niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mvm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MVM_METADATA = Metadata(
-    id="77f08ae920d7900f854bd512d3effcbc6bc7e8b4.boutiques",
+    id="38aecb3cde564424eb11dcefd6d0694fe55948bf.boutiques",
     name="3dMVM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_MVM_METADATA = Metadata(
 
 
 V3dMvmParameters = typing.TypedDict('V3dMvmParameters', {
-    "__STYXTYPE__": typing.Literal["3dMVM"],
+    "@type": typing.NotRequired[typing.Literal["afni/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,
+})
+V3dMvmParametersTagged = typing.TypedDict('V3dMvmParametersTagged', {
+    "@type": typing.Literal["afni/3dMVM"],
     "dbgArgs": typing.NotRequired[str | None],
     "prefix": str,
     "jobs": typing.NotRequired[int | None],
@@ -31,43 +49,11 @@ V3dMvmParameters = typing.TypedDict('V3dMvmParameters', {
     "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(...)`.
+    Output object returned when calling `V3dMvmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +79,7 @@ def v_3d_mvm_params(
     num_glf: int | None = None,
     glf_label: str | None = None,
     glf_code: str | None = None,
-) -> V3dMvmParameters:
+) -> V3dMvmParametersTagged:
     """
     Build parameters.
     
@@ -118,7 +104,7 @@ def v_3d_mvm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMVM",
+        "@type": "afni/3dMVM",
         "prefix": prefix,
         "bsVars": bs_vars,
         "dataTable": data_table,
@@ -165,74 +151,74 @@ def v_3d_mvm_cargs(
     """
     cargs = []
     cargs.append("3dMVM")
-    if params.get("dbgArgs") is not None:
-        cargs.append(params.get("dbgArgs"))
+    if params.get("dbgArgs", None) is not None:
+        cargs.append(params.get("dbgArgs", None))
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("jobs") is not None:
+    if params.get("jobs", None) is not None:
         cargs.extend([
             "-jobs",
-            str(params.get("jobs"))
+            str(params.get("jobs", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
     cargs.extend([
         "-bsVars",
-        params.get("bsVars")
+        params.get("bsVars", None)
     ])
-    if params.get("wsVars") is not None:
+    if params.get("wsVars", None) is not None:
         cargs.extend([
             "-wsVars",
-            params.get("wsVars")
+            params.get("wsVars", None)
         ])
-    if params.get("qVars") is not None:
+    if params.get("qVars", None) is not None:
         cargs.extend([
             "-qVars",
-            params.get("qVars")
+            params.get("qVars", None)
         ])
-    if params.get("qVarCenters") is not None:
+    if params.get("qVarCenters", None) is not None:
         cargs.extend([
             "-qVarCenters",
-            params.get("qVarCenters")
+            params.get("qVarCenters", None)
         ])
-    if params.get("num_glt") is not None:
+    if params.get("num_glt", None) is not None:
         cargs.extend([
             "-num_glt",
-            str(params.get("num_glt"))
+            str(params.get("num_glt", None))
         ])
-    if params.get("gltLabel") is not None:
+    if params.get("gltLabel", None) is not None:
         cargs.extend([
             "-gltLabel",
-            params.get("gltLabel")
+            params.get("gltLabel", None)
         ])
-    if params.get("gltCode") is not None:
+    if params.get("gltCode", None) is not None:
         cargs.extend([
             "-gltCode",
-            params.get("gltCode")
+            params.get("gltCode", None)
         ])
-    if params.get("num_glf") is not None:
+    if params.get("num_glf", None) is not None:
         cargs.extend([
             "-num_glf",
-            str(params.get("num_glf"))
+            str(params.get("num_glf", None))
         ])
-    if params.get("glfLabel") is not None:
+    if params.get("glfLabel", None) is not None:
         cargs.extend([
             "-glfLabel",
-            params.get("glfLabel")
+            params.get("glfLabel", None)
         ])
-    if params.get("glfCode") is not None:
+    if params.get("glfCode", None) is not None:
         cargs.extend([
             "-glfCode",
-            params.get("glfCode")
+            params.get("glfCode", None)
         ])
     cargs.extend([
         "-dataTable",
-        params.get("dataTable")
+        params.get("dataTable", None)
     ])
     return cargs
 
@@ -252,17 +238,19 @@ def v_3d_mvm_outputs(
     """
     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"),
+        outfile_head=execution.output_file(params.get("prefix", None) + "+tlrc.HEAD"),
+        outfile_brik=execution.output_file(params.get("prefix", None) + "+tlrc.BRIK"),
     )
     return ret
 
 
 def v_3d_mvm_execute(
     params: V3dMvmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMvmOutputs:
     """
+    3dMVM
+    
     AFNI Group Analysis Program with Multi-Variate Modeling Approach.
     
     Author: AFNI Developers
@@ -271,10 +259,12 @@ def v_3d_mvm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        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 = execution.params(params)
     cargs = v_3d_mvm_cargs(params, execution)
     ret = v_3d_mvm_outputs(params, execution)
@@ -301,6 +291,8 @@ def v_3d_mvm(
     runner: Runner | None = None,
 ) -> V3dMvmOutputs:
     """
+    3dMVM
+    
     AFNI Group Analysis Program with Multi-Variate Modeling Approach.
     
     Author: AFNI Developers
@@ -328,8 +320,6 @@ def v_3d_mvm(
     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,
@@ -347,13 +337,13 @@ def v_3d_mvm(
         glf_code=glf_code,
         data_table=data_table,
     )
-    return v_3d_mvm_execute(params, execution)
+    return v_3d_mvm_execute(params, runner)
 
 
 __all__ = [
     "V3dMvmOutputs",
-    "V3dMvmParameters",
     "V_3D_MVM_METADATA",
     "v_3d_mvm",
+    "v_3d_mvm_execute",
     "v_3d_mvm_params",
 ]

niwrap_afni/afni/v_3d_mvm_validator.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MVM_VALIDATOR_METADATA = Metadata(
-    id="3810816d3735c07fee9eaec012b3bfc2cb9f95d2.boutiques",
+    id="a3d780f06ce379cf9ef7ff9d1932a56c6f599810.boutiques",
     name="3dMVM_validator",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,58 +14,29 @@ V_3D_MVM_VALIDATOR_METADATA = Metadata(
 
 
 V3dMvmValidatorParameters = typing.TypedDict('V3dMvmValidatorParameters', {
-    "__STYXTYPE__": typing.Literal["3dMVM_validator"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMVM_validator"]],
+    "datatable": InputPathType,
+    "shinyfolder": typing.NotRequired[str | None],
+})
+V3dMvmValidatorParametersTagged = typing.TypedDict('V3dMvmValidatorParametersTagged', {
+    "@type": typing.Literal["afni/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(...)`.
+    Output object returned when calling `V3dMvmValidatorParameters(...)`.
     """
     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:
+) -> V3dMvmValidatorParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +48,7 @@ def v_3d_mvm_validator_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMVM_validator",
+        "@type": "afni/3dMVM_validator",
         "datatable": datatable,
     }
     if shinyfolder is not None:
@@ -100,11 +71,11 @@ def v_3d_mvm_validator_cargs(
     """
     cargs = []
     cargs.append("3dMVM_validator")
-    cargs.append(execution.input_file(params.get("datatable")))
-    if params.get("shinyfolder") is not None:
+    cargs.append(execution.input_file(params.get("datatable", None)))
+    if params.get("shinyfolder", None) is not None:
         cargs.extend([
             "-ShinyFolder",
-            params.get("shinyfolder")
+            params.get("shinyfolder", None)
         ])
     return cargs
 
@@ -124,16 +95,17 @@ def v_3d_mvm_validator_outputs(
     """
     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,
+    runner: Runner | None = None,
 ) -> V3dMvmValidatorOutputs:
     """
+    3dMVM_validator
+    
     Launch the 3dMVM model validation shiny app in a web browser.
     
     Author: AFNI Developers
@@ -142,10 +114,12 @@ def v_3d_mvm_validator_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        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 = execution.params(params)
     cargs = v_3d_mvm_validator_cargs(params, execution)
     ret = v_3d_mvm_validator_outputs(params, execution)
@@ -159,6 +133,8 @@ def v_3d_mvm_validator(
     runner: Runner | None = None,
 ) -> V3dMvmValidatorOutputs:
     """
+    3dMVM_validator
+    
     Launch the 3dMVM model validation shiny app in a web browser.
     
     Author: AFNI Developers
@@ -173,19 +149,17 @@ def v_3d_mvm_validator(
     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)
+    return v_3d_mvm_validator_execute(params, runner)
 
 
 __all__ = [
     "V3dMvmValidatorOutputs",
-    "V3dMvmValidatorParameters",
     "V_3D_MVM_VALIDATOR_METADATA",
     "v_3d_mvm_validator",
+    "v_3d_mvm_validator_execute",
     "v_3d_mvm_validator_params",
 ]

niwrap_afni/afni/v_3d_net_corr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NET_CORR_METADATA = Metadata(
-    id="5670b5b4f9d0ab3696cc0b14e6eaa44805f1ab6c.boutiques",
+    id="843067907bd9f59d5320e8317ba91707fa77c36b.boutiques",
     name="3dNetCorr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3D_NET_CORR_METADATA = Metadata(
 
 
 V3dNetCorrParameters = typing.TypedDict('V3dNetCorrParameters', {
-    "__STYXTYPE__": typing.Literal["3dNetCorr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dNetCorr"]],
+    "prefix": str,
+    "inset": InputPathType,
+    "in_rois": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "fish_z": bool,
+    "part_corr": bool,
+    "ts_out": bool,
+    "ts_label": bool,
+    "ts_indiv": bool,
+    "ts_wb_corr": bool,
+    "ts_wb_Z": bool,
+    "weight_ts": typing.NotRequired[InputPathType | None],
+    "weight_corr": typing.NotRequired[InputPathType | None],
+    "ts_wb_strlabel": bool,
+    "nifti": bool,
+    "output_mask_nonnull": bool,
+    "push_thru_many_zeros": bool,
+    "allow_roi_zeros": bool,
+    "automask_off": bool,
+    "ignore_LT": bool,
+})
+V3dNetCorrParametersTagged = typing.TypedDict('V3dNetCorrParametersTagged', {
+    "@type": typing.Literal["afni/3dNetCorr"],
     "prefix": str,
     "inset": InputPathType,
     "in_rois": InputPathType,
@@ -36,43 +59,11 @@ V3dNetCorrParameters = typing.TypedDict('V3dNetCorrParameters', {
     "automask_off": bool,
     "ignore_LT": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dNetCorr": v_3d_net_corr_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 {
-        "3dNetCorr": v_3d_net_corr_outputs,
-    }.get(t)
 
 
 class V3dNetCorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_net_corr(...)`.
+    Output object returned when calling `V3dNetCorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -114,7 +105,7 @@ def v_3d_net_corr_params(
     allow_roi_zeros: bool = False,
     automask_off: bool = False,
     ignore_lt: bool = False,
-) -> V3dNetCorrParameters:
+) -> V3dNetCorrParametersTagged:
     """
     Build parameters.
     
@@ -154,7 +145,7 @@ def v_3d_net_corr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dNetCorr",
+        "@type": "afni/3dNetCorr",
         "prefix": prefix,
         "inset": inset,
         "in_rois": in_rois,
@@ -197,51 +188,51 @@ def v_3d_net_corr_cargs(
     """
     cargs = []
     cargs.append("3dNetCorr")
-    cargs.append(params.get("prefix"))
-    cargs.append(execution.input_file(params.get("inset")))
-    cargs.append(execution.input_file(params.get("in_rois")))
-    if params.get("mask") is not None:
+    cargs.append(params.get("prefix", None))
+    cargs.append(execution.input_file(params.get("inset", None)))
+    cargs.append(execution.input_file(params.get("in_rois", None)))
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("fish_z"):
+    if params.get("fish_z", False):
         cargs.append("-fish_z")
-    if params.get("part_corr"):
+    if params.get("part_corr", False):
         cargs.append("-part_corr")
-    if params.get("ts_out"):
+    if params.get("ts_out", False):
         cargs.append("-ts_out")
-    if params.get("ts_label"):
+    if params.get("ts_label", False):
         cargs.append("-ts_label")
-    if params.get("ts_indiv"):
+    if params.get("ts_indiv", False):
         cargs.append("-ts_indiv")
-    if params.get("ts_wb_corr"):
+    if params.get("ts_wb_corr", False):
         cargs.append("-ts_wb_corr")
-    if params.get("ts_wb_Z"):
+    if params.get("ts_wb_Z", False):
         cargs.append("-ts_wb_Z")
-    if params.get("weight_ts") is not None:
+    if params.get("weight_ts", None) is not None:
         cargs.extend([
             "-weight_ts",
-            execution.input_file(params.get("weight_ts"))
+            execution.input_file(params.get("weight_ts", None))
         ])
-    if params.get("weight_corr") is not None:
+    if params.get("weight_corr", None) is not None:
         cargs.extend([
             "-weight_corr",
-            execution.input_file(params.get("weight_corr"))
+            execution.input_file(params.get("weight_corr", None))
         ])
-    if params.get("ts_wb_strlabel"):
+    if params.get("ts_wb_strlabel", False):
         cargs.append("-ts_wb_strlabel")
-    if params.get("nifti"):
+    if params.get("nifti", False):
         cargs.append("-nifti")
-    if params.get("output_mask_nonnull"):
+    if params.get("output_mask_nonnull", False):
         cargs.append("-output_mask_nonnull")
-    if params.get("push_thru_many_zeros"):
+    if params.get("push_thru_many_zeros", False):
         cargs.append("-push_thru_many_zeros")
-    if params.get("allow_roi_zeros"):
+    if params.get("allow_roi_zeros", False):
         cargs.append("-allow_roi_zeros")
-    if params.get("automask_off"):
+    if params.get("automask_off", False):
         cargs.append("-automask_off")
-    if params.get("ignore_LT"):
+    if params.get("ignore_LT", False):
         cargs.append("-ignore_LT")
     return cargs
 
@@ -261,12 +252,12 @@ def v_3d_net_corr_outputs(
     """
     ret = V3dNetCorrOutputs(
         root=execution.output_file("."),
-        output_netcc=execution.output_file(params.get("prefix") + "_000.netcc"),
-        output_netts=execution.output_file(params.get("prefix") + "_000.netts"),
-        output_niml=execution.output_file(params.get("prefix") + "_000.niml.dset"),
-        output_roidat=execution.output_file(params.get("prefix") + ".roidat"),
-        output_mask_nnull=execution.output_file(params.get("prefix") + "_mask_nnull"),
-        output_indiv=execution.output_file(params.get("prefix") + "_000_INDIV"),
+        output_netcc=execution.output_file(params.get("prefix", None) + "_000.netcc"),
+        output_netts=execution.output_file(params.get("prefix", None) + "_000.netts"),
+        output_niml=execution.output_file(params.get("prefix", None) + "_000.niml.dset"),
+        output_roidat=execution.output_file(params.get("prefix", None) + ".roidat"),
+        output_mask_nnull=execution.output_file(params.get("prefix", None) + "_mask_nnull"),
+        output_indiv=execution.output_file(params.get("prefix", None) + "_000_INDIV"),
         output_binary_mask_nnull=execution.output_file("PREFIX_mask_nnull"),
     )
     return ret
@@ -274,9 +265,11 @@ def v_3d_net_corr_outputs(
 
 def v_3d_net_corr_execute(
     params: V3dNetCorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dNetCorrOutputs:
     """
+    3dNetCorr
+    
     Compute correlation matrix of a set of ROIs based on mean time series.
     
     Author: AFNI Developers
@@ -285,10 +278,12 @@ def v_3d_net_corr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNetCorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NET_CORR_METADATA)
     params = execution.params(params)
     cargs = v_3d_net_corr_cargs(params, execution)
     ret = v_3d_net_corr_outputs(params, execution)
@@ -320,6 +315,8 @@ def v_3d_net_corr(
     runner: Runner | None = None,
 ) -> V3dNetCorrOutputs:
     """
+    3dNetCorr
+    
     Compute correlation matrix of a set of ROIs based on mean time series.
     
     Author: AFNI Developers
@@ -362,8 +359,6 @@ def v_3d_net_corr(
     Returns:
         NamedTuple of outputs (described in `V3dNetCorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_NET_CORR_METADATA)
     params = v_3d_net_corr_params(
         prefix=prefix,
         inset=inset,
@@ -386,13 +381,13 @@ def v_3d_net_corr(
         automask_off=automask_off,
         ignore_lt=ignore_lt,
     )
-    return v_3d_net_corr_execute(params, execution)
+    return v_3d_net_corr_execute(params, runner)
 
 
 __all__ = [
     "V3dNetCorrOutputs",
-    "V3dNetCorrParameters",
     "V_3D_NET_CORR_METADATA",
     "v_3d_net_corr",
+    "v_3d_net_corr_execute",
     "v_3d_net_corr_params",
 ]