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Merge pull request #288 from populse/add_mrtrix
add mrtrix in capsul
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@@ -4,4 +4,5 @@ | |
| 'ants', | ||
| 'fsl', | ||
| 'matlab', | ||
| 'mrtrix', | ||
| 'spm'] | ||
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| @@ -0,0 +1,97 @@ | ||
| # -*- coding: utf-8 -*- | ||
| from __future__ import absolute_import | ||
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| import os | ||
| from capsul import engine | ||
| import six | ||
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| def init_settings(capsul_engine): | ||
| with capsul_engine.settings as settings: | ||
| settings.ensure_module_fields('mrtrix', | ||
| [dict(name='directory', | ||
| type='string', | ||
| description='Directory where mrtrix is installed') | ||
| ]) | ||
|
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| # init a single config | ||
| config = settings.config('mrtrix', 'global') | ||
| if not config: | ||
| settings.new_config('mrtrix', 'global', | ||
| {capsul_engine.settings.config_id_field: | ||
| 'mrtrix'}) | ||
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| def check_notably_invalid_config(conf): | ||
| ''' | ||
| Checks if the given module config is obviously invalid, for instance | ||
| if a mandatory path is not filled | ||
| Returns | ||
| ------- | ||
| invalid: list | ||
| list of invalid config keys | ||
| ''' | ||
| return getattr(conf, 'directory', None) | ||
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| def activate_configurations(): | ||
| ''' | ||
| Activate the mrtrix module (set env variables) from the global | ||
| configurations, in order to use them via | ||
| :mod:`capsul.in_context.mrtrix` functions | ||
| ''' | ||
| conf = engine.configurations.get('capsul.engine.module.mrtrix', {}) | ||
| mrtrix_dir = conf.get('directory') | ||
| if mrtrix_dir: | ||
| os.environ['MRTRIXPATH'] = six.ensure_str(mrtrix_dir) | ||
| elif 'MRTRIXPATH' in os.environ: | ||
| del os.environ['MRTRIXPATH'] | ||
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| def edition_widget(engine, environment, config_id='mrtrix'): | ||
| ''' Edition GUI for mrtrix config - see | ||
| :class:`~capsul.qt_gui.widgets.settings_editor.SettingsEditor` | ||
| ''' | ||
| from soma.qt_gui.controller_widget import ScrollControllerWidget | ||
| from soma.controller import Controller | ||
| import types | ||
| import traits.api as traits | ||
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| def validate_config(widget): | ||
| widget.update_controller() | ||
| controller = widget.controller_widget.controller | ||
| with widget.engine.settings as session: | ||
| conf = session.config(config_id, widget.environment) | ||
| values = {'config_id': config_id} | ||
| for k in ['directory']: | ||
| value = getattr(controller, k) | ||
| if value is traits.Undefined: | ||
| value = None | ||
| values[k] = value | ||
| if conf is None: | ||
| session.new_config(config_id, widget.environment, values) | ||
| else: | ||
| for k, value in values.items(): | ||
| if k == 'config_id': | ||
| continue | ||
| setattr(conf, k, values[k]) | ||
|
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| controller = Controller() | ||
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| controller.add_trait('directory', | ||
| traits.Directory(traits.Undefined, | ||
| desc='Directory where mrtrix is installed')) | ||
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| conf = engine.settings.select_configurations( | ||
| environment, {'mrtrix': 'any'}) | ||
| if conf: | ||
| fconf = conf.get('capsul.engine.module.mrtrix', {}) | ||
| controller.directory = fconf.get('directory', traits.Undefined) | ||
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| widget = ScrollControllerWidget(controller, live=True) | ||
| widget.engine = engine | ||
| widget.environment = environment | ||
| widget.accept = types.MethodType(validate_config, widget) | ||
|
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||
| return widget |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| # -*- coding: utf-8 -*- | ||
| ''' | ||
| Specific subprocess-like functions to call mrtrix taking into account | ||
| configuration stored in ExecutionContext. To functions and class in | ||
| this module it is mandatory to activate an ExecutionContext (using a | ||
| with statement). For instance:: | ||
| from capsul.engine import capsul_engine | ||
| from capsul.in_context.mrtrix import mrtrix_check_call | ||
| ce = capsul_engine() | ||
| with ce: | ||
| mrtrix_check_call(['mrinfo', '/somewhere/myimage.nii']) | ||
| For calling mrtrix command with this module, the first argument of | ||
| command line must be the mrtrix executable without any path. | ||
| The appropriate path is added from the configuration | ||
| of the ExecutionContext. | ||
| ''' | ||
|
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| from __future__ import absolute_import | ||
|
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| import os | ||
| import os.path as osp | ||
| import soma.subprocess | ||
| from soma.utils.env import parse_env_lines | ||
| import six | ||
|
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| mrtrix_runtime_env = None | ||
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| def mrtrix_command_with_environment(command, use_runtime_env=True): | ||
| ''' | ||
| Given an mrtrix command where first element is a command name without | ||
| any path. Returns the appropriate command to call taking into account | ||
| the mrtrix configuration stored in the | ||
| activated ExecutionContext. | ||
| ''' | ||
|
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| if use_runtime_env and mrtrix_runtime_env: | ||
| c0 = list(osp.split(command[0])) | ||
| c0 = osp.join(*c0) | ||
| cmd = [c0] + command[1:] | ||
| return cmd | ||
|
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| mrtrix_dir = os.environ.get('MRTRIXPATH') | ||
| if mrtrix_dir: | ||
| shell = os.environ.get('SHELL', '/bin/sh') | ||
| if shell.endswith('csh'): | ||
| cmd = [shell, '-c', | ||
| 'setenv MRTRIXPATH "{0}"; setenv PATH "{0}:$PATH";exec {1} '.format( | ||
| mrtrix_dir, command[0]) + \ | ||
| ' '.join("'%s'" % i.replace("'", "\\'") for i in command[1:])] | ||
| else: | ||
| cmd = [shell, '-c', | ||
| 'export MRTRIXPATH="{0}"; export PATH="{0}:$PATH"; exec {1} '.format( | ||
| mrtrix_dir, command[0]) + \ | ||
| ' '.join("'%s'" % i.replace("'", "\\'") for i in command[1:])] | ||
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| return cmd | ||
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| def mrtrix_env(): | ||
| ''' | ||
| get mrtrix env variables | ||
| process | ||
| ''' | ||
| global mrtrix_runtime_env | ||
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| if mrtrix_runtime_env is not None: | ||
| return mrtrix_runtime_env | ||
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| mrtrix_dir = os.environ.get('MRTRIXPATH') | ||
| kwargs = {} | ||
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| cmd = mrtrix_command_with_environment(['env'], use_runtime_env=False) | ||
| new_env = soma.subprocess.check_output(cmd, **kwargs).decode( | ||
| 'utf-8').strip() | ||
| new_env = parse_env_lines(new_env) | ||
| env = {} | ||
| for l in new_env: | ||
| name, val = l.strip().split('=', 1) | ||
| name = six.ensure_str(name) | ||
| val = six.ensure_str(val) | ||
| if name not in ('_', 'SHLVL') and (name not in os.environ | ||
| or os.environ[name] != val): | ||
| env[name] = val | ||
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| # add PATH | ||
| if mrtrix_dir: | ||
| env['PATH'] = os.pathsep.join([mrtrix_dir, os.environ.get('PATH', '')]) | ||
| # cache dict | ||
| mrtrix_runtime_env = env | ||
| return env | ||
|
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| class MrtrixPopen(soma.subprocess.Popen): | ||
| ''' | ||
| Equivalent to Python subprocess.Popen for mrtrix commands | ||
| ''' | ||
| def __init__(self, command, **kwargs): | ||
| cmd = mrtrix_command_with_environment(command) | ||
| super(MrtrixPopen, self).__init__(cmd, **kwargs) | ||
|
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| def mrtrix_call(command, **kwargs): | ||
| ''' | ||
| Equivalent to Python subprocess.call for mrtrix commands | ||
| ''' | ||
| cmd = mrtrix_command_with_environment(command) | ||
| return soma.subprocess.call(cmd, **kwargs) | ||
|
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| def mrtrix_check_call(command, **kwargs): | ||
| ''' | ||
| Equivalent to Python subprocess.check_call for mrtrix commands | ||
| ''' | ||
| cmd = mrtrix_command_with_environment(command) | ||
| return soma.subprocess.check_call(cmd, **kwargs) | ||
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| def mrtrix_check_output(command, **kwargs): | ||
| ''' | ||
| Equivalent to Python subprocess.check_output for mrtrix commands | ||
| ''' | ||
| cmd = mrtrix_command_with_environment(command) | ||
| return soma.subprocess.check_output(cmd, **kwargs) |
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