Merge branch 'main' of https://whale.am28.uni-tuebingen.de/git/awendt/oephys2nix

doc/.gitignore

@@ -3,3 +3,4 @@
 api/
 objects.json
 _site/
+_freeze/

doc/_quarto.yml

@@ -2,8 +2,6 @@
 project:
   type: website
   output-dir: _site
-  preview:
-    port: 7000
 
 format:
   html:
@@ -39,6 +37,7 @@ website:
       - section: "Tutorials"
         contents:
         - "usage.qmd"
+        - "calibration.qmd"
       - section: "API"
         href: "api/index.qmd"
         contents:
@@ -60,4 +59,3 @@ quartodoc:
 
 execute:
   freeze: auto
-

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()
+```

doc/index.qmd

@@ -52,9 +52,12 @@ different sampling rates. If you start a stimulus a TTL pulse is send from
 relacs to the open-ephys recording controler.
 
 :::{.callout-caution}
-The Folder strucutre should be like two folders with one from relacs and one from open-ephys.
+The Folder strucutre should be like two folders with one from relacs and one
+from open-ephys.
 ```bash
 relax_folder/
 open-ephys_folder/
 ```
+the name `relacs` and `open-ephys` is essential for finding the different data
+streams so make sure they are present in the folder names.
 :::

doc/usage.qmd

@@ -1,3 +1,11 @@
 ---
 title: How to use it
 ---
+
+If you have a folder or multiple folders with each containing two recordings one from `relacs` and one from `open-ephys` you can simply run the CLI like this:
+
+```{python}
+# leave out the ! at the beginning if you running this in your shell
+!oephys2nix ../oephys2nix/test/Test1/
+```
+which provides you with information about the transition of the stimuli into the new file.

oephys2nix/logging.py

@@ -5,14 +5,28 @@ from rich.logging import RichHandler
 DEFAULT_LOG_LEVEL = "DEBUG"
 
 
-def setup_logging(logger: logging.Logger, level=DEFAULT_LOG_LEVEL):
+def setup_logging(logger: logging.Logger, verbosity: int):
+    level = logging.WARNING  # Default level
+
+    if verbosity == 0:
+        level = logging.ERROR
+    elif verbosity == 1:
+        level = logging.INFO
+    elif verbosity >= 2:
+        level = logging.DEBUG
+        print("Debugging enabled.")
+    else:
+        print("Invalid verbosity level. Defaulting to WARNING.")
+
     if logger.hasHandlers():
         logger.handlers.clear()
-    stream_handler = RichHandler(rich_tracebacks=True, show_path=False)
+    stream_handler = RichHandler(rich_tracebacks=True, show_path=level == logging.DEBUG)
     stream_handler.setLevel(level)
     fmt_shell = "%(filename)s:%(lineno)d - %(message)s"
     shell_formatter = logging.Formatter(fmt_shell)
     stream_handler.setFormatter(shell_formatter)
     logger.addHandler(stream_handler)
     logger.setLevel(level)
+    logger.propagate = False
+    # logging.basicConfig(level=level, handlers=[stream_handler], force=True)
     logging.getLogger(__name__).info(f"Logging configured with level {level}.")

oephys2nix/main.py

@@ -1,5 +1,6 @@
 import logging
 from pathlib import Path
+from typing import Annotated
 
 import nixio
 import typer
@@ -12,7 +13,6 @@ from oephys2nix.tonix import RawToNix
 
 app = typer.Typer()
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 console = Console()
 
 
@@ -30,8 +30,11 @@ def main(
     no_ttl: bool = typer.Option(False, help="For recordings that did not have a ttl pulse"),
     overwrite: bool = typer.Option(default=True, help="Overwrites nix file"),
     debug: bool = typer.Option(default=True, help="Shows more information and plots the results"),
+    verbose: Annotated[int, typer.Option("--verbose", "-v", count=True)] = 0,
 ) -> None:
     """Combines open ephys data with relacs data from data_path to a new nix file."""
+
+    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"))
@@ -88,10 +91,10 @@ def main(
         stim = StimulusToNix(open_ephys, str(relacs), str(nix_path))
         stim.create_repros_automatically()
         stim.print_table()
-        stim.checks()
+        # stim.checks()
 
-        if debug:
-            stim.plot_stimulus()
+        # if debug:
+        #     stim.plot_stimulus()
 
 
 if __name__ == "__main__":

oephys2nix/stimulus_recreation.py

@@ -15,11 +15,9 @@ from rich.table import Table
 from rlxnix.plugins.efish.utils import extract_am
 from scipy import signal
 
-from oephys2nix.logging import setup_logging
 from oephys2nix.metadata import create_dict_from_section, create_metadata_from_dict
 
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 console = Console()
 
 
@@ -452,8 +450,6 @@ 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
-            embed()
-            exit()
 
             if "FileStimulus" in repro_n.name:
                 repro_n.stimulus_folder = "/home/alexander/stimuli/whitenoise/"

oephys2nix/tonix.py

@@ -11,7 +11,6 @@ from oephys2nix.logging import setup_logging
 from oephys2nix.metadata import create_dict_from_section, create_metadata_from_dict
 
 log = logging.getLogger(__name__)
-setup_logging(log, level="DEBUG")
 
 
 class RawToNix:

pyproject.toml

@@ -18,6 +18,9 @@ oephys2nix = "oephys2nix.main:app"
 
 [project.optional-dependencies]
 docs = [
+    "jupyter>=1.1.1",
+    "jupyterlab>=4.4.9",
+    "plotly>=6.3.1",
     "quartodoc>=0.11.1",
 ]