def drawThreshMask(self, worm_img, worm_qimg, row_data, read_center=True):
#in very old versions of the tracker I didn't save the area in trajectories table,
#let's assign a default value to deal with this cases
if 'area' in row_data:
min_blob_area = row_data['area'] / 2
else:
min_blob_area = 10
c1, c2 = (row_data['coord_x'],
row_data['coord_y']) if read_center else (-1, -1)
worm_mask, worm_cnt, _ = getWormMask(
worm_img,
row_data['threshold'],
strel_size=self.strel_size,
roi_center_x=c1,
roi_center_y=c2,
min_blob_area=min_blob_area,
is_light_background=self.is_light_background)
worm_mask = QImage(worm_mask.data, worm_mask.shape[1],
worm_mask.shape[0], worm_mask.strides[0],
QImage.Format_Indexed8)
worm_mask = worm_mask.convertToFormat(QImage.Format_RGB32,
Qt.AutoColor)
worm_mask = QPixmap.fromImage(worm_mask)
worm_mask = worm_mask.createMaskFromColor(Qt.black)
p = QPainter(worm_qimg)
p.setPen(QColor(0, 204, 102))
p.drawPixmap(worm_qimg.rect(), worm_mask, worm_mask.rect())
if False:
#test skeletonization
skeleton, ske_len, cnt_side1, cnt_side2, cnt_widths, cnt_area = \
getSkeleton(worm_cnt, np.zeros(0), 49)
for cnt in skeleton, cnt_side1, cnt_side2:
p.setPen(Qt.black)
polyline = QPolygonF()
for point in cnt:
polyline.append(QPointF(*point))
p.drawPolyline(polyline)
p.end()
def drawThreshMask(self, worm_img, worm_qimg, row_data, read_center = True):
worm_mask = getWormMask(worm_img, row_data['threshold'])
min_mask_area = row_data['area']/2
if read_center:
worm_cnt, _ = binaryMask2Contour(worm_mask, roi_center_x = row_data['coord_y'], roi_center_y = row_data['coord_x'], min_mask_area = min_mask_area)
else:
worm_cnt, _ = binaryMask2Contour(worm_mask, min_mask_area = min_mask_area)
worm_mask = np.zeros_like(worm_mask)
cv2.drawContours(worm_mask, [worm_cnt.astype(np.int32)], 0, 1, -1)
worm_mask = QImage(worm_mask.data, worm_mask.shape[1],
worm_mask.shape[0], worm_mask.strides[0], QImage.Format_Indexed8)
worm_mask = worm_mask.convertToFormat(QImage.Format_RGB32, Qt.AutoColor)
worm_mask = worm_mask.scaled(worm_qimg.width(),worm_qimg.height(), Qt.KeepAspectRatio)
worm_mask = QPixmap.fromImage(worm_mask)
worm_mask = worm_mask.createMaskFromColor(Qt.black)
p = QPainter(worm_qimg)
p.setPen(QColor(0,204,102))
p.drawPixmap(worm_qimg.rect(), worm_mask, worm_mask.rect())
p.end()
def updateROIcanvas(self, wormCanvas, worm_index_roi, comboBox_ROI, isDrawSkel):
if not isinstance(self.frame_data, pd.DataFrame):
wormCanvas.clear()
return
#update valid index for the comboBox
comboBox_ROI.clear()
comboBox_ROI.addItem(str(worm_index_roi))
for ind in self.frame_data[self.worm_index_str].data:
comboBox_ROI.addItem(str(ind))
#extract individual worm ROI
good = self.frame_data[self.worm_index_str] == worm_index_roi
roi_data = self.frame_data.loc[good].squeeze()
if roi_data.size == 0:
wormCanvas.clear()
return
if np.isnan(roi_data['coord_x']) or np.isnan(roi_data['coord_y']):
return #invalid coordinate, nothing to do here
worm_roi, roi_corner = getWormROI(self.original_image, roi_data['coord_x'], roi_data['coord_y'], roi_data['roi_size'])
roi_corner = roi_corner+1
#worm_roi, roi_corner = self.original_image, np.zeros(2)
roi_ori_size = worm_roi.shape
worm_roi = np.ascontiguousarray(worm_roi)
#worm_roi = cv2.cvtColor(worm_img, cv2.COLOR_GRAY2RGB);
worm_img = QImage(worm_roi.data, worm_roi.shape[1], worm_roi.shape[0], worm_roi.strides[0], QImage.Format_Indexed8)
worm_img = worm_img.convertToFormat(QImage.Format_RGB32, Qt.AutoColor)
canvas_size = min(wormCanvas.height(),wormCanvas.width())
worm_img = worm_img.scaled(canvas_size,canvas_size, Qt.KeepAspectRatio)#, Qt.SmoothTransformation)
if isDrawSkel:
if roi_data['has_skeleton']==1:
c_ratio_y = worm_img.width()/roi_ori_size[1];
c_ratio_x = worm_img.height()/roi_ori_size[0];
skel_id = int(roi_data['skeleton_id'])
qPlg = {}
for tt in ['skeleton', 'contour_side1', 'contour_side2']:
dat = self.skel_dat[tt][skel_id];
dat[:,0] = (dat[:,0]-roi_corner[0])*c_ratio_x
dat[:,1] = (dat[:,1]-roi_corner[1])*c_ratio_y
#dat = (self.skel_dat[tt][skel_id] - 0)*c_ratio
qPlg[tt] = QPolygonF()
for p in dat:
qPlg[tt].append(QPointF(*p))
if 'is_good_skel' in roi_data and roi_data['is_good_skel'] == 0:
self.skel_colors = {'skeleton':(102, 0, 0 ),
'contour_side1':(102, 0, 0 ), 'contour_side2':(102, 0, 0 )}
else:
self.skel_colors = {'skeleton':(27, 158, 119 ),
'contour_side1':(217, 95, 2), 'contour_side2':(231, 41, 138)}
pen = QPen()
pen.setWidth(2)
painter = QPainter()
painter.begin(worm_img)
for tt, color in self.skel_colors.items():
pen.setColor(QColor(*color))
painter.setPen(pen)
painter.drawPolyline(qPlg[tt])
pen.setColor(Qt.black)
painter.setBrush(Qt.white)
painter.setPen(pen)
radius = 3#*c_ratio_x
painter.drawEllipse(qPlg['skeleton'][0], radius, radius)
painter.end()
elif roi_data['has_skeleton']==0:
worm_mask = getWormMask(worm_roi, roi_data['threshold'])
worm_cnt, _ = binaryMask2Contour(worm_mask)
worm_mask = np.zeros_like(worm_mask)
cv2.drawContours(worm_mask, [worm_cnt.astype(np.int32)], 0, 1, -1)
worm_mask = QImage(worm_mask.data, worm_mask.shape[1],
worm_mask.shape[0], worm_mask.strides[0], QImage.Format_Indexed8)
worm_mask = worm_mask.convertToFormat(QImage.Format_RGB32, Qt.AutoColor)
worm_mask = worm_mask.scaled(canvas_size,canvas_size,
Qt.KeepAspectRatio)#, Qt.SmoothTransformation)
worm_mask = QPixmap.fromImage(worm_mask)
worm_mask = worm_mask.createMaskFromColor(Qt.black)
p = QPainter(worm_img)
p.setPen(QColor(0,204,102))
p.drawPixmap(worm_img.rect(), worm_mask, worm_mask.rect())
p.end()
pixmap = QPixmap.fromImage(worm_img)
wormCanvas.setPixmap(pixmap);
