microspheres · TCAcycle · Oct 25, 2018 · Oct 25, 2018 · Oct 25, 2018 · Oct 25, 2018
diff --git a/LabView Code/DAQ/DAQ.vi b/LabView Code/DAQ/DAQ.vi
diff --git a/LabView Code/DAQ/Get Full Terminal Name.vi b/LabView Code/DAQ/Get Full Terminal Name.vi
diff --git a/LabView Code/DAQ/arange (SubVI).vi b/LabView Code/DAQ/arange (SubVI).vi
diff --git a/LabView Code/DAQ/boolean_run_tilt_stage.vi b/LabView Code/DAQ/boolean_run_tilt_stage.vi
diff --git a/LabView Code/DAQ/change_voltages_in_process_list.vi b/LabView Code/DAQ/change_voltages_in_process_list.vi
diff --git a/LabView Code/DAQ/check_folder (SubVI).vi b/LabView Code/DAQ/check_folder (SubVI).vi
diff --git a/LabView Code/DAQ/check_if_should_flash (SubVI).vi b/LabView Code/DAQ/check_if_should_flash (SubVI).vi
diff --git a/LabView Code/DAQ/clean_up_data_tasks (SubVI).vi b/LabView Code/DAQ/clean_up_data_tasks (SubVI).vi
diff --git a/LabView Code/DAQ/clean_up_instruments (SubVI).vi b/LabView Code/DAQ/clean_up_instruments (SubVI).vi
diff --git a/LabView Code/DAQ/create_file_name (SubVI).vi b/LabView Code/DAQ/create_file_name (SubVI).vi
diff --git a/LabView Code/DAQ/create_process_list (SubVI).vi b/LabView Code/DAQ/create_process_list (SubVI).vi
diff --git a/LabView Code/DAQ/dipole_voltage_control(Sub VI).vi b/LabView Code/DAQ/dipole_voltage_control(Sub VI).vi
diff --git a/LabView Code/DAQ/dipole_voltage_control_logic(SubVI).vi b/LabView Code/DAQ/dipole_voltage_control_logic(SubVI).vi
diff --git a/LabView Code/DAQ/flash_lamp (SubVI).vi b/LabView Code/DAQ/flash_lamp (SubVI).vi
diff --git a/LabView Code/DAQ/initialize_instruments (SubVI).vi b/LabView Code/DAQ/initialize_instruments (SubVI).vi
diff --git a/LabView Code/DAQ/make_synth_array (SubVI).vi b/LabView Code/DAQ/make_synth_array (SubVI).vi
diff --git a/LabView Code/DAQ/make_tilt_stage_array (SubVI).vi b/LabView Code/DAQ/make_tilt_stage_array (SubVI).vi
diff --git a/LabView Code/DAQ/name_dipole_voltage.vi b/LabView Code/DAQ/name_dipole_voltage.vi
diff --git a/LabView Code/DAQ/read_data (SubVI).vi b/LabView Code/DAQ/read_data (SubVI).vi
diff --git a/LabView Code/DAQ/save_data (SubVI).vi b/LabView Code/DAQ/save_data (SubVI).vi
diff --git a/LabView Code/DAQ/set_dipole_voltage.vi b/LabView Code/DAQ/set_dipole_voltage.vi
diff --git a/LabView Code/DAQ/set_instruments (SubVI).vi b/LabView Code/DAQ/set_instruments (SubVI).vi
diff --git a/LabView Code/DAQ/take_data (SubVI).vi b/LabView Code/DAQ/take_data (SubVI).vi
diff --git a/LabView Code/DAQ/variable_steps_logic.vi b/LabView Code/DAQ/variable_steps_logic.vi
diff --git a/LabView Code/Examples/Tilt Stage/Command VIs/SetAcceleration.vi b/LabView Code/Examples/Tilt Stage/Command VIs/SetAcceleration.vi
diff --git a/LabView Code/Examples/Tilt Stage/Command VIs/SetVelocity.vi b/LabView Code/Examples/Tilt Stage/Command VIs/SetVelocity.vi
diff --git a/LabView Code/Examples/Tilt Stage/Device VIs/DeviceOpen.vi b/LabView Code/Examples/Tilt Stage/Device VIs/DeviceOpen.vi
diff --git a/LabView Code/Examples/Tilt Stage/Device VIs/GetMasterDeviceAddress.vi b/LabView Code/Examples/Tilt Stage/Device VIs/GetMasterDeviceAddress.vi
diff --git a/LabView Code/Examples/Tilt Stage/Device VIs/InitSingleDevice.vi b/LabView Code/Examples/Tilt Stage/Device VIs/InitSingleDevice.vi
diff --git a/LabView Code/FPGA code/FPGA Bitfiles/EOM.vi b/LabView Code/FPGA code/FPGA Bitfiles/EOM.vi
diff --git a/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_ErjQEsBLsCA.lvbitx b/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_ErjQEsBLsCA.lvbitx
diff --git a/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw.lvbitx b/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw.lvbitx
diff --git a/...de/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211021.lvbitx b/...de/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211021.lvbitx
diff --git a/...de/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211022.lvbitx b/...de/FPGA Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211022.lvbitx
diff --git a/...A Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211028_notch.lvbitx b/...A Bitfiles/Microspherefeedb_FPGATarget2_(FPGA)PIDXYZlase_Y-TtBVY85Jw20211028_notch.lvbitx
diff --git a/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_MultiChannelfFee_SMENcAWM-fA.lvbitx b/.../FPGA code/FPGA Bitfiles/Microspherefeedb_FPGATarget2_MultiChannelfFee_SMENcAWM-fA.lvbitx
diff --git a/LabView Code/FPGA code/Microsphere feedback.aliases b/LabView Code/FPGA code/Microsphere feedback.aliases
@@ -1,3 +1,3 @@
 [My Computer]
-My Computer = "192.168.1.3"
+My Computer = "169.254.107.234"
 
diff --git a/LabView Code/FPGA code/Microsphere feedback.lvlps b/LabView Code/FPGA code/Microsphere feedback.lvlps
@@ -1,3 +1,3 @@
 [ProjectWindow_Data]
-ProjectExplorer.ClassicPosition[String] = "165,1005,935,1796"
+ProjectExplorer.ClassicPosition[String] = "274,808,1042,1599"
 
diff --git a/LabView Code/FPGA code/Microsphere feedback.lvproj b/LabView Code/FPGA code/Microsphere feedback.lvproj
diff --git a/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/(FPGA)_PIDXYZ_laserPID)_COMtemp.vi b/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/(FPGA)_PIDXYZ_laserPID)_COMtemp.vi
diff --git a/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/(FPGA)_PIDXYZ_laserPID)_COMtemp2.vi b/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/(FPGA)_PIDXYZ_laserPID)_COMtemp2.vi
diff --git a/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/BeadCoolerFixedZ(SubVI).vi b/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/BeadCoolerFixedZ(SubVI).vi
diff --git a/...nelFeedbackCooling FPGA/MultiChannelFeedbackCooling_aod_feedback(Host)_PIDXYZ_laserPID.vi b/...nelFeedbackCooling FPGA/MultiChannelFeedbackCooling_aod_feedback(Host)_PIDXYZ_laserPID.vi
diff --git a/.../FPGA code/MultiChannelFeedbackCooling FPGA/MultiChannelfFeedbackCooling (FPGA)_PIDXYZ.vi b/.../FPGA code/MultiChannelFeedbackCooling FPGA/MultiChannelfFeedbackCooling (FPGA)_PIDXYZ.vi
diff --git a/...e/MultiChannelFeedbackCooling FPGA/MultiChannelfFeedbackCooling (FPGA)_PIDXYZ_laserPID.vi b/...e/MultiChannelFeedbackCooling FPGA/MultiChannelfFeedbackCooling (FPGA)_PIDXYZ_laserPID.vi
diff --git a/...Code/FPGA code/MultiChannelFeedbackCooling FPGA/feedback(Host)_PIDXYZ_laserPID_COMTEMP.vi b/...Code/FPGA code/MultiChannelFeedbackCooling FPGA/feedback(Host)_PIDXYZ_laserPID_COMTEMP.vi
diff --git a/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/rangelimiter.vi b/LabView Code/FPGA code/MultiChannelFeedbackCooling FPGA/rangelimiter.vi
diff --git a/LabView Code/FPGA code/newgauge.vi b/LabView Code/FPGA code/newgauge.vi
diff --git a/LabView Code/Gwinstek_chan_1_2.vi b/LabView Code/Gwinstek_chan_1_2.vi
diff --git a/LabView Code/Gwinstek_chan_1_2_sub.vi b/LabView Code/Gwinstek_chan_1_2_sub.vi
diff --git a/LabView Code/Gwinstek_sub.vi b/LabView Code/Gwinstek_sub.vi
diff --git a/LabView Code/Microsphere_Control.aliases b/LabView Code/Microsphere_Control.aliases
@@ -1,3 +1,3 @@
 [My Computer]
-My Computer = "192.168.1.3"
+My Computer = "169.254.107.234"
 
diff --git a/LabView Code/Microsphere_Control.lvlps b/LabView Code/Microsphere_Control.lvlps
@@ -1,3 +1,3 @@
 [ProjectWindow_Data]
-ProjectExplorer.ClassicPosition[String] = "275,1027,681,1399"
+ProjectExplorer.ClassicPosition[String] = "86,345,873,880"
 
diff --git a/LabView Code/Microsphere_Control.lvproj b/LabView Code/Microsphere_Control.lvproj
diff --git a/LabView Code/TIC Query Command daq.vi b/LabView Code/TIC Query Command daq.vi
diff --git a/LabView Code/TIC Query Command.vi b/LabView Code/TIC Query Command.vi
diff --git a/LabView Code/TIC Read Gauge Pressure or Volts daq.vi b/LabView Code/TIC Read Gauge Pressure or Volts daq.vi
diff --git a/LabView Code/TIC Read Gauge Pressure or Volts.vi b/LabView Code/TIC Read Gauge Pressure or Volts.vi
diff --git a/LabView Code/Turbo Instrument Controller.llb b/LabView Code/Turbo Instrument Controller.llb
diff --git a/LabView Code/VISA_Query.vi b/LabView Code/VISA_Query.vi
diff --git a/LabView Code/bead_dropper.vi b/LabView Code/bead_dropper.vi
diff --git a/LabView Code/bead_dropper_Gadi.vi b/LabView Code/bead_dropper_Gadi.vi
diff --git a/LabView Code/get_position_robust (SubVI).vi b/LabView Code/get_position_robust (SubVI).vi
diff --git a/LabView Code/initialize_oscilloscope_chan1.vi b/LabView Code/initialize_oscilloscope_chan1.vi
diff --git a/LabView Code/move_tilt_stage_simpler(Sub VI).vi b/LabView Code/move_tilt_stage_simpler(Sub VI).vi
diff --git a/LabView Code/open_stage_simpler (SubVI).vi b/LabView Code/open_stage_simpler (SubVI).vi
diff --git a/LabView Code/open_tilt_stage_motor.vi b/LabView Code/open_tilt_stage_motor.vi
diff --git a/LabView Code/oscilloscopes_Acquire_Multiple_Waveforms.vi b/LabView Code/oscilloscopes_Acquire_Multiple_Waveforms.vi
diff --git a/LabView Code/pressures.vi b/LabView Code/pressures.vi
diff --git a/LabView Code/pressures_sub.vi b/LabView Code/pressures_sub.vi
diff --git a/LabView Code/read_preassures_TIC_daq.vi b/LabView Code/read_preassures_TIC_daq.vi
diff --git a/LabView Code/relative_move_robust (SubVI).vi b/LabView Code/relative_move_robust (SubVI).vi
diff --git a/LabView Code/set_QWP.vi b/LabView Code/set_QWP.vi
diff --git a/LabView Code/set_synth.vi b/LabView Code/set_synth.vi
diff --git a/LabView Code/set_tilt_stage_simpler (SubVI).vi b/LabView Code/set_tilt_stage_simpler (SubVI).vi
diff --git a/LabView Code/sweep_Gadi.vi b/LabView Code/sweep_Gadi.vi
diff --git a/LabView Code/test_gwintek.vi b/LabView Code/test_gwintek.vi
diff --git a/h5binaries/hdf5.lib b/h5binaries/hdf5.lib
diff --git a/h5binaries/szip.lib b/h5binaries/szip.lib
diff --git a/h5binaries/zlib.lib b/h5binaries/zlib.lib
diff --git a/scripts/43.6 b/scripts/43.6
diff --git a/scripts/49.5 b/scripts/49.5
diff --git a/scripts/60.8 b/scripts/60.8
diff --git a/scripts/68.7 b/scripts/68.7
diff --git a/scripts/72.9 b/scripts/72.9
diff --git a/scripts/AOM_characterization.py b/scripts/AOM_characterization.py
@@ -0,0 +1,49 @@
+import numpy, h5py, matplotlib
+import matplotlib.pyplot as plt
+import os
+import scipy.signal as sp
+import numpy as np
+import bead_util as bu
+import glob
+
+FPGAout = r"X_PM_Y_SYNTH.h5"
+path = r"C:\data\AOM"
+
+NFFT = 2**17
+
+def getdata(fname):
+	print "Opening file: ", fname
+	## guess at file type from extension
+	_, fext = os.path.splitext( fname )
+	if( fext == ".h5"):
+		f = h5py.File(fname,'r')
+		dset = f['beads/data/pos_data']
+		dat = numpy.transpose(dset)
+		#max_volt = dset.attrs['max_volt']
+		#nbit = dset.attrs['nbit']
+		Fs = dset.attrs['Fsamp']
+
+		#dat = 1.0*dat*max_volt/nbit
+                dat = dat * 10./(2**15 - 1)
+
+	else:
+		dat = numpy.loadtxt(fname, skiprows = 5, usecols = [2, 3, 4, 5, 6] )
+
+	xpsd, freqs = matplotlib.mlab.psd(dat[:, bu.xi]-numpy.mean(dat[:, bu.xi]), Fs = Fs, NFFT = NFFT)
+
+        ypsd, freqs = matplotlib.mlab.psd(dat[:, bu.yi]-numpy.mean(dat[:, bu.yi]), Fs = Fs, NFFT = NFFT)
+
+	return [freqs, xpsd, ypsd, dat[:, bu.xi], dat[:, bu.yi]]
+
+a = getdata(os.path.join(path, FPGAout))
+t = range(len(a[3]))
+
+print a[3]
+
+
+fig = plt.figure()
+plt.plot(a[3], a[4],label="PM vs synth")
+plt.legend()
+plt.xlabel("PM [V]")
+plt.ylabel("synth [V]")
+plt.show()
diff --git a/scripts/COM_motion_camera.py b/scripts/COM_motion_camera.py
@@ -0,0 +1,215 @@
+from PIL import Image
+import glob, os
+import cv2
+import matplotlib.pyplot as plt
+import h5py
+import numpy as np
+import numpy, matplotlib
+import read_log_camera as rlc
+import os
+from scipy.signal import find_peaks
+from skimage.util import img_as_ubyte, crop
+from skimage.filters import threshold_otsu
+from skimage.feature import register_translation
+from skimage.transform import rotate
+import multiprocessing as mp
+import time
+
+pathlist = [r"C:\data\20200313\two_spheres\15um_german\2\only_1_sphere",  ]
+
+#pathlist = glob.glob(os.path.join(r"C:\data\20200311\two_spheres\15um_german\3", "*", ""))
+#pathlist = pathlist + glob.glob(os.path.join(r"C:\data\20200311\two_spheres\15um_german\3", "*", ""))
+#pathlist = pathlist + glob.glob(os.path.join(r"C:\data\20200311\two_spheres\15um_german\4", "*", ""))
+
+#pathlist = [r"C:\data\20200313\two_spheres\15um_german\2\1"]
+#print pathlist
+see_frame = False
+use_threshold = True # always set True
+
+use_rotation = True
+
+# FB on the bottom for march 13
+coorL = [33-12, 25-12, 105+12, 95+12]
+coorR = [160-12, 13-12, 270+12, 90+12]
+
+# # march 11
+#coorL = [47, 35, 133, 110]
+#coorR = [222, 22, 345, 98]
+
+upsample = 100 # the result looks the same with upsample = 1000
+
+def get_files_path(path):
+    file_list = glob.glob(path+"\*.tiff")
+    return file_list
+
+def list_file_time_order(filelist):
+    filelist.sort(key=os.path.getmtime)
+    return filelist
+
+
+def get_sub_image(name, coordinates): # this returnd the cropped images
+    im = Image.open(name)
+    left, top, right, bottom = coordinates
+    im = im.crop((left, top, right, bottom))
+    return im
+
+def rot_special(image, angle, N_crop):
+    image = rotate(image*1.0, angle*1.0)
+    image = image[N_crop:len(image) - N_crop]
+    image = np.rot90(image)
+    image = image[N_crop:len(image) - N_crop]
+    image = np.rot90(image)
+    image = np.rot90(image)
+    image = np.rot90(image)
+    return image
+
+
+# this is for displaying the image cropped
+path = pathlist[0]
+filelist = get_files_path(path)
+filelist = list_file_time_order(filelist)
+imageL = get_sub_image(filelist[400], coorL)
+imageR = get_sub_image(filelist[400], coorR)
+imageL = img_as_ubyte(imageL)
+imageR = img_as_ubyte(imageR)
+if use_threshold:
+    values = np.linspace(0.05, 0.5, 15)
+    threshL = threshold_otsu(imageL)
+    threshR = threshold_otsu(imageR)
+    imageLstat = imageL
+    imageRstat = imageR
+    imageL = np.ones(imageL.shape)
+    imageR = np.ones(imageR.shape)
+    for i in values:
+        imageLa = imageLstat > i*threshL
+        imageRa = imageRstat > i*threshR
+        imageL = imageL + imageLa*1.
+        imageR = imageR + imageRa*1.
+
+plt.figure()
+plt.imshow(imageL)
+
+plt.figure()
+if use_rotation:
+    imageR = rot_special(imageL, 0, 16)
+plt.imshow(imageR)
+
+if see_frame:
+    plt.show()
+# this ends the crop view
+
+
+def threshold(imageL, imageR): # returns 2 iamages with threshold
+    values = np.linspace(0.05, 0.5, 15)
+    threshL = threshold_otsu(imageL)
+    threshR = threshold_otsu(imageR)
+    imageLstat = imageL
+    imageRstat = imageR
+    imageL = np.zeros(imageL.shape)
+    imageR = np.zeros(imageR.shape) 
+    for i in values:
+        imageLa = imageLstat > i*threshL
+        imageRa = imageRstat > i*threshR
+        imageL = imageL + imageLa*1.
+        imageR = imageR + imageRa*1.
+    return [imageL, imageR]
+
+
+def positionLR(nameref, name, coorL, coorR, angle): # outputs the sphere position for each frame name
+    imageLref = get_sub_image(nameref, coorL)
+    imageRref = get_sub_image(nameref, coorR)
+    imageLref = img_as_ubyte(imageLref)
+    imageRref = img_as_ubyte(imageRref)
+
+    imageL = get_sub_image(name, coorL)
+    imageR = get_sub_image(name, coorR)
+    imageL = img_as_ubyte(imageL)
+    imageR = img_as_ubyte(imageR)
+
+    if use_rotation:
+        imageLref = rot_special(imageLref, angle, 16)
+        imageRref = rot_special(imageRref, angle, 16)
+        imageL = rot_special(imageL, angle, 16)
+        imageR = rot_special(imageR, angle, 16)
+
+    if use_threshold: # i think it is alwasys good that the ref image is thresholded, that is why the comment in the line below
+        #imageL, imageR = threshold(imageL, imageR)
+        imageLref, imageRref = threshold(imageLref, imageRref)
+
+    shiftL, errorL, diffphaseL = register_translation(imageLref, imageL, upsample_factor = upsample)
+    shiftR, errorR, diffphaseR = register_translation(imageRref, imageR, upsample_factor = upsample)
+
+    sl = shiftL[1]
+    sr = shiftR[1]
+    slx = shiftL[0]
+    srx = shiftR[0]
+
+    #print "L", SL
+    #print "R", SR
+
+    return [sl, sr, slx, srx]
+
+
+def positionALL(filelist, coorL, coorR, angle): # uses positionLR to generate a timestream for a filelits of images
+    R = []
+    L = []
+    Rx = []
+    Lx = []
+    # a = 0
+    nameref = filelist[0]
+    for i in filelist:
+        l, r, lx, rx = positionLR(nameref, i, coorL, coorR, angle)
+        R.append(r)
+        L.append(l)
+        Rx.append(rx)
+        Lx.append(lx)
+        # print a
+        # a = a + 1
+    R = np.array(R)
+    L = np.array(L)
+    Rx = np.array(Rx)
+    Lx = np.array(Lx)
+    return [L, R, Lx, Rx]
+
+def calculate_path(path, angle): # gets a folder, generate a filelist and saves the timestream
+    filelist = get_files_path(path)
+    filelist = list_file_time_order(filelist)
+
+    L, R, Lx, Rx = positionALL(filelist, coorL, coorR, angle)
+    L = L - np.mean(L)
+    R = R - np.mean(R)
+    Lx = Lx - np.mean(Lx)
+    Rx = Rx - np.mean(Rx)
+
+    save = [L, R, Lx, Rx]
+    if use_threshold:
+        if use_rotation:
+            pathsave = path + "\\timestream_with_threshold_" + str(angle) + ".npy"
+        else:
+            pathsave = path + "\\timestream_with_threshold.npy"
+    else:
+        pathsave = path + "\\timestream.npy"
+
+    np.save(pathsave, save)
+
+    print path
+    seconds = time.time()
+    local_time = time.ctime(seconds)
+    print "time saved: ", local_time
+
+    return []
+
+
+angles = [-16, -12, -8, -4, 0, 4, 8, 12, 16]
+
+for i in angles:
+    calculate_path(pathlist[0], i)
+
+#for i in pathlist:
+#    calculate_path(i)
+
+#if __name__ == '__main__':
+
+#    mp.freeze_support()
+#    pool = mp.Pool(processes = 1)
+#    pool.map(calculate_path, pathlist)