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

niwrap_freesurfer/freesurfer/csvprint.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CSVPRINT_METADATA = Metadata(
-    id="88fe426126aea1052da673cfeee9f2078fb01491.boutiques",
+    id="d678521bcbfff71f3853debd657f7f1d29702d43.boutiques",
     name="csvprint",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ CSVPRINT_METADATA = Metadata(
 
 
 CsvprintParameters = typing.TypedDict('CsvprintParameters', {
-    "__STYXTYPE__": typing.Literal["csvprint"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/csvprint"]],
+    "infile": InputPathType,
+})
+CsvprintParametersTagged = typing.TypedDict('CsvprintParametersTagged', {
+    "@type": typing.Literal["freesurfer/csvprint"],
     "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 {
-        "csvprint": csvprint_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 CsvprintOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `csvprint(...)`.
+    Output object returned when calling `CsvprintParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class CsvprintOutputs(typing.NamedTuple):
 
 def csvprint_params(
     infile: InputPathType,
-) -> CsvprintParameters:
+) -> CsvprintParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def csvprint_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "csvprint",
+        "@type": "freesurfer/csvprint",
         "infile": infile,
     }
     return params
@@ -91,7 +64,7 @@ def csvprint_cargs(
     """
     cargs = []
     cargs.append("csvprint")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def csvprint_outputs(
 
 def csvprint_execute(
     params: CsvprintParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CsvprintOutputs:
     """
+    csvprint
+    
     Command-line tool for printing CSV files.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def csvprint_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CsvprintOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CSVPRINT_METADATA)
     params = execution.params(params)
     cargs = csvprint_cargs(params, execution)
     ret = csvprint_outputs(params, execution)
@@ -143,6 +120,8 @@ def csvprint(
     runner: Runner | None = None,
 ) -> CsvprintOutputs:
     """
+    csvprint
+    
     Command-line tool for printing CSV files.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def csvprint(
     Returns:
         NamedTuple of outputs (described in `CsvprintOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CSVPRINT_METADATA)
     params = csvprint_params(
         infile=infile,
     )
-    return csvprint_execute(params, execution)
+    return csvprint_execute(params, runner)
 
 
 __all__ = [
     "CSVPRINT_METADATA",
     "CsvprintOutputs",
-    "CsvprintParameters",
     "csvprint",
+    "csvprint_execute",
     "csvprint_params",
 ]

niwrap_freesurfer/freesurfer/dcmdir_info_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMDIR_INFO_MGH_METADATA = Metadata(
-    id="8a0c29bc82d0c5ee9d5b9085f7f1bd5a728df60b.boutiques",
+    id="ff157bb6f0f3351f04caa2610173225c28c8297c.boutiques",
     name="dcmdir-info-mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,56 +14,29 @@ DCMDIR_INFO_MGH_METADATA = Metadata(
 
 
 DcmdirInfoMghParameters = typing.TypedDict('DcmdirInfoMghParameters', {
-    "__STYXTYPE__": typing.Literal["dcmdir-info-mgh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dcmdir-info-mgh"]],
+    "dicomdir": str,
+    "unpackdir": typing.NotRequired[str | None],
+    "version": bool,
+    "help": bool,
+    "nopre": bool,
+})
+DcmdirInfoMghParametersTagged = typing.TypedDict('DcmdirInfoMghParametersTagged', {
+    "@type": typing.Literal["freesurfer/dcmdir-info-mgh"],
     "dicomdir": str,
     "unpackdir": typing.NotRequired[str | None],
     "version": bool,
     "help": bool,
     "nopre": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dcmdir-info-mgh": dcmdir_info_mgh_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 {
-        "dcmdir-info-mgh": dcmdir_info_mgh_outputs,
-    }.get(t)
 
 
 class DcmdirInfoMghOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcmdir_info_mgh(...)`.
+    Output object returned when calling `DcmdirInfoMghParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    converted_mgz_files: OutputPathType
-    """Converted DICOM files to MGZ format with naming sequencename_runR.mgz,
-    where R is the run number"""
 
 
 def dcmdir_info_mgh_params(
@@ -72,7 +45,7 @@ def dcmdir_info_mgh_params(
     version: bool = False,
     help_: bool = False,
     nopre: bool = False,
-) -> DcmdirInfoMghParameters:
+) -> DcmdirInfoMghParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +60,7 @@ def dcmdir_info_mgh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcmdir-info-mgh",
+        "@type": "freesurfer/dcmdir-info-mgh",
         "dicomdir": dicomdir,
         "version": version,
         "help": help_,
@@ -115,15 +88,15 @@ def dcmdir_info_mgh_cargs(
     cargs.append("dcmdir-info-mgh")
     cargs.extend([
         "-mgh",
-        params.get("dicomdir")
+        params.get("dicomdir", None)
     ])
-    if params.get("unpackdir") is not None:
-        cargs.append(params.get("unpackdir"))
-    if params.get("version"):
+    if params.get("unpackdir", None) is not None:
+        cargs.append(params.get("unpackdir", None))
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("nopre"):
+    if params.get("nopre", False):
         cargs.append("--nopre")
     return cargs
 
@@ -143,16 +116,17 @@ def dcmdir_info_mgh_outputs(
     """
     ret = DcmdirInfoMghOutputs(
         root=execution.output_file("."),
-        converted_mgz_files=execution.output_file("sequencename_run*.mgz"),
     )
     return ret
 
 
 def dcmdir_info_mgh_execute(
     params: DcmdirInfoMghParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DcmdirInfoMghOutputs:
     """
+    dcmdir-info-mgh
+    
     Scans a DICOM directory and extracts information about each series.
     
     Author: FreeSurfer Developers
@@ -161,10 +135,12 @@ def dcmdir_info_mgh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DcmdirInfoMghOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMDIR_INFO_MGH_METADATA)
     params = execution.params(params)
     cargs = dcmdir_info_mgh_cargs(params, execution)
     ret = dcmdir_info_mgh_outputs(params, execution)
@@ -181,6 +157,8 @@ def dcmdir_info_mgh(
     runner: Runner | None = None,
 ) -> DcmdirInfoMghOutputs:
     """
+    dcmdir-info-mgh
+    
     Scans a DICOM directory and extracts information about each series.
     
     Author: FreeSurfer Developers
@@ -198,8 +176,6 @@ def dcmdir_info_mgh(
     Returns:
         NamedTuple of outputs (described in `DcmdirInfoMghOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCMDIR_INFO_MGH_METADATA)
     params = dcmdir_info_mgh_params(
         dicomdir=dicomdir,
         unpackdir=unpackdir,
@@ -207,13 +183,13 @@ def dcmdir_info_mgh(
         help_=help_,
         nopre=nopre,
     )
-    return dcmdir_info_mgh_execute(params, execution)
+    return dcmdir_info_mgh_execute(params, runner)
 
 
 __all__ = [
     "DCMDIR_INFO_MGH_METADATA",
     "DcmdirInfoMghOutputs",
-    "DcmdirInfoMghParameters",
     "dcmdir_info_mgh",
+    "dcmdir_info_mgh_execute",
     "dcmdir_info_mgh_params",
 ]

niwrap_freesurfer/freesurfer/dcmdjpeg_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMDJPEG_FS_METADATA = Metadata(
-    id="359bc973b8599706e77b1aca498ebac2ce7ef402.boutiques",
+    id="7d851e4223498a0783e1f0f02a5344daf4d5e472.boutiques",
     name="dcmdjpeg.fs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,51 @@ DCMDJPEG_FS_METADATA = Metadata(
 
 
 DcmdjpegFsParameters = typing.TypedDict('DcmdjpegFsParameters', {
-    "__STYXTYPE__": typing.Literal["dcmdjpeg.fs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dcmdjpeg.fs"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "help": bool,
+    "version": bool,
+    "arguments": bool,
+    "quiet": bool,
+    "verbose": bool,
+    "debug": bool,
+    "log_level": typing.NotRequired[str | None],
+    "log_config": typing.NotRequired[InputPathType | None],
+    "read_file": bool,
+    "read_file_only": bool,
+    "read_dataset": bool,
+    "conv_photometric": bool,
+    "conv_lossy": bool,
+    "conv_guess": bool,
+    "conv_guess_lossy": bool,
+    "conv_always": bool,
+    "conv_never": bool,
+    "planar_auto": bool,
+    "color_by_pixel": bool,
+    "color_by_plane": bool,
+    "uid_default": bool,
+    "uid_always": bool,
+    "workaround_pred6": bool,
+    "workaround_incpl": bool,
+    "write_file": bool,
+    "write_dataset": bool,
+    "write_xfer_little": bool,
+    "write_xfer_big": bool,
+    "write_xfer_implicit": bool,
+    "enable_new_vr": bool,
+    "disable_new_vr": bool,
+    "group_length_recalc": bool,
+    "group_length_create": bool,
+    "group_length_remove": bool,
+    "length_explicit": bool,
+    "length_undefined": bool,
+    "padding_retain": bool,
+    "padding_off": bool,
+    "padding_create": typing.NotRequired[list[float] | None],
+})
+DcmdjpegFsParametersTagged = typing.TypedDict('DcmdjpegFsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dcmdjpeg.fs"],
     "input_file": InputPathType,
     "output_file": str,
     "help": bool,
@@ -57,43 +101,11 @@ DcmdjpegFsParameters = typing.TypedDict('DcmdjpegFsParameters', {
     "padding_off": bool,
     "padding_create": typing.NotRequired[list[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 {
-        "dcmdjpeg.fs": dcmdjpeg_fs_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 {
-        "dcmdjpeg.fs": dcmdjpeg_fs_outputs,
-    }.get(t)
 
 
 class DcmdjpegFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcmdjpeg_fs(...)`.
+    Output object returned when calling `DcmdjpegFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -143,7 +155,7 @@ def dcmdjpeg_fs_params(
     padding_retain: bool = False,
     padding_off: bool = False,
     padding_create: list[float] | None = None,
-) -> DcmdjpegFsParameters:
+) -> DcmdjpegFsParametersTagged:
     """
     Build parameters.
     
@@ -197,7 +209,7 @@ def dcmdjpeg_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcmdjpeg.fs",
+        "@type": "freesurfer/dcmdjpeg.fs",
         "input_file": input_file,
         "output_file": output_file,
         "help": help_,
@@ -261,94 +273,94 @@ def dcmdjpeg_fs_cargs(
     """
     cargs = []
     cargs.append("dcmdjpeg.fs")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("help"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("help", False):
         cargs.append("-h")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("arguments"):
+    if params.get("arguments", False):
         cargs.append("--arguments")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-q")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-d")
-    if params.get("log_level") is not None:
+    if params.get("log_level", None) is not None:
         cargs.extend([
             "-ll",
-            params.get("log_level")
+            params.get("log_level", None)
         ])
-    if params.get("log_config") is not None:
+    if params.get("log_config", None) is not None:
         cargs.extend([
             "-lc",
-            execution.input_file(params.get("log_config"))
+            execution.input_file(params.get("log_config", None))
         ])
-    if params.get("read_file"):
+    if params.get("read_file", False):
         cargs.append("+f")
-    if params.get("read_file_only"):
+    if params.get("read_file_only", False):
         cargs.append("+fo")
-    if params.get("read_dataset"):
+    if params.get("read_dataset", False):
         cargs.append("-f")
-    if params.get("conv_photometric"):
+    if params.get("conv_photometric", False):
         cargs.append("+cp")
-    if params.get("conv_lossy"):
+    if params.get("conv_lossy", False):
         cargs.append("+cl")
-    if params.get("conv_guess"):
+    if params.get("conv_guess", False):
         cargs.append("+cg")
-    if params.get("conv_guess_lossy"):
+    if params.get("conv_guess_lossy", False):
         cargs.append("+cgl")
-    if params.get("conv_always"):
+    if params.get("conv_always", False):
         cargs.append("+ca")
-    if params.get("conv_never"):
+    if params.get("conv_never", False):
         cargs.append("+cn")
-    if params.get("planar_auto"):
+    if params.get("planar_auto", False):
         cargs.append("+pa")
-    if params.get("color_by_pixel"):
+    if params.get("color_by_pixel", False):
         cargs.append("+px")
-    if params.get("color_by_plane"):
+    if params.get("color_by_plane", False):
         cargs.append("+pl")
-    if params.get("uid_default"):
+    if params.get("uid_default", False):
         cargs.append("+ud")
-    if params.get("uid_always"):
+    if params.get("uid_always", False):
         cargs.append("+ua")
-    if params.get("workaround_pred6"):
+    if params.get("workaround_pred6", False):
         cargs.append("+w6")
-    if params.get("workaround_incpl"):
+    if params.get("workaround_incpl", False):
         cargs.append("+wi")
-    if params.get("write_file"):
+    if params.get("write_file", False):
         cargs.append("+F")
-    if params.get("write_dataset"):
+    if params.get("write_dataset", False):
         cargs.append("-F")
-    if params.get("write_xfer_little"):
+    if params.get("write_xfer_little", False):
         cargs.append("+te")
-    if params.get("write_xfer_big"):
+    if params.get("write_xfer_big", False):
         cargs.append("+tb")
-    if params.get("write_xfer_implicit"):
+    if params.get("write_xfer_implicit", False):
         cargs.append("+ti")
-    if params.get("enable_new_vr"):
+    if params.get("enable_new_vr", False):
         cargs.append("+u")
-    if params.get("disable_new_vr"):
+    if params.get("disable_new_vr", False):
         cargs.append("-u")
-    if params.get("group_length_recalc"):
+    if params.get("group_length_recalc", False):
         cargs.append("+g=")
-    if params.get("group_length_create"):
+    if params.get("group_length_create", False):
         cargs.append("+g")
-    if params.get("group_length_remove"):
+    if params.get("group_length_remove", False):
         cargs.append("-g")
-    if params.get("length_explicit"):
+    if params.get("length_explicit", False):
         cargs.append("+e")
-    if params.get("length_undefined"):
+    if params.get("length_undefined", False):
         cargs.append("-e")
-    if params.get("padding_retain"):
+    if params.get("padding_retain", False):
         cargs.append("-p=")
-    if params.get("padding_off"):
+    if params.get("padding_off", False):
         cargs.append("-p")
-    if params.get("padding_create") is not None:
+    if params.get("padding_create", None) is not None:
         cargs.extend([
             "+p",
-            *map(str, params.get("padding_create"))
+            *map(str, params.get("padding_create", None))
         ])
     return cargs
 
@@ -368,16 +380,18 @@ def dcmdjpeg_fs_outputs(
     """
     ret = DcmdjpegFsOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def dcmdjpeg_fs_execute(
     params: DcmdjpegFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DcmdjpegFsOutputs:
     """
+    dcmdjpeg.fs
+    
     A tool to decode JPEG-compressed DICOM files.
     
     Author: FreeSurfer Developers
@@ -386,10 +400,12 @@ def dcmdjpeg_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DcmdjpegFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMDJPEG_FS_METADATA)
     params = execution.params(params)
     cargs = dcmdjpeg_fs_cargs(params, execution)
     ret = dcmdjpeg_fs_outputs(params, execution)
@@ -442,6 +458,8 @@ def dcmdjpeg_fs(
     runner: Runner | None = None,
 ) -> DcmdjpegFsOutputs:
     """
+    dcmdjpeg.fs
+    
     A tool to decode JPEG-compressed DICOM files.
     
     Author: FreeSurfer Developers
@@ -498,8 +516,6 @@ def dcmdjpeg_fs(
     Returns:
         NamedTuple of outputs (described in `DcmdjpegFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCMDJPEG_FS_METADATA)
     params = dcmdjpeg_fs_params(
         input_file=input_file,
         output_file=output_file,
@@ -543,13 +559,13 @@ def dcmdjpeg_fs(
         padding_off=padding_off,
         padding_create=padding_create,
     )
-    return dcmdjpeg_fs_execute(params, execution)
+    return dcmdjpeg_fs_execute(params, runner)
 
 
 __all__ = [
     "DCMDJPEG_FS_METADATA",
     "DcmdjpegFsOutputs",
-    "DcmdjpegFsParameters",
     "dcmdjpeg_fs",
+    "dcmdjpeg_fs_execute",
     "dcmdjpeg_fs_params",
 ]