import microscope
m=microscope.Microscope(port="COM4", debug=True)
def take_mosaic(microscope, rows, columns, abc=False):
x_fov=m.fov()[0]
y_fov=m.fov()[1]
overlap=0.9
x_move=x_fov*overlap
y_move=y_fov*overlap
start_x=m.get_x_position()
start_y=m.get_y_position()
x=start_x
y=start_y
microscope.enable_raster_rotation()
# Empirically determined on my scope as the delta between the stage xy and image xy -JK
microscope.set_raster_rotation(3)
photo=0
for row in range(0,rows):
for column in range(0,columns):
if photo == 14:
ack = raw_input('Please save buffered images and hit any key to continue...')
photo=0
microscope.trigger_abc()
microscope.take_photo()
photo+=1
microscope.set_x_position(microscope.get_x_position() + x_move)
microscope.set_y_position(microscope.get_y_position() + y_move)
microscope.set_x_position(start_x)
microscope.disable_raster_rotation()
def take_series(microscope, af=False, abc=False):
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)
df = data_file.Datafile(filename="drift_81217.hdf5"
) #creates the .hdf5 file to save the data
data_gr = df.new_group(
"test_data", "A file of data collected to test this code works")
#puts the data file into a group with description
image = get_numpy_image(camera, greyscale=True) #takes template photo
templ8 = image[100:-100, 100:-100] #crops image
loop = True
tweet = True
import microscope
import picamera
import numpy as np
import matplotlib.pyplot as plt
import time
#resolution=(3280,2464)
#m = microscope.Microscope(picamera.PiCamera(resolution=(640,480)), None)
m = microscope.Microscope(picamera.PiCamera(resolution=(3280 / 1, 2464 / 1)),
None)
m.cam.start_preview()
time.sleep(2)
image = m.rgb_image()
m.cam.stop_preview()
plt.figure()
plt.imshow(image)
plt.figure()
plt.imshow(microscope.decimate_to((100, 100), image))
plt.show()