From 3b8f8ddb0a1fad27f7bc74f09f6e367d3bc3d37f Mon Sep 17 00:00:00 2001
From: amitjans <amitjans@ethz.ch>
Date: Fri, 2 Jul 2021 17:33:32 +0200
Subject: [PATCH] Solve trap state and delete useless files. Change realtive
height of peak width measure
---
".\\features\\noise.npy" | Bin 144 -> 0 bytes
features/region.npy | Bin 160 -> 0 bytes
tools.py | 39 ++++++++++++++++++---------------------
3 files changed, 18 insertions(+), 21 deletions(-)
delete mode 100644 ".\\features\\noise.npy"
delete mode 100644 features/region.npy
diff --git "a/.\\features\\noise.npy" "b/.\\features\\noise.npy"
deleted file mode 100644
index 8f073d57a5a1b037dfc41eefd3595f3724c10a34..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 144
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mXCxM+0{I$7I+{8PwF(pfuB756EwVCR4&vXO9`3s>?*ITn<ws
diff --git a/features/region.npy b/features/region.npy
deleted file mode 100644
index 2f93132a326b48942dae8c06b3e3fbf0b56fb039..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 160
zcmbR27wQ`j$;eQ~P_3SlTAW;@Zl$1ZlWC!@qoAIaUsO_*m=~X4l#&V(cT3DEP6dh=
mXCxM+0{I$7ItoUbItsN4WCN~+j0|AV52amMApA}y2n_)8ARTxB
diff --git a/tools.py b/tools.py
index 4d856b1..0978320 100644
--- a/tools.py
+++ b/tools.py
@@ -82,8 +82,8 @@ class Main:
'linearity': 'cloud',
'max_int': -1,
'num_pixels': -1,
- 'noise_mean': self.trap_state.noise[0],
- 'noise_std': self.trap_state.noise[1],
+ 'noise_mean': int(self.trap_state.noise[0]),
+ 'noise_std': int(self.trap_state.noise[1]),
'reorder_avg': self.count_avg.moving_avg,
'reorder_flag': -1,
'max_spot_size': -1,
@@ -98,6 +98,7 @@ class Main:
output['time'] = 60 - int(running_time)
if running_time >= 60:
self.init_time = time.time()
+ self.trap_state.update_trap_state()
# Save variables in self.memory
self._save_in_memory(output)
@@ -155,8 +156,8 @@ class Main:
'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],
+ 'noise_mean': int(self.trap_state.noise[0]),
+ 'noise_std': int(self.trap_state.noise[1]),
'reorder_avg': self.count_avg.moving_avg,
'reorder_flag': reorder_flag,
'max_spot_size': int(max_spot_size),
@@ -270,7 +271,7 @@ class Memory:
try:
max_value = self.memory[self.max_idx]
except IndexError:
- max_value = np.empty((1, 3))
+ max_value = [[-1, -1, -1]]
return max_value
@@ -318,7 +319,6 @@ class TrapState:
self.noise = [0, 0]
self.empty = True
- self.update_trap_state()
self.toggle_ions()
def update_trap_state(self):
@@ -326,9 +326,6 @@ class TrapState:
Measures contrast (and noise) of the image and determines the state of the trap.
This function is executed every 60 seconds.
"""
- _thread = threading.Timer(60, self.update_trap_state)
- _thread.daemon = True
- _thread.start()
# Measure contrast and noise
contrast, self.noise = _contrast_and_noise()
@@ -341,7 +338,7 @@ class TrapState:
elif not self.empty and contrast:
self.trap_state = 'Crystallized ions'
elif not self.empty and not contrast:
- self.trap_state = 'Bad detection: No contrast but ions detected'
+ self.trap_state = 'No contrast but ions detected'
else:
self.trap_state = 'Empty'
@@ -384,6 +381,7 @@ def load_image():
sem = acquire_semaphore_read(settings.SEM_NAME)
shm = SharedArray.attach(settings.SHM_NAME) >> 4
image = shm.copy()
+
del shm
release_semaphore_read(sem)
return image
@@ -446,16 +444,16 @@ def ion_roundness(image, center):
c_x = center[0]
c_y = center[1]
- image_copy = image_copy[c_x - 25 : c_x + 25, c_y - 25 : c_y + 25] # crop the image
+ image_copy = image_copy[max(0, c_x - 25) : c_x + 25, max(0, c_y - 25) : c_y + 25] # crop the image
# get coordinates of ion pixels
- # TODO: fix this (sometimes the image_copy is empty)
pca_input = np.swapaxes(np.stack(np.where(image_copy > image_copy.max()*0.5)), 0, 1)
+
if len(pca_input) > 1:
pca = PCA(n_components=2) # compute PCA
pca.fit(pca_input)
var1, var2 = pca.explained_variance_ # return variance of 2 principal components
- roundness = var2 / var1 # if the ion is a circle, var1 / var2 = 1
+ roundness = var2 / var1 # if the ion is a circle, var2 / var1 = 1
else:
roundness = 0
@@ -757,9 +755,10 @@ def _contrast_and_noise():
time.sleep(1) # wait one second
img2 = load_image() # load image
_laser_switch(True) # turn on laser
+ time.sleep(1)
except requests.exceptions.ConnectionError:
warnings.warn("Connection to API couldn't be stablished.")
- return None, [0, 0]
+ return None, [-1, -1]
max2 = _max_coord(img2)
try:
@@ -823,7 +822,7 @@ def _ion_max_spot_size(y):
Return max width of peaks.
"""
y = _smooth(y, window_len=15, window='hamming')
- width, _, _, _ = peak_widths(y, [np.argmax(y)], rel_height=0.75)
+ width, _, _, _ = peak_widths(y, [np.argmax(y)], rel_height=0.5)
return np.max(width)
@@ -906,11 +905,9 @@ def _ion_distance(coord):
def _compare_coord(coord1, coord2):
same_coord = False
- same_len = len(coord1) == len(coord2)
- same_type = all(coord1[:, 2] == coord2[:, 2])
- same_pos = np.abs(coord1[:, :2] - coord2[:, :2]).sum()
-
- if same_len and same_type and same_pos < 30:
- same_coord = True
+ if len(coord1) == len(coord2):
+ if all(coord1[:, 2] == coord2[:, 2]):
+ if np.abs(coord1[:, :2] - coord2[:, :2]).sum() < 30:
+ same_coord = True
return same_coord
\ No newline at end of file
--
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