spacr 0.0.20__py3-none-any.whl → 0.0.35__py3-none-any.whl

spacr/alpha.py

@@ -1,18 +1,295 @@
-def gui_mask():
-    from .cli import get_arg_parser
-    from .version import version_str
+from skimage import measure, feature
+from skimage.filters import gabor
+from skimage.color import rgb2gray
+from skimage.feature.texture import greycomatrix, greycoprops, local_binary_pattern
+from skimage.util import img_as_ubyte
+import numpy as np
+import pandas as pd
+from scipy.stats import skew, kurtosis, entropy, hmean, gmean, mode
+import pywt
 
-    args = get_arg_parser().parse_args()
+import os
+import pandas as pd
+from PIL import Image
+from torchvision import transforms
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+from torch_geometric.data import Data, DataLoader
+from torch_geometric.nn import GCNConv, global_mean_pool
+from torch.optim import Adam
+
+# Step 1: Data Preparation
+
+# Load images
+def load_images(image_dir):
+    images = {}
+    for filename in os.listdir(image_dir):
+        if filename.endswith(".png"):
+            img = Image.open(os.path.join(image_dir, filename))
+            images[filename] = img
+    return images
+
+# Load sequencing data
+def load_sequencing_data(seq_file):
+    seq_data = pd.read_csv(seq_file)
+    return seq_data
+
+# Step 2: Data Representation
+
+# Image Representation (Using a simple CNN for feature extraction)
+class CNNFeatureExtractor(nn.Module):
+    def __init__(self):
+        super(CNNFeatureExtractor, self).__init__()
+        self.conv1 = nn.Conv2d(3, 16, kernel_size=3, stride=1, padding=1)
+        self.conv2 = nn.Conv2d(16, 32, kernel_size=3, stride=1, padding=1)
+        self.fc = nn.Linear(32 * 8 * 8, 128)  # Assuming input images are 64x64
+
+    def forward(self, x):
+        x = F.relu(self.conv1(x))
+        x = F.max_pool2d(x, 2)
+        x = F.relu(self.conv2(x))
+        x = F.max_pool2d(x, 2)
+        x = x.view(x.size(0), -1)
+        x = self.fc(x)
+        return x
+
+# Graph Representation
+def create_graph(wells, sequencing_data):
+    nodes = []
+    edges = []
+    node_features = []
+    
+    for well in wells:
+        # Add node for each well
+        nodes.append(well)
+        
+        # Get sequencing data for the well
+        seq_info = sequencing_data[sequencing_data['well'] == well]
+        
+        # Create node features based on gene knockouts and abundances
+        features = torch.tensor(seq_info['abundance'].values, dtype=torch.float)
+        node_features.append(features)
+        
+        # Define edges (for simplicity, assume fully connected graph)
+        for other_well in wells:
+            if other_well != well:
+                edges.append((wells.index(well), wells.index(other_well)))
+    
+    edge_index = torch.tensor(edges, dtype=torch.long).t().contiguous()
+    x = torch.stack(node_features)
+    
+    data = Data(x=x, edge_index=edge_index)
+    return data
+
+# Step 3: Model Architecture
+
+class GraphTransformer(nn.Module):
+    def __init__(self, in_channels, hidden_channels, out_channels):
+        super(GraphTransformer, self).__init__()
+        self.conv1 = GCNConv(in_channels, hidden_channels)
+        self.conv2 = GCNConv(hidden_channels, hidden_channels)
+        self.fc = nn.Linear(hidden_channels, out_channels)
+        self.attention = nn.MultiheadAttention(hidden_channels, num_heads=8)
+
+    def forward(self, x, edge_index, batch):
+        x = F.relu(self.conv1(x, edge_index))
+        x = F.relu(self.conv2(x, edge_index))
+        
+        # Apply attention mechanism
+        x, _ = self.attention(x.unsqueeze(1), x.unsqueeze(1), x.unsqueeze(1))
+        x = x.squeeze(1)
+        
+        x = global_mean_pool(x, batch)
+        x = self.fc(x)
+        return x
+
+# Step 4: Training
+
+# Training Loop
+def train(model, data_loader, criterion, optimizer, epochs=10):
+    model.train()
+    for epoch in range(epochs):
+        for data in data_loader:
+            optimizer.zero_grad()
+            out = model(data.x, data.edge_index, data.batch)
+            loss = criterion(out, data.y)
+            loss.backward()
+            optimizer.step()
+        print(f'Epoch {epoch+1}, Loss: {loss.item()}')
+        
+def evaluate(model, data_loader):
+    model.eval()
+    correct = 0
+    total = 0
+    with torch.no_grad():
+        for data in data_loader:
+            out = model(data.x, data.edge_index, data.batch)
+            _, predicted = torch.max(out, 1)
+            total += data.y.size(0)
+            correct += (predicted == data.y).sum().item()
+    accuracy = correct / total
+    print(f'Accuracy: {accuracy * 100:.2f}%')
+
+def spacr_transformer(image_dir, seq_file, nr_grnas=1350, lr=0.001, mode='train'):
+    images = load_images(image_dir)
     
-    if args.version:
-        print(version_str)
-        return
+    sequencing_data = load_sequencing_data(seq_file)
+    wells = sequencing_data['well'].unique()
+    graph_data = create_graph(wells, sequencing_data)
+    model = GraphTransformer(in_channels=nr_grnas, hidden_channels=128, out_channels=nr_grnas)
+    criterion = nn.CrossEntropyLoss()
+    optimizer = Adam(model.parameters(), lr=lr)
+    data_list = [graph_data]
+    loader = DataLoader(data_list, batch_size=1, shuffle=True)
+    if mode == 'train':
+        train(model, loader, criterion, optimizer)
+    elif mode == 'eval':
+        evaluate(model, loader)
+    else:
+        raise ValueError('Invalid mode. Use "train" or "eval".')
 
-    if args.headless:
-        settings = {}
-        spacr.core.preprocess_generate_masks(settings['src'], settings=settings, advanced_settings={})
-        return
+def _calculate_glcm_features(intensity_image):
+    glcm = greycomatrix(img_as_ubyte(intensity_image), distances=[1, 2, 3, 4], angles=[0, np.pi/4, np.pi/2, 3*np.pi/4], symmetric=True, normed=True)
+    features = {}
+    for prop in ['contrast', 'dissimilarity', 'homogeneity', 'energy', 'correlation', 'ASM']:
+        for i, distance in enumerate([1, 2, 3, 4]):
+            for j, angle in enumerate([0, np.pi/4, np.pi/2, 3*np.pi/4]):
+                features[f'glcm_{prop}_d{distance}_a{angle}'] = greycoprops(glcm, prop)[i, j]
+    return features
+
+def _calculate_lbp_features(intensity_image, P=8, R=1):
+    lbp = local_binary_pattern(intensity_image, P, R, method='uniform')
+    lbp_hist, _ = np.histogram(lbp, density=True, bins=np.arange(0, P + 3), range=(0, P + 2))
+    return {f'lbp_{i}': val for i, val in enumerate(lbp_hist)}
+
+def _calculate_wavelet_features(intensity_image, wavelet='db1'):
+    coeffs = pywt.wavedec2(intensity_image, wavelet=wavelet, level=3)
+    features = {}
+    for i, coeff in enumerate(coeffs):
+        if isinstance(coeff, tuple):
+            for j, subband in enumerate(coeff):
+                features[f'wavelet_coeff_{i}_{j}_mean'] = np.mean(subband)
+                features[f'wavelet_coeff_{i}_{j}_std'] = np.std(subband)
+                features[f'wavelet_coeff_{i}_{j}_energy'] = np.sum(subband**2)
+        else:
+            features[f'wavelet_coeff_{i}_mean'] = np.mean(coeff)
+            features[f'wavelet_coeff_{i}_std'] = np.std(coeff)
+            features[f'wavelet_coeff_{i}_energy'] = np.sum(coeff**2)
+    return features
+
+
+from .measure import _estimate_blur, _calculate_correlation_object_level, _calculate_homogeneity, _periphery_intensity, _outside_intensity, _calculate_radial_distribution, _create_dataframe, _extended_regionprops_table, _calculate_correlation_object_level
+
+def _intensity_measurements(cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask, channel_arrays, settings, sizes=[3, 6, 12, 24], periphery=True, outside=True):
+    radial_dist = settings['radial_dist']
+    calculate_correlation = settings['calculate_correlation']
+    homogeneity = settings['homogeneity']
+    distances = settings['homogeneity_distances']
+    
+    intensity_props = ["label", "centroid_weighted", "centroid_weighted_local", "max_intensity", "mean_intensity", "min_intensity", "integrated_intensity"]
+    additional_props = ["standard_deviation_intensity", "median_intensity", "sum_intensity", "intensity_range", "mean_absolute_deviation_intensity", "skewness_intensity", "kurtosis_intensity", "variance_intensity", "mode_intensity", "energy_intensity", "entropy_intensity", "harmonic_mean_intensity", "geometric_mean_intensity"]
+    col_lables = ['region_label', 'mean', '5_percentile', '10_percentile', '25_percentile', '50_percentile', '75_percentile', '85_percentile', '95_percentile']
+    cell_dfs, nucleus_dfs, pathogen_dfs, cytoplasm_dfs = [], [], [], []
+    ls = ['cell','nucleus','pathogen','cytoplasm']
+    labels = [cell_mask, nucleus_mask, pathogen_mask, cytoplasm_mask]
+    dfs = [cell_dfs, nucleus_dfs, pathogen_dfs, cytoplasm_dfs]
+    
+    for i in range(0,channel_arrays.shape[-1]):
+        channel = channel_arrays[:, :, i]
+        for j, (label, df) in enumerate(zip(labels, dfs)):
+            
+            if np.max(label) == 0:
+                empty_df = pd.DataFrame()
+                df.append(empty_df)
+                continue
+                
+            mask_intensity_df = _extended_regionprops_table(label, channel, intensity_props)
+            
+            # Additional intensity properties
+            region_props = measure.regionprops_table(label, intensity_image=channel, properties=['label'])
+            intensity_values = [channel[region.coords[:, 0], region.coords[:, 1]] for region in measure.regionprops(label)]
+            additional_data = {prop: [] for prop in additional_props}
+            
+            for values in intensity_values:
+                if len(values) == 0:
+                    continue
+                additional_data["standard_deviation_intensity"].append(np.std(values))
+                additional_data["median_intensity"].append(np.median(values))
+                additional_data["sum_intensity"].append(np.sum(values))
+                additional_data["intensity_range"].append(np.max(values) - np.min(values))
+                additional_data["mean_absolute_deviation_intensity"].append(np.mean(np.abs(values - np.mean(values))))
+                additional_data["skewness_intensity"].append(skew(values))
+                additional_data["kurtosis_intensity"].append(kurtosis(values))
+                additional_data["variance_intensity"].append(np.var(values))
+                additional_data["mode_intensity"].append(mode(values)[0][0])
+                additional_data["energy_intensity"].append(np.sum(values**2))
+                additional_data["entropy_intensity"].append(entropy(values))
+                additional_data["harmonic_mean_intensity"].append(hmean(values))
+                additional_data["geometric_mean_intensity"].append(gmean(values))
+            
+            for prop in additional_props:
+                region_props[prop] = additional_data[prop]
+            
+            additional_df = pd.DataFrame(region_props)
+            mask_intensity_df = pd.concat([mask_intensity_df.reset_index(drop=True), additional_df.reset_index(drop=True)], axis=1)
+            
+            if homogeneity:
+                homogeneity_df = _calculate_homogeneity(label, channel, distances)
+                mask_intensity_df = pd.concat([mask_intensity_df.reset_index(drop=True), homogeneity_df], axis=1)
+
+            if periphery:
+                if ls[j] == 'nucleus' or ls[j] == 'pathogen':
+                    periphery_intensity_stats = _periphery_intensity(label, channel)
+                    mask_intensity_df = pd.concat([mask_intensity_df, pd.DataFrame(periphery_intensity_stats, columns=[f'periphery_{stat}' for stat in col_lables])],axis=1)
+
+            if outside:
+                if ls[j] == 'nucleus' or ls[j] == 'pathogen':
+                    outside_intensity_stats = _outside_intensity(label, channel)
+                    mask_intensity_df = pd.concat([mask_intensity_df, pd.DataFrame(outside_intensity_stats, columns=[f'outside_{stat}' for stat in col_lables])], axis=1)
+
+            # Adding GLCM features
+            glcm_features = _calculate_glcm_features(channel)
+            for k, v in glcm_features.items():
+                mask_intensity_df[f'{ls[j]}_channel_{i}_{k}'] = v
+
+            # Adding LBP features
+            lbp_features = _calculate_lbp_features(channel)
+            for k, v in lbp_features.items():
+                mask_intensity_df[f'{ls[j]}_channel_{i}_{k}'] = v
+            
+            # Adding Wavelet features
+            wavelet_features = _calculate_wavelet_features(channel)
+            for k, v in wavelet_features.items():
+                mask_intensity_df[f'{ls[j]}_channel_{i}_{k}'] = v
+
+            blur_col = [_estimate_blur(channel[label == region_label]) for region_label in mask_intensity_df['label']]
+            mask_intensity_df[f'{ls[j]}_channel_{i}_blur'] = blur_col
+
+            mask_intensity_df.columns = [f'{ls[j]}_channel_{i}_{col}' if col != 'label' else col for col in mask_intensity_df.columns]
+            df.append(mask_intensity_df)
+    
+    if radial_dist:
+        if np.max(nucleus_mask) != 0:
+            nucleus_radial_distributions = _calculate_radial_distribution(cell_mask, nucleus_mask, channel_arrays, num_bins=6)
+            nucleus_df = _create_dataframe(nucleus_radial_distributions, 'nucleus')
+            dfs[1].append(nucleus_df)
+            
+        if np.max(nucleus_mask) != 0:
+            pathogen_radial_distributions = _calculate_radial_distribution(cell_mask, pathogen_mask, channel_arrays, num_bins=6)
+            pathogen_df = _create_dataframe(pathogen_radial_distributions, 'pathogen')
+            dfs[2].append(pathogen_df)
+        
+    if calculate_correlation:
+        if channel_arrays.shape[-1] >= 2:
+            for i in range(channel_arrays.shape[-1]):
+                for j in range(i+1, channel_arrays.shape[-1]):
+                    chan_i = channel_arrays[:, :, i]
+                    chan_j = channel_arrays[:, :, j]
+                    for m, mask in enumerate(labels):
+                        coloc_df = _calculate_correlation_object_level(chan_i, chan_j, mask, settings)
+                        coloc_df.columns = [f'{ls[m]}_channel_{i}_channel_{j}_{col}' for col in coloc_df.columns]
+                        dfs[m].append(coloc_df)
+    
+    return pd.concat(cell_dfs, axis=1), pd.concat(nucleus_dfs, axis=1), pd.concat(pathogen_dfs, axis=1), pd.concat(cytoplasm_dfs, axis=1)
 
-    global vars_dict, root
-    root, vars_dict = initiate_mask_root(1000, 1500)
-    root.mainloop()

spacr/annotate_app.py

@@ -13,7 +13,7 @@ from ttkthemes import ThemedTk
 
 from .logger import log_function_call
 
-from .gui_utils import ScrollableFrame, set_default_font, set_dark_style, create_dark_mode
+from .gui_utils import ScrollableFrame, set_default_font, set_dark_style, create_dark_mode, style_text_boxes, create_menu_bar
 
 class ImageApp:
     """
@@ -38,7 +38,7 @@ class ImageApp:
     - db_update_thread (threading.Thread): A thread for updating the database.
     """
 
-    def _init_(self, root, db_path, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate'):
+    def __init__(self, root, db_path, image_type=None, channels=None, grid_rows=None, grid_cols=None, image_size=(200, 200), annotation_column='annotate'):
         """
         Initializes an instance of the ImageApp class.
 
@@ -383,7 +383,7 @@ def annotate(db, image_type=None, channels=None, geom="1000x1100", img_size=(200
     root = tk.Tk()
     root.geometry(geom)
     app = ImageApp(root, db, image_type=image_type, channels=channels, image_size=img_size, grid_rows=rows, grid_cols=columns, annotation_column=annotation_column)
-    
+    #app = ImageApp()
     next_button = tk.Button(root, text="Next", command=app.next_page)
     next_button.grid(row=app.grid_rows, column=app.grid_cols - 1)
     back_button = tk.Button(root, text="Back", command=app.previous_page)
@@ -425,7 +425,8 @@ def initiate_annotation_app_root(width, height):
     root = ThemedTk(theme=theme)
     style = ttk.Style(root)
     set_dark_style(style)
-    set_default_font(root, font_name="Arial", size=10)
+    style_text_boxes(style)
+    set_default_font(root, font_name="Arial", size=8)
     root.geometry(f"{width}x{height}")
     root.title("Annotation App")
 
@@ -473,6 +474,7 @@ def initiate_annotation_app_root(width, height):
         new_root = tk.Tk()
         new_root.geometry(f"{width}x{height}")
         new_root.title("Mask Application")
+        
 
         # Start the annotation application in the new root window
         app_instance = annotate(db, image_type, channels, annotation_column, geom, img_size, rows, columns)
@@ -482,7 +484,7 @@ def initiate_annotation_app_root(width, height):
     create_dark_mode(root, style, console_output=None)
 
     run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run", command=run_app)
-    run_button.grid(row=row, column=0, columnspan=2, pady=10)
+    run_button.grid(row=row, column=0, columnspan=2, pady=10, padx=10)
 
     return root
 

spacr/chris.py

@@ -0,0 +1,50 @@
+import pandas as pd 
+import numpy as np
+from .core import _permutation_importance, _shap_analysis
+
+def join_measurments_and_annotation(src, tables = ['cell', 'nucleus', 'pathogen','cytoplasm']):
+    
+    from .io import _read_and_merge_data, _read_db
+    
+    db_loc = [src+'/measurements/measurements.db']
+    loc = src+'/measurements/measurements.db'
+    df, _ = _read_and_merge_data(db_loc, 
+                                 tables, 
+                                 verbose=True, 
+                                 include_multinucleated=True, 
+                                 include_multiinfected=True, 
+                                 include_noninfected=True)
+    
+    paths_df = _read_db(loc, tables=['png_list'])
+
+    merged_df = pd.merge(df, paths_df[0], on='prcfo', how='left')
+
+    return merged_df
+
+def plate_heatmap(src, model_type='xgboost', variable='predictions', grouping='mean', min_max='allq', cmap='viridis', channel_of_interest=3, min_count=25, n_estimators=100, col_to_compare='col', pos='c1', neg='c2', exclude=None, n_repeats=10, clean=True, nr_to_plot=20, verbose=False, n_jobs=-1):
+    from .io import _read_and_merge_data
+    from .plot import _plot_plates
+
+    db_loc = [src+'/measurements/measurements.db']
+    tables = ['cell', 'nucleus', 'pathogen','cytoplasm']
+    include_multinucleated, include_multiinfected, include_noninfected = True, 2.0, True
+    
+    df = join_measurments_and_annotation(src, tables=['cell', 'nucleus', 'pathogen', 'cytoplasm'])
+        
+    if not channel_of_interest is None:
+        df['recruitment'] = df[f'pathogen_channel_{channel_of_interest}_mean_intensity']/df[f'cytoplasm_channel_{channel_of_interest}_mean_intensity']
+        feature_string = f'channel_{channel_of_interest}'
+    else:
+        feature_string = None
+    
+    output = _permutation_importance(df, feature_string, col_to_compare, pos, neg, exclude, n_repeats, clean, nr_to_plot, n_estimators=n_estimators, random_state=42, model_type=model_type, n_jobs=n_jobs)
+    
+    _shap_analysis(output[3], output[4], output[5])
+
+    features = output[0].select_dtypes(include=[np.number]).columns.tolist()
+
+    if not variable in features:
+        raise ValueError(f"Variable {variable} not found in the dataframe. Please choose one of the following: {features}")
+    
+    plate_heatmap = _plot_plates(output[0], variable, grouping, min_max, cmap, min_count)
+    return [output, plate_heatmap]