pysnt.setup_utils module#

Setup utilities for PySNT.

This module provides helper functions for setting up PySNT, including Fiji path configuration and environment setup with persistent configuration storage.

get_config_dir() → Path[source]#

Get platform-specific config directory.

Returns:: Platform-specific configuration directory for pysnt (following XDG base directory specification)
Return type:: Path

load_config() → Dict[str, Any][source]#

Load configuration from platform-specific config file.

Returns:: Configuration dictionary, empty if file doesn’t exist or is invalid
Return type:: Dict[str, Any]

save_config(config: Dict[str, Any]) → bool[source]#

Save configuration to platform-specific config file.

Parameters:: config (Dict[str, Any]) – Configuration dictionary to save
Returns:: True if saved successfully, False otherwise
Return type:: bool

set_fiji_path(fiji_path: str, validate: bool = True) → bool[source]#

Set and persist the Fiji installation path.

Parameters:

fiji_path (str) – Path to Fiji installation
validate (bool, default True) – Whether to validate the path before saving

Returns:

True if path was set successfully, False otherwise

Return type:

bool

Examples

>>> # Set Fiji path
>>> pysnt.setup_utils.set_fiji_path("/Applications/Fiji.app")
>>>
>>> # Set without validation (use with caution)
>>> pysnt.setup_utils.set_fiji_path("/custom/fiji/path", validate=False)

get_fiji_path() → str | None[source]#

Get the currently configured Fiji path.

Returns the path from the first available source in priority order: 1. FIJI_PATH environment variable 2. Config file 3. None if not found

Returns:: Current Fiji path if configured, None otherwise
Return type:: str or None

Examples

>>> # Check current Fiji path
>>> path = pysnt.setup_utils.get_fiji_path()
>>> if path:
...     print(f"Fiji configured at: {path}")
... else:
...     print("Fiji path not configured")

clear_fiji_path(reset_env: bool = False) → bool[source]#

Clear the saved Fiji path from configuration.

Parameters:: reset_env (bool, default False) – If True, also clears the FIJI_PATH environment variable for the current session. If False, only clears the saved configuration file.
Returns:: True if cleared successfully, False otherwise
Return type:: bool

Examples

>>> # Clear saved Fiji path only
>>> pysnt.setup_utils.clear_fiji_path()
>>>
>>> # Clear both saved path and environment variable
>>> pysnt.setup_utils.clear_fiji_path(reset_env=True)

reset_fiji_path() → bool[source]#

Completely reset Fiji path configuration.

This clears both the saved configuration file and the FIJI_PATH environment variable for the current session.

Returns:: True if reset successfully, False otherwise
Return type:: bool

Examples

>>> # Completely reset Fiji configuration
>>> pysnt.setup_utils.reset_fiji_path()

get_config_info() → Dict[str, Any][source]#

Get information about the current configuration.

Returns:: Dictionary containing configuration information
Return type:: Dict[str, Any]

Examples

>>> # Get config info
>>> info = pysnt.setup_utils.get_config_info()
>>> print(f"Config directory: {info['config_dir']}")
>>> print(f"Config file exists: {info['config_exists']}")
>>> print(f"Fiji path: {info['fiji_path']}")

is_fiji_valid() → bool[source]#

Quick check if the current Fiji configuration is valid with SNT plugin.

Returns:: True if Fiji is configured with SNT plugin, False otherwise
Return type:: bool

Examples

>>> # Quick validation check
>>> if not pysnt.setup_utils.is_fiji_valid():
...     print("Fiji with SNT not configured properly!")
...     exit(1)
>>>
>>> # Use in scripts
>>> import sys
>>> import pysnt.setup_utils as setup
>>> if not setup.is_fiji_valid():
...     print("Error: Fiji installation not found or SNT plugin missing")
...     print("Run: python -m pysnt.setup_utils --auto-detect")
...     sys.exit(1)

get_fiji_status() → Dict[str, Any][source]#

Get detailed status of the current Fiji configuration/

Returns:: Dictionary with detailed status information including: - configured: bool - Whether any Fiji path is configured - path: str or None - The effective Fiji path - exists: bool - Whether the path exists - valid: bool - Whether it’s a valid Fiji installation with SNT - issues: List[str] - List of any issues found (including SNT-specific)
Return type:: Dict[str, Any]

Examples

>>> # Get detailed status
>>> status = pysnt.setup_utils.get_fiji_status()
>>> if not status['valid']:
...     print(f"Fiji/SNT issues: {', '.join(status['issues'])}")

show_config_status()[source]#

Display current Fiji configuration status in a user-friendly format.

Examples

>>> # Show current configuration
>>> pysnt.setup_utils.show_config_status()

auto_detect_and_configure() → str | None[source]#

Try to auto-detect a valid Fiji installation and save to config if found.

Returns:: Path to detected Fiji installation if found and configured, None otherwise
Return type:: str or None

Examples

>>> # Auto-detect and configure Fiji
>>> path = pysnt.setup_utils.auto_detect_and_configure()
>>> if path:
...     print(f"Fiji configured at: {path}")
... else:
...     print("No Fiji installation detected")

setup_fiji_environment(fiji_path: str, permanent: bool = False) → bool[source]#

Set up Fiji environment variable.

Parameters:

fiji_path (str) – Path to Fiji installation
permanent (bool, default False) – Whether to attempt permanent setup (adds to shell profile)

Returns:

True if setup was successful

Return type:

bool

find_fiji_installations() → List[str][source]#

Search for Fiji installations on the system.

Returns:: List of found Fiji installation paths
Return type:: List[str]

check_fiji_installation(fiji_path: str) → dict[source]#

Check and validate a Fiji installation serving SNT.

Parameters:: fiji_path (str) – Path to check
Returns:: Dictionary with validation results including: - path: str - The path that was checked - exists: bool - Whether the path exists - is_fiji: bool - Whether it appears to be a Fiji installation - has_snt: bool - Whether SNT plugin is found - executables: List[str] - Found executables - has_plugins: bool - Whether plugins directory exists - has_jars: bool - Whether jars directory exists - snt_jars: List[str] - Found SNT jar files - issues: List[str] - List of issues found
Return type:: dict

print_fiji_status(fiji_path: str)[source]#

Print detailed status of a Fiji installation with SNT plugin check.

Parameters:: fiji_path (str) – Path to check

interactive_fiji_setup()[source]#: Interactive setup wizard for Fiji configuration with persistent storage.