niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/dcm2niix_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCM2NIIX_AFNI_METADATA = Metadata(
-    id="7cf66629029a0771961d7c7125e4684dcd412a4d.boutiques",
+    id="e5ea5e9f3b64f6321fbd04c6f810e3b7cbd7551b.boutiques",
     name="dcm2niix_afni",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,39 @@ DCM2NIIX_AFNI_METADATA = Metadata(
 
 
 Dcm2niixAfniParameters = typing.TypedDict('Dcm2niixAfniParameters', {
-    "__STYXTYPE__": typing.Literal["dcm2niix_afni"],
+    "@type": typing.NotRequired[typing.Literal["afni/dcm2niix_afni"]],
+    "input_folder": str,
+    "compression_level": typing.NotRequired[int | None],
+    "adjacent_dicoms": typing.NotRequired[str | None],
+    "bids_sidecar": typing.NotRequired[str | None],
+    "anonymize_bids": typing.NotRequired[str | None],
+    "comment": typing.NotRequired[str | None],
+    "directory_search_depth": typing.NotRequired[int | None],
+    "export_format": typing.NotRequired[str | None],
+    "filename_template": typing.NotRequired[str | None],
+    "generate_defaults": typing.NotRequired[str | None],
+    "ignore_images": typing.NotRequired[str | None],
+    "lossless_scale": typing.NotRequired[str | None],
+    "merge_slices": typing.NotRequired[str | None],
+    "series_crc_number": typing.NotRequired[list[str] | None],
+    "output_directory": typing.NotRequired[str | None],
+    "phillips_scaling": typing.NotRequired[str | None],
+    "rename_dicoms": typing.NotRequired[str | None],
+    "single_file_mode": typing.NotRequired[str | None],
+    "up_to_date": bool,
+    "verbose": typing.NotRequired[str | None],
+    "write_behavior": typing.NotRequired[int | None],
+    "crop_3d": typing.NotRequired[str | None],
+    "gz_compress": typing.NotRequired[str | None],
+    "big_endian": typing.NotRequired[str | None],
+    "progress": typing.NotRequired[str | None],
+    "ignore_trigger_times": bool,
+    "terse": bool,
+    "version": bool,
+    "xml": bool,
+})
+Dcm2niixAfniParametersTagged = typing.TypedDict('Dcm2niixAfniParametersTagged', {
+    "@type": typing.Literal["afni/dcm2niix_afni"],
     "input_folder": str,
     "compression_level": typing.NotRequired[int | None],
     "adjacent_dicoms": typing.NotRequired[str | None],
@@ -45,48 +77,16 @@ Dcm2niixAfniParameters = typing.TypedDict('Dcm2niixAfniParameters', {
     "version": bool,
     "xml": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dcm2niix_afni": dcm2niix_afni_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 {
-        "dcm2niix_afni": dcm2niix_afni_outputs,
-    }.get(t)
 
 
 class Dcm2niixAfniOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcm2niix_afni(...)`.
+    Output object returned when calling `Dcm2niixAfniParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    nifti_files: OutputPathType
-    """The main output NIfTI files"""
+    output_directory: OutputPathType | None
+    """The directory containing main output NIfTI files"""
 
 
 def dcm2niix_afni_params(
@@ -119,7 +119,7 @@ def dcm2niix_afni_params(
     terse: bool = False,
     version: bool = False,
     xml_: bool = False,
-) -> Dcm2niixAfniParameters:
+) -> Dcm2niixAfniParametersTagged:
     """
     Build parameters.
     
@@ -172,7 +172,7 @@ def dcm2niix_afni_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcm2niix_afni",
+        "@type": "afni/dcm2niix_afni",
         "input_folder": input_folder,
         "up_to_date": up_to_date,
         "ignore_trigger_times": ignore_trigger_times,
@@ -244,131 +244,131 @@ def dcm2niix_afni_cargs(
     """
     cargs = []
     cargs.append("dcm2niix_afni")
-    cargs.append(params.get("input_folder"))
-    if params.get("compression_level") is not None:
+    cargs.append(params.get("input_folder", None))
+    if params.get("compression_level", None) is not None:
         cargs.extend([
             "-1..-9",
-            str(params.get("compression_level"))
+            str(params.get("compression_level", None))
         ])
-    if params.get("adjacent_dicoms") is not None:
+    if params.get("adjacent_dicoms", None) is not None:
         cargs.extend([
             "-a",
-            params.get("adjacent_dicoms")
+            params.get("adjacent_dicoms", None)
         ])
-    if params.get("bids_sidecar") is not None:
+    if params.get("bids_sidecar", None) is not None:
         cargs.extend([
             "-b",
-            params.get("bids_sidecar")
+            params.get("bids_sidecar", None)
         ])
-    if params.get("anonymize_bids") is not None:
+    if params.get("anonymize_bids", None) is not None:
         cargs.extend([
             "-ba",
-            params.get("anonymize_bids")
+            params.get("anonymize_bids", None)
         ])
-    if params.get("comment") is not None:
+    if params.get("comment", None) is not None:
         cargs.extend([
             "-c",
-            params.get("comment")
+            params.get("comment", None)
         ])
-    if params.get("directory_search_depth") is not None:
+    if params.get("directory_search_depth", None) is not None:
         cargs.extend([
             "-d",
-            str(params.get("directory_search_depth"))
+            str(params.get("directory_search_depth", None))
         ])
-    if params.get("export_format") is not None:
+    if params.get("export_format", None) is not None:
         cargs.extend([
             "-e",
-            params.get("export_format")
+            params.get("export_format", None)
         ])
-    if params.get("filename_template") is not None:
+    if params.get("filename_template", None) is not None:
         cargs.extend([
             "-f",
-            params.get("filename_template")
+            params.get("filename_template", None)
         ])
-    if params.get("generate_defaults") is not None:
+    if params.get("generate_defaults", None) is not None:
         cargs.extend([
             "-g",
-            params.get("generate_defaults")
+            params.get("generate_defaults", None)
         ])
-    if params.get("ignore_images") is not None:
+    if params.get("ignore_images", None) is not None:
         cargs.extend([
             "-i",
-            params.get("ignore_images")
+            params.get("ignore_images", None)
         ])
-    if params.get("lossless_scale") is not None:
+    if params.get("lossless_scale", None) is not None:
         cargs.extend([
             "-l",
-            params.get("lossless_scale")
+            params.get("lossless_scale", None)
         ])
-    if params.get("merge_slices") is not None:
+    if params.get("merge_slices", None) is not None:
         cargs.extend([
             "-m",
-            params.get("merge_slices")
+            params.get("merge_slices", None)
         ])
-    if params.get("series_crc_number") is not None:
+    if params.get("series_crc_number", None) is not None:
         cargs.extend([
             "-n",
-            *params.get("series_crc_number")
+            *params.get("series_crc_number", None)
         ])
-    if params.get("output_directory") is not None:
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
-    if params.get("phillips_scaling") is not None:
+    if params.get("phillips_scaling", None) is not None:
         cargs.extend([
             "-p",
-            params.get("phillips_scaling")
+            params.get("phillips_scaling", None)
         ])
-    if params.get("rename_dicoms") is not None:
+    if params.get("rename_dicoms", None) is not None:
         cargs.extend([
             "-r",
-            params.get("rename_dicoms")
+            params.get("rename_dicoms", None)
         ])
-    if params.get("single_file_mode") is not None:
+    if params.get("single_file_mode", None) is not None:
         cargs.extend([
             "-s",
-            params.get("single_file_mode")
+            params.get("single_file_mode", None)
         ])
-    if params.get("up_to_date"):
+    if params.get("up_to_date", False):
         cargs.append("-u")
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-v",
-            params.get("verbose")
+            params.get("verbose", None)
         ])
-    if params.get("write_behavior") is not None:
+    if params.get("write_behavior", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("write_behavior"))
+            str(params.get("write_behavior", None))
         ])
-    if params.get("crop_3d") is not None:
+    if params.get("crop_3d", None) is not None:
         cargs.extend([
             "-x",
-            params.get("crop_3d")
+            params.get("crop_3d", None)
         ])
-    if params.get("gz_compress") is not None:
+    if params.get("gz_compress", None) is not None:
         cargs.extend([
             "-z",
-            params.get("gz_compress")
+            params.get("gz_compress", None)
         ])
-    if params.get("big_endian") is not None:
+    if params.get("big_endian", None) is not None:
         cargs.extend([
             "--big-endian",
-            params.get("big_endian")
+            params.get("big_endian", None)
         ])
-    if params.get("progress") is not None:
+    if params.get("progress", None) is not None:
         cargs.extend([
             "--progress",
-            params.get("progress")
+            params.get("progress", None)
         ])
-    if params.get("ignore_trigger_times"):
+    if params.get("ignore_trigger_times", False):
         cargs.append("--ignore_trigger_times")
-    if params.get("terse"):
+    if params.get("terse", False):
         cargs.append("--terse")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("xml"):
+    if params.get("xml", False):
         cargs.append("--xml")
     return cargs
 
@@ -388,16 +388,18 @@ def dcm2niix_afni_outputs(
     """
     ret = Dcm2niixAfniOutputs(
         root=execution.output_file("."),
-        nifti_files=execution.output_file("<OUTPUT_DIRECTORY>/*.nii"),
+        output_directory=execution.output_file(params.get("output_directory", None)) if (params.get("output_directory") is not None) else None,
     )
     return ret
 
 
 def dcm2niix_afni_execute(
     params: Dcm2niixAfniParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Dcm2niixAfniOutputs:
     """
+    dcm2niix_afni
+    
     DICOM to NIfTI converter optimized for AFNI.
     
     Author: AFNI Developers
@@ -406,10 +408,12 @@ def dcm2niix_afni_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Dcm2niixAfniOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCM2NIIX_AFNI_METADATA)
     params = execution.params(params)
     cargs = dcm2niix_afni_cargs(params, execution)
     ret = dcm2niix_afni_outputs(params, execution)
@@ -450,6 +454,8 @@ def dcm2niix_afni(
     runner: Runner | None = None,
 ) -> Dcm2niixAfniOutputs:
     """
+    dcm2niix_afni
+    
     DICOM to NIfTI converter optimized for AFNI.
     
     Author: AFNI Developers
@@ -505,8 +511,6 @@ def dcm2niix_afni(
     Returns:
         NamedTuple of outputs (described in `Dcm2niixAfniOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCM2NIIX_AFNI_METADATA)
     params = dcm2niix_afni_params(
         input_folder=input_folder,
         compression_level=compression_level,
@@ -538,13 +542,13 @@ def dcm2niix_afni(
         version=version,
         xml_=xml_,
     )
-    return dcm2niix_afni_execute(params, execution)
+    return dcm2niix_afni_execute(params, runner)
 
 
 __all__ = [
     "DCM2NIIX_AFNI_METADATA",
     "Dcm2niixAfniOutputs",
-    "Dcm2niixAfniParameters",
     "dcm2niix_afni",
+    "dcm2niix_afni_execute",
     "dcm2niix_afni_params",
 ]

niwrap_afni/afni/dicom_hdr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_HDR_METADATA = Metadata(
-    id="06030930d3116d7bf58316357750a3ae68688ced.boutiques",
+    id="f0edec277c064e3934045c9faf56bc0c162e5eeb.boutiques",
     name="dicom_hdr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ DICOM_HDR_METADATA = Metadata(
 
 
 DicomHdrParameters = typing.TypedDict('DicomHdrParameters', {
-    "__STYXTYPE__": typing.Literal["dicom_hdr"],
+    "@type": typing.NotRequired[typing.Literal["afni/dicom_hdr"]],
+    "files": list[InputPathType],
+    "hex": bool,
+    "noname": bool,
+    "sexinfo": bool,
+    "mulfram": bool,
+    "v_dump": typing.NotRequired[float | None],
+    "no_length": bool,
+    "slice_times": bool,
+    "slice_times_verb": bool,
+    "siemens_csa_data": bool,
+})
+DicomHdrParametersTagged = typing.TypedDict('DicomHdrParametersTagged', {
+    "@type": typing.Literal["afni/dicom_hdr"],
     "files": list[InputPathType],
     "hex": bool,
     "noname": bool,
@@ -26,42 +39,11 @@ DicomHdrParameters = typing.TypedDict('DicomHdrParameters', {
     "slice_times_verb": bool,
     "siemens_csa_data": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dicom_hdr": dicom_hdr_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 DicomHdrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dicom_hdr(...)`.
+    Output object returned when calling `DicomHdrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def dicom_hdr_params(
     slice_times: bool = False,
     slice_times_verb: bool = False,
     siemens_csa_data: bool = False,
-) -> DicomHdrParameters:
+) -> DicomHdrParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +82,7 @@ def dicom_hdr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dicom_hdr",
+        "@type": "afni/dicom_hdr",
         "files": files,
         "hex": hex_,
         "noname": noname,
@@ -131,27 +113,27 @@ def dicom_hdr_cargs(
     """
     cargs = []
     cargs.append("dicom_hdr")
-    cargs.extend([execution.input_file(f) for f in params.get("files")])
-    if params.get("hex"):
+    cargs.extend([execution.input_file(f) for f in params.get("files", None)])
+    if params.get("hex", False):
         cargs.append("-hex")
-    if params.get("noname"):
+    if params.get("noname", False):
         cargs.append("-noname")
-    if params.get("sexinfo"):
+    if params.get("sexinfo", False):
         cargs.append("-sexinfo")
-    if params.get("mulfram"):
+    if params.get("mulfram", False):
         cargs.append("-mulfram")
-    if params.get("v_dump") is not None:
+    if params.get("v_dump", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("v_dump"))
+            str(params.get("v_dump", None))
         ])
-    if params.get("no_length"):
+    if params.get("no_length", False):
         cargs.append("-no_length")
-    if params.get("slice_times"):
+    if params.get("slice_times", False):
         cargs.append("-slice_times")
-    if params.get("slice_times_verb"):
+    if params.get("slice_times_verb", False):
         cargs.append("-slice_times_verb")
-    if params.get("siemens_csa_data"):
+    if params.get("siemens_csa_data", False):
         cargs.append("-siemens_csa_data")
     return cargs
 
@@ -177,9 +159,11 @@ def dicom_hdr_outputs(
 
 def dicom_hdr_execute(
     params: DicomHdrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DicomHdrOutputs:
     """
+    dicom_hdr
+    
     A tool to print DICOM file information to stdout.
     
     Author: AFNI Developers
@@ -188,10 +172,12 @@ def dicom_hdr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DicomHdrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_HDR_METADATA)
     params = execution.params(params)
     cargs = dicom_hdr_cargs(params, execution)
     ret = dicom_hdr_outputs(params, execution)
@@ -213,6 +199,8 @@ def dicom_hdr(
     runner: Runner | None = None,
 ) -> DicomHdrOutputs:
     """
+    dicom_hdr
+    
     A tool to print DICOM file information to stdout.
     
     Author: AFNI Developers
@@ -237,8 +225,6 @@ def dicom_hdr(
     Returns:
         NamedTuple of outputs (described in `DicomHdrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DICOM_HDR_METADATA)
     params = dicom_hdr_params(
         files=files,
         hex_=hex_,
@@ -251,13 +237,13 @@ def dicom_hdr(
         slice_times_verb=slice_times_verb,
         siemens_csa_data=siemens_csa_data,
     )
-    return dicom_hdr_execute(params, execution)
+    return dicom_hdr_execute(params, runner)
 
 
 __all__ = [
     "DICOM_HDR_METADATA",
     "DicomHdrOutputs",
-    "DicomHdrParameters",
     "dicom_hdr",
+    "dicom_hdr_execute",
     "dicom_hdr_params",
 ]