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SegmentTrackSingleCycleGUI_v4_0.py
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"""This is the main window of the software to exytract and analyze bursty time series.
This is version 4.0. Since October 2021.
"""
import os
import sys
import glob
import time
import traceback
from importlib import reload
from functools import reduce
import numpy as np
import pyqtgraph as pg
import tifffile
import skimage.morphology as skmr
from PyQt5.QtCore import Qt
from PyQt5 import QtGui, QtWidgets, QtCore
from openpyxl import load_workbook
import AnalysisConverter
import NucleiDetectLog
import NucleiDetect
import NucleiSegmentStackMultiCore
import NucleiConnectMultiCore
import NucleiSpotsConnection
import MultiLoadLsmOrTif5D
import MultiLoadCzi5D
import MultiLoadLif5D
import SpotsConnection
import LabelsModify
import AnalysisSaver
import SpotsDetectionChopper
import SpotsDetection3D
import ParametersExtraction
import FalseColored3Ch
import BurstStatisticWriter
import FromTile2GlobCoordinate
import FromJournal2Fitting
import RemoveBadNuclei
import AnalysisLoader
import MultiTracePlotting_v2
import VisualNucSpot_v2
import ComprehensiveBurstAnalysisWriter
import ComprehensiveActivationWriter
import RemoveShortTraces2
import MergeXlsFiles
import WriteSteadySpotsBursting
import MultiColorIntensityGenerator
import WriteSptsIntsMinusBkg
import WriteSptsIntsDividedByBkg
import AvSpotsTime
import TimeavSptsIntensity
import SpatialDividedByBkg
import PopUpTool
import GalleryDividedByBackground
import CalibrationSpatial
import RescueFunctions
import SpotTracker
import VisualTracked
import TracesImage
class MainWindow(QtWidgets.QMainWindow):
"""Main windows: coordinates all the actions, algorithms, visualization tools and analysis tools"""
def __init__(self, parent=None):
QtWidgets.QMainWindow.__init__(self, parent)
widget = QtWidgets.QWidget(self)
self.setCentralWidget(widget)
exit_action = QtWidgets.QAction(QtGui.QIcon('Icons/exit.png'), '&Exit', self)
exit_action.setShortcut('Ctrl+Q')
exit_action.setStatusTip("Exit application")
exit_action.triggered.connect(self.close)
multiload_action = QtWidgets.QAction(QtGui.QIcon('Icons/load-hi.png'), "&Load data file", self)
multiload_action.setShortcut('Ctrl+L')
multiload_action.setStatusTip("Load .tif, .lsm, .czi or .lif files: if they are more than one, they will be concatenate")
multiload_action.triggered.connect(self.load_several_files)
load_analysis_action = QtWidgets.QAction(QtGui.QIcon('Icons/load-hi.png'), "&Load analysis", self)
load_analysis_action.setShortcut('Ctrl+A')
load_analysis_action.setStatusTip("Load analysis")
load_analysis_action.triggered.connect(self.load_analysis)
save_action = QtWidgets.QAction(QtGui.QIcon('Icons/save-md.png'), "&Save analysis", self)
save_action.setShortcut('Ctrl+S')
save_action.setStatusTip("Save analysis")
save_action.triggered.connect(self.find_zero_in_mtss)
rescue_analysis_action = QtWidgets.QAction(QtGui.QIcon('Icons/float-blisters.png'), "&Rescue analysis", self)
rescue_analysis_action.setShortcut('Ctrl+K')
rescue_analysis_action.setStatusTip("Rescue analysis")
rescue_analysis_action.triggered.connect(self.rescue_analysis)
popup_nuclei_raw_action = QtWidgets.QAction("&Pop-up Raw Nuclei", self)
popup_nuclei_raw_action.setStatusTip("Generate figures with the raw nuclei data")
popup_nuclei_raw_action.triggered.connect(self.popup_nuclei_raw)
popup_nuclei_detected_action = QtWidgets.QAction("&Pop-up Detected Nuclei", self)
popup_nuclei_detected_action.setStatusTip("Generate figures with the detected nuclei")
popup_nuclei_detected_action.triggered.connect(self.popup_nuclei_detected)
popup_nuclei_segmented_action = QtWidgets.QAction("&Pop-up Segmented Nuclei", self)
popup_nuclei_segmented_action.setStatusTip("Generate figures with the detected nuclei")
popup_nuclei_segmented_action.triggered.connect(self.popup_nuclei_segmented)
popup_nuclei_tracked_action = QtWidgets.QAction("&Pop-up Tracked Nuclei", self)
popup_nuclei_tracked_action.setStatusTip("Generate figures with the tracked nuclei")
popup_nuclei_tracked_action.triggered.connect(self.popup_nuclei_trackeded)
popup_spots_raw_action = QtWidgets.QAction("&Pop-up Raw Spots", self)
popup_spots_raw_action.setStatusTip("Generate figures with the raw spots")
popup_spots_raw_action.triggered.connect(self.popup_spots_raw)
popup_spots_segm_action = QtWidgets.QAction("&Pop-up Segmented Spots", self)
popup_spots_segm_action.setStatusTip("Generate figures with the segmented spots")
popup_spots_segm_action.triggered.connect(self.popup_spots_segm)
popup_nucactive_action = QtWidgets.QAction(QtGui.QIcon('Icons/popup.png'), "&Pop-up Active Nuclei", self)
popup_nucactive_action.setStatusTip("Generate a figure with the active nuclei map")
popup_nucactive_action.triggered.connect(self.popup_nucactive)
del_frame_action = QtWidgets.QAction(QtGui.QIcon('Icons/delete_frame.png'), "&Delete Current Frame", self)
del_frame_action.setStatusTip("Delete the current frame from raw data")
del_frame_action.triggered.connect(self.del_frame)
roi_crop_action = QtWidgets.QAction(QtGui.QIcon('Icons/crop.png'), "&Crop Stack", self)
roi_crop_action.setStatusTip("Define a ROI to crop data stack")
roi_crop_action.triggered.connect(self.roi_crop)
activ_dynamic_fitting_action = QtWidgets.QAction("&Activation Dynamic", self)
activ_dynamic_fitting_action.setStatusTip("Perform an analysis on the dynamic of nuclei activation")
activ_dynamic_fitting_action.triggered.connect(self.act_dynamic_study)
test_spots_detection_action = QtWidgets.QAction(QtGui.QIcon('Icons/sccpre.png'), "&Test Spots Detection", self)
test_spots_detection_action.setStatusTip("Test the spots detection on a sample of your data")
test_spots_detection_action.triggered.connect(self.test_spots_detection)
test_nuclei_detection_action = QtWidgets.QAction(QtGui.QIcon('Icons/sccpre.png'), "&Test Nuclei Detection", self)
test_nuclei_detection_action.setStatusTip("Test the nuclei detection on a sample of your data")
test_nuclei_detection_action.triggered.connect(self.test_nuclei_detection)
test_nuclei_detection_action.setShortcut("Ctrl+N")
spatial_comprehensive_action = QtWidgets.QAction(QtGui.QIcon('Icons/geo_pin.jpg'), "&Spatial Comprehensive", self)
spatial_comprehensive_action.setStatusTip('Perform a comprehensive spatial analysis for bursting')
spatial_comprehensive_action.triggered.connect(self.spatial_comprehensive)
spatial_comprehensive_action.setShortcut('Ctrl+H')
single_nucleus_action = QtWidgets.QAction(QtGui.QIcon('Icons/plot_single_trace.png'), "&Single Nucleus Inspection", self)
single_nucleus_action.setStatusTip('Perform a comprehensive spatial analysis for bursting')
single_nucleus_action.triggered.connect(self.single_nucleus)
single_nucleus_action.setShortcut('Ctrl+B')
multi_plot_show_action = QtWidgets.QAction(QtGui.QIcon('Icons/plot_multi_trace.png'), "&Show Multi Plot", self)
multi_plot_show_action.setStatusTip("Inspection of All Spots Traces")
multi_plot_show_action.triggered.connect(self.multi_plot_show)
multi_plot_show_action.setShortcut('Ctrl+M')
set_color_channel_action = QtWidgets.QAction(QtGui.QIcon('Icons/set_channels.png'), "&Set Channels Numbers", self)
set_color_channel_action.setStatusTip("&Set Channels Numbers")
set_color_channel_action.triggered.connect(self.set_color_channel)
multi_color_intensity_action = QtWidgets.QAction(QtGui.QIcon('Icons/multi_color_icon.png'), "&Multi Color Intensity", self)
multi_color_intensity_action.setStatusTip("Visualize spots intensity as color on nuclei")
multi_color_intensity_action.triggered.connect(self.multi_color_intensity)
multi_color_intensity_action.setShortcut('Ctrl+Y')
spts_intensity_minus_bkg_action = QtWidgets.QAction(QtGui.QIcon('Icons/background_remove.jpg'), "&Spots Remove Bkg", self)
spts_intensity_minus_bkg_action.setStatusTip("Write an .xls file with the intensity of the spots minus the background")
spts_intensity_minus_bkg_action.triggered.connect(self.spts_intensity_minus_bkg)
timeav_spts_intensity_action = QtWidgets.QAction(QtGui.QIcon('Icons/clessidra.svg'), "&Time Average Spots by Bkg", self)
timeav_spts_intensity_action.setStatusTip("Write an .xls file with the average time intensity of the spots normalized by the background")
timeav_spts_intensity_action.triggered.connect(self.timeav_spts_intensity)
timeav_spts_intensity_action.setShortcut('Ctrl+E')
check_saturation_action = QtWidgets.QAction(QtGui.QIcon('Icons/check_saturation.png'), "&Check Saturation", self)
check_saturation_action.setStatusTip('Inspection of All Spots Traces')
check_saturation_action.triggered.connect(self.check_saturation)
calibration_spatial_action = QtWidgets.QAction(QtGui.QIcon('Icons/caliber.png'), '&Traces Calibration', self)
calibration_spatial_action.setStatusTip("Shows the gallery of the spots spatially selected divided by the background")
calibration_spatial_action.triggered.connect(self.calibration_spatial)
traces_image_action = QtWidgets.QAction(QtGui.QIcon('Icons/foot_traces.png'), '&Traces Image', self)
traces_image_action.setStatusTip("Plot the traces as a image, even pooling togheter several analyses")
traces_image_action.triggered.connect(self.traces_image)
rmv_mitoticalTS_action = QtWidgets.QAction(QtGui.QIcon('Icons/eraser.png'), '&Remove Mitotical TS', self)
rmv_mitoticalTS_action.setStatusTip("Pop up tool to remove mitotical spots")
rmv_mitoticalTS_action.triggered.connect(self.rmv_mitoticalTS)
rmv_mitoticalTS_action.setShortcut('Ctrl+U')
# sisters_split_action = QtWidgets.QAction(QtGui.QIcon('Icons/sisters_split.png'), '&Allele Split', self)
# sisters_split_action.setStatusTip("Split the sister chromatine tracking")
# sisters_split_action.triggered.connect(self.sisters_split)
# sisters_split_action.setShortcut('Ctrl+G')
remove_nucsdust_action = QtWidgets.QAction(QtGui.QIcon('Icons/duster.png'), '&Remove Nuclear Dust', self)
remove_nucsdust_action.setStatusTip("Remove small objects detected in the nuclei channel")
remove_nucsdust_action.triggered.connect(self.remove_nucsdust)
remove_nucsdust_action.setShortcut('Ctrl+O')
analysis_conversion_action = QtWidgets.QAction('&Analysis Converter', self)
analysis_conversion_action.setStatusTip("Convert analysis 3.3 -> 4.0")
analysis_conversion_action.triggered.connect(self.analysis_conversion)
self.statusBar()
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(multiload_action)
fileMenu.addAction(save_action)
fileMenu.addAction(load_analysis_action)
fileMenu.addAction(rescue_analysis_action)
fileMenu.addAction(exit_action)
modifyMenu = menubar.addMenu('&Modify')
modifyMenu.addAction(roi_crop_action)
modifyMenu.addAction(del_frame_action)
modifyMenu.addAction(set_color_channel_action)
modifyMenu.addAction(rmv_mitoticalTS_action)
modifyMenu.addAction(remove_nucsdust_action)
testMenu = menubar.addMenu('&Test Analysis')
testMenu.addAction(test_nuclei_detection_action)
testMenu.addAction(test_spots_detection_action)
checkMenu = menubar.addMenu('&Check Data')
checkMenu.addAction(check_saturation_action)
posterioriMenu = menubar.addMenu('&Post Processing')
posterioriMenu.addAction(spatial_comprehensive_action)
posterioriMenu.addAction(single_nucleus_action)
posterioriMenu.addAction(multi_plot_show_action)
posterioriMenu.addAction(multi_color_intensity_action)
posterioriMenu.addAction(spts_intensity_minus_bkg_action)
posterioriMenu.addAction(timeav_spts_intensity_action)
posterioriMenu.addAction(calibration_spatial_action)
posterioriMenu.addAction(traces_image_action)
# posterioriMenu.addAction(sisters_split_action)
popupMenu = menubar.addMenu('&PopUp')
popup_nuclei = popupMenu.addMenu(QtGui.QIcon('Icons/popup.png'), "PopUp Nuclei")
popup_nuclei.addAction(popup_nuclei_raw_action)
popup_nuclei.addAction(popup_nuclei_detected_action)
popup_nuclei.addAction(popup_nuclei_segmented_action)
popup_nuclei.addAction(popup_nuclei_tracked_action)
popup_spots = popupMenu.addMenu(QtGui.QIcon('Icons/popup.png'), "PopUp Spots")
popup_spots.addAction(popup_spots_raw_action)
popup_spots.addAction(popup_spots_segm_action)
popupMenu.addAction(popup_nucactive_action)
momentaryMenu = menubar.addMenu("&Temporary")
momentaryMenu.addAction(activ_dynamic_fitting_action)
momentaryMenu.addAction(analysis_conversion_action)
# helpMenu = menubar.addMenu('&Help')
frame1 = pg.ImageView(self)
frame1.ui.roiBtn.hide()
frame1.ui.menuBtn.hide()
frame2 = pg.ImageView(self)
frame2.ui.roiBtn.hide()
frame2.ui.menuBtn.hide()
frame2.ui.histogram.hide()
frame3 = pg.ImageView(self)
frame3.ui.roiBtn.hide()
frame3.ui.menuBtn.hide()
frame4 = pg.ImageView(self)
frame4.ui.roiBtn.hide()
frame4.ui.menuBtn.hide()
frame4.ui.histogram.hide()
fname_edt = QtWidgets.QLineEdit(self)
fname_edt.setToolTip('Name of the file you are working on')
sld1 = QtWidgets.QSlider(QtCore.Qt.Horizontal, self)
sld1.valueChanged.connect(self.sld1_update)
start_cut_btn = QtWidgets.QPushButton("Start", self)
start_cut_btn.clicked.connect(self.start_cut)
start_cut_btn.setToolTip('Select the first frame to consider')
start_cut_btn.setFixedSize(50, 25)
end_cut_btn = QtWidgets.QPushButton("End", self)
end_cut_btn.clicked.connect(self.end_cut)
end_cut_btn.setToolTip('Select the last frame to consider')
end_cut_btn.setFixedSize(50, 25)
reload_cut_btn = QtWidgets.QPushButton("Reload", self)
reload_cut_btn.clicked.connect(self.reload_files)
reload_cut_btn.setToolTip('Reload selected files')
reload_cut_btn.setFixedSize(110, 25)
auto_run_btn = QtWidgets.QPushButton("Auto Run", self)
auto_run_btn.clicked.connect(self.auto_run)
auto_run_btn.setToolTip('Run all the unsupervised analysis in a row')
auto_run_btn.setFixedSize(110, 25)
auto_run_btn.setEnabled(False)
auto_run_tggl = QtWidgets.QCheckBox('Enable Auto', self)
auto_run_tggl.stateChanged.connect(self.auto_run_enable)
auto_run_tggl.setFixedSize(110, 25)
nuc_detect_btn = QtWidgets.QPushButton("N-Detect", self)
nuc_detect_btn.clicked.connect(self.nuclei_detection)
nuc_detect_btn.setToolTip('Nuclei detection')
nuc_detect_btn.setFixedSize(110, 25)
param_detect_lbl = QtWidgets.QLabel("Gauss Size", self)
param_detect_lbl.setFixedSize(60, 25)
param_detect_edt = QtWidgets.QLineEdit(self)
param_detect_edt.textChanged[str].connect(self.param_detect_var)
param_detect_edt.setToolTip('Sets the size of the Gaussian Filter for the pre-smoothing (1.5) or for the logharitmic detection (0.995 - 1.005)')
param_detect_edt.setFixedSize(35, 25)
param_detect_box = QtWidgets.QHBoxLayout()
param_detect_box.addWidget(param_detect_lbl)
param_detect_box.addWidget(param_detect_edt)
gaus_log_detect_combo = QtWidgets.QComboBox(self)
gaus_log_detect_combo.addItem("Gauss Flt")
gaus_log_detect_combo.addItem("Log Flt")
gaus_log_detect_combo.setCurrentIndex(0)
gaus_log_detect_combo.setToolTip('Switch between a linear nuclei detection and a logaritmic nuclei detection')
gaus_log_detect_combo.activated[str].connect(self.gaus_log_detect)
nuc_segment_btn = QtWidgets.QPushButton("N-Segment", self)
nuc_segment_btn.clicked.connect(self.nuclei_segmentation)
nuc_segment_btn.setToolTip('Nuclei Segmentation')
nuc_segment_btn.setFixedSize(110, 25)
gfilt_water_lbl = QtWidgets.QLabel('W-Shed', self)
gfilt_water_lbl.setFixedSize(60, 25)
gfilt_water_edt = QtWidgets.QLineEdit(self)
gfilt_water_edt.textChanged[str].connect(self.gfilt_water_var)
gfilt_water_edt.setToolTip('Sets the size parameter for the Water Shed algorithm, suggested value 7')
gfilt_water_edt.setFixedSize(35, 25)
circ_thr_lbl = QtWidgets.QLabel('Circ Thr', self)
circ_thr_lbl.setFixedSize(60, 25)
circ_thr_edt = QtWidgets.QLineEdit(self)
circ_thr_edt.textChanged[str].connect(self.circ_thr_var)
circ_thr_edt.setToolTip('Circularity Threshold of the detected nuclei, suggested value is 0.65')
circ_thr_edt.setFixedSize(35, 25)
modify_segm_btn = QtWidgets.QPushButton("Modify Segm", self)
modify_segm_btn.clicked.connect(self.modify_tool)
modify_segm_btn.setToolTip('Modify Nuclei Segmentation')
modify_segm_btn.setFixedSize(110, 25)
nuc_track_btn = QtWidgets.QPushButton("N-Track", self)
nuc_track_btn.clicked.connect(self.nuclei_tracking)
nuc_track_btn.setToolTip('Nuclei Tracking')
nuc_track_btn.setFixedSize(110, 25)
dist_thr_lbl = QtWidgets.QLabel('Dist Thr', self)
dist_thr_lbl.setFixedSize(60, 25)
dist_thr_edt = QtWidgets.QLineEdit(self)
dist_thr_edt.textChanged[str].connect(self.dist_thr_var)
dist_thr_edt.setToolTip('Distance threshold to track nuclei; suggested value 10')
dist_thr_edt.setFixedSize(35, 25)
spots_thr_lbl = QtWidgets.QLabel('Spots Thr', self)
spots_thr_lbl.setFixedSize(60, 25)
spots_thr_edt = QtWidgets.QLineEdit(self)
spots_thr_edt.textChanged[str].connect(self.spots_thr_var)
spots_thr_edt.setToolTip('Intensity threshold to segment spots: it is expressed in terms of standard deviation, suggested value 7')
spots_thr_edt.setFixedSize(35, 25)
volume_thr_lbl = QtWidgets.QLabel('Vol Thr', self)
volume_thr_lbl.setFixedSize(60, 25)
volume_thr_edt = QtWidgets.QLineEdit(self)
volume_thr_edt.textChanged[str].connect(self.volume_thr_var)
volume_thr_edt.setToolTip('Threshold volume on spot detection: suggested value 5')
volume_thr_edt.setFixedSize(35, 25)
spots_detect_btn = QtWidgets.QPushButton("S-Detect", self)
spots_detect_btn.clicked.connect(self.spots_detect)
spots_detect_btn.setToolTip('Spots Detection')
spots_detect_btn.setFixedSize(110, 25)
spots_visual_btn = QtWidgets.QPushButton("Visualize Spots", self)
spots_visual_btn.clicked.connect(self.spots_visual)
spots_visual_btn.setToolTip('Updates Spots Detection')
spots_visual_btn.setFixedSize(110, 25)
nuc_spots_conn_btn = QtWidgets.QPushButton("S-N Connect", self)
nuc_spots_conn_btn.clicked.connect(self.nuc_spots_conn)
nuc_spots_conn_btn.setToolTip('Connect Spots to Nuclei')
nuc_spots_conn_btn.setFixedSize(110, 25)
fake_coloured_time_btn = QtWidgets.QPushButton("False Clrs Time", self)
fake_coloured_time_btn.clicked.connect(self.fake_coloured_time)
fake_coloured_time_btn.setToolTip('Generate false coloured movie with time information')
fake_coloured_time_btn.setFixedSize(110, 25)
time_step_lbl = QtWidgets.QLabel('T Step', self)
time_step_lbl.setFixedSize(50, 25)
time_step_edt = QtWidgets.QLineEdit(self)
time_step_edt.textChanged[str].connect(self.time_step_var)
time_step_edt.setToolTip('Duration in seconds of the time step')
time_step_edt.setFixedSize(55, 25)
busy_lbl = QtWidgets.QLabel("Ready")
busy_lbl.setStyleSheet('color: green')
busy_box = QtWidgets.QHBoxLayout()
busy_box.addWidget(busy_lbl)
busy_box.addStretch()
time_lbl = QtWidgets.QLabel("time " + '0', self)
time_lbl.setFixedSize(110, 13)
frame_numb_lbl = QtWidgets.QLabel("frame " + '0', self)
frame_numb_lbl.setFixedSize(110, 13)
hor_line_one = QtWidgets.QFrame()
hor_line_one.setFrameStyle(QtWidgets.QFrame.HLine)
hor_line_two = QtWidgets.QFrame()
hor_line_two.setFrameStyle(QtWidgets.QFrame.HLine)
cut_box_h = QtWidgets.QHBoxLayout()
cut_box_h.addWidget(start_cut_btn)
cut_box_h.addWidget(end_cut_btn)
cut_box = QtWidgets.QVBoxLayout()
cut_box.addLayout(cut_box_h)
cut_box.addWidget(reload_cut_btn)
h1box = QtWidgets.QHBoxLayout()
h1box.addWidget(frame1)
h1box.addWidget(frame2)
h2box = QtWidgets.QHBoxLayout()
h2box.addWidget(frame3)
h2box.addWidget(frame4)
v2box = QtWidgets.QVBoxLayout()
v2box.addWidget(fname_edt)
v2box.addLayout(h1box)
v2box.addLayout(h2box)
v2box.addWidget(sld1)
v2box.addLayout(busy_box)
key_ver1 = QtWidgets.QVBoxLayout()
key_ver1.addWidget(hor_line_one)
key_ver1.addWidget(auto_run_tggl)
key_ver1.addWidget(auto_run_btn)
key_ver1.addWidget(hor_line_two)
key_ver1.addLayout(param_detect_box)
key_ver1.addWidget(gaus_log_detect_combo)
key_ver1.addWidget(nuc_detect_btn)
key_ver1.addStretch()
gseg_hor = QtWidgets.QHBoxLayout()
gseg_hor.addWidget(gfilt_water_lbl)
gseg_hor.addWidget(gfilt_water_edt)
circ_thr_hor = QtWidgets.QHBoxLayout()
circ_thr_hor.addWidget(circ_thr_lbl)
circ_thr_hor.addWidget(circ_thr_edt)
key_ver2 = QtWidgets.QVBoxLayout()
key_ver2.addLayout(gseg_hor)
key_ver2.addLayout(circ_thr_hor)
key_ver2.addWidget(nuc_segment_btn)
key_ver2.addStretch()
dist_thr_hor = QtWidgets.QHBoxLayout()
dist_thr_hor.addWidget(dist_thr_lbl)
dist_thr_hor.addWidget(dist_thr_edt)
key_modifing = QtWidgets.QVBoxLayout()
key_modifing.addWidget(modify_segm_btn)
key_ver3 = QtWidgets.QVBoxLayout()
key_ver3.addLayout(dist_thr_hor)
key_ver3.addWidget(nuc_track_btn)
key_ver3.addStretch()
spots_thr_hor = QtWidgets.QHBoxLayout()
spots_thr_hor.addWidget(spots_thr_lbl)
spots_thr_hor.addWidget(spots_thr_edt)
volume_thr_hor = QtWidgets.QHBoxLayout()
volume_thr_hor.addWidget(volume_thr_lbl)
volume_thr_hor.addWidget(volume_thr_edt)
key_ver4 = QtWidgets.QVBoxLayout()
key_ver4.addLayout(spots_thr_hor)
key_ver4.addLayout(volume_thr_hor)
key_ver4.addWidget(spots_detect_btn)
key_ver4.addStretch()
key_ver4.addWidget(nuc_spots_conn_btn)
key_ver4.addWidget(spots_visual_btn)
key_ver4.addWidget(fake_coloured_time_btn)
key_time_step = QtWidgets.QHBoxLayout()
key_time_step.addWidget(time_step_lbl)
key_time_step.addWidget(time_step_edt)
key_tot = QtWidgets.QVBoxLayout()
key_tot.addLayout(cut_box)
key_tot.addStretch()
key_tot.addLayout(key_ver1)
key_tot.addLayout(key_ver2)
key_tot.addLayout(key_modifing)
key_tot.addLayout(key_ver3)
key_tot.addStretch()
key_tot.addLayout(key_ver4)
key_tot.addStretch()
key_tot.addLayout(key_time_step)
key_tot.addWidget(time_lbl)
key_tot.addWidget(frame_numb_lbl)
layout = QtWidgets.QHBoxLayout(widget)
layout.addLayout(v2box)
layout.addLayout(key_tot)
mycmap = np.fromfile("mycmap.bin", "uint16").reshape((10000, 3)) # / 255.0
self.colors4map = []
for k in range(mycmap.shape[0]):
self.colors4map.append(mycmap[k, :])
self.colors4map[0] = np.array([0, 0, 0])
self.frame1 = frame1
self.frame2 = frame2
self.frame3 = frame3
self.frame4 = frame4
self.fname_edt = fname_edt
self.sld1 = sld1
self.nuc_segment_btn = nuc_segment_btn
self.auto_run_btn = auto_run_btn
self.nuc_detect_btn = nuc_detect_btn
self.gfilt_water_lbl = gfilt_water_lbl
self.gfilt_water_edt = gfilt_water_edt
self.circ_thr_lbl = circ_thr_lbl
self.circ_thr_edt = circ_thr_edt
self.modify_segm_btn = modify_segm_btn
self.nuc_track_btn = nuc_track_btn
self.dist_thr_lbl = dist_thr_lbl
self.dist_thr_edt = dist_thr_edt
self.spots_thr_edt = spots_thr_edt
self.volume_thr_edt = volume_thr_edt
self.volume_thr_lbl = volume_thr_lbl
self.spots_detect_btn = spots_detect_btn
self.param_detect_lbl = param_detect_lbl
self.param_detect_edt = param_detect_edt
self.gaus_log_detect_combo = gaus_log_detect_combo
self.time_step_edt = time_step_edt
self.gaus_log_detect_value = "Gauss Flt"
self.data_flag = 0
self.labbs_flag = 0
self.nuclei_flag = 0
self.nuclei_t_visual_flag = 0
self.spots_segm_flag = 0
self.spots_trk_flag = 0
self.start_cut_value = 0
self.end_cut_value = 0
self.bm_dm_am = 0
self.log_flag = 0
self.nucs_spts_ch = np.array([1, 0])
self.busy_lbl = busy_lbl
self.t_track_end_value = 0
self.time_lbl = time_lbl
self.frame_numb_lbl = frame_numb_lbl
self.software_version = "SegmentTrackSingleCycleGUI_v4.0"
self.setGeometry(100, 100, 1200, 800)
self.setWindowTitle(self.software_version)
self.setWindowIcon(QtGui.QIcon('Icons/MLL_Logo2.png'))
self.show()
def closeEvent(self, event):
"Close the GUI, asking confirmation"
quit_msg = "Are you sure you want to exit the program?"
reply = QtWidgets.QMessageBox.question(self, 'Message', quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
if reply == QtWidgets.QMessageBox.Yes:
event.accept()
else:
event.ignore()
def busy_indicator(self):
"""Write a red text (BUSY) as a label on the GUI (bottom left)"""
self.busy_lbl.setText("Busy")
self.busy_lbl.setStyleSheet('color: red')
def ready_indicator(self):
"""Write a green text (READY) as a label on the GUI (bottom left)"""
self.busy_lbl.setText("Ready")
self.busy_lbl.setStyleSheet('color: green')
def auto_run_enable(self, state):
"""Enable the possibility to run all the unsupervised part in a row"""
if state == QtCore.Qt.Checked:
self.auto_run_btn.setEnabled(True)
self.nuc_detect_btn.setEnabled(False)
self.nuc_segment_btn.setEnabled(False)
self.spots_detect_btn.setEnabled(False)
else:
self.auto_run_btn.setEnabled(False)
self.nuc_detect_btn.setEnabled(True)
self.nuc_segment_btn.setEnabled(True)
self.spots_detect_btn.setEnabled(True)
def roi_crop(self):
"""Call CroppingTool Tool"""
self.mpp8 = CroppingTool(self.filedata.imarray_red, self.filedata.imarray_green)
self.mpp8.show()
self.mpp8.procStart.connect(self.crop_tool_sgnl)
def load_several_files(self):
"""Load, concatenate and visualize raw data to start the analysis"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
self.fnames = QtWidgets.QFileDialog.getOpenFileNames(None, "Select czi (or lsm) data files to concatenate...", filter="*.lsm *.czi *.tif *.lif")[0]
if str(self.fnames[0])[-3:] == 'lsm' or str(self.fnames[0])[-3:] == 'tif':
self.filedata = MultiLoadLsmOrTif5D.MultiLoadLsmOrTif5D(self.fnames, self.nucs_spts_ch)
self.time_step_edt.setText(str(self.filedata.time_step_value))
if str(self.fnames[0])[-3:] == 'czi':
self.filedata = MultiLoadCzi5D.MultiProcLoadCzi5D(self.fnames, self.nucs_spts_ch)
self.time_step_edt.setText(str(self.filedata.time_step_value))
if str(self.fnames[0])[-3:] == 'lif':
self.filedata = MultiLoadLif5D.MultiLoadLif5D(self.fnames, self.nucs_spts_ch)
self.time_step_edt.setText(str(self.filedata.time_step_value))
self.frame1.setImage(self.filedata.imarray_red[0, :, :])
self.frame3.setImage(self.filedata.imarray_green[0, :, :])
self.data_flag = 1
self.sld1.setMaximum(self.filedata.imarray_red.shape[0] - 1)
self.sld1.setValue(0)
joined_fnames = ' '
for s in range(len(self.fnames)):
joined_fnames += str(self.fnames[s]) + ' ----- '
self.fname_edt.setText(joined_fnames)
except Exception:
traceback.print_exc()
self.ready_indicator()
def load_analysis(self):
"""Load an already done analysis"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
foldername = str(QtWidgets.QFileDialog.getExistingDirectory(None, "Select the folder with the analyzed data"))
self.fname_edt.setText(foldername)
app.processEvents()
app.processEvents()
self.filedata = AnalysisLoader.RawData(foldername)
self.spots_3D = AnalysisLoader.SpotsIntsVol(foldername)
self.features_3D = AnalysisLoader.Features(foldername)
self.nucs_spts_ch = np.fromfile(foldername + '/nucs_spts_ch.bin', "uint16")
self.nuclei_tracked = np.load(foldername + '/nuclei_tracked.npy')
self.labbs = np.sign(self.nuclei_tracked)
# wb = open_workbook(foldername + '/journal.xls')
wb = load_workbook(foldername + '/journal.xlsx')
s_wb = wb.worksheets[0]
# if s_wb.col(1)[1].value == "Log Flt":
if s_wb["B2"].value == "Log Flt":
self.gaus_log_detect_combo.setCurrentIndex(0)
self.param_detect_lbl.setText("Gauss Size")
else:
self.gaus_log_detect_combo.setCurrentIndex(1)
self.param_detect_lbl.setText("Thr Coeff")
self.param_detect_edt.setText(str(s_wb["B3"].value))
self.gfilt_water_edt.setText(str(int(s_wb["B4"].value)))
self.circ_thr_edt.setText(str(s_wb["B5"].value))
self.dist_thr_edt.setText(str(int(s_wb["B6"].value)))
self.spots_thr_edt.setText(str(s_wb["B7"].value))
self.volume_thr_edt.setText(str(int(s_wb["B8"].value)))
self.time_step_edt.setText(str(float(s_wb["B12"].value)))
self.gaus_log_detect_value = s_wb["B2"].value
self.gfilt_water_value = int(s_wb["B4"].value)
self.circ_thr_value = s_wb["B5"].value
self.dist_thr_value = int(s_wb["B6"].value)
self.spots_thr_value = s_wb["B7"].value
self.volume_thr_value = int(s_wb["B8"].value)
self.max_dist = int(s_wb["B11"].value)
self.time_step_value = float(s_wb["B12"].value)
self.px_brd = int(s_wb["B13"].value)
self.nuclei_seg = np.zeros(self.filedata.imarray_red.shape, dtype=np.uint32)
for t in range(self.nuclei_tracked.shape[0]):
self.nuclei_seg[t, :, :] = skmr.label(self.nuclei_tracked[t, :, :], connectivity=1)
self.sld1.setMaximum(self.filedata.imarray_red.shape[0] - 1)
self.data_flag = 1
self.nuclei_t_visual_flag = 1
self.spots_segm_flag = 1
self.frame1.setImage(self.filedata.imarray_red[0, :, :])
self.frame3.setImage(self.filedata.imarray_green[0, :, :])
self.frame2.setImage(self.nuclei_tracked[0, :, :], levels=(0, self.nuclei_tracked.max()))
self.mycmap = pg.ColorMap(np.linspace(0, 1, self.nuclei_tracked.max()), color=self.colors4map)
self.frame2.setColorMap(self.mycmap)
self.fnames = foldername
self.nuc_spots_conn4load_analysis()
except Exception:
traceback.print_exc()
self.ready_indicator()
def start_cut(self):
"""Select the current frame as first frame to analyze"""
self.filedata.imarray_red = self.filedata.imarray_red[self.sld1.value():, :, :]
self.filedata.imarray_green = self.filedata.imarray_green[self.sld1.value():, :, :]
self.filedata.green4D = self.filedata.green4D[self.sld1.value():, :, :, :]
self.start_cut_value = self.sld1.value()
self.sld1.setMaximum(self.filedata.imarray_red[:, 0, 0].size - 1)
self.sld1.setValue(0)
def end_cut(self):
"""Select the current frame as last frame to analyze"""
self.filedata.imarray_red = self.filedata.imarray_red[:self.sld1.value() + 1, :, :]
self.filedata.imarray_green = self.filedata.imarray_green[:self.sld1.value() + 1, :, :]
self.filedata.green4D = self.filedata.green4D[:self.sld1.value() + 1, :, :, :]
self.end_cut_value = self.sld1.value()
self.sld1.setMaximum(self.filedata.imarray_red[:, 0, 0].size - 1)
self.sld1.setValue(self.filedata.imarray_red[:, 0, 0].size - 1)
def reload_files(self):
"""reload( and concatenate the files already selected"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
if str(self.fnames[0])[-3:] == 'lsm' or str(self.fnames[0])[-3:] == 'tif':
self.filedata = MultiLoadLsmOrTif5D.MultiLoadLsmOrTif5D(self.fnames, self.nucs_spts_ch)
if str(self.fnames[0])[-3:] == 'czi':
self.filedata = MultiLoadCzi5D.MultiProcLoadCzi5D(self.fnames, self.nucs_spts_ch)
self.frame1.setImage(self.filedata.imarray_red[0, :, :])
self.frame3.setImage(self.filedata.imarray_green[0, :, :])
self.data_flag = 1
self.sld1.setMaximum(self.filedata.imarray_red[:, 0, 0].size - 1)
self.sld1.setValue(0)
except Exception:
traceback.print_exc()
self.ready_indicator()
def sld1_update(self):
self.time_lbl.setText("time " + time.strftime("%M:%S", time.gmtime(self.sld1.value() * self.time_step_value)))
self.frame_numb_lbl.setText("frame " + str(self.sld1.value()))
if self.data_flag == 1:
self.frame1.setImage(self.filedata.imarray_red[self.sld1.value(), :, :])
self.frame3.setImage(self.filedata.imarray_green[self.sld1.value(), :, :])
if self.labbs_flag == 1:
self.frame2.setImage(np.sign(self.labbs[self.sld1.value(), :, :]))
if self.nuclei_flag == 1:
self.frame2.setImage(self.nuclei_seg[self.sld1.value(), :, :])
if self.nuclei_t_visual_flag == 1:
self.frame2.setImage(self.nuclei_tracked[self.sld1.value(), :, :], levels=(0, self.nuclei_tracked.max()))
if self.spots_segm_flag == 1:
self.frame4.setImage(np.sign(self.spots_3D.spots_ints[self.sld1.value(), :, :]))
if self.spots_trk_flag == 1:
self.frame4.setImage(np.sign(self.spots_tracked_3D[self.sld1.value(), :, :]))
def find_zero_in_mtss(self):
"""Launch the tool to set the time zero on the mitosis"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
self.mpp17 = CheckSelectedRawData(self.filedata.imarray_red[0], self.nucs_spts_ch)
self.mpp17.show()
except Exception:
traceback.print_exc()
self.ready_indicator()
self.mpp17.procStart.connect(self.loop_for_find_mtss)
def loop_for_find_mtss(self):
"""Manage the possible situation of the tool to check the zero"""
if self.mpp17.flag_yes_no == "yes":
self.time_zero = self.mpp17.pz[0] - self.mpp17.mtss_frame
print(self.time_zero)
self.save_analysis()
self.mpp17.close()
if self.mpp17.flag_yes_no == "no":
print("no")
self.mpp17.close()
self.find_zero_in_mtss()
def save_analysis(self):
"""Save the analysis"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
fwritename = QtWidgets.QFileDialog.getSaveFileName()[0]
reload(AnalysisSaver)
reload(WriteSptsIntsDividedByBkg)
AnalysisSaver.AnalysisSaver(fwritename, self.fnames, self.nuc_active.nuclei_active3c, self.nuclei_tracked, self.spots_tracked_3D, self.features_3D, self.nuc_active.n_active_vector,
self.filedata.imarray_red, self.filedata.imarray_green, self.spots_3D, self.gfilt_water_value, self.circ_thr_value, self.dist_thr_value, self.spots_thr_value,
self.volume_thr_value, self.start_cut_value, self.end_cut_value, self.nuc_active.popt, self.nuc_active.perr, self.max_dist, self.gaus_log_detect_value,
self.param_detect_value, self.time_step_value, self.time_zero, self.px_brd, self.filedata.pix_size, self.filedata.pix_size_Z, self.nucs_spts_ch, self.t_track_end_value, self.software_version)
BurstStatisticWriter.BurstStatisticWriter(fwritename, self.features_3D)
WriteSptsIntsDividedByBkg.WriteSptsIntsDividedByBkg(fwritename, self.filedata.green4D, self.spots_3D, self.spots_tracked_3D)
os.remove('rescue_fnames.txt')
rescue_del = glob.glob("*.npy")
for k in rescue_del:
os.remove(k)
except Exception:
traceback.print_exc()
self.ready_indicator()
def gaus_log_detect(self, text):
"""Change label for nucs detection parameters"""
self.gaus_log_detect_value = text
if text == "Gauss Flt":
self.param_detect_lbl.setText("Gauss Size")
else:
self.param_detect_lbl.setText("Thr Coeff")
def param_detect_var(self, text):
"""Set nuclei detection parameter"""
self.param_detect_value = float(text)
def gfilt_water_var(self, text):
"""Set gaussian filter kernel size for water shed pre smoothing"""
self.gfilt_water_value = int(text)
def circ_thr_var(self, text):
"""Set circularity parameter"""
self.circ_thr_value = float(text)
def dist_thr_var(self, text):
self.dist_thr_value = float(text)
def spots_thr_var(self, text):
self.spots_thr_value = float(text)
def volume_thr_var(self, text):
self.volume_thr_value = int(text)
def time_step_var(self, text):
self.time_step_value = float(text)
def popup_nuclei_raw(self):
"""Popup raw nuclei"""
PopUpTool.PopUpTool(self.filedata.imarray_red, 'Nuclei Raw Data')
def popup_nuclei_detected(self):
"""Popup detected nuclei"""
PopUpTool.PopUpTool(np.sign(self.labbs), 'Detected Nuclei')
def popup_nuclei_segmented(self):
"""Popup segmented nuclei"""
PopUpTool.PopUpToolWithMap(self.nuclei_seg, 'Segmented Nuclei', self.mycmap)
def popup_nuclei_trackeded(self):
""""Popup tracked nuclei"""
PopUpTool.PopUpToolWithMap(self.nuclei_tracked, 'Tracked Nuclei', self.mycmap)
def popup_spots_raw(self):
"""Popup green raw data"""
PopUpTool.PopUpTool(self.filedata.imarray_green, 'Spots Raw Data')
def popup_spots_segm(self):
"""Popup tracked spots"""
PopUpTool.PopUpTool(np.sign(self.spots_tracked_3D), 'Segmented Spots')
def popup_nucactive(self):
"""Popup false colored movie"""
pg.image(self.nuc_active.nuclei_active3c, title="Active Nuclei")
pg.plot(self.nuc_active.n_active_vector, pen='r', symbol='x')
def nuclei_detection(self):
"""Detect raw data nuclei"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
if self.gaus_log_detect_value == "Log Flt":
self.labbs = NucleiDetectLog.NucleiDetectLog(self.filedata.imarray_red, self.param_detect_value).labbs
else:
self.labbs = NucleiDetect.NucleiDetect(self.filedata.imarray_red, self.param_detect_value).labbs
self.labbs_flag = 1
self.nuclei_flag = 0
self.nuclei_t_visual_flag = 0
self.frame2.setImage(np.sign(self.labbs[self.sld1.value(), :, :]))
np.save('rescue_labbs', self.labbs)
np.save('rescue_rawnucs', self.filedata.imarray_red)
if self.gaus_log_detect_value == "Log Flt":
np.save('rescue_labbs_info', np.array([self.param_detect_value, 1]))
else:
np.save('rescue_labbs_info', np.array([self.param_detect_value, 0]))
file = open('rescue_fnames.txt', "w")
file.write(self.fnames[0])
for k in range(1, len(self.fnames)):
file.write('\n' + self.fnames[k])
file.close()
except Exception:
traceback.print_exc()
self.ready_indicator()
def nuclei_segmentation(self):
"""Segments detected nuclei"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
self.nuclei_seg = NucleiSegmentStackMultiCore.NucleiSegmentStackMultiCore(self.labbs, self.circ_thr_value, self.gfilt_water_value).nuclei_labels
self.labbs_flag = 0
self.nuclei_flag = 1
self.nuclei_t_visual_flag = 0
self.frame2.setImage(self.nuclei_seg[self.sld1.value(), :, :])
self.mycmap = pg.ColorMap(np.linspace(0, 1, self.nuclei_seg.max()), color=self.colors4map)
self.frame2.setColorMap(self.mycmap)
np.save('rescue_nuclei_seg', self.nuclei_seg)
np.save('rescue_nuclei_seg_info', np.array([self.circ_thr_value, self.gfilt_water_value]))
except Exception:
traceback.print_exc()
self.ready_indicator()
def nuclei_tracking(self):
"""Track segmented nuclei"""
self.busy_indicator()
app.processEvents()
app.processEvents()
try:
# self.px_brd = BorderPixelRemove.getNumb()
self.px_brd = 3
nuclei_tracked = NucleiConnectMultiCore.NucleiConnectMultiCore(self.nuclei_seg, self.dist_thr_value).nuclei_tracked
self.nuclei_tracked = RemoveBadNuclei.RemoveBorderNuclei(nuclei_tracked, self.px_brd).nuclei_tracked
self.labbs_flag = 0
self.nuclei_flag = 0
self.nuclei_t_visual_flag = 1
self.frame2.setImage(self.nuclei_tracked[self.sld1.value(), :, :], levels=(0, self.nuclei_tracked.max()))
self.mycmap = pg.ColorMap(np.linspace(0, 1, self.nuclei_tracked.max()), color=self.colors4map)
self.frame2.setColorMap(self.mycmap)
np.save('rescue_nuclei_tracked', self.nuclei_tracked)
np.save('rescue_nuclei_tracked_info', np.array([self.dist_thr_value, self.px_brd]))