spacr 0.0.17__py3-none-any.whl → 0.0.20__py3-none-any.whl

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-0.0.17.dist-info/RECORD

@@ -1,34 +0,0 @@
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-spacr/__main__.py,sha256=_qRkhbFrH_cXr7AZs6KHL8Hh4VApqNdpNCtiKn2ePTo,285
-spacr/annotate_app.py,sha256=IPgZfS4TrSqbJr81P1FWUNOgCPPcS6EdQjUsXRwY-4E,19932
-spacr/cli.py,sha256=-cmIoI_E9UY_yimlMlSJDZrJGWOYwLZvnu8wU4lbC-A,12273
-spacr/core.py,sha256=r-i3EwmFXnLDidxmkWTs5-RwGZ-wy4IcnKJF5ntYf-M,109296
-spacr/graph_learning.py,sha256=IcjucYUjam8Oxck0h_pKSeyJ8ccYGniLqY-V8VUpUR8,3645
-spacr/gui_classify_app.py,sha256=vbweYUe4o4kF5aSvfHjIrAfMKq-6kFlO7otiZji1jZc,8439
-spacr/gui_mask_app.py,sha256=YSo72KqcQ3hlMwTerJmk4yS3c6Xt6Hcdc85GGluMlQE,8964
-spacr/gui_measure_app.py,sha256=157tCdhe__RViwj5pPUXP1g22HIgArAskaq5TmwIiM0,8534
-spacr/gui_sim_app.py,sha256=92pdbUb8n7hdNdPgXibtsBaMMFJTnzgdwajmzi6xsC4,8409
-spacr/gui_temp.py,sha256=pq286z2oULO6ed97YoHxv7RfdbY2enGoFQWpHC2JyH8,8473
-spacr/gui_utils.py,sha256=HlsTg98PvaM4AYEkVpqkAMbxDtneHtzogIQ01T2r3ZE,28582
-spacr/io.py,sha256=cvvAn9268jomFGfOFUtCZb1kPfvsbvmWqbvw2BMVRpw,95523
-spacr/logger.py,sha256=7Zqr3TuuOQLWT32gYr2q1qvv7x0a2JhLANmZcnBXAW8,670
-spacr/mask_app.py,sha256=B6-zYXVFg-cc58gLcz-Ry6LClO2jxLitL6B2ACb0HTw,39278
-spacr/measure.py,sha256=WFaPOysbCVM5f48NbBjBJj5JR-hZOWi4iFpai350Cqs,51366
-spacr/old_code.py,sha256=dbgDULLqhDQhB7ASWJZk3W9pm2MSA-8t-IR-mn70-mw,3280
-spacr/plot.py,sha256=9PNQNuI83SNzw3guEHGfrWJ2rCxdSP_jtO09dQaronI,54566
-spacr/sim.py,sha256=tl40lgTMeeJSyBq_c-Rn54C9Ri0FJ2zLkLLLPLSjz3o,51534
-spacr/test_annotate_app.py,sha256=yBWl_80PgP9jo1ClN0E1zSJVvzDeLCZHrlAvciS5KaY,2283
-spacr/test_plot.py,sha256=K2LhpbWtrpQ0BWhEKZOJi4E-NsmS0U8yjBdKxCwwAAc,2075
-spacr/test_train.py,sha256=qN3N6UvgeK2P-nQlG1HGgsTVZu4XYxXYI-oY7B5AioM,1217
-spacr/test_utils.py,sha256=0MUYmaqEJqUpTXKgj4mhdhUwWtzYkJLFV11T3wR826Q,1307
-spacr/timelapse.py,sha256=_j6cSVaxOhM7mTfJuNNRKogJaIGz_fM92MIegE6Ykh0,25355
-spacr/train.py,sha256=r77zLvLFMzx6MJxXG3JjynD8qTWYM9pNgrChEXYQhtY,25631
-spacr/umap.py,sha256=4QSrQ16Og-Ijq-SwguMQT2f20UWz1LE5HQeSLmzSl8c,29370
-spacr/utils.py,sha256=cyk0MMxCKCOUU3-vuGVxV9VUp0OOF7LaLs-UBCXAI3w,116764
-spacr/version.py,sha256=axH5tnGwtgSnJHb5IDhiu4Zjk5GhLyAEDRe-rnaoFOA,409
-spacr-0.0.17.dist-info/LICENSE,sha256=SR-2MeGc6SCM1UORJYyarSWY_A-JaOMFDj7ReSs9tRM,1083
-spacr-0.0.17.dist-info/METADATA,sha256=GuZ8EJR5Gxzv4mrXh4s8njEkMLty3eYGPksfh8q6yog,4108
-spacr-0.0.17.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-spacr-0.0.17.dist-info/entry_points.txt,sha256=5uyJaAxWCbjWYwP15InAKU1yFxTwyuvCGtIGceso1es,290
-spacr-0.0.17.dist-info/top_level.txt,sha256=GJPU8FgwRXGzKeut6JopsSRY2R8T3i9lDgya42tLInY,6
-spacr-0.0.17.dist-info/RECORD,,