def load_microscope(npzfile=None,
save_settings=False,
dummy_stage=True,
**kwargs):
"""Create a microscope object with specified settings. (context manager)
This will read microscope settings from a .npz file, and/or from
keyword arguments. It will then create the microscope object, and
close it at the end of the with statement. Keyword arguments will
override settings specified in the file.
If save_settings is
True, it will attempt to save the microscope's settings at the end of
the with block, to the same filename. If save_settings_on_exit is set
to a string, it should save instead to that filename.
"""
settings = {}
try:
npz = np.load(npzfile)
for k in npz:
settings[k] = npz[k]
except:
pass
settings.update(kwargs)
if "stage_port" in settings:
stage_port = settings["stage_port"]
del settings["stage_port"]
else:
stage_port = None
# Open the hardware connections
with closing(DummyStage() if dummy_stage else OpenFlexureStage(stage_port)) as stage, \
closing(PiCamera(**extract_settings(settings, picamera_init_settings))) as camera:
ms = Microscope(camera, stage)
for k, v in extract_settings(settings,
picamera_later_settings).items():
setattr(ms.camera, k, v)
yield ms # The contents of the with block from which we're called happen here
if save_settings:
if save_settings is True:
save_settings = npzfile
ms.save_settings(save_settings)
def __init__(self):
#defines some camera parameters
camera_resolution = (3280, 2464)
#camera_resolution = (1024, 768)
self.camera = picamera.PiCamera(resolution = camera_resolution)
# some initial default values - modified in microscope_config.txt
time.sleep(2)
config = initialise_config()
# automatically determine the port name
self.arduino_port = config.detect_arduino_port()
self.stage = OpenFlexureStage(self.arduino_port)
#self.step = 300 # step of motor movement
config.read_config_file()
self.camera.shutter_speed = int(config.shutter_speed)
self.camera.exposure_mode = 'off'
self.camera.awb_mode = config.awb_mode
self.camera.awb_gains = (float(config.red_gain), float(config.blue_gain))
self.camera.iso = int(config.iso)
self.camera.saturation = int(config.saturation)
self.camera.brightness = 50
self.camera.annotate_text_size = int(camera_resolution[0]*0.03) # reasonable ratio for any resolution
import microscope
import picamera
import data_file
from openflexure_stage import OpenFlexureStage
import threading
import matplotlib.pyplot as plt
import matplotlib
import data_file
import h5py
import tweepy
import twitter_keys
if __name__ == "__main__":
with picamera.PiCamera(resolution=(
640, 480)) as camera, OpenFlexureStage('/dev/ttyUSB0') as stage:
#authorises the program to acces the twitter account
auth = tweepy.OAuthHandler(twitter_keys.consumer_key,
twitter_keys.consumer_secret)
auth.set_access_token(twitter_keys.access_token,
twitter_keys.access_token_secret)
api = tweepy.API(auth)
N_frames = 100
counter = 0
#loads camera from picamera and set the stage as the arduino, lower resolution can speed up the programme
ms = microscope.Microscope(camera, stage)
ms.freeze_camera_settings()
frame = get_numpy_image(camera, True)
with closing(DummyStage() if dummy_stage else OpenFlexureStage(stage_port)) as stage, \
closing(PiCamera(**extract_settings(settings, picamera_init_settings))) as camera:
ms = Microscope(camera, stage)
for k, v in extract_settings(settings,
picamera_later_settings).items():
setattr(ms.camera, k, v)
yield ms # The contents of the with block from which we're called happen here
if save_settings:
if save_settings is True:
save_settings = npzfile
ms.save_settings(save_settings)
if __name__ == "__main__":
with picamera.PiCamera() as camera, \
OpenFlexureStage("/dev/ttyUSB0") as stage:
# camera.resolution=(640,480)
camera.start_preview()
ms = Microscope(camera, stage)
ms.freeze_camera_settings(iso=100)
camera.shutter_speed = camera.shutter_speed / 4
backlash = 128
for step, n in [(1000, 10), (200, 10), (100, 10), (50, 10)]:
dz = (np.arange(n) - (n - 1) / 2.0) * step
pos, sharps = ms.autofocus(dz, backlash=backlash)
plt.plot(pos, sharps, 'o-')
import numpy as np
from scipy import ndimage, signal
import sys
import time
from camera_stuff import get_numpy_image, find_template
import microscope
import picamera
import data_file
from openflexure_stage import OpenFlexureStage
import h5py
from contextlib import closing
if __name__ == "__main__":
with picamera.PiCamera(resolution = (640, 480)) as camera, \
OpenFlexureStage('/dev/ttyUSB0') as stage, \
closing(data_file.Datafile(filename = "orthogonality_15123.hdf5")) as df:
side_length = 4000
points = 10
stage.backlash = 256
camera.start_preview()
image = get_numpy_image(camera, greyscale=True).astype(np.float32)
background = cv2.GaussianBlur(image, (41, 41), 0)
templ8 = (image - background)[100:-100, 100:-100]
stage_centre = stage.position
import time
from camera_stuff import get_numpy_image, find_template
import microscope
import picamera
import data_file
from openflexure_stage import OpenFlexureStage
import threading
import matplotlib.pyplot as plt
import matplotlib
import data_file
import h5py
if __name__ == "__main__":
with picamera.PiCamera(resolution=(640, 480),
framerate=100) as camera, OpenFlexureStage(
'/dev/ttyUSB0') as stage:
N_frames = 1000
#loads camera from picamera and set the stage as the arduino, lower resolution can speed up the programme
camera.start_preview() #shows preview of camera
ms = microscope.Microscope(camera, stage)
ms.freeze_camera_settings()
frame = get_numpy_image(camera, True)
print "Frame is {}".format(frame.shape) #print resolution
backlash = 128 #counters backlash
stage.move_rel([-backlash, -backlash, -backlash])
stage.move_rel([backlash, backlash, backlash]) #energise motors
stage.backlash = backlash
raise ValueError("Error setting output filepath. Valid filepaths should"
" either be [creatable] directories, or end with a "
"filename that contains '%d' and ends in '.jpg' or '.jpeg'")
#run microscope_control.py directly
if __name__ == '__main__':
pass
argv = docopt.docopt(__doc__, options_first=True)
stage = OpenFlexureStage('/dev/ttyUSB0')
if argv['move']:
x, y, z = [int(argv.get(d, 0)) for d in ['<x>', '<y>', '<z>']]
print ("moving", x, y, z)
stage.move_rel([x, y, z])
elif argv['focus']:
stage.focus_rel(int(argv['<z>']))
else: #if argv['control']:
def move_stage_with_keyboard(stdscr):
stdscr.addstr(0,0,"wasd to move in X/Y, qe for Z\n"
"r/f to decrease/increase step.\n"
"v/b to start/stop video preview.\n"
"i/o to zoom in/out.\n"
"t/g to adjust contrast, y/h to adjust brightness.\n"
"j to save jpeg file, k to change output path.\n"
from openflexure_stage import OpenFlexureStage
import numpy as np
import matplotlib.pyplot as plt
if __name__ == "__main__":
with OpenFlexureStage("COM3") as stage:
#with OpenFlexureStage("/dev/ttyUSB1") as stage:
gains = stage.light_sensor_gain_values
print gains
f, axes = plt.subplots(1, len(gains))
for i in range(len(gains)):
stage.light_sensor_gain = gains[i]
print "Gain is {}".format(stage.light_sensor_gain)
#print "Integration time is {} ms".format(stage.light_sensor_integration_time)
print "Reading sensor",
readings = np.zeros(50)
for j in range(len(readings)):
readings[j] = stage.light_sensor_intensity
print ".",
print "done"
print "reading {}+/-{}".format(np.mean(readings), np.std(readings))
axes[i].plot(readings)
plt.show()
#import libraries
import numpy as np
from openflexure_stage import OpenFlexureStage
import time
from contextlib import closing
import h5py
import data_file
if __name__ == "__main__":
with OpenFlexureStage('/dev/ttyUSB0') as stage, closing(
data_file.Datafile(filename="background.hdf5")) as df:
n = 200
output = np.zeros((2, n))
data_gr = df.new_group("data", "A file of data collected")
for gain in [1, 25, 428, 9876]:
gain_group = df.new_group("Gain",
"Measurements for one gain",
parent=data_gr)
stage.light_sensor_gain = gain
data = np.zeros(n)
for i in range(n):
data[i] = stage.light_sensor_fullspectrum
time.sleep(5)
mean = np.mean(data)
error = np.std(data)
print "When gain = %d: \nMean background signal = %d +/- %d \n" % (
gain, mean, error)
df.add_data(data, gain_group, "data")
#import libraries
import numpy as np
import io
import sys
import time
import data_file
from openflexure_stage import OpenFlexureStage
import threading
import matplotlib.pyplot as plt
import matplotlib
import data_file
import h5py
if __name__ == "__main__":
with OpenFlexureStage('COM3') as stage:
i = -1
buffer = np.zeros(50)
gains = stage.light_sensor_gain_values
plt.ion()
f, ax = plt.subplots(1, 1)
line = plt.plot(buffer)[0]
while True:
try:
i = (i + 1) % len(buffer)
buffer[i] = stage.light_sensor_intensity
line.set_ydata(buffer)
ax.relim()
ax.autoscale_view()
f.canvas.draw()
return filepath
else:
raise ValueError(
"Error setting output filepath. Valid filepaths should"
" either be [creatable] directories, or end with a "
"filename that contains '%d' and ends in '.jpg' or '.jpeg'")
#run microscope_control.py directly
if __name__ == '__main__':
pass
argv = docopt.docopt(__doc__, options_first=True)
stage = OpenFlexureStage('/dev/ttyUSB0')
if argv['move']:
x, y, z = [int(argv.get(d, 0)) for d in ['<x>', '<y>', '<z>']]
print("moving", x, y, z)
stage.move_rel([x, y, z])
elif argv['focus']:
stage.focus_rel(int(argv['<z>']))
else: #if argv['control']:
def move_stage_with_keyboard(stdscr):
stdscr.addstr(
0, 0, "wasd to move in X/Y, qe for Z\n"
"r/f to decrease/increase step.\n"
"v/b to start/stop video preview.\n"
"i/o to zoom in/out.\n"
class camera_control():
def __init__(self):
#defines some camera parameters
camera_resolution = (3280, 2464)
#camera_resolution = (1024, 768)
self.camera = picamera.PiCamera(resolution = camera_resolution)
# some initial default values - modified in microscope_config.txt
time.sleep(2)
config = initialise_config()
# automatically determine the port name
self.arduino_port = config.detect_arduino_port()
self.stage = OpenFlexureStage(self.arduino_port)
#self.step = 300 # step of motor movement
config.read_config_file()
self.camera.shutter_speed = int(config.shutter_speed)
self.camera.exposure_mode = 'off'
self.camera.awb_mode = config.awb_mode
self.camera.awb_gains = (float(config.red_gain), float(config.blue_gain))
self.camera.iso = int(config.iso)
self.camera.saturation = int(config.saturation)
self.camera.brightness = 50
self.camera.annotate_text_size = int(camera_resolution[0]*0.03) # reasonable ratio for any resolution
def stage_library(self, command, direction):
"""Use this class from kivy interface to use motors, change picamera etc.
in case there is no stage connected, use the exception to avoid crash"""
try:
if command == 'move_x':
if direction == '+':
self.stage.move_rel([-self.step,0,0])
else:
self.stage.move_rel([self.step,0,0])
if command == 'move_y':
if direction == '+':
self.stage.move_rel([0,self.step,0])
else:
self.stage.move_rel([0,-self.step,0])
if command == 'move_z':
if direction == '+':
self.stage.move_rel([0,0,self.step])
else:
self.stage.move_rel([0,0,-self.step])
if command == 'change_self.step':
if direction == '+':
self.step = self.step*2
else:
self.step = self.step/2
except IOError:
# When there is no actual motorised stage connected, do nothing
pass
def camera_library(self, argv, *value):
"Use this function from kivy interface to change picamera etc."
if argv == 'start_preview':
self.camera.start_preview()
elif argv == 'stop_preview':
self.camera.stop_preview()
elif argv == 'reduced_size_preview':
self.camera.start_preview(fullscreen = False, window = value[0])
elif argv == 'fullscreen_preview':
self.camera.start_preview(fullscreen = True)
elif argv == 'set_contrast':
self.camera.contrast = int(value[0])
elif argv == 'set_brightness':
self.camera.brightness = int(value[0])
elif argv == 'set_white_balance':
self.camera.awb_gains = (value[0],value[1])
elif argv == 'set_iso':
self.camera.iso = int(value[0])
elif argv == 'set_shutter_speed':
self.camera.shutter_speed = int(value[0])
elif argv == 'set_saturation':
self.camera.saturation = int(value[0])
elif argv == 'change_annotation':
self.camera.annotate_text = value[0]
# 'save_image' cannot be the last elif for some reason?
elif argv == 'save_image':
# remove any text overlay
folder = value[0]
if not os.path.isdir(folder):
os.mkdir(folder)
image_filepath = value[1]
# format can be 'jpg', 'jpeg', 'raw', 'png'
file_format = value[2]
while True:
# if there is a file with same name, add a -new behind file name
if os.path.isfile(image_filepath+'.jpeg') or os.path.isfile(image_filepath+'.png'):
image_filepath = image_filepath + '-new.'
else:
break
if file_format == 'raw':
self.camera.capture(image_filepath + '.jpeg', format = 'jpeg', bayer = True)
elif file_format == 'png':
self.camera.capture(image_filepath + '.png', format = 'png')
else:
self.camera.capture(image_filepath + '.jpeg', format = 'jpeg')
time.sleep(2)
self.camera.annotate_text = "Image saved as {}".format(image_filepath)
elif argv == 'zoom_in' or 'zoom_out':
if argv == 'zoom_in':
self.fov = self.fov*3/4
elif argv == 'zoom_out' and self.fov < 1:
self.fov = self.fov*4/3
self.camera.zoom = (0.5-self.fov/2, 0.5-self.fov/2, self.fov, self.fov)
self.camera.annotate_text = 'magnification: {0:.2f}X'.format(1/self.fov)
