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GEPARD
Commit 92f24fb4 authored by Josef Brandt's avatar Josef Brandt
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Particle Painting seems to be stable

parent 156ef9b8
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Showing with 71 additions and 83 deletions
analysis/particleContainer.py
View file @ 92f24fb4
......@@ -178,10 +178,8 @@ class ParticleContainer(object):
def getMeasurementPixelCoords(self):
coords = []
# for particle in self.particles:
# for measurement in particle.getMeasurements():
for meas in self.measurements:
coords.append([meas.pixelcoord_x, meas.pixelcoord_y])
coords.append([meas.pixelcoord_x, meas.pixelcoord_y])
return coords
def getNumberOfParticlesOfAssignment(self, assignment):
......
analysis/particlePainter.py
View file @ 92f24fb4
......@@ -23,7 +23,6 @@ from PyQt5 import QtWidgets, QtCore, QtGui
import numpy as np
import cv2
class ParticlePainter(QtWidgets.QGraphicsItem):
def __init__(self, editorParent, img, topLeft):
super(ParticlePainter, self).__init__()
......@@ -38,22 +37,20 @@ class ParticlePainter(QtWidgets.QGraphicsItem):
self.painting = False
self.erasing = False
self.minRadius = 10
self.minRadius = 5
self.maxRadius = 500
self.radius = 30
self.brect = QtCore.QRectF(0,0,1,1)
self.imgToPixmap()
self.setPixmap()
self.setBrect()
def imgToPixmap(self):
img = self.img.repeat(3).reshape(self.img.shape[0], self.img.shape[1],3)
def setPixmap(self):
img = self.img.repeat(3).reshape(self.img.shape[0], self.img.shape[1], 3)
height, width, channel = img.shape
assert channel==3
bytesPerLine = 3 * width
pix = QtGui.QPixmap()
pix.convertFromImage(QtGui.QImage(img.data, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
self.pixmap = pix
self.pixmap = QtGui.QPixmap()
self.pixmap.convertFromImage(QtGui.QImage(img.data, width, height, bytesPerLine, QtGui.QImage.Format_RGB888))
def setBrect(self):
x0 = self.topLeft[1]
......@@ -101,49 +98,65 @@ class ParticlePainter(QtWidgets.QGraphicsItem):
elif event.key() == QtCore.Qt.Key_Return:
self.editorParent.acceptPaintedResult()
def drawParticle(self, pos):
pixelPos = round(pos.y()-self.topLeft[0]), round(pos.x()-self.topLeft[1])
x_min, x_max = round(pixelPos[1]-self.radius/2), round(pixelPos[1]+self.radius/2)
y_min, y_max = round(pixelPos[0]-self.radius/2), round(pixelPos[0]+self.radius/2)
def drawParticle(self, pixelPos):
x_min, x_max = round(pixelPos.x()-self.radius), round(pixelPos.x()+self.radius)
y_min, y_max = round(pixelPos.y()-self.radius), round(pixelPos.y()+self.radius)
x_shift = y_shift = 0
x_shift = y_shift = int(0)
if x_min < 0:
x_shift = x_min
elif x_min >= self.img.shape[1]:
x_shift = x_min + 1 - self.img.shape[1]
x_shift = int(x_min)
self.topLeft[1] -= abs(x_min)
elif x_max >= self.img.shape[1]:
x_shift = int(x_max + 1 - self.img.shape[1])
if y_min < 0:
y_shift = y_min
elif y_min >= self.img.shape[0]:
y_shift = y_min + 1 - self.img.shape[0]
self.topLeft[0] -= abs(y_min)
y_shift = int(y_min)
elif y_max >= self.img.shape[0]:
y_shift = int(y_max + 1 - self.img.shape[0])
if x_shift != 0 or y_shift != 0:
x_range = self.img.shape[1] + abs(x_shift)
y_range = self.img.shape[0] + abs(y_shift)
x_range = int(self.img.shape[1] + abs(x_shift))
y_range = int(self.img.shape[0] + abs(y_shift))
newImg = np.zeros((y_range, x_range))
if x_shift < 0:
if y_shift == 0:
newImg[abs(x_shift):, :] = self.img
elif y_shift < 0:
if y_shift < 0:
newImg[abs(y_shift):, abs(x_shift):] = self.img
elif y_shift == 0:
newImg[:, abs(x_shift):] = self.img
elif y_shift > 0:
newImg[:self.img.shape[0], abs(x_shift):] = self.img
elif x_shift == 0:
if y_shift < 0:
newImg[abs(y_shift):, :] = self.img
elif y_shift == 0:
newImg[:, :] = self.img
elif y_shift > 0:
newImg[:self.img.shape[0], :] = self.img
elif x_shift > 0:
if y_shift < 0:
newImg[abs(y_shift):, :self.img.shape[1]] = self.img
elif y_shift == 0:
newImg[:, :self.img.shape[1]] = self.img
elif y_shift > 0:
newImg[:y_shift, :self.img.shape[1]] = self.img
self.img = np.uint8(newImg)
self.setBrect()
center = (int(pixelPos.x()), int(pixelPos.y()))
# img, xmin, ymin, padding = self.contoursToImg(self.contours)
# center = (int(pos.x()+self.radius), int(pos.y()+self.radius))
# if self.painting:
# cv2.circle(img, center, self.radius, 255, -1)
# elif self.erasing:
# cv2.circle(img, center, self.radius, 0, -1)
#
# img = np.uint8(img)
# self.contours = self.imgToCnt(img, xmin, ymin, padding)
# self.getBrectAndPolygon()
# self.update()
if self.painting:
cv2.circle(self.img, center, self.radius, 255, -1)
elif self.erasing:
cv2.circle(self.img, center, self.radius, 0, -1)
self.setPixmap()
self.update()
def paint(self, painter, option, widget):
painter.setPen(QtCore.Qt.white)
painter.drawRect(self.brect)
......
analysis/particleeditor.py
View file @ 92f24fb4
......@@ -189,9 +189,10 @@ class ParticleEditor(QtCore.QObject):
self.storedAssignmend = newAssignment
contours = self.particleContainer.getParticleContoursByIndex(contourIndices)
topLeft = self.getTopLeft(contours)
img, self.xmin, self.ymin, self.padding = self.contoursToImg(contours)
# topLeft = self.getTopLeft(contours)
# img, self.xmin, self.ymin, self.padding = self.contoursToImg(contours, padding=0)
img, xmin, ymin, self.padding = self.contoursToImg(contours, padding=0)
topLeft = [ymin, xmin]
self.particlePainter = ParticlePainter(self, img, topLeft)
self.viewparent.normalSize()
......@@ -201,7 +202,10 @@ class ParticleEditor(QtCore.QObject):
def acceptPaintedResult(self):
try:
newContour = self.mergeContours(self.particlePainter.contours)
img = self.particlePainter.img
xmin = self.particlePainter.topLeft[1]
ymin = self.particlePainter.topLeft[0]
newContour = self.imgToCnt(img, xmin, ymin, 0)
except NotConnectedContoursError:
self.storedIndices = []
self.storedAssignmend = None
......@@ -258,7 +262,7 @@ class ParticleEditor(QtCore.QObject):
if len(contours)>1:
QtWidgets.QMessageBox.critical(self.viewparent, 'ERROR!',
'Particle contours are not connected and cannot be combined!')
'Particle contours are not connected or have holes.\nThat is currently not supported!')
raise NotConnectedContoursError
newContour = contours[0]
......@@ -273,7 +277,7 @@ class ParticleEditor(QtCore.QObject):
#draw contours
xmin = cnt[:,0,:][:, 0].min()
ymin= cnt[:,0,:][:, 1].min()
return ymin, xmin
return [ymin, xmin]
def mergeParticlesInParticleContainerAndSampleView(self, indices, newContour, stats, assignment):
self.viewparent.addParticleContourToIndex(newContour, len(self.viewparent.contourItems)-1)
......
gepard.py
View file @ 92f24fb4
......@@ -326,12 +326,11 @@ if __name__ == '__main__':
if not os.path.exists(logpath):
os.mkdir(logpath)
logname = os.path.join(logpath, 'logfile.txt')
#
# fp = open(logname, "a")
# sys.stderr = fp
# sys.stdout = fp
print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()),
flush=True)
fp = open(logname, "a")
sys.stderr = fp
sys.stdout = fp
print("starting GEPARD at: " + strftime("%d %b %Y %H:%M:%S", localtime()), flush=True)
gepard = GEPARDMainWindow(logpath)
gepard.showMaximized()
......
sampleview.py
View file @ 92f24fb4
......@@ -268,14 +268,9 @@ class SampleView(QtWidgets.QGraphicsView):
if self.particleEditor is None:
self.particleEditor = ParticleEditor(self, self.dataset.particleContainer)
#try disconnecting the signals. If they are connected multiple times, the functions will run accordingly...
# tryDisconnectingSignal(self.particleEditor.particleContoursChanged)
tryDisconnectingSignal(self.particleEditor.particleAssignmentChanged)
# self.particleEditor.particleContoursChanged.connect(self.resetParticleContours)
if self.analysiswidget is not None:
# self.particleEditor.particleContoursChanged.connect(self.analysiswidget.updateHistogramsAndContours)
self.particleEditor.particleAssignmentChanged.connect(self.analysiswidget.updateHistogramsAndContours)
def setMicroscopeMode(self):
......@@ -381,9 +376,7 @@ class SampleView(QtWidgets.QGraphicsView):
self.dataset.readin = False
else:
return
# x, y, z = self.dataset.mapToLengthRaman([p0.x(), p0.y()],
# microscopeMode=self.microscopeMode,
# noz=(False if self.mode=="RamanScan" else True))
noz = (self.mode in ['OpticalScan', 'RamanScan'])
x, y, z = self.dataset.mapToLengthRaman([pos.x(), pos.y()], microscopeMode=self.microscopeMode, noz=noz)
if z is not None:
......
viewitems.py
View file @ 92f24fb4
......@@ -29,7 +29,6 @@ class SegmentationContour(QtWidgets.QGraphicsItem):
self.setZValue(1)
self.setPos(pos[0], pos[1])
self.setFlag(QtWidgets.QGraphicsItem.ItemIsSelectable)
# self.setAcceptedMouseButtons(QtCore.Qt.AllButtons)
self.brect = QtCore.QRectF(0,0,1,1)
self.contourData = contourData
......@@ -55,10 +54,7 @@ class SegmentationContour(QtWidgets.QGraphicsItem):
def boundingRect(self):
return self.brect
# def createRamanScanIndices(self):
def setIndex(self, index):
self.particleIndex = index
......@@ -83,13 +79,6 @@ class SegmentationContour(QtWidgets.QGraphicsItem):
painter.drawPolygon(self.polygon)
# def mousePressEvent(self, event):
# print('press in contour')
#
# def mouseMoveEvent(self, event):
# print('move in contour')
#
def contextMenuEvent(self, event):
if self.isSelected:
self.contextMenu = ParticleContextMenu(self.viewparent)
......@@ -169,14 +158,6 @@ class RamanScanIndicator(QtWidgets.QGraphicsItem):
font.setPointSize(10)
painter.setFont(font)
painter.drawText(rect, QtCore.Qt.AlignCenter, str(self.number))
# def mousePressEvent(self, event):
# p = event.pos()
# x, y = p.x(), p.y()
# r = np.sqrt(x**2+y**2)
# if r<self.radius:
# self.view.selectRamanScanPoint(self.number, r)
# super().mouseReleaseEvent(event)
class ScanIndicator(QtWidgets.QGraphicsItem):
......
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