spacr 0.3.2__py3-none-any.whl → 0.3.22__py3-none-any.whl

spacr/utils.py

@@ -1,4 +1,4 @@
-import os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, gzip, subprocess, time, requests
+import os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, gzip, subprocess, time, requests, ast
 
 import numpy as np
 import pandas as pd
@@ -37,6 +37,7 @@ from torchvision import models
 from torchvision.models.resnet import ResNet18_Weights, ResNet34_Weights, ResNet50_Weights, ResNet101_Weights, ResNet152_Weights
 import torchvision.transforms as transforms
 from torchvision.models import resnet50
+from torchvision.utils import make_grid
 
 import seaborn as sns
 import matplotlib.pyplot as plt
@@ -66,13 +67,84 @@ from huggingface_hub import list_repo_files
 import umap.umap_ as umap
 #import umap
 
+def load_settings(csv_file_path, show=False, setting_key='setting_key', setting_value='setting_value'):
+    """
+    Convert a CSV file with 'settings_key' and 'settings_value' columns into a dictionary.
+    Handles special cases where values are lists, tuples, booleans, None, integers, floats, and nested dictionaries.
+
+    Args:
+        csv_file_path (str): The path to the CSV file.
+        show (bool): Whether to display the dataframe (for debugging).
+        setting_key (str): The name of the column that contains the setting keys.
+        setting_value (str): The name of the column that contains the setting values.
+
+    Returns:
+        dict: A dictionary where 'settings_key' are the keys and 'settings_value' are the values.
+    """
+    # Read the CSV file into a DataFrame
+    df = pd.read_csv(csv_file_path)
+
+    if show:
+        display(df)
+
+    # Ensure the columns 'setting_key' and 'setting_value' exist
+    if setting_key not in df.columns or setting_value not in df.columns:
+        raise ValueError(f"CSV file must contain {setting_key} and {setting_value} columns.")
+
+    def parse_value(value):
+        """Parse the string value into the appropriate Python data type."""
+        # Handle empty values
+        if pd.isna(value) or value == '':
+            return None
+
+        # Handle boolean values
+        if value == 'True':
+            return True
+        if value == 'False':
+            return False
+
+        # Handle lists, tuples, dictionaries, and other literals
+        if value.startswith(('(', '[', '{')):  # If it starts with (, [ or {, use ast.literal_eval
+            try:
+                parsed_value = ast.literal_eval(value)
+                # If parsed_value is a dict, recursively parse its values
+                if isinstance(parsed_value, dict):
+                    parsed_value = {k: parse_value(v) for k, v in parsed_value.items()}
+                return parsed_value
+            except (ValueError, SyntaxError):
+                pass  # If there's an error, return the value as-is
+        
+        # Handle numeric values (integers and floats)
+        try:
+            if '.' in value:
+                return float(value)  # If it contains a dot, convert to float
+            return int(value)  # Otherwise, convert to integer
+        except ValueError:
+            pass  # If it's not a valid number, return the value as-is
+
+        # Return the original value if no other type matched
+        return value
+
+    # Convert the DataFrame to a dictionary, with parsing of each value
+    result_dict = {key: parse_value(value) for key, value in zip(df[setting_key], df[setting_value])}
+
+    return result_dict
+
+
 def save_settings(settings, name='settings', show=False):
     
     settings_df = pd.DataFrame(list(settings.items()), columns=['Key', 'Value'])
     if show:
         display(settings_df)
-    settings_csv = os.path.join(settings['src'],'settings',f'{name}.csv')
-    os.makedirs(os.path.join(settings['src'],'settings'), exist_ok=True)
+    
+    if isinstance(settings['src'], list):
+        src = settings['src'][0]
+        name = f"{name}_list"
+    else:
+        src = settings['src']
+
+    settings_csv = os.path.join(src,'settings',f'{name}.csv')
+    os.makedirs(os.path.join(src,'settings'), exist_ok=True)
     settings_df.to_csv(settings_csv, index=False)
 
 def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
@@ -2987,7 +3059,6 @@ def preprocess_image(image_path, image_size=224, channels=[1,2,3], normalize=Tru
     input_tensor = transform(image).unsqueeze(0)
     return image, input_tensor
 
-
 class SaliencyMapGenerator:
     def __init__(self, model):
         self.model = model
@@ -3008,17 +3079,63 @@ class SaliencyMapGenerator:
         saliency = X.grad.abs()
         return saliency
 
-    def plot_saliency_maps(self, X, y, saliency, class_names):
+    def compute_saliency_and_predictions(self, X):
+        self.model.eval()
+        X.requires_grad_()
+
+        # Forward pass to get predictions (logits)
+        scores = self.model(X).squeeze()
+
+        # Get predicted class (0 or 1 for binary classification)
+        predictions = (scores > 0).long()
+
+        # Compute saliency maps
+        self.model.zero_grad()
+        target_scores = scores * (2 * predictions - 1)
+        target_scores.backward(torch.ones_like(target_scores))
+
+        saliency = X.grad.abs()
+
+        return saliency, predictions
+    
+    def plot_saliency_grid(self, X, saliency, predictions, mode='mean'):
         N = X.shape[0]
+        rows = (N + 7) // 8  # Ensure we can handle batches of different sizes
+        fig, axs = plt.subplots(rows, 8, figsize=(16, rows * 2))
+
         for i in range(N):
-            plt.subplot(2, N, i + 1)
-            plt.imshow(X[i].permute(1, 2, 0).cpu().numpy())
-            plt.axis('off')
-            plt.title(class_names[y[i]])
-            plt.subplot(2, N, N + i + 1)
-            plt.imshow(saliency[i].cpu().numpy(), cmap=plt.cm.hot)
-            plt.axis('off')
-        plt.gcf().set_size_inches(12, 5)
+            ax = axs[i // 8, i % 8]
+
+            if mode == 'mean':
+                saliency_map = saliency[i].mean(dim=0).cpu().numpy()  # Mean saliency over channels
+                ax.imshow(X[i].permute(1, 2, 0).detach().cpu().numpy())  # Added .detach() here
+                ax.imshow(saliency_map, cmap='jet', alpha=0.5)
+
+            elif mode == 'channel':
+                # Plot individual channels in a loop if the image has multiple channels
+                for j in range(X.shape[1]):
+                    saliency_map = saliency[i, j].cpu().numpy()
+                    ax.imshow(saliency_map, cmap='jet')
+                    ax.axis('off')
+
+            elif mode == '3-channel' and X.shape[1] == 3:
+                saliency_map = saliency[i].cpu().numpy().transpose(1, 2, 0)
+                ax.imshow(saliency_map)
+                    
+            elif mode == '2-channel' and X.shape[1] == 2:
+                saliency_map = saliency[i].cpu().numpy().transpose(1, 2, 0)
+                ax.imshow(saliency_map)
+
+            # Add class label in top-left corner
+            ax.text(5, 25, str(predictions[i].item()), fontsize=12, color='white', weight='bold',
+                    bbox=dict(facecolor='black', alpha=0.7, boxstyle='round,pad=0.2'))
+            ax.axis('off')
+
+        # Turn off unused axes
+        for j in range(N, rows * 8):
+            fig.delaxes(axs[j // 8, j % 8])
+
+        plt.tight_layout(pad=0)
         plt.show()
 
 def preprocess_image(image_path, normalize=True, image_size=224, channels=[1,2,3]):
@@ -4548,3 +4665,25 @@ def download_models(repo_id="einarolafsson/models", local_dir=None, retries=5, d
             time.sleep(delay)
 
     raise Exception("Failed to download model files after multiple attempts.")
+
+def generate_cytoplasm_mask(nucleus_mask, cell_mask):
+        
+    """
+    Generates a cytoplasm mask from nucleus and cell masks.
+    
+    Parameters:
+    - nucleus_mask (np.array): Binary or segmented mask of the nucleus (non-zero values represent nucleus).
+    - cell_mask (np.array): Binary or segmented mask of the whole cell (non-zero values represent cell).
+    
+    Returns:
+    - cytoplasm_mask (np.array): Mask for the cytoplasm (1 for cytoplasm, 0 for nucleus and pathogens).
+    """
+    
+    # Make sure the nucleus and cell masks are numpy arrays
+    nucleus_mask = np.array(nucleus_mask)
+    cell_mask = np.array(cell_mask)
+    
+    # Generate cytoplasm mask
+    cytoplasm_mask = np.where(np.logical_or(nucleus_mask != 0), 0, cell_mask)
+    
+    return cytoplasm_mask

{spacr-0.3.2.dist-info → spacr-0.3.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.3.2
+Version: 0.3.22
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -10,34 +10,41 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: torch<3.0,>=2.0
-Requires-Dist: torchvision<1.0,>=0.1
-Requires-Dist: torch-geometric<3.0,>=2.5
 Requires-Dist: numpy<2.0,>=1.26.4
-Requires-Dist: bottleneck<2.0,>=1.3.6
-Requires-Dist: numexpr<3.0,>=2.8.4
 Requires-Dist: pandas<3.0,>=2.2.1
-Requires-Dist: statsmodels<1.0,>=0.14.1
+Requires-Dist: scipy<2.0,>=1.12.0
+Requires-Dist: cellpose<4.0,>=3.0.6
 Requires-Dist: scikit-image<1.0,>=0.22.0
 Requires-Dist: scikit-learn<2.0,>=1.4.1
-Requires-Dist: seaborn<1.0,>=0.13.2
-Requires-Dist: matplotlib<4.0,>=3.8.3
-Requires-Dist: shap<1.0,>=0.45.0
-Requires-Dist: pillow<11.0,>=10.2.0
-Requires-Dist: imageio<3.0,>=2.34.0
-Requires-Dist: scipy<2.0,>=1.12.0
-Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: mahotas<2.0,>=1.4.13
 Requires-Dist: btrack<1.0,>=0.6.5
 Requires-Dist: trackpy<1.0,>=0.6.2
-Requires-Dist: cellpose<4.0,>=3.0.6
-Requires-Dist: IPython<9.0,>=8.18.1
+Requires-Dist: statsmodels<1.0,>=0.14.1
+Requires-Dist: shap<1.0,>=0.45.0
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchvision<1.0,>=0.1
+Requires-Dist: torch-geometric<3.0,>=2.5
+Requires-Dist: torchcam<1.0,>=0.4.0
+Requires-Dist: transformers<5.0,>=4.45.2
+Requires-Dist: segmentation-models-pytorch>=0.3.3
+Requires-Dist: monai>=1.3.0
+Requires-Dist: captum<1.0,>=0.7.0
+Requires-Dist: seaborn<1.0,>=0.13.2
+Requires-Dist: matplotlib<4.0,>=3.8.3
+Requires-Dist: adjustText<2.0,>=1.2.0
+Requires-Dist: bottleneck<2.0,>=1.3.6
+Requires-Dist: numexpr<3.0,>=2.8.4
 Requires-Dist: opencv-python-headless<5.0,>=4.9.0.80
+Requires-Dist: pillow<11.0,>=10.2.0
+Requires-Dist: tifffile>=2023.4.12
+Requires-Dist: nd2reader<4.0,>=3.3.0
+Requires-Dist: czifile
+Requires-Dist: imageio<3.0,>=2.34.0
+Requires-Dist: pingouin<1.0,>=0.5.5
 Requires-Dist: umap-learn<1.0,>=0.5.6
 Requires-Dist: ttkthemes<4.0,>=3.2.2
 Requires-Dist: xgboost<3.0,>=2.0.3
 Requires-Dist: PyWavelets<2.0,>=1.6.0
-Requires-Dist: torchcam<1.0,>=0.4.0
 Requires-Dist: ttf-opensans>=2020.10.30
 Requires-Dist: customtkinter<6.0,>=5.2.2
 Requires-Dist: biopython<2.0,>=1.80
@@ -50,19 +57,15 @@ Requires-Dist: tables<4.0,>=3.8.0
 Requires-Dist: rapidfuzz<4.0,>=3.9
 Requires-Dist: keyring<16.0,>=15.1
 Requires-Dist: screeninfo<1.0,>=0.8.1
-Requires-Dist: ipykernel
-Requires-Dist: gdown
 Requires-Dist: fastremap>=1.14.1
-Requires-Dist: monai>=1.3.0
 Requires-Dist: pytz>=2023.3.post1
-Requires-Dist: segmentation-models-pytorch>=0.3.3
-Requires-Dist: tifffile>=2023.4.12
 Requires-Dist: tqdm>=4.65.0
 Requires-Dist: wandb>=0.16.2
 Requires-Dist: openai<2.0,>=1.50.2
-Requires-Dist: nd2reader<4.0,>=3.3.0
-Requires-Dist: czifile
-Requires-Dist: adjustText<2.0,>=1.2.0
+Requires-Dist: gdown
+Requires-Dist: IPython<9.0,>=8.18.1
+Requires-Dist: ipykernel
+Requires-Dist: ipywidgets<9.0,>=8.1.2
 Requires-Dist: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
 Requires-Dist: pytest<3.11,>=3.9; extra == "dev"

{spacr-0.3.2.dist-info → spacr-0.3.22.dist-info}/RECORD

@@ -8,26 +8,26 @@ spacr/app_measure.py,sha256=_K7APYIeOKpV6e_LcqabBjvEi7mfq9Fch8175x1x0k8,162
 spacr/app_sequencing.py,sha256=DjG26jy4cpddnV8WOOAIiExtOe9MleVMY4MFa5uTo5w,157
 spacr/app_umap.py,sha256=ZWAmf_OsIKbYvolYuWPMYhdlVe-n2CADoJulAizMiEo,153
 spacr/cellpose.py,sha256=zv4BzhaP2O-mtQ-pUfYvpOyxgn1ke_bDWgdHD5UWm9I,13942
-spacr/core.py,sha256=KNsjpQR_L5mAABrJ4U_JMNsUMav81ILvnjL0Jf2ohU8,43858
-spacr/deep_spacr.py,sha256=HT7x_xHoM8s-AX6aSEHv4mf4wMld9PNDTgzsX-0FqO4,39416
+spacr/core.py,sha256=G_x-w7FRIHNfSOoPaIZPSf_A7mVj7PA7o9HQZ4nIu5o,48231
+spacr/deep_spacr.py,sha256=iPJhwhNQKF0_PmQ3RXi_gK7BKvIb5m54DeYZRlXBqMU,46081
 spacr/gui.py,sha256=ndmWP4F0QO5j6DM6MNzoGtzv_7Yj4LTW2SLi9URBZIQ,8055
 spacr/gui_core.py,sha256=OJQxzpehIyDzjSjIsvxSHat4NIjkqjX0VZAUQTnzEzg,40921
 spacr/gui_elements.py,sha256=3ru8FPZtXCZSj7167GJj18-Zo6TVebhAzkit-mmqmTI,135342
 spacr/gui_utils.py,sha256=76utRICvY0k_6X8CA1P_TmYBJARp4b87OkI9t39tldA,45822
-spacr/io.py,sha256=_P0Rb1ftBlheb9Yd0Bm8py_MeV2bh0ZxDlVRYOZAfBY,144579
+spacr/io.py,sha256=Xy1Drm5NPhxvwE1nyJVd2SQu3yTynlnvSrjlRuFXwBw,143371
 spacr/logger.py,sha256=lJhTqt-_wfAunCPl93xE65Wr9Y1oIHJWaZMjunHUeIw,1538
 spacr/measure.py,sha256=8MRjQdB-2n8JVLjEpF3cxvfT-Udug27uJ2ErJJ5t1ic,56000
 spacr/mediar.py,sha256=FwLvbLQW5LQzPgvJZG8Lw7GniA2vbZx6Jv6vIKu7I5c,14743
-spacr/ml.py,sha256=uf43GIxxgSasq9OiWQYnQO0fV3d5yTPEHkV78jHb-i4,42540
+spacr/ml.py,sha256=3XiQUfhhseCz9cZXhaVkCCv_qfqoZCdXGnO_p3ulwo4,47131
 spacr/openai.py,sha256=5vBZ3Jl2llYcW3oaTEXgdyCB2aJujMUIO5K038z7w_A,1246
-spacr/plot.py,sha256=kPVUlMaRSH2zZIm64o8FmhHILMCRRmzs-uFVPQEIupw,85281
+spacr/plot.py,sha256=eZcs-CQrDTENXVeMY8y8N8VZnmPePO-kAWdoaweFmW8,105540
 spacr/sequencing.py,sha256=t18mgpK6rhWuB1LtFOsPxqgpFXxuUmrD06ecsaVQ0Gw,19655
-spacr/settings.py,sha256=IaRnHXRVrkOOfA0ymavXOJTjPE56_BdOPrbEHq7oONQ,73508
+spacr/settings.py,sha256=YExChD7DWY_cJyaPGKDTpFajsXXi5ZQ8P0XR9ZQf8CE,73560
 spacr/sim.py,sha256=1xKhXimNU3ukzIw-3l9cF3Znc_brW8h20yv8fSTzvss,71173
-spacr/submodules.py,sha256=ojBFEnOZ_YTGcOvSFEAPP6J7-w08QIAFJLEPYjUCkMM,18337
+spacr/submodules.py,sha256=AB7s6-cULsaqz-haAaCtXfGEIi8uPZGT4xoCslUJC3Y,18391
 spacr/timelapse.py,sha256=FSYpUtAVy6xc3lwprRYgyDTT9ysUhfRQ4zrP9_h2mvg,39465
-spacr/toxo.py,sha256=nkV8w1wvaEsDFoSIOVvU5UcIIaTngHfgKNhhZYzBDyY,9893
-spacr/utils.py,sha256=nW4s7wy4spk3T3yYTQGLvonDz5KX6t_d0NKiHcqMPN0,193044
+spacr/toxo.py,sha256=us3pQyULtMTyfTq0MWPn4QJTTmQ6BwAJKChNf75jo3I,10082
+spacr/utils.py,sha256=brlNXsDcsKyHjJ2IodB0KyMQkEpQfMBp5QZCCb0vdz8,198459
 spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
 spacr/resources/MEDIAR/.gitignore,sha256=Ff1q9Nme14JUd-4Q3jZ65aeQ5X4uttptssVDgBVHYo8,152
 spacr/resources/MEDIAR/LICENSE,sha256=yEj_TRDLUfDpHDNM0StALXIt6mLqSgaV2hcCwa6_TcY,1065
@@ -150,9 +150,9 @@ spacr/resources/icons/umap.png,sha256=dOLF3DeLYy9k0nkUybiZMe1wzHQwLJFRmgccppw-8b
 spacr/resources/images/plate1_E01_T0001F001L01A01Z01C02.tif,sha256=Tl0ZUfZ_AYAbu0up_nO0tPRtF1BxXhWQ3T3pURBCCRo,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A02Z01C01.tif,sha256=m8N-V71rA1TT4dFlENNg8s0Q0YEXXs8slIn7yObmZJQ,7958528
 spacr/resources/images/plate1_E01_T0001F001L01A03Z01C03.tif,sha256=Pbhk7xn-KUP6RSIhJsxQcrHFImBm3GEpLkzx7WOc-5M,7958528
-spacr-0.3.2.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.3.2.dist-info/METADATA,sha256=T4leZtOLZyUy19ueD2g_TmAQdTRCbkS29QJXcVf6ciw,5837
-spacr-0.3.2.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
-spacr-0.3.2.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
-spacr-0.3.2.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.3.2.dist-info/RECORD,,
+spacr-0.3.22.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.3.22.dist-info/METADATA,sha256=wHP5zD5dSSsxLHNjlr3-OALEmhzL7gexG_uqX6M0OWc,5949
+spacr-0.3.22.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+spacr-0.3.22.dist-info/entry_points.txt,sha256=BMC0ql9aNNpv8lUZ8sgDLQMsqaVnX5L535gEhKUP5ho,296
+spacr-0.3.22.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.3.22.dist-info/RECORD,,