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gui3d.py
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gui3d.py
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"""
Copyright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import sys, os, pathlib, warnings, datetime, time
from qtpy import QtGui, QtCore
from superqt import QRangeSlider
from qtpy.QtWidgets import QScrollArea, QMainWindow, QApplication, QWidget, QScrollBar, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar, QLineEdit, QMessageBox, QGroupBox
import pyqtgraph as pg
import numpy as np
from scipy.stats import mode
import cv2
from . import guiparts, menus, io
from .. import models, core, dynamics, version
from ..utils import download_url_to_file, masks_to_outlines, diameters
from ..io import get_image_files, imsave, imread
from ..transforms import resize_image, normalize99 #fixed import
from ..plot import disk
from ..transforms import normalize99_tile, smooth_sharpen_img
from .gui import MainW
try:
import matplotlib.pyplot as plt
MATPLOTLIB = True
except:
MATPLOTLIB = False
def avg3d(C):
""" smooth value of c across nearby points
(c is center of grid directly below point)
b -- a -- b
a -- c -- a
b -- a -- b
"""
Ly, Lx = C.shape
# pad T by 2
T = np.zeros((Ly+2, Lx+2), np.float32)
M = np.zeros((Ly, Lx), np.float32)
T[1:-1, 1:-1] = C.copy()
y,x = np.meshgrid(np.arange(0,Ly,1,int), np.arange(0,Lx,1,int), indexing='ij')
y += 1
x += 1
a = 1./2 #/(z**2 + 1)**0.5
b = 1./(1+2**0.5) #(z**2 + 2)**0.5
c = 1.
M = (b*T[y-1, x-1] + a*T[y-1, x] + b*T[y-1, x+1] +
a*T[y, x-1] + c*T[y, x] + a*T[y, x+1] +
b*T[y+1, x-1] + a*T[y+1, x] + b*T[y+1, x+1])
M /= 4*a + 4*b + c
return M
def interpZ(mask, zdraw):
""" find nearby planes and average their values using grid of points
zfill is in ascending order
"""
ifill = np.ones(mask.shape[0], "bool")
zall = np.arange(0, mask.shape[0], 1, int)
ifill[zdraw] = False
zfill = zall[ifill]
zlower = zdraw[np.searchsorted(zdraw, zfill, side='left')-1]
zupper = zdraw[np.searchsorted(zdraw, zfill, side='right')]
for k,z in enumerate(zfill):
Z = zupper[k] - zlower[k]
zl = (z-zlower[k])/Z
plower = avg3d(mask[zlower[k]]) * (1-zl)
pupper = avg3d(mask[zupper[k]]) * zl
mask[z] = (plower + pupper) > 0.33
#Ml, norml = avg3d(mask[zlower[k]], zl)
#Mu, normu = avg3d(mask[zupper[k]], 1-zl)
#mask[z] = (Ml + Mu) / (norml + normu) > 0.5
return mask, zfill
def run(image=None):
from ..io import logger_setup
logger, log_file = logger_setup()
# Always start by initializing Qt (only once per application)
warnings.filterwarnings("ignore")
app = QApplication(sys.argv)
icon_path = pathlib.Path.home().joinpath('.cellpose', 'logo.png')
guip_path = pathlib.Path.home().joinpath('.cellpose', 'cellpose_gui.png')
style_path = pathlib.Path.home().joinpath('.cellpose', 'style_choice.npy')
if not icon_path.is_file():
cp_dir = pathlib.Path.home().joinpath('.cellpose')
cp_dir.mkdir(exist_ok=True)
print('downloading logo')
download_url_to_file('https://www.cellpose.org/static/images/cellpose_transparent.png', icon_path, progress=True)
if not guip_path.is_file():
print('downloading help window image')
download_url_to_file('https://www.cellpose.org/static/images/cellpose_gui.png', guip_path, progress=True)
if not style_path.is_file():
print('downloading style classifier')
download_url_to_file('https://www.cellpose.org/static/models/style_choice.npy', style_path, progress=True)
icon_path = str(icon_path.resolve())
app_icon = QtGui.QIcon()
app_icon.addFile(icon_path, QtCore.QSize(16, 16))
app_icon.addFile(icon_path, QtCore.QSize(24, 24))
app_icon.addFile(icon_path, QtCore.QSize(32, 32))
app_icon.addFile(icon_path, QtCore.QSize(48, 48))
app_icon.addFile(icon_path, QtCore.QSize(64, 64))
app_icon.addFile(icon_path, QtCore.QSize(256, 256))
app.setWindowIcon(app_icon)
app.setStyle("Fusion")
app.setPalette(guiparts_old.DarkPalette())
#app.setStyleSheet("QLineEdit { color: yellow }")
# models.download_model_weights() # does not exist
MainW_3d(image=image, logger=logger)
ret = app.exec_()
sys.exit(ret)
class MainW_3d(MainW):
def __init__(self, image=None, logger=None):
# MainW init
MainW.__init__(self, image=image, logger=logger)
# turn off single stroke
self.SCheckBox.setChecked(False)
### add orthoviews and z-bar
# ortho crosshair lines
self.vLine = pg.InfiniteLine(angle=90, movable=False)
self.hLine = pg.InfiniteLine(angle=0, movable=False)
self.vLineOrtho = [pg.InfiniteLine(angle=90, movable=False), pg.InfiniteLine(angle=90, movable=False)]
self.hLineOrtho = [pg.InfiniteLine(angle=0, movable=False), pg.InfiniteLine(angle=0, movable=False)]
self.make_orthoviews()
# z scrollbar underneath
self.scroll = QScrollBar(QtCore.Qt.Horizontal)
self.scroll.setMaximum(10)
self.scroll.valueChanged.connect(self.move_in_Z)
self.lmain.addWidget(self.scroll, 40,9,1,30)
b = 22
b+=1
label = QLabel('3D stitch threshold:')
label.setToolTip('for 3D volumes, turn on stitch_threshold to stitch masks across planes instead of running cellpose in 3D (see docs for details)')
label.setFont(self.medfont)
self.segBoxG.addWidget(label, b, 0,1,6)
self.stitch_threshold = QLineEdit()
self.stitch_threshold.setText('0.0')
self.stitch_threshold.setFixedWidth(40)
self.stitch_threshold.setFont(self.medfont)
self.stitch_threshold.setToolTip('for 3D volumes, turn on stitch_threshold to stitch masks across planes instead of running cellpose in 3D (see docs for details)')
self.segBoxG.addWidget(self.stitch_threshold, b,7,1,2)
b+=1
self.orthobtn = QCheckBox('ortho')
self.orthobtn.setToolTip('activate orthoviews with 3D image')
self.orthobtn.setFont(self.medfont)
self.orthobtn.setChecked(False)
self.l0.addWidget(self.orthobtn, b,0,1,2)
self.orthobtn.toggled.connect(self.toggle_ortho)
label = QLabel('dz:')
label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
label.setFont(self.medfont)
self.l0.addWidget(label, b, 2,1,1)
self.dz = 10
self.dzedit = QLineEdit()
self.dzedit.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
self.dzedit.setText(str(self.dz))
self.dzedit.returnPressed.connect(self.update_ortho)
self.dzedit.setFixedWidth(40)
self.dzedit.setFont(self.medfont)
self.l0.addWidget(self.dzedit, b, 3,1,2)
label = QLabel('z-aspect:')
label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
label.setFont(self.medfont)
self.l0.addWidget(label, b, 5,1,2)
self.zaspect = 1.0
self.zaspectedit = QLineEdit()
self.zaspectedit.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
self.zaspectedit.setText(str(self.zaspect))
self.zaspectedit.returnPressed.connect(self.update_ortho)
self.zaspectedit.setFixedWidth(40)
self.zaspectedit.setFont(self.medfont)
self.l0.addWidget(self.zaspectedit, b, 7,1,2)
b+=1
# add z position underneath
self.currentZ = 0
label = QLabel('Z:')
label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
self.l0.addWidget(label, b, 5,1,2)
self.zpos = QLineEdit()
self.zpos.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter)
self.zpos.setText(str(self.currentZ))
self.zpos.returnPressed.connect(self.update_ztext)
self.zpos.setFixedWidth(40)
self.zpos.setFont(self.medfont)
self.l0.addWidget(self.zpos, b, 7,1,2)
# if called with image, load it
if image is not None:
self.filename = image
io._load_image(self, self.filename, load_3D=True)
self.load_3D = True
def add_mask(self, points=None, color=(100,200,50), dense=True):
# points is list of strokes
points_all = np.concatenate(points, axis=0)
# loop over z values
median = []
zdraw = np.unique(points_all[:,0])
zrange = np.arange(zdraw.min(), zdraw.max()+1, 1, int)
zmin = zdraw.min()
pix = np.zeros((2,0), "uint16")
mall = np.zeros((len(zrange), self.Ly, self.Lx), "bool")
k=0
for z in zdraw:
ars, acs, vrs, vcs = np.zeros(0, "int"), np.zeros(0, "int"), np.zeros(0, "int"), np.zeros(0, "int")
for stroke in points:
stroke = np.concatenate(stroke, axis=0).reshape(-1, 4)
iz = stroke[:,0] == z
vr = stroke[iz,1]
vc = stroke[iz,2]
if iz.sum() > 0:
# get points inside drawn points
mask = np.zeros((np.ptp(vr)+4, np.ptp(vc)+4), np.uint8)
pts = np.stack((vc-vc.min()+2,vr-vr.min()+2), axis=-1)[:,np.newaxis,:]
mask = cv2.fillPoly(mask, [pts], (255,0,0))
ar, ac = np.nonzero(mask)
ar, ac = ar+vr.min()-2, ac+vc.min()-2
# get dense outline
contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
pvc, pvr = contours[-2][0].squeeze().T
vr, vc = pvr + vr.min() - 2, pvc + vc.min() - 2
# concatenate all points
ar, ac = np.hstack((np.vstack((vr, vc)), np.vstack((ar, ac))))
# if these pixels are overlapping with another cell, reassign them
ioverlap = self.cellpix[z][ar, ac] > 0
if (~ioverlap).sum() < 8:
print('ERROR: cell too small without overlaps, not drawn')
return None
elif ioverlap.sum() > 0:
ar, ac = ar[~ioverlap], ac[~ioverlap]
# compute outline of new mask
mask = np.zeros((np.ptp(ar)+4, np.ptp(ac)+4), np.uint8)
mask[ar-ar.min()+2, ac-ac.min()+2] = 1
contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
pvc, pvr = contours[-2][0].squeeze().T
vr, vc = pvr + ar.min() - 2, pvc + ac.min() - 2
ars = np.concatenate((ars, ar), axis=0)
acs = np.concatenate((acs, ac), axis=0)
vrs = np.concatenate((vrs, vr), axis=0)
vcs = np.concatenate((vcs, vc), axis=0)
self.draw_mask(z, ars, acs, vrs, vcs, color)
median.append(np.array([np.median(ars), np.median(acs)]))
mall[z-zmin, ars, acs] = True
pix = np.append(pix, np.vstack((ars, acs)), axis=-1)
mall = mall[:, pix[0].min():pix[0].max()+1, pix[1].min():pix[1].max()+1].astype(np.float32)
ymin, xmin = pix[0].min(), pix[1].min()
if len(zdraw) > 1:
mall, zfill = interpZ(mall, zdraw - zmin)
for z in zfill:
mask = mall[z].copy()
ar, ac = np.nonzero(mask)
ioverlap = self.cellpix[z+zmin][ar+ymin, ac+xmin] > 0
if (~ioverlap).sum() < 5:
print('WARNING: stroke on plane %d not included due to overlaps'%z)
elif ioverlap.sum() > 0:
mask[ar[ioverlap], ac[ioverlap]] = 0
ar, ac = ar[~ioverlap], ac[~ioverlap]
# compute outline of mask
outlines = masks_to_outlines(mask)
vr, vc = np.nonzero(outlines)
vr, vc = vr+ymin, vc+xmin
ar, ac = ar+ymin, ac+xmin
self.draw_mask(z+zmin, ar, ac, vr, vc, color)
self.zdraw.append(zdraw)
return median
def move_in_Z(self):
if self.loaded:
self.currentZ = min(self.NZ, max(0, int(self.scroll.value())))
self.zpos.setText(str(self.currentZ))
self.update_plot()
self.draw_layer()
self.update_layer()
def make_orthoviews(self):
self.pOrtho, self.imgOrtho, self.layerOrtho = [], [], []
for j in range(2):
self.pOrtho.append(pg.ViewBox(
lockAspect=True,
name=f'plotOrtho{j}',
border=[100, 100, 100],
invertY=True,
enableMouse=False
))
self.pOrtho[j].setMenuEnabled(False)
self.imgOrtho.append(pg.ImageItem(viewbox=self.pOrtho[j], parent=self))
self.imgOrtho[j].autoDownsample = False
self.layerOrtho.append(pg.ImageItem(viewbox=self.pOrtho[j], parent=self))
self.layerOrtho[j].setLevels([0.,255.])
#self.pOrtho[j].scene().contextMenuItem = self.pOrtho[j]
self.pOrtho[j].addItem(self.imgOrtho[j])
self.pOrtho[j].addItem(self.layerOrtho[j])
self.pOrtho[j].addItem(self.vLineOrtho[j], ignoreBounds=False)
self.pOrtho[j].addItem(self.hLineOrtho[j], ignoreBounds=False)
self.pOrtho[0].linkView(self.pOrtho[0].YAxis, self.p0)
self.pOrtho[1].linkView(self.pOrtho[1].XAxis, self.p0)
def add_orthoviews(self):
self.yortho = self.Ly//2
self.xortho = self.Lx//2
if self.NZ > 1:
self.update_ortho()
self.win.addItem(self.pOrtho[0], 0, 1, rowspan=1, colspan=1)
self.win.addItem(self.pOrtho[1], 1, 0, rowspan=1, colspan=1)
qGraphicsGridLayout = self.win.ci.layout
qGraphicsGridLayout.setColumnStretchFactor(0, 2)
qGraphicsGridLayout.setColumnStretchFactor(1, 1)
qGraphicsGridLayout.setRowStretchFactor(0, 2)
qGraphicsGridLayout.setRowStretchFactor(1, 1)
#self.p0.linkView(self.p0.YAxis, self.pOrtho[0])
#self.p0.linkView(self.p0.XAxis, self.pOrtho[1])
self.pOrtho[0].setYRange(0,self.Lx)
self.pOrtho[0].setXRange(-self.dz/3,self.dz*2 + self.dz/3)
self.pOrtho[1].setYRange(-self.dz/3,self.dz*2 + self.dz/3)
self.pOrtho[1].setXRange(0,self.Ly)
#self.pOrtho[0].setLimits(minXRange=self.dz*2+self.dz/3*2)
#self.pOrtho[1].setLimits(minYRange=self.dz*2+self.dz/3*2)
self.p0.addItem(self.vLine, ignoreBounds=False)
self.p0.addItem(self.hLine, ignoreBounds=False)
self.p0.setYRange(0,self.Lx)
self.p0.setXRange(0,self.Ly)
self.win.show()
self.show()
#self.p0.linkView(self.p0.XAxis, self.pOrtho[1])
def remove_orthoviews(self):
self.win.removeItem(self.pOrtho[0])
self.win.removeItem(self.pOrtho[1])
self.p0.removeItem(self.vLine)
self.p0.removeItem(self.hLine)
self.win.show()
self.show()
def update_crosshairs(self):
self.yortho = min(self.Ly-1, max(0, int(self.yortho)))
self.xortho = min(self.Lx-1, max(0, int(self.xortho)))
self.vLine.setPos(self.xortho)
self.hLine.setPos(self.yortho)
self.vLineOrtho[1].setPos(self.xortho)
self.hLineOrtho[1].setPos(self.zc)
self.vLineOrtho[0].setPos(self.zc)
self.hLineOrtho[0].setPos(self.yortho)
def update_ortho(self):
if self.NZ>1 and self.orthobtn.isChecked():
dzcurrent = self.dz
self.dz = min(100, max(3,int(self.dzedit.text() )))
self.zaspect = max(0.01, min(100., float(self.zaspectedit.text())))
self.dzedit.setText(str(self.dz))
self.zaspectedit.setText(str(self.zaspect))
if self.dz != dzcurrent:
self.pOrtho[0].setXRange(-self.dz/3,self.dz*2 + self.dz/3)
self.pOrtho[1].setYRange(-self.dz/3,self.dz*2 + self.dz/3)
dztot = min(self.NZ, self.dz * 2)
y = self.yortho
x = self.xortho
z = self.currentZ
if dztot == self.NZ:
zmin, zmax = 0, self.NZ
else:
if z-self.dz < 0:
zmin = 0
zmax = zmin + self.dz*2
elif z+self.dz >= self.NZ:
zmax = self.NZ
zmin = zmax - self.dz*2
else:
zmin, zmax = z-self.dz, z+self.dz
self.zc = z - zmin
self.update_crosshairs()
if self.view==0 or self.view==4:
for j in range(2):
if j==0:
if self.view==0:
image = self.stack[zmin:zmax, :, x].transpose(1,0,2)
else:
image = self.stack_filtered[zmin:zmax, :, x].transpose(1,0,2)
else:
image = self.stack[zmin:zmax, y, :] if self.view==0 else self.stack_filtered[zmin:zmax, y, :]
if self.nchan == 1:
# show single channel
image = image[...,0]
if self.color==0:
self.imgOrtho[j].setImage(image, autoLevels=False, lut=None)
if self.nchan > 1:
levels = np.array([self.saturation[0][self.currentZ],
self.saturation[1][self.currentZ],
self.saturation[2][self.currentZ]])
self.imgOrtho[j].setLevels(levels)
else:
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
elif self.color>0 and self.color<4:
if self.nchan > 1:
image = image[...,self.color-1]
self.imgOrtho[j].setImage(image, autoLevels=False, lut=self.cmap[self.color])
if self.nchan > 1:
self.imgOrtho[j].setLevels(self.saturation[self.color-1][self.currentZ])
else:
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
elif self.color==4:
image = image.astype(np.float32).mean(axis=-1).astype(np.uint8)
self.imgOrtho[j].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
elif self.color==5:
image = image.astype(np.float32).mean(axis=-1).astype(np.uint8)
self.imgOrtho[j].setImage(image, autoLevels=False, lut=self.cmap[0])
self.imgOrtho[j].setLevels(self.saturation[0][self.currentZ])
self.pOrtho[0].setAspectLocked(lock=True, ratio=self.zaspect)
self.pOrtho[1].setAspectLocked(lock=True, ratio=1./self.zaspect)
else:
image = np.zeros((10,10), np.uint8)
self.imgOrtho[0].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[0].setLevels([0.0, 255.0])
self.imgOrtho[1].setImage(image, autoLevels=False, lut=None)
self.imgOrtho[1].setLevels([0.0, 255.0])
self.win.show()
self.show()
def toggle_ortho(self):
if self.orthobtn.isChecked():
self.add_orthoviews()
else:
self.remove_orthoviews()
def plot_clicked(self, event):
if event.button()==QtCore.Qt.LeftButton \
and not event.modifiers() & (QtCore.Qt.ShiftModifier | QtCore.Qt.AltModifier)\
and not self.removing_region:
if event.double():
try:
self.p0.setYRange(0,self.Ly+self.pr)
except:
self.p0.setYRange(0,self.Ly)
self.p0.setXRange(0,self.Lx)
elif self.loaded and not self.in_stroke:
if self.orthobtn.isChecked():
items = self.win.scene().items(event.scenePos())
for x in items:
if x==self.p0:
pos = self.p0.mapSceneToView(event.scenePos())
x = int(pos.x())
y = int(pos.y())
if y>=0 and y<self.Ly and x>=0 and x<self.Lx:
self.yortho = y
self.xortho = x
self.update_ortho()
def update_plot(self):
super().update_plot()
if self.NZ>1 and self.orthobtn.isChecked():
self.update_ortho()
self.win.show()
self.show()
def keyPressEvent(self, event):
if self.loaded:
if not (event.modifiers() & (QtCore.Qt.ControlModifier | QtCore.Qt.ShiftModifier | QtCore.Qt.AltModifier) or self.in_stroke):
updated = False
if len(self.current_point_set) > 0:
if event.key() == QtCore.Qt.Key_Return:
self.add_set()
if self.NZ>1:
if event.key() == QtCore.Qt.Key_Left:
self.currentZ = max(0,self.currentZ-1)
self.scroll.setValue(self.currentZ)
updated = True
elif event.key() == QtCore.Qt.Key_Right:
self.currentZ = min(self.NZ-1, self.currentZ+1)
self.scroll.setValue(self.currentZ)
updated = True
else:
if event.key() == QtCore.Qt.Key_X:
self.MCheckBox.toggle()
if event.key() == QtCore.Qt.Key_Z:
self.OCheckBox.toggle()
if event.key() == QtCore.Qt.Key_Left or event.key() == QtCore.Qt.Key_A:
self.currentZ = max(0,self.currentZ-1)
self.scroll.setValue(self.currentZ)
updated = True
elif event.key() == QtCore.Qt.Key_Right or event.key() == QtCore.Qt.Key_D:
self.currentZ = min(self.NZ-1, self.currentZ+1)
self.scroll.setValue(self.currentZ)
updated = True
elif event.key() == QtCore.Qt.Key_PageDown:
self.view = (self.view+1)%(5)
self.ViewDropDown.setCurrentIndex(self.view)
elif event.key() == QtCore.Qt.Key_PageUp:
self.view = (self.view-1)%(5)
self.ViewDropDown.setCurrentIndex(self.view)
# can change background or stroke size if cell not finished
if event.key() == QtCore.Qt.Key_Up or event.key() == QtCore.Qt.Key_W:
self.color = (self.color-1)%(6)
self.RGBDropDown.setCurrentIndex(self.color)
elif event.key() == QtCore.Qt.Key_Down or event.key() == QtCore.Qt.Key_S:
self.color = (self.color+1)%(6)
self.RGBDropDown.setCurrentIndex(self.color)
elif event.key() == QtCore.Qt.Key_R:
if self.color!=1:
self.color = 1
else:
self.color = 0
self.RGBDropDown.setCurrentIndex(self.color)
elif event.key() == QtCore.Qt.Key_G:
if self.color!=2:
self.color = 2
else:
self.color = 0
self.RGBDropDown.setCurrentIndex(self.color)
elif event.key() == QtCore.Qt.Key_B:
if self.color!=3:
self.color = 3
else:
self.color = 0
self.RGBDropDown.setCurrentIndex(self.color)
elif (event.key() == QtCore.Qt.Key_Comma or
event.key() == QtCore.Qt.Key_Period):
count = self.BrushChoose.count()
gci = self.BrushChoose.currentIndex()
if event.key() == QtCore.Qt.Key_Comma:
gci = max(0, gci-1)
else:
gci = min(count-1, gci+1)
self.BrushChoose.setCurrentIndex(gci)
self.brush_choose()
if not updated:
self.update_plot()
if event.key() == QtCore.Qt.Key_Minus or event.key() == QtCore.Qt.Key_Equal:
self.p0.keyPressEvent(event)
def update_ztext(self):
zpos = self.currentZ
try:
zpos = int(self.zpos.text())
except:
print('ERROR: zposition is not a number')
self.currentZ = max(0, min(self.NZ-1, zpos))
self.zpos.setText(str(self.currentZ))
self.scroll.setValue(self.currentZ)