From 617a64f910c38145996d5d3ebd4e02eb2851ac01 Mon Sep 17 00:00:00 2001
From: David Mets <dgmets@gamil.com>
Date: Fri, 8 Mar 2024 12:26:38 -0800
Subject: [PATCH] linting of test_assay_growth_curve_chlamy.py

---
 test_assay_growth_curve_chlamy.py | 73 ++++++++++++++++---------------
 1 file changed, 37 insertions(+), 36 deletions(-)

diff --git a/test_assay_growth_curve_chlamy.py b/test_assay_growth_curve_chlamy.py
index a33caba..f911fa7 100644
--- a/test_assay_growth_curve_chlamy.py
+++ b/test_assay_growth_curve_chlamy.py
@@ -1,59 +1,60 @@
-
 import sys as sys
+import time as tm
+
 import cam_tools as ct
-import matplotlib.pyplot as plt
 import serial as ser
-import time as tm
 
-'''This is a script that highlights most of the functions available in cam_tools.py.
+"""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 
+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'''
+for 48 hours"""
 
-dev=ser.Serial('/dev/ttyACM0') # establish serial communication with microcontroller
+dev = ser.Serial("/dev/ttyACM0")  # establish serial communication with microcontroller
 
-dev.write(b'SET LED_TRANS_STATUS 1;') # turn off the LED
+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()
+    sys.exit()
 
-system = ct.ps.System.GetInstance() #start the communication to the cameras
+system = ct.ps.System.GetInstance()  # start the communication to the cameras
 
-cam_list=system.GetCameras() #get the handles of the cameras
+cam_list = system.GetCameras()  # get the handles of the cameras
 
-cam=cam_list[0] #set a handle for a specific camera
+cam = cam_list[0]  # set a handle for a specific camera
 
-cam.Init() #initialze the 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  
+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
+bcode = ct.bcode_read()  # get barcode from usb barcode reader
 
-input('hit enter to start assay') #start the assay
+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
+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
+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
+dev.write(b"SET LED_TRANS_STATUS 1;")  # turn off the led
 
-del cam #turn off the camera
+del cam  # turn off the camera
 
-cam_list.Clear() # de-initialize the cameras
+cam_list.Clear()  # de-initialize the cameras
 
-system.ReleaseInstance() #release the handlers
+system.ReleaseInstance()  # release the handlers