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

niwrap_afni/afni/cifti_tool.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CIFTI_TOOL_METADATA = Metadata(
-    id="d35c1bdf886b6ca8faed8f62946bf8ec095c0a8c.boutiques",
+    id="5dccf8e632c65fb5c70327668e713fb4c23945df.boutiques",
     name="cifti_tool",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ CIFTI_TOOL_METADATA = Metadata(
 
 
 CiftiToolParameters = typing.TypedDict('CiftiToolParameters', {
-    "__STYXTYPE__": typing.Literal["cifti_tool"],
+    "@type": typing.NotRequired[typing.Literal["afni/cifti_tool"]],
+    "input_file": InputPathType,
+    "as_cext": bool,
+    "disp_cext": bool,
+    "eval_cext": bool,
+    "eval_type": typing.NotRequired[typing.Literal["has_data", "has_bdata", "num_tokens", "show", "show_names", "show_summary", "show_text_data"] | None],
+    "output_file": typing.NotRequired[str | None],
+    "verbose_level": typing.NotRequired[float | None],
+    "verbose_read_level": typing.NotRequired[float | None],
+    "both_verbose_levels": typing.NotRequired[float | None],
+})
+CiftiToolParametersTagged = typing.TypedDict('CiftiToolParametersTagged', {
+    "@type": typing.Literal["afni/cifti_tool"],
     "input_file": InputPathType,
     "as_cext": bool,
     "disp_cext": bool,
@@ -25,43 +37,11 @@ CiftiToolParameters = typing.TypedDict('CiftiToolParameters', {
     "verbose_read_level": typing.NotRequired[float | None],
     "both_verbose_levels": 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 {
-        "cifti_tool": cifti_tool_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 {
-        "cifti_tool": cifti_tool_outputs,
-    }.get(t)
 
 
 class CiftiToolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `cifti_tool(...)`.
+    Output object returned when calling `CiftiToolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def cifti_tool_params(
     verbose_level: float | None = None,
     verbose_read_level: float | None = None,
     both_verbose_levels: float | None = None,
-) -> CiftiToolParameters:
+) -> CiftiToolParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +77,7 @@ def cifti_tool_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "cifti_tool",
+        "@type": "afni/cifti_tool",
         "input_file": input_file,
         "as_cext": as_cext,
         "disp_cext": disp_cext,
@@ -133,38 +113,38 @@ def cifti_tool_cargs(
     cargs.append("cifti_tool")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("as_cext"):
+    if params.get("as_cext", False):
         cargs.append("-as_cext")
-    if params.get("disp_cext"):
+    if params.get("disp_cext", False):
         cargs.append("-disp_cext")
-    if params.get("eval_cext"):
+    if params.get("eval_cext", False):
         cargs.append("-eval_cext")
-    if params.get("eval_type") is not None:
+    if params.get("eval_type", None) is not None:
         cargs.extend([
             "-eval_type",
-            params.get("eval_type")
+            params.get("eval_type", None)
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-output",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("verbose_level") is not None:
+    if params.get("verbose_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbose_level"))
+            str(params.get("verbose_level", None))
         ])
-    if params.get("verbose_read_level") is not None:
+    if params.get("verbose_read_level", None) is not None:
         cargs.extend([
             "-verb_read",
-            str(params.get("verbose_read_level"))
+            str(params.get("verbose_read_level", None))
         ])
-    if params.get("both_verbose_levels") is not None:
+    if params.get("both_verbose_levels", None) is not None:
         cargs.extend([
             "-vboth",
-            str(params.get("both_verbose_levels"))
+            str(params.get("both_verbose_levels", None))
         ])
     return cargs
 
@@ -184,16 +164,18 @@ def cifti_tool_outputs(
     """
     ret = CiftiToolOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        output_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def cifti_tool_execute(
     params: CiftiToolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CiftiToolOutputs:
     """
+    cifti_tool
+    
     Example tool for reading/writing CIFTI-2 datasets.
     
     Author: AFNI Developers
@@ -202,10 +184,12 @@ def cifti_tool_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CiftiToolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CIFTI_TOOL_METADATA)
     params = execution.params(params)
     cargs = cifti_tool_cargs(params, execution)
     ret = cifti_tool_outputs(params, execution)
@@ -226,6 +210,8 @@ def cifti_tool(
     runner: Runner | None = None,
 ) -> CiftiToolOutputs:
     """
+    cifti_tool
+    
     Example tool for reading/writing CIFTI-2 datasets.
     
     Author: AFNI Developers
@@ -246,8 +232,6 @@ def cifti_tool(
     Returns:
         NamedTuple of outputs (described in `CiftiToolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CIFTI_TOOL_METADATA)
     params = cifti_tool_params(
         input_file=input_file,
         as_cext=as_cext,
@@ -259,13 +243,13 @@ def cifti_tool(
         verbose_read_level=verbose_read_level,
         both_verbose_levels=both_verbose_levels,
     )
-    return cifti_tool_execute(params, execution)
+    return cifti_tool_execute(params, runner)
 
 
 __all__ = [
     "CIFTI_TOOL_METADATA",
     "CiftiToolOutputs",
-    "CiftiToolParameters",
     "cifti_tool",
+    "cifti_tool_execute",
     "cifti_tool_params",
 ]

niwrap_afni/afni/cjpeg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CJPEG_METADATA = Metadata(
-    id="2c8dea63ef6018ee1b6008e2b8bd11dd5b58bb30.boutiques",
+    id="e4ed2b716c90dcf5f3798fae90dd725dfa8f4e46.boutiques",
     name="cjpeg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ CJPEG_METADATA = Metadata(
 
 
 CjpegParameters = typing.TypedDict('CjpegParameters', {
-    "__STYXTYPE__": typing.Literal["cjpeg"],
+    "@type": typing.NotRequired[typing.Literal["afni/cjpeg"]],
+    "quality": typing.NotRequired[float | None],
+    "grayscale": bool,
+    "optimize": bool,
+    "baseline": bool,
+    "progressive": bool,
+    "outfile": str,
+    "infile": InputPathType,
+})
+CjpegParametersTagged = typing.TypedDict('CjpegParametersTagged', {
+    "@type": typing.Literal["afni/cjpeg"],
     "quality": typing.NotRequired[float | None],
     "grayscale": bool,
     "optimize": bool,
@@ -23,43 +33,11 @@ CjpegParameters = typing.TypedDict('CjpegParameters', {
     "outfile": str,
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "cjpeg": cjpeg_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 {
-        "cjpeg": cjpeg_outputs,
-    }.get(t)
 
 
 class CjpegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `cjpeg(...)`.
+    Output object returned when calling `CjpegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def cjpeg_params(
     optimize: bool = False,
     baseline: bool = False,
     progressive: bool = False,
-) -> CjpegParameters:
+) -> CjpegParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def cjpeg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "cjpeg",
+        "@type": "afni/cjpeg",
         "grayscale": grayscale,
         "optimize": optimize,
         "baseline": baseline,
@@ -119,21 +97,21 @@ def cjpeg_cargs(
     """
     cargs = []
     cargs.append("cjpeg")
-    if params.get("quality") is not None:
+    if params.get("quality", None) is not None:
         cargs.extend([
             "-quality",
-            str(params.get("quality"))
+            str(params.get("quality", None))
         ])
-    if params.get("grayscale"):
+    if params.get("grayscale", False):
         cargs.append("-grayscale")
-    if params.get("optimize"):
+    if params.get("optimize", False):
         cargs.append("-optimize")
-    if params.get("baseline"):
+    if params.get("baseline", False):
         cargs.append("-baseline")
-    if params.get("progressive"):
+    if params.get("progressive", False):
         cargs.append("-progressive")
-    cargs.append(params.get("outfile"))
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(params.get("outfile", None))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -152,16 +130,18 @@ def cjpeg_outputs(
     """
     ret = CjpegOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("outfile")),
+        outfile=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def cjpeg_execute(
     params: CjpegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CjpegOutputs:
     """
+    cjpeg
+    
     Compresses an image file to a JPEG file.
     
     Author: AFNI Developers
@@ -170,10 +150,12 @@ def cjpeg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CjpegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CJPEG_METADATA)
     params = execution.params(params)
     cargs = cjpeg_cargs(params, execution)
     ret = cjpeg_outputs(params, execution)
@@ -192,6 +174,8 @@ def cjpeg(
     runner: Runner | None = None,
 ) -> CjpegOutputs:
     """
+    cjpeg
+    
     Compresses an image file to a JPEG file.
     
     Author: AFNI Developers
@@ -210,8 +194,6 @@ def cjpeg(
     Returns:
         NamedTuple of outputs (described in `CjpegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CJPEG_METADATA)
     params = cjpeg_params(
         quality=quality,
         grayscale=grayscale,
@@ -221,13 +203,13 @@ def cjpeg(
         outfile=outfile,
         infile=infile,
     )
-    return cjpeg_execute(params, execution)
+    return cjpeg_execute(params, runner)
 
 
 __all__ = [
     "CJPEG_METADATA",
     "CjpegOutputs",
-    "CjpegParameters",
     "cjpeg",
+    "cjpeg_execute",
     "cjpeg_params",
 ]

niwrap_afni/afni/clust_exp_hist_table_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CLUST_EXP_HIST_TABLE_PY_METADATA = Metadata(
-    id="2236ab9d18b996789c02458fc65933f93e485f82.boutiques",
+    id="1463a61d8d642f1da2ae42321f37e18bffcb4d50.boutiques",
     name="ClustExp_HistTable.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ CLUST_EXP_HIST_TABLE_PY_METADATA = Metadata(
 
 
 ClustExpHistTablePyParameters = typing.TypedDict('ClustExpHistTablePyParameters', {
-    "__STYXTYPE__": typing.Literal["ClustExp_HistTable.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/ClustExp_HistTable.py"]],
+    "stat_dset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "overwrite": bool,
+})
+ClustExpHistTablePyParametersTagged = typing.TypedDict('ClustExpHistTablePyParametersTagged', {
+    "@type": typing.Literal["afni/ClustExp_HistTable.py"],
     "stat_dset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "session": typing.NotRequired[str | None],
     "overwrite": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ClustExp_HistTable.py": clust_exp_hist_table_py_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 {
-        "ClustExp_HistTable.py": clust_exp_hist_table_py_outputs,
-    }.get(t)
 
 
 class ClustExpHistTablePyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `clust_exp_hist_table_py(...)`.
+    Output object returned when calling `ClustExpHistTablePyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def clust_exp_hist_table_py_params(
     prefix: str | None = None,
     session: str | None = None,
     overwrite: bool = False,
-) -> ClustExpHistTablePyParameters:
+) -> ClustExpHistTablePyParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def clust_exp_hist_table_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ClustExp_HistTable.py",
+        "@type": "afni/ClustExp_HistTable.py",
         "stat_dset": stat_dset,
         "overwrite": overwrite,
     }
@@ -111,19 +86,19 @@ def clust_exp_hist_table_py_cargs(
     cargs.append("ClustExp_HistTable.py")
     cargs.extend([
         "-StatDSET",
-        execution.input_file(params.get("stat_dset"))
+        execution.input_file(params.get("stat_dset", 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("session") is not None:
+    if params.get("session", None) is not None:
         cargs.extend([
             "-session",
-            params.get("session")
+            params.get("session", None)
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
     return cargs
 
@@ -143,18 +118,20 @@ def clust_exp_hist_table_py_outputs(
     """
     ret = ClustExpHistTablePyOutputs(
         root=execution.output_file("."),
-        group_table=execution.output_file(params.get("prefix") + "_GroupTable.csv") if (params.get("prefix") is not None) else None,
+        group_table=execution.output_file(params.get("prefix", None) + "_GroupTable.csv") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def clust_exp_hist_table_py_execute(
     params: ClustExpHistTablePyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ClustExpHistTablePyOutputs:
     """
-    Script to extract the data table from history of datasets from 3dttest++, 3dMVM,
-    or 3dLME.
+    ClustExp_HistTable.py
+    
+    Script to extract the data table from history of datasets from 3dttest++,
+    3dMVM, or 3dLME.
     
     Author: AFNI Developers
     
@@ -162,10 +139,12 @@ def clust_exp_hist_table_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ClustExpHistTablePyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CLUST_EXP_HIST_TABLE_PY_METADATA)
     params = execution.params(params)
     cargs = clust_exp_hist_table_py_cargs(params, execution)
     ret = clust_exp_hist_table_py_outputs(params, execution)
@@ -181,8 +160,10 @@ def clust_exp_hist_table_py(
     runner: Runner | None = None,
 ) -> ClustExpHistTablePyOutputs:
     """
-    Script to extract the data table from history of datasets from 3dttest++, 3dMVM,
-    or 3dLME.
+    ClustExp_HistTable.py
+    
+    Script to extract the data table from history of datasets from 3dttest++,
+    3dMVM, or 3dLME.
     
     Author: AFNI Developers
     
@@ -198,21 +179,19 @@ def clust_exp_hist_table_py(
     Returns:
         NamedTuple of outputs (described in `ClustExpHistTablePyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CLUST_EXP_HIST_TABLE_PY_METADATA)
     params = clust_exp_hist_table_py_params(
         stat_dset=stat_dset,
         prefix=prefix,
         session=session,
         overwrite=overwrite,
     )
-    return clust_exp_hist_table_py_execute(params, execution)
+    return clust_exp_hist_table_py_execute(params, runner)
 
 
 __all__ = [
     "CLUST_EXP_HIST_TABLE_PY_METADATA",
     "ClustExpHistTablePyOutputs",
-    "ClustExpHistTablePyParameters",
     "clust_exp_hist_table_py",
+    "clust_exp_hist_table_py_execute",
     "clust_exp_hist_table_py_params",
 ]