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mm3_CellTrackGUI.py
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#! /usr/bin/env python3
from __future__ import print_function, division
from PyQt5.QtWidgets import (QApplication, QMainWindow, QGraphicsScene, QGraphicsView,
QRadioButton, QButtonGroup, QVBoxLayout, QHBoxLayout,
QWidget, QLabel, QAction, QDockWidget, QPushButton, QGraphicsItem,
QGridLayout, QGraphicsLineItem, QGraphicsPathItem, QGraphicsPixmapItem,
QGraphicsEllipseItem, QGraphicsTextItem, QInputDialog)
from PyQt5.QtGui import (QIcon, QImage, QPainter, QPen, QPixmap, qGray, QColor, QPainterPath, QBrush,
QTransform, QPolygonF, QFont, QPaintDevice)
from PyQt5.QtCore import Qt, QPoint, QRectF, QLineF
from skimage import io, img_as_ubyte, color, draw, measure, morphology, feature
import numpy as np
from matplotlib import pyplot as plt
import argparse
import glob
from pprint import pprint # for human readable file output
import pickle as pickle
import sys
import re
import os
import random
import yaml
import multiprocessing
import pandas as pd
sys.path.insert(0, '/home/wanglab/src/mm3/') # Jeremy's path to mm3 folder
sys.path.insert(0, '/home/wanglab/src/mm3/sup/')
import mm3_helpers as mm3
import mm3_plots
class Window(QMainWindow):
def __init__(self, parent=None):
super(Window, self).__init__(parent)
top = 400
left = 400
width = 800
height = 600
self.setWindowTitle("Update your tracking results and save for deep learning.")
self.setGeometry(top,left,width,height)
# load specs file
with open(os.path.join(params['ana_dir'], 'specs.yaml'), 'r') as specs_file:
specs = yaml.safe_load(specs_file)
self.frames = FrameImgWidget(specs=specs)
# make scene the central widget
self.setCentralWidget(self.frames)
eventButtonGroup = QButtonGroup()
migrateButton = QRadioButton("Migration")
migrateButton.setShortcut("Ctrl+V")
migrateButton.setToolTip("(Ctrl+V) Draw white migration lines\nbetween cells in adjacent frames.\nHINT: You can draw a migraton line over multiple frames at once.")
migrateButton.clicked.connect(self.frames.scene.set_migration)
migrateButton.click()
eventButtonGroup.addButton(migrateButton)
childrenButton = QRadioButton("Children")
childrenButton.setShortcut("Ctrl+C")
childrenButton.setToolTip("(Ctrl+C) Draw green children lines\nbetween a parent cell and its two children.")
childrenButton.clicked.connect(self.frames.scene.set_children)
eventButtonGroup.addButton(childrenButton)
# born button isn't really necessary, since we can get all that information
# from the children events that are already present
# bornButton = QRadioButton("Born")
# bornButton.setShortcut("Ctrl+C")
# bornButton.clicked.connect(self.threeFrames.scene.set_born)
# eventButtonGroup.addButton(bornButton)
dieButton = QRadioButton("Die")
dieButton.setShortcut("Ctrl+X")
dieButton.setToolTip("(Ctrl+X) Indicate a cell died between\nthe current frame and the next frame.")
dieButton.clicked.connect(self.frames.scene.set_die)
eventButtonGroup.addButton(dieButton)
appearButton = QRadioButton("Appear")
appearButton.setShortcut("Ctrl+A")
appearButton.setToolTip("(Ctrl+A) Denotes a cell appeared,\nor entered the field of view at this frame.")
appearButton.clicked.connect(self.frames.scene.set_appear)
eventButtonGroup.addButton(appearButton)
disappearButton = QRadioButton("Disappear")
disappearButton.setShortcut("Ctrl+D")
disappearButton.setToolTip("(Ctrl+D) Indicate a cell leaves\nthe field of view after this frame.")
disappearButton.clicked.connect(self.frames.scene.set_disappear)
eventButtonGroup.addButton(disappearButton)
oneCellButton = QRadioButton("One cell")
oneCellButton.setShortcut("Ctrl+1")
oneCellButton.setToolTip("(Ctrl+1) Indicate an ellipse represents a single cell.")
oneCellButton.clicked.connect(self.frames.scene.set_one)
eventButtonGroup.addButton(oneCellButton)
twoCellButton = QRadioButton("Two cells")
twoCellButton.setShortcut("Ctrl+2")
twoCellButton.setToolTip("(Ctrl+2) Indicate an ellipse represents two cells.")
twoCellButton.clicked.connect(self.frames.scene.set_two)
eventButtonGroup.addButton(twoCellButton)
threeCellButton = QRadioButton("Three cells")
threeCellButton.setShortcut("Ctrl+3")
threeCellButton.setToolTip("(Ctrl+3) Indicate an ellipse represents three cells.")
threeCellButton.clicked.connect(self.frames.scene.set_three)
eventButtonGroup.addButton(threeCellButton)
zeroCellButton = QRadioButton("Zero cells")
zeroCellButton.setShortcut("Ctrl+0")
zeroCellButton.setToolTip("(Ctrl+0) Indicate an ellipse represents three cells.")
zeroCellButton.clicked.connect(self.frames.scene.set_zero)
eventButtonGroup.addButton(zeroCellButton)
removeEventsButton = QRadioButton("Remove events")
removeEventsButton.setShortcut("Ctrl+R")
removeEventsButton.setToolTip("(Ctrl+R) Eliminate events belonging entirely to this\ncell, and emantating from this cell.")
removeEventsButton.clicked.connect(self.frames.scene.remove_all_cell_events)
eventButtonGroup.addButton(removeEventsButton)
# falselyJoinedButton = QRadioButton("Falsely joined")
# falselyJoinedButton.clicked.connect(self.frames.scene.set_falsely_joined)
# falselyJoinedButton.setShortcut("Ctrl+F")
# falselyJoinedButton.setToolTip("(Ctrl+F) If two cells in frame i join\nto one cell in frame i+1, draw red lines\njoining them.")
# eventButtonGroup.addButton(falselyJoinedButton)
# clearAllEventsButton = QPushButton("Remove all\ntracking events")
# clearAllEventsButton.clicked.connect(self.frames.scene.clear_all_events)
# maskEditModeButton = QPushButton("Enter mask\nedit mode")
# maskEditModeButton.clicked.connect(self.frames.enter_mask_edit_mode)
#
# trackEditModeButton = QPushButton("Enter track\nedit mode")
# trackEditModeButton.clicked.connect(self.frames.enter_track_edit_mode)
# splitEllipseButton = QPushButton("Delete ellipse")
# splitEllipseButton.clicked.connect(self.frames.scene.split_ellipse)
# drawEllipseButton = QPushButton("Draw ellipse")
# drawEllipseButton.clicked.connect(self.frames.scene.draw_ellipse)
eventButtonLayout = QVBoxLayout()
eventButtonLayout.addWidget(migrateButton)
eventButtonLayout.addWidget(childrenButton)
# eventButtonLayout.addWidget(bornButton)
eventButtonLayout.addWidget(dieButton)
eventButtonLayout.addWidget(appearButton)
eventButtonLayout.addWidget(disappearButton)
eventButtonLayout.addWidget(zeroCellButton)
eventButtonLayout.addWidget(oneCellButton)
eventButtonLayout.addWidget(twoCellButton)
eventButtonLayout.addWidget(threeCellButton)
# eventButtonLayout.addWidget(falselyJoinedButton)
eventButtonLayout.addWidget(removeEventsButton)
# eventButtonLayout.addWidget(clearAllEventsButton)
# eventButtonLayout.addWidget(maskEditModeButton)
# eventButtonLayout.addWidget(trackEditModeButton)
# eventButtonLayout.addWidget(splitEllipseButton)
eventButtonGroupWidget = QWidget()
eventButtonGroupWidget.setLayout(eventButtonLayout)
eventButtonDockWidget = QDockWidget()
eventButtonDockWidget.setWidget(eventButtonGroupWidget)
self.addDockWidget(Qt.LeftDockWidgetArea, eventButtonDockWidget)
goToPeakButton = QPushButton('Go to fov/peak')
goToPeakButton.clicked.connect(self.frames.get_fov_peak_dialog)
advancePeakButton = QPushButton("Next peak")
advancePeakButton.clicked.connect(self.frames.scene.next_peak)
priorPeakButton = QPushButton("Prior peak")
priorPeakButton.clicked.connect(self.frames.scene.prior_peak)
advanceFOVButton = QPushButton("Next FOV")
advanceFOVButton.clicked.connect(self.frames.scene.next_fov)
priorFOVButton = QPushButton("Prior FOV")
priorFOVButton.clicked.connect(self.frames.scene.prior_fov)
saveUpdatedTracksButton = QPushButton("Save updated tracking info\nfor neural net training data")
saveUpdatedTracksButton.setShortcut("Ctrl+S")
saveUpdatedTracksButton.clicked.connect(self.frames.scene.save_updates)
fileAdvanceLayout = QVBoxLayout()
fileAdvanceLayout.addWidget(goToPeakButton)
fileAdvanceLayout.addWidget(advancePeakButton)
fileAdvanceLayout.addWidget(priorPeakButton)
fileAdvanceLayout.addWidget(advanceFOVButton)
fileAdvanceLayout.addWidget(priorFOVButton)
fileAdvanceLayout.addWidget(saveUpdatedTracksButton)
fileAdvanceGroupWidget = QWidget()
fileAdvanceGroupWidget.setLayout(fileAdvanceLayout)
fileAdvanceDockWidget = QDockWidget()
fileAdvanceDockWidget.setWidget(fileAdvanceGroupWidget)
self.addDockWidget(Qt.RightDockWidgetArea, fileAdvanceDockWidget)
class FrameImgWidget(QWidget):
# class for setting three frames side-by-side as a central widget in a QMainWindow object
def __init__(self,specs):
super(FrameImgWidget, self).__init__()
print("Starting in track edit mode.")
# add images and cell regions as ellipses to each frame in a QGraphicsScene object
self.specs = specs
self.scene = TrackItem(self.specs)
self.view = View(self)
self.view.setScene(self.scene)
def get_fov_peak_dialog(self):
fov_id, pressed = QInputDialog.getInt(self,
"Type your desired FOV",
"fov_id (should be an integer):")
if pressed:
fov_id = fov_id
peak_id, pressed = QInputDialog.getInt(self,
"Go to peak",
"peak_id (should be an integer):")
if pressed:
peak_id = peak_id
self.scene.go_to_fov_and_peak_id(fov_id,peak_id)
# def enter_mask_edit_mode(self):
# print("Entering mask edit mode.")
# ###### NOTE: consider prompting to save track edits prior to switching modes
# self.scene.clear()
# self.scene = MaskItem(self.specs)
# self.view = View(self)
# self.view.setScene(self.scene)
#
# def enter_track_edit_mode(self):
# print("Entering track edit mode.")
# ###### NOTE: consider prompting to save new masks prior to switching modes
# self.scene.clear()
# self.scene = TrackItem(self.specs)
# self.view = View(self)
# self.view.setScene(self.scene)
class View(QGraphicsView):
'''
Re-implementation of QGraphicsView to accept mouse+Ctrl event
as a zoom transformation
'''
def __init__(self, parent):
super(View, self).__init__(parent)
# set upper and lower bounds on zooming
self.setTransformationAnchor(QGraphicsView.AnchorViewCenter)
self.maxScale = 2.5
self.minScale = 0.3
def wheelEvent(self, event):
if event.modifiers() == Qt.ControlModifier:
self.setTransformationAnchor(QGraphicsView.AnchorUnderMouse)
m11 = self.transform().m11() # horizontal scale factor
m12 = self.transform().m12()
m13 = self.transform().m13()
m21 = self.transform().m21()
m22 = self.transform().m22() # vertizal scale factor
m23 = self.transform().m23()
m31 = self.transform().m31()
m32 = self.transform().m32()
m33 = self.transform().m33()
adjust = event.angleDelta().y()/120 * 0.1
if (m11 >= self.maxScale) and (adjust > 0):
m11 = m11
m22 = m22
elif (m11 <= self.minScale) and (adjust < 0):
m11 = m11
m22 = m22
else:
m11 += adjust
m22 += adjust
self.setTransform(QTransform(m11, m12, m13, m21, m22, m23, m31, m32, m33))
elif event.modifiers() == Qt.AltModifier:
self.setTransformationAnchor(QGraphicsView.NoAnchor)
adjust = event.angleDelta().x()/120 * 50
self.translate(adjust,0)
else:
QGraphicsView.wheelEvent(self, event)
# class CellItem(QGraphicsItem):
# '''
# Re-implementation of a QGraphicsItem to enable drawing of cell regions.
# '''
# def __init__(self, region, parent):
# super(CellItem, self).__init__()
#
# graphic = region['region_graphic']
#
# top_left = QPoint(graphic['left_x'],graphic['top_y'])
# bottom_right = QPoint(graphic['right_x'],graphic['bottom_y'])
# coords = graphic['coords']
#
# pen = graphic['pen']
# brush = graphic['brush']
#
# rr = coords[:,0]
# cc = coords[:,1]
# for i in range(len(rr)):
# x = cc[i]
# y = rr[i]
# point = QPoint(x,y)
# if i == 0:
# path = QPainterPath(point)
# else:
# path.moveTo(point)
# path.setFillRule(Qt.WindingFill)
# self.paint(path, pen, brush, top_left, bottom_right)
#
# def boundingRect(self, top_left, bottom_right):
# rect = QRectF(top_left, bottom_right)
# return(rect)
#
# def paint(self, path, pen, brush, top_left, bottom_right):
# rect = self.boundingRect(top_left, bottom_right)
# painter = QPainter()
# painter.setPen(pen)
# painter.setBrush(brush)
# painter.drawPath(path)
#
# def type(self):
# return("CellItem")
class TrackItem(QGraphicsScene):
# add more functionality for setting event type, i.e., parent-child, migrate, death, leave frame, etc..
def __init__(self,specs):
super(TrackItem, self).__init__()
self.specs = specs
# add QImages to scene (try three frames)
self.fov_id_list = [fov_id for fov_id in specs.keys()]
# self.center_frame_index = 1
self.fovIndex = 0
self.fov_id = self.fov_id_list[self.fovIndex]
self.peak_id_list_in_fov = [peak_id for peak_id in specs[self.fov_id].keys() if specs[self.fov_id][peak_id] == 1]
self.peakIndex = 0
self.peak_id = self.peak_id_list_in_fov[self.peakIndex]
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
# read in images
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# time_int = params['moviemaker']['seconds_per_time_index']/60
cell_filename = os.path.join(params['cell_dir'], 'complete_cells.pkl')
cell_filename_all = os.path.join(params['cell_dir'], 'all_cells.pkl')
with open(cell_filename, 'rb') as cell_file:
self.Cells = pickle.load(cell_file)
# mm3.calculate_pole_age(self.Cells) # add poleage
with open(cell_filename_all, 'rb') as cell_file:
self.All_Cells = pickle.load(cell_file)
plot_dir = os.path.join(params['cell_dir'], '20190312_plots')
if not os.path.exists(plot_dir):
os.makedirs(plot_dir)
lin_dir = os.path.join(plot_dir, 'lineage_plots_full')
if not os.path.exists(lin_dir):
os.makedirs(lin_dir)
# look for previously edited info and load it if it is found
self.get_track_pickle()
# self.no_track_pickle_lookup()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.drawing = False
self.remove_events = False
self.brushSize = 2
self.brushColor = QColor('black')
self.lastPoint = QPoint()
self.pen = QPen()
# class options
self.event_types_list = ["ChildLine",
"MigrationLine",
"DieSymbol",
"AppearSymbol",
"BornSymbol",
"DisappearSymbol",
"FalseJoinLine",
"OneCellSymbol",
"TwoCellSymbol",
"ThreeCellSymbol",
"ZeroCellSymbol"]
self.line_events_list = ["ChildLine","MigrationLine","FalseJoinLine"]
self.end_check_events_list = ["AppearSymbol","ZeroCellSymbol"]
# the below lookup table may need reworked to handle migration and child lines to/from a cell
# or the handling may be better done in the update_cell_info function
self.event_type_index_lookup = {"MigrationLine":0, "ChildLine":1,
"DieSymbol":2, "BornSymbol":3,
"AppearSymbol":4, "DisappearSymbol":5,
"FalseJoinLine":6,
"OneCellSymbol":7,
"TwoCellSymbol":8,
"ThreeCellSymbol":9,
"ZeroCellSymbol":10}
# given an event type for a cell, what are the event types that are incompatible within that same cell?
self.forbidden_events_lookup = {"MigrationStart":["ChildStart","DisappearSymbol","DieSymbol","MigrationStart","FalseJoinStart","ZeroCellSymbol"],
"MigrationEnd":["ChildEnd","AppearSymbol","BornSymbol","MigrationEnd","FalseJoinEnd","ZeroCellSymbol"],
"ChildStart":["MigrationStart","DisappearSymbol","DieSymbol","ChildStart","FalseJoinStart","ZeroCellSymbol"],
"ChildEnd":["MigrationEnd","AppearSymbol","ChildEnd","FalseJoinEnd","ZeroCellSymbol"],
"BornSymbol":["MigrationEnd","AppearSymbol","BornSymbol","FalseJoinEnd","ZeroCellSymbol"],
"AppearSymbol":["MigrationEnd","ChildEnd","BornSymbol","AppearSymbol","FalseJoinEnd","ZeroCellSymbol"],
"DisappearSymbol":["MigrationStart","ChildStart","DieSymbol","DisappearSymbol","FalseJoinStart","ZeroCellSymbol"],
"DieSymbol":["MigrationStart","ChildStart","DisappearSymbol","DieSymbol","FalseJoinStart","ZeroCellSymbol"],
"FalseJoinStart":["MigrationStart","ChildStart","DisappearSymbol","DieSymbol","FalseJoinStart","ZeroCellSymbol"],
"FalseJoinEnd":["ChildEnd","AppearSymbol","BornSymbol","MigrationEnd","ZeroCellSymbol"],
"ZeroCellSymbol":["OneCellSymbol","TwoCellSymbol","ThreeCellSymbol","MigrationStart",
"MigrationEnd","ChildStart","ChildEnd","BornSymbol",
"AppearSymbol","DisappearSymbol","DieSymbol","FalseJoinStart","FalseJoinEnd"],
"OneCellSymbol":["ZeroCellSymbol","TwoCellSymbol","ThreeCellSymbol"],
"TwoCellSymbol":["ZeroCellSymbol","OneCellSymbol","ThreeCellSymbol"],
"ThreeCellSymbol":["ZeroCellSymbol","OneCellSymbol","TwoCellSymbol"]}
self.migration = False
self.die = False
self.children = False
self.birth = False
self.appear = False
self.disappear = False
self.falsely_joined_cells = False
self.one_cell = False
self.two_cells = False
self.three_cells = False
# apply cell events to the scene
self.draw_cell_events()
def save_updates(self):
track_info = self.track_info
for t, time_info in track_info.items():
for region_label, region in time_info['regions'].items():
if 'region_graphic' in track_info[t]['regions'][region_label]:
if 'pen' in track_info[t]['regions'][region_label]['region_graphic']:
track_info[t]['regions'][region_label]['region_graphic'].pop('pen')
if 'brush' in track_info[t]['regions'][region_label]['region_graphic']:
track_info[t]['regions'][region_label]['region_graphic'].pop('brush')
with open(self.pickle_file_name, 'wb') as track_file:
try:
pickle.dump(track_info, track_file)
track_file.close()
print("Saved updated tracking information to {}.".format(self.pickle_file_name))
except Exception as e:
track_file.close()
print(str(e))
df_file_name = '/home/wanglab/src/mm3/track_training_file_paths.csv'
# df_file_name = '/Users/jt/code/mm3/track_training_file_paths.csv'
track_file_name_df = pd.read_csv(df_file_name)
# if the current training data isn't yet in the dataframe, add it and save the updated dataframe
if not self.pickle_file_name in track_file_name_df.file_path.values:
print("Appending file name {} as new row in {}.".format(self.pickle_file_name, df_file_name))
track_file_name_df = track_file_name_df.append({'file_path':self.pickle_file_name, 'include':1}, ignore_index=True)
track_file_name_df.to_csv(df_file_name,index=False)
def no_track_pickle_lookup(self):
self.track_info = self.create_tracking_information(self.fov_id, self.peak_id, self.labelStack, self.phaseStack)
def get_track_pickle(self):
self.pickle_file_name = os.path.join(params['cell_dir'], '{}_xy{:0=3}_p{:0=4}_updated_tracks.pkl'.format(params['experiment_name'], self.fov_id, self.peak_id))
# look for previously updated tracking information and load that if it is found.
if not os.path.isfile(self.pickle_file_name):
# get tracking information in a format usable and updatable by qgraphicsscene
self.track_info = self.create_tracking_information(self.fov_id, self.peak_id, self.labelStack, self.phaseStack)
else:
with open(self.pickle_file_name, 'rb') as pickle_file:
try:
print("Found updated track information in {}. Uploading and plotting it.".format(self.pickle_file_name))
self.track_info = pickle.load(pickle_file)
except Exception as e:
print("Could not load pickle file specified.")
print(e)
def go_to_fov_and_peak_id(self, fov_id, peak_id):
# start by removing all current graphics items from the scene, the scene here being 'self'
self.clear()
self.fov_id = fov_id
self.fovIndex = self.fov_id_list.index(self.fov_id)
self.peak_id_list_in_fov = [peak_id for peak_id in self.specs[self.fov_id].keys() if self.specs[self.fov_id][peak_id] == 1]
self.peak_id = peak_id
print(self.peak_id)
# Now we'll look up the peakIndex
self.peakIndex = self.peak_id_list_in_fov.index(self.peak_id)
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# look for previously edited info and load it if it is found
self.get_track_pickle()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.draw_cell_events()
def next_peak(self):
# start by removing all current graphics items from the scene, the scene here being 'self'
self.clear()
# self.center_frame_index = 1
self.peakIndex += 1
self.peak_id = self.peak_id_list_in_fov[self.peakIndex]
# print(self.peak_id)
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# look for previously edited info and load it if it is found
self.get_track_pickle()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.draw_cell_events()
def prior_peak(self):
# start by removing all current graphics items from the scene, the scene here being 'self'
self.clear()
# self.center_frame_index = 1
self.peakIndex -= 1
self.peak_id = self.peak_id_list_in_fov[self.peakIndex]
# print(self.peak_id)
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
# print(self.phaseImgPath)
# print(self.labelImgPath)
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# look for previously edited info and load it if it is found
self.get_track_pickle()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.draw_cell_events()
def next_fov(self):
# start by removing all current graphics items from the scene, the scene here being 'self'
self.clear()
# self.center_frame_index = 1
self.fovIndex += 1
self.fov_id = self.fov_id_list[self.fovIndex]
self.peak_id_list_in_fov = [peak_id for peak_id in self.specs[self.fov_id].keys() if self.specs[self.fov_id][peak_id] == 1]
self.peakIndex = 0
self.peak_id = self.peak_id_list_in_fov[self.peakIndex]
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
# print(self.phaseImgPath)
# print(self.labelImgPath)
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# look for previously edited info and load it if it is found
self.get_track_pickle()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.draw_cell_events()
def prior_fov(self):
# start by removing all current graphics items from the scene, the scene here being 'self'
self.clear()
# self.center_frame_index = 1
self.fovIndex -= 1
self.fov_id = self.fov_id_list[self.fovIndex]
self.peak_id_list_in_fov = [peak_id for peak_id in self.specs[self.fov_id].keys() if self.specs[self.fov_id][peak_id] == 1]
self.peakIndex = 0
self.peak_id = self.peak_id_list_in_fov[self.peakIndex]
# construct image stack file names from params
self.phaseImgPath = os.path.join(params['chnl_dir'], "{}_xy{:0=3}_p{:0=4}_{}.tif".format(params['experiment_name'], self.fov_id, self.peak_id, params['phase_plane']))
self.labelImgPath = os.path.join(params['seg_dir'], "{}_xy{:0=3}_p{:0=4}_seg_unet.tif".format(params['experiment_name'], self.fov_id, self.peak_id))
self.labelStack = io.imread(self.labelImgPath)
self.phaseStack = io.imread(self.phaseImgPath)
# look for previously edited info and load it if it is found
self.get_track_pickle()
self.all_frames_by_time_dict = self.all_phase_img_and_regions()
self.draw_cell_events()
def all_phase_img_and_regions(self):
frame_dict_by_time = {}
xPos = 0
for time in self.track_info.keys():
frame_index = time-1
frame, regions = self.phase_img_and_regions(frame_index)
frame_dict_by_time[time] = self.addPixmap(frame)
frame_dict_by_time[time].time = time
self.add_regions_to_frame(regions, frame_dict_by_time[time])
frame_dict_by_time[time].setPos(xPos, 0)
xPos += frame_dict_by_time[time].pixmap().width()
return(frame_dict_by_time)
def phase_img_and_regions(self, frame_index, watershed=False):
time = frame_index+1
phaseImg = self.phaseStack[frame_index,:,:]
maskImg = self.labelStack[frame_index,:,:]
originalImgMax = np.max(phaseImg)
phaseImg = phaseImg/originalImgMax
phaseImg = color.gray2rgb(phaseImg)
RGBImg = (phaseImg*255).astype('uint8')
originalHeight, originalWidth, originalChannelNumber = RGBImg.shape
phaseQimage = QImage(RGBImg, originalWidth, originalHeight,
RGBImg.strides[0], QImage.Format_RGB888)#.scaled(512, 512, aspectRatioMode=Qt.KeepAspectRatio)
phaseQpixmap = QPixmap(phaseQimage)
phaseQpixmap.time = time
# create transparent rbg overlay to grab colors from for drawing cell regions as QGraphicsPathItems
RGBLabelImg = color.label2rgb(maskImg, bg_label=0)
RGBLabelImg = (RGBLabelImg*255).astype('uint8')
originalHeight, originalWidth, RGBLabelChannelNumber = RGBLabelImg.shape
RGBLabelImg = QImage(RGBLabelImg, originalWidth, originalHeight, RGBLabelImg.strides[0], QImage.Format_RGB888)#.scaled(512, 512, aspectRatioMode=Qt.KeepAspectRatio)
# pprint(regions)
time_regions_and_events = self.track_info[time]
regions = time_regions_and_events['regions']
time_regions_and_events['time'] = time
for region_id in regions.keys():
brush = QBrush()
brush.setStyle(Qt.SolidPattern)
pen = QPen()
pen.setStyle(Qt.SolidLine)
props = regions[region_id]['props']
coords = props.coords
min_row, min_col, max_row, max_col = props.bbox
label = props.label
centroidY,centroidX = props.centroid
brushColor = RGBLabelImg.pixelColor(centroidX,centroidY)
brushColor.setAlphaF(0.15)
brush.setColor(brushColor)
pen.setColor(brushColor)
regions[region_id]['region_graphic'] = {'top_y':min_row, 'bottom_y':max_row,
'left_x':min_col, 'right_x':max_col,
'coords':coords,
'pen':pen, 'brush':brush}
return(phaseQpixmap, time_regions_and_events)
def create_tracking_information(self, fov_id, peak_id, label_stack, phase_stack):
# Complete_Lineages = mm3_plots.organize_cells_by_channel(self.Cells, self.specs)
# All_Lineages = mm3_plots.organize_cells_by_channel(self.All_Cells, self.specs)
t_adj = 1
# correct for occasional missing of a frame by our microscope
dt = phase_stack.dtype
for k,img in enumerate(phase_stack):
# if the mean phase image signal is less than 200, add its index to list
if ((dt == 'uint16') and (np.mean(img) < 200)):
label_stack[k,...] = label_stack[k-1,...]
elif ((dt == 'uint8') and (np.mean(img) < 200/(2**16-1)*(2**8-1))):
label_stack[k,...] = label_stack[k-1,...]
regions_by_time = {frame+t_adj: measure.regionprops(label_stack[frame,:,:]) for frame in range(label_stack.shape[0])}
regions_and_events_by_time = {frame+t_adj : {'regions' : {}, 'matrix' : None} for frame in range(label_stack.shape[0])}
# loop through regions and add them to the main dictionary.
for t, regions in regions_by_time.items():
# this is a list, while we want it to be a dictionary with the region label as the key
for region in regions:
default_events = np.zeros(12, dtype=np.int)
default_events[11] = 1 # set N to 1
regions_and_events_by_time[t]['regions'][region.label] = {'props' : region,
'events' : default_events}
# create default interaction matrix
# Now that we know how many regions there are per time point, we will create a default matrix which indicates how regions are connected to each between this time point, t, and the next one, t+1. The row index will be the region label of the region in t, and the column index will be the region label of the region in t+1.
# If a region migrates from t to t+1, its row should have a sum of 1 corresponding from which region (row) to which region (column) it moved. If the region divided, then both of the daughter columns will get value 1.
# Note that the regions are labeled from 1, but Numpy arrays and indexed from zero. We can use this to store some additional informaiton. If a region disappears, it will receive a 1 in the column with index 0.
# In the last time point all regions will be connected to the disappear column
for t, t_data in regions_and_events_by_time.items():
n_regions_in_t = len(regions_by_time[t])
if t+1 in regions_by_time:
n_regions_in_t_plus_1 = len(regions_by_time[t+1])
else:
n_regions_in_t_plus_1 = 0
t_data['matrix'] = np.zeros((n_regions_in_t+1, n_regions_in_t_plus_1+1), dtype=np.int)
# Loop over cells and edit event information
# We will use the cell dictionary All_Cells. Complete_Cells is a subset of All_Cells which is just those cells that have both a mother and a daughter. These are the brighter lines on the lineage plot.
# Each cell object has a number of attributes that are useful to us. For example find cell f01p0077t0003r02 on the lineage plot and then take a look at its attributes below.
# We will go through each cell by its time points and edit the events associated with that region.
# We will also edit the matrix when appropriate.
# pull out only the cells in of this FOV
cells_tmp = mm3_plots.find_cells_of_fov_and_peak(self.All_Cells, fov_id, peak_id)
print('There are {} cells for this channel'.format(len(cells_tmp)))
for cell_id, cell_tmp in cells_tmp.items():
# Check for when cell has less time points than it should
if (cell_tmp.times[-1] - cell_tmp.times[0])+1 > len(cell_tmp.times):
print('Cell {} has less time points than it should, skipping.'.format(cell_id))
continue
# Go over the time points of this cell and edit appropriate information main dictionary
for i, t in enumerate(cell_tmp.times):
# get the region label
label_tmp = cell_tmp.labels[i]
# M migration, event 0
# If the cell has another time point after this one then it must have migrated
if i != len(cell_tmp.times)-1:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][0] = 1
# update matrix using this region label and the next one
regions_and_events_by_time[t]['matrix'][label_tmp, cell_tmp.labels[i+1]] = 1
# S division, 1
if cell_tmp.daughters and i == len(cell_tmp.times)-1:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][1] = 1
# daughter 1 and 2 label
# d1_label = self.All_Cells[cell_tmp.daughters[0].id].labels[0]
d1_label = self.All_Cells[cell_tmp.daughters[0].id].labels[0]
try:
# d2_label = self.All_Cells[cell_tmp.daughters[1].id].labels[0]
d2_label = self.All_Cells[cell_tmp.daughters[1].id].labels[0]
regions_and_events_by_time[t]['matrix'][label_tmp, d1_label] = 1
regions_and_events_by_time[t]['matrix'][label_tmp, d2_label] = 1
except IndexError as e:
print("At timepoint {} there was an index error in assigning daughters: {}".format(t,e))
# A apoptosis, 2
try:
if cell_tmp.death and i == len(cell_tmp.times)-1:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][2] = 1
# skip here if no death attribute. Of course can update data with input from user.
except AttributeError as e:
print(e)
# B birth, 3
if cell_tmp.parent and i == 0:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][3] = 1
# I appears, 4
if not t == 1:
if not cell_tmp.parent and i == 0:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][4] = 1
# O disappears, 5
if not cell_tmp.daughters and i == len(cell_tmp.times)-1:
regions_and_events_by_time[t]['regions'][label_tmp]['events'][5] = 1
regions_and_events_by_time[t]['matrix'][label_tmp, 0] = 1
# F false join of cells into a single region, 6
# set to zero, since this is difficult to infer here, and will
# probably need done by our eventual algorithm
regions_and_events_by_time[t]['regions'][label_tmp]['events'][6] = 0
# One cell in detection, 7
regions_and_events_by_time[t]['regions'][label_tmp]['events'][7] = 1
# Two cells in detection, 8, keep set to 0. User will update as necessary
# regions_and_events_by_time[t]['regions'][label_tmp]['events'][8] = 1
# Three or more cells in detection, 9, keep set to 0. User will update as necessary
# regions_and_events_by_time[t]['regions'][label_tmp]['events'][9] = 1
# Zero cells in detection, 10, keep set to 0. User will update as necessary
# regions_and_events_by_time[t]['regions'][label_tmp]['events'][10] = 1
# N no data, 10 - Set this to zero as this region as been checked.
regions_and_events_by_time[t]['regions'][label_tmp]['events'][11] = 0
# Set remaining regions to event space [0 0 0 0 1 1]
# Also make their appropriate matrix value 1, which should be in the first column.
for t, t_data in regions_and_events_by_time.items():
for region, region_data in t_data['regions'].items():
if region_data['events'][11] == 1:
region_data['events'][7] = 1
t_data['matrix'][region, 0] = 1
return(regions_and_events_by_time)
def add_regions_to_frame(self, regions_and_events, frame):
# loop through cells within this frame and add their ellipses as children of their corresponding qpixmap object
regions = regions_and_events['regions']
# print(regions_and_events)
frame_time = regions_and_events['time']
for region_id in regions.keys():
region = regions[region_id]
# construct the ellipse
graphic = region['region_graphic']
top_left = QPoint(graphic['left_x'],graphic['top_y'])
bottom_right = QPoint(graphic['right_x'],graphic['bottom_y'])
rect = QRectF(top_left,bottom_right)
# painter_path = graphic['path']
pen = graphic['pen']
brush = graphic['brush']
# cell = CellItem(region, parent=frame)
# instantiate a QGraphicsEllipseItem
ellipse = QGraphicsEllipseItem(rect, frame)
# add cell information to the QGraphicsEllipseItem
ellipse.cellMatrix = regions_and_events['matrix']
ellipse.cellEvents = regions_and_events['regions'][region_id]['events']
ellipse.cellProps = regions_and_events['regions'][region_id]['props']
ellipse.time = frame_time
ellipse.setBrush(brush)
ellipse.setPen(pen)
# # add cell information to the QGraphicsPathItem
# path = QGraphicsPathItem(painter_path, frame)
# path.cellMatrix = regions_and_events['matrix']
# path.cellEvents = regions_and_events['regions'][region_id]['events']
# path.cellProps = regions_and_events['regions'][region_id]['props']
# path.time = frame_time
# path.setBrush(brush)
# path.setPen(pen)
# set up QPainter object to actually paint the QGraphicsPathItem
# painter = QPainter()
# paint_device = QPaintDevice()
# painter.begin(paint_device)
# painter.setPen(pen)
# painter.setBrush(brush)
# painter.drawPath(painter_path)
# painter.end()
# path.paint()
#
def draw_cell_events(self, start_time=1, end_time=None, update=False, original_event_type=None):
# Here is where we will draw the intial lines and symbols representing
# cell events and linkages between cells.
# Set up a list of time points at which we will re-draw events
# the ability to create this list greatkt increases the speed of re-drawing
# events after an update.
if end_time is not None:
max_time = end_time
else: max_time = np.max([item.time for item in self.items() if item.type() == 7])
valid_times = [i for i in range(start_time, max_time+1)]
# track_info is a dictionary, the keys of which are 1-indexed frame numbers
# for each frame, there is a dictionary with the following keys: 'matrix' and 'regions'
# 'matrix' is a 2D array, for which the row index is the region label at time t, and the column index is the region label at time t+1
# If a region disappears from t to t+1, it will receive a 1 in the column with index 0.
# 'regions' is a dictionary with each region's label as a separate key.
# Each region in 'regions' is another dictionary, with 'events', which contains a 1D array identifying the events that correspond to the connections in 'matrix',
# and 'props', which contains all region properties that measure.regionprops retuns for the labelled image at time t.
# The 'events' array is binary. The events are [migration, division, death, birth, appearance, disappearance, no_data], where a 0 at a given position in the 'events'
# array indicates the given event did not occur, and a 1 indicates it did occur.
# loop through frames at valid times
for time in valid_times:
if time in self.all_frames_by_time_dict:
frame = self.all_frames_by_time_dict[time]
# if the frame has child items
if len(frame.childItems()) > 0:
for startItem in frame.childItems():
# test if this is an ellipse item. If it is, draw event symbols.
if startItem.type() == 4:
# remove all previously drawn events belonging entirely to,
# or emanating from, this cell.
if update:
items, items_list = self.get_all_cell_event_items(startItem, return_forbidden_items_list=True)
for i, item_type in enumerate(items_list):
if item_type not in ["ChildEnd","MigrationEnd","FalseJoinEnd"]:
self.removeItem(items[i])
cell_properties = startItem.cellProps
cell_label = cell_properties.label
cell_interactions = startItem.cellMatrix[cell_label,:]
cell_events = startItem.cellEvents
# print(cell_events)
# print(cell_interactions)
# get centroid of cell represented by this qgraphics item
firstPointY = cell_properties.centroid[0]
firstPointX = cell_properties.centroid[1] + startItem.parentItem().x()
firstPoint = QPoint(firstPointX, firstPointY)
# which events happened to this cell?
event_indices = np.where(cell_events == 1)[0]
if 2 in event_indices:
# If the second element in event_indices was 1, the cell dies between this frame and the next.
self.set_die()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)
# Ignoring "born" events in the GUI, and keeping their management
# strictly in the back-end, since we can infer "born" from
# whether a cell has a ChildLine that terminates within it.
# if 3 in event_indices:
# # if the third element in event_indices was 1,
# # the cell cell was born between this frame and the previous one.
# self.set_born()
# self.eventItem = self.set_event_item()
# self.addItem(self.eventItem)
if 4 in event_indices:
# if the fourth element in event_indices was 1,
# the cell cell appeared between this frame and the previous one.
self.set_appear()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)
if 5 in event_indices:
# if the fifth element in event_indices was 1,
# the cell cell disappeared between this frame and the previous one.
self.set_disappear()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)
if 7 in event_indices:
# if the seventh element in event_indices was 1,
# there is one cell in this detection
self.set_one()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)
if 8 in event_indices:
# if the eighth element in event_indices was 1,
# there are two cells in this detection
self.set_two()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)
if 9 in event_indices:
# if the ninth element in event_indices was 1,
# there are three or more cells in this detection
self.set_three()
eventItem = self.set_event_item(firstPoint=firstPoint, startItem=startItem)
self.addItem(eventItem)