prepare for new version

.gitignore

@@ -182,4 +182,5 @@ cython_debug/
 flares-*
 *.flare
 *.cfg
-tempCodeRunnerFile.py
+tempCodeRunnerFile.py
+*.pkl

changelog.md

@@ -1,5 +1,6 @@
-# Version 1.6.1
+# Version 1.7.0
 
+- This is potentially a save-changing release due to adding more data into the save file. Please update your project files to ensure compatibility
 - Renamed all instances of "Inter" to properly read as "Intra" and changed "Cross" to now read as "Inter"
 - Changed RESAMPLE to only apply where it is required to avoid having Functional Connectivity analysis methods running on data that has been resampled
 - Added parameters that appear when attempting to generate results from the Participant and Intra-Group Functional Connectivity viewers and removed the non-functional placeholder parameters

flares.py

@@ -163,6 +163,42 @@ QC_METRIC_LABELS = {
 }
 
 
+ROI_MAP = {
+    'ROI_OccipitoParietal_BA18_19_7': [
+        'S1_D1', 'S1_D2', 'S4_D3'
+    ],
+    'ROI_SuperiorParietal_BA7_5': [
+        'S2_D1', 'S3_D1', 'S2_D2', 'S2_D4', 'S4_D4'
+    ],
+    'ROI_TPJ_AngularGyrus_BA39_19_40': [
+        'S4_D2', 'S5_D3', 'S4_D5', 'S5_D5'
+    ],
+    # --- SPLIT BA40 REGIONS ---
+    'ROI_Posterior_BA40_Parietal': [
+        'S6_D4', 'S6_D5'
+    ],
+    'ROI_Anterior_BA40_Sensorimotor': [
+        'S10_D5', 'S8_D5'
+    ],
+    # --------------------------
+    'ROI_Supramarginal_Inferior_BA40_6': [
+        'S6_D6'
+    ],
+    'ROI_VentralSomatosensory_BA1_2_3_43_48': [
+        'S8_D6', 'S9_D6'
+    ],
+    'ROI_Sensorimotor_BA1_2_3_4_6': [
+        'S6_D8', 'S10_D8'
+    ],
+    'ROI_DLPFC_FEF_BA6_8_9': [
+        'S7_D7', 'S7_D8'
+    ],
+    'ROI_Broca_VLPFC_BA6_44_45_4': [
+        'S9_D7', 'S10_D7'
+    ]
+}
+
+
 DOWNSAMPLE: bool
 DOWNSAMPLE_FREQUENCY: int
 
@@ -303,6 +339,7 @@ GROUP: str = "Default"
 FOLDING_BYP: bool = False
 
 FEATURE_1: bool = False
+FEATURE_2: bool = False
 
 # Ensure that we are working in the directory of this file
 script_dir = os.path.dirname(os.path.abspath(__file__))
@@ -610,10 +647,19 @@ def process_multiple_participants(file_paths, file_params, file_metadata,
     process_multiple_participants._success_count = success_count["value"]
     process_multiple_participants._failed_stages = failed_stages["value"]
 
+    successes = [r for r in qc_rows if r.get("status") == "success"]
+    population_flags = flag_population_outliers(successes)
+
+    for path, flags in population_flags.items():
+        metric_summary = ", ".join(f"{f['metric']}={f['value']} (median={f['median']:.1f}, z={f['z']})" for f in flags)
+        n_metrics_flagged = len(flags)
+        severity = "STRONG" if n_metrics_flagged >= 3 else "possible"
+        logger.warning(f"{severity} outlier: {path} - flagged on {n_metrics_flagged} metric(s): {metric_summary}")
+
     if qc_summary_path and qc_rows:
         if FEATURE_1:
             try:
-                write_qc_excel_summary(qc_rows, qc_summary_path)
+                write_qc_excel_summary(qc_rows, qc_summary_path, population_flags=population_flags)
                 logger.info(f"QC summary written to {qc_summary_path} ({len(qc_rows)} participant(s))")
             except Exception as e:
                 logger.error(f"Failed to write QC summary: {e}")
@@ -622,6 +668,86 @@ def process_multiple_participants(file_paths, file_params, file_metadata,
 
 
 
+def flag_population_outliers(
+    qc_rows: list[dict],
+    metrics: list[str] | None = None,
+    z_threshold: float = 2.5,
+) -> dict[str, list[dict]]:
+    """
+    Given QC metrics collected across an entire batch (each participant
+    processed with identical, fixed thresholds - nothing adaptive changes
+    per-participant), flags participants whose value on a given metric is
+    a statistical outlier relative to the rest of the batch.
+
+    This does NOT change what gets marked as a bad channel, and does NOT
+    imply anything is wrong with the metric thresholds themselves - it
+    answers a different question: "given everyone went through the same
+    pipeline with the same settings, does this participant's result look
+    unusual compared to everyone else who did." A real, uniformly bad
+    dataset (e.g. wrong population for the config) would show up as
+    outliers across MULTIPLE metrics; a participant with one borderline
+    metric and nothing else is much weaker evidence of a real problem.
+
+    Uses a modified z-score (median + MAD-based, not mean + std) since
+    QC metric distributions across a real population are often skewed by
+    a few genuinely bad files - MAD-based scoring is robust to those
+    outliers dominating the very estimate used to detect them, unlike a
+    standard mean/std z-score.
+
+    Parameters
+    ----------
+    qc_rows : list of per-participant QC dicts (successful runs only -
+        filter out FAILED entries before calling this).
+    metrics : list of QC dict keys to check. Defaults to the standard
+        bad-channel-count metrics if not specified.
+    z_threshold : float, default 2.5
+        Modified z-score magnitude above which a participant is flagged
+        for that metric. 2.5 is a commonly used, moderately conservative
+        starting point for outlier flagging - not validated against your
+        specific data, worth adjusting based on what you see in practice.
+
+    Returns
+    -------
+    dict[str, list[dict]]
+        Keyed by file_path, listing which metric(s) that participant was
+        flagged as an outlier on and by how much, e.g.
+        {"sub-07.snirf": [{"metric": "n_bad_sci", "z": 3.1, "value": 22, "median": 3}]}
+    """
+    if metrics is None:
+        metrics = [
+            "n_bad_sci", "n_bad_snr", "n_bad_psp", "n_bad_coeff_var",
+            "n_bad_mad", "n_bad_psd_noise", "n_bad_dropout",
+            "n_bad_channels_total", "pct_bad_channels",
+        ]
+
+    flagged: dict[str, list[dict]] = {}
+
+    for metric in metrics:
+        values = np.array([row.get(metric) for row in qc_rows if row.get(metric) is not None], dtype=float)
+        if len(values) < 4:
+            logger.info(f"Skipping outlier check for '{metric}' - too few participants ({len(values)}) for a meaningful comparison.")
+            continue
+
+        median = np.median(values)
+        mad = np.median(np.abs(values - median))
+        if mad == 0:
+            continue  # every participant identical on this metric - nothing to flag
+
+        for row in qc_rows:
+            val = row.get(metric)
+            if val is None:
+                continue
+            modified_z = 0.6745 * (val - median) / mad
+            if abs(modified_z) >= z_threshold:
+                path = row.get("file_path", "unknown")
+                flagged.setdefault(path, []).append({
+                    "metric": metric, "z": round(float(modified_z), 2),
+                    "value": val, "median": float(median),
+                })
+
+    return flagged
+
+
 def markbad(data, ax, ch_names: list[str]) -> None:
     """
     Add a strikethrough to a plot for channels marked as bad.
@@ -1239,16 +1365,13 @@ def calculate_peak_power(data: BaseRaw, time_window: int = 3, threshold: float =
     psp = scores.mean(axis=1)
     bad_channels = list(compress(cast(list[str], data.ch_names), psp < threshold))
 
-    plot_data = data.copy()
-    plot_data.info["bads"] = bad_channels
-
     existing_bads = set(data.info.get("bads", []))
     data.info["bads"] = list(existing_bads | set(bad_channels))
 
     # Determine the colors based on the threshold, and create the figures
     color_stops = ([0.0, threshold, threshold+0.1, threshold+0.2, 1.0], [0.0, threshold, threshold, 1.0])
-    psp1, psp2 = plot_timechannel_quality_metrics(plot_data, scores, times, color_stops, threshold, "Peak Spectral Power")
-    print(f"thresh: {threshold}")
+    psp1, psp2 = plot_timechannel_quality_metrics(data, scores, times, color_stops, threshold, "Peak Spectral Power")
+
 
     return list(compress(cast(list[str], getattr(data, "ch_names")), psp < threshold)), psp1, psp2
 
@@ -5128,6 +5251,89 @@ def find_bad_channels_coeff_var(raw, coeff_var_threshold=25.0):
 
 
 
+def detect_hbo_hbr_anticorrelation(raw_haemo, threshold: float = -0.2):
+    """
+    Flags channels where HbO and HbR are NOT showing the expected
+    physiologically anti-correlated relationship. Real hemodynamic response
+    typically shows HbO rising while HbR falls (and vice versa) - a channel
+    pair with weak or positive correlation is a common signature of motion
+    artifact or poor optode coupling that other QC metrics can miss, since
+    it's checking signal SHAPE/relationship rather than amplitude, variance,
+    or noise level.
+
+    IMPORTANT: must be run on raw_haemo BEFORE enhance_negative_correlation
+    (or any similar correction step) - that step actively forces HbO/HbR
+    anti-correlation, so measuring this diagnostic afterward would just be
+    checking whether the correction worked, not the underlying data quality.
+
+    Parameters
+    ----------
+    raw_haemo : BaseRaw
+        Haemoglobin-concentration data (post Beer-Lambert, pre-correction).
+    threshold : float, default -0.2
+        Channels with HbO/HbR correlation ABOVE this value are flagged as
+        bad (i.e. not sufficiently anti-correlated). -0.2 is a permissive
+        starting point - real channels often land well below this (-0.5 to
+        -0.9), but very low SNR or task designs can naturally weaken the
+        correlation without indicating artifact, so this shouldn't be set
+        aggressively without checking against your own known-good data.
+
+    Returns
+    -------
+    tuple[list[str], Figure]
+        - list[str]: channel names (both hbo AND hbr for each flagged pair)
+          below the anti-correlation threshold.
+        - Figure: bar chart of correlation per channel pair, matching the
+          visual style of detect_sensor_dropout.
+    """
+    ch_names = raw_haemo.ch_names
+    data = raw_haemo.get_data()
+
+    base_names = sorted({ch.split()[0] for ch in ch_names})
+    correlations = {}
+    bad_bases = []
+
+    for base in base_names:
+        try:
+            hbo_idx = ch_names.index(f"{base} hbo")
+            hbr_idx = ch_names.index(f"{base} hbr")
+        except ValueError:
+            continue  # channel doesn't have both chromophores present
+
+        hbo_signal = data[hbo_idx]
+        hbr_signal = data[hbr_idx]
+
+        if np.std(hbo_signal) == 0 or np.std(hbr_signal) == 0:
+            corr = 0.0  # flat channel - can't meaningfully correlate
+        else:
+            corr = float(np.corrcoef(hbo_signal, hbr_signal)[0, 1])
+
+        correlations[base] = corr
+        if corr > threshold:
+            bad_bases.append(base)
+            print(f"Flagged {base}: HbO/HbR correlation = {corr:.3f} (expected below {threshold})")
+
+    bad_names = [ch for ch in ch_names if ch.split()[0] in bad_bases]
+
+    fig, ax = plt.subplots(figsize=(10, 5), constrained_layout=True)
+    bases_sorted = list(correlations.keys())
+    corr_values = [correlations[b] for b in bases_sorted]
+    colors = ['coral' if c > threshold else 'skyblue' for c in corr_values]
+
+    ax.bar(range(len(corr_values)), corr_values, color=colors)
+    ax.axhline(threshold, color='red', linestyle='--', label=f'Threshold ({threshold})')
+    ax.axhline(0, color='black', linewidth=0.8)
+    ax.set_title("HbO/HbR Anti-Correlation Check")
+    ax.set_ylabel("Pearson r (HbO vs HbR)")
+    ax.set_xlabel("Channel Pair Index")
+    ax.legend()
+    plt.close(fig)
+
+    print(f"Anti-correlation check: flagged {len(bad_bases)} optode pair(s).")
+    return bad_names, fig
+
+
+
 def hr_calc(raw, seconds_to_strip_hr, l_freq, h_freq, search_min, search_max, max_low_hr, max_high_hr, smoothing_window_hr, hr_window, short_channels, short_channels_threshold, verbosity, psd_confidence_threshold: float = 3.0, band_halfwidth_hz: float = 0.3):
     if short_channels:
         short_chans = get_short_channels(raw, max_dist=short_channels_threshold)
@@ -5745,6 +5951,12 @@ def process_participant(file_path, file_start, progress_callback=None):
     logger.info("Step 17 Completed.")
     step_start = lap(step_start, timings, "Step 17")
 
+    bad_anticorr = []
+    if FEATURE_2 and not FOLDING_BYP:
+        bad_anticorr, fig_anticorr = detect_hbo_hbr_anticorrelation(raw_haemo, threshold=-0.2)
+        _enqueue("HbO-HbR Anti-Correlation", fig_anticorr, png_queue)
+    qc["n_bad_anticorrelation"] = len(bad_anticorr)
+
     # Step 18: Enhance Negative Correlation
     if ENHANCE_NEGATIVE_CORRELATION and not FOLDING_BYP:
         raw_haemo = enhance_negative_correlation(raw_haemo)
@@ -5877,6 +6089,27 @@ def process_participant(file_path, file_start, progress_callback=None):
     if progress_callback: progress_callback(27)
     logger.info("27")
     step_start = lap(step_start, timings, "Step 27")
+
+
+    # Step 27.5: Extract FIR Waveform Features & Enqueue Metric Plots
+    fir_feature_dict = {'features': np.array([]), 'feature_names': [], 'feature_channels': []}
+
+    # if HRF_MODEL.lower() == "fir":
+    #     try:
+    #         fir_feature_dict = extract_fir_features_real_data(
+    #             raw=raw_haemo,
+    #             target_condition=None,  # e.g., 'reach'
+    #             fir_delays=FIR_DELAYS,               # e.g., np.arange(0, 15)
+    #             selected_metrics=tuple(METRIC_REGISTRY.keys()),   # e.g., ('Peak_Amp', 'TTP', 'AUC')
+    #             roi_map=ROI_MAP,
+    #             glm_est=glm_est,
+    #             df_design_matrix=df_design_matrix,
+    #             png_queue=png_queue
+    #         )
+    #         logger.info("Step 27.5: FIR features successfully extracted and metric images enqueued.")
+    #     except Exception as e:
+    #         logger.warning(f"Step 27.5 Failed to extract FIR features: {e}")
+
      
     # Step 28: Finishing Up
     png_queue.put(None)   # sentinel
@@ -5895,7 +6128,7 @@ def process_participant(file_path, file_start, progress_callback=None):
         logger.info(f"  {name:<25} {elapsed:7.3f}s")
 
     logger.info(f"Total processing time: {sum(timings.values()):.3f}s")
-    return raw_haemo, epochs, df_cha, df_roi, df_design_matrix, config_dict, fig_bytes_dict, contrast_results_dict, roi_channel_map, qc, True
+    return raw_haemo, epochs, df_cha, df_roi, df_design_matrix, config_dict, fig_bytes_dict, contrast_results_dict, roi_channel_map, fir_feature_dict, qc, True
 
 
 
@@ -6769,7 +7002,11 @@ def peak_power_fast(
     return raw, scores, times
 
 
-def write_qc_excel_summary(qc_rows: list[dict], output_path: str) -> None:
+def write_qc_excel_summary(
+    qc_rows: list[dict],
+    output_path: str,
+    population_flags: dict[str, list[dict]] | None = None,
+) -> None:
     """
     Writes one Excel workbook summarizing QC metrics across all participants
     in a batch run - participants as columns, metrics as rows, each row
@@ -6838,18 +7075,23 @@ def write_qc_excel_summary(qc_rows: list[dict], output_path: str) -> None:
 
         header_range = f"{first_col_letter}1:{last_col_letter}1"
         if key in QC_METRIC_DEVIATION_BASED:
-            # "worst" = furthest from the row's own median
-            worst_formula = (
-                f"=INDEX({header_range},MATCH(MAX(ABS({data_range}-MEDIAN({data_range}))),"
-                f"ABS({data_range}-MEDIAN({data_range})),0))"
-            )
-        elif QC_METRIC_DIRECTIONS[key]:  # lower is better -> worst = max
-            worst_formula = f"=INDEX({header_range},MATCH(MAX({data_range}),{data_range},0))"
-        else:  # higher is better -> worst = min
-            worst_formula = f"=INDEX({header_range},MATCH(MIN({data_range}),{data_range},0))"
-
-        ws.cell(row=row_num, column=worst_col, value=worst_formula).font = body_font
-
+            row_values = [row.get(key) for row in successes if row.get(key) is not None]
+            row_paths = [row.get("file_path") for row in successes if row.get(key) is not None]
+            if row_values:
+                med = float(np.median(row_values))
+                deviations = [abs(v - med) for v in row_values]
+                worst_idx = int(np.argmax(deviations))
+                worst_value = row_paths[worst_idx]
+            else:
+                worst_value = ""
+            ws.cell(row=row_num, column=worst_col, value=worst_value).font = body_font
+        else:
+            # existing live-formula path for direction-based metrics, unchanged
+            if QC_METRIC_DIRECTIONS[key]:
+                worst_formula = f"=INDEX({header_range},MATCH(MAX({data_range}),{data_range},0))"
+            else:
+                worst_formula = f"=INDEX({header_range},MATCH(MIN({data_range}),{data_range},0))"
+            ws.cell(row=row_num, column=worst_col, value=worst_formula).font = body_font
         # --- Color scale, direction-aware ---
         if key in QC_METRIC_DEVIATION_BASED:
             # color by |value - row median| via a helper column pattern isn't
@@ -6876,9 +7118,32 @@ def write_qc_excel_summary(qc_rows: list[dict], output_path: str) -> None:
             )
         ws.conditional_formatting.add(data_range, rule)
 
+    if population_flags:
+        outlier_row = len(metric_keys) + 2
+        ws.cell(row=outlier_row, column=1, value="Population Outlier Flags").font = label_font
+
+        any_flags = bool(population_flags)
+        for i, row in enumerate(successes):
+            col = i + 2
+            path = row.get("file_path", "")
+            flags = population_flags.get(path, []) if population_flags else []
+            if flags:
+                text = "; ".join(f"{f['metric']} (z={f['z']})" for f in flags)
+                c = ws.cell(row=outlier_row, column=col, value=text)
+                c.fill = PatternFill(
+                    start_color="FFEB84" if len(flags) < 3 else "F8696B",
+                    end_color="FFEB84" if len(flags) < 3 else "F8696B",
+                    fill_type="solid",
+                )
+            else:
+                c = ws.cell(row=outlier_row, column=col, value="No outliers detected")
+                c.fill = PatternFill(start_color="C6EFCE", end_color="C6EFCE", fill_type="solid")
+            c.font = body_font
+            c.alignment = Alignment(horizontal="center")
+
     # --- Failed participants block, separate and clearly marked ---
     if failures:
-        fail_row_start = len(metric_keys) + 4
+        fail_row_start = len(metric_keys) + 5
         ws.cell(row=fail_row_start, column=1, value="FAILED PARTICIPANTS").font = Font(name="Arial", bold=True, size=12, color="CC0000")
         for i, row in enumerate(failures):
             r = fail_row_start + 1 + i
@@ -6888,6 +7153,11 @@ def write_qc_excel_summary(qc_rows: list[dict], output_path: str) -> None:
             err_cell = ws.cell(row=r, column=2, value=row.get("error", "unknown error"))
             err_cell.font = body_font
             err_cell.fill = fail_fill
+    else:
+        fail_row_start = len(metric_keys) + 5
+        c = ws.cell(row=fail_row_start, column=1, value="All participants processed successfully - no failures.")
+        c.font = Font(name="Arial", bold=True, size=11, color="006100")
+        c.fill = PatternFill(start_color="C6EFCE", end_color="C6EFCE", fill_type="solid")
 
     ws.column_dimensions['A'].width = 32
     for i in range(n_participants):
@@ -6897,6 +7167,240 @@ def write_qc_excel_summary(qc_rows: list[dict], output_path: str) -> None:
     wb.save(output_path)
 
 
+METRIC_REGISTRY = {
+    'Peak_Amp': 'Peak_Amp',
+    'TTP': 'Time_to_Peak',
+    'AUC': 'AUC',
+    'Rising_Slope': 'Rising_Slope',
+    'Recovery_Slope': 'Recovery_Slope',
+    'FWHM': 'FWHM',
+    'Onset_Latency': 'Onset_Latency',
+    'P2P_Amp': 'Peak_to_Peak_Amp',
+    'Signal_Std': 'Signal_Std',
+    'RMS': 'RMS'
+}
+
+
+def plot_and_enqueue_waveform_metrics(
+    roi_curves, 
+    fir_delays, 
+    selected_metrics, 
+    target_condition='reach', 
+    png_queue=None
+):
+    """
+    Generates and enqueues visual plots for every calculated waveform metric
+    across all Regions of Interest (ROIs).
+    """
+    # Structure metric values per ROI
+    metric_data = {METRIC_REGISTRY[m]: {} for m in selected_metrics}
+
+    for (chromo, roi_name), roi_fir_curve in roi_curves.items():
+        metrics = compute_waveform_metrics(roi_fir_curve, fir_delays=fir_delays, selected_metrics=selected_metrics)
+        for m_key, val in zip(selected_metrics, metrics):
+            label = METRIC_REGISTRY[m_key]
+            metric_data[label][f"{roi_name} ({chromo.upper()})"] = val
+
+    # Generate an image for each metric across ROIs
+    for metric_label, roi_dict in metric_data.items():
+        if not roi_dict:
+            continue
+            
+        fig, ax = plt.subplots(figsize=(8, 4.5))
+        rois = list(roi_dict.keys())
+        values = list(roi_dict.values())
+
+        colors = ['#2b5c8f' if v >= 0 else '#d9534f' for v in values]
+        ax.bar(rois, values, color=colors, alpha=0.85, edgecolor='black')
+        
+        ax.axhline(0, color='black', linewidth=0.8, linestyle='--')
+        ax.set_title(f"FIR Waveform Metric: {metric_label} [{target_condition}]", fontsize=12, fontweight='bold')
+        ax.set_xlabel("Region of Interest (ROI)", fontsize=10)
+        ax.set_ylabel(metric_label, fontsize=10)
+        plt.xticks(rotation=35, ha='right')
+        plt.grid(axis='y', linestyle=':', alpha=0.6)
+        plt.tight_layout()
+
+        # Enqueue figure or close
+        if png_queue is not None:
+            _enqueue(f"FIR Waveform Metric - {metric_label}", fig, png_queue)
+        else:
+            plt.close(fig)
+
+
+def _compute_roi_fir_curves(
+    raw=None, 
+    target_condition='reach', 
+    fir_delays=np.arange(0, 15),
+    roi_map=ROI_MAP, 
+    chromophores=('hbr',),
+    glm_est=None,
+    df_design_matrix=None
+):
+    """
+    Shared FIR-GLM curve extraction. If `glm_est` and `df_design_matrix` are supplied,
+    it reuses pre-calculated GLM results directly to avoid duplicate processing.
+    """
+    roi_curves = {}
+
+    # --- SHORT-CIRCUIT: Reuse pre-calculated GLM estimation if available ---
+    if glm_est is not None and df_design_matrix is not None:
+        if hasattr(glm_est, 'to_dataframe'):
+            glm_df = glm_est.to_dataframe().reset_index()
+        elif isinstance(glm_est, pd.DataFrame):
+            glm_df = glm_est.copy()
+        else:
+            raise ValueError("Unsupported format for precalculated glm_est.")
+
+        glm_df.columns = [str(col).lower() for col in glm_df.columns]
+        cond_col = 'condition' if 'condition' in glm_df.columns else 'regressor'
+        ch_col = 'ch_name' if 'ch_name' in glm_df.columns else ('source' if 'source' in glm_df.columns else 'channel')
+
+        print("Available conditions in GLM:", glm_df[cond_col].unique())
+        fir_df = glm_df[glm_df[cond_col].astype(str).str.lower().str.contains(target_condition.lower())].copy()
+        print(f"Matched rows for '{target_condition}': {len(fir_df)}")
+
+        if fir_df.empty:
+            logger.warning(f"Condition '{target_condition}' not found in precalculated GLM estimates.")
+            return roi_curves
+
+        for chromo in chromophores:
+            chromo_df = fir_df[fir_df[ch_col].str.lower().str.contains(chromo.lower())] if ch_col in fir_df.columns else fir_df
+            
+            ch_curves = {}
+            for ch_name, ch_group in chromo_df.groupby(ch_col):
+                pair = ch_name.split(' ')[0]
+                ch_curves[pair] = ch_group['theta'].values if 'theta' in ch_group.columns else ch_group['beta'].values
+
+            print("Extracted channel keys:", list(ch_curves.keys())[:5])
+
+            for roi_name, channels in roi_map.items():
+                matching_curves = [ch_curves[ch] for ch in channels if ch in ch_curves]
+                if matching_curves:
+                    roi_curves[(chromo, roi_name)] = np.mean(matching_curves, axis=0)
+
+        return roi_curves
+
+
+def extract_fir_features_real_data(
+    raw=None, 
+    target_condition=None,
+    fir_delays=np.arange(0, 15), 
+    selected_metrics=('Peak_Amp',), 
+    roi_map=ROI_MAP,
+    glm_est=None,
+    df_design_matrix=None,
+    png_queue=None
+):
+    """
+    Extracts FIR scalar waveform metrics, plots and enqueues figures for each
+    waveform metric, and returns all outputs collapsed into a single dictionary variable.
+    """
+
+    raw_cols = [
+        col for col in df_design_matrix.columns 
+        if not any(k in col.lower() for k in ['drift', 'constant', 'short', 'nuisance'])
+    ]
+    
+    # Strip '_delay_0', '_delay_1', etc. to get base condition names
+    target_conditions = list(dict.fromkeys(
+        col.split('_delay_')[0] if '_delay_' in col else col 
+        for col in raw_cols
+    ))
+
+    collapsed_features = []
+    feature_names = []
+    feature_channels = []
+
+    # 2. Iterate over EVERY condition
+    for cond in target_conditions:
+        try:
+            roi_curves = _compute_roi_fir_curves(
+                raw=raw, 
+                target_condition=cond, 
+                fir_delays=fir_delays,
+                roi_map=roi_map, 
+                chromophores=('hbr',),
+                glm_est=glm_est,
+                df_design_matrix=df_design_matrix
+            )
+
+            if not roi_curves:
+                print("999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999")
+                continue
+
+            metric_labels = [METRIC_REGISTRY[m] for m in selected_metrics]
+
+            # Extract metrics per ROI for this condition
+            for (chromo, roi_name), roi_fir_curve in roi_curves.items():
+                metrics = compute_waveform_metrics(roi_fir_curve, fir_delays=fir_delays, selected_metrics=selected_metrics)
+                collapsed_features.extend(metrics)
+                # Prefix feature names with condition
+                feature_names.extend([f"{cond}_{roi_name}_{m}" for m in metric_labels])
+                feature_channels.extend([roi_name] * len(metric_labels))
+
+            # Enqueue plots for this specific condition
+            plot_and_enqueue_waveform_metrics(
+                roi_curves=roi_curves,
+                fir_delays=fir_delays,
+                selected_metrics=selected_metrics,
+                target_condition=cond,
+                png_queue=png_queue
+            )
+        except Exception as e:
+            logger.warning(f"Failed extracting FIR metrics for condition '{cond}': {e}")
+
+    return {
+        'features': np.array(collapsed_features),
+        'feature_names': feature_names,
+        'feature_channels': feature_channels
+    }
+
+def compute_waveform_metrics(fir_curve, fir_delays, selected_metrics=('Peak_Amp',)):
+    peak_idx = np.argmax(fir_curve)
+    peak_amp = fir_curve[peak_idx]
+    ttp = fir_delays[peak_idx]
+
+    calculated_metrics = {}
+
+    if 'Peak_Amp' in selected_metrics:
+        calculated_metrics['Peak_Amp'] = peak_amp
+
+    if 'TTP' in selected_metrics:
+        calculated_metrics['TTP'] = ttp
+
+    if 'AUC' in selected_metrics:
+        trapz_fn = getattr(np, 'trapezoid', getattr(np, 'trapz', None))
+        calculated_metrics['AUC'] = trapz_fn(fir_curve, fir_delays)
+
+    if 'Rising_Slope' in selected_metrics:
+        calculated_metrics['Rising_Slope'] = (peak_amp - fir_curve[0]) / (ttp - fir_delays[0]) if ttp > fir_delays[0] else 0.0
+
+    if 'Recovery_Slope' in selected_metrics:
+        calculated_metrics['Recovery_Slope'] = (fir_curve[-1] - peak_amp) / (fir_delays[-1] - ttp) if fir_delays[-1] > ttp else 0.0
+
+    if 'FWHM' in selected_metrics:
+        half_max = peak_amp / 2.0
+        above_half = np.where(fir_curve >= half_max)[0]
+        calculated_metrics['FWHM'] = fir_delays[above_half[-1]] - fir_delays[above_half[0]] if len(above_half) > 1 else 0.0
+
+    if 'Onset_Latency' in selected_metrics:
+        onset_thresh = 0.2 * peak_amp
+        above_onset = np.where(fir_curve >= onset_thresh)[0]
+        calculated_metrics['Onset_Latency'] = fir_delays[above_onset[0]] if len(above_onset) > 0 else 0.0
+
+    if 'P2P_Amp' in selected_metrics:
+        calculated_metrics['P2P_Amp'] = peak_amp - np.min(fir_curve)
+
+    if 'Signal_Std' in selected_metrics:
+        calculated_metrics['Signal_Std'] = np.std(fir_curve)
+
+    if 'RMS' in selected_metrics:
+        calculated_metrics['RMS'] = np.sqrt(np.mean(fir_curve**2))
+
+    return [calculated_metrics[m] for m in selected_metrics]
+
+
 if __name__ == "__main__":
     print("This file has no functionality when not used in tandem with the FLARES application.")
         

main.py

@@ -1215,6 +1215,8 @@ class MainApplication(QMainWindow):
             data_map["fig_bytes_dict"],
             data_map["contrast_results_dict"],
             data_map["roi_channel_map_dict"],
+            data_map["fir_feature_dict"],
+            data_map["qc_dict"],
             self.folding_bypass,
         ]
 

project_manager.py

@@ -336,7 +336,7 @@ class ProjectManager:
 
             has_data = any(len(getattr(app, item["key"], {})) > 0 for item in DATA_SCHEMA)
             if hasattr(app, "button1"):
-                app.button1.setVisible(not has_data)
+                app.button1.setVisible(has_data)
             if hasattr(app, "button3"):
                 app.button3.setVisible(has_data)
 

src/analysis/exporttocsv.py

@@ -32,20 +32,27 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
         design_matrix_dict: dict[str, DataFrame],
         contrast_results_dict: dict[str, dict[str, Any]],
         group_dict: dict[str, str],
-        config_dict: dict[str, dict[str, Any]]
+        config_dict: dict[str, dict[str, Any]],
+        fir_feature_dict: dict[str, dict[str, Any]],
+        qc_dict: dict[str, dict[str, Any]],
     ) -> None:
         
         super().__init__("ExportToCSV")
         self.setWindowTitle(f"Export To CSV Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.cha_dict = cha_dict
-        # self.df_ind = df_ind_dict
-        # self.design_matrix = design_matrix_dict
-        # self.contrast_results_dict = contrast_results_dict
-        # self.group = group_dict
+        self.df_ind_dict = df_ind_dict
+        self.design_matrix = design_matrix_dict
+        self.contrast_results_dict = contrast_results_dict
+        self.group_dict = group_dict
         self.config_dict = config_dict
+        self.fir_feature_dict = fir_feature_dict
+        self.qc_dict = qc_dict
         
-        self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)", "2 (Export Configuration to CSV)", "3 (Paragraph of Configuration)"])
+        self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)", "2 (Export Configuration to CSV)", "3 (Paragraph of Configuration)", "4 (Export FIR Waveform Features to CSV)",
+            "5 (Export Quality Control Metrics to CSV)",
+            "6 (Export Master Consolidated Matrix [All Participants into 1 CSV])"
+        ])
         
     
     def process_request(self):
@@ -113,6 +120,68 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
                         magic_string = self.gen_magic_str(first_params)
                         self.placeholder_label.setText(magic_string)
 
+                    # elif idx == 4:
+                    #     # FIR Waveform Features Export
+                    #     fir_data = self.fir_feature_dict.get(file_path)
+                    #     if fir_data and isinstance(fir_data, dict):
+                    #         names = fir_data.get("feature_names", [])
+                    #         vals = fir_data.get("features", [])
+                    #         chans = fir_data.get("feature_channels", [])
+
+                    #         fir_df = DataFrame({
+                    #             "Feature_Name": names,
+                    #             "Channel": chans if len(chans) == len(names) else ["N/A"] * len(names),
+                    #             "Value": vals
+                    #         })
+                    #         save_path = os.path.join(output_dir, f"{base_filename}_fir_features.csv")
+                    #         fir_df.to_csv(save_path, index=False)
+                    #         success_count += 1
+
+                    # elif idx == 5:
+                    #     # Quality Control (QC) Metrics Export
+                    #     qc_data = self.qc_dict.get(file_path)
+                    #     if qc_data and isinstance(qc_data, dict):
+                    #         qc_df = DataFrame(list(qc_data.items()), columns=["Metric", "Value"])
+                    #         save_path = os.path.join(output_dir, f"{base_filename}_qc_metrics.csv")
+                    #         qc_df.to_csv(save_path, index=False)
+                    #         success_count += 1
+
+                    # elif idx == 6:
+                    #     # Master Consolidated Matrix (1 single CSV combining all selected participants)
+                    #     save_path = os.path.join(output_dir, f"{APP_NAME}_master_consolidated.csv")
+                    #     if not os.path.exists(save_path):
+                    #         master_rows: list[dict[str, Any]] = []
+                    #         for fp in selected_file_paths:
+                    #             abs_path = os.path.abspath(fp)
+                    #             grp = self.group_dict.get(fp, "Unknown")
+                    #             row: dict[str, Any] = {"Participant": abs_path, "Group": grp}
+
+                    #             # QC Metrics
+                    #             qc_info = self.qc_dict.get(fp, {})
+                    #             if isinstance(qc_info, dict):
+                    #                 for mk, mv in qc_info.items():
+                    #                     row[f"QC_{mk}"] = mv
+
+                    #             # FIR Features
+                    #             fir_info = self.fir_feature_dict.get(fp, {})
+                    #             print("1")
+                    #             if isinstance(fir_info, dict):
+                    #                 print("2")
+                    #                 f_names = fir_info.get("feature_names", [])
+                    #                 f_vals = fir_info.get("features", [])
+                    #                 print("3")
+                    #                 if len(f_names) == len(f_vals):
+                    #                     print("4")
+                    #                     for fn, fv in zip(f_names, f_vals):
+                    #                         row[f"FIR_{fn}"] = fv
+
+                    #             master_rows.append(row)
+
+                    #         if master_rows:
+                    #             df_master = DataFrame(master_rows)
+                    #             df_master.to_csv(save_path, index=False)
+                    #             success_count += 1
+
                     else:
                         print(f"No method defined for index {idx}")
                 

src/shared/shareddata.py

@@ -64,7 +64,9 @@ DATA_SCHEMA = [
     {"key": "config_dict",           "help": "Dict[file_path, dict]: Processing configuration parameters"},
     {"key": "fig_bytes_dict",        "help": "Dict[file_path, dict]: Serialized figure data"},
     {"key": "contrast_results_dict", "help": "Dict[file_path, dict]: Calculated contrast statistical results"},
-    {"key": "roi_channel_map_dict",  "help": "Dict[file_path, dict]: Calculated contrast statistical results"},
+    {"key": "roi_channel_map_dict",  "help": "Dict[file_path, dict]: ROI channel mappings"},
+    {"key": "fir_feature_dict",      "help": "Dict[file_path, dict]: Extracted FIR waveform features (features, names, channels)"},
+    {"key": "qc_dict",               "help": "Dict[file_path, dict]: Quality control metrics"},
     {"key": "valid_dict",            "help": "Dict[file_path, bool]: Boolean validity status per file"}
 ]
 

src/window/viewerlauncher.py

@@ -44,6 +44,8 @@ class ViewerLauncherWidget(QWidget):
         fig_bytes_dict: dict[str, dict[str, bytes]],
         contrast_results_dict: dict[str, dict[str, Any]],
         roi_channel_map_dict: dict[str, dict[str, str]],
+        fir_feature_dict: dict[str, dict[str, Any]],
+        qc_dict: dict[str, dict[str, Any]],
         folding_bypass: bool,
     ) -> None:
         
@@ -62,7 +64,7 @@ class ViewerLauncherWidget(QWidget):
             ("Inter-Group Stats Viewer", InterGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, roi_channel_map_dict, group_dict], True),
             ("Intra-Group Brain and Image Viewer", IntraGroupBrainImageWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
             ("Inter-Group Brain and Image Viewer", InterGroupBrainImageWidget, [haemo_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
-            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, config_dict], True)
+            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, config_dict, fir_feature_dict, qc_dict], True)
         ]
 
         layout = QVBoxLayout(self)