spacr 0.0.18__py3-none-any.whl → 0.0.21__py3-none-any.whl

{spacr-0.0.18.dist-info → spacr-0.0.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: spacr
-Version: 0.0.18
+Version: 0.0.21
 Summary: Spatial phenotype analysis of crisp screens (SpaCr)
 Home-page: https://github.com/EinarOlafsson/spacr
 Author: Einar Birnir Olafsson
@@ -9,29 +9,32 @@ Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
-Requires-Dist: torch
-Requires-Dist: torchvision
-Requires-Dist: torch-geometric
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: statsmodels
-Requires-Dist: scikit-image
-Requires-Dist: scikit-learn
-Requires-Dist: seaborn
-Requires-Dist: matplotlib
-Requires-Dist: pillow
-Requires-Dist: imageio
-Requires-Dist: scipy
-Requires-Dist: ipywidgets
-Requires-Dist: mahotas
-Requires-Dist: btrack
-Requires-Dist: trackpy
-Requires-Dist: cellpose
-Requires-Dist: IPython
-Requires-Dist: opencv-python-headless
-Requires-Dist: umap
-Requires-Dist: ttkthemes
-Requires-Dist: lxml
+Requires-Dist: torch >=2.2.1
+Requires-Dist: torchvision >=0.17.1
+Requires-Dist: torch-geometric >=2.5.1
+Requires-Dist: numpy >=1.26.4
+Requires-Dist: pandas >=2.2.1
+Requires-Dist: statsmodels >=0.14.1
+Requires-Dist: scikit-image >=0.22.0
+Requires-Dist: scikit-learn >=1.4.1
+Requires-Dist: seaborn >=0.13.2
+Requires-Dist: matplotlib >=3.8.3
+Requires-Dist: shap >=0.45.0
+Requires-Dist: pillow >=10.2.0
+Requires-Dist: imageio >=2.34.0
+Requires-Dist: scipy >=1.12.0
+Requires-Dist: ipywidgets >=8.1.2
+Requires-Dist: mahotas >=1.4.13
+Requires-Dist: btrack >=0.6.5
+Requires-Dist: trackpy >=0.6.2
+Requires-Dist: cellpose >=3.0.6
+Requires-Dist: IPython >=8.18.1
+Requires-Dist: opencv-python-headless >=4.9.0.80
+Requires-Dist: umap >=0.1.1
+Requires-Dist: ttkthemes >=3.2.2
+Requires-Dist: xgboost >=2.0.3
+Requires-Dist: PyWavelets >=1.6.0
+Requires-Dist: lxml >=5.1.0
 Provides-Extra: dev
 Requires-Dist: pytest >=3.9 ; extra == 'dev'
 Provides-Extra: full
@@ -49,7 +52,7 @@ Requires-Dist: opencv-python-headless ; extra == 'headless'
 <tr>
 <td>
   
-Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions for generating cellpose masks -> single object images and measurements -> annotation and classification of single object images. Spacr uses batch normalization to facilitate accurate segmentation of objects with low foreground representation.
+Spatial phenotype analysis of CRISPR-Cas9 screens (SpaCr). The spatial organization of organelles and proteins within cells constitutes a key level of functional regulation. In the context of infectious disease, the spatial relationships between host cell structures and intracellular pathogens are critical to understand host clearance mechanisms and how pathogens evade them. Spacr is a Python-based software package for generating single cell image data for deep-learning sub-cellular/cellular phenotypic classification from pooled genetic CRISPR-Cas9 screens. Spacr provides a flexible toolset to extract single cell images and measurements from high content cell painting experiments, train deep-learning models to classify cellular/ subcellular phenotypes, simulate and analyze pooled CRISPR-Cas9 imaging screens.
 
 </td>
 <td>
@@ -68,16 +71,18 @@ Spatial phenotype analysis of crisp screens (SpaCr). A collection of functions f
 
 - **Crop Images:** Objects (e.g. cells) can be saved as PNGs from the object area or bounding box area of each object. Object paths are saved in an sql database that can be annotated and used to train CNNs/Transformer models for classefication tasks.
 
-- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing, 
+- **Train CNNs or Transformers:** Train Torch Convolutional Neural Networks (CNNs) or Transformers to classify single object images. Train Torch models with IRM/ERM, checkpointing.
 
 - **Manual Annotation:** Supports manual annotation of single cell images and segmentation to refine training datasets for training CNNs/Transformers or cellpose, respectively.
 
 - **Finetune Cellpose Models:** Adjust pre-existing Cellpose models to your specific dataset for improved performance.
 
-- **Timelapse Data Support:** Includes support for analyzing timelapse data.
+- **Timelapse Data Support:** Track objects in timelapse image data.
 
 - **Simulations:** Simulate spatial phenotype screens.
 
+- **Misc:** Analyze Ca oscillation, recruitment, infection rate, plaque size/count.
+
 ## Installation
 
 spacr requires Tkinter for its graphical user interface features.

spacr-0.0.21.dist-info/RECORD

@@ -0,0 +1,33 @@
+spacr/__init__.py,sha256=mDi-Qu5r1vZnqIbUBV1JAoSq-mxmMEOmni1JSG2e4Wo,879
+spacr/__main__.py,sha256=_qRkhbFrH_cXr7AZs6KHL8Hh4VApqNdpNCtiKn2ePTo,285
+spacr/alpha.py,sha256=1LUtTaeVHqcTMxoCMA7mlsNYyaR0KEaXglwXsUQLwKo,13776
+spacr/annotate_app.py,sha256=jtm1HgWngv9BTsyVzdmBqg1flbmbXs9JkP6CB4wmOH8,19951
+spacr/cli.py,sha256=507jfOOEV8BoL4eeUcblvH-iiDHdBrEVJLu1ghAAPSc,1800
+spacr/core.py,sha256=_R8gXNnjf680yrnbCi2piWQUz7PDbqWYn7SL5MACLfo,156457
+spacr/foldseek.py,sha256=cWtLzvFF2O_mq5I71UMiuU9DTvDCp7wl6aaWAZRrBZc,33970
+spacr/get_alfafold_structures.py,sha256=n0g8gne-oyAV3Uo6qxZoJq5X1cUUyD8u0pOC_W2PX40,3541
+spacr/graph_learning.py,sha256=sD4eOC7Q16rr7WO20mCi_E16_LqioGUUgPamAHIIeNI,12568
+spacr/graph_learning_lap.py,sha256=MyNRLb63gsjBlui-ByZ0anHugYulL6M-OsGm8rnGBmE,3385
+spacr/gui_classify_app.py,sha256=-I06tVoA3U0jaAoTs32H1Y5ACMz6QBaEM1NEfg5w-9c,7965
+spacr/gui_mask_app.py,sha256=wb1w_-U1RTJFfRCGfdrkku4FVULSA_2gFZyVM9oQlB0,8752
+spacr/gui_measure_app.py,sha256=9mAw3Tiuq61uKTzMVslr0MgD8m1Lv5PNI0K4-gQiuXE,8061
+spacr/gui_sim_app.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+spacr/gui_utils.py,sha256=NlgGFt62yqYnusv4yT1yjPcjd-v29N4IYukkJkEdL28,30493
+spacr/io.py,sha256=gcQJ-WOzwDzRZsIzzIoMKIbhFN5AP9lYy2HCv9fG8CU,108683
+spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
+spacr/mask_app.py,sha256=B6-zYXVFg-cc58gLcz-Ry6LClO2jxLitL6B2ACb0HTw,39278
+spacr/measure.py,sha256=_f6UDugw75rILEg0uo2-QsUGUvc4AQdrdHl-BPZk74I,54686
+spacr/old_code.py,sha256=KxljHpKNsV5EfX9ifN2xJTnUeqAhyabZyfDWd5THOOc,11226
+spacr/plot.py,sha256=VtDKTJ_zo8CAVC3ILuIN_wUP6197vq089wNZuom7T8g,61655
+spacr/sim.py,sha256=2NR5hm--HVcYQnj1SCHoUCVbh_b2XUjjjfoAUIXFwnQ,72997
+spacr/timelapse.py,sha256=plPjR8nZ7_Q50VAvMvHK2TUE4F-vh7R23JnI6tSW02g,39661
+spacr/train.py,sha256=lp66dWYkiMMlgdYlMjAsJnkIZFWLizKB-xwyVnKgFBs,25904
+spacr/umap.py,sha256=4QSrQ16Og-Ijq-SwguMQT2f20UWz1LE5HQeSLmzSl8c,29370
+spacr/utils.py,sha256=r0BjycEXqr48m0xEW9o14bLPj62JNpmEUBaBwR817Bw,121205
+spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
+spacr-0.0.21.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
+spacr-0.0.21.dist-info/METADATA,sha256=u93xu8dbff0h_8p25GP5yi49sUOh7GS-axPRbik4qRk,4973
+spacr-0.0.21.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+spacr-0.0.21.dist-info/entry_points.txt,sha256=5uyJaAxWCbjWYwP15InAKU1yFxTwyuvCGtIGceso1es,290
+spacr-0.0.21.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
+spacr-0.0.21.dist-info/RECORD,,

{spacr-0.0.18.dist-info → spacr-0.0.21.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

spacr/gui_temp.py

@@ -1,212 +0,0 @@
-import sys, ctypes, csv, matplotlib
-import tkinter as tk
-from tkinter import ttk, scrolledtext
-from ttkthemes import ThemedTk
-from matplotlib.figure import Figure
-from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
-from matplotlib.figure import Figure
-matplotlib.use('Agg')
-from tkinter import filedialog
-from multiprocessing import Process, Queue, Value
-import traceback
-
-try:
-    ctypes.windll.shcore.SetProcessDpiAwareness(True)
-except AttributeError:
-    pass
-
-from .logger import log_function_call
-from .gui_utils import ScrollableFrame, StdoutRedirector, create_dark_mode, set_dark_style, set_default_font, mask_variables, generate_fields, check_mask_gui_settings, add_mask_gui_defaults, preprocess_generate_masks_wrapper, process_stdout_stderr
-from .gui_utils import safe_literal_eval, clear_canvas, main_thread_update_function
-
-thread_control = {"run_thread": None, "stop_requested": False}
-
-@log_function_call
-def initiate_abort():
-    global thread_control
-    if thread_control.get("stop_requested") is not None:
-        thread_control["stop_requested"].value = 1
-
-    if thread_control.get("run_thread") is not None:
-        thread_control["run_thread"].join(timeout=5)
-        if thread_control["run_thread"].is_alive():
-            thread_control["run_thread"].terminate()
-        thread_control["run_thread"] = None
-        
-@log_function_call
-def run_mask_gui(q, fig_queue, stop_requested):
-    global vars_dict
-    process_stdout_stderr(q)
-    try:
-        settings = check_mask_gui_settings(vars_dict)
-        settings = add_mask_gui_defaults(settings)
-        #for key in settings:
-        #    value = settings[key]
-        #    print(key, value, type(value))
-        preprocess_generate_masks_wrapper(settings, q, fig_queue)
-    except Exception as e:
-        q.put(f"Error during processing: {e}")
-        traceback.print_exc()
-    finally:
-        stop_requested.value = 1
-    
-@log_function_call
-def start_process(q, fig_queue):
-    global thread_control
-    if thread_control.get("run_thread") is not None:
-        initiate_abort()
-
-    stop_requested = Value('i', 0)  # multiprocessing shared value for inter-process communication
-    thread_control["stop_requested"] = stop_requested
-    thread_control["run_thread"] = Process(target=run_mask_gui, args=(q, fig_queue, stop_requested))
-    thread_control["run_thread"].start()
-    
-def import_settings(scrollable_frame):
-    global vars_dict, original_variables_structure
-
-    csv_file_path = filedialog.askopenfilename(filetypes=[("CSV files", "*.csv")])
-    
-    if not csv_file_path:
-        return
-    
-    imported_variables = {}
-
-    with open(csv_file_path, newline='') as csvfile:
-        reader = csv.DictReader(csvfile)
-        for row in reader:
-            key = row['Key']
-            value = row['Value']
-            # Evaluate the value safely using safe_literal_eval
-            imported_variables[key] = safe_literal_eval(value)
-
-    # Track changed variables and apply the imported ones, printing changes as we go
-    for key, var in vars_dict.items():
-        if key in imported_variables and var.get() != imported_variables[key]:
-            print(f"Updating '{key}' from '{var.get()}' to '{imported_variables[key]}'")
-            var.set(imported_variables[key])
-    
-@log_function_call
-def initiate_mask_root(width, height):
-    global root, vars_dict, q, canvas, fig_queue, canvas_widget, thread_control
-        
-    theme = 'breeze'
-    
-    if theme in ['clam']:
-        root = tk.Tk()
-        style = ttk.Style(root)
-        style.theme_use(theme) #plastik, clearlooks, elegance, default was clam #alt, breeze, arc
-        set_dark_style(style)
-    elif theme in ['breeze']:
-        root = ThemedTk(theme="breeze")
-        style = ttk.Style(root)
-        set_dark_style(style)
-        
-    set_default_font(root, font_name="Arial", size=10)
-    #root.state('zoomed')  # For Windows to maximize the window
-    root.attributes('-fullscreen', True)
-    root.geometry(f"{width}x{height}")
-    root.title("SpaCer: generate masks")
-    fig_queue = Queue()
-            
-    def _process_fig_queue():
-        global canvas
-        try:
-            while not fig_queue.empty():
-                clear_canvas(canvas)
-                fig = fig_queue.get_nowait()
-                #set_fig_text_properties(fig, font_size=8)
-                for ax in fig.get_axes():
-                    ax.set_xticks([])  # Remove x-axis ticks
-                    ax.set_yticks([])  # Remove y-axis ticks
-                    ax.xaxis.set_visible(False)  # Hide the x-axis
-                    ax.yaxis.set_visible(False)  # Hide the y-axis
-                    #ax.title.set_fontsize(14) 
-                #disable_interactivity(fig)
-                fig.tight_layout()
-                fig.set_facecolor('#333333')
-                canvas.figure = fig
-                fig_width, fig_height = canvas_widget.winfo_width(), canvas_widget.winfo_height()
-                fig.set_size_inches(fig_width / fig.dpi, fig_height / fig.dpi, forward=True)
-                canvas.draw_idle() 
-        except Exception as e:
-            traceback.print_exc()
-            #pass
-        finally:
-            canvas_widget.after(100, _process_fig_queue)
-            
-    # Process queue for console output
-    def _process_console_queue():
-        while not q.empty():
-            message = q.get_nowait()
-            console_output.insert(tk.END, message)
-            console_output.see(tk.END)
-        console_output.after(100, _process_console_queue)
-        
-    # Vertical container for settings and console
-    vertical_container = tk.PanedWindow(root, orient=tk.HORIZONTAL) #VERTICAL
-    vertical_container.pack(fill=tk.BOTH, expand=True)
-
-    # Scrollable Frame for user settings
-    scrollable_frame = ScrollableFrame(vertical_container, bg='#333333')
-    vertical_container.add(scrollable_frame, stretch="always")
-
-    # Setup for user input fields (variables)
-    variables = mask_variables()
-    vars_dict = generate_fields(variables, scrollable_frame)
-    
-    # Horizontal container for Matplotlib figure and the vertical pane (for settings and console)
-    horizontal_container = tk.PanedWindow(vertical_container, orient=tk.VERTICAL) #HORIZONTAL
-    vertical_container.add(horizontal_container, stretch="always")
-
-    # Matplotlib figure setup
-    figure = Figure(figsize=(30, 4), dpi=100, facecolor='#333333')
-    plot = figure.add_subplot(111)
-    plot.plot([], [])  # This creates an empty plot.
-    plot.axis('off')
-
-    # Embedding the Matplotlib figure in the Tkinter window
-    canvas = FigureCanvasTkAgg(figure, master=horizontal_container)
-    canvas.get_tk_widget().configure(cursor='arrow', background='#333333', highlightthickness=0)
-    #canvas.get_tk_widget().configure(cursor='arrow')
-    canvas_widget = canvas.get_tk_widget()
-    horizontal_container.add(canvas_widget, stretch="always")
-    canvas.draw()
-
-    # Console output setup below the settings
-    console_output = scrolledtext.ScrolledText(vertical_container, height=10)
-    vertical_container.add(console_output, stretch="always")
-
-    # Queue and redirection setup for updating console output safely
-    q = Queue()
-    sys.stdout = StdoutRedirector(console_output)
-    sys.stderr = StdoutRedirector(console_output)
-    
-    # This is your GUI setup where you create the Run button
-    run_button = ttk.Button(scrollable_frame.scrollable_frame, text="Run",command=lambda: start_process(q, fig_queue))
-    run_button.grid(row=40, column=0, pady=10)
-    
-    abort_button = ttk.Button(scrollable_frame.scrollable_frame, text="Abort", command=initiate_abort)
-    abort_button.grid(row=40, column=1, pady=10)
-    
-    progress_label = ttk.Label(scrollable_frame.scrollable_frame, text="Processing: 0%", background="#333333", foreground="white")
-    progress_label.grid(row=41, column=0, columnspan=2, sticky="ew", pady=(5, 0))
-    
-    # Create the Import Settings button
-    import_btn = tk.Button(root, text="Import Settings", command=lambda: import_settings(scrollable_frame))
-    import_btn.pack(pady=20)
-    
-    _process_console_queue()
-    _process_fig_queue()
-    create_dark_mode(root, style, console_output)
-    
-    root.after(100, lambda: main_thread_update_function(root, q, fig_queue, canvas_widget, progress_label))
-    
-    return root, vars_dict
-
-def gui_mask():
-    global vars_dict, root
-    root, vars_dict = initiate_mask_root(1000, 1500)
-    root.mainloop()
-
-if __name__ == "__main__":
-    gui_mask()

spacr/test_annotate_app.py

@@ -1,58 +0,0 @@
-import unittest
-from unittest.mock import MagicMock
-from annotate_app import ImageApp
-from PIL import Image
-
-class TestImageApp(unittest.TestCase):
-    def setUp(self):
-        self.root = MagicMock()
-        self.db_path = '/path/to/database.db'
-        self.image_type = 'png'
-        self.channels = ['r', 'g']
-        self.grid_rows = 2
-        self.grid_cols = 2
-        self.image_size = (200, 200)
-        self.annotation_column = 'annotate'
-        self.image_app = ImageApp(self.root, self.db_path, self.image_type, self.channels, self.grid_rows, self.grid_cols, self.image_size, self.annotation_column)
-
-    def test_normalize_image(self):
-        img = Image.open('/path/to/image.png')
-        normalized_img = self.image_app.normalize_image(img)
-        self.assertIsInstance(normalized_img, Image.Image)
-        self.assertEqual(normalized_img.mode, 'RGB')
-
-    def test_add_colored_border(self):
-        img = Image.open('/path/to/image.png')
-        border_width = 5
-        border_color = 'teal'
-        bordered_img = self.image_app.add_colored_border(img, border_width, border_color)
-        self.assertIsInstance(bordered_img, Image.Image)
-        self.assertEqual(bordered_img.mode, 'RGB')
-
-    def test_filter_channels(self):
-        img = Image.open('/path/to/image.png')
-        filtered_img = self.image_app.filter_channels(img)
-        self.assertIsInstance(filtered_img, Image.Image)
-        self.assertEqual(filtered_img.mode, 'L')
-
-    def test_load_single_image(self):
-        path_annotation_tuple = ('/path/to/image.png', 1)
-        img, annotation = self.image_app.load_single_image(path_annotation_tuple)
-        self.assertIsInstance(img, Image.Image)
-        self.assertEqual(img.mode, 'RGB')
-        self.assertEqual(annotation, 1)
-
-    def test_get_on_image_click(self):
-        path = '/path/to/image.png'
-        label = MagicMock()
-        img = Image.open('/path/to/image.png')
-        callback = self.image_app.get_on_image_click(path, label, img)
-        event = MagicMock(num=1)
-        callback(event)
-        self.assertEqual(self.image_app.pending_updates[path], 1)
-        event = MagicMock(num=3)
-        callback(event)
-        self.assertEqual(self.image_app.pending_updates[path], 2)
-
-if __name__ == '__main__':
-    unittest.main()

spacr/test_plot.py

@@ -1,43 +0,0 @@
-import unittest
-from unittest.mock import MagicMock
-from spacr.plot import _save_scimg_plot
-from unittest.mock import patch
-
-class TestSaveScimgPlot(unittest.TestCase):
-    def setUp(self):
-        self.src = "/path/to/images"
-        self.nr_imgs = 16
-        self.channel_indices = [0, 1, 2]
-        self.um_per_pixel = 0.1
-        self.scale_bar_length_um = 10
-        self.standardize = True
-        self.fontsize = 8
-        self.show_filename = True
-        self.channel_names = None
-        self.dpi = 300
-        self.plot = False
-        self.i = 1
-        self.all_folders = 1
-
-    def test_save_scimg_plot(self):
-        # Mock necessary dependencies
-        _save_figure_mock = MagicMock()
-        _visualize_scimgs_mock = MagicMock(return_value="mocked_figure")
-        _plot_images_on_grid_mock = MagicMock(return_value="mocked_figure")
-
-        # Patch the dependencies
-        with patch('spacr.plot._save_figure', _save_figure_mock), \
-             patch('spacr.plot._visualize_scimgs', _visualize_scimgs_mock), \
-             patch('spacr.plot._plot_images_on_grid', _plot_images_on_grid_mock):
-            
-            # Call the function
-            _save_scimg_plot(self.src, self.nr_imgs, self.channel_indices, self.um_per_pixel, self.scale_bar_length_um, self.standardize, self.fontsize, self.show_filename, self.channel_names, self.dpi, self.plot, self.i, self.all_folders)
-        
-        # Add your assertions here
-        _visualize_scimgs_mock.assert_called_with(self.src, self.channel_indices, self.um_per_pixel, self.scale_bar_length_um, self.show_filename, self.standardize, self.nr_imgs, self.fontsize, self.channel_names, self.plot)
-        _save_figure_mock.assert_called_with("mocked_figure", self.src, text='all_channels')
-        _plot_images_on_grid_mock.assert_called_with("mocked_figure", self.channel_indices, self.um_per_pixel, self.scale_bar_length_um, self.fontsize, self.show_filename, self.channel_names, self.plot)
-        # Add more assertions for other function calls if needed
-
-if __name__ == '__main__':
-    unittest.main()

spacr/test_train.py

@@ -1,39 +0,0 @@
-import unittest
-from unittest.mock import MagicMock
-from spacr.train import train_model
-
-class TestTrainModel(unittest.TestCase):
-    def test_train_model_erm(self):
-        # Mock necessary dependencies
-        train_loaders = [
-            MagicMock(),  # training data loader 1
-            MagicMock()   # training data loader 2
-        ]
-        val_loaders = [
-            MagicMock()   # validation data loader
-        ]
-        test_loaders = [
-            MagicMock()   # test data loader
-        ]
-
-        # Call the function
-        train_model('/path/to/save', 'model_type', train_loaders, ['loader1', 'loader2'], train_mode='erm', epochs=100, val_loaders=val_loaders, test_loaders=test_loaders)
-
-        # Add your assertions here
-        # ...
-
-    def test_train_model_irm(self):
-        # Mock necessary dependencies
-        train_loaders = [
-            MagicMock(),  # training data loader 1
-            MagicMock()   # training data loader 2
-        ]
-
-        # Call the function
-        train_model('/path/to/save', 'model_type', train_loaders, ['loader1', 'loader2'], train_mode='irm', epochs=100)
-
-        # Add your assertions here
-        # ...
-
-if __name__ == '__main__':
-    unittest.main()

spacr/test_utils.py

@@ -1,33 +0,0 @@
-import unittest
-import numpy as np
-from spacr.utils import _filter_cp_masks
-
-class TestFilterCPMasks(unittest.TestCase):
-    def test_filter_cp_masks(self):
-        # Create dummy inputs
-        masks = [np.array([[1, 1, 0], [1, 0, 0], [0, 0, 0]]), np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]])]
-        flows = [np.array([[0, 0, 0], [0, 0, 0], [0, 0, 0]])]
-        filter_size = True
-        minimum_size = 2
-        maximum_size = 5
-        remove_border_objects = True
-        merge = True
-        filter_dimm = True
-        batch = np.zeros((2, 3, 3, 3))
-        moving_avg_q1 = 0.0
-        moving_avg_q3 = 0.0
-        moving_count = 0
-        plot = False
-        figuresize = (10, 10)
-
-        # Call the function
-        filtered_masks = _filter_cp_masks(masks, flows, filter_size, minimum_size, maximum_size, remove_border_objects, merge, filter_dimm, batch, moving_avg_q1, moving_avg_q3, moving_count, plot, figuresize)
-
-        # Add your assertions here
-        self.assertEqual(len(filtered_masks), 2)
-        self.assertTrue(np.array_equal(filtered_masks[0], np.array([[1, 1, 0], [1, 0, 0], [0, 0, 0]])))
-        self.assertTrue(np.array_equal(filtered_masks[1], np.array([[1, 1, 1], [1, 1, 1], [1, 1, 1]])))
-        # Add more assertions as needed
-
-if __name__ == '__main__':
-    unittest.main()

spacr-0.0.18.dist-info/RECORD

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