ZaksPhysicsLibrary 1.2.2__tar.gz → 1.3.0__tar.gz

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ZaksPhysicsLibrary
-Version: 1.2.2
+Version: 1.3.0
 Summary: Data processing and analysis library for TDT, Oxysoft NIRS, and Terranova EFNMR lab data
 Author: zakgm2
 License-Expression: MIT

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/PhysicsLibrary/__init__.py

@@ -7,14 +7,13 @@ Data processing and analysis library for Physics Analysis GUI.
 from importlib.metadata import version as _version, PackageNotFoundError
 
 try:
-    __version__ = _version("PhysicsLibrary")
+    __version__ = _version("ZaksPhysicsLibrary")
 except PackageNotFoundError:
     __version__ = "unknown"
 
 from .file_parser_generic import load_any_file
 
 from .dataset import (
-    choose_file,
     detect_format,
     detect_format_file,
     DataFormat,

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/PhysicsLibrary/analysis.py

@@ -14,26 +14,40 @@ from scipy.signal import detrend, find_peaks
 from scipy.optimize import curve_fit
 
 
-def get_zscore_slice(time_array, signal, center_t, window=30):
+def get_zscore_slice(time_array, signal, center_t, window=None, pre=None, post=None):
     """
     Extract and z-score a time window around an event.
 
+    Supports either a symmetric `window` (split evenly before/after
+    center_t, legacy behaviour) or an asymmetric `pre`/`post` pair — e.g.
+    10s before the event and 20s after. If pre/post are given they take
+    precedence over window.
+
     Parameters
     ----------
     time_array : array
     signal : array
     center_t : float
         Event time in seconds
-    window : float
-        Total window size in seconds
+    window : float or None
+        Total window size in seconds, split evenly before/after center_t.
+        Ignored if pre/post are given.
+    pre : float or None
+        Seconds before center_t to include. Defaults to window/2.
+    post : float or None
+        Seconds after center_t to include. Defaults to window/2.
 
     Returns
     -------
     (time segment, z-scored signal)
     """
-    half_win  = window / 2
-    start_idx = np.searchsorted(time_array, center_t - half_win)
-    end_idx   = np.searchsorted(time_array, center_t + half_win)
+    if pre is None or post is None:
+        half_win = (window if window is not None else 30) / 2
+        pre  = pre  if pre  is not None else half_win
+        post = post if post is not None else half_win
+
+    start_idx = np.searchsorted(time_array, center_t - pre)
+    end_idx   = np.searchsorted(time_array, center_t + post)
 
     seg_y = signal[start_idx:end_idx]
     seg_x = time_array[start_idx:end_idx]
@@ -41,8 +55,11 @@ def get_zscore_slice(time_array, signal, center_t, window=30):
     # Clip extreme artefacts before z-scoring so outliers don't dominate the baseline std.
     seg_y = np.clip(seg_y, -5, 5)
 
-    baseline_end    = len(seg_y) // 2
-    baseline_period = seg_y[:baseline_end]
+    # Baseline is the pre-event portion — the part of the window that
+    # actually precedes the event, not just "the first half of the segment"
+    # (those differ once pre != post).
+    baseline_mask   = seg_x < center_t
+    baseline_period = seg_y[baseline_mask] if baseline_mask.any() else seg_y
     mu  = np.mean(baseline_period)
     std = np.std(baseline_period)
 
@@ -95,7 +112,7 @@ def bin_for_heatmap(z_seg, num_bins=300):
     return np.array([np.mean(z_seg[bin_edges[i]:bin_edges[i+1]]) for i in range(num_bins)])
 
 
-def compute_fft_slice(time_array, signal, center_t, fs, window=30):
+def compute_fft_slice(time_array, signal, center_t, fs, window=None, pre=None, post=None):
     """
     Extract a time window around center_t and compute its FFT.
 
@@ -103,6 +120,10 @@ def compute_fft_slice(time_array, signal, center_t, fs, window=30):
     the DC spike and slow drift, making physiological frequencies
     (breathing ~0.3 Hz, heart rate ~1 Hz) visible.
 
+    Supports either a symmetric `window` (split evenly before/after
+    center_t, legacy behaviour) or an asymmetric `pre`/`post` pair. If
+    pre/post are given they take precedence over window.
+
     Parameters
     ----------
     time_array : array
@@ -111,8 +132,13 @@ def compute_fft_slice(time_array, signal, center_t, fs, window=30):
         Center time in seconds
     fs : float
         Sampling frequency in Hz
-    window : float
-        Total window size in seconds
+    window : float or None
+        Total window size in seconds, split evenly before/after center_t.
+        Ignored if pre/post are given.
+    pre : float or None
+        Seconds before center_t to include. Defaults to window/2.
+    post : float or None
+        Seconds after center_t to include. Defaults to window/2.
 
     Returns
     -------
@@ -121,9 +147,13 @@ def compute_fft_slice(time_array, signal, center_t, fs, window=30):
     seg_x : array
     seg_y : array
     """
-    half_win  = window / 2
-    start_idx = np.searchsorted(time_array, center_t - half_win)
-    end_idx   = np.searchsorted(time_array, center_t + half_win)
+    if pre is None or post is None:
+        half_win = (window if window is not None else 30) / 2
+        pre  = pre  if pre  is not None else half_win
+        post = post if post is not None else half_win
+
+    start_idx = np.searchsorted(time_array, center_t - pre)
+    end_idx   = np.searchsorted(time_array, center_t + post)
 
     seg_y = signal[start_idx:end_idx]
     seg_x = time_array[start_idx:end_idx]

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/PhysicsLibrary/dataset.py

@@ -2,8 +2,8 @@
 dataset.py
 ----------
 The universal Dataset container returned by every loader, plus format
-detection and folder selection. No parsing logic lives here — that's in
-loaders/.
+detection. No parsing logic lives here — that's in loaders/. No GUI
+concerns either — folder/file selection is a caller responsibility.
 """
 
 from __future__ import annotations
@@ -11,33 +11,11 @@ from __future__ import annotations
 import os
 from dataclasses import dataclass, field
 from enum import Enum, auto
-from tkinter import filedialog
 from typing import Optional
 
 import numpy as np
 
 
-# ---------------------------------------------------------------------------
-# Folder selection
-# ---------------------------------------------------------------------------
-
-def choose_file(parent_window=None) -> tuple[Optional[str], Optional[str]]:
-    """
-    Opens a native folder selection dialog.
-
-    Returns
-    -------
-    (folder_path, folder_name)  or  (None, None) if cancelled.
-    """
-    folder_path = filedialog.askdirectory(
-        parent=parent_window,
-        title="Open Lab Data Folder",
-    )
-    if not folder_path:
-        return None, None
-    return folder_path, os.path.basename(folder_path)
-
-
 # ---------------------------------------------------------------------------
 # Universal output struct
 # ---------------------------------------------------------------------------

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/PhysicsLibrary/processing_TDT.py

@@ -118,6 +118,30 @@ def get_tdt_struct(path):
     """
     Load a Tucker-Davis Technologies (TDT) recording block.
 
+    Streams and scalars are read in a single call (unaffected by the issue
+    below). Epoc stores are auto-discovered from the block's own headers
+    and then read ONE STORE AT A TIME, each with its own fresh
+    tdt.read_block() call:
+
+    - The `tdt` SDK has a bug where reading multiple epoc stores together
+      breaks if any store has a mismatched onset/offset count (e.g. a
+      strobe/epoch that was still active when the recording was stopped —
+      a completely normal way for a session to end). Reading one store per
+      call sidesteps it; a store that still fails to a genuine data issue
+      is skipped with a warning rather than crashing the entire load.
+    - Store names must come from each store's own `.name` attribute, not
+      the header dict's key — TDT sanitizes store codes containing `/`
+      into a trailing-underscore Python attribute name (e.g. dict key
+      "EE1_" but the real store code passed to `store=` is "EE1/").
+    - Epoc reads must NOT reuse the cached `headers=` object from the
+      initial header scan — doing so carries over the same mismatched
+      onset/offset state that causes the crash in the first place. Only
+      the streams/scalars read benefits from header reuse.
+
+    This entirely auto-discovers whatever stores a given recording
+    contains — nothing about store names/types is hardcoded, so it works
+    for any TDT block regardless of how it was configured in Synapse.
+
     Parameters
     ----------
     path : str
@@ -126,11 +150,36 @@ def get_tdt_struct(path):
     Returns
     -------
     object
-        Parsed TDT data structure.
+        Parsed TDT data structure (data.streams, data.epocs, data.scalars).
     """
-    data = tdt.read_block(path)
+    import warnings
+
+    heads = tdt.read_block(path, headers=1)
+    if heads is None:
+        raise Exception("TDT returned an empty object.")
+
+    data = tdt.read_block(path, headers=heads, evtype=['streams', 'scalars'], verbose=0)
     if data is None:
         raise Exception("TDT returned an empty object.")
+
+    epoc_stores = [(key, s.name) for key, s in heads.stores.items()
+                   if getattr(s, 'type_str', None) == 'epocs']
+
+    for key, real_name in epoc_stores:
+        try:
+            # No headers= reuse here — see docstring.
+            ep = tdt.read_block(path, store=real_name, evtype=['epocs'], verbose=0)
+        except Exception as e:
+            warnings.warn(
+                f"Skipping epoc store '{key}' ({real_name}): {e}",
+                RuntimeWarning, stacklevel=2,
+            )
+            continue
+        if not ep.epocs:
+            continue
+        store_key = next(iter(ep.epocs.keys()))
+        setattr(data.epocs, key, ep.epocs[store_key])
+
     return data
 
 
@@ -220,34 +269,75 @@ def correct_bleaching(y, fs):
 
 def get_event_markers(data):
     """
-    Extract behavioral event markers from TDT epoc data.
+    Extract behavioral event markers from every populated TDT epoc store.
+
+    A recording can easily have a dozen+ epoc stores (I/O strobes, Epoch
+    Event Storage, free-text notes, a 1-second Tick reference, ...) —
+    every one of them becomes its own marker group here, tagged by store
+    name via the 'store' key, so a caller (e.g. a GUI) can let the user
+    toggle each store's markers independently instead of dumping every
+    store onto the plot at once (which overlaps into an unreadable mess).
+
+    The 'Note' store keeps its original behaviour: each onset becomes a
+    marker labeled with the actual note text (from Notes.txt), since
+    that's the one store meant for free-text annotations. Every other
+    epoc store gets one marker per onset event, labeled with the store
+    name.
+
+    Nothing about which stores exist is hardcoded — this walks whatever
+    data.epocs actually contains, so it works for any TDT block.
 
     Returns
     -------
     list of dict
         Each dict contains:
-        - time
-        - label
-        - color
+        - time  : float
+        - label : str
+        - color : str
+        - store : str  (source epoc store name, for grouping/toggling)
     """
-    if not hasattr(data.epocs, 'Note'):
+    if not hasattr(data, 'epocs'):
         return []
 
-    notes  = data.epocs.Note.notes
-    onsets = data.epocs.Note.onset
-
-    # Experiment-specific label→colour mapping; unknown labels default to black.
-    color_map = {'Clap': 'red', 'Sucrose': 'green', 'Stop': 'blue'}
-    markers   = []
-
-    for n, t in zip(notes, onsets):
-        note_str = n.decode() if isinstance(n, bytes) else str(n)
-        note_str = note_str.strip()
-        markers.append({
-            'time':  t,
-            'label': note_str,
-            'color': color_map.get(note_str, 'black'),
-        })
+    # Experiment-specific label→colour mapping for Note text; every other
+    # store cycles through a fixed palette so each store gets a distinct,
+    # consistent colour across redraws.
+    note_color_map = {'Clap': 'red', 'Sucrose': 'green', 'Stop': 'blue'}
+    palette = ['black', 'purple', 'orange', 'saddlebrown', 'teal', 'magenta',
+               'darkgreen', 'navy', 'gray', 'olive']
+
+    markers = []
+    store_keys = sorted(k for k in data.epocs.keys())
+
+    for i, store_key in enumerate(store_keys):
+        epoc = data.epocs[store_key]
+        onsets = getattr(epoc, 'onset', [])
+        if len(onsets) == 0:
+            continue
+
+        display_name = store_key.rstrip('_')  # cosmetic: TDT pads slash-containing codes with a trailing "_"
+
+        if store_key == 'Note':
+            notes = getattr(epoc, 'notes', [])
+            for n, t in zip(notes, onsets):
+                note_str = n.decode() if isinstance(n, bytes) else str(n)
+                note_str = note_str.strip()
+                markers.append({
+                    'time':  float(t),
+                    'label': note_str,
+                    'color': note_color_map.get(note_str, 'black'),
+                    'store': display_name,
+                })
+        else:
+            color = palette[i % len(palette)]
+            for t in onsets:
+                markers.append({
+                    'time':  float(t),
+                    'label': display_name,
+                    'color': color,
+                    'store': display_name,
+                })
+
     return markers
 
 

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/ZaksPhysicsLibrary.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ZaksPhysicsLibrary
-Version: 1.2.2
+Version: 1.3.0
 Summary: Data processing and analysis library for TDT, Oxysoft NIRS, and Terranova EFNMR lab data
 Author: zakgm2
 License-Expression: MIT

{zaksphysicslibrary-1.2.2 → zaksphysicslibrary-1.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ZaksPhysicsLibrary"
-version = "1.2.2"
+version = "1.3.0"
 description = "Data processing and analysis library for TDT, Oxysoft NIRS, and Terranova EFNMR lab data"
 requires-python = ">=3.10"
 readme = "README.md"