From 4c0f2b6301293f62258ac34fa607a1ad8210ed96 Mon Sep 17 00:00:00 2001
From: Florian Dworkowski <florian.dworkowski@psi.ch>
Date: Mon, 7 Sep 2026 16:41:10 +0200
Subject: [PATCH 1/2] moved working copy from RHEL8 to outdated git

---
 camerata/deprecated/main.old.py               | 134 ++++++++++++++++++
 camerata/{ => deprecated}/main_less_simple.py |   0
 camerata/{ => deprecated}/main_simple.py      |   0
 camerata/main.py                              |  97 ++++++-------
 4 files changed, 174 insertions(+), 57 deletions(-)
 create mode 100755 camerata/deprecated/main.old.py
 rename camerata/{ => deprecated}/main_less_simple.py (100%)
 rename camerata/{ => deprecated}/main_simple.py (100%)

diff --git a/camerata/deprecated/main.old.py b/camerata/deprecated/main.old.py
new file mode 100755
index 0000000..d53dbe0
--- /dev/null
+++ b/camerata/deprecated/main.old.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()
+
+
+
diff --git a/camerata/main_less_simple.py b/camerata/deprecated/main_less_simple.py
similarity index 100%
rename from camerata/main_less_simple.py
rename to camerata/deprecated/main_less_simple.py
diff --git a/camerata/main_simple.py b/camerata/deprecated/main_simple.py
similarity index 100%
rename from camerata/main_simple.py
rename to camerata/deprecated/main_simple.py
diff --git a/camerata/main.py b/camerata/main.py
index d53dbe0..2427a10 100755
--- a/camerata/main.py
+++ b/camerata/main.py
@@ -3,35 +3,26 @@
 from time import sleep
 from collections import deque
 import numpy as np
-import scipy.signal
+from scipy import 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
-
-
+cam_name = "SARES11-SPEC125-M2.jet_projection"
+um_per_px = 3.33 # calibrated as of feb 6 2024 
+buffer_length = 1000
+shots = 10
+fftthresh = 10000
 
 def get_data(cam):
-    img = 0
-    for i in range(1):
-        img += cam.get()
+    jet = np.empty((shots, 500)) 
+    for i in range(shots):
+        jet[i] = 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
+    proj = jet.max(axis=0)
+    return proj 
 
 
 def find_spacing(py, extend=5):
@@ -40,14 +31,14 @@ def find_spacing(py, extend=5):
     if extend > 1:
         py = np.concatenate((py, np.zeros(len(py) * extend)))
 
-    spectrum = np.abs(np.fft.fft(py))
+    spectrum = np.abs(np.fft.fft(py))**2
     freq = np.fft.fftfreq(len(spectrum))
 
     which = (freq > 0.005)
     spectrum = spectrum[which]
     freq = freq[which]
 
-    index_peaks = scipy.signal.find_peaks(spectrum)[0]
+    index_peaks = signal.find_peaks(spectrum)[0]
     peaks_pos = freq[index_peaks]
     peak_height = spectrum[index_peaks]
 
@@ -60,42 +51,40 @@ def make_xs(arr):
 
 
 # create channel
-cam = BS(cam_name + ".roi_signal_x_profile", modulo=5)
-cropped, width, proj = get_data(cam)
+cam = BS(cam_name)
+proj = get_data(cam)
 pixel_proj  = make_xs(proj)
-pixel_width = make_xs(width)
 
+plt.fig.set_figheight(8)
+plt.fig.set_figwidth(8)
 
-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.subplot(221)
 plt.title("projection")
 pln_proj = plt.plot(proj, pixel_proj)
+plt.xlim(-45,45)
+plt.gca().invert_yaxis()
+plt.grid()
 
-plt.subplot(323)
-plt.title("projection")
-pln_width = plt.plot([0])
-
-plt.subplot(324)
+plt.subplot(222)
 plt.title("FFT")
 plt.xlabel("frequency in 1/pixel")
 pln_fft_spec = plt.plot([0])
-plt.xlim(0,0.2)
+plt.xlim(0,0.25)
+plt.grid()
+#plt.ylim(0,500000)
 pln_fft_cut  = plt.plot([0])
 
-plt.subplot(313)
+plt.subplot(212)
 plt.title(f"spacing assuming {um_per_px} μm per pixel")
 pln_spac = plt.plot([0], 'o')
-plt.ylim(0,250)
-plt.tight_layout()
+pln_spac.ax.axhline(y=95, color='r') # 95um spacing set for CRY4 expt
+plt.xlabel('1000 (*10) most recent images')
+plt.ylabel('ladder spacing in $\mu$m')
+plt.ylim(0,150)
+plt.xlim(0,buffer_length)
 
+plt.grid()
+plt.tight_layout()
 
 spacings = deque(maxlen=buffer_length)
 
@@ -103,32 +92,26 @@ for counter in plt.show():
     print(counter)
     next(bsstream)
 
+    proj = get_data(cam)
 
-    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)
+    if spectrum.max() > fftthresh:
+        spacings.append(spac)
+    else:
+        spacings.append(np.nan)
 
     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")
-
+    pln_fft_spec.ax.set_title(f"FFT; current spacing: {spac:.1f} μm")
 
     # this, I need to move into the library
-    ps = [pln_proj, pln_width, pln_spac, pln_fft_spec]
+    ps = [pln_proj, pln_spac, pln_fft_spec]
     for p in ps:
         p.ax.relim()
         p.ax.autoscale_view()
 
-
-
 bsstream.close()
-
-
-
-- 
2.54.0


From bbc09780b975c063bc69fb5b4b1f9bed899dc8b3 Mon Sep 17 00:00:00 2001
From: Florian Dworkowski <florian.dworkowski@psi.ch>
Date: Mon, 7 Sep 2026 16:58:18 +0200
Subject: [PATCH 2/2] updated run from RHEL8

---
 run | 31 +++++++++----------------------
 1 file changed, 9 insertions(+), 22 deletions(-)

diff --git a/run b/run
index d997964..08c75e2 100755
--- a/run
+++ b/run
@@ -1,24 +1,5 @@
 #!/bin/bash
 
-# The following block allows to use the `run` script like this
-# ```
-# ln -s run a_script.sh
-# ./a_script.sh
-# ```
-# which then runs `./run a_script.py`
-
-fn=$(basename $0)
-if [ "$fn" != "run" ]; then
-  dn=$(dirname "$0")
-  sn=$(basename "$0" .sh)
-  dn="${dn}/run"
-  sn="${sn}.py"
-  echo "Running: $dn $sn"
-  $dn $sn
-  exit
-fi
-
-###
 
 function help() {
   echo "Load conda env and run a script"
@@ -42,8 +23,14 @@ if [[ -z $@ ]]; then
   exit 1
 fi
 
-source /sf/alvra/applications/miniconda3/etc/profile.d/conda.sh
-conda activate adaq
-source /sf/eido/source-python
+#!/usr/bin/env python
+
+#source /sf/alvra/applications/miniconda3/etc/profile.d/conda.sh
+#conda activate adaq
+#source /sf/eido/applications/miniconda3/etc/profile.d/conda.sh
+#conda activate slic-3.8-update6
+source /sf/daq/source-conda
+conda activate slic
+source /sf/daq/source-python
 $@
 
-- 
2.54.0