M3Drop 0.4.42__py3-none-any.whl → 0.4.45__py3-none-any.whl

m3Drop/CoreCPU.py

@@ -0,0 +1,508 @@
+import time
+import psutil
+import h5py
+import numpy as np
+import anndata
+import pandas as pd
+import os
+import sys
+import pickle
+
+# [OPTIMIZATION] Use Numba for near-C++ speed on CPU
+try:
+    import numba
+    from numba import jit, prange
+except ImportError:
+    print("CRITICAL ERROR: 'numba' not found. Please install it (pip install numba) for CPU optimization.")
+    sys.exit(1)
+
+import statsmodels.api as sm
+import matplotlib.pyplot as plt
+from scipy.stats import norm
+from scipy import sparse
+from statsmodels.stats.multitest import multipletests
+
+# [FIX] Strict Relative Import
+# This ensures that if ControlDeviceCPU fails to load (e.g. missing dependency), 
+# the real error is shown instead of being masked.
+from .ControlDeviceCPU import ControlDevice
+
+# ==========================================
+#        NUMBA KERNELS (CPU OPTIMIZED)
+# ==========================================
+
+@jit(nopython=True, cache=True)
+def nan_replace_cpu(x):
+    """Replaces NaNs with 0 and Infs with 0 or 1."""
+    flat = x.ravel()
+    for i in range(flat.size):
+        val = flat[i]
+        if np.isnan(val):
+            flat[i] = 0.0
+        elif np.isinf(val):
+            flat[i] = 1.0 if val > 0 else 0.0
+    return x.reshape(x.shape)
+
+@jit(nopython=True, parallel=True, fastmath=True)
+def dropout_prob_kernel_cpu(tj, ti, total, exp_size, out_matrix):
+    """
+    Calculates dropout probabilities using Negative Binomial logic.
+    Parallelized across CPU cores.
+    """
+    rows = out_matrix.shape[0]
+    cols = out_matrix.shape[1]
+    
+    # Numba handles the broadcasting loops explicitly for max speed
+    for r in prange(rows):
+        ti_val = ti[r]
+        for c in range(cols):
+            mu = (tj[c] * ti_val) / total
+            size_val = exp_size[c]
+            
+            base = (mu / size_val) + 1.0
+            if base < 1e-12:
+                base = 1e-12
+            
+            # pow(base, -size_val)
+            val = base ** (-size_val)
+            
+            if np.isnan(val):
+                out_matrix[r, c] = 0.0
+            elif np.isinf(val):
+                out_matrix[r, c] = 1.0 if val > 0 else 0.0
+            else:
+                out_matrix[r, c] = val
+
+@jit(nopython=True, cache=True)
+def dropout_variance_inplace_cpu(p):
+    """Calculates variance p * (1 - p) in-place."""
+    flat = p.ravel()
+    for i in range(flat.size):
+        val = flat[i]
+        flat[i] = val - (val * val)
+
+# ==========================================
+#        STAGE 1: MASK GENERATION
+# ==========================================
+
+def ConvertDataSparseCPU(input_filename: str, output_mask_filename: str, mode: str = "auto", manual_target: int = 3000):
+    start_time = time.perf_counter()
+    print(f"FUNCTION: ConvertDataSparseCPU() | FILE: {input_filename}")
+
+    device = ControlDevice.from_h5ad(input_filename, mode=mode, manual_target=manual_target)
+    n_cells = device.total_rows
+    n_genes = device.n_genes
+
+    with h5py.File(input_filename, 'r') as f_in:
+        x_group_in = f_in['X']
+        print(f"Phase [1/1]: identifying expressed genes...")
+        genes_to_keep_mask = np.zeros(n_genes, dtype=bool)
+        
+        h5_indptr = x_group_in['indptr']
+        h5_indices = x_group_in['indices']
+
+        current_row = 0
+        while current_row < n_cells:
+            # Overhead 1.0 is fine for sparse scan on CPU
+            end_row = device.get_next_chunk(current_row, mode='sparse', overhead_multiplier=1.0)
+            if end_row is None or end_row <= current_row: break
+
+            chunk_size = end_row - current_row
+            print(f"Phase [1/1]: Scanning rows {end_row} of {n_cells} | Chunk: {chunk_size}", end='\r')
+
+            start_idx, end_idx = h5_indptr[current_row], h5_indptr[end_row]
+            if start_idx == end_idx:
+                current_row = end_row
+                continue
+
+            indices = h5_indices[start_idx:end_idx]
+            unique_indices = np.unique(indices)
+            genes_to_keep_mask[unique_indices] = True
+            
+            current_row = end_row
+
+        n_genes_to_keep = int(np.sum(genes_to_keep_mask))
+        print(f"\nPhase [1/1]: COMPLETE | Result: {n_genes_to_keep} / {n_genes} genes retained.")
+
+        print(f"Saving mask to {output_mask_filename}...")
+        with open(output_mask_filename, 'wb') as f:
+            pickle.dump(genes_to_keep_mask, f)
+
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.2f} seconds.\n")
+
+# ==========================================
+#        STAGE 2: STATISTICS
+# ==========================================
+
+def hidden_calc_valsCPU(filename: str, mask_filename: str, mode: str = "auto", manual_target: int = 3000) -> dict:
+    start_time = time.perf_counter()
+    print(f"FUNCTION: hidden_calc_valsCPU() | FILE: {filename}")
+
+    # 1. Load Mask
+    with open(mask_filename, 'rb') as f: mask = pickle.load(f)
+    ng_filtered = int(np.sum(mask))
+    
+    # 2. Init Device
+    with h5py.File(filename, 'r') as f:
+        indptr_cpu = f['X']['indptr'][:]
+        total_rows = len(indptr_cpu) - 1
+        
+    device = ControlDevice(
+        indptr=indptr_cpu, 
+        total_rows=total_rows, 
+        n_genes=ng_filtered, 
+        mode=mode, 
+        manual_target=manual_target
+    )
+    nc = device.total_rows
+
+    adata_meta = anndata.read_h5ad(filename, backed='r')
+    tis = np.zeros(nc, dtype='float64')
+    cell_non_zeros = np.zeros(nc, dtype='int64')
+    tjs = np.zeros(ng_filtered, dtype=np.float64)
+    gene_non_zeros = np.zeros(ng_filtered, dtype=np.int32)
+
+    print("Phase [1/2]: Calculating statistics...")
+    with h5py.File(filename, 'r') as f_in:
+        x_group = f_in['X']
+        h5_indptr = x_group['indptr']
+        h5_data = x_group['data']
+        h5_indices = x_group['indices']
+
+        current_row = 0
+        while current_row < nc:
+            end_row = device.get_next_chunk(current_row, mode='sparse', overhead_multiplier=1.1)
+            if end_row is None or end_row <= current_row: break
+
+            chunk_size = end_row - current_row
+            print(f"Phase [1/2]: Processing {end_row} of {nc} | Chunk: {chunk_size}", end='\r')
+
+            start_idx, end_idx = h5_indptr[current_row], h5_indptr[end_row]
+            data = np.array(h5_data[start_idx:end_idx], dtype=np.float64)
+            indices = np.array(h5_indices[start_idx:end_idx])
+            indptr = np.array(h5_indptr[current_row:end_row+1] - h5_indptr[current_row])
+
+            # Use Scipy CSR for CPU operations
+            chunk_csr = sparse.csr_matrix((data, indices, indptr), shape=(chunk_size, len(mask)))
+            
+            # --- VIRTUAL FILTER + CEIL ---
+            chunk_csr = chunk_csr[:, mask]
+            chunk_csr.data = np.ceil(chunk_csr.data)
+            # -----------------------------
+
+            tis[current_row:end_row] = np.array(chunk_csr.sum(axis=1)).flatten()
+            cell_non_zeros[current_row:end_row] = np.diff(chunk_csr.indptr)
+
+            # Numpy 'add.at' equivalent for sparse accumulation
+            np.add.at(tjs, chunk_csr.indices, chunk_csr.data)
+            
+            unique_indices, counts = np.unique(chunk_csr.indices, return_counts=True)
+            np.add.at(gene_non_zeros, unique_indices, counts)
+            
+            current_row = end_row
+
+    print(f"\nPhase [1/2]: COMPLETE{' ' * 50}")
+
+    print("Phase [2/2]: Finalizing stats...")
+    dis = ng_filtered - cell_non_zeros
+    djs = nc - gene_non_zeros
+    total = tjs.sum()
+    print("Phase [2/2]: COMPLETE")
+
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.2f} seconds.\n")
+
+    filtered_var_index = adata_meta.var.index[mask]
+
+    return {
+        "tis": pd.Series(tis, index=adata_meta.obs.index),
+        "tjs": pd.Series(tjs, index=filtered_var_index),
+        "dis": pd.Series(dis, index=adata_meta.obs.index),
+        "djs": pd.Series(djs, index=filtered_var_index),
+        "total": total,
+        "nc": nc,
+        "ng": ng_filtered
+    }
+
+def NBumiFitModelCPU(raw_filename: str, mask_filename: str, stats: dict, mode: str = "auto", manual_target: int = 3000) -> dict:
+    start_time = time.perf_counter()
+    print(f"FUNCTION: NBumiFitModelCPU() | FILE: {raw_filename}")
+
+    with open(mask_filename, 'rb') as f: mask = pickle.load(f)
+    ng_filtered = stats['ng']
+    
+    with h5py.File(raw_filename, 'r') as f:
+        indptr_cpu = f['X']['indptr'][:]
+        total_rows = len(indptr_cpu) - 1
+    device = ControlDevice(indptr=indptr_cpu, total_rows=total_rows, n_genes=ng_filtered, mode=mode, manual_target=manual_target)
+    nc = device.total_rows
+    
+    tjs = stats['tjs'].values
+    tis = stats['tis'].values
+    total = stats['total']
+    
+    # Numpy arrays
+    sum_x_sq = np.zeros(ng_filtered, dtype=np.float64)
+    sum_2xmu = np.zeros(ng_filtered, dtype=np.float64)
+    
+    print("Phase [1/3]: Pre-calculating sum of squared expectations...")
+    sum_tis_sq = np.sum(tis**2)
+    sum_mu_sq = (tjs**2 / total**2) * sum_tis_sq
+    print("Phase [1/3]: COMPLETE")
+    
+    print("Phase [2/3]: Calculating variance components...")
+    with h5py.File(raw_filename, 'r') as f_in:
+        x_group = f_in['X']
+        h5_indptr = x_group['indptr']
+        h5_data = x_group['data']
+        h5_indices = x_group['indices']
+        
+        current_row = 0
+        while current_row < nc:
+            # L3 optimization is critical here for CPU performance
+            end_row = device.get_next_chunk(current_row, mode='sparse', overhead_multiplier=1.1)
+            if end_row is None or end_row <= current_row: break
+            
+            chunk_size = end_row - current_row
+            print(f"Phase [2/3]: Processing {end_row} of {nc} | Chunk: {chunk_size}", end='\r')
+            
+            start_idx, end_idx = h5_indptr[current_row], h5_indptr[end_row]
+            data = np.array(h5_data[start_idx:end_idx], dtype=np.float64)
+            indices = np.array(h5_indices[start_idx:end_idx])
+            indptr = np.array(h5_indptr[current_row:end_row+1] - h5_indptr[current_row])
+            
+            chunk_csr = sparse.csr_matrix((data, indices, indptr), shape=(chunk_size, len(mask)))
+            chunk_csr = chunk_csr[:, mask]
+            chunk_csr.data = np.ceil(chunk_csr.data)
+
+            # Accumulate X^2
+            np.add.at(sum_x_sq, chunk_csr.indices, chunk_csr.data**2)
+            
+            # Vectorized term calculation for 2 * x * mu
+            # To avoid expanding dense matrices, we iterate over CSR structure manually or use broadcasting
+            # For CPU, iterating over the non-zeros is efficient enough
+            
+            # Map row indices to global cell indices
+            row_indices = np.repeat(np.arange(chunk_size), np.diff(chunk_csr.indptr)) + current_row
+            global_tis = tis[row_indices]
+            
+            term_vals = 2 * chunk_csr.data * tjs[chunk_csr.indices] * global_tis / total
+            np.add.at(sum_2xmu, chunk_csr.indices, term_vals)
+            
+            current_row = end_row
+    
+    print(f"\nPhase [2/3]: COMPLETE {' ' * 50}")
+    
+    print("Phase [3/3]: Finalizing dispersion...")
+    sum_sq_dev = sum_x_sq - sum_2xmu + sum_mu_sq
+    var_obs = sum_sq_dev / (nc - 1)
+    
+    sizes = np.full(ng_filtered, 10000.0)
+    numerator = (tjs**2 / total**2) * sum_tis_sq
+    denominator = sum_sq_dev - tjs
+    
+    stable_mask = denominator > 1e-6
+    sizes[stable_mask] = numerator[stable_mask] / denominator[stable_mask]
+    sizes[sizes <= 0] = 10000.0
+    
+    print("Phase [3/3]: COMPLETE")
+    
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.2f} seconds.\n")
+    
+    return {
+        'var_obs': pd.Series(var_obs, index=stats['tjs'].index),
+        'sizes': pd.Series(sizes, index=stats['tjs'].index),
+        'vals': stats
+    }
+
+def NBumiFitDispVsMeanCPU(fit: dict, suppress_plot=True):
+    vals = fit['vals']
+    size_g = fit['sizes'].values
+    tjs = vals['tjs'].values
+    mean_expression = tjs / vals['nc']
+    
+    forfit = (np.isfinite(size_g)) & (size_g < 1e6) & (mean_expression > 1e-3) & (size_g > 0)
+    log2_mean_expr = np.log2(mean_expression, where=(mean_expression > 0))
+    
+    higher = log2_mean_expr > 4
+    if np.sum(higher & forfit) > 2000:
+        forfit = higher & forfit
+
+    y = np.log(size_g[forfit])
+    x = np.log(mean_expression[forfit])
+    
+    X = sm.add_constant(x)
+    model = sm.OLS(y, X).fit()
+    
+    if not suppress_plot:
+        plt.figure(figsize=(7, 6))
+        plt.scatter(x, y, alpha=0.5, s=1)
+        plt.plot(x, model.fittedvalues, color='red')
+        plt.show()
+
+    return model.params
+
+def NBumiFeatureSelectionHighVarCPU(fit: dict) -> pd.DataFrame:
+    start_time = time.perf_counter()
+    print(f"FUNCTION: NBumiFeatureSelectionHighVarCPU()")
+
+    vals = fit['vals']
+    coeffs = NBumiFitDispVsMeanCPU(fit, suppress_plot=True)
+    mean_expression = vals['tjs'].values / vals['nc']
+
+    with np.errstate(divide='ignore', invalid='ignore'):
+        log_mean_expression = np.log(mean_expression)
+        log_mean_expression[np.isneginf(log_mean_expression)] = 0
+        exp_size = np.exp(coeffs[0] + coeffs[1] * log_mean_expression)
+        res = np.log(fit['sizes'].values) - np.log(exp_size)
+
+    results_df = pd.DataFrame({'Gene': fit['sizes'].index, 'Residual': res})
+    final_table = results_df.sort_values(by='Residual', ascending=True)
+    
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.4f} seconds.\n")
+    return final_table
+
+def NBumiFeatureSelectionCombinedDropCPU(
+    fit: dict, 
+    raw_filename: str, 
+    method="fdr_bh", 
+    qval_thresh=0.05, 
+    mode: str = "auto", 
+    manual_target: int = 3000
+) -> pd.DataFrame:
+    
+    start_time = time.perf_counter()
+    print(f"FUNCTION: NBumiFeatureSelectionCombinedDropCPU() | FILE: {raw_filename}")
+    
+    ng_filtered = fit['vals']['ng']
+
+    with h5py.File(raw_filename, 'r') as f:
+        indptr_cpu = f['X']['indptr'][:]
+        total_rows = len(indptr_cpu) - 1
+    device = ControlDevice(indptr=indptr_cpu, total_rows=total_rows, n_genes=ng_filtered, mode=mode, manual_target=manual_target)
+    nc = device.total_rows
+
+    print("Phase [1/3]: Initializing arrays...")
+    vals = fit['vals']
+    coeffs = NBumiFitDispVsMeanCPU(fit, suppress_plot=True)
+
+    tjs = vals['tjs'].values
+    tis = vals['tis'].values
+    total = vals['total']
+
+    mean_expression = vals['tjs'].values / nc
+    with np.errstate(divide='ignore'):
+        exp_size = np.exp(coeffs[0] + coeffs[1] * np.log(mean_expression))
+    
+    # Pre-allocate accumulators
+    p_sum = np.zeros(ng_filtered, dtype=np.float64)
+    p_var_sum = np.zeros(ng_filtered, dtype=np.float64)
+    print("Phase [1/3]: COMPLETE")
+
+    print("Phase [2/3]: Calculating dropout stats (Virtual)...")
+    
+    current_row = 0
+    while current_row < nc:
+        # Dense mode allows Numba to rip through the data
+        end_row = device.get_next_chunk(current_row, mode='dense', overhead_multiplier=1.1)
+        if end_row is None or end_row <= current_row: break
+        
+        chunk_size = end_row - current_row
+        print(f"Phase [2/3]: Processing {end_row} of {nc} | Chunk: {chunk_size}", end='\r')
+
+        tis_chunk = tis[current_row:end_row]
+        work_matrix = np.empty((chunk_size, ng_filtered), dtype=np.float64)
+        
+        # CALL NUMBA KERNEL
+        dropout_prob_kernel_cpu(
+            tjs,
+            tis_chunk,
+            total,
+            exp_size,
+            work_matrix 
+        )
+
+        p_sum += work_matrix.sum(axis=0) 
+        
+        # In-place variance calc
+        dropout_variance_inplace_cpu(work_matrix)
+        p_var_sum += work_matrix.sum(axis=0)
+        
+        current_row = end_row
+    
+    print(f"\nPhase [2/3]: COMPLETE {' ' * 50}")
+
+    print("Phase [3/3]: Statistical testing...")
+    
+    droprate_exp = p_sum / nc
+    droprate_exp_err = np.sqrt(p_var_sum / (nc**2))
+    droprate_obs = vals['djs'].values / nc
+    
+    diff = droprate_obs - droprate_exp
+    combined_err = np.sqrt(droprate_exp_err**2 + (droprate_obs * (1 - droprate_obs) / nc))
+    
+    with np.errstate(divide='ignore', invalid='ignore'):
+        Zed = diff / combined_err
+    
+    pvalue = norm.sf(Zed)
+    
+    results_df = pd.DataFrame({'Gene': vals['tjs'].index, 'p.value': pvalue, 'effect_size': diff})
+    results_df = results_df.sort_values(by='p.value')
+    
+    qval = multipletests(results_df['p.value'].fillna(1), method=method)[1]
+    results_df['q.value'] = qval
+    final_table = results_df[results_df['q.value'] < qval_thresh]
+    
+    print("Phase [3/3]: COMPLETE")
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.2f} seconds.\n")
+    
+    return final_table[['Gene', 'effect_size', 'p.value', 'q.value']]
+
+def NBumiCombinedDropVolcanoCPU(results_df: pd.DataFrame, qval_thresh=0.05, effect_size_thresh=0.25, top_n_genes=10, suppress_plot=False, plot_filename=None):
+    start_time = time.perf_counter()
+    print(f"FUNCTION: NBumiCombinedDropVolcanoCPU()")
+    
+    # Standard Matplotlib code - safe for CPU
+    df = results_df.copy()
+    if (df['q.value'] == 0).any():
+        non_zero_min = df[df['q.value'] > 0]['q.value'].min()
+        df['q.value'] = df['q.value'].replace(0, non_zero_min)
+
+    df['-log10_qval'] = -np.log10(df['q.value'])
+    df['color'] = 'grey'
+    df.loc[(df['q.value'] < qval_thresh) & (df['effect_size'] > effect_size_thresh), 'color'] = 'red'
+    df.loc[(df['q.value'] < qval_thresh) & (df['effect_size'] < -effect_size_thresh), 'color'] = 'blue'
+
+    plt.figure(figsize=(10, 8))
+    plt.scatter(df['effect_size'], df['-log10_qval'], c=df['color'], s=10, alpha=0.6, edgecolors='none')
+    
+    plt.axvline(x=effect_size_thresh, linestyle='--', color='grey', linewidth=0.8)
+    plt.axvline(x=-effect_size_thresh, linestyle='--', color='grey', linewidth=0.8)
+    plt.axhline(y=-np.log10(qval_thresh), linestyle='--', color='grey', linewidth=0.8)
+
+    top_genes = df.nsmallest(top_n_genes, 'q.value')
+    for i, row in top_genes.iterrows():
+        plt.text(row['effect_size'], row['-log10_qval'], row['Gene'], fontsize=9, fontweight='bold')
+
+    plt.title('Volcano Plot: Dropout Rate vs Significance (CPU)')
+    plt.xlabel('Effect Size (Observed - Expected Dropout Rate)')
+    plt.ylabel('-log10 (FDR Adjusted p-value)')
+    plt.grid(True, linestyle='--', alpha=0.3)
+    ax = plt.gca()
+
+    if plot_filename:
+        print(f"Saving plot to: {plot_filename}")
+        plt.savefig(plot_filename, dpi=300, bbox_inches='tight')
+        
+    if not suppress_plot:
+        plt.show()
+        
+    plt.close()
+    
+    end_time = time.perf_counter()
+    print(f"Total time: {end_time - start_time:.2f} seconds.\n")
+    return ax