ethoscopy 2.1.0__tar.gz → 2.2.1__tar.gz

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/.github/workflows/release.yml

@@ -3,9 +3,6 @@ name: Release to PyPI
 on:
   release:
     types: [published]
-  push:
-    tags:
-      - 'v*.*.*'
 
 jobs:
   test:
@@ -58,16 +55,7 @@ jobs:
       run: |
         twine check dist/*
 
-    - name: Publish to Test PyPI
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
-      run: |
-        twine upload --repository testpypi dist/*
-
     - name: Publish to PyPI
-      if: github.event_name == 'release'
       env:
         TWINE_USERNAME: __token__
         TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/CLAUDE.md

@@ -36,48 +36,62 @@ pip install -e ".[dev]"
 ```
 
 ### Testing
-- **No formal test suite found** - project relies on Jupyter notebooks for validation
-- Use the tutorial notebooks in `tutorial_notebook/` for testing functionality
-- Run notebooks: `jupyter notebook tutorial_notebook/`
+- **Pytest suite in `tests/`**: `python -m pytest tests/ -q` (~230 tests, seconds to run)
+- **Caveat**: `pytest.ini` declares its section as `[tool:pytest]`, which is the
+  *setup.cfg* spelling — pytest silently ignores the file, so `addopts` (coverage,
+  `--strict-markers`) and the `markers` registrations do **not** apply. Renaming the
+  section to `[pytest]` would switch on `--cov-fail-under=70` and `--strict-markers`
+  for the whole suite; check it passes before doing so.
+- Tutorial notebooks in `tutorial_notebook/` complement the suite for end-to-end checks
 
 ### Docker Environment
 - **Docker available** for JupyterHub deployment
 - Build: `JUPYTER_HUB_TAG=5.3.0 ETHOSCOPE_LAB_TAG=1.0 docker compose build`
 - Run: `docker compose up -d` (from Docker/ directory)
 
-### Troubleshooting: Database "Malformed" Errors
+### Opening databases: WAL mode and read-only mounts
 
-**Problem**: Intermittent "database disk image is malformed" errors when loading ethoscope data in Docker
+Ethoscopes record in **WAL** (Write-Ahead Logging) mode and the results tree is
+normally mounted read-only (`:ro` in Docker). That combination has broken loading
+repeatedly — as `database disk image is malformed`, and as
+`unable to open database file` on `SELECT * FROM ROI_MAP`.
 
-**Root Cause**: SQLite databases in WAL (Write-Ahead Logging) mode on read-only Docker mounts
+**How `_connect_db()` handles it** (load.py)
 
-**Solution Options**:
-1. **Convert databases to DELETE mode** (recommended for immediate fix)
-   ```bash
-   # Using the conversion script (from project root)
-   python3 scripts/convert_wal_to_delete.py /mnt/ethoscope_data/results --verbose
+ethoscopy never writes to these files, so the connection is *always* read-only —
+this also stops a load from checkpointing or truncating raw data as a side effect.
+It walks an ordered ladder of open modes, `_READ_STRATEGIES`, and **probes each
+one with a real statement** before returning it:
 
-   # Or using bash wrapper
-   ./scripts/convert_databases.sh /mnt/ethoscope_data/results
-   ```
+| rung | reads | notes |
+|---|---|---|
+| `mode=ro` | every recoverable state, incl. WAL with `-shm`, corrupt `-shm`, hot rollback journal | the only mode that sees data still in an uncheckpointed `-wal` |
+| `immutable=1` | WAL database whose sidecars are absent on a read-only mount | ignores the `-wal`; warns via `_warn_if_wal_ignored()` if it would hide committed rows |
 
-2. **Improved connection handling** (v2.0.4+)
-   - The `_connect_db()` function in `load.py` now detects WAL mode automatically
-   - Uses `mode=ro&nolock=1` URI parameters for WAL databases on read-only mounts
-   - Includes retry logic in `read_single_roi_optimized()` for resilience
+Two traps worth not rediscovering:
 
-**Key Implementation Details** (load.py):
-- Lines 18-70: `_connect_db()` - Smart connection with WAL detection and appropriate parameters
-- Lines 943-979: Retry logic in `read_single_roi_optimized()` - Handles transient errors with fresh connections
+- **Never use `mode=ro&nolock=1`.** SQLite rejects it for *every* WAL database.
+- **`sqlite3.connect()` never touches the file**, so a bad URI opens "successfully"
+  and only fails on the first query — past any `try/except` around the connect
+  call. That is why every rung is probed, and it is how the `nolock=1` bug survived
+  a fallback that looked like it covered the case.
+- `immutable=1` will also "open" a **missing** path, *creating* an empty database
+  and reporting `no such table: ROI_MAP`. `_connect_db()` checks the file exists first.
 
-**Testing After Changes**:
-```python
-import ethoscopy as etho
-metadata = etho.link_meta_index('metadata.csv', '/mnt/ethoscope_results')
-data = etho.load_ethoscope(metadata, reference_hour=9.0, FUN=etho.sleep_annotation)
-# Should load all ROIs without "malformed" errors
+`read_single_roi_optimized()` retries a failed read with `_connect_db(path,
+degraded=True)`, which skips to the last rung — a retry with the default ladder
+would just pick the same failing mode again.
+
+**Optional**: convert databases to DELETE mode to avoid the question entirely
+```bash
+python3 scripts/convert_wal_to_delete.py /mnt/ethoscope_data/results --verbose
+./scripts/convert_databases.sh /mnt/ethoscope_data/results   # bash wrapper
 ```
 
+**Tests**: `tests/test_load_wal.py` builds real SQLite files in each on-disk state
+(read-only and writable directories) rather than mocking sqlite3 — the failures
+being guarded against come from SQLite itself and only appear when a statement runs.
+
 **See Also**: `Docker/README.md` for detailed database preparation instructions
 
 ## Architecture and Code Structure

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/.env.dummy.example

@@ -16,6 +16,10 @@ ALLOWED_USERS=amadabhushi,ggilestro,mjoyce,lguo,labguest1,labguest2,labguest3,la
 # Comma-separated list of admin users
 ADMIN_USERS=ggilestro
 
+# Superusers see /home as their JupyterLab root and can browse/open/run
+# notebooks across every user. Defaults to ADMIN_USERS if unset.
+SUPERUSERS=ggilestro
+
 # Docker user/group (optional, defaults to 1000:1000)
 UID=1000
 GID=1000

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/.env.github.example

@@ -30,6 +30,10 @@ ALLOWED_USERS=username1,username2,username3
 # Comma-separated list of admin users (GitHub usernames)
 ADMIN_USERS=your-github-username
 
+# Superusers see /home as their JupyterLab root and can browse/open/run
+# notebooks across every user. Defaults to ADMIN_USERS if unset.
+SUPERUSERS=your-github-username
+
 # Docker user/group (optional, defaults to 1000:1000)
 UID=1000
 GID=1000

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/.env.google.example

@@ -32,6 +32,10 @@ ALLOWED_USERS=user1,user2,user3
 # Comma-separated list of admin users
 ADMIN_USERS=your-email-username
 
+# Superusers see /home as their JupyterLab root and can browse/open/run
+# notebooks across every user. Defaults to ADMIN_USERS if unset.
+SUPERUSERS=your-email-username
+
 # Docker user/group (optional, defaults to 1000:1000)
 UID=1000
 GID=1000

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/.env.keycloak.example

@@ -44,6 +44,10 @@ ALLOWED_USERS=amadabhushi,ggilestro,mjoyce,lguo,labguest1,labguest2,labguest3,la
 # Comma-separated list of admin users
 ADMIN_USERS=ggilestro
 
+# Superusers see /home as their JupyterLab root and can browse/open/run
+# notebooks across every user. Defaults to ADMIN_USERS if unset.
+SUPERUSERS=ggilestro
+
 # Docker user/group (optional, defaults to 1000:1000)
 UID=1000
 GID=1000

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/Dockerfile

@@ -66,7 +66,7 @@ RUN ln -s /bin/tar /bin/gtar && \
 # JUPYTER INSTALLATION AND CONFIGURATION
 # ============================================================================
 
-# Install JupyterLab (version 3.6.4)
+# Install JupyterLab (latest 4.x; pip resolves the newest compatible release)
 RUN pip3 install jupyterlab --ignore-installed
 
 # To upgrade to version 4.0.2 (commented out)
@@ -75,6 +75,14 @@ RUN pip3 install jupyterlab --ignore-installed
 # Install Jupyter extensions (compatible with 3.x only)
 RUN pip3 install jupyterlab-spreadsheet-editor
 
+# AI assistant: Copilot-style inline completions + chat panel.
+# Reason: lightweight (declares only jupyter-server as its Jupyter dep), so it
+# does NOT pull in jupyter-collaboration / server-documents like jupyter-ai does
+# — that RTC stack is what caused "File ID could not be retrieved" on file open.
+# Pinned for reproducible builds. Supports OpenRouter via its OpenAI-compatible
+# provider (base URL https://openrouter.ai/api/v1).
+RUN pip3 install --no-cache-dir "notebook-intelligence==5.1.0"
+
 # ============================================================================
 # PYTHON PACKAGES AND ETHOSCOPE SETUP
 # ============================================================================
@@ -87,9 +95,18 @@ RUN pip3 install \
         seaborn \
         bokeh \
         lifelines \
+        ipywidgets \
+        ipympl \
         opencv-python \
         mysql-connector \
-        ethoscopy
+        scikit-learn \
+        statsmodels \
+        pingouin \
+        openpyxl \
+        pyarrow \
+        tqdm \
+        jupyterlab-git \
+        ethoscopy==2.2.0
        # pycatch22
 
 # Pre-populate tutorial datasets inside the installed package so non-root

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/README_AUTH.md

@@ -15,6 +15,7 @@ This JupyterHub deployment supports multiple authentication methods, configurabl
   - [Adding New Users (OAuth)](#adding-new-users-oauth)
   - [Adding New Users (Dummy Auth)](#adding-new-users-dummy-auth)
   - [Making Users Admins](#making-users-admins)
+  - [Granting Cross-User File Access (Superusers)](#granting-cross-user-file-access-superusers)
 - [Switching Authentication Methods](#switching-authentication-methods)
 - [Dockerfile Optimization](#dockerfile-optimization)
 - [Troubleshooting](#troubleshooting)
@@ -388,6 +389,33 @@ docker compose restart
 - Navigate to: `https://jupyter.lab.gilest.ro/hub/admin`
 - You should see the admin panel with all users listed
 
+### Granting Cross-User File Access (Superusers)
+
+By default JupyterLab roots each user's file browser at their own home (`/home/<username>`). A **superuser** instead gets `/home` as their root, so they can browse, open, and run notebooks across every user's directory directly from their own JupyterLab session.
+
+This works because all single-user servers in this deployment run under the same container UID (see `ConfigUserSpawner` in `config/jupyterhub_config.py`), so filesystem-level access to all homes already exists — `SUPERUSERS` simply surfaces it in the UI.
+
+**Configuration**:
+
+```bash
+# .env
+SUPERUSERS=ggilestro,jdoe
+```
+
+If `SUPERUSERS` is unset, it defaults to `ADMIN_USERS`.
+
+**Apply changes**:
+```bash
+docker compose restart
+```
+
+**Verify**:
+- Log in as a superuser
+- The JupyterLab file browser should list every user's home folder
+- Opening another user's `.ipynb` runs it in place; edits and kernel output write back to that user's home
+
+**Security note**: Regular users are not isolated from each other at the filesystem level in this setup — anyone with a JupyterLab terminal can already `cd` into another user's home. `SUPERUSERS` only changes what is shown by default in the file browser. True per-user isolation would require a different spawner (e.g. `DockerSpawner` or `KubeSpawner` with distinct UIDs).
+
 ---
 
 ## Dockerfile Optimization

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/config/jupyterhub_config.py

@@ -120,6 +120,17 @@ else:
     # Use imported list from users.py
     c.Authenticator.admin_users = ADMIN_USERS
 
+# Superusers: users whose JupyterLab file browser is rooted at /home instead
+# of their own home, so they can browse/open/run notebooks across every user.
+# Reason: all single-user servers run as the same container UID (see
+# ConfigUserSpawner below), so filesystem access already exists — this just
+# exposes it in the UI. Defaults to admins; override with SUPERUSERS env var.
+superusers_env = os.getenv('SUPERUSERS')
+if superusers_env is not None:
+    SUPERUSERS = {u.strip() for u in superusers_env.split(',') if u.strip()}
+else:
+    SUPERUSERS = set(c.Authenticator.admin_users)
+
 # ============================================================================
 # CUSTOM SPAWNER (Preserved - critical for current setup)
 # ============================================================================
@@ -129,25 +140,48 @@ class ConfigUserSpawner(LocalProcessSpawner):
     def make_preexec_fn(self, name):
         """Don't try to switch users - run everything as current user"""
         return None
-    
+
     def user_env(self, env):
         """Set user environment without system user lookup"""
         env = env.copy()
         home_dir = f'/home/{self.user.name}'
-        
+
         # Ensure home directory exists with proper permissions
         os.makedirs(home_dir, mode=0o755, exist_ok=True)
-        
+
         # Set environment variables
         env['USER'] = self.user.name
         env['HOME'] = home_dir
         env['SHELL'] = '/bin/bash'
         env['LOGNAME'] = self.user.name
-        
+
+        # Notebook Intelligence (AI assistant): forward central LLM config from
+        # the container environment so students never enter API keys themselves
+        # (avoids keys leaking into dotfiles, cf. the pxin OpenAI-key incident).
+        # LiteLLM reads OPENROUTER_API_KEY directly and routes the
+        # `openrouter/...` model id; values come from .env via docker-compose.
+        for _key in (
+            'OPENROUTER_API_KEY',
+            'NBI_CHAT_MODEL_PROVIDER', 'NBI_CHAT_MODEL_ID',
+            'NBI_INLINE_COMPLETION_MODEL_PROVIDER', 'NBI_INLINE_COMPLETION_MODEL_ID',
+        ):
+            _val = os.getenv(_key)
+            if _val:
+                env[_key] = _val
+
         return env
 
 c.JupyterHub.spawner_class = ConfigUserSpawner
-c.Spawner.notebook_dir = '/home/{username}'
+
+
+def _set_notebook_dir(spawner):
+    if spawner.user.name in SUPERUSERS:
+        spawner.notebook_dir = '/home'
+    else:
+        spawner.notebook_dir = f'/home/{spawner.user.name}'
+
+
+c.Spawner.pre_spawn_hook = _set_notebook_dir
 
 # Timeouts
 c.Spawner.http_timeout = 60

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/Docker/docker-compose.yml

@@ -6,13 +6,14 @@ services:
       dockerfile: Dockerfile
       args:
         JUPYTER_HUB_TAG: ${JUPYTER_HUB_TAG:-5.4.0}
-    image: ggilestro/ethoscope-lab:${ETHOSCOPE_LAB_TAG:-1.2}
+    image: ggilestro/ethoscope-lab:${ETHOSCOPE_LAB_TAG:-1.3}
     container_name: ethoscope-lab
     ports:
       - 8082:8000
     volumes:
       - /mnt/ethoscope_data/results:/mnt/ethoscope_results:ro
       - /mnt/ethoscope_data/ethoscope_metadata:/opt/ethoscope_metadata
+      - /mnt/data/projects:/mnt/data/projects:ro
       - /mnt/homes:/home
       - /mnt/cache:/home/cache
       - ./jupyterhub_data:/srv/jupyterhub/
@@ -34,6 +35,7 @@ services:
       - DUMMY_PASSWORD=${DUMMY_PASSWORD:-ethoscope}
       - ALLOWED_USERS=${ALLOWED_USERS}
       - ADMIN_USERS=${ADMIN_USERS}
+      - SUPERUSERS=${SUPERUSERS}
       # OAuth settings (only needed when using OAuth authenticators)
       - OAUTH_CLIENT_ID=${OAUTH_CLIENT_ID}
       - OAUTH_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
@@ -47,6 +49,14 @@ services:
       - GITHUB_ORG=${GITHUB_ORG}
       - GOOGLE_HOSTED_DOMAIN=${GOOGLE_HOSTED_DOMAIN}
       - GITLAB_URL=${GITLAB_URL}
+      # Notebook Intelligence (AI assistant) — central OpenRouter config.
+      # Put OPENROUTER_API_KEY in .env (gitignored). Models are overridable;
+      # verify/adjust slugs at https://openrouter.ai/models
+      - OPENROUTER_API_KEY=${OPENROUTER_API_KEY}
+      - NBI_CHAT_MODEL_PROVIDER=${NBI_CHAT_MODEL_PROVIDER:-litellm-compatible}
+      - NBI_CHAT_MODEL_ID=${NBI_CHAT_MODEL_ID:-openrouter/anthropic/claude-sonnet-4.5}
+      - NBI_INLINE_COMPLETION_MODEL_PROVIDER=${NBI_INLINE_COMPLETION_MODEL_PROVIDER:-litellm-compatible}
+      - NBI_INLINE_COMPLETION_MODEL_ID=${NBI_INLINE_COMPLETION_MODEL_ID:-openrouter/openai/gpt-4o-mini}
 
     user: "${UID:-1000}:${GID:-1000}" # Adjust to your own user. Make sure this matches the permissions of your /mnt/{homes,cache} folder
     restart: always

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: ethoscopy
-Version: 2.1.0
+Version: 2.2.1
 Summary: "A python based toolkit to download and anlyse data from the Ethoscope hardware system."
 Author-email: Lblackhurst29 <lblackhurst29@gmail.com>
 License-File: LICENSE
@@ -23,6 +23,7 @@ Requires-Dist: plotly<6.0.0,>=5.22.0
 Requires-Dist: pywavelets<2.0.0,>=1.6.0
 Requires-Dist: seaborn<0.14.0,>=0.13.2
 Requires-Dist: tabulate<0.10.0,>=0.9.0
+Requires-Dist: tqdm<5.0,>=4.66
 Provides-Extra: dev
 Requires-Dist: black<25.0.0,>=24.0.0; extra == 'dev'
 Requires-Dist: ipykernel<7.0.0,>=6.29.5; extra == 'dev'

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ethoscopy"
-version = "2.1.0"
+version = "2.2.1"
 description = "\"A python based toolkit to download and anlyse data from the Ethoscope hardware system.\""
 authors = [{name = "Lblackhurst29",email = "lblackhurst29@gmail.com"}]
 readme = "README.md"
@@ -15,6 +15,7 @@ dependencies = [
     "pywavelets>=1.6.0,<2.0.0",
     "astropy>=7.0,<8.0",
     "nbformat>=5.10.4,<6.0.0",
+    "tqdm>=4.66,<5.0",
 ]
 requires-python = ">=3.12,<4.0"
 classifiers = [

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/src/ethoscopy/behavpy_core.py

@@ -9,6 +9,7 @@ from hmmlearn import hmm
 from scipy.signal import find_peaks
 from scipy.stats import zscore
 from tabulate import tabulate
+from tqdm.auto import tqdm
 
 from ethoscopy.analyse import max_velocity_detector
 from ethoscopy.misc.general_functions import concat, rle
@@ -2330,9 +2331,7 @@ class behavpy_core(pd.DataFrame):
         seq_test = np.concatenate(test, 0)
         seq_test = seq_test.reshape(-1, 1)
 
-        for i in range(iterations):
-            print(f"Iteration {i+1} of {iterations}")
-
+        for i in tqdm(range(iterations), desc="HMM training", unit="iter"):
             init_params = ""
             # h = hmm.MultinomialHMM(n_components = n_states, n_iter = hmm_iterations, tol = tol, params = 'ste', verbose = verbose)
             h = hmm.CategoricalHMM(
@@ -2397,11 +2396,13 @@ class behavpy_core(pd.DataFrame):
             h.fit(seq_train, len_seq_train)
 
             # Boolean output of if the number of runs convererged on set of appropriate probabilites for s, t, an e
-            print(
+            tqdm.write(
                 "True Convergence:"
                 + str(h.monitor_.history[-1] - h.monitor_.history[-2] < h.monitor_.tol)
             )
-            print("Final log liklihood score:" + str(h.score(seq_train, len_seq_train)))
+            tqdm.write(
+                "Final log liklihood score:" + str(h.score(seq_train, len_seq_train))
+            )
 
             # On first iteration save and print the first trained matrix
             if i == 0:
@@ -2410,9 +2411,11 @@ class behavpy_core(pd.DataFrame):
                     if h.score(seq_test, len_seq_test) > h_old.score(
                         seq_test, len_seq_test
                     ):
-                        print("New Matrix:")
+                        tqdm.write("New Matrix:")
                         df_t = pd.DataFrame(h.transmat_, index=states, columns=states)
-                        print(tabulate(df_t, headers="keys", tablefmt="github") + "\n")
+                        tqdm.write(
+                            tabulate(df_t, headers="keys", tablefmt="github") + "\n"
+                        )
 
                         with open(file_name, "wb") as file:
                             pickle.dump(h, file)
@@ -2426,9 +2429,9 @@ class behavpy_core(pd.DataFrame):
                 if h.score(seq_test, len_seq_test) > h_old.score(
                     seq_test, len_seq_test
                 ):
-                    print("New Matrix:")
+                    tqdm.write("New Matrix:")
                     df_t = pd.DataFrame(h.transmat_, index=states, columns=states)
-                    print(tabulate(df_t, headers="keys", tablefmt="github") + "\n")
+                    tqdm.write(tabulate(df_t, headers="keys", tablefmt="github") + "\n")
                     with open(file_name, "wb") as file:
                         pickle.dump(h, file)
 

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/src/ethoscopy/behavpy_plotly.py

@@ -6,6 +6,7 @@ import pandas as pd
 import plotly.graph_objs as go
 from plotly.subplots import make_subplots
 from scipy.stats import zscore
+from tqdm.auto import tqdm
 
 from ethoscopy.behavpy_draw import behavpy_draw
 from ethoscopy.behavpy_seaborn import behavpy_seaborn
@@ -3559,10 +3560,16 @@ class behavpy_plotly(behavpy_draw):
         min_t = []
         max_t = []
 
-        for c, (df, b) in enumerate(zip(decoded, b_list)):
+        for c, (df, b) in enumerate(
+            tqdm(
+                list(zip(decoded, b_list)),
+                desc="Plotting",
+                unit="fly",
+                total=len(decoded),
+            )
+        ):
             df["colour"] = df["previous_state"].map(colours_index)
             id = df.first_valid_index()
-            print(f"Plotting: {id}")
 
             if stim_df is not None:
                 df2 = stim_df.xmv("id", id)

{ethoscopy-2.1.0 → ethoscopy-2.2.1}/src/ethoscopy/behavpy_seaborn.py

@@ -6,6 +6,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import seaborn as sns
+from tqdm.auto import tqdm
 
 from ethoscopy.behavpy_draw import behavpy_draw
 from ethoscopy.misc.circadian_bars import circadian_bars
@@ -3000,9 +3001,7 @@ class behavpy_seaborn(behavpy_draw):
         min_t = []
         max_t = []
 
-        for ax, data in enumerate(decoded):
-            print(f"Plotting: {data.index[0]}")
-
+        for ax, data in enumerate(tqdm(decoded, desc="Plotting", unit="fly")):
             data["bin"] = data["bin"] / (60 * 60)
             st = data["state"].to_numpy()
             time = data["bin"].to_numpy()