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

niwrap_afni/afni/v__command_globb.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__COMMAND_GLOBB_METADATA = Metadata(
-    id="5f14a5e6156977564d2f36a3dee265f9e274c661.boutiques",
+    id="953bb7b12ef5b6600c31268fb6295e56ede7c7ab.boutiques",
     name="@CommandGlobb",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,54 +14,27 @@ V__COMMAND_GLOBB_METADATA = Metadata(
 
 
 VCommandGlobbParameters = typing.TypedDict('VCommandGlobbParameters', {
-    "__STYXTYPE__": typing.Literal["@CommandGlobb"],
+    "@type": typing.NotRequired[typing.Literal["afni/@CommandGlobb"]],
+    "program_command": str,
+    "output_dir": str,
+    "extension": typing.NotRequired[str | None],
+    "brick_list": list[str],
+})
+VCommandGlobbParametersTagged = typing.TypedDict('VCommandGlobbParametersTagged', {
+    "@type": typing.Literal["afni/@CommandGlobb"],
     "program_command": str,
     "output_dir": str,
     "extension": typing.NotRequired[str | None],
     "brick_list": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@CommandGlobb": v__command_globb_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 {
-        "@CommandGlobb": v__command_globb_outputs,
-    }.get(t)
 
 
 class VCommandGlobbOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__command_globb(...)`.
+    Output object returned when calling `VCommandGlobbParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType
-    """Output files generated by the specified program command line."""
 
 
 def v__command_globb_params(
@@ -69,7 +42,7 @@ def v__command_globb_params(
     output_dir: str,
     brick_list: list[str],
     extension: str | None = None,
-) -> VCommandGlobbParameters:
+) -> VCommandGlobbParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +60,7 @@ def v__command_globb_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@CommandGlobb",
+        "@type": "afni/@CommandGlobb",
         "program_command": program_command,
         "output_dir": output_dir,
         "brick_list": brick_list,
@@ -114,20 +87,20 @@ def v__command_globb_cargs(
     cargs.append("@CommandGlobb")
     cargs.extend([
         "-com",
-        params.get("program_command")
+        params.get("program_command", None)
     ])
     cargs.extend([
         "-session",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
-    if params.get("extension") is not None:
+    if params.get("extension", None) is not None:
         cargs.extend([
             "-newext",
-            params.get("extension")
+            params.get("extension", None)
         ])
     cargs.extend([
         "-list",
-        *params.get("brick_list")
+        *params.get("brick_list", None)
     ])
     return cargs
 
@@ -147,16 +120,17 @@ def v__command_globb_outputs(
     """
     ret = VCommandGlobbOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("output_dir") + "/*"),
     )
     return ret
 
 
 def v__command_globb_execute(
     params: VCommandGlobbParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VCommandGlobbOutputs:
     """
+    @CommandGlobb
+    
     A command-line tool to execute a specified program command line on a list of
     input bricks.
     
@@ -166,10 +140,12 @@ def v__command_globb_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VCommandGlobbOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMMAND_GLOBB_METADATA)
     params = execution.params(params)
     cargs = v__command_globb_cargs(params, execution)
     ret = v__command_globb_outputs(params, execution)
@@ -185,6 +161,8 @@ def v__command_globb(
     runner: Runner | None = None,
 ) -> VCommandGlobbOutputs:
     """
+    @CommandGlobb
+    
     A command-line tool to execute a specified program command line on a list of
     input bricks.
     
@@ -206,21 +184,19 @@ def v__command_globb(
     Returns:
         NamedTuple of outputs (described in `VCommandGlobbOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__COMMAND_GLOBB_METADATA)
     params = v__command_globb_params(
         program_command=program_command,
         output_dir=output_dir,
         extension=extension,
         brick_list=brick_list,
     )
-    return v__command_globb_execute(params, execution)
+    return v__command_globb_execute(params, runner)
 
 
 __all__ = [
     "VCommandGlobbOutputs",
-    "VCommandGlobbParameters",
     "V__COMMAND_GLOBB_METADATA",
     "v__command_globb",
+    "v__command_globb_execute",
     "v__command_globb_params",
 ]

niwrap_afni/afni/v__compute_gcor.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__COMPUTE_GCOR_METADATA = Metadata(
-    id="5b49288dc45e60df83fcd651b8cdf3b983aa266d.boutiques",
+    id="ff28d4939bf8b46e877006f649680caefff5f639.boutiques",
     name="@compute_gcor",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__COMPUTE_GCOR_METADATA = Metadata(
 
 
 VComputeGcorParameters = typing.TypedDict('VComputeGcorParameters', {
-    "__STYXTYPE__": typing.Literal["@compute_gcor"],
+    "@type": typing.NotRequired[typing.Literal["afni/@compute_gcor"]],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "corr_vol_prefix": typing.NotRequired[str | None],
+    "initial_trs": typing.NotRequired[float | None],
+    "no_demean": bool,
+    "save_tmp": bool,
+    "verbose": typing.NotRequired[float | None],
+})
+VComputeGcorParametersTagged = typing.TypedDict('VComputeGcorParametersTagged', {
+    "@type": typing.Literal["afni/@compute_gcor"],
     "input": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "corr_vol_prefix": typing.NotRequired[str | None],
@@ -23,43 +33,11 @@ VComputeGcorParameters = typing.TypedDict('VComputeGcorParameters', {
     "save_tmp": bool,
     "verbose": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@compute_gcor": v__compute_gcor_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 {
-        "@compute_gcor": v__compute_gcor_outputs,
-    }.get(t)
 
 
 class VComputeGcorOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__compute_gcor(...)`.
+    Output object returned when calling `VComputeGcorParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +55,7 @@ def v__compute_gcor_params(
     no_demean: bool = False,
     save_tmp: bool = False,
     verbose: float | None = None,
-) -> VComputeGcorParameters:
+) -> VComputeGcorParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def v__compute_gcor_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@compute_gcor",
+        "@type": "afni/@compute_gcor",
         "input": input_,
         "no_demean": no_demean,
         "save_tmp": save_tmp,
@@ -124,27 +102,27 @@ def v__compute_gcor_cargs(
     """
     cargs = []
     cargs.append("@compute_gcor")
-    cargs.append(execution.input_file(params.get("input")))
-    if params.get("mask") is not None:
-        cargs.append(execution.input_file(params.get("mask")))
-    if params.get("corr_vol_prefix") is not None:
+    cargs.append(execution.input_file(params.get("input", None)))
+    if params.get("mask", None) is not None:
+        cargs.append(execution.input_file(params.get("mask", None)))
+    if params.get("corr_vol_prefix", None) is not None:
         cargs.extend([
             "-corr_vol",
-            params.get("corr_vol_prefix")
+            params.get("corr_vol_prefix", None)
         ])
-    if params.get("initial_trs") is not None:
+    if params.get("initial_trs", None) is not None:
         cargs.extend([
             "-nfirst",
-            str(params.get("initial_trs"))
+            str(params.get("initial_trs", None))
         ])
-    if params.get("no_demean"):
+    if params.get("no_demean", False):
         cargs.append("-no_demean")
-    if params.get("save_tmp"):
+    if params.get("save_tmp", False):
         cargs.append("-savetmp")
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
     return cargs
 
@@ -164,17 +142,19 @@ def v__compute_gcor_outputs(
     """
     ret = VComputeGcorOutputs(
         root=execution.output_file("."),
-        corr_vol_brik=execution.output_file(params.get("corr_vol_prefix") + "+tlrc.BRIK") if (params.get("corr_vol_prefix") is not None) else None,
-        corr_vol_head=execution.output_file(params.get("corr_vol_prefix") + "+tlrc.HEAD") if (params.get("corr_vol_prefix") is not None) else None,
+        corr_vol_brik=execution.output_file(params.get("corr_vol_prefix", None) + "+tlrc.BRIK") if (params.get("corr_vol_prefix") is not None) else None,
+        corr_vol_head=execution.output_file(params.get("corr_vol_prefix", None) + "+tlrc.HEAD") if (params.get("corr_vol_prefix") is not None) else None,
     )
     return ret
 
 
 def v__compute_gcor_execute(
     params: VComputeGcorParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VComputeGcorOutputs:
     """
+    @compute_gcor
+    
     Compute GCOR, the global correlation.
     
     Author: AFNI Developers
@@ -183,10 +163,12 @@ def v__compute_gcor_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VComputeGcorOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMPUTE_GCOR_METADATA)
     params = execution.params(params)
     cargs = v__compute_gcor_cargs(params, execution)
     ret = v__compute_gcor_outputs(params, execution)
@@ -205,6 +187,8 @@ def v__compute_gcor(
     runner: Runner | None = None,
 ) -> VComputeGcorOutputs:
     """
+    @compute_gcor
+    
     Compute GCOR, the global correlation.
     
     Author: AFNI Developers
@@ -223,8 +207,6 @@ def v__compute_gcor(
     Returns:
         NamedTuple of outputs (described in `VComputeGcorOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__COMPUTE_GCOR_METADATA)
     params = v__compute_gcor_params(
         input_=input_,
         mask=mask,
@@ -234,13 +216,13 @@ def v__compute_gcor(
         save_tmp=save_tmp,
         verbose=verbose,
     )
-    return v__compute_gcor_execute(params, execution)
+    return v__compute_gcor_execute(params, runner)
 
 
 __all__ = [
     "VComputeGcorOutputs",
-    "VComputeGcorParameters",
     "V__COMPUTE_GCOR_METADATA",
     "v__compute_gcor",
+    "v__compute_gcor_execute",
     "v__compute_gcor_params",
 ]

niwrap_afni/afni/v__compute_oc_weights.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__COMPUTE_OC_WEIGHTS_METADATA = Metadata(
-    id="8cbef05597be3ac05a382bf27e8ef50be3a6cef0.boutiques",
+    id="22729c57ac0f8061c696e52f5cfb71514654aab2.boutiques",
     name="@compute_OC_weights",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V__COMPUTE_OC_WEIGHTS_METADATA = Metadata(
 
 
 VComputeOcWeightsParameters = typing.TypedDict('VComputeOcWeightsParameters', {
-    "__STYXTYPE__": typing.Literal["@compute_OC_weights"],
+    "@type": typing.NotRequired[typing.Literal["afni/@compute_OC_weights"]],
+    "echo_times": typing.NotRequired[str | None],
+    "echo_times_file": typing.NotRequired[InputPathType | None],
+    "echo_dsets": list[str],
+    "prefix": typing.NotRequired[str | None],
+    "def_to_equal": typing.NotRequired[str | None],
+    "oc_method": typing.NotRequired[str | None],
+    "sum_weight_tolerance": typing.NotRequired[float | None],
+    "t2_star_limit": typing.NotRequired[float | None],
+    "work_dir": typing.NotRequired[str | None],
+    "verbosity": bool,
+})
+VComputeOcWeightsParametersTagged = typing.TypedDict('VComputeOcWeightsParametersTagged', {
+    "@type": typing.Literal["afni/@compute_OC_weights"],
     "echo_times": typing.NotRequired[str | None],
     "echo_times_file": typing.NotRequired[InputPathType | None],
     "echo_dsets": list[str],
@@ -26,43 +39,11 @@ VComputeOcWeightsParameters = typing.TypedDict('VComputeOcWeightsParameters', {
     "work_dir": typing.NotRequired[str | None],
     "verbosity": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@compute_OC_weights": v__compute_oc_weights_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 {
-        "@compute_OC_weights": v__compute_oc_weights_outputs,
-    }.get(t)
 
 
 class VComputeOcWeightsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__compute_oc_weights(...)`.
+    Output object returned when calling `VComputeOcWeightsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def v__compute_oc_weights_params(
     t2_star_limit: float | None = None,
     work_dir: str | None = None,
     verbosity: bool = False,
-) -> VComputeOcWeightsParameters:
+) -> VComputeOcWeightsParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +86,7 @@ def v__compute_oc_weights_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@compute_OC_weights",
+        "@type": "afni/@compute_OC_weights",
         "echo_dsets": echo_dsets,
         "verbosity": verbosity,
     }
@@ -143,51 +124,51 @@ def v__compute_oc_weights_cargs(
     """
     cargs = []
     cargs.append("@compute_OC_weights")
-    if params.get("echo_times") is not None:
+    if params.get("echo_times", None) is not None:
         cargs.extend([
             "-echo_times",
-            params.get("echo_times")
+            params.get("echo_times", None)
         ])
-    if params.get("echo_times_file") is not None:
+    if params.get("echo_times_file", None) is not None:
         cargs.extend([
             "-echo_times_file",
-            execution.input_file(params.get("echo_times_file"))
+            execution.input_file(params.get("echo_times_file", None))
         ])
     cargs.extend([
         "-echo_dsets",
-        *params.get("echo_dsets")
+        *params.get("echo_dsets", None)
     ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("def_to_equal") is not None:
+    if params.get("def_to_equal", None) is not None:
         cargs.extend([
             "-def_to_equal",
-            params.get("def_to_equal")
+            params.get("def_to_equal", None)
         ])
-    if params.get("oc_method") is not None:
+    if params.get("oc_method", None) is not None:
         cargs.extend([
             "-oc_method",
-            params.get("oc_method")
+            params.get("oc_method", None)
         ])
-    if params.get("sum_weight_tolerance") is not None:
+    if params.get("sum_weight_tolerance", None) is not None:
         cargs.extend([
             "-sum_weight_tolerance",
-            str(params.get("sum_weight_tolerance"))
+            str(params.get("sum_weight_tolerance", None))
         ])
-    if params.get("t2_star_limit") is not None:
+    if params.get("t2_star_limit", None) is not None:
         cargs.extend([
             "-t2_star_limit",
-            str(params.get("t2_star_limit"))
+            str(params.get("t2_star_limit", None))
         ])
-    if params.get("work_dir") is not None:
+    if params.get("work_dir", None) is not None:
         cargs.extend([
             "-work_dir",
-            params.get("work_dir")
+            params.get("work_dir", None)
         ])
-    if params.get("verbosity"):
+    if params.get("verbosity", False):
         cargs.append("-verb")
     return cargs
 
@@ -207,16 +188,18 @@ def v__compute_oc_weights_outputs(
     """
     ret = VComputeOcWeightsOutputs(
         root=execution.output_file("."),
-        output_oc_weights=execution.output_file(params.get("prefix") + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
+        output_oc_weights=execution.output_file(params.get("prefix", None) + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__compute_oc_weights_execute(
     params: VComputeOcWeightsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VComputeOcWeightsOutputs:
     """
+    @compute_OC_weights
+    
     Compute optimal combined weights dataset for multi-echo EPI data.
     
     Author: AFNI Developers
@@ -225,10 +208,12 @@ def v__compute_oc_weights_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VComputeOcWeightsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__COMPUTE_OC_WEIGHTS_METADATA)
     params = execution.params(params)
     cargs = v__compute_oc_weights_cargs(params, execution)
     ret = v__compute_oc_weights_outputs(params, execution)
@@ -250,6 +235,8 @@ def v__compute_oc_weights(
     runner: Runner | None = None,
 ) -> VComputeOcWeightsOutputs:
     """
+    @compute_OC_weights
+    
     Compute optimal combined weights dataset for multi-echo EPI data.
     
     Author: AFNI Developers
@@ -276,8 +263,6 @@ def v__compute_oc_weights(
     Returns:
         NamedTuple of outputs (described in `VComputeOcWeightsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__COMPUTE_OC_WEIGHTS_METADATA)
     params = v__compute_oc_weights_params(
         echo_times=echo_times,
         echo_times_file=echo_times_file,
@@ -290,13 +275,13 @@ def v__compute_oc_weights(
         work_dir=work_dir,
         verbosity=verbosity,
     )
-    return v__compute_oc_weights_execute(params, execution)
+    return v__compute_oc_weights_execute(params, runner)
 
 
 __all__ = [
     "VComputeOcWeightsOutputs",
-    "VComputeOcWeightsParameters",
     "V__COMPUTE_OC_WEIGHTS_METADATA",
     "v__compute_oc_weights",
+    "v__compute_oc_weights_execute",
     "v__compute_oc_weights_params",
 ]