Merge 91810f5 into ce9afe0

docs/metadata.rst

@@ -57,8 +57,7 @@ used.
 
 Paths to individual files within the dataset are provided using keys listed
 below. These paths should be given relative to ``data_dir``. If ``data_dir`` is
-flat (no subdirectories), these should be simply the file names. Only
-``data_file`` is required.
+flat (no subdirectories), these should be simply the file names.
 
 ======================  ========================================================
 Key                     Description

neurotic/datasets/data.py

@@ -31,7 +31,8 @@ def load_dataset(metadata, lazy=False, signal_group_mode='split-all', filter_eve
 
     The ``data_file`` in ``metadata`` is read into a Neo :class:`Block
     <neo.core.Block>` using an automatically detected :mod:`neo.io` class
-    if ``lazy=False`` or a :mod:`neo.rawio` class if ``lazy=True``.
+    if ``lazy=False`` or a :mod:`neo.rawio` class if ``lazy=True``. If
+    ``data_file`` is unspecified, an empty Neo Block is created instead.
 
     Epochs and events loaded from ``annotations_file`` and
     ``epoch_encoder_file`` and spike trains loaded from ``tridesclous_file``
@@ -44,8 +45,14 @@ def load_dataset(metadata, lazy=False, signal_group_mode='split-all', filter_eve
     signal.
     """
 
-    # read in the electrophysiology data
-    blk = _read_data_file(metadata, lazy, signal_group_mode)
+    if metadata.get('data_file', None) is not None:
+        # read in the electrophysiology data
+        blk = _read_data_file(metadata, lazy, signal_group_mode)
+    else:
+        # create an empty Block
+        blk = neo.Block()
+        seg = neo.Segment()
+        blk.segments.append(seg)
 
     # update the real-world start time of the data if provided
     if metadata.get('rec_datetime', None) is not None:
@@ -80,11 +87,15 @@ def load_dataset(metadata, lazy=False, signal_group_mode='split-all', filter_eve
         blk.segments[0].spiketrains += _run_amplitude_discriminators(metadata, blk)
 
     # read in spikes identified by spike sorting using tridesclous
-    t_start = blk.segments[0].analogsignals[0].t_start
-    t_stop = blk.segments[0].analogsignals[0].t_stop
-    sampling_period = blk.segments[0].analogsignals[0].sampling_period
     spikes_dataframe = _read_spikes_file(metadata, blk)
-    blk.segments[0].spiketrains += _create_neo_spike_trains_from_dataframe(spikes_dataframe, metadata, t_start, t_stop, sampling_period)
+    if spikes_dataframe is not None:
+        if blk.segments[0].analogsignals:
+            t_start = blk.segments[0].analogsignals[0].t_start                 # assuming all AnalogSignals start at the same time
+            t_stop = blk.segments[0].analogsignals[0].t_stop                   # assuming all AnalogSignals start at the same time
+            sampling_period = blk.segments[0].analogsignals[0].sampling_period # assuming all AnalogSignals have the same sampling rate
+            blk.segments[0].spiketrains += _create_neo_spike_trains_from_dataframe(spikes_dataframe, metadata, t_start, t_stop, sampling_period)
+        else:
+            logger.warning('Ignoring tridesclous_file because the sampling rate and start time could not be inferred from analog signals')
 
     # calculate smoothed firing rates from spike trains if not using lazy
     # loading of signals
@@ -189,6 +200,10 @@ def _read_data_file(metadata, lazy=False, signal_group_mode='split-all'):
         # some IOs do not have signal_group_mode
         blk = io.read_block(lazy=lazy)
 
+    if lazy and isinstance(io, neo.rawio.baserawio.BaseRawIO):
+        # store the rawio for use with AnalogSignalFromNeoRawIOSource
+        blk.rawio = io
+
     # load all objects except analog signals
     if lazy:
 

neurotic/datasets/metadata.py

@@ -338,7 +338,7 @@ def _defaults_for_key(key):
         'epoch_encoder_file': None,
 
         # list of labels for epoch encoder
-        'epoch_encoder_possible_labels': ['Type 1', 'Type 2', 'Type 3'],
+        'epoch_encoder_possible_labels': [],
 
         # list of dicts giving name, channel, units, amplitude window, epoch window, color for each unit
         # - e.g. [{'name': 'Unit X', 'channel': 'Channel A', 'units': 'uV', 'amplitude': [75, 150], 'epoch': 'Type 1', 'color': 'ff0000'}, ...]

neurotic/gui/config.py

@@ -15,7 +15,6 @@
 import neo
 import ephyviewer
 
-from ..datasets.data import _get_io
 from ..datasets.metadata import _abs_path
 from ..gui.epochencoder import NeuroticWritableEpochSource
 
@@ -101,6 +100,10 @@ def __init__(self, metadata, blk, lazy = False):
         }
 
         # hide and disable viewers for which inputs are missing
+        if not self.blk.segments[0].analogsignals:
+            self.viewer_settings['traces']['show'] = False
+            self.viewer_settings['traces']['disabled'] = True
+            self.viewer_settings['traces']['reason'] = 'Cannot enable because there are no signals'
         if not [sig.annotations['rauc_sig'] for sig in blk.segments[0].analogsignals if 'rauc_sig' in sig.annotations]:
             self.viewer_settings['traces_rauc']['show'] = False
             self.viewer_settings['traces_rauc']['disabled'] = True
@@ -304,13 +307,20 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
 
         if self.is_shown('traces'):
 
-            # get a Neo IO object appropriate for the data file type
-            io = _get_io(self.metadata)
+            lazy_load_signals = False
+            if self.lazy:
+                # check whether blk contains a rawio, which would have been put
+                # there by _read_data_file if lazy=True and if Neo has a RawIO
+                # that supports the file format
+                if hasattr(self.blk, 'rawio') and isinstance(self.blk.rawio, neo.rawio.baserawio.BaseRawIO):
+                    io = self.blk.rawio
+                    if io.support_lazy:
+                        lazy_load_signals = True
 
-            if self.lazy and io.support_lazy:
+            if lazy_load_signals:
 
                 # Intan-specific tricks
-                if type(io) is neo.io.IntanIO:
+                if isinstance(io, neo.io.IntanIO):
                     # dirty trick for getting ungrouped channels into a single source
                     io.header['signal_channels']['group_id'] = 0
 
@@ -326,7 +336,7 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                     ylabel = p['ylabel']
 
                     # Intan-specific tricks
-                    if type(io) is neo.io.IntanIO:
+                    if isinstance(io, neo.io.IntanIO):
                         # append custom channel names stored in data file to ylabels
                         if custom_channel_names[p['channel']] != ylabel:
                             ylabel += ' ({})'.format(custom_channel_names[p['channel']])
@@ -625,7 +635,7 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
 
         if self.is_shown('epoch_encoder') and self.metadata.get('epoch_encoder_file', None) is not None:
 
-            possible_labels = self.metadata['epoch_encoder_possible_labels']
+            possible_labels = self.metadata.get('epoch_encoder_possible_labels', [])
 
             # append labels found in the epoch encoder file but not in the
             # epoch_encoder_possible_labels list, preserving the original
@@ -635,21 +645,29 @@ def create_ephyviewer_window(self, theme='light', support_increased_line_width=F
                 if label not in possible_labels:
                     possible_labels.append(label)
 
-            writable_epoch_source = NeuroticWritableEpochSource(
-                filename = _abs_path(self.metadata, 'epoch_encoder_file'),
-                possible_labels = possible_labels,
-            )
+            if not possible_labels:
 
-            epoch_encoder = ephyviewer.EpochEncoder(source = writable_epoch_source, name = 'epoch encoder')
-            epoch_encoder.params['exclusive_mode'] = False
-            win.add_view(epoch_encoder)
+                # an empty epoch encoder file and an empty list of possible
+                # labels were provided
+                logger.warning('Ignoring epoch_encoder_file because epoch_encoder_possible_labels was unspecified')
 
-            # set the theme
-            if theme != 'original':
-                epoch_encoder.params['background_color'] = self.themes[theme]['background_color']
-                epoch_encoder.params['vline_color'] = self.themes[theme]['vline_color']
-                epoch_encoder.params['label_fill_color'] = self.themes[theme]['label_fill_color']
-                # TODO add support for combo_cmap
+            else:
+
+                writable_epoch_source = NeuroticWritableEpochSource(
+                    filename = _abs_path(self.metadata, 'epoch_encoder_file'),
+                    possible_labels = possible_labels,
+                )
+
+                epoch_encoder = ephyviewer.EpochEncoder(source = writable_epoch_source, name = 'epoch encoder')
+                epoch_encoder.params['exclusive_mode'] = False
+                win.add_view(epoch_encoder)
+
+                # set the theme
+                if theme != 'original':
+                    epoch_encoder.params['background_color'] = self.themes[theme]['background_color']
+                    epoch_encoder.params['vline_color'] = self.themes[theme]['vline_color']
+                    epoch_encoder.params['label_fill_color'] = self.themes[theme]['label_fill_color']
+                    # TODO add support for combo_cmap
 
         ########################################################################
         # VIDEO