niwrap-afni 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_afni/afni/v_3d_nwarp_xyz.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_NWARP_XYZ_METADATA = Metadata(
-    id="5a16d2bee46238f64451cbe6e0fea267dd5ecf53.boutiques",
+    id="1ad64cabce09853e006ac8e3b63d94912f629b5c.boutiques",
     name="3dNwarpXYZ",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,8 +15,10 @@ V_3D_NWARP_XYZ_METADATA = Metadata(
 
 V3dNwarpXyzParameters = typing.TypedDict('V3dNwarpXyzParameters', {
     "__STYX_TYPE__": typing.Literal["3dNwarpXYZ"],
-    "warp_spec": str,
     "xyzfile": InputPathType,
+    "warp_spec": str,
+    "iwarp": bool,
+    "output_file": str,
 })
 
 
@@ -63,22 +65,28 @@ class V3dNwarpXyzOutputs(typing.NamedTuple):
 
 
 def v_3d_nwarp_xyz_params(
-    warp_spec: str,
     xyzfile: InputPathType,
+    warp_spec: str,
+    output_file: str,
+    iwarp: bool = False,
 ) -> V3dNwarpXyzParameters:
     """
     Build parameters.
     
     Args:
-        warp_spec: Warp specification as in 3dNwarpApply.
         xyzfile: XYZ coordinate file containing 3 columns.
+        warp_spec: Warp specification as in 3dNwarpApply.
+        output_file: Warped XYZ coordinates output file.
+        iwarp: Compute the inverse warp for each input (x,y,z) triple.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dNwarpXYZ",
-        "warp_spec": warp_spec,
         "xyzfile": xyzfile,
+        "warp_spec": warp_spec,
+        "iwarp": iwarp,
+        "output_file": output_file,
     }
     return params
 
@@ -98,15 +106,14 @@ def v_3d_nwarp_xyz_cargs(
     """
     cargs = []
     cargs.append("3dNwarpXYZ")
-    cargs.append("[OPTIONS]")
-    cargs.append("-nwarp")
+    cargs.append(execution.input_file(params.get("xyzfile")))
     cargs.extend([
         "-nwarp",
         params.get("warp_spec")
     ])
-    cargs.append(execution.input_file(params.get("xyzfile")))
-    cargs.append(">")
-    cargs.append("[OUTPUT_FILE]")
+    if params.get("iwarp"):
+        cargs.append("-iwarp")
+    cargs.append("> " + params.get("output_file"))
     return cargs
 
 
@@ -125,7 +132,7 @@ def v_3d_nwarp_xyz_outputs(
     """
     ret = V3dNwarpXyzOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file("[OUTPUT_FILE]"),
+        output_file=execution.output_file(params.get("output_file")),
     )
     return ret
 
@@ -156,8 +163,10 @@ def v_3d_nwarp_xyz_execute(
 
 
 def v_3d_nwarp_xyz(
-    warp_spec: str,
     xyzfile: InputPathType,
+    warp_spec: str,
+    output_file: str,
+    iwarp: bool = False,
     runner: Runner | None = None,
 ) -> V3dNwarpXyzOutputs:
     """
@@ -169,8 +178,10 @@ def v_3d_nwarp_xyz(
     URL: https://afni.nimh.nih.gov/
     
     Args:
-        warp_spec: Warp specification as in 3dNwarpApply.
         xyzfile: XYZ coordinate file containing 3 columns.
+        warp_spec: Warp specification as in 3dNwarpApply.
+        output_file: Warped XYZ coordinates output file.
+        iwarp: Compute the inverse warp for each input (x,y,z) triple.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dNwarpXyzOutputs`).
@@ -178,8 +189,10 @@ def v_3d_nwarp_xyz(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_NWARP_XYZ_METADATA)
     params = v_3d_nwarp_xyz_params(
-        warp_spec=warp_spec,
         xyzfile=xyzfile,
+        warp_spec=warp_spec,
+        iwarp=iwarp,
+        output_file=output_file,
     )
     return v_3d_nwarp_xyz_execute(params, execution)
 

niwrap_afni/afni/v_3d_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_OVERLAP_METADATA = Metadata(
-    id="a1bc040d8dc7e5b89536a75a10ba6ad55a1ecc95.boutiques",
+    id="55cf3c3d26402707160ae90ffa63fe67eaa8da85.boutiques",
     name="3dOverlap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,7 @@ V3dOverlapParameters = typing.TypedDict('V3dOverlapParameters', {
     "__STYX_TYPE__": typing.Literal["3dOverlap"],
     "dataset1": InputPathType,
     "dataset2": list[InputPathType],
+    "save_prefix": typing.NotRequired[str | None],
 })
 
 
@@ -58,15 +59,16 @@ class V3dOverlapOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_brik: OutputPathType
+    output_brik: OutputPathType | None
     """BRIK file with count of overlaps at each voxel (if -save is used)"""
-    output_head: OutputPathType
+    output_head: OutputPathType | None
     """HEAD file with count of overlaps at each voxel (if -save is used)"""
 
 
 def v_3d_overlap_params(
     dataset1: InputPathType,
     dataset2: list[InputPathType],
+    save_prefix: str | None = None,
 ) -> V3dOverlapParameters:
     """
     Build parameters.
@@ -74,6 +76,8 @@ def v_3d_overlap_params(
     Args:
         dataset1: First input dataset (e.g. dset1+orig).
         dataset2: Second input dataset (e.g. dset2+orig).
+        save_prefix: Save the count of overlaps at each voxel into a dataset\
+            with the given prefix.
     Returns:
         Parameter dictionary
     """
@@ -82,6 +86,8 @@ def v_3d_overlap_params(
         "dataset1": dataset1,
         "dataset2": dataset2,
     }
+    if save_prefix is not None:
+        params["save_prefix"] = save_prefix
     return params
 
 
@@ -100,9 +106,13 @@ def v_3d_overlap_cargs(
     """
     cargs = []
     cargs.append("3dOverlap")
-    cargs.append("[OPTIONS]")
     cargs.append(execution.input_file(params.get("dataset1")))
     cargs.extend([execution.input_file(f) for f in params.get("dataset2")])
+    if params.get("save_prefix") is not None:
+        cargs.extend([
+            "-save",
+            params.get("save_prefix")
+        ])
     return cargs
 
 
@@ -121,8 +131,8 @@ def v_3d_overlap_outputs(
     """
     ret = V3dOverlapOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file("[SAVE_PREFIX]+orig.BRIK"),
-        output_head=execution.output_file("[SAVE_PREFIX]+orig.HEAD"),
+        output_brik=execution.output_file(params.get("save_prefix") + "+orig.BRIK") if (params.get("save_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("save_prefix") + "+orig.HEAD") if (params.get("save_prefix") is not None) else None,
     )
     return ret
 
@@ -154,6 +164,7 @@ def v_3d_overlap_execute(
 def v_3d_overlap(
     dataset1: InputPathType,
     dataset2: list[InputPathType],
+    save_prefix: str | None = None,
     runner: Runner | None = None,
 ) -> V3dOverlapOutputs:
     """
@@ -166,6 +177,8 @@ def v_3d_overlap(
     Args:
         dataset1: First input dataset (e.g. dset1+orig).
         dataset2: Second input dataset (e.g. dset2+orig).
+        save_prefix: Save the count of overlaps at each voxel into a dataset\
+            with the given prefix.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dOverlapOutputs`).
@@ -175,6 +188,7 @@ def v_3d_overlap(
     params = v_3d_overlap_params(
         dataset1=dataset1,
         dataset2=dataset2,
+        save_prefix=save_prefix,
     )
     return v_3d_overlap_execute(params, execution)
 

niwrap_afni/afni/v_3d_par2_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PAR2_AFNI_METADATA = Metadata(
-    id="955afce507c339e4fbf43caaf056ad39a659f439.boutiques",
+    id="abf07fa80d8ac5cc00c4348273246690b0e76d2a.boutiques",
     name="3dPAR2AFNI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,11 +17,14 @@ V3dPar2AfniParameters = typing.TypedDict('V3dPar2AfniParameters', {
     "__STYX_TYPE__": typing.Literal["3dPAR2AFNI"],
     "input_file": InputPathType,
     "skip_outliers_test": bool,
+    "output_nifti": bool,
     "output_analyze": bool,
     "output_dir": typing.NotRequired[str | None],
     "verbose_flag": bool,
     "gzip_files": bool,
+    "byte_swap_2": bool,
     "byte_swap_4": bool,
+    "help_flag": bool,
 })
 
 
@@ -70,11 +73,14 @@ class V3dPar2AfniOutputs(typing.NamedTuple):
 def v_3d_par2_afni_params(
     input_file: InputPathType,
     skip_outliers_test: bool = False,
+    output_nifti: bool = False,
     output_analyze: bool = False,
     output_dir: str | None = None,
     verbose_flag: bool = False,
     gzip_files: bool = False,
+    byte_swap_2: bool = False,
     byte_swap_4: bool = False,
+    help_flag: bool = False,
 ) -> V3dPar2AfniParameters:
     """
     Build parameters.
@@ -83,6 +89,8 @@ def v_3d_par2_afni_params(
         input_file: Input PAR file (e.g., subject1.PAR).
         skip_outliers_test: Skip the outliers test when converting 4D files.\
             The default is to perform the outliers test.
+        output_nifti: Output NIfTI files instead of HEAD/BRIK. The default is\
+            to create HEAD/BRIK files.
         output_analyze: Output ANALYZE files instead of HEAD/BRIK.
         output_dir: The name of the directory where the created files should be\
             placed. If this directory does not exist, the program exits without\
@@ -90,8 +98,11 @@ def v_3d_par2_afni_params(
         verbose_flag: Be verbose in operation.
         gzip_files: Gzip the files created. The default is not to gzip the\
             files.
+        byte_swap_2: 2-Byte-swap the files created. The default is not to 2\
+            byte-swap.
         byte_swap_4: 4-Byte-swap the files created. The default is not to 4\
             byte-swap.
+        help_flag: Display help message.
     Returns:
         Parameter dictionary
     """
@@ -99,10 +110,13 @@ def v_3d_par2_afni_params(
         "__STYXTYPE__": "3dPAR2AFNI",
         "input_file": input_file,
         "skip_outliers_test": skip_outliers_test,
+        "output_nifti": output_nifti,
         "output_analyze": output_analyze,
         "verbose_flag": verbose_flag,
         "gzip_files": gzip_files,
+        "byte_swap_2": byte_swap_2,
         "byte_swap_4": byte_swap_4,
+        "help_flag": help_flag,
     }
     if output_dir is not None:
         params["output_dir"] = output_dir
@@ -127,6 +141,8 @@ def v_3d_par2_afni_cargs(
     cargs.append(execution.input_file(params.get("input_file")))
     if params.get("skip_outliers_test"):
         cargs.append("-s")
+    if params.get("output_nifti"):
+        cargs.append("-n")
     if params.get("output_analyze"):
         cargs.append("-a")
     if params.get("output_dir") is not None:
@@ -138,8 +154,12 @@ def v_3d_par2_afni_cargs(
         cargs.append("-v")
     if params.get("gzip_files"):
         cargs.append("-g")
+    if params.get("byte_swap_2"):
+        cargs.append("-2")
     if params.get("byte_swap_4"):
         cargs.append("-4")
+    if params.get("help_flag"):
+        cargs.append("-h")
     return cargs
 
 
@@ -190,11 +210,14 @@ def v_3d_par2_afni_execute(
 def v_3d_par2_afni(
     input_file: InputPathType,
     skip_outliers_test: bool = False,
+    output_nifti: bool = False,
     output_analyze: bool = False,
     output_dir: str | None = None,
     verbose_flag: bool = False,
     gzip_files: bool = False,
+    byte_swap_2: bool = False,
     byte_swap_4: bool = False,
+    help_flag: bool = False,
     runner: Runner | None = None,
 ) -> V3dPar2AfniOutputs:
     """
@@ -208,6 +231,8 @@ def v_3d_par2_afni(
         input_file: Input PAR file (e.g., subject1.PAR).
         skip_outliers_test: Skip the outliers test when converting 4D files.\
             The default is to perform the outliers test.
+        output_nifti: Output NIfTI files instead of HEAD/BRIK. The default is\
+            to create HEAD/BRIK files.
         output_analyze: Output ANALYZE files instead of HEAD/BRIK.
         output_dir: The name of the directory where the created files should be\
             placed. If this directory does not exist, the program exits without\
@@ -215,8 +240,11 @@ def v_3d_par2_afni(
         verbose_flag: Be verbose in operation.
         gzip_files: Gzip the files created. The default is not to gzip the\
             files.
+        byte_swap_2: 2-Byte-swap the files created. The default is not to 2\
+            byte-swap.
         byte_swap_4: 4-Byte-swap the files created. The default is not to 4\
             byte-swap.
+        help_flag: Display help message.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPar2AfniOutputs`).
@@ -226,11 +254,14 @@ def v_3d_par2_afni(
     params = v_3d_par2_afni_params(
         input_file=input_file,
         skip_outliers_test=skip_outliers_test,
+        output_nifti=output_nifti,
         output_analyze=output_analyze,
         output_dir=output_dir,
         verbose_flag=verbose_flag,
         gzip_files=gzip_files,
+        byte_swap_2=byte_swap_2,
         byte_swap_4=byte_swap_4,
+        help_flag=help_flag,
     )
     return v_3d_par2_afni_execute(params, execution)
 

niwrap_afni/afni/v_3d_pfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PFM_METADATA = Metadata(
-    id="c5e5e30b454a1a81f02535de2e794be7d716492a.boutiques",
+    id="96e747e1055107a8734dd4f14bdc3fe2e1d0dca3.boutiques",
     name="3dPFM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,21 @@ V_3D_PFM_METADATA = Metadata(
 
 V3dPfmParameters = typing.TypedDict('V3dPfmParameters', {
     "__STYX_TYPE__": typing.Literal["3dPFM"],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "algorithm": typing.NotRequired[str | None],
+    "criteria": typing.NotRequired[str | None],
+    "nonzeros": typing.NotRequired[float | None],
+    "maxiter": typing.NotRequired[float | None],
+    "maxiterfactor": typing.NotRequired[float | None],
+    "tr": typing.NotRequired[float | None],
+    "hrf": typing.NotRequired[str | None],
+    "hrf_vol": typing.NotRequired[InputPathType | None],
+    "idx_hrf": typing.NotRequired[InputPathType | None],
+    "LHS": typing.NotRequired[list[InputPathType] | None],
+    "jobs": typing.NotRequired[float | None],
+    "nSeg": typing.NotRequired[float | None],
+    "verb": typing.NotRequired[float | None],
 })
 
 
@@ -113,17 +128,79 @@ class V3dPfmOutputs(typing.NamedTuple):
 
 
 def v_3d_pfm_params(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    algorithm: str | None = None,
+    criteria: str | None = None,
+    nonzeros: float | None = None,
+    maxiter: float | None = None,
+    maxiterfactor: float | None = None,
+    tr: float | None = None,
+    hrf: str | None = None,
+    hrf_vol: InputPathType | None = None,
+    idx_hrf: InputPathType | None = None,
+    lhs: list[InputPathType] | None = None,
+    jobs: float | None = None,
+    n_seg: float | None = None,
+    verb: float | None = None,
 ) -> V3dPfmParameters:
     """
     Build parameters.
     
     Args:
+        input_: Specify the dataset to analyze (e.g., epi.nii).
+        mask: Process voxels inside this mask only. Default is no masking.
+        algorithm: Regularization function used for HRF deconvolution (dantzig\
+            or lasso).
+        criteria: Model selection criterion for HRF deconvolution (BIC or AIC).
+        nonzeros: Choose estimate with a fixed number of nonzero coefficients.
+        maxiter: Maximum number of iterations in the homotopy procedure\
+            (absolute value).
+        maxiterfactor: Maximum number of iterations relative to the number of\
+            volumes.
+        tr: Repetition time or sampling period of the input data.
+        hrf: Haemodynamic response function used for deconvolution.
+        hrf_vol: 3D+time dataset with voxel/nodes/vertex -dependent HRFs.
+        idx_hrf: 3D dataset with voxel-dependent indexes for HRF.
+        lhs: Additional regressors to be fitted to the dataset.
+        jobs: Number of parallel jobs to use in processing.
+        n_seg: Divide into segments to report progress.
+        verb: Verbosity level (0 for quiet, 1 for talkative).
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dPFM",
+        "input": input_,
     }
+    if mask is not None:
+        params["mask"] = mask
+    if algorithm is not None:
+        params["algorithm"] = algorithm
+    if criteria is not None:
+        params["criteria"] = criteria
+    if nonzeros is not None:
+        params["nonzeros"] = nonzeros
+    if maxiter is not None:
+        params["maxiter"] = maxiter
+    if maxiterfactor is not None:
+        params["maxiterfactor"] = maxiterfactor
+    if tr is not None:
+        params["tr"] = tr
+    if hrf is not None:
+        params["hrf"] = hrf
+    if hrf_vol is not None:
+        params["hrf_vol"] = hrf_vol
+    if idx_hrf is not None:
+        params["idx_hrf"] = idx_hrf
+    if lhs is not None:
+        params["LHS"] = lhs
+    if jobs is not None:
+        params["jobs"] = jobs
+    if n_seg is not None:
+        params["nSeg"] = n_seg
+    if verb is not None:
+        params["verb"] = verb
     return params
 
 
@@ -142,7 +219,80 @@ def v_3d_pfm_cargs(
     """
     cargs = []
     cargs.append("3dPFM")
-    cargs.append("[PARAMETERS]")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("algorithm") is not None:
+        cargs.extend([
+            "-algorithm",
+            params.get("algorithm")
+        ])
+    if params.get("criteria") is not None:
+        cargs.extend([
+            "-criteria",
+            params.get("criteria")
+        ])
+    if params.get("nonzeros") is not None:
+        cargs.extend([
+            "-nonzeros",
+            str(params.get("nonzeros"))
+        ])
+    if params.get("maxiter") is not None:
+        cargs.extend([
+            "-maxiter",
+            str(params.get("maxiter"))
+        ])
+    if params.get("maxiterfactor") is not None:
+        cargs.extend([
+            "-maxiterfactor",
+            str(params.get("maxiterfactor"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("hrf") is not None:
+        cargs.extend([
+            "-hrf",
+            params.get("hrf")
+        ])
+    if params.get("hrf_vol") is not None:
+        cargs.extend([
+            "-hrf_vol",
+            execution.input_file(params.get("hrf_vol"))
+        ])
+    if params.get("idx_hrf") is not None:
+        cargs.extend([
+            "-idx_hrf",
+            execution.input_file(params.get("idx_hrf"))
+        ])
+    if params.get("LHS") is not None:
+        cargs.extend([
+            "-LHS",
+            *[execution.input_file(f) for f in params.get("LHS")]
+        ])
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    if params.get("nSeg") is not None:
+        cargs.extend([
+            "-nSeg",
+            str(params.get("nSeg"))
+        ])
+    if params.get("verb") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb"))
+        ])
     return cargs
 
 
@@ -217,6 +367,21 @@ def v_3d_pfm_execute(
 
 
 def v_3d_pfm(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    algorithm: str | None = None,
+    criteria: str | None = None,
+    nonzeros: float | None = None,
+    maxiter: float | None = None,
+    maxiterfactor: float | None = None,
+    tr: float | None = None,
+    hrf: str | None = None,
+    hrf_vol: InputPathType | None = None,
+    idx_hrf: InputPathType | None = None,
+    lhs: list[InputPathType] | None = None,
+    jobs: float | None = None,
+    n_seg: float | None = None,
+    verb: float | None = None,
     runner: Runner | None = None,
 ) -> V3dPfmOutputs:
     """
@@ -228,6 +393,24 @@ def v_3d_pfm(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        input_: Specify the dataset to analyze (e.g., epi.nii).
+        mask: Process voxels inside this mask only. Default is no masking.
+        algorithm: Regularization function used for HRF deconvolution (dantzig\
+            or lasso).
+        criteria: Model selection criterion for HRF deconvolution (BIC or AIC).
+        nonzeros: Choose estimate with a fixed number of nonzero coefficients.
+        maxiter: Maximum number of iterations in the homotopy procedure\
+            (absolute value).
+        maxiterfactor: Maximum number of iterations relative to the number of\
+            volumes.
+        tr: Repetition time or sampling period of the input data.
+        hrf: Haemodynamic response function used for deconvolution.
+        hrf_vol: 3D+time dataset with voxel/nodes/vertex -dependent HRFs.
+        idx_hrf: 3D dataset with voxel-dependent indexes for HRF.
+        lhs: Additional regressors to be fitted to the dataset.
+        jobs: Number of parallel jobs to use in processing.
+        n_seg: Divide into segments to report progress.
+        verb: Verbosity level (0 for quiet, 1 for talkative).
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPfmOutputs`).
@@ -235,6 +418,21 @@ def v_3d_pfm(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_PFM_METADATA)
     params = v_3d_pfm_params(
+        input_=input_,
+        mask=mask,
+        algorithm=algorithm,
+        criteria=criteria,
+        nonzeros=nonzeros,
+        maxiter=maxiter,
+        maxiterfactor=maxiterfactor,
+        tr=tr,
+        hrf=hrf,
+        hrf_vol=hrf_vol,
+        idx_hrf=idx_hrf,
+        lhs=lhs,
+        jobs=jobs,
+        n_seg=n_seg,
+        verb=verb,
     )
     return v_3d_pfm_execute(params, execution)