groups") is not None:
+        cargs.extend([
+            "-groups",
+            *params.get("groups")
+        ])
+    if params.get("cio"):
+        cargs.append("-cio")
+    if params.get("HKtest"):
+        cargs.append("-HKtest")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("max_zeros") is not None:
+        cargs.extend([
+            "-max_zeros",
+            str(params.get("max_zeros"))
+        ])
+    if params.get("missing_data") is not None:
+        cargs.extend([
+            "-missing_data",
+            *params.get("missing_data")
+        ])
+    if params.get("model_outliers"):
+        cargs.append("-model_outliers")
+    if params.get("n_nonzero") is not None:
+        cargs.extend([
+            "-n_nonzero",
+            str(params.get("n_nonzero"))
+        ])
+    if params.get("no_HKtest"):
+        cargs.append("-no_HKtest")
+    if params.get("no_model_outliers"):
+        cargs.append("-no_model_outliers")
+    if params.get("no_residual_Z"):
+        cargs.append("-no_residual_Z")
+    if params.get("residual_Z"):
+        cargs.append("-residual_Z")
+    if params.get("Rio"):
+        cargs.append("-Rio")
+    if params.get("equal_variance"):
+        cargs.append("-equal_variance")
+    if params.get("unequal_variance"):
+        cargs.append("-unequal_variance")
+    if params.get("verb") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb"))
+        ])
+    if params.get("dbgArgs"):
+        cargs.append("-dbgArgs")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("conditions") is not None:
+        cargs.extend([
+            "-conditions",
+            *params.get("conditions")
+        ])
+    if params.get("no_tstat"):
+        cargs.append("-no_tstat")
     return cargs
 
 
@@ -109,7 +324,7 @@ def v_3d_mema_outputs(
     """
     ret = V3dMemaOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("[PREFIX].nii.gz"),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
     )
     return ret
 
@@ -140,6 +355,33 @@ def v_3d_mema_execute(
 
 
 def v_3d_mema(
+    prefix: str,
+    set_: list[str],
+    jobs: float | None = None,
+    covariates: InputPathType | None = None,
+    covariates_center: str | None = None,
+    covariates_model: str | None = None,
+    covariates_name: list[str] | None = None,
+    groups: list[str] | None = None,
+    cio: bool = False,
+    hktest: bool = False,
+    mask: InputPathType | None = None,
+    max_zeros: float | None = None,
+    missing_data: list[str] | None = None,
+    model_outliers: bool = False,
+    n_nonzero: float | None = None,
+    no_hktest: bool = False,
+    no_model_outliers: bool = False,
+    no_residual_z: bool = False,
+    residual_z: bool = False,
+    rio: bool = False,
+    equal_variance: bool = False,
+    unequal_variance: bool = False,
+    verb: float | None = None,
+    dbg_args: bool = False,
+    help_: bool = False,
+    conditions: list[str] | None = None,
+    no_tstat: bool = False,
     runner: Runner | None = None,
 ) -> V3dMemaOutputs:
     """
@@ -151,6 +393,35 @@ def v_3d_mema(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        prefix: Output prefix (just prefix, no view+suffix needed).
+        set_: Set data for one of the test variables.
+        jobs: Number of jobs for parallel computing.
+        covariates: Specify the name of a text file containing a table for the\
+            covariate(s).
+        covariates_center: Specify the center values for covariates.
+        covariates_model: Specify how covariates should be modeled.
+        covariates_name: Specify the name of each covariate.
+        groups: Label of groups, used for output naming.
+        cio: Use AFNI's C io functions.
+        hktest: Perform Hartung-Knapp adjustment for the output t-statistic.
+        mask: Only process voxels inside the specified mask.
+        max_zeros: Specify how many beta/t-statistics can be zero.
+        missing_data: Specify missing data handling.
+        model_outliers: Model outliers with a Laplace distribution.
+        n_nonzero: Number of non-zero beta values required.
+        no_hktest: Specify not to use Hartung-Knapp adjustment.
+        no_model_outliers: Specify not to model outliers.
+        no_residual_z: Do not output residuals and their Z values.
+        residual_z: Output residuals and their Z values.
+        rio: Use R's io functions.
+        equal_variance: Assume same cross-subjects variability between groups.
+        unequal_variance: Model cross-subject variability difference between\
+            groups.
+        verb: Specify verbosity level.
+        dbg_args: Output missing data debug file.
+        help_: Show help message.
+        conditions: Name of 1 or 2 conditions, tasks, or GLTs.
+        no_tstat: Do not compute t-statistics.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMemaOutputs`).
@@ -158,6 +429,33 @@ def v_3d_mema(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_MEMA_METADATA)
     params = v_3d_mema_params(
+        prefix=prefix,
+        jobs=jobs,
+        set_=set_,
+        covariates=covariates,
+        covariates_center=covariates_center,
+        covariates_model=covariates_model,
+        covariates_name=covariates_name,
+        groups=groups,
+        cio=cio,
+        hktest=hktest,
+        mask=mask,
+        max_zeros=max_zeros,
+        missing_data=missing_data,
+        model_outliers=model_outliers,
+        n_nonzero=n_nonzero,
+        no_hktest=no_hktest,
+        no_model_outliers=no_model_outliers,
+        no_residual_z=no_residual_z,
+        residual_z=residual_z,
+        rio=rio,
+        equal_variance=equal_variance,
+        unequal_variance=unequal_variance,
+        verb=verb,
+        dbg_args=dbg_args,
+        help_=help_,
+        conditions=conditions,
+        no_tstat=no_tstat,
     )
     return v_3d_mema_execute(params, execution)
 

niwrap_afni/afni/v_3d_mepfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEPFM_METADATA = Metadata(
-    id="44860000dde3dcae9381914d7a939fdce74cff79.boutiques",
+    id="32cebfe19ae42e608df27da2db7aceaf30da29c6.boutiques",
     name="3dMEPFM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -150,7 +150,6 @@ def v_3d_mepfm_cargs(
             "-verb",
             str(params.get("verbosity"))
         ])
-    cargs.append("[OTHER_OPTIONS]")
     return cargs