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

niwrap_afni/afni/p2dsetstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 P2DSETSTAT_METADATA = Metadata(
-    id="425596bb580582f82bf97f7e288cb9c38b721949.boutiques",
+    id="23edaf6df2aa7e769c710a218ab8bd8e6572d021.boutiques",
     name="p2dsetstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,8 @@ P2dsetstatParameters = typing.TypedDict('P2dsetstatParameters', {
     "__STYX_TYPE__": typing.Literal["p2dsetstat"],
     "dataset": str,
     "pvalue": float,
+    "bisided": bool,
+    "twosided": bool,
     "onesided": bool,
     "quiet": bool,
 })
@@ -67,6 +69,8 @@ class P2dsetstatOutputs(typing.NamedTuple):
 def p2dsetstat_params(
     dataset: str,
     pvalue: float,
+    bisided: bool = False,
+    twosided: bool = False,
     onesided: bool = False,
     quiet: bool = False,
 ) -> P2dsetstatParameters:
@@ -80,6 +84,8 @@ def p2dsetstat_params(
             (because of the square-brackets). 'i' can be either a number or a\
             string label selector.
         pvalue: Input p-value P, which MUST be in the interval [0,1].
+        bisided: Two-sided test.
+        twosided: Two-sided test.
         onesided: One-sided test.
         quiet: Output only the final statistic value.
     Returns:
@@ -89,6 +95,8 @@ def p2dsetstat_params(
         "__STYXTYPE__": "p2dsetstat",
         "dataset": dataset,
         "pvalue": pvalue,
+        "bisided": bisided,
+        "twosided": twosided,
         "onesided": onesided,
         "quiet": quiet,
     }
@@ -118,6 +126,10 @@ def p2dsetstat_cargs(
         "-pval",
         str(params.get("pvalue"))
     ])
+    if params.get("bisided"):
+        cargs.append("-bisided")
+    if params.get("twosided"):
+        cargs.append("-2sided")
     if params.get("onesided"):
         cargs.append("-1sided")
     if params.get("quiet"):
@@ -172,6 +184,8 @@ def p2dsetstat_execute(
 def p2dsetstat(
     dataset: str,
     pvalue: float,
+    bisided: bool = False,
+    twosided: bool = False,
     onesided: bool = False,
     quiet: bool = False,
     runner: Runner | None = None,
@@ -190,6 +204,8 @@ def p2dsetstat(
             (because of the square-brackets). 'i' can be either a number or a\
             string label selector.
         pvalue: Input p-value P, which MUST be in the interval [0,1].
+        bisided: Two-sided test.
+        twosided: Two-sided test.
         onesided: One-sided test.
         quiet: Output only the final statistic value.
         runner: Command runner.
@@ -201,6 +217,8 @@ def p2dsetstat(
     params = p2dsetstat_params(
         dataset=dataset,
         pvalue=pvalue,
+        bisided=bisided,
+        twosided=twosided,
         onesided=onesided,
         quiet=quiet,
     )

niwrap_afni/afni/plugout_drive.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PLUGOUT_DRIVE_METADATA = Metadata(
-    id="65a44f6f7d92c1ad9ba4ed1d48f6c277a7f935fb.boutiques",
+    id="322abb84ee04acd16878a832336aea8a4c964855.boutiques",
     name="plugout_drive",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,12 +16,20 @@ PLUGOUT_DRIVE_METADATA = Metadata(
 PlugoutDriveParameters = typing.TypedDict('PlugoutDriveParameters', {
     "__STYX_TYPE__": typing.Literal["plugout_drive"],
     "host": typing.NotRequired[str | None],
+    "shm": bool,
     "verbose": bool,
     "port": typing.NotRequired[float | None],
     "maxwait": typing.NotRequired[float | None],
     "name": typing.NotRequired[str | None],
     "command": typing.NotRequired[list[str] | None],
     "quit": bool,
+    "np": typing.NotRequired[float | None],
+    "npq": typing.NotRequired[float | None],
+    "npb": typing.NotRequired[float | None],
+    "max_port_bloc": bool,
+    "max_port_bloc_quiet": bool,
+    "num_assigned_ports": bool,
+    "num_assigned_ports_quiet": bool,
 })
 
 
@@ -66,12 +74,20 @@ class PlugoutDriveOutputs(typing.NamedTuple):
 
 def plugout_drive_params(
     host: str | None = None,
+    shm: bool = False,
     verbose: bool = False,
     port: float | None = None,
     maxwait: float | None = None,
     name: str | None = None,
     command: list[str] | None = None,
     quit_: bool = False,
+    np: float | None = None,
+    npq: float | None = None,
+    npb: float | None = None,
+    max_port_bloc: bool = False,
+    max_port_bloc_quiet: bool = False,
+    num_assigned_ports: bool = False,
+    num_assigned_ports_quiet: bool = False,
 ) -> PlugoutDriveParameters:
     """
     Build parameters.
@@ -79,6 +95,8 @@ def plugout_drive_params(
     Args:
         host: Connect to AFNI running on the specified host using TCP/IP.\
             Default is 'localhost'.
+        shm: Connect to the current host using shared memory for large data\
+            transfers.
         verbose: Verbose mode.
         port: Use TCP/IP port number. Default is 8099.
         maxwait: Maximum wait time in seconds for AFNI to connect. Default is 9\
@@ -89,13 +107,28 @@ def plugout_drive_params(
             SomeFunction"'.
         quit_: Quit after executing all -com commands. Default is to wait for\
             more commands.
+        np: Provide a port offset to allow multiple instances of AFNI <-->\
+            SUMA, etc., on the same machine.
+        npq: Like -np but quieter in the face of adversity.
+        npb: Similar to -np, but using a block for easier usage.
+        max_port_bloc: Print the current value of MAX_BLOC and exit.
+        max_port_bloc_quiet: Print MAX_BLOC value and exit quietly.
+        num_assigned_ports: Print the number of assigned ports used by AFNI and\
+            exit.
+        num_assigned_ports_quiet: Print the number of assigned ports used by\
+            AFNI and exit quietly.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "plugout_drive",
+        "shm": shm,
         "verbose": verbose,
         "quit": quit_,
+        "max_port_bloc": max_port_bloc,
+        "max_port_bloc_quiet": max_port_bloc_quiet,
+        "num_assigned_ports": num_assigned_ports,
+        "num_assigned_ports_quiet": num_assigned_ports_quiet,
     }
     if host is not None:
         params["host"] = host
@@ -107,6 +140,12 @@ def plugout_drive_params(
         params["name"] = name
     if command is not None:
         params["command"] = command
+    if np is not None:
+        params["np"] = np
+    if npq is not None:
+        params["npq"] = npq
+    if npb is not None:
+        params["npb"] = npb
     return params
 
 
@@ -130,6 +169,8 @@ def plugout_drive_cargs(
             "-host",
             params.get("host")
         ])
+    if params.get("shm"):
+        cargs.append("-shm")
     if params.get("verbose"):
         cargs.append("-v")
     if params.get("port") is not None:
@@ -154,6 +195,29 @@ def plugout_drive_cargs(
         ])
     if params.get("quit"):
         cargs.append("-quit")
+    if params.get("np") is not None:
+        cargs.extend([
+            "-np",
+            str(params.get("np"))
+        ])
+    if params.get("npq") is not None:
+        cargs.extend([
+            "-npq",
+            str(params.get("npq"))
+        ])
+    if params.get("npb") is not None:
+        cargs.extend([
+            "-npb",
+            str(params.get("npb"))
+        ])
+    if params.get("max_port_bloc"):
+        cargs.append("-max_port_bloc")
+    if params.get("max_port_bloc_quiet"):
+        cargs.append("-max_port_bloc_quiet")
+    if params.get("num_assigned_ports"):
+        cargs.append("-num_assigned_ports")
+    if params.get("num_assigned_ports_quiet"):
+        cargs.append("-num_assigned_ports_quiet")
     return cargs
 
 
@@ -203,12 +267,20 @@ def plugout_drive_execute(
 
 def plugout_drive(
     host: str | None = None,
+    shm: bool = False,
     verbose: bool = False,
     port: float | None = None,
     maxwait: float | None = None,
     name: str | None = None,
     command: list[str] | None = None,
     quit_: bool = False,
+    np: float | None = None,
+    npq: float | None = None,
+    npb: float | None = None,
+    max_port_bloc: bool = False,
+    max_port_bloc_quiet: bool = False,
+    num_assigned_ports: bool = False,
+    num_assigned_ports_quiet: bool = False,
     runner: Runner | None = None,
 ) -> PlugoutDriveOutputs:
     """
@@ -222,6 +294,8 @@ def plugout_drive(
     Args:
         host: Connect to AFNI running on the specified host using TCP/IP.\
             Default is 'localhost'.
+        shm: Connect to the current host using shared memory for large data\
+            transfers.
         verbose: Verbose mode.
         port: Use TCP/IP port number. Default is 8099.
         maxwait: Maximum wait time in seconds for AFNI to connect. Default is 9\
@@ -232,6 +306,16 @@ def plugout_drive(
             SomeFunction"'.
         quit_: Quit after executing all -com commands. Default is to wait for\
             more commands.
+        np: Provide a port offset to allow multiple instances of AFNI <-->\
+            SUMA, etc., on the same machine.
+        npq: Like -np but quieter in the face of adversity.
+        npb: Similar to -np, but using a block for easier usage.
+        max_port_bloc: Print the current value of MAX_BLOC and exit.
+        max_port_bloc_quiet: Print MAX_BLOC value and exit quietly.
+        num_assigned_ports: Print the number of assigned ports used by AFNI and\
+            exit.
+        num_assigned_ports_quiet: Print the number of assigned ports used by\
+            AFNI and exit quietly.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PlugoutDriveOutputs`).
@@ -240,12 +324,20 @@ def plugout_drive(
     execution = runner.start_execution(PLUGOUT_DRIVE_METADATA)
     params = plugout_drive_params(
         host=host,
+        shm=shm,
         verbose=verbose,
         port=port,
         maxwait=maxwait,
         name=name,
         command=command,
         quit_=quit_,
+        np=np,
+        npq=npq,
+        npb=npb,
+        max_port_bloc=max_port_bloc,
+        max_port_bloc_quiet=max_port_bloc_quiet,
+        num_assigned_ports=num_assigned_ports,
+        num_assigned_ports_quiet=num_assigned_ports_quiet,
     )
     return plugout_drive_execute(params, execution)
 

niwrap_afni/afni/prompt_popup.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PROMPT_POPUP_METADATA = Metadata(
-    id="56ce96c081577f794f865f7030869659d97db1e1.boutiques",
+    id="c24519073e7efb98045929a1a4d42a4a25f3e8ef.boutiques",
     name="prompt_popup",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,8 +15,11 @@ PROMPT_POPUP_METADATA = Metadata(
 
 PromptPopupParameters = typing.TypedDict('PromptPopupParameters', {
     "__STYX_TYPE__": typing.Literal["prompt_popup"],
+    "message": str,
     "message_pause": typing.NotRequired[str | None],
+    "buttons": typing.NotRequired[list[str] | None],
     "buttons_b": typing.NotRequired[list[str] | None],
+    "timeout": typing.NotRequired[float | None],
     "timeout_to": typing.NotRequired[float | None],
 })
 
@@ -61,27 +64,42 @@ class PromptPopupOutputs(typing.NamedTuple):
 
 
 def prompt_popup_params(
+    message: str,
     message_pause: str | None = None,
+    buttons: list[str] | None = None,
     buttons_b: list[str] | None = None,
+    timeout: float | None = None,
     timeout_to: float | None = None,
 ) -> PromptPopupParameters:
     """
     Build parameters.
     
     Args:
+        message: Pops a window prompting the user with MESSAGE. If MESSAGE is\
+            '-', it is read from stdin.
         message_pause: Same as -message to match the old prompt_user.
+        buttons: What do you want the buttons to say? You can give up to three\
+            -button for three buttons. Returns integer 1, 2, or 3. If there is no\
+            -button, there will be one button 'Ok'.
         buttons_b: Same as -button.
+        timeout: Timeout in seconds of prompt message. Default answer is\
+            returned if TT seconds elapse without user input.
         timeout_to: Same as -timeout TT.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "prompt_popup",
+        "message": message,
     }
     if message_pause is not None:
         params["message_pause"] = message_pause
+    if buttons is not None:
+        params["buttons"] = buttons
     if buttons_b is not None:
         params["buttons_b"] = buttons_b
+    if timeout is not None:
+        params["timeout"] = timeout
     if timeout_to is not None:
         params["timeout_to"] = timeout_to
     return params
@@ -102,16 +120,30 @@ def prompt_popup_cargs(
     """
     cargs = []
     cargs.append("prompt_popup")
+    cargs.extend([
+        "-message",
+        params.get("message")
+    ])
     if params.get("message_pause") is not None:
         cargs.extend([
             "-pause",
             params.get("message_pause")
         ])
+    if params.get("buttons") is not None:
+        cargs.extend([
+            "-button",
+            *params.get("buttons")
+        ])
     if params.get("buttons_b") is not None:
         cargs.extend([
             "-b",
             *params.get("buttons_b")
         ])
+    if params.get("timeout") is not None:
+        cargs.extend([
+            "-timeout",
+            str(params.get("timeout"))
+        ])
     if params.get("timeout_to") is not None:
         cargs.extend([
             "-to",
@@ -165,8 +197,11 @@ def prompt_popup_execute(
 
 
 def prompt_popup(
+    message: str,
     message_pause: str | None = None,
+    buttons: list[str] | None = None,
     buttons_b: list[str] | None = None,
+    timeout: float | None = None,
     timeout_to: float | None = None,
     runner: Runner | None = None,
 ) -> PromptPopupOutputs:
@@ -179,8 +214,15 @@ def prompt_popup(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        message: Pops a window prompting the user with MESSAGE. If MESSAGE is\
+            '-', it is read from stdin.
         message_pause: Same as -message to match the old prompt_user.
+        buttons: What do you want the buttons to say? You can give up to three\
+            -button for three buttons. Returns integer 1, 2, or 3. If there is no\
+            -button, there will be one button 'Ok'.
         buttons_b: Same as -button.
+        timeout: Timeout in seconds of prompt message. Default answer is\
+            returned if TT seconds elapse without user input.
         timeout_to: Same as -timeout TT.
         runner: Command runner.
     Returns:
@@ -189,8 +231,11 @@ def prompt_popup(
     runner = runner or get_global_runner()
     execution = runner.start_execution(PROMPT_POPUP_METADATA)
     params = prompt_popup_params(
+        message=message,
         message_pause=message_pause,
+        buttons=buttons,
         buttons_b=buttons_b,
+        timeout=timeout,
         timeout_to=timeout_to,
     )
     return prompt_popup_execute(params, execution)

niwrap_afni/afni/prompt_user.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PROMPT_USER_METADATA = Metadata(
-    id="eeffbea4e522408c1d4978572830a23c9b27d7fb.boutiques",
+    id="50f7b3456cf7fa2cd699f8ebd295c575df5c9675.boutiques",
     name="prompt_user",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,7 @@ PROMPT_USER_METADATA = Metadata(
 PromptUserParameters = typing.TypedDict('PromptUserParameters', {
     "__STYX_TYPE__": typing.Literal["prompt_user"],
     "pause_message": str,
+    "timeout": typing.NotRequired[float | None],
     "timeout_alias": typing.NotRequired[float | None],
 })
 
@@ -61,6 +62,7 @@ class PromptUserOutputs(typing.NamedTuple):
 
 def prompt_user_params(
     pause_message: str,
+    timeout: float | None = None,
     timeout_alias: float | None = None,
 ) -> PromptUserParameters:
     """
@@ -69,6 +71,8 @@ def prompt_user_params(
     Args:
         pause_message: Pops a window prompting the user with MESSAGE. If\
             MESSAGE is '-', it is read from stdin.
+        timeout: Timeout in seconds for the prompt message. Default answer is\
+            returned if TT seconds elapse without user input.
         timeout_alias: Alias for -timeout.
     Returns:
         Parameter dictionary
@@ -77,6 +81,8 @@ def prompt_user_params(
         "__STYXTYPE__": "prompt_user",
         "pause_message": pause_message,
     }
+    if timeout is not None:
+        params["timeout"] = timeout
     if timeout_alias is not None:
         params["timeout_alias"] = timeout_alias
     return params
@@ -101,6 +107,11 @@ def prompt_user_cargs(
         "<-pause>",
         params.get("pause_message")
     ])
+    if params.get("timeout") is not None:
+        cargs.extend([
+            "-timeout",
+            str(params.get("timeout"))
+        ])
     if params.get("timeout_alias") is not None:
         cargs.extend([
             "-to",
@@ -154,6 +165,7 @@ def prompt_user_execute(
 
 def prompt_user(
     pause_message: str,
+    timeout: float | None = None,
     timeout_alias: float | None = None,
     runner: Runner | None = None,
 ) -> PromptUserOutputs:
@@ -167,6 +179,8 @@ def prompt_user(
     Args:
         pause_message: Pops a window prompting the user with MESSAGE. If\
             MESSAGE is '-', it is read from stdin.
+        timeout: Timeout in seconds for the prompt message. Default answer is\
+            returned if TT seconds elapse without user input.
         timeout_alias: Alias for -timeout.
         runner: Command runner.
     Returns:
@@ -176,6 +190,7 @@ def prompt_user(
     execution = runner.start_execution(PROMPT_USER_METADATA)
     params = prompt_user_params(
         pause_message=pause_message,
+        timeout=timeout,
         timeout_alias=timeout_alias,
     )
     return prompt_user_execute(params, execution)