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

niwrap_afni/afni/fat_proc_convert_dcm_dwis.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_CONVERT_DCM_DWIS_METADATA = Metadata(
-    id="012a1abbcf7ef5f5ce0b2e253bfc3807310bf236.boutiques",
+    id="819854f3caefcd724b79e423c240789a1b1ea953.boutiques",
     name="fat_proc_convert_dcm_dwis",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ FAT_PROC_CONVERT_DCM_DWIS_METADATA = Metadata(
 
 
 FatProcConvertDcmDwisParameters = typing.TypedDict('FatProcConvertDcmDwisParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_convert_dcm_dwis"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_convert_dcm_dwis"]],
+    "dicom_dir": str,
+    "output_prefix": str,
+    "nifti_files": typing.NotRequired[list[InputPathType] | None],
+    "bvec_files": typing.NotRequired[list[InputPathType] | None],
+    "bval_files": typing.NotRequired[list[InputPathType] | None],
+    "work_dir": typing.NotRequired[str | None],
+    "orientation": typing.NotRequired[str | None],
+    "origin_xyz": typing.NotRequired[list[float] | None],
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "no_flip": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "reorient_off": bool,
+    "no_clean": bool,
+    "no_cmd_out": bool,
+    "no_qc_view": bool,
+    "do_movie": typing.NotRequired[str | None],
+})
+FatProcConvertDcmDwisParametersTagged = typing.TypedDict('FatProcConvertDcmDwisParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_convert_dcm_dwis"],
     "dicom_dir": str,
     "output_prefix": str,
     "nifti_files": typing.NotRequired[list[InputPathType] | None],
@@ -34,43 +55,11 @@ FatProcConvertDcmDwisParameters = typing.TypedDict('FatProcConvertDcmDwisParamet
     "no_qc_view": bool,
     "do_movie": 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 {
-        "fat_proc_convert_dcm_dwis": fat_proc_convert_dcm_dwis_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 {
-        "fat_proc_convert_dcm_dwis": fat_proc_convert_dcm_dwis_outputs,
-    }.get(t)
 
 
 class FatProcConvertDcmDwisOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_convert_dcm_dwis(...)`.
+    Output object returned when calling `FatProcConvertDcmDwisParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -111,7 +100,7 @@ def fat_proc_convert_dcm_dwis_params(
     no_cmd_out: bool = False,
     no_qc_view: bool = False,
     do_movie: str | None = None,
-) -> FatProcConvertDcmDwisParameters:
+) -> FatProcConvertDcmDwisParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +134,7 @@ def fat_proc_convert_dcm_dwis_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_convert_dcm_dwis",
+        "@type": "afni/fat_proc_convert_dcm_dwis",
         "dicom_dir": dicom_dir,
         "output_prefix": output_prefix,
         "flip_x": flip_x,
@@ -191,42 +180,42 @@ def fat_proc_convert_dcm_dwis_cargs(
     """
     cargs = []
     cargs.append("fat_proc_convert_dcm_dwis")
-    cargs.append(params.get("dicom_dir"))
-    cargs.append(params.get("output_prefix"))
-    if params.get("nifti_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("nifti_files")])
-    if params.get("bvec_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("bvec_files")])
-    if params.get("bval_files") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("bval_files")])
-    if params.get("work_dir") is not None:
-        cargs.append(params.get("work_dir"))
-    if params.get("orientation") is not None:
-        cargs.append(params.get("orientation"))
-    if params.get("origin_xyz") is not None:
-        cargs.extend(map(str, params.get("origin_xyz")))
-    if params.get("flip_x"):
+    cargs.append(params.get("dicom_dir", None))
+    cargs.append(params.get("output_prefix", None))
+    if params.get("nifti_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("nifti_files", None)])
+    if params.get("bvec_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("bvec_files", None)])
+    if params.get("bval_files", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("bval_files", None)])
+    if params.get("work_dir", None) is not None:
+        cargs.append(params.get("work_dir", None))
+    if params.get("orientation", None) is not None:
+        cargs.append(params.get("orientation", None))
+    if params.get("origin_xyz", None) is not None:
+        cargs.extend(map(str, params.get("origin_xyz", None)))
+    if params.get("flip_x", False):
         cargs.append("-flip_x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-flip_y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-flip_z")
-    if params.get("no_flip"):
+    if params.get("no_flip", False):
         cargs.append("-no_flip")
-    if params.get("qc_prefix") is not None:
-        cargs.append(params.get("qc_prefix"))
-    if params.get("reorient_off"):
+    if params.get("qc_prefix", None) is not None:
+        cargs.append(params.get("qc_prefix", None))
+    if params.get("reorient_off", False):
         cargs.append("-reorig_reorient_off")
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    if params.get("no_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
-    if params.get("do_movie") is not None:
+    if params.get("do_movie", None) is not None:
         cargs.extend([
             "-do_movie",
-            params.get("do_movie")
+            params.get("do_movie", None)
         ])
     return cargs
 
@@ -246,23 +235,26 @@ def fat_proc_convert_dcm_dwis_outputs(
     """
     ret = FatProcConvertDcmDwisOutputs(
         root=execution.output_file("."),
-        output_nifti=execution.output_file(params.get("output_prefix") + ".nii.gz"),
-        output_rvec=execution.output_file(params.get("output_prefix") + ".rvec"),
-        output_bval=execution.output_file(params.get("output_prefix") + ".bval"),
-        output_mat_a=execution.output_file(params.get("output_prefix") + "_matA.dat"),
-        output_mat_t=execution.output_file(params.get("output_prefix") + "_matT.dat"),
-        output_cvec=execution.output_file(params.get("output_prefix") + "_cvec.dat"),
+        output_nifti=execution.output_file(params.get("output_prefix", None) + ".nii.gz"),
+        output_rvec=execution.output_file(params.get("output_prefix", None) + ".rvec"),
+        output_bval=execution.output_file(params.get("output_prefix", None) + ".bval"),
+        output_mat_a=execution.output_file(params.get("output_prefix", None) + "_matA.dat"),
+        output_mat_t=execution.output_file(params.get("output_prefix", None) + "_matT.dat"),
+        output_cvec=execution.output_file(params.get("output_prefix", None) + "_cvec.dat"),
     )
     return ret
 
 
 def fat_proc_convert_dcm_dwis_execute(
     params: FatProcConvertDcmDwisParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcConvertDcmDwisOutputs:
     """
-    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format, reorient
-    volumetric data, and glue together multiple sessions/directories of data.
+    fat_proc_convert_dcm_dwis
+    
+    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format,
+    reorient volumetric data, and glue together multiple sessions/directories of
+    data.
     
     Author: AFNI Developers
     
@@ -270,10 +262,12 @@ def fat_proc_convert_dcm_dwis_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcConvertDcmDwisOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_CONVERT_DCM_DWIS_METADATA)
     params = execution.params(params)
     cargs = fat_proc_convert_dcm_dwis_cargs(params, execution)
     ret = fat_proc_convert_dcm_dwis_outputs(params, execution)
@@ -303,8 +297,11 @@ def fat_proc_convert_dcm_dwis(
     runner: Runner | None = None,
 ) -> FatProcConvertDcmDwisOutputs:
     """
-    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format, reorient
-    volumetric data, and glue together multiple sessions/directories of data.
+    fat_proc_convert_dcm_dwis
+    
+    Convert sets of DWIs in DICOM format into 'nicer' volume+grad format,
+    reorient volumetric data, and glue together multiple sessions/directories of
+    data.
     
     Author: AFNI Developers
     
@@ -340,8 +337,6 @@ def fat_proc_convert_dcm_dwis(
     Returns:
         NamedTuple of outputs (described in `FatProcConvertDcmDwisOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_CONVERT_DCM_DWIS_METADATA)
     params = fat_proc_convert_dcm_dwis_params(
         dicom_dir=dicom_dir,
         output_prefix=output_prefix,
@@ -362,13 +357,13 @@ def fat_proc_convert_dcm_dwis(
         no_qc_view=no_qc_view,
         do_movie=do_movie,
     )
-    return fat_proc_convert_dcm_dwis_execute(params, execution)
+    return fat_proc_convert_dcm_dwis_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_CONVERT_DCM_DWIS_METADATA",
     "FatProcConvertDcmDwisOutputs",
-    "FatProcConvertDcmDwisParameters",
     "fat_proc_convert_dcm_dwis",
+    "fat_proc_convert_dcm_dwis_execute",
     "fat_proc_convert_dcm_dwis_params",
 ]

niwrap_afni/afni/fat_proc_decmap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_PROC_DECMAP_METADATA = Metadata(
-    id="45121a70c28df707b0e175b9138ea43971564311.boutiques",
+    id="ca491f287d5cb34d79116906fd02296391367e14.boutiques",
     name="fat_proc_decmap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ FAT_PROC_DECMAP_METADATA = Metadata(
 
 
 FatProcDecmapParameters = typing.TypedDict('FatProcDecmapParameters', {
-    "__STYXTYPE__": typing.Literal["fat_proc_decmap"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_proc_decmap"]],
+    "in_fa": InputPathType,
+    "in_v1": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "fa_thr": typing.NotRequired[float | None],
+    "fa_sca": typing.NotRequired[float | None],
+    "workdir": typing.NotRequired[str | None],
+    "no_clean": bool,
+    "qc_prefix": typing.NotRequired[str | None],
+    "no_cmd_out": bool,
+    "no_qc_view": bool,
+})
+FatProcDecmapParametersTagged = typing.TypedDict('FatProcDecmapParametersTagged', {
+    "@type": typing.Literal["afni/fat_proc_decmap"],
     "in_fa": InputPathType,
     "in_v1": InputPathType,
     "prefix": str,
@@ -27,43 +41,11 @@ FatProcDecmapParameters = typing.TypedDict('FatProcDecmapParameters', {
     "no_cmd_out": bool,
     "no_qc_view": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_proc_decmap": fat_proc_decmap_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 {
-        "fat_proc_decmap": fat_proc_decmap_outputs,
-    }.get(t)
 
 
 class FatProcDecmapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_proc_decmap(...)`.
+    Output object returned when calling `FatProcDecmapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +78,7 @@ def fat_proc_decmap_params(
     qc_prefix: str | None = None,
     no_cmd_out: bool = False,
     no_qc_view: bool = False,
-) -> FatProcDecmapParameters:
+) -> FatProcDecmapParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +103,7 @@ def fat_proc_decmap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_proc_decmap",
+        "@type": "afni/fat_proc_decmap",
         "in_fa": in_fa,
         "in_v1": in_v1,
         "prefix": prefix,
@@ -159,46 +141,46 @@ def fat_proc_decmap_cargs(
     cargs.append("fat_proc_decmap")
     cargs.extend([
         "-in_fa",
-        execution.input_file(params.get("in_fa"))
+        execution.input_file(params.get("in_fa", None))
     ])
     cargs.extend([
         "-in_v1",
-        execution.input_file(params.get("in_v1"))
+        execution.input_file(params.get("in_v1", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("fa_thr") is not None:
+    if params.get("fa_thr", None) is not None:
         cargs.extend([
             "-fa_thr",
-            str(params.get("fa_thr"))
+            str(params.get("fa_thr", None))
         ])
-    if params.get("fa_sca") is not None:
+    if params.get("fa_sca", None) is not None:
         cargs.extend([
             "-fa_sca",
-            str(params.get("fa_sca"))
+            str(params.get("fa_sca", None))
         ])
-    if params.get("workdir") is not None:
+    if params.get("workdir", None) is not None:
         cargs.extend([
             "-workdir",
-            params.get("workdir")
+            params.get("workdir", None)
         ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("qc_prefix") is not None:
+    if params.get("qc_prefix", None) is not None:
         cargs.extend([
             "-qc_prefix",
-            params.get("qc_prefix")
+            params.get("qc_prefix", None)
         ])
-    if params.get("no_cmd_out"):
+    if params.get("no_cmd_out", False):
         cargs.append("-no_cmd_out")
-    if params.get("no_qc_view"):
+    if params.get("no_qc_view", False):
         cargs.append("-no_qc_view")
     return cargs
 
@@ -218,21 +200,23 @@ def fat_proc_decmap_outputs(
     """
     ret = FatProcDecmapOutputs(
         root=execution.output_file("."),
-        outfile_dec_rgb=execution.output_file(params.get("prefix") + "_dec.nii.gz"),
-        outfile_dec_unwt_thr=execution.output_file(params.get("prefix") + "_dec_unwt_thr.nii.gz"),
-        outfile_dec_sca=execution.output_file(params.get("prefix") + "_dec_sca*.nii.gz"),
-        qc_dec_images=execution.output_file(params.get("prefix") + "_qc_dec*.png"),
-        qc_dec_unwt_thrx_images=execution.output_file(params.get("prefix") + "_qc_dec_unwt_thrx*.png"),
-        qc_dec_sca_images=execution.output_file(params.get("prefix") + "_qc_dec_sca*.png"),
+        outfile_dec_rgb=execution.output_file(params.get("prefix", None) + "_dec.nii.gz"),
+        outfile_dec_unwt_thr=execution.output_file(params.get("prefix", None) + "_dec_unwt_thr.nii.gz"),
+        outfile_dec_sca=execution.output_file(params.get("prefix", None) + "_dec_sca.nii.gz"),
+        qc_dec_images=execution.output_file(params.get("prefix", None) + "_qc_dec.png"),
+        qc_dec_unwt_thrx_images=execution.output_file(params.get("prefix", None) + "_qc_dec_unwt_thrx.png"),
+        qc_dec_sca_images=execution.output_file(params.get("prefix", None) + "_qc_dec_sca.png"),
     )
     return ret
 
 
 def fat_proc_decmap_execute(
     params: FatProcDecmapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatProcDecmapOutputs:
     """
+    fat_proc_decmap
+    
     This program makes a directionally encoded color (DEC) map for DTI results.
     
     Author: AFNI Developers
@@ -241,10 +225,12 @@ def fat_proc_decmap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatProcDecmapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_PROC_DECMAP_METADATA)
     params = execution.params(params)
     cargs = fat_proc_decmap_cargs(params, execution)
     ret = fat_proc_decmap_outputs(params, execution)
@@ -267,6 +253,8 @@ def fat_proc_decmap(
     runner: Runner | None = None,
 ) -> FatProcDecmapOutputs:
     """
+    fat_proc_decmap
+    
     This program makes a directionally encoded color (DEC) map for DTI results.
     
     Author: AFNI Developers
@@ -294,8 +282,6 @@ def fat_proc_decmap(
     Returns:
         NamedTuple of outputs (described in `FatProcDecmapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_PROC_DECMAP_METADATA)
     params = fat_proc_decmap_params(
         in_fa=in_fa,
         in_v1=in_v1,
@@ -309,13 +295,13 @@ def fat_proc_decmap(
         no_cmd_out=no_cmd_out,
         no_qc_view=no_qc_view,
     )
-    return fat_proc_decmap_execute(params, execution)
+    return fat_proc_decmap_execute(params, runner)
 
 
 __all__ = [
     "FAT_PROC_DECMAP_METADATA",
     "FatProcDecmapOutputs",
-    "FatProcDecmapParameters",
     "fat_proc_decmap",
+    "fat_proc_decmap_execute",
     "fat_proc_decmap_params",
 ]