niwrap-afni 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_afni/afni/v_3d_toy_prog.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TOY_PROG_METADATA = Metadata(
-    id="1311a81e171aae35dd519b54379bb3bfad692a46.boutiques",
+    id="690427ee59940bfcf8d97ee3a7fbced4f0a52ee5.boutiques",
     name="3dToyProg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,6 +19,16 @@ V3dToyProgParameters = typing.TypedDict('V3dToyProgParameters', {
     "output_prefix": typing.NotRequired[str | None],
     "mask_dataset": typing.NotRequired[InputPathType | None],
     "output_datum": typing.NotRequired[typing.Literal["float", "short"] | None],
+    "mini_help": bool,
+    "help": bool,
+    "extreme_help": bool,
+    "help_view": bool,
+    "help_web": bool,
+    "help_find": typing.NotRequired[str | None],
+    "help_raw": bool,
+    "help_spx": bool,
+    "help_aspx": bool,
+    "help_all_opts": bool,
 })
 
 
@@ -66,6 +76,16 @@ def v_3d_toy_prog_params(
     output_prefix: str | None = None,
     mask_dataset: InputPathType | None = None,
     output_datum: typing.Literal["float", "short"] | None = None,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    help_view: bool = False,
+    help_web: bool = False,
+    help_find: str | None = None,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_aspx: bool = False,
+    help_all_opts: bool = False,
 ) -> V3dToyProgParameters:
     """
     Build parameters.
@@ -76,12 +96,39 @@ def v_3d_toy_prog_params(
         mask_dataset: Restrict analysis to non-zero voxels in the mask dataset.
         output_datum: Output datum type for one of the datasets. Choose from\
             'float' or 'short'. Default is 'float'.
+        mini_help: Mini help, at time, same as -help in many cases.
+        help_: The entire help output.
+        extreme_help: Extreme help, same as -help in majority of cases.
+        help_view: Open help in text editor. AFNI will try to find a GUI editor\
+            on your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        help_web: Open help in web browser. AFNI will try to find a browser on\
+            your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        help_find: Look for lines in this program's -help output that match\
+            (approximately) WORD.
+        help_raw: Help string unedited.
+        help_spx: Help string in sphinx loveliness, but do not try to\
+            autoformat.
+        help_aspx: Help string in sphinx with autoformatting of options, etc.
+        help_all_opts: Try to identify all options for the program from the\
+            output of its -help option. Some options might be missed and others\
+            misidentified. Use this output for hints only.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dToyProg",
         "input_dataset": input_dataset,
+        "mini_help": mini_help,
+        "help": help_,
+        "extreme_help": extreme_help,
+        "help_view": help_view,
+        "help_web": help_web,
+        "help_raw": help_raw,
+        "help_spx": help_spx,
+        "help_aspx": help_aspx,
+        "help_all_opts": help_all_opts,
     }
     if output_prefix is not None:
         params["output_prefix"] = output_prefix
@@ -89,6 +136,8 @@ def v_3d_toy_prog_params(
         params["mask_dataset"] = mask_dataset
     if output_datum is not None:
         params["output_datum"] = output_datum
+    if help_find is not None:
+        params["help_find"] = help_find
     return params
 
 
@@ -126,6 +175,29 @@ def v_3d_toy_prog_cargs(
             "-datum",
             params.get("output_datum")
         ])
+    if params.get("mini_help"):
+        cargs.append("-h")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("extreme_help"):
+        cargs.append("-HELP")
+    if params.get("help_view"):
+        cargs.append("-h_view")
+    if params.get("help_web"):
+        cargs.append("-h_web")
+    if params.get("help_find") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("help_find")
+        ])
+    if params.get("help_raw"):
+        cargs.append("-h_raw")
+    if params.get("help_spx"):
+        cargs.append("-h_spx")
+    if params.get("help_aspx"):
+        cargs.append("-h_aspx")
+    if params.get("help_all_opts"):
+        cargs.append("-all_opts")
     return cargs
 
 
@@ -177,6 +249,16 @@ def v_3d_toy_prog(
     output_prefix: str | None = None,
     mask_dataset: InputPathType | None = None,
     output_datum: typing.Literal["float", "short"] | None = None,
+    mini_help: bool = False,
+    help_: bool = False,
+    extreme_help: bool = False,
+    help_view: bool = False,
+    help_web: bool = False,
+    help_find: str | None = None,
+    help_raw: bool = False,
+    help_spx: bool = False,
+    help_aspx: bool = False,
+    help_all_opts: bool = False,
     runner: Runner | None = None,
 ) -> V3dToyProgOutputs:
     """
@@ -192,6 +274,24 @@ def v_3d_toy_prog(
         mask_dataset: Restrict analysis to non-zero voxels in the mask dataset.
         output_datum: Output datum type for one of the datasets. Choose from\
             'float' or 'short'. Default is 'float'.
+        mini_help: Mini help, at time, same as -help in many cases.
+        help_: The entire help output.
+        extreme_help: Extreme help, same as -help in majority of cases.
+        help_view: Open help in text editor. AFNI will try to find a GUI editor\
+            on your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        help_web: Open help in web browser. AFNI will try to find a browser on\
+            your machine. You can control which it should use by setting\
+            environment variable AFNI_GUI_EDITOR.
+        help_find: Look for lines in this program's -help output that match\
+            (approximately) WORD.
+        help_raw: Help string unedited.
+        help_spx: Help string in sphinx loveliness, but do not try to\
+            autoformat.
+        help_aspx: Help string in sphinx with autoformatting of options, etc.
+        help_all_opts: Try to identify all options for the program from the\
+            output of its -help option. Some options might be missed and others\
+            misidentified. Use this output for hints only.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dToyProgOutputs`).
@@ -203,6 +303,16 @@ def v_3d_toy_prog(
         output_prefix=output_prefix,
         mask_dataset=mask_dataset,
         output_datum=output_datum,
+        mini_help=mini_help,
+        help_=help_,
+        extreme_help=extreme_help,
+        help_view=help_view,
+        help_web=help_web,
+        help_find=help_find,
+        help_raw=help_raw,
+        help_spx=help_spx,
+        help_aspx=help_aspx,
+        help_all_opts=help_all_opts,
     )
     return v_3d_toy_prog_execute(params, execution)
 

niwrap_afni/afni/v_3d_tsgen.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TSGEN_METADATA = Metadata(
-    id="99758b64781663ffd508cccdf61b5f963c784b4a.boutiques",
+    id="23ea0ec274045284df882fa88ec58e47ba43443f.boutiques",
     name="3dTSgen",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -27,6 +27,7 @@ V3dTsgenParameters = typing.TypedDict('V3dTsgenParameters', {
     "signal_coef": typing.NotRequired[str | None],
     "noise_coef": typing.NotRequired[str | None],
     "bucket_config": typing.NotRequired[str | None],
+    "brick_config": typing.NotRequired[str | None],
 })
 
 
@@ -82,6 +83,7 @@ def v_3d_tsgen_params(
     signal_coef: str | None = None,
     noise_coef: str | None = None,
     bucket_config: str | None = None,
+    brick_config: str | None = None,
 ) -> V3dTsgenParameters:
     """
     Build parameters.
@@ -106,6 +108,9 @@ def v_3d_tsgen_params(
         bucket_config: Create one AFNI 'bucket' dataset containing n\
             sub-bricks. n=0 creates the default output. Output 'bucket' is written\
             to prefixname.
+        brick_config: Specify content for sub-brick in the form 'm t k label'\
+            where m is the sub-brick number, t is 'scoef' or 'ncoef', k is\
+            parameter index, and label is a descriptive label.
     Returns:
         Parameter dictionary
     """
@@ -130,6 +135,8 @@ def v_3d_tsgen_params(
         params["noise_coef"] = noise_coef
     if bucket_config is not None:
         params["bucket_config"] = bucket_config
+    if brick_config is not None:
+        params["brick_config"] = brick_config
     return params
 
 
@@ -197,6 +204,11 @@ def v_3d_tsgen_cargs(
             "-bucket",
             params.get("bucket_config")
         ])
+    if params.get("brick_config") is not None:
+        cargs.extend([
+            "-brick",
+            params.get("brick_config")
+        ])
     return cargs
 
 
@@ -257,6 +269,7 @@ def v_3d_tsgen(
     signal_coef: str | None = None,
     noise_coef: str | None = None,
     bucket_config: str | None = None,
+    brick_config: str | None = None,
     runner: Runner | None = None,
 ) -> V3dTsgenOutputs:
     """
@@ -287,6 +300,9 @@ def v_3d_tsgen(
         bucket_config: Create one AFNI 'bucket' dataset containing n\
             sub-bricks. n=0 creates the default output. Output 'bucket' is written\
             to prefixname.
+        brick_config: Specify content for sub-brick in the form 'm t k label'\
+            where m is the sub-brick number, t is 'scoef' or 'ncoef', k is\
+            parameter index, and label is a descriptive label.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTsgenOutputs`).
@@ -306,6 +322,7 @@ def v_3d_tsgen(
         signal_coef=signal_coef,
         noise_coef=noise_coef,
         bucket_config=bucket_config,
+        brick_config=brick_config,
     )
     return v_3d_tsgen_execute(params, execution)
 

niwrap_afni/afni/v_3d_tsort.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TSORT_METADATA = Metadata(
-    id="28c28b79e328ac59d8297a59e0298ad19fb48796.boutiques",
+    id="0baecbfda8717ca32038a0d906eaab9d406613ee.boutiques",
     name="3dTsort",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,7 @@ V3dTsortParameters = typing.TypedDict('V3dTsortParameters', {
     "__STYX_TYPE__": typing.Literal["3dTsort"],
     "input_file": InputPathType,
     "prefix": typing.NotRequired[str | None],
+    "inc": bool,
     "dec": bool,
     "rank": bool,
     "ind": bool,
@@ -73,6 +74,7 @@ class V3dTsortOutputs(typing.NamedTuple):
 def v_3d_tsort_params(
     input_file: InputPathType,
     prefix: str | None = None,
+    inc: bool = False,
     dec: bool = False,
     rank: bool = False,
     ind: bool = False,
@@ -88,6 +90,7 @@ def v_3d_tsort_params(
     Args:
         input_file: Input dataset to be sorted.
         prefix: Prefix for the output dataset.
+        inc: Sort into increasing order (default).
         dec: Sort into decreasing order.
         rank: Output rank instead of sorted values; ranks range from 1 to Nvals.
         ind: Output sorting index (0 to Nvals -1).
@@ -103,6 +106,7 @@ def v_3d_tsort_params(
     params = {
         "__STYXTYPE__": "3dTsort",
         "input_file": input_file,
+        "inc": inc,
         "dec": dec,
         "rank": rank,
         "ind": ind,
@@ -139,6 +143,8 @@ def v_3d_tsort_cargs(
             "-prefix",
             params.get("prefix")
         ])
+    if params.get("inc"):
+        cargs.append("-inc")
     if params.get("dec"):
         cargs.append("-dec")
     if params.get("rank"):
@@ -208,6 +214,7 @@ def v_3d_tsort_execute(
 def v_3d_tsort(
     input_file: InputPathType,
     prefix: str | None = None,
+    inc: bool = False,
     dec: bool = False,
     rank: bool = False,
     ind: bool = False,
@@ -228,6 +235,7 @@ def v_3d_tsort(
     Args:
         input_file: Input dataset to be sorted.
         prefix: Prefix for the output dataset.
+        inc: Sort into increasing order (default).
         dec: Sort into decreasing order.
         rank: Output rank instead of sorted values; ranks range from 1 to Nvals.
         ind: Output sorting index (0 to Nvals -1).
@@ -246,6 +254,7 @@ def v_3d_tsort(
     params = v_3d_tsort_params(
         input_file=input_file,
         prefix=prefix,
+        inc=inc,
         dec=dec,
         rank=rank,
         ind=ind,

niwrap_afni/afni/v_3d_tstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TSTAT_METADATA = Metadata(
-    id="2c3351f9c202b2f87198789eb63df2ff52ca3826.boutiques",
+    id="e1660f36f2b134d3f7b3ce6ea6944f69d67b9501.boutiques",
     name="3dTstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,8 +15,11 @@ V_3D_TSTAT_METADATA = Metadata(
 
 V3dTstatParameters = typing.TypedDict('V3dTstatParameters', {
     "__STYX_TYPE__": typing.Literal["3dTstat"],
+    "in_file": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "num_threads": typing.NotRequired[int | None],
+    "options": typing.NotRequired[str | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
     "sum": bool,
     "abssum": bool,
     "sos": bool,
@@ -73,8 +76,6 @@ V3dTstatParameters = typing.TypedDict('V3dTstatParameters', {
     "mask_mset": typing.NotRequired[InputPathType | None],
     "mrange": typing.NotRequired[str | None],
     "cmask": typing.NotRequired[str | None],
-    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
-    "in_file": InputPathType,
 })
 
 
@@ -124,6 +125,8 @@ def v_3d_tstat_params(
     in_file: InputPathType,
     mask: InputPathType | None = None,
     num_threads: int | None = None,
+    options: str | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     sum_: bool = False,
     abssum: bool = False,
     sos: bool = False,
@@ -180,7 +183,6 @@ def v_3d_tstat_params(
     mask_mset: InputPathType | None = None,
     mrange: str | None = None,
     cmask: str | None = None,
-    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
 ) -> V3dTstatParameters:
     """
     Build parameters.
@@ -189,6 +191,8 @@ def v_3d_tstat_params(
         in_file: Input file to 3dtstat.
         mask: Mask file.
         num_threads: Set number of threads.
+        options: Selected statistical output.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
         sum_: Compute sum of input voxels.
         abssum: Compute absolute sum of input voxels.
         sos: Compute sum of squares.
@@ -262,12 +266,12 @@ def v_3d_tstat_params(
             values between 'a' and 'b' (inclusive) will be used.
         cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
             program, and produce a mask from the resulting 3D brick.
-        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dTstat",
+        "in_file": in_file,
         "sum": sum_,
         "abssum": abssum,
         "sos": sos,
@@ -318,12 +322,15 @@ def v_3d_tstat_params(
         "firstvalue": firstvalue,
         "tdiff": tdiff,
         "nscale": nscale,
-        "in_file": in_file,
     }
     if mask is not None:
         params["mask"] = mask
     if num_threads is not None:
         params["num_threads"] = num_threads
+    if options is not None:
+        params["options"] = options
+    if outputtype is not None:
+        params["outputtype"] = outputtype
     if prefix is not None:
         params["prefix"] = prefix
     if datum is not None:
@@ -336,8 +343,6 @@ def v_3d_tstat_params(
         params["mrange"] = mrange
     if cmask is not None:
         params["cmask"] = cmask
-    if outputtype is not None:
-        params["outputtype"] = outputtype
     return params
 
 
@@ -356,6 +361,7 @@ def v_3d_tstat_cargs(
     """
     cargs = []
     cargs.append("3dTstat")
+    cargs.append(execution.input_file(params.get("in_file")))
     if params.get("mask") is not None:
         cargs.extend([
             "-mask",
@@ -363,6 +369,10 @@ def v_3d_tstat_cargs(
         ])
     if params.get("num_threads") is not None:
         cargs.append(str(params.get("num_threads")))
+    if params.get("options") is not None:
+        cargs.append(params.get("options"))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
     if params.get("sum"):
         cargs.append("-sum")
     if params.get("abssum"):
@@ -493,9 +503,6 @@ def v_3d_tstat_cargs(
             "-cmask",
             params.get("cmask")
         ])
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    cargs.append(execution.input_file(params.get("in_file")))
     return cargs
 
 
@@ -547,6 +554,8 @@ def v_3d_tstat(
     in_file: InputPathType,
     mask: InputPathType | None = None,
     num_threads: int | None = None,
+    options: str | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     sum_: bool = False,
     abssum: bool = False,
     sos: bool = False,
@@ -603,7 +612,6 @@ def v_3d_tstat(
     mask_mset: InputPathType | None = None,
     mrange: str | None = None,
     cmask: str | None = None,
-    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     runner: Runner | None = None,
 ) -> V3dTstatOutputs:
     """
@@ -617,6 +625,8 @@ def v_3d_tstat(
         in_file: Input file to 3dtstat.
         mask: Mask file.
         num_threads: Set number of threads.
+        options: Selected statistical output.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
         sum_: Compute sum of input voxels.
         abssum: Compute absolute sum of input voxels.
         sos: Compute sum of squares.
@@ -690,7 +700,6 @@ def v_3d_tstat(
             values between 'a' and 'b' (inclusive) will be used.
         cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
             program, and produce a mask from the resulting 3D brick.
-        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTstatOutputs`).
@@ -698,8 +707,11 @@ def v_3d_tstat(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_TSTAT_METADATA)
     params = v_3d_tstat_params(
+        in_file=in_file,
         mask=mask,
         num_threads=num_threads,
+        options=options,
+        outputtype=outputtype,
         sum_=sum_,
         abssum=abssum,
         sos=sos,
@@ -756,8 +768,6 @@ def v_3d_tstat(
         mask_mset=mask_mset,
         mrange=mrange,
         cmask=cmask,
-        outputtype=outputtype,
-        in_file=in_file,
     )
     return v_3d_tstat_execute(params, execution)
 

niwrap_afni/afni/v_3d_undump.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_UNDUMP_METADATA = Metadata(
-    id="d8ab76cb95ed8dc992c00cf2e9245c240a475a40.boutiques",
+    id="f0b8af447cf310eefc98d5d8262aaf16f8069930.boutiques",
     name="3dUndump",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -23,6 +23,7 @@ V3dUndumpParameters = typing.TypedDict('V3dUndumpParameters', {
     "datatype": typing.NotRequired[str | None],
     "dval": typing.NotRequired[float | None],
     "fval": typing.NotRequired[float | None],
+    "ijk": bool,
     "xyz": bool,
     "sphere_radius": typing.NotRequired[float | None],
     "cube_mode": bool,
@@ -84,6 +85,7 @@ def v_3d_undump_params(
     datatype: str | None = None,
     dval: float | None = None,
     fval: float | None = None,
+    ijk: bool = False,
     xyz: bool = False,
     sphere_radius: float | None = None,
     cube_mode: bool = False,
@@ -111,6 +113,7 @@ def v_3d_undump_params(
             not have a value supplied in the input file [default = 1].
         fval: 'fff' is the fill value, used for each voxel in the output\
             dataset that is NOT listed in the input file [default = 0].
+        ijk: Coordinates in the input file are (i,j,k) index triples.
         xyz: Coordinates in the input file are (x,y,z) spatial coordinates, in\
             mm.
         sphere_radius: Specifies that a sphere of radius 'rrr' will be filled\
@@ -129,6 +132,7 @@ def v_3d_undump_params(
     params = {
         "__STYXTYPE__": "3dUndump",
         "input_files": input_files,
+        "ijk": ijk,
         "xyz": xyz,
         "cube_mode": cube_mode,
         "head_only": head_only,
@@ -208,6 +212,8 @@ def v_3d_undump_cargs(
             "-fval",
             str(params.get("fval"))
         ])
+    if params.get("ijk"):
+        cargs.append("-ijk")
     if params.get("xyz"):
         cargs.append("-xyz")
     if params.get("sphere_radius") is not None:
@@ -287,6 +293,7 @@ def v_3d_undump(
     datatype: str | None = None,
     dval: float | None = None,
     fval: float | None = None,
+    ijk: bool = False,
     xyz: bool = False,
     sphere_radius: float | None = None,
     cube_mode: bool = False,
@@ -319,6 +326,7 @@ def v_3d_undump(
             not have a value supplied in the input file [default = 1].
         fval: 'fff' is the fill value, used for each voxel in the output\
             dataset that is NOT listed in the input file [default = 0].
+        ijk: Coordinates in the input file are (i,j,k) index triples.
         xyz: Coordinates in the input file are (x,y,z) spatial coordinates, in\
             mm.
         sphere_radius: Specifies that a sphere of radius 'rrr' will be filled\
@@ -346,6 +354,7 @@ def v_3d_undump(
         datatype=datatype,
         dval=dval,
         fval=fval,
+        ijk=ijk,
         xyz=xyz,
         sphere_radius=sphere_radius,
         cube_mode=cube_mode,