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

niwrap_afni/afni/dicom_hinfo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_HINFO_METADATA = Metadata(
-    id="86b86805a9240d1e9926ec2238c1b43833f0390d.boutiques",
+    id="2da4137ffb7a00f1751a6350ead114c9f0d440cc.boutiques",
     name="dicom_hinfo",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ DICOM_HINFO_METADATA = Metadata(
 
 
 DicomHinfoParameters = typing.TypedDict('DicomHinfoParameters', {
-    "__STYXTYPE__": typing.Literal["dicom_hinfo"],
+    "@type": typing.NotRequired[typing.Literal["afni/dicom_hinfo"]],
+    "tag": list[str],
+    "sepstr": typing.NotRequired[str | None],
+    "full_entry": bool,
+    "no_name": bool,
+    "namelast": bool,
+    "files": list[InputPathType],
+})
+DicomHinfoParametersTagged = typing.TypedDict('DicomHinfoParametersTagged', {
+    "@type": typing.Literal["afni/dicom_hinfo"],
     "tag": list[str],
     "sepstr": typing.NotRequired[str | None],
     "full_entry": bool,
@@ -22,42 +31,11 @@ DicomHinfoParameters = typing.TypedDict('DicomHinfoParameters', {
     "namelast": bool,
     "files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dicom_hinfo": dicom_hinfo_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 {
-    }.get(t)
 
 
 class DicomHinfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dicom_hinfo(...)`.
+    Output object returned when calling `DicomHinfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def dicom_hinfo_params(
     full_entry: bool = False,
     no_name: bool = False,
     namelast: bool = False,
-) -> DicomHinfoParameters:
+) -> DicomHinfoParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def dicom_hinfo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dicom_hinfo",
+        "@type": "afni/dicom_hinfo",
         "tag": tag,
         "full_entry": full_entry,
         "no_name": no_name,
@@ -116,20 +94,20 @@ def dicom_hinfo_cargs(
     cargs.append("dicom_hinfo")
     cargs.extend([
         "-tag",
-        *params.get("tag")
+        *params.get("tag", None)
     ])
-    if params.get("sepstr") is not None:
+    if params.get("sepstr", None) is not None:
         cargs.extend([
             "-sepstr",
-            params.get("sepstr")
+            params.get("sepstr", None)
         ])
-    if params.get("full_entry"):
+    if params.get("full_entry", False):
         cargs.append("-full_entry")
-    if params.get("no_name"):
+    if params.get("no_name", False):
         cargs.append("-no_name")
-    if params.get("namelast"):
+    if params.get("namelast", False):
         cargs.append("-namelast")
-    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    cargs.extend([execution.input_file(f) for f in params.get("files", None)])
     return cargs
 
 
@@ -154,9 +132,11 @@ def dicom_hinfo_outputs(
 
 def dicom_hinfo_execute(
     params: DicomHinfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DicomHinfoOutputs:
     """
+    dicom_hinfo
+    
     Prints selected information from one or more DICOM files to stdout.
     
     Author: AFNI Developers
@@ -165,10 +145,12 @@ def dicom_hinfo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DicomHinfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_HINFO_METADATA)
     params = execution.params(params)
     cargs = dicom_hinfo_cargs(params, execution)
     ret = dicom_hinfo_outputs(params, execution)
@@ -186,6 +168,8 @@ def dicom_hinfo(
     runner: Runner | None = None,
 ) -> DicomHinfoOutputs:
     """
+    dicom_hinfo
+    
     Prints selected information from one or more DICOM files to stdout.
     
     Author: AFNI Developers
@@ -205,8 +189,6 @@ def dicom_hinfo(
     Returns:
         NamedTuple of outputs (described in `DicomHinfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DICOM_HINFO_METADATA)
     params = dicom_hinfo_params(
         tag=tag,
         sepstr=sepstr,
@@ -215,13 +197,13 @@ def dicom_hinfo(
         namelast=namelast,
         files=files,
     )
-    return dicom_hinfo_execute(params, execution)
+    return dicom_hinfo_execute(params, runner)
 
 
 __all__ = [
     "DICOM_HINFO_METADATA",
     "DicomHinfoOutputs",
-    "DicomHinfoParameters",
     "dicom_hinfo",
+    "dicom_hinfo_execute",
     "dicom_hinfo_params",
 ]

niwrap_afni/afni/dicom_to_raw.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_TO_RAW_METADATA = Metadata(
-    id="ca648caf3773ae863aa716fd8d0405d25e6caa2c.boutiques",
+    id="0a2cbde328d9c72d2d7fb7cc92352b0a51cb72ce.boutiques",
     name="dicom_to_raw",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ DICOM_TO_RAW_METADATA = Metadata(
 
 
 DicomToRawParameters = typing.TypedDict('DicomToRawParameters', {
-    "__STYXTYPE__": typing.Literal["dicom_to_raw"],
+    "@type": typing.NotRequired[typing.Literal["afni/dicom_to_raw"]],
+    "input_dicom": InputPathType,
+})
+DicomToRawParametersTagged = typing.TypedDict('DicomToRawParametersTagged', {
+    "@type": typing.Literal["afni/dicom_to_raw"],
     "input_dicom": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dicom_to_raw": dicom_to_raw_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 {
-        "dicom_to_raw": dicom_to_raw_outputs,
-    }.get(t)
 
 
 class DicomToRawOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dicom_to_raw(...)`.
+    Output object returned when calling `DicomToRawParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class DicomToRawOutputs(typing.NamedTuple):
 
 def dicom_to_raw_params(
     input_dicom: InputPathType,
-) -> DicomToRawParameters:
+) -> DicomToRawParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def dicom_to_raw_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dicom_to_raw",
+        "@type": "afni/dicom_to_raw",
         "input_dicom": input_dicom,
     }
     return params
@@ -94,7 +66,7 @@ def dicom_to_raw_cargs(
     """
     cargs = []
     cargs.append("dicom_to_raw")
-    cargs.append(execution.input_file(params.get("input_dicom")))
+    cargs.append(execution.input_file(params.get("input_dicom", None)))
     return cargs
 
 
@@ -113,16 +85,18 @@ def dicom_to_raw_outputs(
     """
     ret = DicomToRawOutputs(
         root=execution.output_file("."),
-        output_raw_file=execution.output_file(pathlib.Path(params.get("input_dicom")).name + ".raw.0001"),
+        output_raw_file=execution.output_file(pathlib.Path(params.get("input_dicom", None)).name + ".raw.0001"),
     )
     return ret
 
 
 def dicom_to_raw_execute(
     params: DicomToRawParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DicomToRawOutputs:
     """
+    dicom_to_raw
+    
     Reads images from DICOM file and writes them to raw file(s).
     
     Author: AFNI Developers
@@ -131,10 +105,12 @@ def dicom_to_raw_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DicomToRawOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_TO_RAW_METADATA)
     params = execution.params(params)
     cargs = dicom_to_raw_cargs(params, execution)
     ret = dicom_to_raw_outputs(params, execution)
@@ -147,6 +123,8 @@ def dicom_to_raw(
     runner: Runner | None = None,
 ) -> DicomToRawOutputs:
     """
+    dicom_to_raw
+    
     Reads images from DICOM file and writes them to raw file(s).
     
     Author: AFNI Developers
@@ -159,18 +137,16 @@ def dicom_to_raw(
     Returns:
         NamedTuple of outputs (described in `DicomToRawOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DICOM_TO_RAW_METADATA)
     params = dicom_to_raw_params(
         input_dicom=input_dicom,
     )
-    return dicom_to_raw_execute(params, execution)
+    return dicom_to_raw_execute(params, runner)
 
 
 __all__ = [
     "DICOM_TO_RAW_METADATA",
     "DicomToRawOutputs",
-    "DicomToRawParameters",
     "dicom_to_raw",
+    "dicom_to_raw_execute",
     "dicom_to_raw_params",
 ]

niwrap_afni/afni/dimon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DIMON_METADATA = Metadata(
-    id="c892c771a45028c51f21626d1cce300d014da2d2.boutiques",
+    id="5ab73709e46bdb383910ed3cb7eef84a4ba8075a.boutiques",
     name="Dimon",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ DIMON_METADATA = Metadata(
 
 
 DimonParameters = typing.TypedDict('DimonParameters', {
-    "__STYXTYPE__": typing.Literal["Dimon"],
+    "@type": typing.NotRequired[typing.Literal["afni/Dimon"]],
+    "infile_prefix": str,
+    "infile_pattern": typing.NotRequired[str | None],
+    "infile_list": typing.NotRequired[InputPathType | None],
+    "rt_cmd": typing.NotRequired[str | None],
+    "host": typing.NotRequired[str | None],
+    "drive_afni": typing.NotRequired[str | None],
+    "drive_wait": typing.NotRequired[str | None],
+    "te_list": typing.NotRequired[str | None],
+    "sort_method": typing.NotRequired[str | None],
+})
+DimonParametersTagged = typing.TypedDict('DimonParametersTagged', {
+    "@type": typing.Literal["afni/Dimon"],
     "infile_prefix": str,
     "infile_pattern": typing.NotRequired[str | None],
     "infile_list": typing.NotRequired[InputPathType | None],
@@ -25,48 +37,14 @@ DimonParameters = typing.TypedDict('DimonParameters', {
     "te_list": typing.NotRequired[str | None],
     "sort_method": 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 {
-        "Dimon": dimon_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 {
-        "Dimon": dimon_outputs,
-    }.get(t)
 
 
 class DimonOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dimon(...)`.
+    Output object returned when calling `DimonParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    sorted_files: OutputPathType
-    """Sorted input files with specified prefix"""
     sorted_files_details: OutputPathType | None
     """Details about sorted files"""
 
@@ -81,7 +59,7 @@ def dimon_params(
     drive_wait: str | None = None,
     te_list: str | None = None,
     sort_method: str | None = None,
-) -> DimonParameters:
+) -> DimonParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +77,7 @@ def dimon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "Dimon",
+        "@type": "afni/Dimon",
         "infile_prefix": infile_prefix,
     }
     if infile_pattern is not None:
@@ -138,47 +116,47 @@ def dimon_cargs(
     cargs.append("Dimon")
     cargs.extend([
         "-infile_prefix",
-        params.get("infile_prefix")
+        params.get("infile_prefix", None)
     ])
-    if params.get("infile_pattern") is not None:
+    if params.get("infile_pattern", None) is not None:
         cargs.extend([
             "-infile_pattern",
-            params.get("infile_pattern")
+            params.get("infile_pattern", None)
         ])
-    if params.get("infile_list") is not None:
+    if params.get("infile_list", None) is not None:
         cargs.extend([
             "-infile_list",
-            execution.input_file(params.get("infile_list"))
+            execution.input_file(params.get("infile_list", None))
         ])
-    if params.get("rt_cmd") is not None:
+    if params.get("rt_cmd", None) is not None:
         cargs.extend([
             "-rt_cmd",
-            params.get("rt_cmd")
+            params.get("rt_cmd", None)
         ])
-    if params.get("host") is not None:
+    if params.get("host", None) is not None:
         cargs.extend([
             "-host",
-            params.get("host")
+            params.get("host", None)
         ])
-    if params.get("drive_afni") is not None:
+    if params.get("drive_afni", None) is not None:
         cargs.extend([
             "-drive_afni",
-            params.get("drive_afni")
+            params.get("drive_afni", None)
         ])
-    if params.get("drive_wait") is not None:
+    if params.get("drive_wait", None) is not None:
         cargs.extend([
             "-drive_wait",
-            params.get("drive_wait")
+            params.get("drive_wait", None)
         ])
-    if params.get("te_list") is not None:
+    if params.get("te_list", None) is not None:
         cargs.extend([
             "-te_list",
-            params.get("te_list")
+            params.get("te_list", None)
         ])
-    if params.get("sort_method") is not None:
+    if params.get("sort_method", None) is not None:
         cargs.extend([
             "-sort_method",
-            params.get("sort_method")
+            params.get("sort_method", None)
         ])
     return cargs
 
@@ -198,17 +176,18 @@ def dimon_outputs(
     """
     ret = DimonOutputs(
         root=execution.output_file("."),
-        sorted_files=execution.output_file(params.get("infile_prefix") + "*"),
-        sorted_files_details=execution.output_file(pathlib.Path(params.get("infile_list")).name + "_details") if (params.get("infile_list") is not None) else None,
+        sorted_files_details=execution.output_file(pathlib.Path(params.get("infile_list", None)).name + "_details") if (params.get("infile_list") is not None) else None,
     )
     return ret
 
 
 def dimon_execute(
     params: DimonParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DimonOutputs:
     """
+    Dimon
+    
     Monitor real-time acquisition of DICOM image files.
     
     Author: AFNI Developers
@@ -217,10 +196,12 @@ def dimon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DimonOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DIMON_METADATA)
     params = execution.params(params)
     cargs = dimon_cargs(params, execution)
     ret = dimon_outputs(params, execution)
@@ -241,6 +222,8 @@ def dimon(
     runner: Runner | None = None,
 ) -> DimonOutputs:
     """
+    Dimon
+    
     Monitor real-time acquisition of DICOM image files.
     
     Author: AFNI Developers
@@ -261,8 +244,6 @@ def dimon(
     Returns:
         NamedTuple of outputs (described in `DimonOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DIMON_METADATA)
     params = dimon_params(
         infile_prefix=infile_prefix,
         infile_pattern=infile_pattern,
@@ -274,13 +255,13 @@ def dimon(
         te_list=te_list,
         sort_method=sort_method,
     )
-    return dimon_execute(params, execution)
+    return dimon_execute(params, runner)
 
 
 __all__ = [
     "DIMON_METADATA",
     "DimonOutputs",
-    "DimonParameters",
     "dimon",
+    "dimon_execute",
     "dimon_params",
 ]