From 764ee40b4359c140ad351f9d03cc16187d3981ba Mon Sep 17 00:00:00 2001
From: wendtalexander <wendtalexander@protonmail.com>
Date: Sun, 19 Oct 2025 10:04:25 +0200
Subject: [PATCH] [doc] adding calibration doc

---
 doc/calibration.qmd | 122 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)
 create mode 100644 doc/calibration.qmd

diff --git a/doc/calibration.qmd b/doc/calibration.qmd
new file mode 100644
index 0000000..81cbc36
--- /dev/null
+++ b/doc/calibration.qmd
@@ -0,0 +1,122 @@
+---
+title: Calibration
+---
+
+### Calibration of the Amplitude
+```{python}
+import rlxnix as rlx
+import plotly.graph_objects as go
+import numpy as np
+from plotly.subplots import make_subplots
+
+
+dataset = rlx.Dataset("../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")
+repro_d = dataset.repro_runs("CalibEfield_1")[0]
+repro_r = relacs.repro_runs("CalibEfield_1")[0]
+
+fig = make_subplots(
+rows=4,
+cols=1,
+shared_xaxes=True,
+subplot_titles=(
+	"Stimulus Comparison",
+	"Local EOD Comparison",
+	"Global EOD Comparison",
+	"Sinus Comparison",
+),)
+
+
+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")
+
+local_eod_oe, t = repro_d.trace_data("local-eod")
+local_eod_re, t_r = repro_r.trace_data("LocalEOD-1")
+
+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")
+# 2. Add traces to the FIRST subplot (row=1, col=1)
+# Note: Plotly rows and columns are 1-indexed
+fig.add_trace(
+    go.Scatter(x=t_r, y=stimulus_re, name="stimulus (relacs)", line_color="blue"),
+    row=1,
+    col=1,
+)
+fig.add_trace(
+    go.Scatter(
+        x=t,
+        y=stimulus_oe - np.mean(stimulus_oe), # The same data transformation
+        name="stimulus (open-ephys)",
+        line_color="red",
+    ),
+    row=1,
+    col=1,
+)
+fig.add_trace(
+    go.Scatter(x=t, y=ttl, name="ttl-line", line_color="black"),
+    row=1,
+    col=1,
+)
+
+
+# 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,
+    col=1,
+)
+fig.add_trace(
+    go.Scatter(x=t, y=local_eod_oe, name="local EOD (open-ephys)", line_color="red"),
+    row=2,
+    col=1,
+)
+
+
+# 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,
+    col=1,
+)
+fig.add_trace(
+    go.Scatter(
+        x=t, y=global_eod_oe, name="global EOD (open-ephys)", line_color="red"
+    ),
+    row=3,
+    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,
+    col=1,
+)
+fig.add_trace(
+    go.Scatter(x=t, y=sinus, name="sinus (open-ephys)", line_color="red"),
+    row=4,
+    col=1,
+)
+
+
+# 6. Update the layout for a cleaner look
+fig.update_layout(
+    title_text="Relacs vs. Open Ephys Data Alignment",
+    height=800, # Set the figure height in pixels
+    # Control the legend
+    legend=dict(orientation="h", yanchor="bottom", y=1.02, xanchor="right", x=1),
+)
+# 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()
+```