spacr 0.2.4__py3-none-any.whl → 0.2.8__py3-none-any.whl

spacr/utils.py

@@ -1,4 +1,4 @@
-import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, signal
+import sys, os, re, sqlite3, torch, torchvision, random, string, shutil, cv2, tarfile, glob, psutil, platform, gzip, subprocess
 
 import numpy as np
 from cellpose import models as cp_models
@@ -87,33 +87,18 @@ from scipy.stats import f_oneway, kruskal
 from sklearn.cluster import KMeans
 from scipy import stats
 
-def print_progress_v1(files_processed, files_to_process, n_jobs, time_ls=None, batch_size=None, operation_type=""):
-    if isinstance(files_processed, list):
-        files_processed = len(files_processed)
-    if isinstance(files_to_process, list):
-        files_to_process = len(files_to_process)
-    if isinstance(batch_size, list):
-        batch_size = len(batch_size)
-
-    if time_ls is not None:
-        average_time = np.mean(time_ls) if len(time_ls) > 0 else 0
-        time_left = (((files_to_process-files_processed)*average_time)/n_jobs)/60
-        if batch_size is None:
-            print(f'Time/image: {average_time:.3f}sec')
-            print(f'Time_left: {time_left:.3f} min.')
-        else:
-            average_time_img = average_time/batch_size
-            print(f'Time/batch:{average_time:.3f}sec')
-            print(f'Time/image {average_time_img:.3f}')
-            print(f'Time_left: {time_left:.3f} min.')
-            
-    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type}')
+def save_settings(settings, name='settings'):
+    
+    settings_df = pd.DataFrame(list(settings.items()), columns=['Key', 'Value'])
+    settings_csv = os.path.join(settings['src'],'settings',f'{name}.csv')
+    os.makedirs(os.path.join(settings['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=""):
     if isinstance(files_processed, list):
-        files_processed = len(files_processed)
+        files_processed = len(set(files_processed))
     if isinstance(files_to_process, list):
-        files_to_process = len(files_to_process)
+        files_to_process = len(set(files_to_process))
     if isinstance(batch_size, list):
         batch_size = len(batch_size)
 
@@ -137,10 +122,9 @@ def print_progress(files_processed, files_to_process, n_jobs, time_ls=None, batc
         else:
             average_time_img = average_time / batch_size
             time_info = f'Time/batch: {average_time:.3f}sec, Time/image: {average_time_img:.3f}sec, Time_left: {time_left:.3f} min.'
-
-    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type} {time_info}')
-
-
+    else:
+        time_info = None
+    print(f'Progress: {files_processed}/{files_to_process}, operation_type: {operation_type}, {time_info}')
 
 def reset_mp():
     current_method = get_start_method()
@@ -1670,7 +1654,7 @@ def split_my_dataset(dataset, split_ratio=0.1):
     val_dataset = Subset(dataset, val_indices)
     return train_dataset, val_dataset
 
-def classification_metrics(all_labels, prediction_pos_probs, loader_name, loss, epoch):
+def classification_metrics(all_labels, prediction_pos_probs, loss, epoch):
     """
     Calculate classification metrics for binary classification.
 
@@ -1719,11 +1703,9 @@ def classification_metrics(all_labels, prediction_pos_probs, loader_name, loss,
     else:
         acc_nc = np.nan
     data_dict = {'accuracy': acc_all, 'neg_accuracy': acc_nc, 'pos_accuracy': acc_pc, 'loss':loss.item(),'prauc':pr_auc, 'optimal_threshold':optimal_threshold}
-    data_df = pd.DataFrame(data_dict, index=[str(epoch)+'_'+loader_name]) 
+    data_df = pd.DataFrame(data_dict, index=[str(epoch)]) 
     return data_df
     
-
-
 def compute_irm_penalty(losses, dummy_w, device):
     """
     Computes the Invariant Risk Minimization (IRM) penalty.
@@ -1761,7 +1743,7 @@ def compute_irm_penalty(losses, dummy_w, device):
 #    summary(base_model, (channels, height, width))
 #    return
 
-def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_checkpoint=False, channels=3, height=224, width=224, chan_dict=None, num_classes=2):
+def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_checkpoint=False, channels=3, height=224, width=224, chan_dict=None, num_classes=2, verbose=False):
     """
     Choose a model for classification.
 
@@ -1793,7 +1775,7 @@ def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_chec
         print(f'Invalid model_type: {model_type}. Compatible model_types: {model_types}')
         return
 
-    print(f'\rModel parameters: Architecture: {model_type} init_weights: {init_weights} dropout_rate: {dropout_rate} use_checkpoint: {use_checkpoint}', end='\r', flush=True)
+    print(f'Model parameters: Architecture: {model_type} init_weights: {init_weights} dropout_rate: {dropout_rate} use_checkpoint: {use_checkpoint}', end='\r', flush=True)
     
     if model_type == 'custom':
         
@@ -1804,8 +1786,8 @@ def choose_model(model_type, device, init_weights=True, dropout_rate=0, use_chec
     else:
         print(f'Compatible model_types: {model_types}')
         raise ValueError(f"Invalid model_type: {model_type}")
-
-    print(base_model)
+    if verbose:
+        print(base_model)
     
     return base_model
 
@@ -2989,11 +2971,13 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
     if restore_type == None:
         if model_name in ['cyto', 'cyto2', 'cyto3', 'nuclei']:
             model = cp_models.Cellpose(gpu=torch.cuda.is_available(), model_type=model_name, device=device)
-
+            return model
     else:
         if object_type == 'nucleus':
             restore = f'{type}_nuclei'
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="nuclei",restore_type=restore, chan2_restore=False, device=device)
+            return model
+
         else:
             restore = f'{type}_cyto3'
             if model_name =='cyto2':
@@ -3001,8 +2985,7 @@ def _choose_model(model_name, device, object_type='cell', restore_type=None, obj
             if model_name =='cyto':
                 chan2_restore = False
             model = denoise.CellposeDenoiseModel(gpu=torch.cuda.is_available(), model_type="cyto3",restore_type=restore, chan2_restore=chan2_restore, device=device)
-    
-    return model
+            return model
 
 class SelectChannels:
     def __init__(self, channels):
@@ -3469,7 +3452,7 @@ def setup_plot(figuresize, black_background):
     fig, ax = plt.subplots(1, 1, figsize=(figuresize, figuresize))
     return fig, ax
 
-def plot_clusters(ax, embedding, labels, colors, cluster_centers, plot_outlines, plot_points, smooth_lines, figuresize=50, dot_size=50, verbose=False):
+def plot_clusters(ax, embedding, labels, colors, cluster_centers, plot_outlines, plot_points, smooth_lines, figuresize=10, dot_size=50, verbose=False):
     unique_labels = np.unique(labels)
     for cluster_label, color, center in zip(unique_labels, colors, cluster_centers):
         cluster_data = embedding[labels == cluster_label]
@@ -3648,22 +3631,22 @@ def delete_folder(folder_path):
 def measure_test_mode(settings):    
 
     if settings['test_mode']:
-        if not os.path.basename(settings['input_folder']) == 'test':
-            all_files = os.listdir(settings['input_folder'])
+        if not os.path.basename(settings['src']) == 'test':
+            all_files = os.listdir(settings['src'])
             random_files = random.sample(all_files, settings['test_nr'])
 
-            src = os.path.join(os.path.dirname(settings['input_folder']),'test', 'merged')
+            src = os.path.join(os.path.dirname(settings['src']),'test', 'merged')
             if os.path.exists(src):
                 delete_folder(src)
             os.makedirs(src, exist_ok=True)
 
             for file in random_files:
-                shutil.copy(os.path.join(settings['input_folder'], file), os.path.join(src,file))
+                shutil.copy(os.path.join(settings['src'], file), os.path.join(src,file))
 
-            settings['input_folder'] = src
+            settings['src'] = src
             print(f'Changed source folder to {src} for test mode')
         else:
-            print(f'Test mode enabled, using source folder {settings["input_folder"]}')
+            print(f'Test mode enabled, using source folder {settings["src"]}')
 
     return settings
 
@@ -4444,3 +4427,20 @@ def correct_masks(src):
     cell_path = os.path.join(src,'norm_channel_stack', 'cell_mask_stack')
     convert_and_relabel_masks(cell_path)
     _load_and_concatenate_arrays(src, [0,1,2,3], 1, 0, 2)
+
+def count_reads_in_fastq(fastq_file):
+    count = 0
+    with gzip.open(fastq_file, "rt") as f:
+        for _ in f:
+            count += 1
+    return count // 4
+
+
+# Function to determine the CUDA version
+def get_cuda_version():
+    try:
+        output = subprocess.check_output(['nvcc', '--version'], stderr=subprocess.STDOUT).decode('utf-8')
+        if 'release' in output:
+            return output.split('release ')[1].split(',')[0].replace('.', '')
+    except (subprocess.CalledProcessError, FileNotFoundError):
+        return None

{spacr-0.2.4.dist-info → spacr-0.2.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.2.4
+Version: 0.2.8
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,43 +9,54 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: torch <3.0,>=2.2.1
-Requires-Dist: torchvision <1.0,>=0.17.1
-Requires-Dist: torch-geometric <3.0,>=2.5.1
-Requires-Dist: numpy <2.0,>=1.26.4
-Requires-Dist: pandas <3.0,>=2.2.1
-Requires-Dist: statsmodels <1.0,>=0.14.1
-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: opencv-python-headless <5.0,>=4.9.0.80
-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
-Requires-Dist: lxml <6.0,>=5.1.0
-Requires-Dist: huggingface-hub <0.25,>=0.24.0
+Requires-Dist: torch<3.0,>=2.0
+Requires-Dist: torchvision<1.0,>=0.1
+Requires-Dist: torch-geometric<3.0,>=2.5
+Requires-Dist: 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: 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: opencv-python-headless<5.0,>=4.9.0.80
+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
+Requires-Dist: lxml<6.0,>=5.1.0
+Requires-Dist: psutil<6.0,>=5.9.8
+Requires-Dist: gputil<2.0,>=1.4.0
+Requires-Dist: gpustat<2.0,>=1.1.1
+Requires-Dist: pyautogui<1.0,>=0.9.54
+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: huggingface-hub<0.25,>=0.24.0
 Provides-Extra: dev
-Requires-Dist: pytest <3.11,>=3.9 ; extra == 'dev'
+Requires-Dist: pytest<3.11,>=3.9; extra == "dev"
 Provides-Extra: full
-Requires-Dist: opencv-python ; extra == 'full'
+Requires-Dist: opencv-python; extra == "full"
 Provides-Extra: headless
-Requires-Dist: opencv-python-headless ; extra == 'headless'
+Requires-Dist: opencv-python-headless; extra == "headless"
 
 .. |Documentation Status| image:: https://readthedocs.org/projects/spacr/badge/?version=latest
    :target: https://spacr.readthedocs.io/en/latest/?badge=latest

spacr-0.2.8.dist-info/RECORD

@@ -0,0 +1,100 @@
+spacr/__init__.py,sha256=8NZIlJOY2OzRCFjXvqusFL7BfyEJwNqB2lL8QNB-Kgo,1141
+spacr/__main__.py,sha256=bkAJJD2kjIqOP-u1kLvct9jQQCeUXzlEjdgitwi1Lm8,75
+spacr/app_annotate.py,sha256=nEIL7Fle9CDKGo3sucG_03DgjUQt5W1M1IHBIpVBr08,2171
+spacr/app_classify.py,sha256=urTP_wlZ58hSyM5a19slYlBxN0PdC-9-ga0hvq8CGWc,165
+spacr/app_make_masks.py,sha256=pqDhRpluiHZz-kPX2Zh_KbYe4TsU43qYBa_7f-rsjpw,1694
+spacr/app_mask.py,sha256=l-dBY8ftzCMdDe6-pXc2Nh_u-idNL9G7UOARiLJBtds,153
+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/chris.py,sha256=YlBjSgeZaY8HPy6jkrT_ISAnCMAKVfvCxF0I9eAZLFM,2418
+spacr/core.py,sha256=B2KMyG6IrVtV9d4XQkXVblbvfFhgcMY2o-mtmqDVDic,146519
+spacr/deep_spacr.py,sha256=a2YewgkQvLV-95NYJAutnojvJmX4S8z_wv6Tb-XIgUI,34484
+spacr/graph_learning.py,sha256=1tR-ZxvXE3dBz1Saw7BeVFcrsUFu9OlUZeZVifih9eo,13070
+spacr/gui.py,sha256=RMg0bgbUpO6JwaWuNVMwuVZ18j4WlER3nW0Eaa0YZ30,7883
+spacr/gui_core.py,sha256=gTgsBzhZ5Q4vl6fT8VwrHWZ6BXWW5FNli8CE3WNMfv0,39986
+spacr/gui_elements.py,sha256=OA514FUVRKAcdu9CFVOt7UEzn1vztakQ-rDyKqV0b9A,129771
+spacr/gui_utils.py,sha256=pq_bmZ527S1j2s6McvqMhHNI05hJycBhHM8GY_jH9Ng,30597
+spacr/io.py,sha256=ZtVNbEom8X8p_KfsuWw0glGwLg6S0CfwwevDPGdfiSc,117342
+spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
+spacr/measure.py,sha256=4rmzH_a5Y0s1qALVi6YRut3xpnkJXs5vzeTPCEf3QS8,54871
+spacr/plot.py,sha256=xVnbML7WpAEzdJdrLeYRk6aPinZSiV2dLAeu4mh7n0k,73963
+spacr/sequencing.py,sha256=y7EB8226B0b0gnGXt6jqBaFVATrM1Y89v3rtHb8XR_k,75746
+spacr/settings.py,sha256=1PE6rQi0JoxbPSwEdEEWlJvrFW-dBkdY0WP461X-4FA,67839
+spacr/sim.py,sha256=FveaVgBi3eypO2oVB5Dx-v0CC1Ny7UPfXkJiiRRodAk,71212
+spacr/sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+spacr/timelapse.py,sha256=KMYCgHzf9LTZe-lWl5mvH2EjbKRE6OhpwdY13wEumGc,39504
+spacr/utils.py,sha256=2v0N1GJPqGyhxLJGSl9cGaaLQr04ehzqcOxiD-zQ1WI,189142
+spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
+spacr/resources/font/open_sans/OFL.txt,sha256=bGMoWBRrE2RcdzDiuYiB8A9OVFlJ0sA2imWwce2DAdo,4484
+"spacr/resources/font/open_sans/OpenSans-Italic-VariableFont_wdth,wght.ttf",sha256=QSoWv9h46CRX_fdlqFM3O2d3-PF3R1srnb4zUezcLm0,580280
+"spacr/resources/font/open_sans/OpenSans-VariableFont_wdth,wght.ttf",sha256=E3RLvAefD0kuT7OxShXSQrjZYA-qzUI9WM35N_6nzms,529700
+spacr/resources/font/open_sans/README.txt,sha256=-ZB4ocy30PWpgUpWm_djuTyBe_NiE1yEFG7H-zODBbA,3518
+spacr/resources/font/open_sans/static/OpenSans-Bold.ttf,sha256=vHPEXlgQoJcevq7062w13shGB9vgLaZ1f59D2Vi22l8,130860
+spacr/resources/font/open_sans/static/OpenSans-BoldItalic.ttf,sha256=tiGd9Fy-5vh25rKPZoNI4YB7H7mtEY6n1ocEHw0zI4Q,136360
+spacr/resources/font/open_sans/static/OpenSans-ExtraBold.ttf,sha256=DAeBB3dmNBMRYr5Go4JFOZBAwr7MSV6T1p2bbt1lqY0,131244
+spacr/resources/font/open_sans/static/OpenSans-ExtraBoldItalic.ttf,sha256=oDRGYhCusJ9__bySUKzNH1w-L7isv9O-iqFUmT7EPZs,136928
+spacr/resources/font/open_sans/static/OpenSans-Italic.ttf,sha256=XqvWf-PYtbXu5kUE6p5KXvdmW2Q1d-8Rfzwy_aZ80p8,136604
+spacr/resources/font/open_sans/static/OpenSans-Light.ttf,sha256=RurTiXjijzKtfcENRn7-jYtXhv-YAgw3GKKW-I738cw,130804
+spacr/resources/font/open_sans/static/OpenSans-LightItalic.ttf,sha256=TqxQLBDa9mCOU-fbhteXaYkDc-u9VHKle7y3V4m8URA,136896
+spacr/resources/font/open_sans/static/OpenSans-Medium.ttf,sha256=KrFWKUJKzobUKdvA5ae-sw0q89uZiisDpxYB7mllwzQ,130976
+spacr/resources/font/open_sans/static/OpenSans-MediumItalic.ttf,sha256=v0NvTDTSySHQ8tSZfnhUBQpg_qqJu6zGBK6JatJUyos,136796
+spacr/resources/font/open_sans/static/OpenSans-Regular.ttf,sha256=ZTBIAnfaYu_eBH6ybnin5TLRz67skWA-aNY4drlmnw0,130832
+spacr/resources/font/open_sans/static/OpenSans-SemiBold.ttf,sha256=5gMTXMOxIAxyYLNPN_nLHyF4pCs2MDfiah4YJ2q3i_A,130760
+spacr/resources/font/open_sans/static/OpenSans-SemiBoldItalic.ttf,sha256=sb8sWCggtXA9vNM5tdyXI1wUUYXQ-ruwnCJO-HIVJms,136724
+spacr/resources/font/open_sans/static/OpenSans_Condensed-Bold.ttf,sha256=CIWGlNIDGR-928YD8NguGNEEwnlBYir6S4_wzKyhK2A,130372
+spacr/resources/font/open_sans/static/OpenSans_Condensed-BoldItalic.ttf,sha256=dd_-wIDY3AM6l5T_JTYUo4D1H34Tmq5I2vEuvpqkrsQ,136240
+spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBold.ttf,sha256=98s7bdAITVn2b6nlI4tLuBkq1pSfmaFnPJELgyripT4,130812
+spacr/resources/font/open_sans/static/OpenSans_Condensed-ExtraBoldItalic.ttf,sha256=Yh7na-RGr-rH4T_uNLv6cGefmQfyALsb1Qrf4c5xp30,136652
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