From 05cadf701f1f0c68ae28d5e55584647f5380b17a Mon Sep 17 00:00:00 2001
From: amitjans <amitjans@ethz.ch>
Date: Tue, 1 Jun 2021 16:40:50 +0200
Subject: [PATCH] reorder
---
app.py | 3 +-
html_settings.py | 13 ---
html_tools.py | 36 --------
main.py | 191 ------------------------------------------
settings.py | 3 +
tools.py | 211 ++++++++++++++++++++++++++++++++++++++++++++++-
6 files changed, 214 insertions(+), 243 deletions(-)
delete mode 100644 html_settings.py
delete mode 100644 html_tools.py
delete mode 100644 main.py
diff --git a/app.py b/app.py
index 1b4a597..b1c5f47 100644
--- a/app.py
+++ b/app.py
@@ -2,8 +2,7 @@
import threading
import cv2
from flask import Flask, render_template, Response
-from html_tools import plot_detection
-from main import Main
+from tools import plot_detection, Main
app = Flask(__name__)
sm = threading.Semaphore(10)
diff --git a/html_settings.py b/html_settings.py
deleted file mode 100644
index 148b2b0..0000000
--- a/html_settings.py
+++ /dev/null
@@ -1,13 +0,0 @@
-"""Settings file"""
-
-# Shared memory name (ion images)
-SHM_NAME = 'shm://zwoioncameraone'
-
-# Semaphore name
-SEM_NAME = '/zwocamdataone'
-
-# Radius of circle that captures the intensity of each ion (plotted on html)
-RADIUS = 15
-
-# Transparency of the circle plotted in the html
-ALPHA = 0.15
diff --git a/html_tools.py b/html_tools.py
deleted file mode 100644
index 9aef80e..0000000
--- a/html_tools.py
+++ /dev/null
@@ -1,36 +0,0 @@
-"""This file contains all the needed functions"""
-import logging
-import numpy as np
-import cv2
-import html_settings
-
-log = logging.getLogger(__name__)
-
-def plot_detection(image, points):
- """
- Use OpenCV to plot the detected ions on the image, following this color code:
- - Red: Bright Ion
- - Green: Bright Ion
- - Blue: Dark Ion
- Code the image into bytes and return it.
- """
- image = cv2.cvtColor(image, cv2.COLOR_GRAY2BGR)
- for point in points:
- if point[2] != 2:
- overlay = image.copy()
- cv2.circle(overlay, tuple(np.flip(point[:2])), radius=html_settings.RADIUS,
- color=(255, 255, 255), thickness=1)
- alpha = html_settings.ALPHA
- image = cv2.addWeighted(overlay, alpha, image, 1 - alpha, 0)
- if point[2] == 1:
- image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 255, 255),
- thickness=-1)
- else:
- image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 255, 0),
- thickness=-1)
- else:
- image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 0, 255),
- thickness=-1)
-
-
- return image
\ No newline at end of file
diff --git a/main.py b/main.py
deleted file mode 100644
index 2ce87c9..0000000
--- a/main.py
+++ /dev/null
@@ -1,191 +0,0 @@
-"""MAIN file"""
-# import matplotlib
-# matplotlib.use('tkagg')
-import time
-import threading
-import warnings
-from multiprocessing import Queue
-import redis
-import numpy as np
-import influxdb
-import settings
-from tools import Memory, MovingAverage, ion_positions, dark_ions, ion_linearity
-from tools import detect_ion_cloud, read_factor, compensate_gradient, acquire_semaphore_write, release_semaphore_write
-from tools import TrapState, max_ion_intensity, detect_dim_ions, load_image, ion_roundness
-
-
-class Main:
- """
- Main class. Does the processing of the images and stores all the outputs.
- """
- def __init__(self, sem):
- """
- Connect to redis and influxdb. Instantiate all the needed classes and variables.
- """
- # Define Semaphore
- self.sm = sem
-
- # Connect to redis and influxdb
- self.conn = redis.Redis('localhost', decode_responses=True)
-
- self.db = influxdb.InfluxDBClient(
- host=settings.DB_HOST,
- port=settings.DB_PORT,
- username=settings.DB_USER,
- password=settings.DB_PWD,
- database=settings.DB_DATASET,
- ssl=False,
- )
-
- # Instantiate classes
- self.memory = Memory()
- self.count_avg = MovingAverage()
- self.trap_state = TrapState()
-
- # Define class attributes
- self.init_time = time.time()
- self.num = 0
- self.output = {}
-
- def start_thread(self):
- """
- Start background thread.
- """
- t = threading.Thread(target=self._background_thread, daemon=True)
- t.start()
-
- def _background_thread(self):
- """
- Apply the processing on the images.
- """
- warnings.simplefilter("once", UserWarning)
- while True:
- dist_factor = read_factor(self.conn)
- image = load_image()
- ion_cloud = detect_ion_cloud(image)
-
- if ion_cloud:
- output = {
- 'image': image,
- 'coord': np.array([[-1, -1, -1]]),
- 'trap_state': self.trap_state.trap_state,
- 'num_ions': -1,
- 'bright_ions': -1,
- 'dim_ions': -1,
- 'dark_ions': -1,
- 'linearity': 'cloud',
- 'max_int': -1,
- 'num_pixels': -1,
- 'noise_mean': self.trap_state.noise[0],
- 'noise_std': self.trap_state.noise[1],
- 'reorder_avg': self.count_avg.moving_avg,
- 'reorder_flag': -1,
- 'max_spot_size': -1,
- 'roundness': -1
- }
-
- elif not ion_cloud:
- output = self._processing(image, dist_factor)
-
- # Update running time
- running_time = time.time() - self.init_time
- output['time'] = 60 - int(running_time)
- if running_time >= 60:
- self.init_time = time.time()
-
- # Save variables in self.memory
- self._save_in_memory(output)
- self.num += 1
-
- # Delete unnecessary variables for html and put output in queue
- del output['num_ions']
- del output['reorder_flag']
- sem = acquire_semaphore_write(self.sm, num_sem=10)
- self.output = output
- release_semaphore_write(sem, num_sem=10)
-
- def _processing(self, image, dist_factor):
- coord, max_spot_size = ion_positions(image)
- if len(coord) > 0:
- roundness = ion_roundness(image, coord[0][:2])
- new_img = compensate_gradient(image, coord)
- max_int, num_pix = max_ion_intensity(new_img, coord)
- coord = detect_dim_ions(new_img, coord, max_int)
- linearity = ion_linearity(coord)
-
- if len(coord) > 1 and dist_factor is not None:
- coord = dark_ions(image, coord, dist_factor)
-
- _, old_idx = self.memory.get_value()
- self.memory.save_value(coord)
- coord, new_idx = self.memory.get_value()
- # If idx changes, it means that ion reordered
- reorder_flag = 0
- if new_idx != old_idx:
- reorder_flag = 1
- self.count_avg.update_count()
-
- # Update trap state
- self.trap_state.update_coord(coord)
-
- num_ions = len(coord)
- num_bright_ions = np.sum(coord[:, 2] == 0).item()
- num_dim_ions = np.sum(coord[:, 2] == 1).item()
- num_dark_ions = np.sum(coord[:, 2] == 2).item()
-
- # Reset self.memory every NUM_ITERATIONS
- if self.num > settings.NUM_ITERATIONS:
- self.memory.reset_memory(coord)
- self.num = 0
-
- return {
- 'image': image,
- 'coord': coord,
- 'trap_state': self.trap_state.trap_state,
- 'num_ions': num_ions,
- 'bright_ions': num_bright_ions,
- 'dim_ions': num_dim_ions,
- 'dark_ions': num_dark_ions,
- 'linearity': linearity,
- 'max_int': int(max_int),
- 'num_pixels': int(num_pix),
- 'noise_mean': self.trap_state.noise[0],
- 'noise_std': self.trap_state.noise[1],
- 'reorder_avg': self.count_avg.moving_avg,
- 'reorder_flag': reorder_flag,
- 'max_spot_size': int(max_spot_size),
- 'roundness': int(roundness)
- }
-
- def _save_in_memory(self, output):
- """
- Save measured variables in shared memory
- """
- self.conn.set(name='/image_analysis/trap_state', value=output['trap_state'], ex=10)
- self.conn.set(name='/image_analysis/num_ions/bright_ions', value=output['bright_ions'], ex=10)
- self.conn.set(name='/image_analysis/num_ions/dim_ions', value=output['dim_ions'], ex=10)
- self.conn.set(name='/image_analysis/num_ions/dark_ions', value=output['dark_ions'], ex=10)
- self.conn.set(name='/image_analysis/linearity', value=output['linearity'], ex=10)
- self.conn.set(name='/image_analysis/ion_intensity/max_int', value=int(output['max_int']), ex=10)
- self.conn.set(name='/image_analysis/ion_intensity/num_pixels', value=int(output['num_pixels']), ex=10)
- self.conn.set(name='/image_analysis/noise/mean', value=output['noise_mean'])
- self.conn.set(name='/image_analysis/noise/std', value=output['noise_std'])
- self.conn.set(name='/image_analysis/reorder/flag', value=output['reorder_flag'], ex=10)
- self.conn.set(name='/image_analysis/reorder/avg', value=output['reorder_avg'], ex=10)
- self.conn.set(name='/image_analysis/time', value=output['time'], ex=10)
- self.conn.set(name='/image_analysis/max_spot_size', value=int(output['max_spot_size']), ex=10)
- self.conn.set(name='/image_analysis/ion_roundness', value=int(output['roundness']), ex=10)
-
- self.db.write_points([{
- 'measurement': 'ion_image',
- 'fields': {
- 'num_ions': output['num_ions'],
- 'num_bright_ions': output['bright_ions'],
- 'num_dim_ions': output['dim_ions'],
- 'num_dark_ions': output['dark_ions'],
- 'reorder_rate': output['reorder_avg'],
- 'max_int': output['max_int'],
- 'max_spot_size': output['max_spot_size'],
- 'ion_roundness': output['roundness']
- }
- }])
\ No newline at end of file
diff --git a/settings.py b/settings.py
index 7b58371..0579433 100644
--- a/settings.py
+++ b/settings.py
@@ -43,3 +43,6 @@ RADIUS = 15
# Area threshold of biggest contour in image (for ion cloud detection)
AREA_THS = 10e3
+
+# Transparency of the circle plotted in the html
+ALPHA = 0.15
diff --git a/tools.py b/tools.py
index f4e0ad2..806ac12 100644
--- a/tools.py
+++ b/tools.py
@@ -1,9 +1,10 @@
"""This file contains all the needed functions"""
-import struct
import time
import warnings
import logging
import threading
+import redis
+import influxdb
import cv2
import requests
import SharedArray
@@ -20,6 +21,184 @@ import settings
log = logging.getLogger(__name__)
+
+class Main:
+ """
+ Main class. Does the processing of the images and stores all the outputs.
+ """
+ def __init__(self, sem):
+ """
+ Connect to redis and influxdb. Instantiate all the needed classes and variables.
+ """
+ # Define Semaphore
+ self.sm = sem
+
+ # Connect to redis and influxdb
+ self.conn = redis.Redis('localhost', decode_responses=True)
+
+ self.db = influxdb.InfluxDBClient(
+ host=settings.DB_HOST,
+ port=settings.DB_PORT,
+ username=settings.DB_USER,
+ password=settings.DB_PWD,
+ database=settings.DB_DATASET,
+ ssl=False,
+ )
+
+ # Instantiate classes
+ self.memory = Memory()
+ self.count_avg = MovingAverage()
+ self.trap_state = TrapState()
+
+ # Define class attributes
+ self.init_time = time.time()
+ self.num = 0
+ self.output = {}
+
+ def start_thread(self):
+ """
+ Start background thread.
+ """
+ t = threading.Thread(target=self._background_thread, daemon=True)
+ t.start()
+
+ def _background_thread(self):
+ """
+ Apply the processing on the images.
+ """
+ warnings.simplefilter("once", UserWarning)
+ while True:
+ dist_factor = read_factor(self.conn)
+ image = load_image()
+ ion_cloud = detect_ion_cloud(image)
+
+ if ion_cloud:
+ output = {
+ 'image': image,
+ 'coord': np.array([[-1, -1, -1]]),
+ 'trap_state': self.trap_state.trap_state,
+ 'num_ions': -1,
+ 'bright_ions': -1,
+ 'dim_ions': -1,
+ 'dark_ions': -1,
+ 'linearity': 'cloud',
+ 'max_int': -1,
+ 'num_pixels': -1,
+ 'noise_mean': self.trap_state.noise[0],
+ 'noise_std': self.trap_state.noise[1],
+ 'reorder_avg': self.count_avg.moving_avg,
+ 'reorder_flag': -1,
+ 'max_spot_size': -1,
+ 'roundness': -1
+ }
+
+ elif not ion_cloud:
+ output = self._processing(image, dist_factor)
+
+ # Update running time
+ running_time = time.time() - self.init_time
+ output['time'] = 60 - int(running_time)
+ if running_time >= 60:
+ self.init_time = time.time()
+
+ # Save variables in self.memory
+ self._save_in_memory(output)
+ self.num += 1
+
+ # Delete unnecessary variables for html and put output in queue
+ del output['num_ions']
+ del output['reorder_flag']
+ sem = acquire_semaphore_write(self.sm, num_sem=10)
+ self.output = output
+ release_semaphore_write(sem, num_sem=10)
+
+ def _processing(self, image, dist_factor):
+ coord, max_spot_size = ion_positions(image)
+ if len(coord) > 0:
+ roundness = ion_roundness(image, coord[0][:2])
+ new_img = compensate_gradient(image, coord)
+ max_int, num_pix = max_ion_intensity(new_img, coord)
+ coord = detect_dim_ions(new_img, coord, max_int)
+ linearity = ion_linearity(coord)
+
+ if len(coord) > 1 and dist_factor is not None:
+ coord = dark_ions(image, coord, dist_factor)
+
+ _, old_idx = self.memory.get_value()
+ self.memory.save_value(coord)
+ coord, new_idx = self.memory.get_value()
+ # If idx changes, it means that ion reordered
+ reorder_flag = 0
+ if new_idx != old_idx:
+ reorder_flag = 1
+ self.count_avg.update_count()
+
+ # Update trap state
+ self.trap_state.update_coord(coord)
+
+ num_ions = len(coord)
+ num_bright_ions = np.sum(coord[:, 2] == 0).item()
+ num_dim_ions = np.sum(coord[:, 2] == 1).item()
+ num_dark_ions = np.sum(coord[:, 2] == 2).item()
+
+ # Reset self.memory every NUM_ITERATIONS
+ if self.num > settings.NUM_ITERATIONS:
+ self.memory.reset_memory(coord)
+ self.num = 0
+
+ return {
+ 'image': image,
+ 'coord': coord,
+ 'trap_state': self.trap_state.trap_state,
+ 'num_ions': num_ions,
+ 'bright_ions': num_bright_ions,
+ 'dim_ions': num_dim_ions,
+ 'dark_ions': num_dark_ions,
+ 'linearity': linearity,
+ 'max_int': int(max_int),
+ 'num_pixels': int(num_pix),
+ 'noise_mean': self.trap_state.noise[0],
+ 'noise_std': self.trap_state.noise[1],
+ 'reorder_avg': self.count_avg.moving_avg,
+ 'reorder_flag': reorder_flag,
+ 'max_spot_size': int(max_spot_size),
+ 'roundness': int(roundness)
+ }
+
+ def _save_in_memory(self, output):
+ """
+ Save measured variables in shared memory
+ """
+ self.conn.set(name='/image_analysis/trap_state', value=output['trap_state'], ex=10)
+ self.conn.set(name='/image_analysis/num_ions/bright_ions', value=output['bright_ions'], ex=10)
+ self.conn.set(name='/image_analysis/num_ions/dim_ions', value=output['dim_ions'], ex=10)
+ self.conn.set(name='/image_analysis/num_ions/dark_ions', value=output['dark_ions'], ex=10)
+ self.conn.set(name='/image_analysis/linearity', value=output['linearity'], ex=10)
+ self.conn.set(name='/image_analysis/ion_intensity/max_int', value=int(output['max_int']), ex=10)
+ self.conn.set(name='/image_analysis/ion_intensity/num_pixels', value=int(output['num_pixels']), ex=10)
+ self.conn.set(name='/image_analysis/noise/mean', value=output['noise_mean'])
+ self.conn.set(name='/image_analysis/noise/std', value=output['noise_std'])
+ self.conn.set(name='/image_analysis/reorder/flag', value=output['reorder_flag'], ex=10)
+ self.conn.set(name='/image_analysis/reorder/avg', value=output['reorder_avg'], ex=10)
+ self.conn.set(name='/image_analysis/time', value=output['time'], ex=10)
+ self.conn.set(name='/image_analysis/max_spot_size', value=int(output['max_spot_size']), ex=10)
+ self.conn.set(name='/image_analysis/ion_roundness', value=int(output['roundness']), ex=10)
+
+ self.db.write_points([{
+ 'measurement': 'ion_image',
+ 'fields': {
+ 'num_ions': output['num_ions'],
+ 'num_bright_ions': output['bright_ions'],
+ 'num_dim_ions': output['dim_ions'],
+ 'num_dark_ions': output['dark_ions'],
+ 'reorder_rate': output['reorder_avg'],
+ 'max_int': output['max_int'],
+ 'max_spot_size': output['max_spot_size'],
+ 'ion_roundness': output['roundness']
+ }
+ }])
+
+
class Memory:
"""
Stores values in memory and counts how many times each value was stored.
@@ -505,6 +684,36 @@ def pos_solver(num):
return solution
+def plot_detection(image, points):
+ """
+ Use OpenCV to plot the detected ions on the image, following this color code:
+ - Red: Bright Ion
+ - Green: Bright Ion
+ - Blue: Dark Ion
+ Code the image into bytes and return it.
+ """
+ image = cv2.cvtColor(image, cv2.COLOR_GRAY2BGR)
+ for point in points:
+ if point[2] != 2:
+ overlay = image.copy()
+ cv2.circle(overlay, tuple(np.flip(point[:2])), radius=settings.RADIUS,
+ color=(255, 255, 255), thickness=1)
+ alpha = settings.ALPHA
+ image = cv2.addWeighted(overlay, alpha, image, 1 - alpha, 0)
+ if point[2] == 1:
+ image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 255, 255),
+ thickness=-1)
+ else:
+ image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 255, 0),
+ thickness=-1)
+ else:
+ image = cv2.circle(image, tuple(np.flip(point[:2])), radius=3, color=(0, 0, 255),
+ thickness=-1)
+
+
+ return image
+
+
def _laser_switch(boolean):
"""
Switch on (True) or off (False) the repumping laser.
--
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