def concatenate_movies_in_folder(pathfilter, output_path, frame_size=(2048,2048,3)):
for file in BatchProcess(pathfilter=pathfilter):
print(pathfilter+file.split('/')[-1])
writevid = WriteVideo(filename=output_path+file.split('/')[-1], frame_size=frame_size)
for filename in BatchProcess(pathfilter=file[:-4]+"*.mp4", reverse_sort=True):
readvid=ReadVideo(filename)
for frame in range(readvid.num_frames):
writevid.add_frame(readvid.read_next_frame())
readvid.close()
writevid.close()
def extract_section_movies_in_folder(pathfilter, output_path, start_frame=0, stop_frame=1, step=1, frame_size=(2048,2048,3)):
for file in BatchProcess(pathfilter=pathfilter):
print(pathfilter+file.split('/')[-1])
writevid = WriteVideo(filename=output_path+file.split('/')[-1], frame_size=frame_size)
for filename in BatchProcess(pathfilter=file[:-4]+"*.mp4", reverse_sort=True):
readvid=ReadVideo(filename)
for frame in range(start_frame,stop_frame,step):
writevid.add_frame(readvid.read_next_frame())
readvid.close()
writevid.close()
frames = range(1, 800, 25)
def click(event, x, y, dummy, dummy2):
global compaction_front
if event == cv2.EVENT_LBUTTONDOWN:
compaction_front.append(x)
print(x)
print(y)
if __name__ == '__main__':
filename = '/media/ppzmis/data/Cracks/2020_02_14/2020_02_14Newno_salt_20uL_A_5fps_2020-02-14-115652-0000.avi'
vidObj = ReadVideo(filename=filename)
angle = -5 + 0.1503646
crack_threshval = 110
frame_index = 110
scale = 300 / 1803.91 # scale in um/pixel taken from
#Different versions of code
frame = vidObj.find_frame(frame_index)
rot_frame = rotate(frame, angle)
gray_frame = cv2.cvtColor(rot_frame, cv2.COLOR_BGR2GRAY)
#BW image with the crack extracted from background
crack_frame = threshold(frame[:, :, 1], thresh=crack_threshval)
crack_frame = rotate(crack_frame, angle)
crack_frame = imfill(crack_frame)
crack_frame = extract_nth_biggest_object(crack_frame, n=0)
from Generic.video import ReadVideo
from Generic.images import display
if __name__ == '__main__':
readvid = ReadVideo()
for i in range(readvid.num_frames):
frame = readvid.read_next_frame()
display(frame)
gray_frame = cv2.cvtColor(rot_frame, cv2.COLOR_BGR2GRAY)
# BW image with the crack extracted from background
crack_frame = frame[:, :,
1] #threshold(frame[:, :, 1], thresh=crack_threshval)
crack_frame = rotate(crack_frame, angle)
crack_frame = imfill(crack_frame)
#crack_frame = extract_nth_biggest_object(crack_frame, n=0)
return crack_frame, rot_frame, gray_frame
if __name__ == '__main__':
#filename = '/media/ppzmis/data/Cracks/2020_03_17/25mMnacl5fps_2020-03-17-110622-0000.avi'
filename = '/media/ppzmis/data/Cracks/2020_02_14/2020_02_14Newno_salt_20uL_A_5fps_2020-02-14-115652-0000.avi'
vidObj = ReadVideo(filename=filename)
angle = angle = 175 #-5+ 0.1503646
fps = 5
output = []
for index in range(0, vidObj.num_frames - 1, 50):
vidObj.set_frame(index)
frame = vidObj.read_next_frame()
crack_frame, rot_frame, gray_frame = processframe(frame, angle)
compact_pos_pixels = find_compaction(rot_frame)
time = (index + 1) / fps
output.append([time, compact_pos_pixels])
print('final')
print(output)
np.savetxt(filename[:-4] + 'pos_compactionb.txt', np.array(output))
from Generic.filedialogs import BatchProcess
from Generic.video import ReadVideo
import numpy as np
from Generic.images import display
import cv2
if __name__ == '__main__':
for file in BatchProcess(
pathfilter=
'/media/ppzmis/data/ActiveMatter/Microscopy/190820bacteriaand500nmparticles/videos/joined/StreamDIC???.mp4'
):
readvid = ReadVideo(filename=file)
frame_init = readvid.read_next_frame() #.astype(np.int32)
counter = 1
sz = np.shape(frame_init)
frame_assemble = np.reshape(frame_init, (sz[0], sz[1] * sz[2]))
for i in range(readvid.num_frames - 1):
frame = readvid.read_next_frame().astype(np.int32)
new_frame = np.reshape(frame, (sz[0], sz[1] * sz[2]))
frame_assemble = np.sum((frame_assemble, new_frame),
axis=0,
dtype=np.int32)
counter = counter + 1
frame = (frame_assemble / counter).astype(np.uint8)
frame_assemble = np.reshape(frame, (sz[0], sz[1], sz[2]))
cv2.imwrite(file[:-4] + '_bkgimg.png', frame_assemble)
readvid.close()
def load_vid(self):
self.readvid=ReadVideo(filename=self.filename)
self.filename = self.readvid.filename
self.framenum = 0
self.framenum_slider.setSliderRangeValues(0, self.readvid.num_frames -1)
self.load_frame()
class MainWindow(QtImageViewer):
def __init__(self, filename=None):
app = QApplication(sys.argv)
super().__init__()
self.filename=filename
self.setup_main_window()
self.load_vid()
sys.exit(app.exec_())
def setup_main_window(self):
# Create window and layout
self.win = QWidget()
self.vbox = QVBoxLayout(self.win)
# Create Image viewer
self.viewer_setup()
self.vbox.addWidget(self.viewer)
self.framenum_slider = Slider(self.win, 'frame number', self.slider_update, 0, 5, 1)
self.vbox.addWidget(self.framenum_slider)
# Finalise window
self.win.setWindowTitle('ParamGui')
self.win.setLayout(self.vbox)
self.win.show()
def viewer_setup(self):
self.viewer = QtImageViewer()
self.viewer.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
self.viewer.setVerticalScrollBarPolicy(Qt.ScrollBarAsNeeded)
self.viewer.leftMouseButtonPressed.connect(self.get_coords)
self.viewer.scrollMouseButton.connect(self._update_frame)
self.viewer.canZoom = True
self.viewer.canPan = True
self.win.resize(1024, 720)
def setup_menubar(self):
exitAct = QAction('&Exit', self)
exitAct.setShortcut('Ctrl+Q')
exitAct.triggered.connect(app.quit)
loadVid = QAction('&Load', self)
loadVid.setShortcut(('Ctrl-O'))
loadVid.triggered.connect(self.load_video)
menubar = self.menuBar()
fileMenu = menubar.addMenu('&File')
fileMenu.addAction((loadVid))
fileMenu.addAction(exitAct)
preferences = menubar.addMenu('&Preferences')
def load_video(self):
self.filename=None
self.load_vid()
def load_vid(self):
self.readvid=ReadVideo(filename=self.filename)
self.filename = self.readvid.filename
self.framenum = 0
self.framenum_slider.setSliderRangeValues(0, self.readvid.num_frames -1)
self.load_frame()
def slider_update(self, val):
print(val)
self.framenum = self.framenum_slider.value()
self.load_frame()
def _update_frame(self, wheel_change):
self.framenum = self.framenum + wheel_change
if self.framenum < 0:
self.framenum = 0
elif self.framenum >= (self.readvid.num_frames - 1):
self.framenum = (self.readvid.num_frames - 1)
self.framenum_slider.sliderCallback(self.framenum)
self.load_frame()
def load_frame(self):
im = self.readvid.find_frame(self.framenum)
pixmap = QPixmap.fromImage(array2qimage(im))
self.viewer.setImage(pixmap)
def _display_img(self, *ims):
if len(ims) == 1:
self.im = ims[0]
else:
self.im = hstack(*ims)
def get_coords(self, x, y):
print('cursor position (x, y) = ({}, {})'.format(int(x), int(y)))