diff --git a/devices/CurrentCamera.properties b/devices/CurrentCamera.properties index 953bff0..595bae3 100644 --- a/devices/CurrentCamera.properties +++ b/devices/CurrentCamera.properties @@ -1,16 +1,16 @@ -#Mon May 29 14:54:24 CEST 2017 +#Tue May 30 17:05:36 CEST 2017 colormap=Flame colormapAutomatic=true -colormapMax=2000.0 -colormapMin=0.0 +colormapMax=35000.0 +colormapMin=300.0 flipHorizontally=false flipVertically=false grayscale=false -imageHeight=2160 -imageWidth=2560 +imageHeight=1680 +imageWidth=1744 invert=false -regionStartX=1 -regionStartY=1 +regionStartX=433 +regionStartY=241 rescaleFactor=1.0 rescaleOffset=0.0 roiHeight=-1 @@ -21,9 +21,9 @@ rotation=0.0 rotationCrop=false scale=1.0 serverURL=localhost\:10000 -spatialCalOffsetX=-96.58536606067958 -spatialCalOffsetY=-67.48201620883489 -spatialCalScaleX=-14.46944297232279 -spatialCalScaleY=-13.605441964787545 +spatialCalOffsetX=-1093.4812581603794 +spatialCalOffsetY=-1098.5114274849898 +spatialCalScaleX=-7.617446798629459 +spatialCalScaleY=-7.774538463917676 spatialCalUnits=mm transpose=false diff --git a/plugins/SchottkyScan.form b/plugins/SchottkyScan.form index e6880af..0120c53 100644 --- a/plugins/SchottkyScan.form +++ b/plugins/SchottkyScan.form @@ -76,10 +76,13 @@ - + + + + diff --git a/plugins/SchottkyScan.java b/plugins/SchottkyScan.java index a7aa7d7..c5e64d0 100644 --- a/plugins/SchottkyScan.java +++ b/plugins/SchottkyScan.java @@ -132,7 +132,7 @@ public class SchottkyScan extends Panel { } }); - panelPars.setBorder(javax.swing.BorderFactory.createTitledBorder("Parameters")); + panelPars.setBorder(javax.swing.BorderFactory.createTitledBorder("Parameters (beam phase)")); spinnerStep.setModel(new javax.swing.SpinnerNumberModel(5.0d, 1.0d, 90.0d, 1.0d)); @@ -305,6 +305,8 @@ public class SchottkyScan extends Panel { .addComponent(plot, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)) .addGap(17, 17, 17)) ); + + panelPars.getAccessibleContext().setAccessibleDescription(""); }// //GEN-END:initComponents private void buttonStartActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartActionPerformed diff --git a/script/CPython/hfitoff.py b/script/CPython/hfitoff.py index be809fa..3b0d5fb 100644 --- a/script/CPython/hfitoff.py +++ b/script/CPython/hfitoff.py @@ -13,11 +13,13 @@ def hfitoff(data, xdeg): xrad = xdeg / 180 * np.pi optimize_func = lambda x: x[0] * np.sin(xrad + x[1]) + x[2] - data fit_amplitude, fit_phase, fit_offset = leastsq(optimize_func, [guess_amplitude, guess_phase, guess_offset])[0] + if fit_amplitude < 0: + fit_amplitude = -fit_amplitude + fit_phase = fit_phase - np.pi fit_xdeg = np.linspace(start, end, 100) fit_data = fit_amplitude * np.sin(fit_xdeg / 180 * np.pi + fit_phase) + fit_offset - ph_crest = 90 - fit_phase / np.pi * 180 - xdeg_max = xdeg[np.argmax(data)] - if start <= ph_crest <= end: - return (fit_amplitude, fit_phase, fit_offset, True, ph_crest, fit_xdeg, fit_data) - else: - return (fit_amplitude, fit_phase, fit_offset, False, xdeg_max, fit_xdeg, fit_data) + fit_phase_deg = fit_phase / np.pi * 180 + ph_crest = 90 - fit_phase_deg + if ph_crest > 180: + ph_crest = ph_crest - 360 + return (fit_amplitude, fit_phase_deg, fit_offset, ph_crest, fit_xdeg, fit_data) diff --git a/script/CPython/wrapper.py b/script/CPython/wrapper.py index 46d632e..b08b2e8 100644 --- a/script/CPython/wrapper.py +++ b/script/CPython/wrapper.py @@ -3,7 +3,7 @@ from jeputils import * def hfitoff(data, xdeg): ret = call_jep("CPython/hfitoff", "hfitoff", [to_npa(data),to_npa(xdeg)]) print ret - return (ret[0], ret[1], ret[2],ret[3], ret[4], ret[5].data,ret[6].data) + return (ret[0], ret[1], ret[2],ret[3], ret[4].data,ret[5].data) def gfitoff(x, y, off=None, amp=None, com=None, sigma=None): ret = call_jep("CPython/gfitoff", "gfitoff", [to_npa(x), to_npa(y), off, amp, com, sigma]) diff --git a/script/Devices/ImageStats.py b/script/Devices/ImageStats.py index 7a4a583..1e5c0d3 100644 --- a/script/Devices/ImageStats.py +++ b/script/Devices/ImageStats.py @@ -1,5 +1,6 @@ from startup import * from ijutils import * +from mathutils import * from ch.psi.pshell.imaging.Overlays import * import ch.psi.pshell.imaging.Pen as Pen import java.awt.Color as Color @@ -8,6 +9,9 @@ import ch.psi.pshell.imaging.ImageListener as ImageListener from operator import add, mul, sub, truediv from ch.psi.pshell.imaging.Utils import sub +REMOVE_BACKGROUND = True +PLOT_PROFILE = True + def get_centroid(source): bi = source.getImage() if bi is None: @@ -33,6 +37,39 @@ def get_centroid(source): +def arroff(a, value = "mean"): + """Subtract offset to all elemets in series. + + Args: + + a(list, tuple, array ...): subscriptable object containing numbers + type(int or str, optional): value to subtract from the array, or "mean" or "min". + + Returns: + List + + """ + if value=="mean": + value = mean(a) + elif value=="min": + value = min(a) + return [x-value for x in a] + + +def arrsubback(data, a, b): + """Subtract offset to all elemets in series. + + Args: + + a(list, tuple, array ...): subscriptable object containing numbers + type(int or str, optional): value to subtract from the array, or "mean" or "min". + + Returns: + List + + """ + return [y-(a*y+b) for y in a] + import ch.psi.pshell.imaging.Filter as Filter @@ -117,23 +154,47 @@ class ImageStats(DeviceBase): self.rms_x_samples, self.rms_y_samples = [], [] for i in range(self.num_images): if type(self.source) is not ch.psi.pshell.imaging.FileSource: + #print "A" self.source.waitNext(5000) + #print "B" #time.sleep(0.2) #print "Ok" #centroid = get_centroid(self.source) #print "cent ", centroid #if centroid is not None: # self.com_x_samples.append(centroid[0]) - # self.com_y_samples.append(centroid[1]) - x_profile = self.source.data.integrateVertically(True) + # self.com_y_samples.append(centroid[1]) + + x_profile = self.source.data.integrateVertically(True) + x_profile_x = self.source.data.getRowSelectionX(True) + y_profile = self.source.data.integrateHorizontally(True) - com_x,rms_x = center_of_mass(x_profile, self.source.data.getRowSelectionX(True)) - com_y,rms_y = center_of_mass(y_profile, self.source.data.getColSelectionX(True)) + y_profile_x = self.source.data.getColSelectionX(True) + + #Remove background + if (self.bg_en == False) and REMOVE_BACKGROUND: + (a, b, amp, com, sigma) = fit_gaussian_linear(x_profile, x_profile_x) + x_profile = [x_profile[i]-(a*x_profile_x[i]+b) for i in range(len(x_profile))] + (a, b, amp, com, sigma) = fit_gaussian_linear(y_profile, y_profile_x) + y_profile = [y_profile[i]-(a*y_profile_x[i]+b) for i in range(len(y_profile))] + com_x,rms_x = center_of_mass(x_profile, x_profile_x) + com_y,rms_y = center_of_mass(y_profile, y_profile_x) self.com_x_samples.append(com_x) self.com_y_samples.append(com_y) self.rms_x_samples.append(rms_x) self.rms_y_samples.append(rms_y) - + if PLOT_PROFILE: + p = get_plots("Profile") + if (p is None) or (len(p)==0): + p = plot([x_profile, y_profile], ["x_profile", "yprofile"], [x_profile_x,y_profile_x], title ="Profile") + else: + p[0].removeMarker(None) + p[1].removeMarker(None) + p[0].getSeries(0).setData(x_profile_x, x_profile) + p[1].getSeries(0).setData(y_profile_x, y_profile) + p[0].addMarker(com_x, None, "COM = " + str(com_x), Color.GREEN) + p[1].addMarker(com_y, None, "COM = " + str(com_y), Color.GREEN) + def setNumberOfImages(self, value): self.num_images = value @@ -182,7 +243,7 @@ if __name__ == "__builtin__": #print get_centroid(simulated_source) add_device(ImageStats("image_stats", cam3), True) - #cam3.waitNext(5000) + cam3.waitNext(2000) image_stats.enableBackground(False) #for i in range (10): # image_stats.update() diff --git a/script/RFscan/SchottkyScan.py b/script/RFscan/SchottkyScan.py index 8dcb1c8..5bf1f1e 100644 --- a/script/RFscan/SchottkyScan.py +++ b/script/RFscan/SchottkyScan.py @@ -1,11 +1,11 @@ import ch.psi.pshell.epics.ControlledVariable as ControlledVariable if get_exec_pars().source == CommandSource.ui: - start = -30.0 - stop = 30.0 + start = -10.0 + stop = 10.0 step = 5.0 - nb = 1 - lat = 0.100 + nb = 3 + lat = 0.300 else: start = args[0] stop = args[1] @@ -13,8 +13,8 @@ else: nb = int(args[3]) lat = args[4] -phase = ControlledVariable("Phase", "SINEG01-RSYS:SET-VSUM-PHASE", "SINEG01-RSYS:GET-VSUM-PHASE") -#phase = ControlledVariable("Phase", "S10CB09-RSYS:SET-VSUM-PHASE", "S10CB09-RSYS:SET-VSUM-PHASE") +phase = ControlledVariable("Phase", "SINEG01-RSYS:SET-BEAM-PHASE", "SINEG01-RSYS:GET-BEAM-PHASE") +#phase = ControlledVariable("Phase", "S10CB09-RSYS:SET-BEAM-PHASE", "S10CB09-RSYS:SET-BEAM-PHASE") phase.config.minValue =-180.0 phase.config.maxValue = 360.0 phase.config.precision = 3 @@ -50,3 +50,13 @@ index_max = y.index(max(y)) phase_ref = x[index_max] - 80 set_return(phase_ref) + +# save the entry in the logbook +#if get_option("Generated data file:\n" + get_exec_pars().path +"\n\n" + "Save to ELOG?", "YesNo") == "Yes": +# log_msg = "Start: %0.1f" % start + "deg\n" +# log_msg = log_msg + "Stop: %0.1f" % stop + "deg\n" +# log_msg = log_msg + "Step: %0.1f" % nb + "deg\n" +# log_msg = log_msg + "Nb samples: %0.0f" % nb + "\n" +# log_msg = log_msg + "Latency: %0.3f" % lat + "s\n" +# log_msg = log_msg + "Data file: " + get_exec_pars().path +# elog("Schottky Scan", log_msg, get_plot_snapshots())