mep-cmap-analyser 0.9.1__tar.gz

mep_cmap_analyser-0.9.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Justin Andrushko, Northumbria University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

mep_cmap_analyser-0.9.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: mep-cmap-analyser
+Version: 0.9.1
+Summary: BIDS-compliant TMS/EMG neurophysiology analysis tool for MEP and CMAP quantification
+Author-email: Justin Andrushko <justin.andrushko@northumbria.ac.uk>
+License: MIT License
+        
+        Copyright (c) 2026 Justin Andrushko, Northumbria University
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/justinAndrushko/mep-cmap-analyser
+Project-URL: Repository, https://github.com/justinAndrushko/mep-cmap-analyser
+Project-URL: Bug Tracker, https://github.com/justinAndrushko/mep-cmap-analyser/issues
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=1.5
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: scipy>=1.10
+Requires-Dist: PyWavelets>=1.4
+Requires-Dist: Pillow>=9.0
+Dynamic: license-file
+
+# MEP-CMAP Analyser
+
+**Version 0.9.1 | May 2026**  
+*Author: Justin Andrushko PhD, Northumbria University*
+
+A BIDS-compliant, open-source tool for processing and quantifying TMS-evoked motor evoked potentials (MEPs) and cortical silent periods (cSPs) from Spike-2 EMG recordings.
+
+\---
+
+## Features
+
+* **Dataset Setup** — multi-file session management with a persistent file queue, BIDS folder auto-detection, processing status tracking, and excluded-file management across sessions
+* **BIDS-compliant** derivatives output with automatic participant/session naming
+* **Per-trial MEP quantification** — PTP amplitude, onset latency, AUC, cSP duration, paired-pulse ratios
+* **Physiologically-bounded MEP onset detection** — peak-anchored backward scan with per-stim-type latency profiles derived from published normative data (TMS: hand/FDI 18–30 ms, vastus lateralis 18–35 ms, leg 28–45 ms; peripheral nerve: upper limb 2–12 ms, lower limb 4–18 ms)
+* **Cortical silent period (cSP) detection** using a vectorised bootstrap threshold method with MEP-anchored search cap
+* **Auto AUC** — onset-to-cSP start computed automatically for all event types; user can override via drag selector
+* **Auto SP and AUC for unreviewed segments** — silent period and AUC computed in the pipeline for any segment not manually reviewed in the Data Inspector
+* **M-wave normalisation** with plateau-based Mmax detection
+* **Paired-pulse ratios** (SICI, ICF, etc.) with flexible per-stim reference assignment in Stage 1a
+* **Data Inspector** — interactive per-trial review with draggable markers, zoom toolbar, AUC selector, silent period annotation; all edits persist across reruns
+* **Filter preview** — real-time frequency response and wavelet time-frequency display
+* **Outlier detection** with interactive review and Z-score thresholding
+* **Multi-channel support** — additional EMG and force channels for visual inspection
+* **Full session persistence** — every adjustable setting (filters, onset detection, CSP, latency profiles, normalisation, inspector edits, analysis options) is saved and restored automatically per file
+* **Group analysis** — Stage 2 merges all processed sessions into a single LME-ready CSV with study design columns (between/within-subject factors, stim roles)
+* **LME-ready trial-level CSV output** with Z-scores, detrended values, normalised PTP, and pooled statistics
+* **Cross-platform** — Windows, macOS, and Linux supported
+
+\---
+
+## Workflow
+
+The tool is organised into four tabs:
+
+### Dataset Setup
+
+Load a study folder or individual files. The tool auto-detects `rawdata/` and `derivatives/` subfolders (BIDS structure) or accepts manual folder selection. The derivatives folder is always placed beside `rawdata/`, never inside it. A persistent file queue tracks processing status across sessions — files are marked Not started, In progress, Needs review, Complete, or Stale.
+
+* Double-click any file to load it
+* Use **Run all unprocessed** to batch process
+* Use **Refresh** to detect newly added files (previously excluded files are remembered and not re-added)
+* Right-click → **Show excluded files** to restore previously removed files
+* Queue state is saved to `dataset\\\_session.json` in the derivatives folder
+
+### Stage 1a — Labels \& Analysis Setup
+
+Appears automatically after a file is loaded. Configure per-stim-type settings:
+
+* Label, colour, gap (ms), CSP detection toggle
+* Stimulation type and muscle group (sets physiological latency bounds for onset detection)
+* Internal normalisation references and plateau tolerance for Mmax detection
+
+Confirming setup auto-switches to Stage 1b. Settings persist between files.
+
+### Stage 1b — Single File Processing
+
+Filter settings (bandpass, notch, mains noise canceller), time window and MEP onset detection parameters, CSP detection settings, outlier review, and analysis options. All settings are saved per file and restored on reload.
+
+When reloading a previously processed file:
+
+* Option to reuse the saved data range, select a new range, or use the whole file
+* Previously adjusted marker positions, notes, exclusions, and AUC windows are restored and carried through the re-analysis
+
+### Stage 2 — Group Analysis LME Setup
+
+Scan the derivatives folder to discover all processed sessions. Assign study design columns (e.g. Group, Condition, Timepoint), configure stim type roles (Reference, Conditioned, M-wave), and click **Build group analysis file** to merge all selected sessions into a single `group\\\_level\\\_LME\\\_ready.csv`.
+
+\---
+
+## Installation
+
+### Option 1: pip (recommended for Python users)
+
+```bash
+pip install mep-cmap-analyser
+mep-cmap
+```
+
+Python 3.9+ required. Tkinter must be available:
+
+* **Windows/Mac**: included with standard Python
+* **Linux (Ubuntu/Debian)**: `sudo apt install python3-tk`
+
+### Option 2: Compiled binaries (no Python required)
+
+Download the latest release for your platform from the [Releases page](https://github.com/justinAndrushko/mep-cmap-analyser/releases):
+
+|Platform|File|
+|-|-|
+|Windows|`MEP-CMAP\\\_Analyser\\\_Windows.zip`|
+|macOS|`MEP-CMAP\\\_Analyser\\\_Mac.zip`|
+|Linux|`MEP-CMAP\\\_Analyser\\\_Linux.tar.gz`|
+
+Unzip and run the executable — no installation required.
+
+### Option 3: Run from source
+
+```bash
+git clone https://github.com/justinAndrushko/mep-cmap-analyser.git
+cd mep-cmap-analyser
+pip install -r requirements.txt
+python MEP\\\_CMAP\\\_Analyser.py
+```
+
+\---
+
+## Quick start
+
+```bash
+# Launch the GUI
+mep-cmap
+
+# Or from Python
+from mep\\\_cmap import run\\\_app
+run\\\_app()
+```
+
+### Scripted pipeline (no GUI)
+
+```python
+from mep\\\_cmap import run\\\_pipeline, PipelineConfig
+
+run\\\_pipeline(
+    input\\\_path   = "path/to/recording.txt",
+    pre\\\_ms       = 20,
+    post\\\_ms      = 400,
+    ptp\\\_start    = 10,
+    ptp\\\_end      = 50,
+    prestim\\\_ms   = 100,
+    marker\\\_name  = "Keyboard",
+)
+```
+
+\---
+
+## Input format
+
+The tool reads **Spike-2 text exports** (`.txt`) containing:
+
+* Waveform channels (EMG, force, etc.)
+* DigMark event timestamps
+
+Files should follow BIDS naming conventions for automatic metadata parsing:
+
+```
+sub-001\\\_ses-01\\\_limb-left\\\_recording.txt
+```
+
+Single-file recordings with multiple stimulus types and multi-file sessions (one file per condition) are both supported.
+
+\---
+
+## Output
+
+Results are saved to a `derivatives/` folder beside (not inside) the raw data folder, following BIDS structure:
+
+```
+study/
+├── rawdata/
+│   └── sub-001/ses-01/...
+└── derivatives/
+    ├── dataset\\\_session.json               ← queue state, processing status, excluded files
+    ├── group\\\_level\\\_LME\\\_ready.csv          ← merged group-level output (Stage 2)
+    └── sub-001/
+        └── ses-01/
+            ├── results/
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_All\\\_stims\\\_trial\\\_summary.csv
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_All\\\_stims\\\_trial\\\_summary.json
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_ptp\\\_results.csv
+            │   └── sub-001\\\_ses-01\\\_limb-left\\\_ptp\\\_results\\\_with\\\_outliers.csv
+            ├── figures/
+            └── sub-001\\\_ses-01\\\_limb-left\\\_session.json  ← per-file session state
+```
+
+### Trial-level CSV columns
+
+|Column|Description|
+|-|-|
+|`PTP(mV)`|MEP peak-to-peak amplitude|
+|`Latency(ms)`|MEP onset latency|
+|`cSP\\\_Duration(ms)`|Cortical silent period duration|
+|`cSP\\\_MEP\\\_Offset(ms)`|Time from stim to cSP onset|
+|`cSP\\\_EMG\\\_Return(ms)`|Time from stim to EMG return after cSP|
+|`MEP\\\_cSP\\\_Ratio`|PTP / cSP duration (Orth \& Rothwell, 2004)|
+|`AUC(mV\\\*s)`|Area under the rectified EMG curve (onset to cSP start)|
+|`Normalised\\\_PTP`|PTP / reference mean (Mmax or single-pulse reference)|
+|`Reference\\\_Type`|How the reference mean was computed|
+|`Reference\\\_Mean(mV)`|Reference amplitude used for normalisation|
+|`Z\\\_PTP\\\_Within`|Z-score within stim type|
+|`Z\\\_PTP\\\_Pooled`|Z-score pooled across all conditions|
+|`PTP\\\_Detrended(mV)`|Linearly detrended PTP amplitude|
+|`Outlier\\\_Decision`|Include / Exclude / Reviewed|
+|`Manual\\\_Note`|Annotator note from Data Inspector|
+
+### Group-level CSV additional columns
+
+|Column|Description|
+|-|-|
+|`participant\\\_id`|BIDS participant identifier|
+|`session`|Session label|
+|`task`|Task label (if assigned)|
+|`timepoint`|Timepoint label (if assigned)|
+|`Limb`|Limb identifier parsed from filename|
+|`Stim\\\_Role`|Role assigned in Stage 2 (Reference, Conditioned, M-wave, etc.)|
+|`\\\[custom columns]`|User-defined between/within-subject factors|
+
+\---
+
+## Building from source (developers)
+
+```bash
+# Windows
+python build\\\_windows.py
+
+# Linux
+python3 -m venv venv\\\_linux
+source venv\\\_linux/bin/activate
+pip install -r requirements.txt
+python3 build\\\_linux.py
+
+# macOS
+python3 build\\\_mac.py
+```
+
+\---
+
+## Citation
+
+If you use this tool in your research, please cite:
+
+> Andrushko, J.W. (2026). MEP-CMAP Analyser (Version 0.9.1) \\\[Software].
+> Northumbria University. https://doi.org/10.5281/zenodo.XXXXXXX
+
+\---
+
+## References
+
+* Orth, M., \& Rothwell, J.C. (2004). The cortical silent period: intrinsic variability and relation to the waveform of the transcranial magnetic stimulation pulse. *Clinical Neurophysiology*, 115(5), 1076–1082.
+* Hupfeld, K.E., Swanson, C.W., Fling, B.W., \& Seidler, R.D. (2021). TMS-induced silent periods: A review of methods and call for consistency. *Journal of Neuroscience Methods*, 346, 108950.
+
+\---
+
+## License
+
+MIT License — see [LICENSE](LICENSE) for details.
+

mep_cmap_analyser-0.9.1/README.md

@@ -0,0 +1,247 @@
+# MEP-CMAP Analyser
+
+**Version 0.9.1 | May 2026**  
+*Author: Justin Andrushko PhD, Northumbria University*
+
+A BIDS-compliant, open-source tool for processing and quantifying TMS-evoked motor evoked potentials (MEPs) and cortical silent periods (cSPs) from Spike-2 EMG recordings.
+
+\---
+
+## Features
+
+* **Dataset Setup** — multi-file session management with a persistent file queue, BIDS folder auto-detection, processing status tracking, and excluded-file management across sessions
+* **BIDS-compliant** derivatives output with automatic participant/session naming
+* **Per-trial MEP quantification** — PTP amplitude, onset latency, AUC, cSP duration, paired-pulse ratios
+* **Physiologically-bounded MEP onset detection** — peak-anchored backward scan with per-stim-type latency profiles derived from published normative data (TMS: hand/FDI 18–30 ms, vastus lateralis 18–35 ms, leg 28–45 ms; peripheral nerve: upper limb 2–12 ms, lower limb 4–18 ms)
+* **Cortical silent period (cSP) detection** using a vectorised bootstrap threshold method with MEP-anchored search cap
+* **Auto AUC** — onset-to-cSP start computed automatically for all event types; user can override via drag selector
+* **Auto SP and AUC for unreviewed segments** — silent period and AUC computed in the pipeline for any segment not manually reviewed in the Data Inspector
+* **M-wave normalisation** with plateau-based Mmax detection
+* **Paired-pulse ratios** (SICI, ICF, etc.) with flexible per-stim reference assignment in Stage 1a
+* **Data Inspector** — interactive per-trial review with draggable markers, zoom toolbar, AUC selector, silent period annotation; all edits persist across reruns
+* **Filter preview** — real-time frequency response and wavelet time-frequency display
+* **Outlier detection** with interactive review and Z-score thresholding
+* **Multi-channel support** — additional EMG and force channels for visual inspection
+* **Full session persistence** — every adjustable setting (filters, onset detection, CSP, latency profiles, normalisation, inspector edits, analysis options) is saved and restored automatically per file
+* **Group analysis** — Stage 2 merges all processed sessions into a single LME-ready CSV with study design columns (between/within-subject factors, stim roles)
+* **LME-ready trial-level CSV output** with Z-scores, detrended values, normalised PTP, and pooled statistics
+* **Cross-platform** — Windows, macOS, and Linux supported
+
+\---
+
+## Workflow
+
+The tool is organised into four tabs:
+
+### Dataset Setup
+
+Load a study folder or individual files. The tool auto-detects `rawdata/` and `derivatives/` subfolders (BIDS structure) or accepts manual folder selection. The derivatives folder is always placed beside `rawdata/`, never inside it. A persistent file queue tracks processing status across sessions — files are marked Not started, In progress, Needs review, Complete, or Stale.
+
+* Double-click any file to load it
+* Use **Run all unprocessed** to batch process
+* Use **Refresh** to detect newly added files (previously excluded files are remembered and not re-added)
+* Right-click → **Show excluded files** to restore previously removed files
+* Queue state is saved to `dataset\\\_session.json` in the derivatives folder
+
+### Stage 1a — Labels \& Analysis Setup
+
+Appears automatically after a file is loaded. Configure per-stim-type settings:
+
+* Label, colour, gap (ms), CSP detection toggle
+* Stimulation type and muscle group (sets physiological latency bounds for onset detection)
+* Internal normalisation references and plateau tolerance for Mmax detection
+
+Confirming setup auto-switches to Stage 1b. Settings persist between files.
+
+### Stage 1b — Single File Processing
+
+Filter settings (bandpass, notch, mains noise canceller), time window and MEP onset detection parameters, CSP detection settings, outlier review, and analysis options. All settings are saved per file and restored on reload.
+
+When reloading a previously processed file:
+
+* Option to reuse the saved data range, select a new range, or use the whole file
+* Previously adjusted marker positions, notes, exclusions, and AUC windows are restored and carried through the re-analysis
+
+### Stage 2 — Group Analysis LME Setup
+
+Scan the derivatives folder to discover all processed sessions. Assign study design columns (e.g. Group, Condition, Timepoint), configure stim type roles (Reference, Conditioned, M-wave), and click **Build group analysis file** to merge all selected sessions into a single `group\\\_level\\\_LME\\\_ready.csv`.
+
+\---
+
+## Installation
+
+### Option 1: pip (recommended for Python users)
+
+```bash
+pip install mep-cmap-analyser
+mep-cmap
+```
+
+Python 3.9+ required. Tkinter must be available:
+
+* **Windows/Mac**: included with standard Python
+* **Linux (Ubuntu/Debian)**: `sudo apt install python3-tk`
+
+### Option 2: Compiled binaries (no Python required)
+
+Download the latest release for your platform from the [Releases page](https://github.com/justinAndrushko/mep-cmap-analyser/releases):
+
+|Platform|File|
+|-|-|
+|Windows|`MEP-CMAP\\\_Analyser\\\_Windows.zip`|
+|macOS|`MEP-CMAP\\\_Analyser\\\_Mac.zip`|
+|Linux|`MEP-CMAP\\\_Analyser\\\_Linux.tar.gz`|
+
+Unzip and run the executable — no installation required.
+
+### Option 3: Run from source
+
+```bash
+git clone https://github.com/justinAndrushko/mep-cmap-analyser.git
+cd mep-cmap-analyser
+pip install -r requirements.txt
+python MEP\\\_CMAP\\\_Analyser.py
+```
+
+\---
+
+## Quick start
+
+```bash
+# Launch the GUI
+mep-cmap
+
+# Or from Python
+from mep\\\_cmap import run\\\_app
+run\\\_app()
+```
+
+### Scripted pipeline (no GUI)
+
+```python
+from mep\\\_cmap import run\\\_pipeline, PipelineConfig
+
+run\\\_pipeline(
+    input\\\_path   = "path/to/recording.txt",
+    pre\\\_ms       = 20,
+    post\\\_ms      = 400,
+    ptp\\\_start    = 10,
+    ptp\\\_end      = 50,
+    prestim\\\_ms   = 100,
+    marker\\\_name  = "Keyboard",
+)
+```
+
+\---
+
+## Input format
+
+The tool reads **Spike-2 text exports** (`.txt`) containing:
+
+* Waveform channels (EMG, force, etc.)
+* DigMark event timestamps
+
+Files should follow BIDS naming conventions for automatic metadata parsing:
+
+```
+sub-001\\\_ses-01\\\_limb-left\\\_recording.txt
+```
+
+Single-file recordings with multiple stimulus types and multi-file sessions (one file per condition) are both supported.
+
+\---
+
+## Output
+
+Results are saved to a `derivatives/` folder beside (not inside) the raw data folder, following BIDS structure:
+
+```
+study/
+├── rawdata/
+│   └── sub-001/ses-01/...
+└── derivatives/
+    ├── dataset\\\_session.json               ← queue state, processing status, excluded files
+    ├── group\\\_level\\\_LME\\\_ready.csv          ← merged group-level output (Stage 2)
+    └── sub-001/
+        └── ses-01/
+            ├── results/
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_All\\\_stims\\\_trial\\\_summary.csv
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_All\\\_stims\\\_trial\\\_summary.json
+            │   ├── sub-001\\\_ses-01\\\_limb-left\\\_ptp\\\_results.csv
+            │   └── sub-001\\\_ses-01\\\_limb-left\\\_ptp\\\_results\\\_with\\\_outliers.csv
+            ├── figures/
+            └── sub-001\\\_ses-01\\\_limb-left\\\_session.json  ← per-file session state
+```
+
+### Trial-level CSV columns
+
+|Column|Description|
+|-|-|
+|`PTP(mV)`|MEP peak-to-peak amplitude|
+|`Latency(ms)`|MEP onset latency|
+|`cSP\\\_Duration(ms)`|Cortical silent period duration|
+|`cSP\\\_MEP\\\_Offset(ms)`|Time from stim to cSP onset|
+|`cSP\\\_EMG\\\_Return(ms)`|Time from stim to EMG return after cSP|
+|`MEP\\\_cSP\\\_Ratio`|PTP / cSP duration (Orth \& Rothwell, 2004)|
+|`AUC(mV\\\*s)`|Area under the rectified EMG curve (onset to cSP start)|
+|`Normalised\\\_PTP`|PTP / reference mean (Mmax or single-pulse reference)|
+|`Reference\\\_Type`|How the reference mean was computed|
+|`Reference\\\_Mean(mV)`|Reference amplitude used for normalisation|
+|`Z\\\_PTP\\\_Within`|Z-score within stim type|
+|`Z\\\_PTP\\\_Pooled`|Z-score pooled across all conditions|
+|`PTP\\\_Detrended(mV)`|Linearly detrended PTP amplitude|
+|`Outlier\\\_Decision`|Include / Exclude / Reviewed|
+|`Manual\\\_Note`|Annotator note from Data Inspector|
+
+### Group-level CSV additional columns
+
+|Column|Description|
+|-|-|
+|`participant\\\_id`|BIDS participant identifier|
+|`session`|Session label|
+|`task`|Task label (if assigned)|
+|`timepoint`|Timepoint label (if assigned)|
+|`Limb`|Limb identifier parsed from filename|
+|`Stim\\\_Role`|Role assigned in Stage 2 (Reference, Conditioned, M-wave, etc.)|
+|`\\\[custom columns]`|User-defined between/within-subject factors|
+
+\---
+
+## Building from source (developers)
+
+```bash
+# Windows
+python build\\\_windows.py
+
+# Linux
+python3 -m venv venv\\\_linux
+source venv\\\_linux/bin/activate
+pip install -r requirements.txt
+python3 build\\\_linux.py
+
+# macOS
+python3 build\\\_mac.py
+```
+
+\---
+
+## Citation
+
+If you use this tool in your research, please cite:
+
+> Andrushko, J.W. (2026). MEP-CMAP Analyser (Version 0.9.1) \\\[Software].
+> Northumbria University. https://doi.org/10.5281/zenodo.XXXXXXX
+
+\---
+
+## References
+
+* Orth, M., \& Rothwell, J.C. (2004). The cortical silent period: intrinsic variability and relation to the waveform of the transcranial magnetic stimulation pulse. *Clinical Neurophysiology*, 115(5), 1076–1082.
+* Hupfeld, K.E., Swanson, C.W., Fling, B.W., \& Seidler, R.D. (2021). TMS-induced silent periods: A review of methods and call for consistency. *Journal of Neuroscience Methods*, 346, 108950.
+
+\---
+
+## License
+
+MIT License — see [LICENSE](LICENSE) for details.
+

mep_cmap_analyser-0.9.1/mep_cmap/__init__.py

@@ -0,0 +1,70 @@
+"""
+mep_cmap
+~~~~~~~~
+MEP-CMAP Analysis Tool — BIDS-compliant TMS/EMG neurophysiology pipeline.
+
+Package layout
+--------------
+compat      — gc patch, numpy shim, tk thread-safety
+bids        — StudyMetadata, BIDS label sanitisation
+utils       — shared helpers (_add_time_and_digmark)
+io          — Spike-2 file reading
+filters     — EMG filter functions
+detection   — MEP onset + CSP bootstrap detection
+pipeline       — PipelineConfig + all pipeline_* subfunctions + run_pipeline
+inspector      — DataInspectorWindow (per-trial interactive review)
+stage2         — Stage2Mixin (group analysis tab)
+filter_preview — FilterPreviewMixin (filter preview popup)
+app            — TMSAnalysisApp (main GUI, inherits stage2 + filter_preview)
+
+Quickstart
+----------
+    python -m mep_cmap          # launch the GUI
+    from mep_cmap import run_app; run_app()
+"""
+
+# compat must be imported first — it disables the cyclic GC and patches tkinter
+from . import compat  # noqa: F401
+
+from .bids      import StudyMetadata, TOOL_VERSION
+from .preferences import prefs, apply_scaling
+from .pipeline  import PipelineConfig, run_pipeline
+from .detection import detect_mep_onset_peak_fraction, detect_csp_bootstrap
+
+__version__ = TOOL_VERSION
+__all__ = [
+    "run_app",
+    "StudyMetadata",
+    "PipelineConfig",
+    "run_pipeline",
+    "detect_mep_onset_peak_fraction",
+    "detect_csp_bootstrap",
+]
+
+
+def run_app():
+    """Launch the MEP-CMAP Analysis GUI."""
+    import sys
+    import tkinter as tk
+
+    # Windows: create Tk root before numpy to avoid Tcl_AsyncDelete crash
+    pre_root = None
+    if sys.platform == "win32":
+        pre_root = tk.Tk()
+        pre_root.withdraw()
+
+    # Now safe to import matplotlib TkAgg backend
+    import matplotlib
+    matplotlib.use("TkAgg")
+    import matplotlib.pyplot as plt
+    from matplotlib.backends.backend_tkagg import (
+        FigureCanvasTkAgg, NavigationToolbar2Tk)
+
+    from .app import TMSAnalysisApp
+
+    root = pre_root if pre_root is not None else tk.Tk()
+    root.tk.call("tk", "scaling", 1.0)
+    root.deiconify()
+
+    app = TMSAnalysisApp(root)
+    root.mainloop()

mep_cmap_analyser-0.9.1/mep_cmap/__main__.py

@@ -0,0 +1,7 @@
+"""
+Entry point for  python -m mep_cmap
+"""
+from mep_cmap import run_app
+
+if __name__ == "__main__":
+    run_app()