Restructure repo: add Python EMG scripts and move ESP32 code to EMG_Arm/

- Add emg_gui.py, learning_data_collection.py, learning_emg_filtering.py
- Add collected EMG data and trained models
- Move ESP32/PlatformIO code into EMG_Arm/ subdirectory
- Add servo control functions for robotic hand (flex/unflex fingers)
- Update .gitignore for Python and PlatformIO
- Exclude large asset files from repo (>100MB)

.gitignore

@@ -1,5 +1,18 @@
-.pio
-.vscode/.browse.c_cpp.db*
-.vscode/c_cpp_properties.json
-.vscode/launch.json
-.vscode/ipch
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.venv/
+venv/
+
+# PlatformIO
+EMG_Arm/.pio/
+EMG_Arm/.vscode/
+
+# Data (uncomment if you want to exclude)
+# collected_data/
+# models/
+
+# OS
+.DS_Store
+Thumbs.db

.vscode/extensions.json

@@ -1,8 +0,0 @@
-{
-    "recommendations": [
-        "pioarduino.pioarduino-ide"
-    ],
-    "unwantedRecommendations": [
-        "ms-vscode.cpptools-extension-pack"
-    ]
-}

EMG_Arm/.gitignore

@@ -0,0 +1,5 @@
+.pio
+.vscode/.browse.c_cpp.db*
+.vscode/c_cpp_properties.json
+.vscode/launch.json
+.vscode/ipch

EMG_Arm/src/main.c

@@ -0,0 +1,180 @@
+
+#include <freertos/FreeRTOS.h>
+#include "driver/gpio.h"
+#include "driver/ledc.h"
+
+// Finger servo pin mappings
+#define thumbServoPin   GPIO_NUM_1
+#define indexServoPin   GPIO_NUM_4
+#define middleServoPin  GPIO_NUM_5
+#define ringServoPin    GPIO_NUM_6
+#define pinkyServoPin   GPIO_NUM_7
+
+// LEDC channels (one per servo)
+#define thumbChannel    LEDC_CHANNEL_0
+#define indexChannel    LEDC_CHANNEL_1
+#define middleChannel   LEDC_CHANNEL_2
+#define ringChannel     LEDC_CHANNEL_3
+#define pinkyChannel    LEDC_CHANNEL_4
+#define deg180 2048
+#define deg0 430
+
+// Arrays for cleaner initialization
+const int servoPins[] = {thumbServoPin, indexServoPin, middleServoPin, ringServoPin, pinkyServoPin};
+const int servoChannels[] = {thumbChannel, indexChannel, middleChannel, ringChannel, pinkyChannel};
+const int numServos = 5;
+
+void servoInit() {
+  // LEDC timer configuration (shared by all servos)
+  ledc_timer_config_t ledc_timer = {};
+  ledc_timer.speed_mode = LEDC_LOW_SPEED_MODE;
+  ledc_timer.timer_num = LEDC_TIMER_0;
+  ledc_timer.duty_resolution = LEDC_TIMER_14_BIT;
+  ledc_timer.freq_hz = 50;
+  ledc_timer.clk_cfg = LEDC_AUTO_CLK;
+  ESP_ERROR_CHECK(ledc_timer_config(&ledc_timer));
+
+  // Initialize each finger servo channel
+  for (int i = 0; i < numServos; i++) {
+    ledc_channel_config_t ledc_channel = {};
+    ledc_channel.speed_mode = LEDC_LOW_SPEED_MODE;
+    ledc_channel.channel = servoChannels[i];
+    ledc_channel.timer_sel = LEDC_TIMER_0;
+    ledc_channel.intr_type = LEDC_INTR_DISABLE;
+    ledc_channel.gpio_num = servoPins[i];
+    ledc_channel.duty = deg0; // Start with fingers open
+    ledc_channel.hpoint = 0;
+    ESP_ERROR_CHECK(ledc_channel_config(&ledc_channel));
+  }
+}
+
+// Flex functions (move to 180 degrees - finger closed)
+void flexThumb() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, thumbChannel, deg180);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, thumbChannel);
+}
+
+void flexIndex() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, indexChannel, deg180);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, indexChannel);
+}
+
+void flexMiddle() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, middleChannel, deg180);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, middleChannel);
+}
+
+void flexRing() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, ringChannel, deg180);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, ringChannel);
+}
+
+void flexPinky() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, pinkyChannel, deg180);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, pinkyChannel);
+}
+
+// Unflex functions (move to 0 degrees - finger open)
+void unflexThumb() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, thumbChannel, deg0);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, thumbChannel);
+}
+
+void unflexIndex() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, indexChannel, deg0);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, indexChannel);
+}
+
+void unflexMiddle() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, middleChannel, deg0);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, middleChannel);
+}
+
+void unflexRing() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, ringChannel, deg0);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, ringChannel);
+}
+
+void unflexPinky() {
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, pinkyChannel, deg0);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, pinkyChannel);
+}
+
+// Combo functions
+void makeFist() {
+  // Set all duties first
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, thumbChannel, deg180);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, indexChannel, deg180);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, middleChannel, deg180);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, ringChannel, deg180);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, pinkyChannel, deg180);
+  // Update all at once
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, thumbChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, indexChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, middleChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, ringChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, pinkyChannel);
+}
+
+void openHand() {
+  // Set all duties first
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, thumbChannel, deg0);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, indexChannel, deg0);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, middleChannel, deg0);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, ringChannel, deg0);
+  ledc_set_duty(LEDC_LOW_SPEED_MODE, pinkyChannel, deg0);
+  // Update all at once
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, thumbChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, indexChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, middleChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, ringChannel);
+  ledc_update_duty(LEDC_LOW_SPEED_MODE, pinkyChannel);
+}
+
+void individualFingerDemo(int delay_ms){
+  flexThumb();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    unflexThumb();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+
+    flexIndex();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    unflexIndex();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+
+    flexMiddle();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    unflexMiddle();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+
+    flexRing();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    unflexRing();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+
+    flexPinky();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    unflexPinky();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+}
+
+void closeOpenDemo(int delay_ms){
+    makeFist();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+    openHand();
+    vTaskDelay(pdMS_TO_TICKS(delay_ms));
+}
+
+void app_main() {
+  servoInit();
+
+  // Demo: flex and unflex each finger in sequence
+  // while(1) {
+  //   individualFingerDemo(1000);
+  // }
+
+  // Demo: close and open hand
+  while(1) {
+    closeOpenDemo(1000);
+  }
+}

learning_emg_filtering.py

@@ -0,0 +1,243 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import h5py
+import pandas as pd
+from scipy.signal import butter, sosfiltfilt
+
+# =============================================================================
+# CONFIGURABLE PARAMETERS
+# =============================================================================
+ZC_THRESHOLD_PERCENT = 0.6   # Zero Crossing threshold as fraction of RMS
+SSC_THRESHOLD_PERCENT = 0.3  # Slope Sign Change threshold as fraction of RMS
+
+file = h5py.File("assets/discrete_gestures_user_000_dataset_000.hdf5", "r")
+
+def print_tree(name, obj):
+    print(name)
+
+file.visititems(print_tree)
+
+print(list(file.keys()))
+
+data = file["data"]
+print(type(data))
+print(data)
+print(data.dtype)
+
+raw = data[:]
+print(raw.shape)
+print(raw.dtype)
+
+emg = raw['emg']     
+time = raw['time']
+print(emg.shape)
+
+dt = np.diff(time)
+fs = 1.0 / np.median(dt)
+print("fs =", fs)
+print("dt min/median/max =", dt.min(), np.median(dt), dt.max())
+
+# 1) pick one channel
+emg_ch = emg[:, 0].astype(np.float32)
+
+# 2) drop the initial transient (recommended)
+drop_s = 0.5
+drop = int(drop_s * fs)
+emg_ch = emg_ch[drop:]
+time_ch = time[drop:]
+
+# 3) design + apply bandpass
+low, high = 20.0, 450.0
+sos = butter(4, [low/(0.5*fs), high/(0.5*fs)], btype="bandpass", output="sos")
+emg_bp = sosfiltfilt(sos, emg_ch)
+
+# 4) RMS envelope extraction
+# Step A: Define window size (150ms)
+window_ms = 150
+window_samples = int(window_ms / 1000 * fs)  # Convert ms to samples
+print(f"Window: {window_ms}ms = {window_samples} samples")
+
+# Step B: Square the bandpassed signal
+emg_squared = emg_bp ** 2
+
+# Step C: Moving average via convolution (rectangular kernel, normalized)
+kernel = np.ones(window_samples) / window_samples
+emg_mean_squared = np.convolve(emg_squared, kernel, mode='same')
+
+# Step D: Square root to complete RMS
+emg_envelope = np.sqrt(emg_mean_squared)
+
+# =============================================================================
+# TIME-DOMAIN FEATURE FUNCTIONS (RMS, WL, ZC, SSC)
+# Computed on band-passed EMG, not RMS envelope.
+# Designed for easy porting to embedded C.
+# =============================================================================
+
+def compute_rms(x):
+    """Root Mean Square: sqrt(mean(x^2))"""
+    return np.sqrt(np.mean(x ** 2))
+
+
+def compute_wl(x):
+    """Waveform Length: sum of absolute differences between consecutive samples."""
+    return np.sum(np.abs(np.diff(x)))
+
+
+def compute_zc(x, threshold):
+    """Zero Crossings: count of sign changes where amplitude change exceeds threshold."""
+    sign_change = x[:-1] * x[1:] < 0
+    amp_diff = np.abs(np.diff(x)) > threshold
+    return np.sum(sign_change & amp_diff)
+
+
+def compute_ssc(x, threshold):
+    """Slope Sign Changes: count of slope direction reversals exceeding threshold."""
+    diff_left = x[1:-1] - x[:-2]
+    diff_right = x[1:-1] - x[2:]
+    return np.sum(diff_left * diff_right > threshold)
+
+
+def compute_all_features_windowed(x, window_len, threshold_zc, threshold_ssc):
+    """
+    Compute RMS, WL, ZC, SSC using non-overlapping windows.
+    Returns arrays of feature values, one per window (for ML).
+    """
+    n_samples = len(x)
+    n_windows = n_samples // window_len
+    x_trim = x[:n_windows * window_len]
+    x_win = x_trim.reshape(n_windows, window_len)
+
+    rms = np.sqrt(np.mean(x_win ** 2, axis=1))
+    wl = np.sum(np.abs(np.diff(x_win, axis=1)), axis=1)
+
+    sign_change = x_win[:, :-1] * x_win[:, 1:] < 0
+    amp_diff = np.abs(np.diff(x_win, axis=1)) > threshold_zc
+    zc = np.sum(sign_change & amp_diff, axis=1)
+
+    diff_left = x_win[:, 1:-1] - x_win[:, :-2]
+    diff_right = x_win[:, 1:-1] - x_win[:, 2:]
+    ssc = np.sum(diff_left * diff_right > threshold_ssc, axis=1)
+
+    return rms, wl, zc, ssc
+
+
+# =============================================================================
+# COMPUTE FEATURES FOR ALL 16 CHANNELS
+# =============================================================================
+
+n_channels = 16
+all_features = {}  # Non-overlapping windows - for ML
+
+for ch in range(n_channels):
+    emg_ch_i = emg[drop:, ch].astype(np.float32)
+    emg_bp_i = sosfiltfilt(sos, emg_ch_i)
+
+    signal_rms_i = np.sqrt(np.mean(emg_bp_i ** 2))
+    threshold_zc_i = ZC_THRESHOLD_PERCENT * signal_rms_i
+    threshold_ssc_i = (SSC_THRESHOLD_PERCENT * signal_rms_i) ** 2
+
+    # Non-overlapping windowed features (for ML)
+    rms_i, wl_i, zc_i, ssc_i = compute_all_features_windowed(
+        emg_bp_i, window_samples, threshold_zc_i, threshold_ssc_i
+    )
+    all_features[ch] = {'rms': rms_i, 'wl': wl_i, 'zc': zc_i, 'ssc': ssc_i}
+
+# Time vector for windowed features
+n_windows = len(all_features[0]['rms'])
+window_centers = np.arange(n_windows) * window_samples + window_samples // 2
+time_windows = time_ch[window_centers]
+
+print(f"\nComputed features for {n_channels} channels")
+print(f"Windows per channel (non-overlapping): {n_windows}")
+print(f"Window size: {window_samples} samples ({window_ms} ms)")
+
+# 5) Load gesture labels (prompts)
+prompts = pd.read_hdf("assets/discrete_gestures_user_000_dataset_000.hdf5", key="prompts")
+print("\nUnique gestures:", prompts['name'].unique())
+
+t_abs = time_ch  # absolute timestamps
+
+# Find first occurrence of each gesture type
+index_gestures = prompts[prompts['name'].str.contains('index')]
+middle_gestures = prompts[prompts['name'].str.contains('middle')]
+thumb_gestures = prompts[prompts['name'].str.contains('thumb')]
+
+# Define plot configurations: 1) Index+Middle combined, 2) Thumb separate
+plot_configs = [
+    {'name': 'Index & Middle Finger', 'start_time': index_gestures['time'].iloc[0], 'filter': 'index|middle'},
+    {'name': 'Thumb', 'start_time': thumb_gestures['time'].iloc[0], 'filter': 'thumb'},
+]
+
+# Color function for markers
+def get_gesture_color(name):
+    if 'index' in name:
+        return 'green'
+    elif 'middle' in name:
+        return 'blue'
+    elif 'thumb' in name:
+        return 'orange'
+    return 'gray'
+
+# =============================================================================
+# 6) PLOT ALL FEATURES (RMS, WL, ZC, SSC) FOR ALL 16 CHANNELS
+# =============================================================================
+
+feature_names = ['rms', 'wl', 'zc', 'ssc']
+feature_titles = ['RMS Envelope', 'Waveform Length (WL)', 'Zero Crossings (ZC)', 'Slope Sign Changes (SSC)']
+feature_colors = ['red', 'blue', 'green', 'purple']
+feature_ylabels = ['Amplitude', 'WL (a.u.)', 'Count', 'Count']
+
+for config in plot_configs:
+    t_start = config['start_time'] - 0.5
+    t_end = t_start + 10.0
+
+    # Mask for windowed time vector
+    mask_win = (time_windows >= t_start) & (time_windows <= t_end)
+    t_win_rel = time_windows[mask_win] - t_start
+
+    # Get gestures in window
+    gesture_mask = (prompts['time'] >= t_start) & (prompts['time'] <= t_end) & \
+                   (prompts['name'].str.contains(config['filter']))
+    gestures_in_window = prompts[gesture_mask]
+
+    # Create one figure per feature
+    for feat_idx, feat_name in enumerate(feature_names):
+        fig, axes = plt.subplots(4, 4, figsize=(10, 8), sharex=True, sharey=True)
+        axes = axes.flatten()
+
+        for ch in range(n_channels):
+            ax = axes[ch]
+
+            # Plot windowed feature
+            feat_data = all_features[ch][feat_name][mask_win]
+            ax.plot(t_win_rel, feat_data, linewidth=1, color=feature_colors[feat_idx])
+            ax.set_title(f"Ch {ch}", fontsize=9)
+
+            # Add gesture markers
+            for _, row in gestures_in_window.iterrows():
+                t_g = row['time'] - t_start
+                color = get_gesture_color(row['name'])
+                ax.axvline(t_g, color=color, linestyle='--', alpha=0.5, linewidth=0.5)
+
+        # Set subtitle based on gesture type
+        if 'Index' in config['name']:
+            subtitle = "(Green=index, Blue=middle)"
+        else:
+            subtitle = "(Orange=thumb)"
+
+        fig.suptitle(f"{feature_titles[feat_idx]} - {config['name']} Gestures\n{subtitle}", fontsize=12)
+        fig.supxlabel("Time (s)")
+        fig.supylabel(feature_ylabels[feat_idx])
+        plt.tight_layout()
+        plt.show()
+
+# =============================================================================
+# SUMMARY: Feature statistics across all channels
+# =============================================================================
+print("\n" + "=" * 60)
+print("FEATURE SUMMARY (all channels, all windows)")
+print("=" * 60)
+for feat_name in ['rms', 'wl', 'zc', 'ssc']:
+    all_vals = np.concatenate([all_features[ch][feat_name] for ch in range(n_channels)])
+    print(f"{feat_name.upper():4s} | min: {all_vals.min():10.4f} | max: {all_vals.max():10.4f} | "
+          f"mean: {all_vals.mean():10.4f} | std: {all_vals.std():10.4f}")

src/main.c

@@ -1,46 +0,0 @@
-
-#include <freertos/FreeRTOS.h>
-#include "driver/gpio.h"
-#include "driver/ledc.h"
-
-#define servoPin GPIO_NUM_4
-#define ledcChannel LEDC_CHANNEL_0
-#define deg180 2048
-#define deg0 430
-
-void servoInit() {
-  // LEDC timer configuration (C++ aggregate initialization)
-  ledc_timer_config_t ledc_timer = {};
-  ledc_timer.speed_mode = LEDC_LOW_SPEED_MODE;
-  ledc_timer.timer_num = LEDC_TIMER_0;
-  ledc_timer.duty_resolution = LEDC_TIMER_14_BIT;
-  ledc_timer.freq_hz = 50;
-  ledc_timer.clk_cfg = LEDC_AUTO_CLK;
-  ESP_ERROR_CHECK(ledc_timer_config(&ledc_timer));
-
-  // LEDC channel configuration
-  ledc_channel_config_t ledc_channel = {};
-  ledc_channel.speed_mode = LEDC_LOW_SPEED_MODE;
-  ledc_channel.channel = ledcChannel;
-  ledc_channel.timer_sel = LEDC_TIMER_0;
-  ledc_channel.intr_type = LEDC_INTR_DISABLE;
-  ledc_channel.gpio_num = servoPin;
-  ledc_channel.duty = deg180; // Start off
-  ledc_channel.hpoint = 0;
-  ESP_ERROR_CHECK(ledc_channel_config(&ledc_channel));
-}
-
-// alternates between 0 and 180 - 2048 is 180 degrees (counterclockwise max)
-void app_main() {
-  servoInit();
-  while(1) {
-    ledc_set_duty(LEDC_LOW_SPEED_MODE, ledcChannel, deg180);
-    ledc_update_duty(LEDC_LOW_SPEED_MODE, ledcChannel);
-    printf("ccwMax\n");
-    vTaskDelay(pdMS_TO_TICKS(1000));
-    ledc_set_duty(LEDC_LOW_SPEED_MODE, ledcChannel, deg0);
-    ledc_update_duty(LEDC_LOW_SPEED_MODE, ledcChannel);
-    vTaskDelay(pdMS_TO_TICKS(1000));
-    printf("cwMax\n");
-  }
-}