[features] adding features

oephys2nix/stimulus_recreation.py

@@ -266,6 +266,8 @@ class StimulusToNix:
             nix_group = self.nix_file.blocks[0].groups[repro.name]
         nix_group.multi_tags.append(nix_mtag)
 
+        self._append_features(repro, nix_mtag)
+
     def _append_tag(self, repro: rlx.Dataset, position: np.ndarray, extent: np.ndarray) -> None:
         """Append tag of the current repro.
 
@@ -321,6 +323,45 @@ class StimulusToNix:
             nix_group = self.nix_file.blocks[0].groups[repro.name]
         nix_group.tags.append(nix_tag)
 
+    def _append_features(self, repro, mtag):
+        s = repro.stimuli[0]
+        if not s.features:
+            log.debug(f"Repro {repro.name} does not have a feature in multitags")
+            return
+        das_names = [f[1] for f in s.features]
+        for das in das_names:
+            arr = self.relacs_block.data_arrays[das]
+            if arr.data.dtype == object:
+                data = arr.data[:].astype(np.dtypes.StringDType)
+            else:
+                data = arr.data[:]
+
+            try:
+                f = self.block.create_data_array(
+                    arr.name,
+                    arr.type,
+                    data=data,
+                    unit=arr.unit,
+                    label=arr.label,
+                )
+                for d in arr.dimensions:
+                    if d.dimension_type == nixio.DimensionType.Set:
+                        f.append_set_dimension(labels=d.labels)
+                    elif d.dimension_type == nixio.DimensionType.Range:
+                        f.append_range_dimension(
+                            np.sort(d.ticks),
+                            labels=d.labels,
+                        )
+                    else:
+                        f.append_sampled_dimension(
+                            d.sampling_interval,
+                            labels=d.labels,
+                        )
+            except DuplicateName:
+                f = self.block.data_arrays[arr.name]
+
+            mtag.create_feature(f, nixio.LinkType.Indexed)
+
     def create_repros_automatically(self) -> None:
         """Create the repros form relacs with the TTL pulses."""
         ttl_oeph = self.block.data_arrays["ttl-line"][:]
@@ -364,7 +405,7 @@ class StimulusToNix:
                         time_ttl, peaks_ttl, current_position
                     )
 
-                if "FICurve" in repro.name:
+                if "FICurve_" in repro.name:
                     position_mtags += 0.2
 
                 self._append_mtag(repro, position_mtags, extents_mtag)

oephys2nix/tonix.py

@@ -1,5 +1,6 @@
 import logging
 import pathlib
+import sys
 
 import nixio
 import numpy as np
@@ -78,7 +79,7 @@ class RawToNix:
 
         efish_group = self.block.create_group("efish", "open-ephys.sampled")
 
-        efish_neo_data = self.neo_data[0].segments[0].analogsignals[2].load()
+        efish_neo_data = self._load_neo_object("Data_ADC")
 
         for i in np.arange(len(efishs)):
             log.debug(f"Appending efish traces {efishs[i]}")
@@ -95,6 +96,14 @@ class RawToNix:
             )
             efish_group.data_arrays.append(data_array)
 
+    def _load_neo_object(self, name: str):
+        for sig in self.neo_data[0].segments[0].analogsignals:
+            if sig.name.endswith(name):
+                return sig.load()
+
+        log.error(f"No {name} found in open ephys data")
+        sys.exit(1)
+
     def append_relacs_lines(self) -> None:
         """Append relacs lines."""
         relacs = [
@@ -129,25 +138,31 @@ class RawToNix:
                 label=efish_relacs_data_array.label,
                 unit=efish_relacs_data_array.unit,
             )
-            if efish_relacs_data_array.dimensions[0].dimension_type == nixio.DimensionType.Sample:
-                data_array.append_sampled_dimension(
-                    efish_relacs_data_array.dimensions[0].sampling_interval,
-                    label="time",
-                    unit="s",
-                )
-            elif efish_relacs_data_array.dimensions[0].dimension_type == nixio.DimensionType.Range:
-                data_array.append_range_dimension(
-                    np.sort(efish_relacs_data_array.dimensions[0].ticks),
-                    label="time",
-                    unit="s",
-                )
+            for d in efish_relacs_data_array.dimensions:
+                if d.dimension_type == nixio.DimensionType.Sample:
+                    data_array.append_sampled_dimension(
+                        efish_relacs_data_array.dimensions[0].sampling_interval,
+                        label="time",
+                        unit="s",
+                    )
+                elif d.dimension_type == nixio.DimensionType.Range:
+                    data_array.append_range_dimension(
+                        np.sort(efish_relacs_data_array.dimensions[0].ticks),
+                        label="time",
+                        unit="s",
+                    )
+                else:
+                    data_array.append_set_dimension(
+                        label="time",
+                        unit="s",
+                    )
 
             efish_group.data_arrays.append(data_array)
 
     def append_raw_data(self) -> None:
         """Append Open-Ephys Raw data."""
         gr = self.block.create_group("neuronal-data", "open-epyhs.sampled")
-        raw_neo_data = self.neo_data[0].segments[0].analogsignals[0].load()
+        raw_neo_data = self._load_neo_object("Data")
 
         log.debug("Appending raw data")
         nix_data_array = self.block.create_data_array(