From c09fc3061b97ca9431eb2cded07853097effb901 Mon Sep 17 00:00:00 2001
From: amitjans <amitjans@ethz.ch>
Date: Mon, 31 May 2021 19:47:07 +0200
Subject: [PATCH] fix gradient compensation
---
main.py | 6 +++---
tools.py | 40 ++++++++++++++--------------------------
2 files changed, 17 insertions(+), 29 deletions(-)
diff --git a/main.py b/main.py
index 15ed4ca..0326b51 100644
--- a/main.py
+++ b/main.py
@@ -49,9 +49,9 @@ while True:
coord, max_spot_size = ion_positions(image)
if len(coord) > 0:
roundness = ion_roundness(image, coord[0][:2])
- new_img = compensate_gradient(image)
- max_int, num_pix = max_ion_intensity(image, coord)
- coord = detect_wrong_isotopes(image, coord, max_int)
+ new_img = compensate_gradient(image, coord)
+ max_int, num_pix = max_ion_intensity(new_img, coord)
+ coord = detect_wrong_isotopes(new_img, coord, max_int)
LINEARITY = ion_linearity(coord)
if len(coord) > 1 and dist_factor is not None:
coord = dark_ions(image, coord)
diff --git a/tools.py b/tools.py
index 963e793..bd87614 100644
--- a/tools.py
+++ b/tools.py
@@ -218,24 +218,12 @@ def ion_positions(image):
Finally return the coordinates together with the maximum ion width.
"""
coordinates, max_width = _max_coord(image, width=True) # measure local max
- # delete local maxima that are not in the same axis as the brightest spot.
- try:
- h_axis = coordinates[0, 0]
- coordinates = coordinates[np.logical_and(coordinates[:, 0] < h_axis + 15,
- coordinates[:, 0] > h_axis - 15)]
- except IndexError:
- pass
-
coordinates += np.flip(settings.REGION[0]) # change reference
coordinates = coordinates[coordinates[:, 1].argsort()] # order
# add 3rd column indicating the ion's state (bright, dark, wrong isotope)
coordinates = np.concatenate((coordinates, np.zeros((len(coordinates[:, 1]), 1))), axis=1)
- if len(coordinates) > 25:
- coordinates = np.empty((0, 3))
- print('We have an ion cloud')
-
- elif len(coordinates) == 0:
+ if len(coordinates) == 0:
coordinates = np.empty((0, 3))
return coordinates.astype(int), max_width
@@ -291,21 +279,18 @@ def ion_linearity(points):
return linearity
-def compensate_gradient(image):
+def compensate_gradient(image, coord):
"""
Measure the intensity gradient of the ions along the x axis and correct it.
Ignore any basckground intensity gradient.
"""
- im_slope = _measure_gradient(image)
-
- background_slope = _measure_gradient(image[np.r_[0:200, image.shape[0]-200:image.shape[0]]])
- slope = im_slope - background_slope
+ slope = _measure_gradient(image, coord)
for i in range(image.shape[1]):
- image[:, i] = image[:, i] - i*slope
+ image[:, i] = np.clip(image[:, i] - i*slope, 0, None)
- return image
+ return image.astype(np.uint16)
def max_ion_intensity(image, centers):
@@ -631,16 +616,19 @@ def _smooth(x, window_len=11, window='hanning'):
return y
-def _measure_gradient(image):
+def _measure_gradient(image, coord):
"""
- Fits the image intensity into a polynomial function of degree one and returns
+ Fits the ion intensity into a polynomial function of degree one and returns
the value of the slope.
"""
- col_int = np.sum(image, axis=0)
- x = np.arange(image.shape[1], step=1)
- m, _ = np.polyfit(x, col_int, deg=1)
+ y = []
+ x = []
+ for pos in coord:
+ y.append(np.sum(image[pos[0] - 30 : pos[0] + 30, pos[1]], axis=0))
+ x.append(pos[1])
+ m, _ = np.polyfit(x, y, deg=1)
- return m/image.shape[0]
+ return m/60
def _ion_intensity(image, center):
--
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