phy 2.1.0rc1__py3-none-any.whl

phy/__init__.py

@@ -0,0 +1,53 @@
+# flake8: noqa
+
+"""phy: interactive visualization and manual spike sorting of large-scale ephys data."""
+
+
+# ------------------------------------------------------------------------------
+# Imports
+# ------------------------------------------------------------------------------
+
+import atexit
+import logging
+import os.path as op
+import sys
+
+from io import StringIO
+
+from phylib.utils import Bunch
+from phylib.utils._misc import _git_version
+from phylib.utils.event import connect, unconnect, emit
+from .utils.config import load_master_config
+from .utils.plugin import IPlugin, get_plugin, discover_plugins
+
+
+# ------------------------------------------------------------------------------
+# Global variables and functions
+# ------------------------------------------------------------------------------
+
+__author__ = 'Cyrille Rossant'
+__email__ = 'cyrille.rossant at gmail.com'
+__version__ = '2.1.0rc1'
+__version_git__ = __version__ + _git_version()
+
+
+# Set a null handler on the root logger
+logger = logging.getLogger()
+logger.setLevel(logging.DEBUG)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+
+
+@atexit.register
+def on_exit():  # pragma: no cover
+    # Close the logging handlers.
+    for handler in logger.handlers:
+        handler.close()
+        logger.removeHandler(handler)
+
+
+def test():  # pragma: no cover
+    """Run the full testing suite of phy."""
+    import pytest
+
+    pytest.main()

phy/apps/__init__.py

@@ -0,0 +1,260 @@
+"""CLI tool."""
+
+
+# ------------------------------------------------------------------------------
+# Imports
+# ------------------------------------------------------------------------------
+
+import logging
+import sys
+from contextlib import contextmanager
+from pathlib import Path
+from traceback import format_exception
+
+import click
+from phylib import _Formatter, _logger_date_fmt, _logger_fmt, add_default_handler  # noqa  # noqa
+
+from phy import __version_git__
+from phy.gui.qt import QtDialogLogger
+from phy.utils.profiling import _enable_pdb, _enable_profiler
+
+from .base import BaseController, FeatureMixin, TemplateMixin, TraceMixin, WaveformMixin  # noqa
+
+logger = logging.getLogger(__name__)
+
+
+# ------------------------------------------------------------------------------
+# CLI utils
+# ------------------------------------------------------------------------------
+
+DEBUG = False
+if '--debug' in sys.argv:  # pragma: no cover
+    DEBUG = True
+    sys.argv.remove('--debug')
+
+
+if '--pdb' in sys.argv:  # pragma: no cover
+    sys.argv.remove('--pdb')
+    _enable_pdb()
+
+
+# Add `profile` in the builtins.
+if '--lprof' in sys.argv or '--prof' in sys.argv:  # pragma: no cover
+    _enable_profiler('--lprof' in sys.argv)
+    if '--prof' in sys.argv:
+        sys.argv.remove('--prof')
+    if '--lprof' in sys.argv:
+        sys.argv.remove('--lprof')
+
+
+# ------------------------------------------------------------------------------
+# Set up logging with the CLI tool
+# ------------------------------------------------------------------------------
+
+
+def exceptionHandler(exception_type, exception, traceback):  # pragma: no cover
+    tb = ''.join(format_exception(exception_type, exception, traceback))
+    logger.error('An error has occurred (%s): %s\n%s', exception_type.__name__, exception, tb)
+
+
+@contextmanager
+def capture_exceptions():  # pragma: no cover
+    """Log exceptions instead of crashing the GUI, and display an error dialog on errors."""
+    logger.debug('Start capturing exceptions.')
+
+    # Add a custom exception hook.
+    excepthook = sys.excepthook
+    sys.excepthook = exceptionHandler
+
+    # Add a dialog exception handler.
+    handler = QtDialogLogger()
+    handler.setLevel(logging.ERROR)
+    logging.getLogger('phy').addHandler(handler)
+
+    yield
+
+    # Reset the original exception hook.
+    sys.excepthook = excepthook
+
+    # Remove the dialog exception handler.
+    logging.getLogger('phy').removeHandler(handler)
+
+    logger.debug('Stop capturing exceptions.')
+
+
+# ------------------------------------------------------------------------------
+# Root CLI tool
+# ------------------------------------------------------------------------------
+
+
+@click.group()
+@click.version_option(version=__version_git__)
+@click.help_option('-h', '--help')
+@click.pass_context
+def phycli(ctx):
+    """Interactive visualization and manual spike sorting of large-scale ephys data."""
+    add_default_handler(level='DEBUG' if DEBUG else 'INFO', logger=logging.getLogger('phy'))
+    add_default_handler(level='DEBUG' if DEBUG else 'INFO', logger=logging.getLogger('phylib'))
+    add_default_handler(level='DEBUG' if DEBUG else 'INFO', logger=logging.getLogger('mtscomp'))
+
+
+# ------------------------------------------------------------------------------
+# GUI command wrapper
+# ------------------------------------------------------------------------------
+
+
+def _gui_command(f):
+    """Command options for GUI commands."""
+    f = click.option(
+        '--clear-cache/--no-clear-cache',
+        default=False,
+        help='Clear the .phy cache in the data directory.',
+    )(f)
+    f = click.option(
+        '--clear-state/--no-clear-state',
+        default=False,
+        help='Clear the GUI state in `~/.phy/` and in `.phy`.',
+    )(f)
+    return f
+
+
+# ------------------------------------------------------------------------------
+# Raw data GUI
+# ------------------------------------------------------------------------------
+
+
+@phycli.command('trace-gui')  # pragma: no cover
+@click.argument('dat-path', type=click.Path(exists=True))
+@click.option('-s', '--sample-rate', type=float)
+@click.option('-d', '--dtype', type=str)
+@click.option('-n', '--n-channels', type=int)
+@click.option('-h', '--offset', type=int)
+@click.option('-f', '--fortran', type=bool, is_flag=True)
+@_gui_command
+@click.pass_context
+def cli_trace_gui(ctx, dat_path, **kwargs):
+    """Launch the trace GUI on a raw data file."""
+    from .trace.gui import trace_gui
+
+    with capture_exceptions():
+        kwargs['n_channels_dat'] = kwargs.pop('n_channels')
+        kwargs['order'] = 'F' if kwargs.pop('fortran', None) else None
+        trace_gui(dat_path, **kwargs)
+
+
+# ------------------------------------------------------------------------------
+# Template GUI
+# ------------------------------------------------------------------------------
+
+
+@phycli.command('template-gui')  # pragma: no cover
+@click.argument('params-path', type=click.Path(exists=True))
+@_gui_command
+@click.pass_context
+def cli_template_gui(ctx, params_path, **kwargs):
+    """Launch the template GUI on a params.py file."""
+    from .template.gui import template_gui
+
+    prof = __builtins__.get('profile', None)
+    with capture_exceptions():
+        if prof:
+            from phy.utils.profiling import _profile
+
+            return _profile(prof, 'template_gui(params_path)', globals(), locals())
+        template_gui(params_path, **kwargs)
+
+
+@phycli.command('template-describe')
+@click.argument('params-path', type=click.Path(exists=True))
+@click.pass_context
+def cli_template_describe(ctx, params_path):
+    """Describe a template file."""
+    from .template.gui import template_describe
+
+    template_describe(params_path)
+
+
+# ------------------------------------------------------------------------------
+# Kwik GUI
+# ------------------------------------------------------------------------------
+
+
+# Create the `phy cluster-manual file.kwik` command.
+@phycli.command('kwik-gui')  # pragma: no cover
+@click.argument('path', type=click.Path(exists=True))
+@click.option('--channel-group', type=int)
+@click.option('--clustering', type=str)
+@_gui_command
+@click.pass_context
+def cli_kwik_gui(ctx, path, channel_group=None, clustering=None, **kwargs):
+    """Launch the Kwik GUI on a Kwik file."""
+    from .kwik.gui import kwik_gui
+
+    with capture_exceptions():
+        assert path
+        kwik_gui(path, channel_group=channel_group, clustering=clustering, **kwargs)
+
+
+@phycli.command('kwik-describe')
+@click.argument('path', type=click.Path(exists=True))
+@click.option('--channel-group', type=int, help='channel group')
+@click.option('--clustering', type=str, help='clustering')
+@click.pass_context
+def cli_kwik_describe(ctx, path, channel_group=0, clustering='main'):
+    """Describe a Kwik file."""
+    from .kwik.gui import kwik_describe
+
+    assert path
+    kwik_describe(path, channel_group=channel_group, clustering=clustering)
+
+
+# ------------------------------------------------------------------------------
+# Conversion
+# ------------------------------------------------------------------------------
+
+
+@phycli.command('alf-convert')
+@click.argument('subdirs', nargs=-1, type=click.Path(exists=True, file_okay=False, dir_okay=True))
+@click.argument('out_dir', type=click.Path())
+@click.pass_context
+def cli_alf_convert(ctx, subdirs, out_dir):
+    """Convert an ephys dataset into ALF. If several directories are specified, it is assumed
+    that each directory contains the data for one probe of the same recording."""
+    from phylib.io.alf import EphysAlfCreator
+    from phylib.io.merge import Merger
+    from phylib.io.model import load_model
+
+    out_dir = Path(out_dir)
+
+    if len(subdirs) >= 2:
+        # Merge in the `merged` subdirectory inside the output directory.
+        m = Merger(subdirs, out_dir / '_tmp_merged')
+        model = m.merge()
+    else:
+        model = load_model(Path(subdirs[0]) / 'params.py')
+
+    c = EphysAlfCreator(model)
+    c.convert(out_dir)
+
+
+# ------------------------------------------------------------------------------
+# Waveform extraction
+# ------------------------------------------------------------------------------
+
+
+@phycli.command('extract-waveforms')
+@click.argument('params-path', type=click.Path(exists=True))
+@click.argument('n_spikes_per_cluster', type=int, default=500)
+@click.option('--nc', type=int, default=16)
+@click.pass_context
+def template_extract_waveforms(
+    ctx, params_path, n_spikes_per_cluster, nc=None
+):  # pragma: no cover
+    """Extract spike waveforms."""
+    from phylib.io.model import load_model
+
+    model = load_model(params_path)
+    model.save_spikes_subset_waveforms(
+        max_n_spikes_per_template=n_spikes_per_cluster, max_n_channels=nc
+    )
+    model.close()