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

niwrap_mrtrix/mrtrix/dcmedit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMEDIT_METADATA = Metadata(
-    id="8cde5cf6f19725e4d438d7089e7f5a9e71f0b93d.boutiques",
+    id="8755d3035d88c63d3618eea7e9e40463fa8a47ee.boutiques",
     name="dcmedit",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,7 +14,13 @@ DCMEDIT_METADATA = Metadata(
 
 
 DcmeditTagParameters = typing.TypedDict('DcmeditTagParameters', {
-    "__STYXTYPE__": typing.Literal["tag"],
+    "@type": typing.NotRequired[typing.Literal["tag"]],
+    "group": str,
+    "element": str,
+    "newvalue": str,
+})
+DcmeditTagParametersTagged = typing.TypedDict('DcmeditTagParametersTagged', {
+    "@type": typing.Literal["tag"],
     "group": str,
     "element": str,
     "newvalue": str,
@@ -22,14 +28,34 @@ DcmeditTagParameters = typing.TypedDict('DcmeditTagParameters', {
 
 
 DcmeditConfigParameters = typing.TypedDict('DcmeditConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+DcmeditConfigParametersTagged = typing.TypedDict('DcmeditConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 DcmeditParameters = typing.TypedDict('DcmeditParameters', {
-    "__STYXTYPE__": typing.Literal["dcmedit"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/dcmedit"]],
+    "anonymise": bool,
+    "id": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[list[DcmeditTagParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DcmeditConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "file": InputPathType,
+})
+DcmeditParametersTagged = typing.TypedDict('DcmeditParametersTagged', {
+    "@type": typing.Literal["mrtrix/dcmedit"],
     "anonymise": bool,
     "id": typing.NotRequired[str | None],
     "tag": typing.NotRequired[list[DcmeditTagParameters] | None],
@@ -43,46 +69,13 @@ DcmeditParameters = typing.TypedDict('DcmeditParameters', {
     "version": bool,
     "file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dcmedit": dcmedit_cargs,
-        "tag": dcmedit_tag_cargs,
-        "config": dcmedit_config_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)
 
 
 def dcmedit_tag_params(
     group: str,
     element: str,
     newvalue: str,
-) -> DcmeditTagParameters:
+) -> DcmeditTagParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +87,7 @@ def dcmedit_tag_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tag",
+        "@type": "tag",
         "group": group,
         "element": element,
         "newvalue": newvalue,
@@ -117,16 +110,16 @@ def dcmedit_tag_cargs(
     """
     cargs = []
     cargs.append("-tag")
-    cargs.append(params.get("group"))
-    cargs.append(params.get("element"))
-    cargs.append(params.get("newvalue"))
+    cargs.append(params.get("group", None))
+    cargs.append(params.get("element", None))
+    cargs.append(params.get("newvalue", None))
     return cargs
 
 
 def dcmedit_config_params(
     key: str,
     value: str,
-) -> DcmeditConfigParameters:
+) -> DcmeditConfigParametersTagged:
     """
     Build parameters.
     
@@ -137,7 +130,7 @@ def dcmedit_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -159,14 +152,14 @@ def dcmedit_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class DcmeditOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcmedit(...)`.
+    Output object returned when calling `DcmeditParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -185,7 +178,7 @@ def dcmedit_params(
     config: list[DcmeditConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> DcmeditParameters:
+) -> DcmeditParametersTagged:
     """
     Build parameters.
     
@@ -221,7 +214,7 @@ def dcmedit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcmedit",
+        "@type": "mrtrix/dcmedit",
         "anonymise": anonymise,
         "info": info,
         "quiet": quiet,
@@ -257,35 +250,35 @@ def dcmedit_cargs(
     """
     cargs = []
     cargs.append("dcmedit")
-    if params.get("anonymise"):
+    if params.get("anonymise", False):
         cargs.append("-anonymise")
-    if params.get("id") is not None:
+    if params.get("id", None) is not None:
         cargs.extend([
             "-id",
-            params.get("id")
+            params.get("id", None)
         ])
-    if params.get("tag") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("tag")] for a in c])
-    if params.get("info"):
+    if params.get("tag", None) is not None:
+        cargs.extend([a for c in [dcmedit_tag_cargs(s, execution) for s in params.get("tag", None)] for a in c])
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [dcmedit_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("file")))
+    cargs.append(execution.input_file(params.get("file", None)))
     return cargs
 
 
@@ -310,9 +303,11 @@ def dcmedit_outputs(
 
 def dcmedit_execute(
     params: DcmeditParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DcmeditOutputs:
     """
+    dcmedit
+    
     Edit DICOM file in-place.
     
     Note that this command simply replaces the existing values without modifying
@@ -332,10 +327,12 @@ def dcmedit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DcmeditOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMEDIT_METADATA)
     params = execution.params(params)
     cargs = dcmedit_cargs(params, execution)
     ret = dcmedit_outputs(params, execution)
@@ -359,6 +356,8 @@ def dcmedit(
     runner: Runner | None = None,
 ) -> DcmeditOutputs:
     """
+    dcmedit
+    
     Edit DICOM file in-place.
     
     Note that this command simply replaces the existing values without modifying
@@ -408,8 +407,6 @@ def dcmedit(
     Returns:
         NamedTuple of outputs (described in `DcmeditOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCMEDIT_METADATA)
     params = dcmedit_params(
         anonymise=anonymise,
         id_=id_,
@@ -424,17 +421,15 @@ def dcmedit(
         version=version,
         file=file,
     )
-    return dcmedit_execute(params, execution)
+    return dcmedit_execute(params, runner)
 
 
 __all__ = [
     "DCMEDIT_METADATA",
-    "DcmeditConfigParameters",
     "DcmeditOutputs",
-    "DcmeditParameters",
-    "DcmeditTagParameters",
     "dcmedit",
     "dcmedit_config_params",
+    "dcmedit_execute",
     "dcmedit_params",
     "dcmedit_tag_params",
 ]

niwrap_mrtrix/mrtrix/dcminfo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DCMINFO_METADATA = Metadata(
-    id="07f39463fe810bd85aa94c83f3e100efd9db5e83.boutiques",
+    id="f02767c67a910f0ef82176cc014707d1d17070a2.boutiques",
     name="dcminfo",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,21 +14,47 @@ DCMINFO_METADATA = Metadata(
 
 
 DcminfoTagParameters = typing.TypedDict('DcminfoTagParameters', {
-    "__STYXTYPE__": typing.Literal["tag"],
+    "@type": typing.NotRequired[typing.Literal["tag"]],
+    "group": str,
+    "element": str,
+})
+DcminfoTagParametersTagged = typing.TypedDict('DcminfoTagParametersTagged', {
+    "@type": typing.Literal["tag"],
     "group": str,
     "element": str,
 })
 
 
 DcminfoConfigParameters = typing.TypedDict('DcminfoConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+DcminfoConfigParametersTagged = typing.TypedDict('DcminfoConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 DcminfoParameters = typing.TypedDict('DcminfoParameters', {
-    "__STYXTYPE__": typing.Literal["dcminfo"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/dcminfo"]],
+    "all": bool,
+    "csa": bool,
+    "phoenix": bool,
+    "tag": typing.NotRequired[list[DcminfoTagParameters] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[DcminfoConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "file": InputPathType,
+})
+DcminfoParametersTagged = typing.TypedDict('DcminfoParametersTagged', {
+    "@type": typing.Literal["mrtrix/dcminfo"],
     "all": bool,
     "csa": bool,
     "phoenix": bool,
@@ -43,45 +69,12 @@ DcminfoParameters = typing.TypedDict('DcminfoParameters', {
     "version": bool,
     "file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dcminfo": dcminfo_cargs,
-        "tag": dcminfo_tag_cargs,
-        "config": dcminfo_config_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)
 
 
 def dcminfo_tag_params(
     group: str,
     element: str,
-) -> DcminfoTagParameters:
+) -> DcminfoTagParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +89,7 @@ def dcminfo_tag_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tag",
+        "@type": "tag",
         "group": group,
         "element": element,
     }
@@ -118,15 +111,15 @@ def dcminfo_tag_cargs(
     """
     cargs = []
     cargs.append("-tag")
-    cargs.append(params.get("group"))
-    cargs.append(params.get("element"))
+    cargs.append(params.get("group", None))
+    cargs.append(params.get("element", None))
     return cargs
 
 
 def dcminfo_config_params(
     key: str,
     value: str,
-) -> DcminfoConfigParameters:
+) -> DcminfoConfigParametersTagged:
     """
     Build parameters.
     
@@ -137,7 +130,7 @@ def dcminfo_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -159,14 +152,14 @@ def dcminfo_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class DcminfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dcminfo(...)`.
+    Output object returned when calling `DcminfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -186,7 +179,7 @@ def dcminfo_params(
     config: list[DcminfoConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> DcminfoParameters:
+) -> DcminfoParametersTagged:
     """
     Build parameters.
     
@@ -214,7 +207,7 @@ def dcminfo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dcminfo",
+        "@type": "mrtrix/dcminfo",
         "all": all_,
         "csa": csa,
         "phoenix": phoenix,
@@ -250,34 +243,34 @@ def dcminfo_cargs(
     """
     cargs = []
     cargs.append("dcminfo")
-    if params.get("all"):
+    if params.get("all", False):
         cargs.append("-all")
-    if params.get("csa"):
+    if params.get("csa", False):
         cargs.append("-csa")
-    if params.get("phoenix"):
+    if params.get("phoenix", False):
         cargs.append("-phoenix")
-    if params.get("tag") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("tag")] for a in c])
-    if params.get("info"):
+    if params.get("tag", None) is not None:
+        cargs.extend([a for c in [dcminfo_tag_cargs(s, execution) for s in params.get("tag", None)] for a in c])
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [dcminfo_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("file")))
+    cargs.append(execution.input_file(params.get("file", None)))
     return cargs
 
 
@@ -302,9 +295,11 @@ def dcminfo_outputs(
 
 def dcminfo_execute(
     params: DcminfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DcminfoOutputs:
     """
+    dcminfo
+    
     Output DICOM fields in human-readable format.
     
     
@@ -319,10 +314,12 @@ def dcminfo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DcminfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DCMINFO_METADATA)
     params = execution.params(params)
     cargs = dcminfo_cargs(params, execution)
     ret = dcminfo_outputs(params, execution)
@@ -347,6 +344,8 @@ def dcminfo(
     runner: Runner | None = None,
 ) -> DcminfoOutputs:
     """
+    dcminfo
+    
     Output DICOM fields in human-readable format.
     
     
@@ -383,8 +382,6 @@ def dcminfo(
     Returns:
         NamedTuple of outputs (described in `DcminfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DCMINFO_METADATA)
     params = dcminfo_params(
         all_=all_,
         csa=csa,
@@ -400,17 +397,15 @@ def dcminfo(
         version=version,
         file=file,
     )
-    return dcminfo_execute(params, execution)
+    return dcminfo_execute(params, runner)
 
 
 __all__ = [
     "DCMINFO_METADATA",
-    "DcminfoConfigParameters",
     "DcminfoOutputs",
-    "DcminfoParameters",
-    "DcminfoTagParameters",
     "dcminfo",
     "dcminfo_config_params",
+    "dcminfo_execute",
     "dcminfo_params",
     "dcminfo_tag_params",
 ]