[tonix] testing data analog signal is at 3 now

oephys2nix/main.py

@@ -35,6 +35,13 @@ def main(
     log.info(f"Selected data_path is {data_path}")
     open_ephys_data_paths = list(Path(data_path).rglob("*open-ephys"))
     relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
+    if not open_ephys_data_paths:
+        log.error("Did not find any open-ephys data")
+        raise typer.Exit()
+
+    if not relacs_data_paths:
+        log.error("Did not find any relacs data")
+        raise typer.Exit()
 
     if len(open_ephys_data_paths) != len(relacs_data_paths):
         log.error(

oephys2nix/stimulus_recreation.py

@@ -25,6 +25,9 @@ console = Console()
 
 class StimulusToNix:
     def __init__(self, open_ephys_path: pathlib.Path, relacs_nix_path: str, nix_file: str):
+        self.relacs_nix_path = relacs_nix_path
+        self.nix_file_path = nix_file
+
         self.dataset = rlx.Dataset(relacs_nix_path)
 
         self.relacs_nix_file = nixio.File.open(relacs_nix_path, nixio.FileMode.ReadOnly)
@@ -34,7 +37,6 @@ class StimulusToNix:
         self.neo_data = OpenEphysBinaryIO(open_ephys_path).read(lazy=True)
         self.fs = self.neo_data[0].segments[0].analogsignals[0].sampling_rate.magnitude
 
-        self.nix_file_path = nix_file
         self.nix_file = nixio.File(nix_file, nixio.FileMode.ReadWrite)
         self.block = self.nix_file.blocks[0]
 
@@ -450,11 +452,8 @@ class StimulusToNix:
         for repro_r, repro_n in zip(self.dataset.repro_runs(), nix_data_set.repro_runs()):
             if repro_n.name.split("_")[0] not in important_repros:
                 continue
-            if "SAM" in repro_n.name:
-                embed()
-                exit()
-            else:
-                continue
+            embed()
+            exit()
 
             if "FileStimulus" in repro_n.name:
                 repro_n.stimulus_folder = "/home/alexander/stimuli/whitenoise/"
@@ -464,10 +463,38 @@ class StimulusToNix:
 
             stim = repro_n.stimuli[0]
             stim_r = repro_r.stimuli[0]
-            v, t = stim.trace_data("local-eod")
-            v_r, t_r = stim_r.trace_data("LocalEOD-1")
-            plt.plot(t_r, v_r, "o--", color="tab:blue", label="relacs")
-            plt.plot(t, v, "o--", color="tab:red", label="open-ephys")
+
+            # stim = repro_n
+            # stim_r = repro_r
+            sinus, t = stim.trace_data("sinus")
+            sinus_r, t_r = stim_r.trace_data("V-1")
+
+            stimulus_oe, t = stim.trace_data("stimulus")
+            stimulus_re, t_r = stim_r.trace_data("GlobalEFieldStimulus")
+
+            local_eod_oe, t = stim.trace_data("local-eod")
+            local_eod_re, t_r = stim_r.trace_data("LocalEOD-1")
+
+            global_eod_oe, t = stim.trace_data("global-eod")
+            global_eod_re, t_r = stim_r.trace_data("EOD")
+
+            ttl, t = stim.trace_data("ttl-line")
+
+            fig, ax = plt.subplots(4, sharex=True)
+            ax[0].plot(t_r, stimulus_re, color="tab:blue", label="relacs")
+            ax[0].plot(t, stimulus_oe - np.mean(stimulus_oe), color="tab:red", label="open-ephys")
+            ax[0].plot(t, ttl, color="black")
+
+            ax[1].plot(t_r, local_eod_re, color="tab:blue", label="relacs")
+            ax[1].plot(t, local_eod_oe, color="tab:red", label="open-ephys")
+
+            ax[2].plot(t_r, global_eod_re, color="tab:blue", label="relacs")
+            ax[2].plot(t, global_eod_oe, color="tab:red", label="open-ephys")
+
+            ax[3].plot(t_r, sinus_r, color="tab:blue", label="relacs")
+            ax[3].plot(t, sinus, color="tab:red", label="open-ephys")
+
+            plt.legend(loc="upper right")
             # plt.plot(stimulus_time, white_noise, "o--", color="tab:orange", label="stimulus")
             # plt.plot(new_t, new_v, "go--", label="resampled")
             for i, (s, r) in enumerate(zip(repro_n.stimuli, repro_r.stimuli)):
@@ -475,7 +502,6 @@ class StimulusToNix:
                 v_r, t_r = r.trace_data("LocalEOD-1")
                 plt.plot(t_r + (i * r.duration), v_r)
                 plt.plot(t + (i * s.duration), v)
-            plt.legend(loc="upper right")
             plt.show()
 
             am = extract_am(v, 30_000)
@@ -490,7 +516,9 @@ class StimulusToNix:
         ttl_oeph = self.block.data_arrays["ttl-line"][:]
 
         time_index = np.arange(len(ttl_oeph))
-        peaks_ttl = time_index[(np.roll(ttl_oeph, 1) < 2) & (ttl_oeph > 2)]
+        peaks_ttl = time_index[
+            (np.roll(ttl_oeph, 1) < self.threshold) & (ttl_oeph > self.threshold)
+        ]
 
         stimulus_oeph = self.block.data_arrays["stimulus"]
         stimulus = self.relacs_block.data_arrays["GlobalEFieldStimulus"]

oephys2nix/tonix.py

@@ -35,23 +35,19 @@ class RawToNix:
         self.block.metadata = sec
 
     def append_fish_lines(self):
-        efishs = [
-            "ttl-line",
-            "global-eod",
-            "stimulus",
-            "local-eod",
-        ]
+        efishs = ["ttl-line", "global-eod", "stimulus", "local-eod", "sinus"]
 
         efish_types = [
             "open-ephys.data.sampled",
             "open-ephys.data.sampled",
             "open-ephys.data.sampled",
             "open-ephys.data.sampled",
+            "open-ephys.data.sampled",
         ]
 
         efish_group = self.block.create_group("efish", "open-ephys.sampled")
 
-        efish_neo_data = self.neo_data[0].segments[0].analogsignals[1].load()
+        efish_neo_data = self.neo_data[0].segments[0].analogsignals[2].load()
 
         for i in np.arange(len(efishs)):
             log.debug(f"Appending efish traces {efishs[i]}")