"""Module that handle the configuration of the software
Load and save the parameters from the miniviewer and the MIA preferences
pop-up in the config.yml file.
:Contains:
:Class:
- Config
"""
##########################################################################
# Populse_mia - Copyright (C) IRMaGe/CEA, 2018
# Distributed under the terms of the CeCILL license, as published by
# the CEA-CNRS-INRIA. Refer to the LICENSE file or to
# http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html
# for details.
##########################################################################
import glob
import logging
import os
import platform
from functools import lru_cache
from pathlib import Path
import yaml
# Capsul import
from capsul.api import capsul_engine
from cryptography.fernet import Fernet
ENCRYPTION_KEY = b"5YSmesxZ4ge9au2Bxe7XDiQ3U5VCdLeRdqimOOggKyc="
logger = logging.getLogger(__name__)
[docs]
class Config:
"""
Object that handles the configuration of the software
:Contains:
:Methods:
- get_admin_hash: get the value of the hash of the admin password
- get_afni_path: returns the path of AFNI
- get_ants_path: returns the path of ANTS
- getBackgroundColor: get background color
- get_capsul_config: get CAPSUL config dictionary
- get_capsul_engine: get a global CapsulEngine object used for all
operations in MIA application
- getChainCursors: returns if the "chain cursors" checkbox of the
mini-viewer is activated
- get_freesurfer_setup: get freesurfer path
- get_fsl_config: returns the path of the FSL config file
- get_mainwindow_maximized: get the maximized (full-screen) flag
- get_mainwindow_size: get the main window size
- get_matlab_command: returns Matlab command
- get_matlab_path: returns the path of Matlab's executable
- get_matlab_standalone_path: returns the path of Matlab Compiler
Runtime
- get_max_projects: returns the maximum number of projects
displayed in the "Saved projects" menu
- get_max_thumbnails: get max thumbnails number at the data
browser bottom
- get_properties_path: returns the software's properties path
- get_mri_conv_path: returns the MRIManager.jar path
- get_mrtrix_path: returns mrtrix path
- getNbAllSlicesMax: returns the maximum number of slices to
display in the mini viewer
- get_opened_projects: returns the opened projects
- get_projects_save_path: returns the folder where the projects
are saved
- get_referential: returns boolean to indicate DataViewer
referential
- get_resources_path: get the resources path
- getShowAllSlices: returns if the "show all slices" checkbox of
the mini viewer is activated
- getSourceImageDir: get the source directory for project images
- get_spm_path: returns the path of SPM12 (license version)
- get_spm_standalone_path: returns the path of SPM12 (standalone
version)
- getTextColor: return the text color
- getThumbnailTag: returns the tag that is displayed in the mini
viewer
- get_use_afni: returns the value of "use afni" checkbox in the
preferences
- get_use_ants: returns the value of "use ants" checkbox in the
preferences
- get_use_clinical: returns the value of "clinical mode" checkbox
in the preferences
- get_use_freesurfer: returns the value of "use freesurfer"
checkbox in the preferences
- get_use_fsl: returns the value of "use fsl" checkbox in the
preferences
- get_use_matlab: returns the value of "use matlab" checkbox in
the preferences
- get_use_matlab_standalone: returns the value of "use matlab
standalone" checkbox in the
preferences
- get_use_mrtrix: returns the value of "use mrtrix" checkbox in
the preferences
- get_user_level: get the user level in the Capsul config
- get_user_mode: returns the value of "user mode" checkbox
in the preferences
- get_use_spm: returns the value of "use spm" checkbox in the
preferences
- get_use_spm_standalone: returns the value of "use spm standalone"
checkbox in the preferences
- getViewerConfig: returns the DataViewer configuration (neuro or
radio), by default neuro
- getViewerFramerate: returns the DataViewer framerate for
automatic time running images
- isAutoSave: checks if auto-save mode is activated
- isControlV1: checks if the selected display of the controller is
of V1 type
- isRadioView: checks if miniviewer in radiological orientation (if
not, then it is in neurological orientation)
- loadConfig: reads the config in the config.yml file
- saveConfig: saves the config to the config.yml file
- set_admin_hash: set the password hash
- set_afni_path: set the path of the AFNI
- set_ants_path: set the path of the ANTS
- set_mrtrix_path: set the path of mrtrix
- setAutoSave: sets the auto-save mode
- setBackgroundColor: sets the background color
- set_capsul_config: set CAPSUL configuration dict into MIA config
- setChainCursors: set the "chain cursors" checkbox of the mini
viewer
- set_clinical_mode: set the value of "clinical mode" in
the preferences
- setControlV1: Set controller display mode (True if V1)
- set_freesurfer_setup: set freesurfer path
- set_fsl_config: set the path of the FSL config file
- set_mainwindow_maximized: set the maximized (fullscreen) flag
- set_mainwindow_size: set main window size
- set_matlab_path: set the path of Matlab's executable
- set_matlab_standalone_path: set the path of Matlab Compiler
Runtime
- set_max_projects: set the maximum number of projects displayed in
the "Saved projects" menu
- set_max_thumbnails: set max thumbnails number at the data browser
bottom
- set_mri_conv_path: set the MRIManager.jar path
- setNbAllSlicesMax: set the maximum number of slices to display in
the mini viewer
- set_opened_projects: set the opened projects
- set_projects_save_path: set the folder where the projects are
saved
- set_radioView: set the orientation in miniviewer (True for
radiological, False for neurological orientation)
- set_referential: set the DataViewer referential
- set_resources_path: Set the resources path
- setShowAllSlices: set the "show all slices" checkbox of the mini
viewer
- setSourceImageDir: set the source directory for project images
- set_spm_path: set the path of SPM12 (license version)
- set_spm_standalone_path: set the path of SPM12 (standalone
version)
- setTextColor: set the text color
- setThumbnailTag: set the tag that is displayed in the mini viewer
- set_use_afni: set the value of "use afni" checkbox in the
preferences
- set_use_ants: set the value of "use ants" checkbox in the
preferences
- set_use_freesurfer: set the value of "use freesurfer" checkbox
in the preferences
- set_use_fsl: set the value of "use fsl" checkbox in the
preferences
- set_use_matlab: set the value of "use matlab" checkbox in the
preferences
- set_use_matlab_standalone: set the value of "use matlab
standalone" checkbox in the
preferences
- set_use_mrtrix: set the value of "use mrtrix" checkbox in the
preferences
- set_user_mode: set the value of "user mode" checkbox in
the preferences
- set_use_spm: set the value of "use spm" checkbox in the
preferences
- set_use_spm_standalone: set the value of "use spm standalone"
checkbox in the preferences
- setViewerConfig: set the Viewer configuration neuro or radio
- setViewerFramerate: set the Viewer frame rate for automatic
running time images
- update_capsul_config: update a global CapsulEngine object used
for all operations in MIA application
"""
capsul_engine = None
[docs]
def __init__(self, properties_path=None):
"""
Initialization of the Config class
:param properties_path (str): If provided, the configuration file
will be loaded/saved from the given
directory. Otherwise, the regular
heuristics will be used to determine the
config path. This option allows to use
an alternative config directory (for
tests for instance).
"""
if properties_path is not None:
self.properties_path = properties_path
if os.environ.get("MIA_DEV_MODE", None) is not None:
self.dev_mode = bool(int(os.environ["MIA_DEV_MODE"]))
else:
# FIXME: What can we do if "MIA_DEV_MODE" is not in os.environ?
logger.warning("MIA_DEV_MODE not found...")
self.config = self.loadConfig()
[docs]
def get_admin_hash(self):
"""
Retrieves the hashed admin password from the configuration.
:return: The hashed admin password if found in config, False if not
present in config.
"""
try:
return self.config["admin_hash"]
except KeyError:
return False
[docs]
def get_afni_path(self):
"""Get the AFNI path.
:return (str): Path to AFNI, or "" if unknown.
"""
return self.config.get("afni", "")
[docs]
def get_ants_path(self):
"""Get the ANTS path.
:return (str): Path to ANTS, or "" if unknown.
"""
return self.config.get("ants", "")
[docs]
def get_freesurfer_setup(self):
"""Get the freesurfer path.
:return (str): Path to freesurfer, or "" if unknown.
"""
return self.config.get("freesurfer_setup", "")
[docs]
def getBackgroundColor(self):
"""Get background color.
:return (str): Background color, or "" if unknown.
"""
return self.config.get("background_color", "")
[docs]
def get_capsul_config(self, sync_from_engine=True):
"""
Retrieve and construct the Capsul configuration dictionary.
This function builds a configuration dictionary for Capsul,
incorporating settings for various neuroimaging tools and processing
engines. It manages configurations for tools like SPM, FSL,
FreeSurfer, MATLAB, AFNI, ANTs, and MRTrix.
The function first retrieves local settings for each tool from the Mia
preferences, then constructs the appropriate configuration structure.
If requested, it can synchronize the configuration with the current
Capsul engine state.
:param sync_from_engine (bool): If True, synchronizes the
configuration with the current Capsul
engine settings after building the
base configuration.
:return (dict): A nested dictionary containing the complete Capsul
configuration, structured with the following main
sections:
- engine_modules: List of available processing modules
- engine: Contains global and environment-specific
settings
- tool-specific configurations (SPM, FSL, etc.)
:Private functions:
- _configure_spm: Configure SPM settings.
- _configure_tool:
"""
def _configure_spm(spm_configs, path, standalone=False):
"""
Helper function to configure SPM settings, preserving existing
configuration IDs if found.
This function either updates an existing SPM configuration or
creates a new one based on the provided parameters. It searches
through existing configurations to find any matching the specified
path and standalone settings. If found, it reuses that
configuration's ID; otherwise, it generates a new one.
:param spm_configs (dict): Dictionary of existing SPM
configurations where keys are
config_ids and values are configuration
dictionaries.
:param path (str): Directory path for the SPM configuration.
:param standalone (bool): Flag indicating whether this is a
standalone configuration.
Defaults to False
"""
found_config = {}
# Look for existing matching configuration
for config_id, config in spm_configs.items():
if (
config.get("standalone") == standalone
and config.get("directory") == path
):
found_config = config
break
# Use existing config_id if found, otherwise create new one
if found_config:
config_id = found_config["config_id"]
else:
config_id = f"spm{'-standalone' if standalone else ''}"
# Update or create configuration
spm_configs.setdefault(config_id, {}).update(
{
"config_id": config_id,
"config_environment": "global",
"directory": path,
"standalone": standalone,
}
)
def _configure_tool(global_config, tool_name, tool_config):
"""
Helper function to configure various neuroimaging tools within
a global configuration.
This function updates or creates tool-specific configurations
within a global configuration dictionary. It handles setup for
neuroimaging tools by managing their paths, configurations, and
setup parameters.
:param global_config (dict): Global configuration dictionary where
tool configurations will be stored.
The tool's settings will be placed
under the key
'capsul.engine.module.{tool_name}'.
:param tool_name (str): Name of the neuroimaging tool being
configured (e.g., 'fsl', 'afni', etc.).
:param tool_config (dict): Tool-specific configuration dictionary
that may contain:
- 'path': Directory path for the tool
installation
- 'config': Path to tool's
configuration file
- 'setup': Setup-specific parameters
for the tool
"""
tool_section = global_config.setdefault(
f"capsul.engine.module.{tool_name}", {}
).setdefault(tool_name, {})
base_config = {
"config_id": tool_name,
"config_environment": "global",
}
if "path" in tool_config:
base_config["directory"] = tool_config["path"]
if "config" in tool_config:
base_config["config"] = tool_config["config"]
base_config["directory"] = os.path.dirname(
os.path.dirname(os.path.dirname(tool_config["config"]))
)
if "setup" in tool_config:
base_config["setup"] = tool_config["setup"]
# TODO: Change FSL subject dir
base_config["subjects_dir"] = ""
tool_section.update(base_config)
capsul_config = self.config.setdefault("capsul_config", {})
capsul_config.setdefault(
"engine_modules",
[
"nipype",
"fsl",
"freesurfer",
"matlab",
"spm",
"fom",
"python",
"afni",
"ants",
"mrtrix",
"somaworkflow",
],
)
# Set up engine configuration structure
engine_config = capsul_config.setdefault("engine", {})
global_config = engine_config.setdefault("global", {})
# Collect all tool configurations
tool_configs = {
"spm": {
"use_standard": self.get_use_spm(),
"path": self.get_spm_path(),
"use_standalone": self.get_use_spm_standalone(),
"standalone_path": self.get_spm_standalone_path(),
},
"matlab": {
"use_standard": self.get_use_matlab(),
"path": self.get_matlab_path(),
"use_standalone": self.get_use_matlab_standalone(),
"standalone_path": self.get_matlab_standalone_path(),
},
"fsl": {
"use": self.get_use_fsl(),
"config": self.get_fsl_config(),
},
"afni": {"use": self.get_use_afni(), "path": self.get_afni_path()},
"ants": {"use": self.get_use_ants(), "path": self.get_ants_path()},
"freesurfer": {
"use": self.get_use_freesurfer(),
"setup": self.get_freesurfer_setup(),
},
"mrtrix": {
"use": self.get_use_mrtrix(),
"path": self.get_mrtrix_path(),
},
}
# Make synchronisation from Mia preferences to Capsul config:
# TODO: We do not deal with the version parameter. This can produce
# hidden configurations (spm and spm12 and spm8 ...)!
# Configure SPM (both standalone and standard versions)
spm_configs = global_config.setdefault("capsul.engine.module.spm", {})
if tool_configs["spm"]["use_standalone"]:
_configure_spm(
spm_configs,
tool_configs["spm"]["standalone_path"],
standalone=True,
)
if tool_configs["spm"]["use_standard"]:
_configure_spm(
spm_configs, tool_configs["spm"]["path"], standalone=False
)
# Configure MATLAB
matlab_config = global_config.setdefault(
"capsul.engine.module.matlab", {}
).setdefault("matlab", {})
if tool_configs["matlab"]["use_standalone"]:
matlab_config.update(
{
"mcr_directory": tool_configs["matlab"]["standalone_path"],
"config_id": "matlab",
"config_environment": "global",
}
)
if tool_configs["matlab"]["use_standard"]:
matlab_config.update(
{
"executable": tool_configs["matlab"]["path"],
"config_id": "matlab",
"config_environment": "global",
}
)
# Configure other tools
for tool in ["fsl", "afni", "ants", "freesurfer", "mrtrix"]:
if tool_configs[tool]["use"]:
_configure_tool(global_config, tool, tool_configs[tool])
# attributes completion
attrs_config = global_config.setdefault(
"capsul.engine.module.attributes", {}
).setdefault("attributes", {})
attrs_config.update(
{
"config_id": "attributes",
"config_environment": "global",
"attributes_schema_paths": [
"capsul.attributes.completion_engine_factory",
"populse_mia.user_interface.pipeline_manager.process_mia",
],
"process_completion": "mia_completion",
}
)
# Synchronise from engine, or not
if sync_from_engine and self.capsul_engine:
for environment in (
self.capsul_engine.settings.get_all_environments
)():
env_config = engine_config.setdefault(environment, {})
# would need a better merging system
env_config.update(
self.capsul_engine.settings.export_config_dict(
environment
)[environment]
)
return capsul_config
[docs]
@staticmethod
@lru_cache(maxsize=1)
def get_capsul_engine():
"""
Get or create a global CapsulEngine singleton for Mia application
operations.
The engine is created only once when first needed (lazy
initialization). Subsequent calls return the same instance.
:return: CapsulEngine: The global CapsulEngine instance.
"""
if Config.capsul_engine is None:
config = Config()
config.get_capsul_config()
Config.capsul_engine = capsul_engine()
Config().update_capsul_config()
return Config.capsul_engine
[docs]
def getChainCursors(self):
"""Get the value of the checkbox 'chain cursor' in miniviewer.
:return (bool): Value of the checkbox.
"""
return self.config.get("chain_cursors", False)
[docs]
def get_fsl_config(self):
"""Get the FSL config file path.
:return (str): Path to the fsl/etc/fslconf/fsl.sh file.
"""
return self.config.get("fsl_config", "")
[docs]
def get_mainwindow_maximized(self):
"""Get the maximized (fullscreen) flag.
:return (bool): Maximized (fullscreen) flag.
"""
return self.config.get("mainwindow_maximized", True)
[docs]
def get_mainwindow_size(self):
"""Get the main window size.
:return (list): Main window size.
"""
return self.config.get("mainwindow_size", None)
[docs]
def get_matlab_command(self):
"""
Retrieves the appropriate Matlab command based on the configuration.
:return (str): The Matlab executable path or None if no path is
specified.
"""
if self.config.get("use_spm_standalone"):
arch_bits, os_name = platform.architecture()
if "Windows" in os_name:
pattern = os.path.join(
self.config["spm_standalone"],
f"spm*_win{arch_bits[:2]}.exe",
)
else:
pattern = os.path.join(
self.config["spm_standalone"], "run_spm*.sh"
)
spm_script = glob.glob(pattern)
# An empty string indicates that the script has not been
# localised, which is bound to cause problems later on.
return (
f"{spm_script[0]} {self.config['matlab_standalone']} script"
if spm_script
else ""
)
return self.config.get("matlab")
[docs]
def get_matlab_path(self):
"""Get the path to the matlab executable.
:return (str): A path.
"""
return self.config.get("matlab", None)
[docs]
def get_matlab_standalone_path(self):
"""Get the path to matlab compiler runtime.
:return (str): A path.
"""
return self.config.get("matlab_standalone", "")
[docs]
def get_max_projects(self):
"""
Retrieves the maximum number of projects displayed in the
"Saved projects" menu.
:return (int): The maximum number of projects. Defaults to 5 if not
specified.
"""
return int(self.config.get("max_projects", 5))
[docs]
def get_max_thumbnails(self):
"""
Retrieves the maximum number of thumbnails displayed in the
mini-viewer at the bottom of the data browser.
:return (int): The maximum number of thumbnails. Defaults to 5 if
not specified.
"""
return int(self.config.get("max_thumbnails", 5))
[docs]
def get_properties_path(self):
"""
Retrieves the path to the folder containing the "processes" and
"properties" directories of Mia.
The properties path is defined in the `configuration_path.yml` file,
located in `~/.populse_mia`.
- In **user mode**, the path is retrieved from the
`properties_user_path` parameter.
- In **developer mode**, the path is retrieved from the
`properties_dev_path` parameter.
If outdated parameters (`mia_path`, `mia_user_path`) are found,
they are automatically updated in the configuration file.
:return (str): The absolute path to the properties folder.
"""
# import verCmp only here to prevent circular import issue
from populse_mia.utils import verCmp
if (
hasattr(self, "properties_path")
and self.properties_path is not None
):
return self.properties_path
dot_mia_config = os.path.expanduser(
"~/.populse_mia/configuration_path.yml"
)
try:
with open(dot_mia_config) as stream:
if verCmp(yaml.__version__, "5.1", "sup"):
mia_home_properties_path = yaml.load(
stream, Loader=yaml.FullLoader
)
else:
mia_home_properties_path = yaml.load(stream)
except yaml.YAMLError as e:
logger.warning(f"{e}")
logger.warning(
"~/.populse_mia/configuration_path.yml cannot be read, the "
"path to the properties folder has not been found.."
)
raise
# Patch for obsolete parameters.
updated = False
for old_key, new_key in [
("mia_path", "properties_user_path"),
("mia_user_path", "properties_user_path"),
]:
if old_key in mia_home_properties_path:
mia_home_properties_path[new_key] = (
mia_home_properties_path.pop(old_key)
)
updated = True
if updated:
with open(dot_mia_config, "w", encoding="utf-8") as configfile:
yaml.dump(
mia_home_properties_path,
configfile,
default_flow_style=False,
allow_unicode=True,
)
try:
key = (
"properties_dev_path"
if self.dev_mode
else "properties_user_path"
)
self.properties_path = os.path.join(
mia_home_properties_path[key],
"dev" if self.dev_mode else "usr",
)
return self.properties_path
except KeyError as e:
logger.warning(f"{e}")
logger.warning(
"Key not found in ~/.populse_mia/configuration_path.yml!"
)
raise
[docs]
def get_mri_conv_path(self):
"""Get the MRIManager.jar path.
:return (str): A path.
"""
return self.config.get("mri_conv_path", "")
[docs]
def get_mrtrix_path(self):
"""Get the mrtrix path
:return (str): A path.
"""
return self.config.get("mrtrix", "")
[docs]
def getNbAllSlicesMax(self):
"""
Get number the maximum number of slices to display in the miniviewer.
:return (int): Maximum number of slices to display in miniviewer.
"""
return int(self.config.get("nb_slices_max", "10"))
[docs]
def get_opened_projects(self):
"""Get opened projects.
:return (list): Opened projects.
"""
return self.config.get("opened_projects", [])
[docs]
def get_projects_save_path(self):
"""Get the path where projects are saved.
:return (str): A path.
"""
return self.config.get("projects_save_path", "")
[docs]
def get_referential(self):
"""
Retrieves the chosen referential from the anatomist_2 data viewer.
:return (str): "0" for World Coordinates, "1" for Image ref.
"""
return self.config.get("ref", "0")
[docs]
def get_resources_path(self):
"""Get the resources path.
:return (str): A path.
"""
return self.config.get("resources_path", "")
[docs]
def getShowAllSlices(self):
"""
Get whether the show_all_slices parameters was enabled or not in
the miniviewer.
:return (bool): True if the show_all_slices parameters was enabled.
"""
return self.config.get("show_all_slices", False)
[docs]
def getSourceImageDir(self):
"""Get the source directory for project images.
:return (str): A path.
"""
return self.config.get("source_image_dir", "")
[docs]
def get_spm_path(self):
"""Get the path of SPM12.
:return (str): A path.
"""
return self.config.get("spm", "")
[docs]
def get_spm_standalone_path(self):
"""Get the path to the SPM12 standalone version.
:return (str): A path.
"""
return self.config.get("spm_standalone", "")
[docs]
def getTextColor(self):
"""Get the text color.
:return (str): The text color.
"""
return self.config.get("text_color", "")
[docs]
def getThumbnailTag(self):
"""Get the tag of the thumbnail displayed in the miniviewer.
:return (str): The tag of the thumbnail displayed in miniviewer.
"""
return self.config.get("thumbnail_tag", "SequenceName")
[docs]
def get_use_afni(self):
"""Get the value of "use afni" checkbox in the preferences.
:return (bool): The value of "use afni" checkbox.
"""
return self.config.get("use_afni", False)
[docs]
def get_use_ants(self):
"""Get the value of "use ants" checkbox in the preferences.
:return (bool): The value of "use ants" checkbox.
"""
return self.config.get("use_ants", False)
[docs]
def get_use_clinical(self):
"""Get the clinical mode in the preferences.
:return (bool): The clinical mode.
"""
return self.config.get("clinical_mode", False)
[docs]
def get_use_fsl(self):
"""Get the value of "use fsl" checkbox in the preferences.
:return (bool): The value of "use fsl" checkbox.
"""
return self.config.get("use_fsl", False)
[docs]
def get_use_freesurfer(self):
"""Get the value of "use freesurfer" checkbox in the preferences.
:return (bool): The value of "use freesurfer" checkbox.
"""
return self.config.get("use_freesurfer", False)
[docs]
def get_use_matlab(self):
"""Get the value of "use matlab" checkbox in the preferences.
:return (bool): The value of "use matlab" checkbox.
"""
return self.config.get("use_matlab", False)
[docs]
def get_use_matlab_standalone(self):
"""
Get the value of "use matlab standalone" checkbox in the preferences.
:return (bool): The value of "use matlab standalone" checkbox.
"""
return self.config.get("use_matlab_standalone", False)
[docs]
def get_user_level(self):
"""Get the user level in the Capsul config.
:return (int): The user level in the Capsul config.
"""
return (
self.config.get("capsul_config", {})
.get("engine", {})
.get("global", {})
.get("capsul.engine.module.axon", {})
.get("user_level", 0)
)
[docs]
def get_user_mode(self):
"""Get if user mode is disabled or enabled in the preferences.
:return (bool): If True, the user mode is enabled.
"""
return self.config.get("user_mode", True)
[docs]
def get_use_mrtrix(self):
"""Get the value of "use mrtrix" checkbox in the preferences.
:return (bool): The value of "use mrtrix" checkbox.
"""
return self.config.get("use_mrtrix", False)
[docs]
def get_use_spm(self):
"""Get the value of "use spm" checkbox in the preferences.
:return (bool): The value of "use spm" checkbox.
"""
return self.config.get("use_spm", False)
[docs]
def get_use_spm_standalone(self):
"""Get the value of "use spm standalone" checkbox in the preferences.
:return (bool): The value of "use spm standalone" checkbox.
"""
return self.config.get("use_spm_standalone", False)
[docs]
def getViewerConfig(self):
"""Get the viewer config "neuro" or "radio", "neuro" by default.
:return (str): The viewer config ("neuro" or "radio").
"""
return self.config.get("config_NeuRad", "neuro")
[docs]
def getViewerFramerate(self):
"""Get the Viewer framerate.
:return (str): The Viewer framerat (ex. "5").
"""
return self.config.get("im_sec", "5")
[docs]
def isAutoSave(self):
"""Get if the auto-save mode is enabled or not.
:return (bool): If True, auto-save mode is enabled.
"""
return self.config.get("auto_save", False)
[docs]
def isControlV1(self):
"""
Gets whether the controller display is of type V1.
:return (bool): If True, V1 controller display.
"""
return self.config.get("control_V1", False)
[docs]
def isRadioView(self):
"""
Get if the display in miniviewer is in radiological orientation.
:return (bool): If True, radiological orientation,
otherwise neurological orientation.
"""
return self.config.get("radio_view", True)
[docs]
def loadConfig(self):
"""Read the config from config.yml file.
Attempts to read an encrypted YAML configuration file from the
properties directory, decrypt it using Fernet encryption, and
parse it as YAML.
:return (dict): Parsed configuration from the YAML file.
Returns empty dict if parsing fails.
"""
# import verCmp only here to prevent circular import issue
from populse_mia.utils import verCmp
fernet = Fernet(ENCRYPTION_KEY)
config_path = (
Path(self.get_properties_path()) / "properties" / "config.yml"
)
if not config_path.exists():
raise yaml.YAMLError(
f"\nThe configuration file '{config_path}' doesn't "
f"exist or is corrupted...\n"
)
try:
encrypted_data = config_path.read_bytes()
decrypted_data = fernet.decrypt(encrypted_data)
# For YAML versions >= 5.1, use FullLoader for better security
if verCmp(yaml.__version__, "5.1", "sup"):
return yaml.load(decrypted_data, Loader=yaml.FullLoader)
else:
# Loader parameter not available in older versions
return yaml.load(decrypted_data)
except yaml.YAMLError as exc:
logger.warning(f"Error loading '{config_path}' file: {exc}")
return {}
[docs]
def saveConfig(self):
"""
Save the current parameters in the config.yml file.
Encrypts and writes the current configuration (self.config) to
config.yml using Fernet encryption. Creates the necessary
directory structure if it doesn't exist. After saving, updates
the capsul configuration.
"""
config_path = (
Path(self.get_properties_path()) / "properties" / "config.yml"
)
# Ensure parent directory exists
config_path.parent.mkdir(parents=True, exist_ok=True)
fernet = Fernet(ENCRYPTION_KEY)
yaml_data = yaml.dump(
self.config, default_flow_style=False, allow_unicode=True
)
encrypted_data = fernet.encrypt(yaml_data.encode())
# Write encrypted configuration
config_path.write_bytes(encrypted_data)
self.update_capsul_config()
[docs]
def set_admin_hash(self, admin_hash):
"""Set the password hash.
:param admin_hash: A string.
"""
self.config["admin_hash"] = admin_hash
# Then save the modification
self.saveConfig()
[docs]
def set_afni_path(self, path):
"""Set the AFNI path.
:param path: A path (str).
"""
self.config["afni"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_ants_path(self, path):
"""Set the ANTS path
:param path: A path (str).
"""
self.config["ants"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_mrtrix_path(self, path):
"""Set the mrtrix path.
:param path: A path (str).
"""
self.config["mrtrix"] = path
# Then save the modification
self.saveConfig()
[docs]
def setAutoSave(self, save):
"""Set auto-save mode.
:param save: A boolean.
"""
self.config["auto_save"] = save
# Then save the modification
self.saveConfig()
[docs]
def setBackgroundColor(self, color):
"""Set background color and save configuration.
:param color: Color string ('Black', 'Blue', 'Green', 'Grey',
'Orange', 'Red', 'Yellow', 'White')
"""
self.config["background_color"] = color
# Then save the modification
self.saveConfig()
[docs]
def set_capsul_config(self, capsul_config_dict):
"""
Update Mia configuration with Capsul settings and synchronize tools
configuration.
Called after editing Capsul config (via File > Mia preferences >
Pipeline tab > Edit CAPSUL config) to synchronize Capsul settings
with Mia preferences. Configures various neuroimaging tools
AFNI, ANTs, FSL, etc.) based on the Capsul engine configuration.
:param capsul_config_dict (dict): Dictionary containing Capsul
configuration with structure:
{
'engine': {
'environment_name': {...configuration...}
},
'engine_modules': [...]
}
:Contains:
:Private function:
- _configure_standalone_spm: Configures standalone SPM and
MCR.
- _configure_matlab_spm: Configures SPM and MATLAB.
- _configure_matlab_only: Configures MATLAB without SPM.
- _configure_mcr_only: Configures MCR without SPM.
- _disable_matlab_spm: Disables all MATLAB and SPM
configurations.
- _get_module_config: Extracts module configuration from the
global Capsul configuration.
"""
def _configure_standalone_spm(self, spm_dir, mcr_dir):
"""
Configures standalone SPM to use the specified SPM and MATLAB
Compiler Runtime (MCR) directories.
:param spm_dir (str): The directory path of the standalone SPM
installation.
:param mcr_dir (str): The directory path of the MATLAB Compiler
Runtime (MCR).
"""
self.set_spm_standalone_path(spm_dir)
self.set_use_spm_standalone(True)
self.set_use_spm(False)
self.set_matlab_standalone_path(mcr_dir)
self.set_use_matlab_standalone(True)
self.set_use_matlab(False)
def _configure_matlab_spm(self, spm_dir, matlab_path):
"""
Configures SPM to use the specified SPM directory with a MATLAB
installation.
:param spm_dir (str): The directory path of the SPM installation.
:param matlab_path (str): The directory path of the MATLAB
installation.
"""
self.set_spm_path(spm_dir)
self.set_use_spm(True)
self.set_use_spm_standalone(False)
self.set_matlab_path(matlab_path)
self.set_use_matlab(True)
self.set_use_matlab_standalone(False)
def _configure_matlab_only(self, matlab_path: str) -> None:
"""
Configures MATLAB without SPM, ensuring that only MATLAB is used.
:param matlab_path (str): The directory path of the MATLAB
installation.
"""
self.set_matlab_path(matlab_path)
self.set_use_matlab(True)
self.set_use_matlab_standalone(False)
self.set_use_spm(False)
self.set_use_spm_standalone(False)
def _configure_mcr_only(self, mcr_dir: str) -> None:
"""
Configures MATLAB Compiler Runtime (MCR) without SPM, ensuring
that only MCR is used.
:param mcr_dir (str): The directory path of the MATLAB Compiler
Runtime (MCR).
"""
self.set_matlab_standalone_path(mcr_dir)
self.set_use_matlab_standalone(True)
self.set_use_matlab(False)
self.set_use_spm(False)
self.set_use_spm_standalone(False)
def _disable_matlab_spm(self) -> None:
"""
Disables all MATLAB and SPM configurations, ensuring that neither
MATLAB nor SPM is used.
"""
self.set_use_matlab(False)
self.set_use_matlab_standalone(False)
self.set_use_spm(False)
self.set_use_spm_standalone(False)
def _get_module_config(module_name: str) -> dict:
"""
Extracts the configuration for a specific module from the global
Capsul configuration.
:param module_name (str): The name of the module to retrieve the
configuration for.
:return (dict): The configuration dictionary of the specified
module, or an empty dictionary if not found.
"""
module_path = f"capsul.engine.module.{module_name}"
module_config = global_config.get(module_path, {})
# TODO: we only take the first element of the dictionary (the one
# that is normally edited in the Capsul config GUI). There is
# actually a problem because this means that there may be
# hidden config(s) ... This can produce bugs and at least
# unpredictable results for the user ...
return next(iter(module_config.values())) if module_config else {}
self.config["capsul_config"] = capsul_config_dict
# Initialize new engine and import configurations
new_engine = capsul_engine()
engine_config = capsul_config_dict.get("engine", {})
for environment, config in engine_config.items():
if environment != "capsul_engine":
new_engine.import_configs(environment, config)
global_config = new_engine.settings.export_config_dict("global").get(
"global", {}
)
# Configure simple tools (AFNI, ANTs, MRtrix)
for tool in ["afni", "ants", "mrtrix"]:
config = _get_module_config(tool)
directory = config.get("directory")
use_tool = bool(directory)
if directory:
getattr(self, f"set_{tool}_path")(directory)
getattr(self, f"set_use_{tool}")(use_tool)
# Configure Freesurfer
freesurfer_config = _get_module_config("freesurfer")
setup_path = freesurfer_config.get("setup")
use_freesurfer = bool(setup_path)
if setup_path:
self.set_freesurfer_setup(setup_path)
self.set_use_freesurfer(use_freesurfer)
# Configure FSL
fsl_config = _get_module_config("fsl")
fsl_conf_path = fsl_config.get("config")
fsl_dir_path = fsl_config.get("directory")
use_fsl = False
if fsl_conf_path:
use_fsl = True
self.set_fsl_config(fsl_conf_path)
# If only the directory parameter has been set, let's try using
# the config parameter = directory/etc/fslconf/fsl.sh:
elif fsl_dir_path:
default_conf = Path(fsl_dir_path) / "etc" / "fslconf" / "fsl.sh"
if default_conf.is_file():
use_fsl = True
self.set_fsl_config(str(default_conf))
else:
logger.warning(
f"Could not determine FSL configuration file from "
f"directory {fsl_dir_path}. FSL is not correctly defined "
f"in preferences (see File > Mia Preferences)."
)
self.set_use_fsl(use_fsl)
# Configure MATLAB/SPM
matlab_config = _get_module_config("matlab")
spm_config = _get_module_config("spm")
matlab_path = matlab_config.get("executable")
mcr_dir = matlab_config.get("mcr_directory")
spm_dir = spm_config.get("directory")
use_spm_standalone = spm_config.get("standalone", False)
use_matlab = bool(matlab_path) and Path(matlab_path).is_file()
use_mcr = bool(mcr_dir) and Path(mcr_dir).is_dir()
spm_dir_valid = bool(spm_dir) and Path(spm_dir).is_dir()
# Determine configuration mode
if spm_dir_valid and use_mcr and use_spm_standalone:
self._configure_standalone_spm(spm_dir, mcr_dir)
elif spm_dir_valid and use_matlab and not use_spm_standalone:
self._configure_matlab_spm(spm_dir, matlab_path)
elif use_matlab:
self._configure_matlab_only(matlab_path)
elif use_mcr:
self._configure_mcr_only(mcr_dir)
else:
self._disable_matlab_spm()
# TODO: Because there are two parameters for matlab (executable and
# mcr_directory) in Capsul config, if the user defines both, we don't
# know which on to choose! Here we choose to favour matlab in front
# of MCR if both are chosen, is it desirable?
if (
use_matlab
and use_mcr
and not (use_spm_standalone or bool(spm_dir))
):
logger.info(
"Both Matlab executable and MCR directory are set in Capsul "
"configuration. Defaulting to Matlab over MCR."
)
self.update_capsul_config()
[docs]
def setChainCursors(self, chain_cursors):
"""Set the value of the checkbox 'chain cursor' in the mini viewer.
:param chain_cursors: A boolean.
"""
self.config["chain_cursors"] = chain_cursors
# Then save the modification
self.saveConfig()
[docs]
def set_clinical_mode(self, clinical_mode):
"""Enable or disable clinical mode.
:param clinical_mode: A boolean.
"""
self.config["clinical_mode"] = clinical_mode
# Then save the modification
self.saveConfig()
[docs]
def setControlV1(self, controlV1):
"""Set controller display mode (True if V1).
:param controlV1: A boolean.
"""
self.config["control_V1"] = controlV1
# Then save the modification
self.saveConfig()
[docs]
def set_fsl_config(self, path):
"""Set the FSL config file.
:param path (str): Path to fsl/etc/fslconf/fsl.sh.
"""
self.config["fsl_config"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_freesurfer_setup(self, path):
"""Set the freesurfer config file.
:param path (str): Path to freesurfer/FreeSurferEnv.sh.
"""
self.config["freesurfer_setup"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_mainwindow_maximized(self, enabled):
"""Set the maximized (full-screen) flag.
:param enabled: A boolean.
"""
self.config["mainwindow_maximized"] = enabled
self.saveConfig()
[docs]
def set_mainwindow_size(self, size):
"""Set main window size.
:param size: A list of two integers.
"""
self.config["mainwindow_size"] = list(size)
self.saveConfig()
[docs]
def set_matlab_path(self, path):
"""Set the path of Matlab's executable.
:param path: A path (str).
"""
self.config["matlab"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_matlab_standalone_path(self, path):
"""Set the path of Matlab Compiler Runtime.
:param path: A path (str).
"""
self.config["matlab_standalone"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_max_projects(self, nb_max_projects):
"""
Set the maximum number of projects displayed in the "Saved projects"
menu.
:param nb_max_projects: An integer.
"""
self.config["max_projects"] = nb_max_projects
# Then save the modification
self.saveConfig()
[docs]
def set_max_thumbnails(self, nb_max_thumbnails):
"""Set max thumbnails number at the data browser bottom.
:param nb_max_thumbnails: An integer.
"""
self.config["max_thumbnails"] = nb_max_thumbnails
# Then save the modification
self.saveConfig()
[docs]
def set_mri_conv_path(self, path):
"""Set the MRIManager.jar path.
:param path: A path (str).
"""
self.config["mri_conv_path"] = path
# Then save the modification
self.saveConfig()
[docs]
def setNbAllSlicesMax(self, nb_slices_max):
"""Set the number of slices to display in the mini-viewer.
:param nb_slices_max (int): maximum number of slices to display.
"""
self.config["nb_slices_max"] = nb_slices_max
# Then save the modification
self.saveConfig()
[docs]
def set_opened_projects(self, new_projects):
"""Set the list of opened projects and saves the modification.
:param new_projects (list[str]): A list of paths.
"""
self.config["opened_projects"] = new_projects
# Then save the modification
self.saveConfig()
[docs]
def set_projects_save_path(self, path):
"""Set the folder where the projects are saved.
:param path: A path (str).
"""
self.config["projects_save_path"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_radioView(self, radio_view):
"""Set the radiological/neurological orientation in mini viewer.
- True for radiological
- False for neurological
:param radio_view: A boolean.
"""
self.config["radio_view"] = radio_view
# Then save the modification
self.saveConfig()
[docs]
def set_referential(self, ref):
"""
Set the referential to "image Ref" or "World Coordinates" in
anatomist_2 data viewer.
:param ref (str): "0" for World Coordinates, "1" for Image Ref.
"""
self.config["ref"] = ref
# Then save the modification
self.saveConfig()
[docs]
def set_resources_path(self, path):
"""Set the resources path.
:param path: A path (str).
"""
self.config["resources_path"] = path
# Then save the modification
self.saveConfig()
[docs]
def setShowAllSlices(self, show_all_slices):
"""Set the show_all_slides setting in miniviewer.
:param show_all_slices: A boolean.
"""
self.config["show_all_slices"] = show_all_slices
# Then save the modification
self.saveConfig()
[docs]
def setSourceImageDir(self, source_image_dir):
"""Set the source directory for project images.
:param source_image_dir: A path (str).
"""
self.config["source_image_dir"] = source_image_dir
# Then save the modification
self.saveConfig()
[docs]
def set_spm_path(self, path):
"""Set the path of SPM (license version).
:param path: A path (str).
"""
self.config["spm"] = path
# Then save the modification
self.saveConfig()
[docs]
def set_spm_standalone_path(self, path):
"""Set the path of SPM (standalone version).
:param path: A path (str).
"""
self.config["spm_standalone"] = path
# Then save the modification
self.saveConfig()
[docs]
def setTextColor(self, color):
"""Set text color and save configuration.
:param color: Color string ('Black', 'Blue', 'Green', 'Grey',
'Orange', 'Red', 'Yellow', 'White')
"""
self.config["text_color"] = color
# Then save the modification
self.saveConfig()
[docs]
def setThumbnailTag(self, thumbnail_tag):
"""Set the tag that is displayed in the mini-viewer.
:param thumbnail_tag: A string.
"""
self.config["thumbnail_tag"] = thumbnail_tag
# Then save the modification
self.saveConfig()
[docs]
def set_use_afni(self, use_afni):
"""Set the value of "use_afni" checkbox in the preferences.
:param use_afni: A boolean.
"""
self.config["use_afni"] = use_afni
# Then save the modification
self.saveConfig()
[docs]
def set_use_ants(self, use_ants):
"""Set the value of "use_ants" checkbox in the preferences.
:param use_ants: A boolean.
"""
self.config["use_ants"] = use_ants
# Then save the modification
self.saveConfig()
[docs]
def set_use_freesurfer(self, use_freesurfer):
"""Set the value of "use_freesurfer" checkbox in the preferences.
:param use_freesurfer: A boolean.
"""
self.config["use_freesurfer"] = use_freesurfer
# Then save the modification
self.saveConfig()
[docs]
def set_use_fsl(self, use_fsl):
"""Set the value of "use_fsl" checkbox in the preferences.
:param use_fsl: A boolean.
"""
self.config["use_fsl"] = use_fsl
# Then save the modification
self.saveConfig()
[docs]
def set_use_matlab(self, use_matlab):
"""Set the value of "use matlab" checkbox in the preferences.
:param use_matlab: A boolean.
"""
self.config["use_matlab"] = use_matlab
# Then save the modification
self.saveConfig()
[docs]
def set_use_matlab_standalone(self, use_matlab_standalone):
"""
Set the value of "use_matlab_standalone" checkbox in the preferences.
:param use_matlab: A boolean.
"""
self.config["use_matlab_standalone"] = use_matlab_standalone
# Then save the modification
self.saveConfig()
[docs]
def set_use_mrtrix(self, use_mrtrix):
"""Set the value of "use_mrtrix" checkbox in the preferences.
:param use_mrtrix: A boolean.
"""
self.config["use_mrtrix"] = use_mrtrix
# Then save the modification
self.saveConfig()
[docs]
def set_user_mode(self, user_mode):
"""Enable or disable user mode.
:param user_mode: A boolean.
"""
self.config["user_mode"] = user_mode
# Then save the modification
self.saveConfig()
[docs]
def set_use_spm(self, use_spm):
"""Set the value of "use spm" checkbox in the preferences.
:param use_spm: A boolean.
"""
self.config["use_spm"] = use_spm
# Then save the modification
self.saveConfig()
[docs]
def set_use_spm_standalone(self, use_spm_standalone):
"""Set the value of "use spm standalone" checkbox in the preferences.
:param use_spm_standalone: A boolean.
"""
self.config["use_spm_standalone"] = use_spm_standalone
# Then save the modification
self.saveConfig()
[docs]
def setViewerConfig(self, config_NeuRad):
"""sets user's configuration neuro or radio for data_viewer.
- neuro: neurological
- radio: radiological
:param config_NeuRad: A string.
"""
self.config["config_NeuRad"] = config_NeuRad
# Then save the modification
self.saveConfig()
[docs]
def setViewerFramerate(self, im_sec):
"""sets user's framerate for data_viewer.
:param im_sec (int): Number of images per second.
"""
self.config["im_sec"] = im_sec
# Then save the modification
self.saveConfig()
[docs]
def update_capsul_config(self):
"""
Updates the global CapsulEngine object used for all operations in
the Mia application.
The CapsulEngine is created once when needed and updated each time
the configuration is saved. This method ensures that all necessary
engine modules are loaded and configurations are properly imported
from the saved settings.
:return (capsul.engine.CapsulEngine): The updated CapsulEngine
object, or None if the engine
is not initialized.
"""
if self.capsul_engine is None:
# Avoid unnecessary updates before the config is actually used
return
capsul_config = self.get_capsul_config(sync_from_engine=False)
engine = Config.capsul_engine
modules = capsul_config.get("engine_modules", []) + [
"fom",
"nipype",
"python",
"fsl",
"freesurfer",
"axon",
"afni",
"ants",
"mrtrix",
"somaworkflow",
]
for module in modules:
engine.load_module(module)
engine_config = capsul_config.get("engine", {})
for environment, config in engine_config.items():
config_copy = dict(config)
if (
"capsul_engine" not in config_copy
or "uses" not in config_copy["capsul_engine"]
):
config_copy["capsul_engine"] = {
"uses": {
engine.settings.module_name(m): "ALL" for m in config
}
}
try:
engine.import_configs(
environment, config_copy, cont_on_error=True
)
except Exception as exc:
logger.warning("An issue was detected in MIA's configuration:")
logger.warning(f"{exc}")
logger.warning(
"Please check the settings in File > "
"Mia Preferences > Pipeline ..."
)
return engine