added lots of .py

camerata/main.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+
+from time import sleep
+from collections import deque
+import numpy as np
+import scipy.signal
+
+from zoetrope import aniplot as plt
+from bstrd import BS, bsstream
+plt.blit = False
+
+
+
+# config
+cam_name = "SARES11-XMI125-C4P1"
+xmin = 0
+xmax = 400
+ymin = 400
+ymax = 700
+proj_axis = 0
+um_per_px = 2.28
+buffer_length = 100
+
+
+
+def get_data(cam):
+    img = 0
+    for i in range(1):
+        img += cam.get()
+        next(bsstream)
+    cropped = img[xmin:xmax, ymin:ymax]
+    projx = cropped.mean(axis=proj_axis)
+    projy = cropped.mean(axis=int(not proj_axis))
+    return cropped, projx, projy
+
+
+def find_spacing(py, extend=5):
+    py -= py.mean()
+
+    if extend > 1:
+        py = np.concatenate((py, np.zeros(len(py) * extend)))
+
+    spectrum = np.abs(np.fft.fft(py))
+    freq = np.fft.fftfreq(len(spectrum))
+
+    which = (freq > 0.005)
+    spectrum = spectrum[which]
+    freq = freq[which]
+
+    index_peaks = scipy.signal.find_peaks(spectrum)[0]
+    peaks_pos = freq[index_peaks]
+    peak_height = spectrum[index_peaks]
+
+    cut_freq = peaks_pos[np.argmax(peak_height)]
+    return freq, spectrum, cut_freq
+
+
+def make_xs(arr):
+    return np.arange(len(arr))
+
+
+# create channel
+cam = BS(cam_name + ".roi_signal_x_profile", modulo=5)
+cropped, width, proj = get_data(cam)
+pixel_proj  = make_xs(proj)
+pixel_width = make_xs(width)
+
+
+plt.fig.set_figheight(12)
+plt.fig.set_figwidth(9)
+
+plt.suptitle(cam_name)
+
+plt.subplot(321)
+plt.title(f"cropped image\n[{xmin}:{xmax}, {ymin}:{ymax}]")
+pimg = plt.imshow(cropped, origin="lower")
+
+plt.subplot(322)
+plt.title("projection")
+pln_proj = plt.plot(proj, pixel_proj)
+
+plt.subplot(323)
+plt.title("projection")
+pln_width = plt.plot([0])
+
+plt.subplot(324)
+plt.title("FFT")
+plt.xlabel("frequency in 1/pixel")
+pln_fft_spec = plt.plot([0])
+plt.xlim(0,0.2)
+pln_fft_cut  = plt.plot([0])
+
+plt.subplot(313)
+plt.title(f"spacing assuming {um_per_px} μm per pixel")
+pln_spac = plt.plot([0], 'o')
+plt.ylim(0,250)
+plt.tight_layout()
+
+
+spacings = deque(maxlen=buffer_length)
+
+for counter in plt.show():
+    print(counter)
+    next(bsstream)
+
+
+    cropped, width, proj = get_data(cam)
+
+    pimg.set(cropped)
+    pln_proj.set(proj, pixel_proj)
+    pln_width.set(pixel_width, width)
+
+    freq, spectrum, cut_freq = find_spacing(proj, extend=10)
+    spac = um_per_px / cut_freq
+    spacings.append(spac)
+
+    pln_spac.set(make_xs(spacings), spacings)
+    pln_fft_spec.set(freq, spectrum)
+    pln_fft_cut.set([cut_freq]*2, [spectrum.min(), spectrum.max()])
+    pln_fft_spec.ax.set_title(f"FFT\ncurrent spacing: {spac:.1f} μm")
+
+
+    # this, I need to move into the library
+    ps = [pln_proj, pln_width, pln_spac, pln_fft_spec]
+    for p in ps:
+        p.ax.relim()
+        p.ax.autoscale_view()
+
+
+
+bsstream.close()
+
+
+