From f6c02be8b3b75b78f2abc9af6d2e3a8b8bc6bded Mon Sep 17 00:00:00 2001
From: amitjans <amitjans@ethz.ch>
Date: Tue, 6 Jul 2021 11:27:37 +0200
Subject: [PATCH] Display dark ion fit error
---
templates/index.html | 7 +++++++
tools.py | 46 ++++++++++++++++++++++++++++++++++++++++----
2 files changed, 49 insertions(+), 4 deletions(-)
diff --git a/templates/index.html b/templates/index.html
index e2fd576..38b5956 100644
--- a/templates/index.html
+++ b/templates/index.html
@@ -23,6 +23,7 @@
<p style="font-size: 23px">Linearity: <span id="linearity" style="color: red"></span></p>
<p style="font-size: 23px">Max spot size: <span id="max_spot_size" style="color: red"></span></p>
<p style="font-size: 23px">Ion roundness: <span id="roundness" style="color: red"></span>%</p>
+ <p style="font-size: 23px">Fit error: <span id="fit_error" style="color: red"></span> (Moving avg: <span id="fit_avg" style="color: red"></span>) <span id="response" style="color: red"></span></p>
<h2 style="font-size: 35px">Stream:</h2>
<span class="img-container">
<img src="{{ url_for('video_feed') }}" width="450" height="350" alt="Streaming">
@@ -36,6 +37,12 @@
for (let key in jsonResponse) {
document.getElementById(key).innerText = jsonResponse[key];
}
+ if (Number(document.getElementById("fit_avg").innerText) >= 20) {
+ document.getElementById("response").innerText = "Calibration needed!"
+ }
+ else{
+ document.getElementById("response").innerText = ""
+ }
};
setInterval(() => {
diff --git a/tools.py b/tools.py
index 9d620a3..4f1b284 100644
--- a/tools.py
+++ b/tools.py
@@ -48,6 +48,7 @@ class Main:
# Instantiate classes
self.memory = Memory()
self.count_avg = MovingAverage()
+ self.fit_avg = FitAverage()
self.trap_state = TrapState()
# Define class attributes
@@ -87,7 +88,9 @@ class Main:
'reorder_avg': self.count_avg.moving_avg,
'reorder_flag': -1,
'max_spot_size': -1,
- 'roundness': -1
+ 'roundness': -1,
+ 'fit_error': -1,
+ 'fit_avg': -1
}
elif not ion_cloud:
@@ -121,7 +124,8 @@ class Main:
linearity = ion_linearity(coord)
if len(coord) > 1 and dist_factor is not None:
- coord = dark_ions(img, coord, dist_factor)
+ coord, fit_error = dark_ions(img, coord, dist_factor)
+ self.fit_avg.update_value(fit_error)
else:
roundness = 0
max_int, num_pix = (0, 0)
@@ -163,7 +167,9 @@ class Main:
'reorder_avg': self.count_avg.moving_avg,
'reorder_flag': reorder_flag,
'max_spot_size': int(max_spot_size),
- 'roundness': int(roundness)
+ 'roundness': int(roundness),
+ 'fit_error': int(fit_error),
+ 'fit_avg': int(self.fit_avg.moving_avg)
}
def _save_in_memory(self, output):
@@ -278,6 +284,38 @@ class Memory:
return max_value
+class FitAverage:
+ """
+ Compute moving average of fit error
+ """
+ def __init__(self):
+ self.value = 0
+ self.value_history = [0]
+ self.moving_avg = 0
+
+ self.update_history()
+
+ def update_history(self):
+ """
+ Every second update history and compute moving average.
+ """
+ _thread = threading.Timer(1, self.update_history)
+ _thread.daemon = True
+ _thread.start()
+ self.value_history.append(self.value)
+ if len(self.value_history) > 60:
+ self.value_history.pop(0)
+ self.moving_avg = np.mean(self.value_history)
+ min_val = min(self.value_history)
+ self.value_history = [i - min_val for i in self.value_history]
+ self.value -= min_val
+
+ def update_value(self, value):
+ """
+ Update value.
+ """
+ self.value = value
+
class MovingAverage:
"""
Keep record of number of reorders of the ions and return a moving average of
@@ -603,7 +641,7 @@ def dark_ions(image, coord, dist_factor):
# warnings.warn("Loss is too high... "
# "Try calculating a new factor value using calibrate() function.")
- return coord
+ return coord, loss.min()
def acquire_semaphore_read(name: str, timeout=1):
--
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