Merge commit '33010f81b0219286f80110e386593df2d629c392' (eaebe41d) · Commits · GEPARD / GEPARD

dataset.py

+25 −5

Original line number	Diff line number	Diff line
		@@ -74,6 +74,18 @@ class DataSet(object):
		self.pshift = None # shift of raman scan position relative to image center
		self.seedpoints = np.array([])
		self.seeddeletepoints = np.array([])
		self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
		'contrastcurve': True,
		'blurRadius': 9,
		'threshold': 0.2,
		'maxholebrightness': 0.5,
		'erodeconvexdefects': 0,
		'minparticlearea': 20,
		'minparticledistance': 20,
		'measurefrac': 1,
		'compactness': 0.1,
		'seedRad': 3}

		self.ramanpoints = []
		self.particlecontours = []
		self.particlestats = []
		@@ -104,8 +116,8 @@ class DataSet(object):
		from opticalscan import loadAndPasteImage

		# try to load png and check for detection contours
		recreatefullimage = recreatefullimage or not os.path.exists(self.getLegacyImageName())
		if not recreatefullimage:
		buggyimage = recreatefullimage
		if not buggyimage and os.path.exists(self.getLegacyImageName()):
		img = cv2imread_fix(self.getLegacyImageName())
		Nc = len(self.particlecontours)
		if Nc>0:
		@@ -113,12 +125,12 @@ class DataSet(object):
		contpixels = img[contour[:,0,1],contour[:,0,0]]
		if np.all(contpixels[:,1]==255) and np.all(contpixels[:,2]==0) \
		and np.all(contpixels[:,0]==0):
		recreatefullimage = True
		if not recreatefullimage:
		buggyimage = True
		if not buggyimage:
		cv2imwrite_fix(self.getImageName(), img)
		del img

		if recreatefullimage:
		if buggyimage:
		print("recreating fullimage from grid data")
		imgdata = None
		zvalimg = None
		@@ -249,3 +261,11 @@ class DataSet(object):
		def save(self):
		saveData(self, self.fname)


		if __name__ == '__main__':
		dset = loadData(r'C:\Users\brandt\Desktop\20180723DemoTZW\20180723DemoTZW.pkl')
		print(dset.detectParams)
		# dset.seedpoints = np.array([])
		# dset.seeddeletepoints = np.array([])
		# dset.save()

		No newline at end of file

detectionview.py

+96 −34

Original line number	Diff line number	Diff line
		@@ -32,7 +32,10 @@ class HistWidget(QtWidgets.QWidget):
		super().__init__(parent)

		self.updateCallbacks(histcallback, curvecallback)
		self.points = np.array([[50,0],[100,150],[200,255]])
		if parent.dataset is None:
		self.points = np.array([[50,0],[100,220],[200,255]])
		else:
		self.points = parent.dataset.detectParams['points']

		self.fig = plt.Figure()
		self.canvas = FigureCanvasQTAgg(self.fig)
		@@ -151,12 +154,12 @@ class ImageView(QtWidgets.QLabel):
		p0 = np.array([p0])
		if len(self.seedpoints)>0:
		arr = np.array(self.seedpoints)
		d = np.linalg.norm(arr-p0, axis=1)
		d = np.linalg.norm(arr[:, :2]-p0, axis=1)
		ind = d>self.seedradius
		self.seedpoints = arr[ind,:].tolist()
		if len(self.seeddeletepoints)>0:
		arr = np.array(self.seeddeletepoints)
		d = np.linalg.norm(arr-p0, axis=1)
		d = np.linalg.norm(arr[:, :2]-p0, axis=1)
		ind = d>self.seedradius
		self.seeddeletepoints = arr[ind,:].tolist()

		@@ -170,9 +173,9 @@ class ImageView(QtWidgets.QLabel):
		self.drag = "add"
		p0 = event.pos()
		if self.drag=="add":
		self.seedpoints.append([p0.x(),p0.y()])
		self.seedpoints.append([p0.x(),p0.y(),self.seedradius])
		elif self.drag=="delete":
		self.seeddeletepoints.append([p0.x(),p0.y()])
		self.seeddeletepoints.append([p0.x(),p0.y(),self.seedradius])
		else:
		self.removeSeeds([p0.x(),p0.y()])

		@@ -183,9 +186,9 @@ class ImageView(QtWidgets.QLabel):
		if self.drag:
		p0 = event.pos()
		if self.drag=="add":
		self.seedpoints.append([p0.x(),p0.y()])
		self.seedpoints.append([p0.x(),p0.y(),self.seedradius])
		elif self.drag=="delete":
		self.seeddeletepoints.append([p0.x(),p0.y()])
		self.seeddeletepoints.append([p0.x(),p0.y(),self.seedradius])
		else:
		self.removeSeeds([p0.x(),p0.y()])
		self.update()
		@@ -205,6 +208,10 @@ class ImageView(QtWidgets.QLabel):
		self.overlay = None

		def updateSeedPoints(self, seedpoints=[], seeddeletepoints=[]):
		# if len(seedpoints) > 0 and len(self.seedpoints) > 0:
		# print(seedpoints[0, :], self.seedpoints[0, :])
		# else:
		# print('else...', len(seedpoints), len(self.seedpoints))
		self.seedpoints = seedpoints
		self.seeddeletepoints = seeddeletepoints

		@@ -231,6 +238,7 @@ class ImageView(QtWidgets.QLabel):
		self.overlay = pix

		def paintEvent(self, event):

		painter = QtGui.QPainter(self)
		painter.drawPixmap(0, 0, self.pixmap())
		painter.setOpacity(self.alpha)
		@@ -247,16 +255,16 @@ class ImageView(QtWidgets.QLabel):
		painter.drawEllipse(p[0]-2, p[1]-2, 5, 5)

		if self.showseedpoints:
		r = self.seedradius
		painter.setPen(QtCore.Qt.magenta)
		painter.setBrush(QtCore.Qt.magenta)
		for p in self.seeddeletepoints:
		painter.drawEllipse(p[0]-r, p[1]-r, 2r, 2r)

		painter.setPen(QtCore.Qt.white)
		painter.setBrush(QtCore.Qt.white)
		for p in self.seedpoints:
		painter.drawEllipse(p[0]-r, p[1]-r, 2r, 2r)
		painter.drawEllipse(p[0]-p[2], p[1]-p[2], 2p[2], 2p[2])

		painter.setPen(QtCore.Qt.magenta) #I think it is more useful when the deletpoints override the seedpoints
		painter.setBrush(QtCore.Qt.magenta)

		for p in self.seeddeletepoints:
		painter.drawEllipse(p[0]-p[2], p[1]-p[2], 2p[2], 2p[2])

		class ParticleDetectionView(QtWidgets.QWidget):
		imageUpdate = QtCore.pyqtSignal(name='imageUpdate')
		@@ -264,10 +272,10 @@ class ParticleDetectionView(QtWidgets.QWidget):

		def __init__(self, img, dataset, parent=None):
		super().__init__(parent, QtCore.Qt.Window)
		self.dataset = dataset
		self.dataset = self.verifySeedpoints(dataset)
		self.img = img
		self.imgclip = 0,0,0,0
		self.seg = Segmentation()
		self.seg = Segmentation(self.dataset)
		self.thread = None

		vbox = QtWidgets.QVBoxLayout()
		@@ -294,6 +302,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
		group = QtWidgets.QGroupBox("Detection settings", self)
		grid = QtWidgets.QGridLayout()
		self.parameters = []
		#create editable parameters:
		for i, p in enumerate(self.seg.parlist):
		label, colstretch = None, 1
		if p.name == "points":
		@@ -371,6 +380,37 @@ class ParticleDetectionView(QtWidgets.QWidget):
		self.setLayout(hbox)
		self.setWindowTitle("Particle Detection")

		def saveDetectParams(self, ds=None):
		if ds is not None:
		for param in self.parameters:
		if param[1] == 'points':
		print(param[0].value())
		try: #is it a spinbox or the histWidget? Read out the value
		ds.detectParams[param[1]] = param[0].value()
		except: #otherwise checkbox -> take its state
		ds.detectParams[param[1]] = param[0].isChecked()
		ds.detectParams['seedRad'] = self.seedradiusedit.value()
		ds.save()

		def verifySeedpoints(self, dataset):
		seedpoints = dataset.seedpoints
		seeddeletepoints = dataset.seeddeletepoints

		if len(seedpoints) > 0: #points are present
		if seedpoints.shape[1] == 2: #old entries with only x,y coordinates
		radii = np.ones((seedpoints.shape[0], 1))*3
		dataset.seedpoints = np.hstack((seedpoints, radii))
		else:
		dataset.seedpoints = np.array([])

		if len(seeddeletepoints) > 0: #points are present
		if seeddeletepoints.shape[1] == 2: #old entries with only x,y coordinates
		radii = np.ones((seeddeletepoints.shape[0], 1))*3
		dataset.seeddeletepoints = np.hstack((seeddeletepoints, radii))
		else:
		dataset.seeddeletepoints = np.array([])
		return dataset

		@QtCore.pyqtSlot()
		def seedChanged(self):
		seedradius = self.seedradiusedit.value()
		@@ -380,20 +420,21 @@ class ParticleDetectionView(QtWidgets.QWidget):
		ind &= (arr0[:,1]>n1-seedradius)&(arr0[:,1]<=n2+seedradius)
		arr0 = arr0[~ind,:]
		else:
		arr0 = arr0.reshape(0,2)
		arr0 = arr0.reshape(0,3)

		if arr1.shape[0]>0:
		arr1 += p0
		arr1[:,:2] += p0
		else:
		arr1 = arr1.reshape(0,2)
		arr1 = arr1.reshape(0,3)
		return np.concatenate((arr0, arr1), axis=0)

		if self.dataset is not None:
		n1,n2,m1,m2 = self.imgclip
		p0 = np.array([[m1,n1]], dtype=np.int32)

		self.dataset.seedpoints = clipdata(self.dataset.seedpoints,
		np.array(self.imglabel.seedpoints, dtype=np.int32),
		p0, n1, n2, m1, m2)

		self.dataset.seeddeletepoints = clipdata(self.dataset.seeddeletepoints,
		np.array(self.imglabel.seeddeletepoints, dtype=np.int32),
		p0, n1, n2, m1, m2)
		@@ -402,23 +443,35 @@ class ParticleDetectionView(QtWidgets.QWidget):
		@QtCore.pyqtSlot()
		def updateImageSeeds(self):
		if self.dataset is not None:
		seedradius = self.seedradiusedit.value()
		# seedradius = self.seedradiusedit.value()
		n1,n2,m1,m2 = self.imgclip
		p0 = np.array([[m1,n1]], dtype=np.int32)
		seedpoints = []
		seeddeletepoints = []

		arr1 = self.dataset.seedpoints
		if arr1.shape[0]>0:
		ind = (arr1[:,0]>m1-seedradius)&(arr1[:,0]<=m2+seedradius)
		ind &= (arr1[:,1]>n1-seedradius)&(arr1[:,1]<=n2+seedradius)
		if np.any(ind):
		seedpoints = (arr1[ind,:]-p0).tolist()
		#what seeds are actually in image view?
		for point in arr1: #Josef says: I replaced the commented logic with the one right here below, as the old one somehow did not work.... The for-loop might become slow at some point??
		if point[0] > (m1-point[2]) and point[0] <= (m2+point[2]) and point[1] > (n1-point[2]) and point[1] <= (n2+point[2]):
		seedpoints.append([point[0] - p0[0][0], point[1] - p0[0][1], point[2]])
		# if arr1.shape[0]>0:
		# ind = (arr1[:,0]>m1-seedradius)&(arr1[:,0]<=m2+seedradius)
		# ind &= (arr1[:,1]>n1-seedradius)&(arr1[:,1]<=n2+seedradius)
		# if np.any(ind):
		# arr1[ind, :2] -= p0
		# seedpoints = arr1.tolist()
		#
		arr2 = self.dataset.seeddeletepoints
		if arr2.shape[0]>0:
		ind = (arr2[:,0]>m1-seedradius)&(arr2[:,0]<=m2+seedradius)
		ind &= (arr2[:,1]>n1-seedradius)&(arr2[:,1]<=n2+seedradius)
		if np.any(ind):
		seeddeletepoints = (arr2[ind,:]-p0).tolist()
		for point in arr2: #Josef says: I replaced the commented logic with the one right here below, as the old one somehow did not work.... The for-loop might become slow at some point??
		if point[0] > (m1-point[2]) and point[0] <= (m2+point[2]) and point[1] > (n1-point[2]) and point[1] <= (n2+point[2]):
		seeddeletepoints.append([point[0] - p0[0][0], point[1] - p0[0][1], point[2]])
		# if arr2.shape[0]>0:
		# ind = (arr2[:,0]>m1-seedradius)&(arr2[:,0]<=m2+seedradius)
		# ind &= (arr2[:,1]>n1-seedradius)&(arr2[:,1]<=n2+seedradius)
		# if np.any(ind):
		# arr2[ind, :2] -= p0
		# seeddeletepoints = arr2.tolist()

		self.imglabel.updateSeedPoints(seedpoints, seeddeletepoints)

		def closeEvent(self, event):
		@@ -436,6 +489,12 @@ class ParticleDetectionView(QtWidgets.QWidget):
		self.lastmove = (self.lastcenter[0]+dp.x(),self.lastcenter[1]+dp.y())
		self.setImageCenter(self.lastmove)

		def wheelEvent(self, event):
		if event.angleDelta().y() > 0:
		self.seedradiusedit.setValue(self.seedradiusedit.value()+1)
		else:
		self.seedradiusedit.setValue(self.seedradiusedit.value()-1)

		def mouseReleaseEvent(self, event):
		if self.drag:
		self.lastcenter = self.lastmove
		@@ -486,6 +545,7 @@ class ParticleDetectionView(QtWidgets.QWidget):
		self.updateImageSeeds()

		def detectShow(self, showname):
		self.saveDetectParams(self.dataset)
		img = self.subimg.copy()
		kwargs = {}
		for ui, name, valuefunc in self.parameters:
		@@ -534,6 +594,7 @@ class ParticleDetectionView(QtWidgets.QWidget):

		@QtCore.pyqtSlot()
		def detectParticles(self):
		self.saveDetectParams(self.dataset)
		if self.thread is not None and self.thread.is_alive():
		self.cancelThread()
		return
		@@ -596,7 +657,8 @@ if __name__ == "__main__":
		from dataset import DataSet
		from time import time

		fname = r"D:\Projekte\Mikroplastik\Waferreinigung_Kerzenfilter\WaferMilliQH118\fullimage.tif"
		# fname = r"D:\Projekte\Mikroplastik\Waferreinigung_Kerzenfilter\WaferMilliQH118\fullimage.tif"
		fname = r"C:\Users\brandt\Desktop\20180723DemoTZW\fullimage.tif"
		app = QtWidgets.QApplication(sys.argv)

		t2 = time()
		@@ -605,8 +667,8 @@ if __name__ == "__main__":
		print("OpenCV read:", t3-t2)
		img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)

		view = ParticleDetectionView(img, None)
		ds = DataSet("dummy")
		view = ParticleDetectionView(img, ds, None)
		view.setDataSet(ds)
		view.show()
		app.exec_()
		No newline at end of file

segmentation.py

+38 −29

Original line number	Diff line number	Diff line
		@@ -41,22 +41,36 @@ class Parameter(object):
		self.show = show

		class Segmentation(object):
		def __init__(self):
		def __init__(self, dataset=None):
		self.cancelcomputation = False
		if dataset is not None:
		self.detectParams = dataset.detectParams
		else:
		self.detectParams = {'points': np.array([[50,0],[100,200],[200,255]]),
		'contrastcurve': True,
		'blurRadius': 9,
		'threshold': 0.2,
		'maxholebrightness': 0.5,
		'erodeconvexdefects': 0,
		'minparticlearea': 20,
		'minparticledistance': 20,
		'measurefrac': 1,
		'compactness': 0.1,
		'seedRad': 3}
		self.initialParameters()

		def initialParameters(self):
		parlist = [Parameter("points", np.ndarray, np.array([[20,0],[50,100],[200,255]]), helptext="Curve contrast"),
		Parameter("contrastcurve", np.bool, True, helptext="Contrast curve", show=True),
		Parameter("blurRadius", int, 9, 3, 99, 1, 2, helptext="Blur radius", show=True),
		Parameter("threshold", float, .2, .01, .9, 2, .02, helptext="Basic threshold", show=True),
		Parameter("maxholebrightness", float, 0.5, 0, 1, 2, 0.02, helptext="Close holes brighter than..", show = True),
		Parameter("erodeconvexdefects", int, 0, 0, 20, helptext="Erode convex defects", show=True),
		Parameter("minparticlearea", int, 20, 10, 1000, 0, 50, helptext="Min. particle pixel area", show=False),
		Parameter("minparticledistance", int, 20, 10, 1000, 0, 5, helptext="Min. distance between particles", show=False),
		Parameter("measurefrac", float, 1, 0, 1, 2, stepsize = 0.05, helptext="measure fraction of particles", show=False),
		parlist = [Parameter("points", np.ndarray, self.detectParams['points'], helptext="Curve contrast"),
		Parameter("contrastcurve", np.bool, self.detectParams['contrastcurve'], helptext="Contrast curve", show=True),
		Parameter("blurRadius", int, self.detectParams['blurRadius'], 3, 99, 1, 2, helptext="Blur radius", show=True),
		Parameter("threshold", float, self.detectParams['threshold'], .01, .9, 2, .02, helptext="Basic threshold", show=True),
		Parameter("maxholebrightness", float, self.detectParams['maxholebrightness'], 0, 1, 2, 0.02, helptext="Close holes brighter than..", show = True),
		Parameter("erodeconvexdefects", int, self.detectParams['erodeconvexdefects'], 0, 20, helptext="Erode convex defects", show=True),
		Parameter("minparticlearea", int, self.detectParams['minparticlearea'], 10, 1000, 0, 50, helptext="Min. particle pixel area", show=False),
		Parameter("minparticledistance", int, self.detectParams['minparticledistance'], 10, 1000, 0, 5, helptext="Min. distance between particles", show=False),
		Parameter("measurefrac", float, self.detectParams['measurefrac'], 0, 1, 2, stepsize = 0.05, helptext="measure fraction of particles", show=False),
		Parameter("sure_fg", None, helptext="Show sure foreground", show=True),
		Parameter("compactness", float, 0.1, 0, 1, 2, 0.05, helptext="watershed compactness", show=False),
		Parameter("compactness", float, self.detectParams['compactness'], 0, 1, 2, 0.05, helptext="watershed compactness", show=False),
		Parameter("watershed", None, helptext="Show watershed markers", show=True),
		]
		# make each parameter accessible via self.name
		@@ -279,10 +293,6 @@ class Segmentation(object):
		if return_step=="contrastcurve": return gray, 0

		# image blur for noise-reduction
		if self.blurRadius%2 != 1:
		self.blurRadius += 1
		print('blur Radius was an even number, incremented blur Radius by 1')

		blur = cv2.medianBlur(gray, self.blurRadius)
		blur = np.uint8(blur*(255/blur.max()))
		if return_step=="blurRadius": return blur, 0
		@@ -330,27 +340,26 @@ class Segmentation(object):

		sure_fg = self.getSureForeground(erthresh, self.minparticledistance, self.minparticlearea)

		# modify sure_fg with seedpoints and deletepoints
		sure_bg = cv2.dilate(erthresh, np.ones((5, 5)), iterations = 1)
		sure_bg = self.closeHoles(sure_bg)

		sure_bg = cv2.dilate(thresh, np.ones((5, 5)), iterations = 1)
		sure_bg = self.closeHoles(sure_bg)

		# modify sure_fg and sure_bg with seedpoints and deletepoints
		if len(deletepoints)>0:
		h, w = sure_fg.shape[:2]
		mask = np.zeros((h+2, w+2), np.uint8)
		for p in np.int32(deletepoints):
		if p[0] >= 0 and p[1] >= 0:
		cv2.floodFill(sure_fg, mask, tuple(p), 0)
		else:
		print('skipped del point at {}'.format(p))
		for p in np.int32(deletepoints):
		cv2.circle(sure_fg, tuple(p), int(seedradius), 0, -1)
		if p[0] > 0 and p[1] > 0:
		cv2.floodFill(sure_fg, mask, tuple([p[0], p[1]]), 0)

		for p in np.int32(seedpoints):
		cv2.circle(sure_fg, tuple(p), int(seedradius), 1, -1)

		sure_bg = cv2.dilate(erthresh, np.ones((5, 5)), iterations = 1)
		sure_bg = self.closeHoles(sure_bg)
		print("sure_fg, sure_bg")
		cv2.circle(sure_fg, tuple([p[0], p[1]]), int(p[2]), 1, -1)
		for p in np.int32(deletepoints):
		cv2.circle(sure_fg, tuple([p[0], p[1]]), int(p[2]), 0, -1)
		cv2.circle(sure_bg, tuple([p[0], p[1]]), int(p[2]), 0, -1)

		sure_bg = cv2.dilate(thresh, np.ones((5, 5)), iterations = 1)
		sure_bg = self.closeHoles(sure_bg)
		print("sure_fg, sure_bg")
		if self.cancelcomputation:
		return None, None, None