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

niwrap_freesurfer/freesurfer/dcmunpack.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMUNPACK_METADATA = Metadata(
-    id="64a19ab70f6129ad53152ddeab602e5432759bab.boutiques",
+    id="a172d3fb8225abb3caf4f7ee8805cdf0967017f5.boutiques",
     name="dcmunpack",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,48 @@ DCMUNPACK_METADATA = Metadata(
 
 
 DcmunpackParameters = typing.TypedDict('DcmunpackParameters', {
-    "__STYXTYPE__": typing.Literal["dcmunpack"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dcmunpack"]],
+    "src": str,
+    "targ": typing.NotRequired[str | None],
+    "run": typing.NotRequired[str | None],
+    "auto_runseq": typing.NotRequired[str | None],
+    "keep_scouts": bool,
+    "scanonly": typing.NotRequired[str | None],
+    "one_per_dir": bool,
+    "ext": typing.NotRequired[str | None],
+    "pre": typing.NotRequired[str | None],
+    "pat": typing.NotRequired[str | None],
+    "no_infodump": bool,
+    "generic": bool,
+    "copy_only": bool,
+    "no_convert": bool,
+    "force_update": bool,
+    "max": bool,
+    "base": bool,
+    "key_string": typing.NotRequired[str | None],
+    "index_out": typing.NotRequired[str | None],
+    "index_in": typing.NotRequired[str | None],
+    "it_dicom": bool,
+    "no_exit_on_error": bool,
+    "run_skip": typing.NotRequired[str | None],
+    "no_rescale_dicom": bool,
+    "rescale_dicom": bool,
+    "no_dwi": bool,
+    "iid": typing.NotRequired[list[float] | None],
+    "ijd": typing.NotRequired[list[float] | None],
+    "ikd": typing.NotRequired[list[float] | None],
+    "extra_info": bool,
+    "first_dicom": bool,
+    "no_dcm2niix": bool,
+    "phase": bool,
+    "fips": typing.NotRequired[str | None],
+    "fips_run": typing.NotRequired[str | None],
+    "xml_only": bool,
+    "log": typing.NotRequired[str | None],
+    "debug": bool,
+})
+DcmunpackParametersTagged = typing.TypedDict('DcmunpackParametersTagged', {
+    "@type": typing.Literal["freesurfer/dcmunpack"],
     "src": str,
     "targ": typing.NotRequired[str | None],
     "run": typing.NotRequired[str | None],
@@ -54,42 +95,11 @@ DcmunpackParameters = typing.TypedDict('DcmunpackParameters', {
     "log": typing.NotRequired[str | None],
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dcmunpack": dcmunpack_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 DcmunpackOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcmunpack(...)`.
+    Output object returned when calling `DcmunpackParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -134,7 +144,7 @@ def dcmunpack_params(
     xml_only: bool = False,
     log: str | None = None,
     debug: bool = False,
-) -> DcmunpackParameters:
+) -> DcmunpackParametersTagged:
     """
     Build parameters.
     
@@ -189,7 +199,7 @@ def dcmunpack_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcmunpack",
+        "@type": "freesurfer/dcmunpack",
         "src": src,
         "keep_scouts": keep_scouts,
         "one_per_dir": one_per_dir,
@@ -266,132 +276,132 @@ def dcmunpack_cargs(
     cargs.append("dcmunpack")
     cargs.extend([
         "-src",
-        params.get("src")
+        params.get("src", None)
     ])
-    if params.get("targ") is not None:
+    if params.get("targ", None) is not None:
         cargs.extend([
             "-targ",
-            params.get("targ")
+            params.get("targ", None)
         ])
-    if params.get("run") is not None:
+    if params.get("run", None) is not None:
         cargs.extend([
             "-run",
-            params.get("run")
+            params.get("run", None)
         ])
-    if params.get("auto_runseq") is not None:
+    if params.get("auto_runseq", None) is not None:
         cargs.extend([
             "-auto-runseq",
-            params.get("auto_runseq")
+            params.get("auto_runseq", None)
         ])
-    if params.get("keep_scouts"):
+    if params.get("keep_scouts", False):
         cargs.append("-keep-scouts")
-    if params.get("scanonly") is not None:
+    if params.get("scanonly", None) is not None:
         cargs.extend([
             "-scanonly",
-            params.get("scanonly")
+            params.get("scanonly", None)
         ])
-    if params.get("one_per_dir"):
+    if params.get("one_per_dir", False):
         cargs.append("-one-per-dir")
-    if params.get("ext") is not None:
+    if params.get("ext", None) is not None:
         cargs.extend([
             "-ext",
-            params.get("ext")
+            params.get("ext", None)
         ])
-    if params.get("pre") is not None:
+    if params.get("pre", None) is not None:
         cargs.extend([
             "-pre",
-            params.get("pre")
+            params.get("pre", None)
         ])
-    if params.get("pat") is not None:
+    if params.get("pat", None) is not None:
         cargs.extend([
             "-pat",
-            params.get("pat")
+            params.get("pat", None)
         ])
-    if params.get("no_infodump"):
+    if params.get("no_infodump", False):
         cargs.append("-no-infodump")
-    if params.get("generic"):
+    if params.get("generic", False):
         cargs.append("-generic")
-    if params.get("copy_only"):
+    if params.get("copy_only", False):
         cargs.append("-copy-only")
-    if params.get("no_convert"):
+    if params.get("no_convert", False):
         cargs.append("-no-convert")
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("-force-update")
-    if params.get("max"):
+    if params.get("max", False):
         cargs.append("-max")
-    if params.get("base"):
+    if params.get("base", False):
         cargs.append("-base")
-    if params.get("key_string") is not None:
+    if params.get("key_string", None) is not None:
         cargs.extend([
             "-key",
-            params.get("key_string")
+            params.get("key_string", None)
         ])
-    if params.get("index_out") is not None:
+    if params.get("index_out", None) is not None:
         cargs.extend([
             "-index-out",
-            params.get("index_out")
+            params.get("index_out", None)
         ])
-    if params.get("index_in") is not None:
+    if params.get("index_in", None) is not None:
         cargs.extend([
             "-index-in",
-            params.get("index_in")
+            params.get("index_in", None)
         ])
-    if params.get("it_dicom"):
+    if params.get("it_dicom", False):
         cargs.append("-itdicom")
-    if params.get("no_exit_on_error"):
+    if params.get("no_exit_on_error", False):
         cargs.append("-no-exit-on-error")
-    if params.get("run_skip") is not None:
+    if params.get("run_skip", None) is not None:
         cargs.extend([
             "-run-skip",
-            params.get("run_skip")
+            params.get("run_skip", None)
         ])
-    if params.get("no_rescale_dicom"):
+    if params.get("no_rescale_dicom", False):
         cargs.append("-no-rescale-dicom")
-    if params.get("rescale_dicom"):
+    if params.get("rescale_dicom", False):
         cargs.append("-rescale-dicom")
-    if params.get("no_dwi"):
+    if params.get("no_dwi", False):
         cargs.append("-no-dwi")
-    if params.get("iid") is not None:
+    if params.get("iid", None) is not None:
         cargs.extend([
             "-iid",
-            *map(str, params.get("iid"))
+            *map(str, params.get("iid", None))
         ])
-    if params.get("ijd") is not None:
+    if params.get("ijd", None) is not None:
         cargs.extend([
             "-ijd",
-            *map(str, params.get("ijd"))
+            *map(str, params.get("ijd", None))
         ])
-    if params.get("ikd") is not None:
+    if params.get("ikd", None) is not None:
         cargs.extend([
             "-ikd",
-            *map(str, params.get("ikd"))
+            *map(str, params.get("ikd", None))
         ])
-    if params.get("extra_info"):
+    if params.get("extra_info", False):
         cargs.append("-extra-info")
-    if params.get("first_dicom"):
+    if params.get("first_dicom", False):
         cargs.append("-first-dicom")
-    if params.get("no_dcm2niix"):
+    if params.get("no_dcm2niix", False):
         cargs.append("-no-dcm2niix")
-    if params.get("phase"):
+    if params.get("phase", False):
         cargs.append("-phase")
-    if params.get("fips") is not None:
+    if params.get("fips", None) is not None:
         cargs.extend([
             "-fips",
-            params.get("fips")
+            params.get("fips", None)
         ])
-    if params.get("fips_run") is not None:
+    if params.get("fips_run", None) is not None:
         cargs.extend([
             "-fips-run",
-            params.get("fips_run")
+            params.get("fips_run", None)
         ])
-    if params.get("xml_only"):
+    if params.get("xml_only", False):
         cargs.append("-xml-only")
-    if params.get("log") is not None:
+    if params.get("log", None) is not None:
         cargs.extend([
             "-log",
-            params.get("log")
+            params.get("log", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
     return cargs
 
@@ -417,9 +427,11 @@ def dcmunpack_outputs(
 
 def dcmunpack_execute(
     params: DcmunpackParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DcmunpackOutputs:
     """
+    dcmunpack
+    
     Sorts and converts a directory of DICOM files (Siemens, GE, Philips) into an
     output hierarchy with nifti (nii), mgh, mgz, or analyze output formats.
     
@@ -429,10 +441,12 @@ def dcmunpack_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DcmunpackOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMUNPACK_METADATA)
     params = execution.params(params)
     cargs = dcmunpack_cargs(params, execution)
     ret = dcmunpack_outputs(params, execution)
@@ -482,6 +496,8 @@ def dcmunpack(
     runner: Runner | None = None,
 ) -> DcmunpackOutputs:
     """
+    dcmunpack
+    
     Sorts and converts a directory of DICOM files (Siemens, GE, Philips) into an
     output hierarchy with nifti (nii), mgh, mgz, or analyze output formats.
     
@@ -540,8 +556,6 @@ def dcmunpack(
     Returns:
         NamedTuple of outputs (described in `DcmunpackOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCMUNPACK_METADATA)
     params = dcmunpack_params(
         src=src,
         targ=targ,
@@ -582,13 +596,13 @@ def dcmunpack(
         log=log,
         debug=debug,
     )
-    return dcmunpack_execute(params, execution)
+    return dcmunpack_execute(params, runner)
 
 
 __all__ = [
     "DCMUNPACK_METADATA",
     "DcmunpackOutputs",
-    "DcmunpackParameters",
     "dcmunpack",
+    "dcmunpack_execute",
     "dcmunpack_params",
 ]

niwrap_freesurfer/freesurfer/deface_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DEFACE_SUBJECT_METADATA = Metadata(
-    id="89832befbb0be4ec4bfd9bda31d48569152b4136.boutiques",
+    id="7c334a149092c36895908dacd855b00538942a5d.boutiques",
     name="deface_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ DEFACE_SUBJECT_METADATA = Metadata(
 
 
 DefaceSubjectParameters = typing.TypedDict('DefaceSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["deface_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/deface_subject"]],
+    "subjects_dir": str,
+    "subject_id": str,
+    "volume_input": InputPathType,
+    "volume_output": str,
+})
+DefaceSubjectParametersTagged = typing.TypedDict('DefaceSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/deface_subject"],
     "subjects_dir": str,
     "subject_id": str,
     "volume_input": InputPathType,
     "volume_output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "deface_subject": deface_subject_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 {
-        "deface_subject": deface_subject_outputs,
-    }.get(t)
 
 
 class DefaceSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `deface_subject(...)`.
+    Output object returned when calling `DefaceSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def deface_subject_params(
     subject_id: str,
     volume_input: InputPathType,
     volume_output: str,
-) -> DefaceSubjectParameters:
+) -> DefaceSubjectParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def deface_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "deface_subject",
+        "@type": "freesurfer/deface_subject",
         "subjects_dir": subjects_dir,
         "subject_id": subject_id,
         "volume_input": volume_input,
@@ -108,19 +83,19 @@ def deface_subject_cargs(
     cargs.append("deface_subject")
     cargs.extend([
         "-sdir",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
     cargs.extend([
         "-id",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     cargs.extend([
         "-i",
-        execution.input_file(params.get("volume_input"))
+        execution.input_file(params.get("volume_input", None))
     ])
     cargs.extend([
         "-o",
-        params.get("volume_output")
+        params.get("volume_output", None)
     ])
     return cargs
 
@@ -140,16 +115,18 @@ def deface_subject_outputs(
     """
     ret = DefaceSubjectOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("volume_output")),
+        output_volume=execution.output_file(params.get("volume_output", None)),
     )
     return ret
 
 
 def deface_subject_execute(
     params: DefaceSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DefaceSubjectOutputs:
     """
+    deface_subject
+    
     Tool for defacing MRI images to anonymize patient data.
     
     Author: FreeSurfer Developers
@@ -158,10 +135,12 @@ def deface_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DefaceSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFACE_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = deface_subject_cargs(params, execution)
     ret = deface_subject_outputs(params, execution)
@@ -177,6 +156,8 @@ def deface_subject(
     runner: Runner | None = None,
 ) -> DefaceSubjectOutputs:
     """
+    deface_subject
+    
     Tool for defacing MRI images to anonymize patient data.
     
     Author: FreeSurfer Developers
@@ -192,21 +173,19 @@ def deface_subject(
     Returns:
         NamedTuple of outputs (described in `DefaceSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DEFACE_SUBJECT_METADATA)
     params = deface_subject_params(
         subjects_dir=subjects_dir,
         subject_id=subject_id,
         volume_input=volume_input,
         volume_output=volume_output,
     )
-    return deface_subject_execute(params, execution)
+    return deface_subject_execute(params, runner)
 
 
 __all__ = [
     "DEFACE_SUBJECT_METADATA",
     "DefaceSubjectOutputs",
-    "DefaceSubjectParameters",
     "deface_subject",
+    "deface_subject_execute",
     "deface_subject_params",
 ]