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fix creation of peaks, apply to config
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@rettigl
rettigl committed Apr 15, 2024
1 parent 211f087 commit d55d47d
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Showing 2 changed files with 56 additions and 97 deletions.
151 changes: 55 additions & 96 deletions specsanalyzer/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,11 +137,11 @@ def convert_image(
try:
fft_filter_params: dict = self._correction_matrix_dict["fft_tool_params"]
(amp, pos_x, pos_y, sig_x, sig_y) = (
fft_filter_params['amplitude'],
fft_filter_params['pos_x'],
fft_filter_params['pos_y'],
fft_filter_params['sigma_x'],
fft_filter_params['sigma_y'],
fft_filter_params["amplitude"],
fft_filter_params["pos_x"],
fft_filter_params["pos_y"],
fft_filter_params["sigma_x"],
fft_filter_params["sigma_y"],
)
fft_filter_peaks = create_fft_params_dict(amp, pos_x, pos_y, sig_x, sig_y)
img = fourier_filter_2d(raw_img, fft_filter_peaks)
Expand Down Expand Up @@ -579,7 +579,6 @@ def cropit(val): # pylint: disable=unused-argument
if apply:
cropit("")


def fft_tool(
self,
raw_image: np.ndarray,
Expand All @@ -594,83 +593,68 @@ def fft_tool(
matplotlib.use("module://ipympl.backend_nbagg")
try:
fft_tool_params = (
kwds["fft_tool_params"] if "fft_tool_params" in kwds
kwds["fft_tool_params"]
if "fft_tool_params" in kwds
else self._correction_matrix_dict["fft_tool_params"]
)
(amp, pos_x, pos_y, sig_x, sig_y) = (
fft_tool_params['amplitude'],
fft_tool_params['pos_x'],
fft_tool_params['pos_y'],
fft_tool_params['sigma_x'],
fft_tool_params['sigma_y'],
fft_tool_params["amplitude"],
fft_tool_params["pos_x"],
fft_tool_params["pos_y"],
fft_tool_params["sigma_x"],
fft_tool_params["sigma_y"],
)
except KeyError:
(amp, pos_x, pos_y, sig_x, sig_y) = (0.95, 86, 116, 13, 22)

fft_filter_peaks = create_fft_params_dict(amp, pos_x, pos_y, sig_x, sig_y)
try:
img = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret="fft"
)
fft_filtered = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret="filtered_fft"
)
img = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="fft")
fft_filtered = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="filtered_fft")

mask = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret="mask"
)
mask = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="mask")

filtered = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret="filtered"
)
filtered = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="filtered")
except IndexError:
print("Load the scan first!")
raise

fig = plt.figure()
ax = fig.add_subplot(3,2,1)
im_fft = ax.imshow(np.abs(img).T, origin='lower', aspect='auto')
ax = fig.add_subplot(3, 2, 1)
im_fft = ax.imshow(np.abs(img).T, origin="lower", aspect="auto")
fig.colorbar(im_fft)

ax.set_title("FFT")
cont = ax.contour(mask.T)

# Plot raw image
ax2 = fig.add_subplot(3,2,2)
fft_filt = ax2.imshow(np.abs(fft_filtered).T, origin='lower', aspect='auto')
ax2 = fig.add_subplot(3, 2, 2)
fft_filt = ax2.imshow(np.abs(fft_filtered).T, origin="lower", aspect="auto")
ax2.set_title("Filtered FFT")
fig.colorbar(fft_filt)

# Plot fft filtered image
ax3 = fig.add_subplot(2,2,3)
filt = ax3.imshow(filtered.T, origin='lower', aspect='auto')
ax3 = fig.add_subplot(2, 2, 3)
filt = ax3.imshow(filtered.T, origin="lower", aspect="auto")
ax3.set_title("Filtered Image")
fig.colorbar(filt)

ax4 = fig.add_subplot(3,2,4)
edc, = ax4.plot(np.sum(filtered, 0), label='EDC')
ax4 = fig.add_subplot(3, 2, 4)
(edc,) = ax4.plot(np.sum(filtered, 0), label="EDC")
ax4.legend()

ax5 = fig.add_subplot(3,2,6)
mdc, = ax5.plot(np.sum(filtered, 1), label='MDC')
ax5 = fig.add_subplot(3, 2, 6)
(mdc,) = ax5.plot(np.sum(filtered, 1), label="MDC")
ax5.legend()
# plt.tight_layout()

posx_slider = ipw.FloatSlider(
description="pos_x",
value=pos_x,
min=0,
max=128,
step=1,
)
description="pos_x",
value=pos_x,
min=0,
max=128,
step=1,
)
posy_slider = ipw.FloatSlider(
description="pos_y",
value=pos_y,
Expand Down Expand Up @@ -707,23 +691,15 @@ def fft_tool(
max=int(np.log10(np.abs(img).max())) + 1,
)

def update(v_vals, posx, posy, sigx, sigy, amp):
fft_filter_peaks = create_fft_params_dict(amp, posx, posy, sigx, sigy)
msk = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret='mask'
)
filtered_new = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret='filtered'
)
def update(v_vals, pos_x, pos_y, sig_x, sig_y, amp):
fft_filter_peaks = create_fft_params_dict(amp, pos_x, pos_y, sig_x, sig_y)
msk = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="mask")
filtered_new = fourier_filter_2d(raw_image, peaks=fft_filter_peaks, ret="filtered")

fft_filtered_new = fourier_filter_2d(
raw_image,
peaks=fft_filter_peaks,
ret='filtered_fft'
ret="filtered_fft",
)

im_fft.set_clim(vmax=v_vals)
Expand All @@ -745,25 +721,33 @@ def update(v_vals, posx, posy, sigx, sigy, amp):
ipw.interact(
update,
amp=amp_slider,
posx=posx_slider,
posy=posy_slider,
sigx=sigx_slider,
sigy=sigy_slider,
pos_x=posx_slider,
pos_y=posy_slider,
sig_x=sigx_slider,
sig_y=sigy_slider,
v_vals=clim_slider,
)

def apply_fft(apply: bool): # pylint: disable=unused-argument
amp = amp_slider.value
pos_x = posx_slider.value
pos_y = posy_slider.value
sig_x = sigx_slider.value
sig_y = sigy_slider.value
self._correction_matrix_dict['fft_tool_params'] = {
self._correction_matrix_dict["fft_tool_params"] = {
"amplitude": amp,
"pos_x": pos_x,
"pos_y": pos_y,
"sigma_x": sig_x,
"sigma_y": sig_y,
}
self.config["fft_filter_peaks"] = create_fft_params_dict(
amp,
pos_x,
pos_y,
sig_x,
sig_y,
)
amp_slider.close()
posx_slider.close()
posy_slider.close()
Expand Down Expand Up @@ -794,36 +778,11 @@ def create_fft_params_dict(amp, posx, posy, sigx, sigy):
"""

fft_filter_peaks = [
{'amplitude': amp,
'pos_x': 1*posx,
'pos_y': 0,
'sigma_x': sigx,
'sigma_y': sigy},
{'amplitude': amp,
'pos_x': 2*posx,
'pos_y': 0,
'sigma_x': sigx,
'sigma_y': sigy},
{'amplitude': amp,
'pos_x': 0,
'pos_y': posy,
'sigma_x': sigx,
'sigma_y': sigy},
{'amplitude': amp,
'pos_x': 1*posx,
'pos_y': posy,
'sigma_x': sigx,
'sigma_y': sigy},
{'amplitude': amp,
'pos_x': 2*posx,
'pos_y': posy,
'sigma_x': sigx,
'sigma_y': sigy},
{'amplitude': amp,
'pos_x': 3*posx,
'pos_y': posy,
'sigma_x': sigx,
'sigma_y': sigy},
{"amplitude": amp, "pos_x": -posx, "pos_y": 0, "sigma_x": sigx, "sigma_y": sigy},
{"amplitude": amp, "pos_x": posx, "pos_y": 0, "sigma_x": sigx, "sigma_y": sigy},
{"amplitude": amp, "pos_x": 0, "pos_y": posy, "sigma_x": sigx, "sigma_y": sigy},
{"amplitude": amp, "pos_x": -posx, "pos_y": posy, "sigma_x": sigx, "sigma_y": sigy},
{"amplitude": amp, "pos_x": posx, "pos_y": posy, "sigma_x": sigx, "sigma_y": sigy},
]

return fft_filter_peaks
2 changes: 1 addition & 1 deletion specsanalyzer/img_tools.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def fourier_filter_2d(
mask -= peak["amplitude"] * gauss2d(
xgrid,
ygrid,
peak["pos_x"],
image_fft.shape[0] / 2 + peak["pos_x"],
peak["pos_y"],
peak["sigma_x"],
peak["sigma_y"],
Expand Down

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