def exposed_load_microscope(self, config_path=default["mm"]["cfg_file"]):
"""initialize MMCore for the given micro-manager config file"""
config_abspath = os.path.abspath(config_path)
# store the current working dir, so that we can change it back after
# device adapters are pointed to the micromanager directory
# changing the working directory to mm_dir is necessary for pymmcore
# to find the device adapters (stored in mm_dir) correctly
working_dir = os.getcwd()
if os.name == 'nt': # check if windows
# ah! the microscope computer
mm_dir = default["mm"]["win_path"]
elif os.name == "posix":
# the dev's linux computer
mm_dir = default["mm"]["linux_path"]
os.chdir(mm_dir)
mmc = pymmcore.CMMCore()
mmc.setDeviceAdapterSearchPaths([mm_dir])
mmc.loadSystemConfiguration(config_abspath)
os.chdir(working_dir)
self.exposed_mmc = mmc
return mmc
def show_frame(self):
# _, frame = self.cap.read()
# frame = cv2.flip(frame, 1)
# cv2image = cv2.cvtColor(frame, cv2.COLOR_BGR2RGBA)
# img = Image.fromarray(cv2image)
# imgtk = ImageTk.PhotoImage(image=img)
# self.lmain.imgtk = imgtk
# self.lmain.configure(image=imgtk)
# self.lmain.after(10, self.show_frame)
mmc = pymmcore.CMMCore()
print('-----setup cam-----')
mm_dir = 'C:/Program Files/Micro-Manager-2.0gamma/'
mmc.setDeviceAdapterSearchPaths([mm_dir])
print(mmc.getVersionInfo())
print(mmc.getAPIVersionInfo())
use_YOLO = False
my_yolo = YOLO() # start yolo session
print('-----load cam-----')
# print(os.path.join(mm_dir, 'MMConfig_1.cfg'))
mmc.loadSystemConfiguration(mm_dir + 'MMConfig_QCam.cfg')
mmc.setExposure(200)
cv2.namedWindow('live', cv2.WINDOW_AUTOSIZE)
mmc.startContinuousSequenceAcquisition(1)
while True:
if mmc.getRemainingImageCount() > 0:
start = timer()
frame = mmc.popNextImage()
# Run detection
if use_YOLO:
alter = contrastStretch(frame, min_range, max_range)
image = Image.fromarray(np.uint8(alter))
output = detect_img(my_yolo, image)
output = np.array(output)
cv2.imshow('live', output)
else:
cv2.imshow('live', frame)
end = timer()
save_time = end - start
if cv2.waitKey(1) & 0xFF == ord(
'q'
): # This break key is critical, otherwise the live image does not load
break
# N = 1024
# for m in range(0,M):
# for n in range(0,N):
# if minI < iI[m,n] < maxI:
# iI[m,n] = iI[m,n]
# elif iI[m,n] < minI:
# iI[m,n] = 0
# elif iI[m,n] > maxI:
# iI[m,n] = 255
# if iI < minI:
# iO = 0
# if iI > maxI:
# iO = 255
return iO
mmc = pymmcore.CMMCore()
print('-----setup cam-----')
mm_dir = 'C:/Program Files/Micro-Manager-2.0gamma/'
mmc.setDeviceAdapterSearchPaths([mm_dir])
print(mmc.getVersionInfo())
print(mmc.getAPIVersionInfo())
use_YOLO = True
my_yolo = YOLO() # start yolo session
print('-----load cam-----')
# print(os.path.join(mm_dir, 'MMConfig_1.cfg'))
mmc.loadSystemConfiguration(mm_dir + 'MMConfig_QCam.cfg')
mmc.setExposure(200)
mmc.snapImage()
im1 = mmc.getImage()
import pymmcore
import configparser
import os.path
#
# At the moment, the only test is that our version number is correct
#
script_dir = os.path.dirname(os.path.realpath(__file__))
setup_cfg = os.path.join(os.path.dirname(script_dir), 'setup.cfg')
config = configparser.ConfigParser()
config.read(setup_cfg)
pymmcore_version = config['metadata']['version'].split('.')
print("Version: {}".format(pymmcore_version))
# getVersionInfo() returns a string like "MMCore version x.y.z"
mmcore_version = pymmcore.CMMCore().getVersionInfo().split()[-1].split('.')
print("MMCore version: {}".format(mmcore_version))
for i in range(3):
if pymmcore_version[i] != mmcore_version[i]:
raise AssertionError('Version mismatch between pymmcore and MMCore')