added chlamy growth curve assay

test_assay_growth_curve_chlamy.py

@@ -0,0 +1,63 @@
+import sys as sys
+import time as tm
+
+import cam_tools as ct
+import serial as ser
+
+"""This is a script that highlights most of the functions available in cam_tools.py.
+It connects to the microcontroller, sets up the camera, turns on the grow lights,
+allows the use of a barcode reader, turns on the LEDs that are useful for Chlamydomonas
+to grow ("grow lights"), then acquires an image using transillumination once an hour
+for 48 hours"""
+
+
+# establish serial communication with microcontroller.
+# expects only one phenotype-o-mat attached to the computer
+dev = ser.Serial("/dev/ttyACM0")
+
+dev.write(b"SET LED_TRANS_STATUS 1;")  # turn off the LED
+
+if not ct.detect_cams():  # make sure there are blackfly cameras attached to the computer
+    sys.exit()
+
+system = ct.ps.System.GetInstance()  # start the communication to the cameras
+
+cam_list = system.GetCameras()  # get the handles of the cameras
+
+cam = cam_list[0]  # set a handle for a specific camera
+
+cam.Init()  # initialze the camera
+
+dev.write(b"SET LED_TRANS_STATUS 0;")  # turn on the led
+dev.write(b"SET LED_460_STATUS 0;")  # turn on grow light
+dev.write(b"SET LED_670_STATUS 0;")  # turn on grow light
+
+bcode = ct.bcode_read()  # get barcode from usb barcode reader
+
+input("hit enter to start assay")  # start the assay
+
+for _n in range(0, 48):
+    ct.set_expos_time(cam, 500)  # set the exposure time
+    dev.write(b"SET LED_460_STATUS 1;")  # turn off grow light
+    dev.write(b"SET LED_670_STATUS 1;")  # turn off grow light
+    dev.write(b"SET LED_TRANS_STATUS 0;")  # turn on the led
+    tm.sleep(5)  # wait 5 seconds
+    images, timestamps = ct.grab_images(
+        cam, n_frames=1
+    )  # get images and timestamps for a vide of 10 seconds length from the camera
+    ct.save_avi(images, barcode=bcode, prefix="algae_growth_curve")  # save images
+    dev.write(b"SET LED_460_STATUS 0;")  # turn on grow light
+    dev.write(b"SET LED_670_STATUS 0;")  # turn on grow light
+    tm.sleep(60 * 60)  # wait 1 hr
+    dev.write(b"SET LED_TRANS_STATUS 1;")  # turn off LED
+
+print(str(timestamps[-1] - timestamps[0]))  # print the total imaging time
+print(str(timestamps[-1] - timestamps[-2]))  # print the time between frames
+
+dev.write(b"SET LED_TRANS_STATUS 1;")  # turn off the led
+
+del cam  # turn off the camera
+
+cam_list.Clear()  # de-initialize the cameras
+
+system.ReleaseInstance()  # release the handlers