microlive 1.0.11__py3-none-any.whl

microlive/gui/main.py

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+"""Entry point for MicroLive GUI application.
+
+This module provides the command-line entry point for launching
+the MicroLive graphical user interface.
+
+Usage:
+    $ microlive
+    
+Or programmatically:
+    from microlive.gui.main import main
+    main()
+"""
+
+import sys
+import os
+
+
+def main():
+    """Launch the MicroLive GUI application."""
+    # Ensure proper Qt platform on macOS
+    if sys.platform == "darwin":
+        os.environ.setdefault("QT_MAC_WANTS_LAYER", "1")
+    
+    # Import Qt after environment setup
+    from PyQt5.QtWidgets import QApplication
+    from PyQt5.QtGui import QIcon, QFont, QPalette, QColor
+    from PyQt5.QtCore import Qt
+    import matplotlib.pyplot as plt
+    
+    # Import the main application window
+    from .app import GUI
+    
+    # Get icon path
+    from ..utils.resources import get_icon_path
+    
+    # Create application
+    app = QApplication(sys.argv)
+    app.setStyle('Fusion')
+    
+    # Set modern font based on platform
+    if sys.platform == 'win32':
+        app.setFont(QFont("Segoe UI", 11))
+    elif sys.platform == 'darwin':
+        app.setFont(QFont("SF Pro", 11))
+    else:
+        app.setFont(QFont("Inter", 11))
+    
+    # Set dark matplotlib style
+    plt.style.use('dark_background')
+    
+    # Set dark palette for the application
+    palette = QPalette()
+    palette.setColor(QPalette.Window, QColor(53, 53, 53))
+    palette.setColor(QPalette.WindowText, Qt.white)
+    palette.setColor(QPalette.Base, QColor(35, 35, 35))
+    palette.setColor(QPalette.AlternateBase, QColor(53, 53, 53))
+    palette.setColor(QPalette.ToolTipBase, Qt.white)
+    palette.setColor(QPalette.ToolTipText, Qt.white)
+    palette.setColor(QPalette.Text, Qt.white)
+    palette.setColor(QPalette.Button, QColor(53, 53, 53))
+    palette.setColor(QPalette.ButtonText, Qt.white)
+    palette.setColor(QPalette.BrightText, Qt.red)
+    palette.setColor(QPalette.Highlight, QColor(142, 45, 197).lighter())
+    palette.setColor(QPalette.HighlightedText, Qt.black)
+    app.setPalette(palette)
+    
+    # Set application metadata
+    app.setApplicationName("MicroLive")
+    app.setApplicationDisplayName("MicroLive")
+    app.setOrganizationName("Zhao Lab")
+    
+    # Set application icon
+    icon_path = get_icon_path()
+    if icon_path and icon_path.exists():
+        app.setWindowIcon(QIcon(str(icon_path)))
+    
+    # Create and show main window
+    window = GUI(icon_path=icon_path)
+    window.show()
+    
+    # Run event loop
+    sys.exit(app.exec_())
+
+
+if __name__ == "__main__":
+    main()

microlive/gui/micro_mac.command

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+#!/bin/bash
+# MicroLive GUI Launcher (macOS)
+
+# Find the conda base directory
+CONDA_BASE=$(conda info --base 2>/dev/null)
+if [ -z "$CONDA_BASE" ]; then
+    echo "Conda does not appear to be installed or not in your PATH."
+    exit 1
+fi
+
+# Source conda's shell functions
+source "$CONDA_BASE/etc/profile.d/conda.sh"
+
+# Activate the 'microlive' environment
+conda activate microlive
+
+# Launch MicroLive using the pip-installed entry point
+microlive

microlive/gui/micro_windows.bat

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+@echo off
+REM =======================================================
+REM MicroLive GUI Launcher (Windows)
+REM This batch file activates the conda environment
+REM and launches MicroLive using the pip-installed entry point.
+REM =======================================================
+
+REM Check if conda is available in PATH.
+where conda >nul 2>&1
+if errorlevel 1 (
+    echo Conda does not appear to be installed or is not in your PATH.
+    pause
+    exit /b 1
+)
+
+REM Activate the 'microlive' environment.
+REM Using "call" is critical in batch files so that the script continues after activation.
+call conda activate microlive
+
+REM Launch MicroLive using the pip-installed entry point
+microlive
+
+REM Optional: Pause at the end so the window doesn't immediately close.
+pause

microlive/imports.py

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+# Import standard libraries
+import sys
+import os
+import pathlib
+import tempfile
+from pathlib import Path
+import warnings
+import getpass
+import importlib
+import random
+import time
+import math
+import socket
+import datetime
+from functools import partial, wraps
+from itertools import compress
+import io
+import traceback
+import subprocess
+import re
+import bisect
+from numba import njit, types
+from numba.typed import List as TypedList
+import cv2
+import io
+import fpdf
+import json
+
+# Import third-party libraries
+import shutil
+import urllib.request
+import gzip
+import inspect
+import numpy as np
+import pandas as pd
+import tifffile
+import matplotlib.pyplot as plt
+from matplotlib import gridspec
+from matplotlib.animation import FuncAnimation, PillowWriter
+import matplotlib.colors as mcolors
+from matplotlib_scalebar.scalebar import ScaleBar
+from matplotlib.font_manager import FontProperties
+import matplotlib.patches as patches
+from matplotlib.ticker import MaxNLocator
+from matplotlib.patches import Rectangle
+from skimage.io import imread
+from skimage.measure import regionprops
+from skimage import exposure  # for adaptive histogram equalization
+from skimage.filters import threshold_local
+from skimage.morphology import disk, binary_opening, binary_closing
+from skimage.measure import label, regionprops
+from skimage.filters import threshold_otsu
+from skimage.transform import hough_circle, hough_circle_peaks
+import openpyxl
+import bigfish.stack as stack
+from PIL import Image
+from joblib import Parallel, delayed
+from scipy.ndimage import binary_opening as binary_opening_ndi 
+from scipy.ndimage import binary_closing as binary_closing_ndi
+from scipy.ndimage import gaussian_filter, binary_dilation,gaussian_filter1d , uniform_filter1d#label
+from scipy.ndimage import label as ndi_label
+from scipy.signal import find_peaks
+from scipy.integrate import odeint, solve_ivp
+from scipy.optimize import curve_fit
+from scipy.stats import linregress, pearsonr, gaussian_kde, mannwhitneyu,ttest_ind
+from statsmodels.stats.multitest import multipletests
+from snapgene_reader import snapgene_file_to_dict, snapgene_file_to_seqrecord
+from IPython.display import Image as IPImage, display
+import ipywidgets as widgets
+import imageio
+import contextlib, io
+_f = io.StringIO()
+with contextlib.redirect_stdout(_f), contextlib.redirect_stderr(_f):
+    from cellpose import models, denoise
+import seaborn as sns
+from dna_features_viewer import GraphicFeature, GraphicRecord, CircularGraphicRecord
+from Bio.Seq import Seq
+from Bio import SeqIO
+from Bio.SeqUtils import CodonAdaptationIndex
+from Bio.SeqRecord import SeqRecord
+from typing import List
+import trackpy as tp
+tp.quiet(suppress=True)
+from PIL import Image
+from matplotlib.colors import LinearSegmentedColormap
+from matplotlib.colors import to_rgb
+
+try:
+    import torch
+except ImportError:
+    print("Warning: napari and/or napari-animation not found. Some functionality will not be available.")
+    napari = None
+
+import logging
+logging.getLogger("root").setLevel(logging.ERROR)
+
+# Suppress Cellpose verbose logging (only show warnings and errors)
+logging.getLogger('cellpose').setLevel(logging.WARNING)
+logging.getLogger('cellpose.core').setLevel(logging.WARNING)
+logging.getLogger('cellpose.models').setLevel(logging.WARNING)
+
+from mpl_toolkits.mplot3d import Axes3D  # For older versions of Matplotlib
+import matplotlib.colors as mcolors
+
+
+# Get the username
+computer_user_name = getpass.getuser()
+
+# =============================================================================
+# Package-aware imports and paths (pip packaging compatible)
+# =============================================================================
+
+# Import MicroLive modules using direct module imports (avoid circular import via __init__.py)
+from microlive.microscopy import *  # Direct module import, not through package __init__
+import microlive.microscopy as mi
+import microlive.ml_spot_detection as ML
+from microlive.utils.resources import get_icon_path, get_model_path
+
+# Get icon path (works both in development and installed modes)
+icon_file = get_icon_path()
+if icon_file is None:
+    warnings.warn("Icon file not found. Some GUI features may not display correctly.")
+
+# Load machine learning model
+try:
+    model_path = get_model_path()
+    if model_path is not None and model_path.exists():
+        model_ML = ML.ParticleDetectionCNN()
+        ML.load_model(model_ML, model_path)
+    else:
+        model_ML = None
+        warnings.warn("ML model not found. ML spot detection will not be available.")
+except Exception as e:
+    model_ML = None
+    warnings.warn(f"Error loading machine learning model: {e}")
+
+
+
+# --- Set microscope folder path based on operating system ---
+if sys.platform.startswith('win'):
+    # Windows example (adjust the path as needed)
+    microscope_folder_path = Path(f"C:/Users/{computer_user_name}/OneDrive - TheUniversityofColoradoDenver/Microscope")
+elif sys.platform.startswith('darwin'):
+    # macOS path (your original path)
+    microscope_folder_path = Path(
+        f"/Users/{computer_user_name}/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/"
+        "General - Zhao (NZ) Lab/Microscope"
+    )
+elif sys.platform.startswith('linux'):
+    # Linux example (adjust as needed)
+    microscope_folder_path = Path(f"/home/{computer_user_name}/Microscope")
+else:
+    # Fallback: use the home directory plus a default folder name
+    microscope_folder_path = Path.home() / "Microscope"
+
+# Suppress warnings
+warnings.filterwarnings("ignore")
+
+
+
+# Define a custom green colormap from black to green
+cdict_green = {
+    'red':   ((0.0, 0.0, 0.0),  # No red at any point
+              (1.0, 0.0, 0.0)),
+    'green': ((0.0, 0.0, 0.0),  # Start with no green
+              (1.0, 1.0, 1.0)), # Full green at the end
+    'blue':  ((0.0, 0.0, 0.0),  # No blue at any point
+              (1.0, 0.0, 0.0))
+}
+cdict_magenta = {
+    'red':   ((0.0, 0.0, 0.0),  # Start with no red
+              (1.0, 1.0, 1.0)), # Full red at the end
+    'green': ((0.0, 0.0, 0.0),  # No green at any point
+              (1.0, 0.0, 0.0)),
+    'blue':  ((0.0, 0.0, 0.0),  # Start with no blue
+              (1.0, 1.0, 1.0))  # Full blue at the end
+}
+cdict_red = {
+    'red':   ((0.0, 0.0, 0.0),  # Start with no red
+              (1.0, 1.0, 1.0)), # Full red at the end
+    'green': ((0.0, 0.0, 0.0),  # No green at any point
+              (1.0, 0.0, 0.0)),
+    'blue':  ((0.0, 0.0, 0.0),  # No blue at any point
+              (1.0, 0.0, 0.0))
+}
+cdict_yellow = {
+    'red':   ((0.0, 0.0, 0.0),  # Start with no red
+              (1.0, 1.0, 1.0)), # Full red at the end
+    'green': ((0.0, 0.0, 0.0),  # Start with no green
+              (1.0, 1.0, 1.0)), # Full green at the end
+    'blue':  ((0.0, 0.0, 0.0),  # No blue at any point
+              (1.0, 0.0, 0.0))
+}
+
+yellow_colormap = LinearSegmentedColormap('BlackYellow', cdict_yellow)
+red_colormap = LinearSegmentedColormap('BlackRed', cdict_red)
+green_colormap = LinearSegmentedColormap('BlackGreen', cdict_green)
+magenta_colormap = LinearSegmentedColormap('BlackMagenta', cdict_magenta)
+
+cmap_list_imagej = [green_colormap, magenta_colormap ,yellow_colormap,red_colormap]
+
+# List of colors for plotting in GUI
+color_green = (0.0, 1.0, 0.0)  # No Red, Full Green, No Blue
+color_magenta = (1.0, 0.0, 1.0)  # Full Red, No Green, Full Blue
+color_red = (1.0, 0.0, 0.0)  # Full Red, No Green, No Blue
+color_yellow = (1.0, 1.0, 0.0)  # Full Red, Full Green, No Blue
+
+list_colors_default = [ color_green, color_magenta, color_yellow, color_red]
+