[pyproject] adding scipy to docs

doc/calibration.qmd

@@ -1,36 +1,45 @@
 ---
 title: Calibration
+format:
+  html:
+    toc: true
+    toc-title: Contents
+    code-block-bg: true
+    code-block-border-left: "#31BAE9"
+    code-line-numbers: true
+    highlight-style: atom-one
+    link-external-icon: true
+    link-external-newwindow: true
+    eqn-number: true
 ---
 
 ### Calibration of the Amplitude
+Lets look at the calibration and the first trial of the recording.
+
 ```{python}
+
+import pathlib
+
 import rlxnix as rlx
 import plotly.graph_objects as go
 import numpy as np
+import scipy.signal as signal
 from plotly.subplots import make_subplots
 
 
-dataset = rlx.Dataset("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2-recording.nix")
+dataset_path = pathlib.Path("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2-recording.nix")
-relacs = rlx.Dataset("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2_relacs/2025-10-08-aa-invivo-2.nix")
+relacs_path  = pathlib.Path("../oephys2nix/test/Test1/2025-10-08-aa-invivo-2_relacs/2025-10-08-aa-invivo-2.nix")
-repro_d = dataset.repro_runs("CalibEfield_1")[0]
-repro_r = relacs.repro_runs("CalibEfield_1")[0]
 
-fig = make_subplots(
+dataset = rlx.Dataset(str(dataset_path))
-rows=4,
+relacs = rlx.Dataset(str(relacs_path))
-cols=1,
-shared_xaxes=True,
-subplot_titles=(
-	"Stimulus Comparison",
-	"Local EOD Comparison",
-	"Global EOD Comparison",
-	"Sinus Comparison",
-),)
 
+#INFO: Select the first stimulus of the calibration repro
+repro_d = dataset.repro_runs("CalibEfield_1")[0].stimuli[2]
+repro_r = relacs.repro_runs("CalibEfield_1")[0].stimuli[2]
 
 sinus, t = repro_d.trace_data("sinus")
 sinus_r, t_r = repro_r.trace_data("V-1")
 
-
 stimulus_oe, t = repro_d.trace_data("stimulus")
 stimulus_re, t_r = repro_r.trace_data("GlobalEFieldStimulus")
 
@@ -41,11 +50,27 @@ global_eod_oe, t = repro_d.trace_data("global-eod")
 global_eod_re, t_r = repro_r.trace_data("EOD")
 
 ttl, t = repro_d.trace_data("ttl-line")
+```
+### Plotting the First trial
+If you zoom in you can see a little delay between the different recording systems. It seems that open-ephys is before the relacs recording.
+
+```{python}
+#| echo: False
 # 2. Add traces to the FIRST subplot (row=1, col=1)
 # Note: Plotly rows and columns are 1-indexed
+fig = make_subplots( rows=5, cols=1, shared_xaxes=True, subplot_titles=("TTL-Line",
+  "Stimulus Comparison", "Local EOD Comparison", "Global EOD Comparison",
+  "Sinus Comparison"))
+
+fig.add_trace(
+    go.Scatter(x=t, y=ttl, name="ttl-line", line_color="magenta"),
+    row=1,
+    col=1,
+)
+
 fig.add_trace(
     go.Scatter(x=t_r, y=stimulus_re, name="stimulus (relacs)", line_color="blue"),
-    row=1,
+    row=2,
     col=1,
 )
 fig.add_trace(
@@ -55,12 +80,7 @@ fig.add_trace(
         name="stimulus (open-ephys)",
         line_color="red",
     ),
-    row=1,
+    row=2,
-    col=1,
-)
-fig.add_trace(
-    go.Scatter(x=t, y=ttl, name="ttl-line", line_color="black"),
-    row=1,
     col=1,
 )
 
@@ -68,12 +88,12 @@ fig.add_trace(
 # 3. Add traces to the SECOND subplot (row=2, col=1)
 fig.add_trace(
     go.Scatter(x=t_r, y=local_eod_re, name="local EOD (relacs)", line_color="blue"),
-    row=2,
+    row=3,
     col=1,
 )
 fig.add_trace(
     go.Scatter(x=t, y=local_eod_oe, name="local EOD (open-ephys)", line_color="red"),
-    row=2,
+    row=3,
     col=1,
 )
 
@@ -81,42 +101,112 @@ fig.add_trace(
 # 4. Add traces to the THIRD subplot (row=3, col=1)
 fig.add_trace(
     go.Scatter(x=t_r, y=global_eod_re, name="global EOD (relacs)", line_color="blue"),
-    row=3,
+    row=4,
     col=1,
 )
 fig.add_trace(
     go.Scatter(
         x=t, y=global_eod_oe, name="global EOD (open-ephys)", line_color="red"
     ),
-    row=3,
+    row=4,
     col=1,
 )
 
-
 # 5. Add traces to the FOURTH subplot (row=4, col=1)
 fig.add_trace(
     go.Scatter(x=t_r, y=sinus_r, name="sinus (relacs)", line_color="blue"),
-    row=4,
+    row=5,
     col=1,
 )
 fig.add_trace(
     go.Scatter(x=t, y=sinus, name="sinus (open-ephys)", line_color="red"),
-    row=4,
+    row=5,
     col=1,
 )
 
-
 # 6. Update the layout for a cleaner look
 fig.update_layout(
-    title_text="Relacs vs. Open Ephys Data Alignment",
+    template="plotly_dark",
     height=800, # Set the figure height in pixels
     # Control the legend
-    legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
+    #legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
+    legend=dict(
+    bgcolor="rgba(0,0,0,0)",   # transparent dark (or use "#1f2630" to match bg)
+    bordercolor="#444",
+    borderwidth=0,
+    font=dict(color="#e5ecf6") # matches plotly_dark foreground
+  )
 )
 # Add a label to the shared x-axis (targeting the last subplot)
 fig.update_xaxes(title_text="Time (s)", row=4, col=1)
 
-
 # 7. Show the figure
 fig.show()
 ```
+### Correlation between the Signals
+
+```{python}
+print(f"Duration of the dataset {repro_d.duration}")
+print(f"Duration of the relacs {repro_r.duration}")
+# Resample the open-ephys data
+sinus_resampled = signal.resample(sinus, len(sinus_r))
+
+```
+
+```{python}
+#| echo: False
+fig = go.Figure()
+fig.add_trace( go.Scatter(x=t_r, y=sinus_r, name="sinus (relacs)", line_color="blue", mode="lines+markers"))
+fig.add_trace( go.Scatter(x=t_r, y=sinus_resampled, name="sinus-resampled (open-ephys)", line_color="red", mode="lines+markers"))
+fig.update_layout(
+    template="plotly_dark",
+    height=500, # Set the figure height in pixels
+    # Control the legend
+    #legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
+    legend=dict(
+    bgcolor="rgba(0,0,0,0)",   # transparent dark (or use "#1f2630" to match bg)
+    bordercolor="#444",
+    borderwidth=0,
+    font=dict(color="#e5ecf6") # matches plotly_dark foreground
+  )
+)
+fig.update_xaxes(range=[0, 0.01])
+```
+We need to scale the two signals
+
+```{python}
+oephys_lanes = [sinus, local_eod_oe, global_eod_oe, stimulus_oe]
+relacs_lanes = [sinus_r, local_eod_re, global_eod_re, stimulus_re]
+names_lanes = ["sinus", "local-eod", "global-eod", "stimulus"]
+lags_lanes = []
+for oephys_lane, relacs_lane, names_lane in zip(oephys_lanes, relacs_lanes, names_lanes, strict=True):
+  print(oephys_lane.shape)
+  print(relacs_lane.shape)
+  oephys_lane_resampled = signal.resample(oephys_lane, len(relacs_lane))
+  correlation = signal.correlate(oephys_lane_resampled, relacs_lane, mode="full")
+  lags = signal.correlation_lags(oephys_lane_resampled.size, relacs_lane.size, mode="full")
+  lag = lags[np.argmax(correlation)]
+  lags_lanes.append(lag)
+  print(f"{names_lane} has a lag of {lag}")
+```
+
+```{python}
+#| echo: False
+fig = go.Figure()
+fig.add_trace( go.Scatter(x=t_r, y=sinus_r, name="sinus (relacs)", line_color="blue", mode="lines+markers"))
+fig.add_trace( go.Scatter(x=t_r, y=np.roll(sinus_resampled, -lags_lanes[0]), name="sinus-resampled (open-ephys)", line_color="red", mode="lines+markers"))
+fig.update_layout(
+    title="Sinus",
+    template="plotly_dark",
+    height=500, # Set the figure height in pixels
+    # Control the legend
+    #legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
+    legend=dict(
+    bgcolor="rgba(0,0,0,0)",   # transparent dark (or use "#1f2630" to match bg)
+    bordercolor="#444",
+    borderwidth=0,
+    font=dict(color="#e5ecf6") # matches plotly_dark foreground
+  )
+)
+fig.update_xaxes(range=[0, 0.01])
+```

oephys2nix/main.py

@@ -3,6 +3,7 @@ from pathlib import Path
 from typing import Annotated
 
 import nixio
+import rlxnix as rlx
 import typer
 from IPython import embed
 from rich.console import Console
@@ -37,11 +38,11 @@ def main(
     setup_logging(logging.getLogger("oephys2nix"), verbosity=verbose)
     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()
 
+    relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
     if not relacs_data_paths:
         log.error("Did not find any relacs data")
         raise typer.Exit()
@@ -97,5 +98,27 @@ def main(
         #     stim.plot_stimulus()
 
 
+@app.command()
+def timeline(
+    data_path: Path = typer.Argument(
+        ...,
+        help="The source directory containing the Open Ephys data.",
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
+    ),
+):
+    relacs_data_paths = list(Path(data_path).rglob("*relacs/*.nix"))
+    if not relacs_data_paths:
+        log.error("Did not find any relacs data")
+        raise typer.Exit()
+
+    dataset = rlx.Dataset(str(relacs_data_paths[0]))
+    dataset.plot_timeline()
+    dataset.close()
+
+
 if __name__ == "__main__":
     app()

pyproject.toml

@@ -22,6 +22,7 @@ docs = [
     "jupyterlab>=4.4.9",
     "plotly>=6.3.1",
     "quartodoc>=0.11.1",
+    "scipy>=1.16.2",
 ]
 
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