Shift calculation tests

config/devices.properties

@@ -1,3 +1,13 @@
+#fe_slit_V_ctr:offset=ch.psi.pshell.epics.ChannelDouble||||
+#fe_slit_V_ctr=ch.psi.pshell.epics.Positioner|X11MA-FE-SV:ctr caget X11MA-FE-SV:t2.D|||true
+#fe_slit_H_ctr_offset=ch.psi.pshell.epics.ChannelDouble||||
+#fe_slit_H_ctr=ch.psi.pshell.epics.Positioner|X11MA-FE-SH:ctr X11MA-FE-SH:t2.D|||true
+fe_slit_V_size_offs=ch.psi.pshell.epics.ChannelDouble|X11MA-FE-DSVER.A|||true
+fe_slit_V_size=ch.psi.pshell.epics.Positioner|X11MA-FE-SV:size X11MA-FE-SV:t2.C|||true
+fe_slit_H_size_offs=ch.psi.pshell.epics.ChannelDouble|X11MA-FE-DSHOR.A|||true
+fe_slit_H_size=ch.psi.pshell.epics.Positioner|X11MA-FE-SH:size X11MA-FE-SH:t2.C|||true
+exit_slit_offset=ch.psi.pshell.epics.ChannelDouble|X11MA-OP2-SL:EOff|||true
+exit_slit=ch.psi.pshell.epics.Motor|X11MA-OP2-SL:TRY|||true
 machine_cur=ch.psi.pshell.epics.ChannelDouble|ARIDI-PCT:CURRENT|Read||true
 field=ch.psi.pshell.epics.ChannelDouble|X11MA-XMCD:Ireadout|Read||true
 pol_mode=ch.psi.pshell.epics.DiscretePositioner|X11MA-ID2:MODE|||true
@@ -68,13 +78,15 @@ eiger_bit_depth=ch.psi.pshell.epics.ChannelInteger|X11MA-ES1-SD1:cam1:BitDepth||
 eiger_mode=ch.psi.pshell.epics.ChannelInteger|X11MA-ES1-SD1:cam1:ImageMode|||true
 eiger_exposure=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1-SD1:cam1:AcquireTime 2|||true
 Ecrbk=ch.psi.pshell.epics.ChannelDouble|X11MA-PGM:CERBK|Read||true
-CADC1=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC1|Read||true
-CADC2=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC2|Read||true
-CADC3=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC3|Read||true
+#CADC1=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC1|Read||true
+#CADC2=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC2|Read||true
+#CADC3=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC3|Read||true
 #CADC4=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC4|Read||true
 #CADC5=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC5|Read||true
 #CADC6=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC6|Read||true
 #CADC7=ch.psi.pshell.epics.ChannelDouble|X11MA-ES1:CADC7|Read||true
 girder_x=ch.psi.pshell.epics.Positioner|X11MA-HG:X_SET X11MA-HG:X1|||true
+cam2=ch.psi.pshell.epics.AreaDetector|X11MA-ES1-CAM2|||true
 image=ch.psi.pshell.imaging.CameraSource|eiger|||true
+image2=ch.psi.pshell.imaging.CameraSource|cam2|||true
 axis=ch.psi.pshell.imaging.MjpegSource|http://axis-x11ma.psi.ch/axis-cgi/mjpg/video.cgi?id=176 true||-200|false

config/scicat.properties

@@ -1,11 +1,11 @@
-#Wed Apr 14 15:11:25 CEST 2021
+#Wed Jun 30 15:27:33 CEST 2021
 environment=prod
 testParameters=-testenv -user slssim\:4DMGBarXmr
-sourceFolder=/sls/X11MA/Data1/e19148
+sourceFolder=/sls/X11MA/Data1/e18900
 prodParameters=\ -user slssim\:4DMGBarXmr
 devParameters=-devenv -user slssim\:slssim
 ownerGroup=
 type=raw
 parameters=-ingest -allowexistingsource -noninteractive -autoarchive
 creationLocation=/PSI/SLS/SIM
-principalInvestigator=arik.beck@psi.ch
+principalInvestigator=

config/session_metadata.properties

@@ -1,5 +1,5 @@
-#Wed May 05 22:02:15 CEST 2021
+#Mon Jun 07 19:28:06 CEST 2021
 keywords=List;[]
-ownerEmail=String;adirajan@uni-mainz.de
+ownerEmail=String;caretta@berkeley.edu
 contactEmail=String;armin.kleibert@psi.ch
-owner=String;Adithya Rajan
+owner=String;Lucas Caretta

config/sessions.properties

@@ -1,2 +1,2 @@
-#Tue May 11 10:49:31 CEST 2021
-SessionCounter=24
+#Wed Jun 30 09:46:41 CEST 2021
+SessionCounter=29

config/settings.properties

@@ -1,19 +1,26 @@
-#Wed May 12 09:47:57 CEST 2021
-proposal=proposal
+#Wed Jun 30 16:03:46 CEST 2021
+HARMONIC_ID_1=1
 RSYNC_USER=
-ENERGY=710
 OUTLIERS_THRESHOLD=1000000000
-proposer=proposer
 NORM_FILE=/sls/X11MA/data/X11MA/Data1/2021/Yona250121/s250121
-AUTO_SWITCH_VALVE=true
+AUTO_SWITCH_VALVE=false
+DRY_RUN=false
+POL_ID_2=Lin_Hor
+OFFSET_ID_1=0.0
+ID=ID2
+OFFSET_ID_2=0.0
+proposal=proposal
+ENERGY=400.0
+proposer=proposer
+POL_ID_1=Circ_Plus
 RSYNC_HOST=
 sample=sample
 RSYNC_PATH=
-DRY_RUN=false
 pgroup=pgroup
-POL_ID_2=Lin_Hor
+ALPHA_ID_2=30.0
+ALPHA_ID_1=0.0
 RSYNC_DEL=true
-ID=ID2
 AVERAGING_DETECTOR=true
 FdaBrowser=false
 authors=author1|author2
+HARMONIC_ID_2=1

config/variables.properties

@@ -1,4 +1,4 @@
-#Wed May 12 09:49:36 CEST 2021
-LastRunDate=210512
-FileSequentialNumber=7552
-DaySequentialNumber=18
+#Wed Jun 30 14:55:49 CEST 2021
+LastRunDate=210630
+FileSequentialNumber=8602
+DaySequentialNumber=44

devices/Position.properties

@@ -0,0 +1,10 @@
+#Mon May 31 14:01:51 CEST 2021
+minValue=NaN
+unit=null
+offset=0.0
+maxValue=NaN
+rotation=false
+precision=-1
+sign_bit=0
+scale=1.0
+resolution=NaN

devices/Time.properties

@@ -0,0 +1,10 @@
+#Mon Jun 07 15:00:54 CEST 2021
+minValue=NaN
+unit=null
+offset=0.0
+maxValue=NaN
+rotation=false
+precision=-1
+sign_bit=0
+scale=1.0
+resolution=NaN

devices/exit_slit.properties

@@ -0,0 +1,18 @@
+#Tue Jun 22 16:58:14 CEST 2021
+precision=5
+scale=1.0
+estbilizationDelay=0
+resolution=1.0
+minValue=-3000.0
+defaultSpeed=200.0
+sign_bit=0
+monitorByPosition=false
+minSpeed=10.0
+offset=0.0
+maxValue=3000.0
+rotation=false
+maxSpeed=200.0
+homingType=None
+startRetries=1
+unit=micron
+hasEnable=false

devices/exit_slit_motor.properties

@@ -0,0 +1,18 @@
+#Mon Jun 07 15:56:05 CEST 2021
+offset=0.0
+maxValue=3000.0
+rotation=false
+precision=5
+scale=1.0
+estbilizationDelay=0
+maxSpeed=NaN
+resolution=1.0
+homingType=None
+startRetries=1
+minValue=-3000.0
+unit=micron
+defaultSpeed=200.0
+hasEnable=false
+sign_bit=0
+monitorByPosition=false
+minSpeed=10.0

devices/exit_slit_old.properties

@@ -0,0 +1,10 @@
+#Mon Jun 07 09:49:47 CEST 2021
+offset=0.0
+maxValue=NaN
+rotation=false
+precision=5
+scale=1.0
+resolution=1.0
+minValue=NaN
+unit=micron
+sign_bit=0

devices/fe_slit_H_size.properties

@@ -0,0 +1,10 @@
+#Wed Jun 30 14:15:27 CEST 2021
+offset=0.0
+maxValue=200.0
+rotation=false
+precision=3
+scale=1.0
+resolution=0.005
+minValue=-200.0
+unit=mm
+sign_bit=0

devices/fe_slit_V_size.properties

@@ -0,0 +1,10 @@
+#Wed Jun 30 10:57:08 CEST 2021
+offset=0.0
+maxValue=200.0
+rotation=false
+precision=3
+scale=1.0
+resolution=0.005
+minValue=-200.0
+unit=mm
+sign_bit=0

devices/image.properties

@@ -1,4 +1,4 @@
-#Tue May 11 10:36:23 CEST 2021
+#Wed Jun 30 12:51:54 CEST 2021
 spatialCalOffsetY=NaN
 spatialCalOffsetX=NaN
 colormapLogarithmic=false
@@ -6,7 +6,7 @@ scale=1.0
 grayscale=false
 spatialCalScaleX=NaN
 spatialCalScaleY=NaN
-colormapMax=1.0
+colormapMax=500.0
 rescaleOffset=0.0
 roiWidth=-1
 colormap=Grayscale

devices/image2.properties

@@ -0,0 +1,25 @@
+#Thu May 27 14:51:41 CEST 2021
+spatialCalOffsetY=NaN
+spatialCalOffsetX=NaN
+colormapLogarithmic=false
+scale=1.0
+grayscale=false
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+colormapMax=255.0
+rescaleOffset=0.0
+roiWidth=-1
+colormap=Grayscale
+invert=false
+colormapMin=0.0
+rotation=0.0
+rotationCrop=false
+rescaleFactor=1.0
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+flipHorizontally=false
+colormapAutomatic=false
+roiY=0
+roiX=0
+transpose=false

devices/shift_0000.png.properties

@@ -0,0 +1,20 @@
+#Wed Jun 23 09:10:47 CEST 2021
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

devices/shift_0001.png.properties

@@ -0,0 +1,20 @@
+#Wed Jun 23 09:20:13 CEST 2021
+spatialCalOffsetY=NaN
+invert=false
+spatialCalOffsetX=NaN
+rotation=0.0
+rotationCrop=false
+scale=1.0
+rescaleFactor=1.0
+grayscale=false
+spatialCalUnits=mm
+flipVertically=false
+roiHeight=-1
+spatialCalScaleX=NaN
+spatialCalScaleY=NaN
+flipHorizontally=false
+roiY=0
+roiX=0
+rescaleOffset=0.0
+transpose=false
+roiWidth=-1

plugins/Align_ComplexEdgeFiltering.java

@@ -0,0 +1,154 @@
+import ij.*;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.plugin.filter.PlugInFilter;
+import ij.process.ImageProcessor;
+import ij.plugin.filter.GaussianBlur;
+import ij.gui.GenericDialog;
+
+/**
+ * This is a template for a plugin that requires one image to
+ * be opened, and takes it as parameter.
+ */
+public class Align_ComplexEdgeFiltering implements PlugInFilter {
+    protected ImagePlus imp;
+    private static double g_sigma = 3.0, g_resolution = 1e-4; //filter parameters
+    private static int filter_output;
+    //private static int filter_type = 0;
+    private GaussianBlur gb = new GaussianBlur();
+    private int[] sobel_r = new int[] {1,0,-1, 2,0,-2, 1,0,-1};
+    private int[] sobel_i = new int[] {1,2,1, 0,0,0, -1,-2,-1};
+
+    String arg;
+    final  java.util.List output = new java.util.ArrayList();
+    public java.util.List getOutput(){
+        return output;
+    }
+    boolean show=true;
+    
+    /**
+     * This method gets called by ImageJ / Fiji to determine
+     * whether the current image is of an appropriate type.
+     *
+     * @param arg can be specified in plugins.config
+     * @param image is the currently opened image
+     */
+    public int setup(String arg, ImagePlus image) {
+        this.imp = image;
+        this.arg = arg;
+        /*
+         * The current return value accepts all gray-scale
+         * images (if you access the pixels with ip.getf(x, y)
+         * anyway, that works quite well.
+         *
+         * It could also be DOES_ALL; you can add "| NO_CHANGES"
+         * to indicate that the current image will not be
+         * changed by this plugin.
+         *
+         * Beware of DOES_STACKS: this will call the run()
+         * method with all slices of the current image
+         * (channels, z-slices and frames, all). Most likely
+         * not what you want.
+         */
+        return DOES_8G | DOES_16 | DOES_32 | NO_CHANGES;// | DOES_STACKS;
+    }
+
+    /**
+     * This method is run when the current image was accepted.
+     *
+     * @param ip is the current slice (typically, plugins use
+     * the ImagePlus set above instead).
+     */
+    public void run(ImageProcessor ip) {
+        if ((arg !=null) && (!arg.isBlank())){
+            String[] tokens = arg.trim().split(",");
+            g_sigma = Double.valueOf(tokens[0].trim());
+            filter_output = Boolean.valueOf(tokens[1].trim().toLowerCase()) ? 0 : 1;
+            try{
+                show = Boolean.valueOf(tokens[2].trim().toLowerCase());
+            } catch (Exception ex){
+                show = false;
+            }
+        } else {
+            String[] filter_outputs = {"complex", "real"};
+            GenericDialog gd = new GenericDialog("Complex Edge Filtering Options:");
+            gd.addSlider("Gaussian blur radius", 0, 20.0, g_sigma);
+            gd.addChoice("Edge filter output:", filter_outputs, filter_outputs[0]);
+            //String[] edge_filters = {"Sobel"};//, "Frei&Chen"};
+            //gd.addChoice("Task:", edge_filters, edge_filters[0]);
+                gd.showDialog();                        // display the dialog; preview runs in the background now
+            if (gd.wasCanceled()) return;
+            g_sigma = gd.getNextNumber();
+            filter_output = gd.getNextChoiceIndex();
+        }
+            //filter_type = gd.getNextChoiceIndex();
+            exec();
+    }
+
+    private void exec() {
+        // display the results
+        if (filter_output == 1) {
+            ImagePlus imp_r = imp.createImagePlus();
+            ImageStack stack_r = new ImageStack(imp.getWidth(), imp.getHeight());
+        
+            for (int i = 1; i <= imp.getImageStackSize(); i++) {
+                ImageProcessor ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat();
+                // Gaussian blurring
+                gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution);
+                // Sobel edge filtering
+                ip_r.filter(ImageProcessor.FIND_EDGES);
+            
+                stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r);
+                IJ.showProgress(i, imp.getImageStackSize());
+            }
+            
+            //real
+            imp_r.setStack("EdgeReal_" + imp.getTitle(), stack_r);
+            imp_r.resetDisplayRange();
+            if (show){
+                imp_r.show();
+                imp_r.updateAndDraw();
+            }
+            output.add(imp_r);
+            
+        } else {
+            ImagePlus imp_r = imp.createImagePlus();
+            ImageStack stack_r = new ImageStack(imp.getWidth(), imp.getHeight());
+
+            ImagePlus imp_i = imp.createImagePlus();
+            ImageStack stack_i = new ImageStack(imp.getWidth(), imp.getHeight());
+        
+            for (int i = 1; i <= imp.getImageStackSize(); i++) {
+                ImageProcessor ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat();
+                // Gaussian blurring
+                gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution);
+                ImageProcessor ip_i = ip_r.duplicate();
+                // Sobel edge filtering
+                ip_r.convolve3x3(sobel_r);
+                ip_i.convolve3x3(sobel_i);
+            
+                stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r);
+                stack_i.addSlice(imp.getStack().getSliceLabel(i), ip_i);
+                IJ.showProgress(i, imp.getImageStackSize());
+            }
+                        
+            //real
+            imp_r.setStack("EdgeReal_" + imp.getTitle(), stack_r);
+            imp_r.resetDisplayRange();
+            if (show){
+                imp_r.show();
+                imp_r.updateAndDraw();
+            }
+            output.add(imp_r);
+        
+            //imag
+            imp_i.setStack("EdgeImag_" + imp.getTitle(), stack_i);
+            imp_i.resetDisplayRange();
+            if (show){
+                imp_i.show();
+                imp_i.updateAndDraw();
+            }
+            output.add(imp_i);
+        }
+    }
+}

plugins/Align_ComputeShifts.java

@@ -0,0 +1,717 @@
+import ij.*;
+import ij.process.*;
+import ij.gui.*;
+import java.awt.*;
+import ij.plugin.PlugIn;
+import ij.WindowManager;
+//import edu.emory.mathcs.jtransforms.fft.*;
+//import edu.emory.mathcs.utils.*;
+import org.jtransforms.fft.*;
+import org.jtransforms.utils.*;
+import flanagan.complex.*;
+import flanagan.math.*;
+import ij.plugin.frame.RoiManager;
+import ij.gui.Roi;
+
+
+public class Align_ComputeShifts implements PlugIn {
+    protected ImagePlus imp_r, imp_i;
+    protected int reference_slide;
+    protected Roi roi;
+    protected int usfac;
+    protected boolean debug = true;
+    double[][] shifts;
+    boolean allShifts;
+    
+    static boolean isPowerOf2(int n) {
+        if (n == 0)
+            return false;
+
+        while (n != 1) {
+            if (n % 2 != 0)
+                return false;
+            n = n / 2;
+        }
+        return true;
+    }
+    
+
+     public void setup(int upscaleFactor, boolean allShifts, ImagePlus imp_r, ImagePlus imp_i, 
+            int reference_slide,  Roi roi) {
+         if (imp_r==null){
+            throw new RuntimeException("Real part image must exist!");
+         }
+
+         if (roi==null){
+            roi = new Roi(0,0,imp_r.getWidth(), imp_r.getHeight());
+         }
+        Rectangle box = roi.getBounds();
+        //if (!ConcurrencyUtils.isPowerOf2(box.height) || !ConcurrencyUtils.isPowerOf2(box.width)) {
+        if (!isPowerOf2(box.height) || !isPowerOf2(box.width)) {
+            throw new RuntimeException("The selected ROI height and with must be a power of 2");
+        }
+
+         this.usfac = upscaleFactor;
+         this.allShifts = allShifts;
+         this.imp_r = imp_r;
+         this.imp_i = imp_i;
+         this.reference_slide=reference_slide;
+         this.roi = roi;
+        
+     }
+
+    public void run(String arg) {   
+            if (allShifts) {
+                calculateAllShiftsRun();
+                
+            } else {
+                calculateShiftsRun();
+            }
+            return;
+    }
+
+    private void calculateShiftsRun() {
+        // perform the FFT of each slice
+        
+        IJ.showStatus("1/2 Perform FFT of each slice");
+        ComplexMatrix[] ffts = computeFFT();
+        
+        // calculate shifts
+        IJ.showStatus("2/2 Calculate shifts between slices");
+        shifts = calculateShifts(ffts);
+
+        /*
+        // save shifts
+        ShiftsIO sio = new ShiftsIO();
+        sio.save(shifts, "directshifts");
+       */
+    }
+
+   public double[][] getShifts(){
+        return shifts;
+   }
+
+    private void calculateAllShiftsRun() {
+        // perform the FFT of each slice
+        IJ.showStatus("1/2 Perform FFT of each slice");
+        ComplexMatrix[] ffts = computeFFT();
+
+        // calculate shifts
+        IJ.showStatus("2/2 Calculate shifts between slices");
+        shifts = calculateAllShifts(ffts);
+
+        /*
+        // save shifts
+        ShiftsIO sio = new ShiftsIO();
+        sio.save(shifts, "allshifts");
+        */
+    }
+
+    // perform the FFT of each slice
+    private ComplexMatrix[] computeFFT() {
+        
+        int slices = imp_r.getStackSize();
+        
+        ComplexMatrix[] ffts = new ComplexMatrix[slices];
+        for (int i=1; i <= slices; i++) {
+            if (imp_i == null) {
+                ImageProcessor ip = imp_r.getStack().getProcessor(i);
+                ip.setRoi(roi);
+                ImageProcessor curr = ip.crop().convertToFloat();
+                double[][] data = ImageProcessor_to_FFTArray2D(curr);   
+                ffts[i-1] = fft2(data);
+            } else {
+                ImageProcessor ip1, ip2;
+                ip1 = imp_r.getStack().getProcessor(i);
+                ip1.setRoi(roi);
+                ImageProcessor curr_r = ip1.crop().convertToFloat();
+                ip2 = imp_i.getStack().getProcessor(i);
+                ip2.setRoi(roi);
+                ImageProcessor curr_i = ip2.crop().convertToFloat();
+                double[][] data = ImageProcessor_to_FFTComplexArray2D(curr_r, curr_i);
+                ffts[i-1] = cfft2(data);
+            }
+            IJ.showProgress(i, slices);
+        }
+
+        return ffts;
+    }
+
+    //calculate the shifts between ffts
+    private double[][] calculateShifts(ComplexMatrix[] ffts) {
+        
+        double[][] shifts = new double[ffts.length][6];        
+        for (int i = 0; i < ffts.length; i++) {
+            shifts[i][0] = reference_slide; shifts[i][1] = i+1;
+            double[] temp = DFTRegistration(ffts[reference_slide - 1], ffts[i]);
+            shifts[i][2] = temp[2]; shifts[i][3] = temp[3];
+            shifts[i][4] = temp[0]; shifts[i][5] = temp[1];            
+            IJ.showProgress(i + 1, ffts.length);
+        }
+        return shifts; // [ref, drifted, dr, dc, error, diffphase]
+    
+    }
+
+    //calculate all the shifts between ffts
+    private double[][] calculateAllShifts(ComplexMatrix[] ffts) {
+
+        double[][] shifts = new double[ffts.length*(ffts.length-1)/2][6];
+        int id = 0;
+        for (int i = 0; i < ffts.length-1; i++) {
+            for (int j = i+1; j < ffts.length; j++) {
+                shifts[id][0] = i+1; shifts[id][1] = j+1;
+                double[] temp = DFTRegistration(ffts[i], ffts[j]);
+                shifts[id][2] = temp[2]; shifts[id][3] = temp[3];
+                shifts[id][4] = temp[0]; shifts[id][5] = temp[1];
+                id = id + 1;
+                IJ.showProgress(id + 1, ffts.length*(ffts.length-1)/2);
+            }
+        }
+        
+        return shifts; // [ref,drifted,dr,dc,error, diffphase]
+    }
+    
+    // compute 2D fft from an image
+    private ComplexMatrix fft2(double[][] data) {
+
+        int h = data.length;
+        int w = data[0].length;
+        DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+        
+        fft.realForward(data);
+        ComplexMatrix m = FFTArray2D_to_ComplexMatrix(data, h, w);
+
+        return m;
+    }
+
+    // compute complex 2D fft from an image
+    private ComplexMatrix cfft2(double[][] data) {
+
+        int h = data.length;
+        int w = data[0].length;
+        DoubleFFT_2D fft = new DoubleFFT_2D(h, w/2);
+        
+        fft.complexForward(data);
+        ComplexMatrix m = FFTComplexArray2D_to_ComplexMatrix(data, h, w/2);
+
+        return m;
+    }
+    
+    // compute inverse 2D fft from a complex matrix
+    private double[][] ifft2(ComplexMatrix m) {
+        int w = m.getNcol();
+        int h = m.getNrow();
+        
+        DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+        
+        double[][] data = ComplexMatrix_to_FFTArray2D(m);   
+        fft.realInverse(data, true);
+
+        return data;
+    }
+    
+    // compute complex inverse 2D fft from a complex matrix
+    private ComplexMatrix cifft2(ComplexMatrix m) {
+        int w = m.getNcol();
+        int h = m.getNrow();
+        
+        DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+        
+        double[][] data = new double[h][2*w];
+        for (int j=0; j<h; j++) {
+            for (int i=0; i<w; i++) {
+                data[j][2*i] = m.getElementReference(j, i).getReal();
+                data[j][2*i+1] = m.getElementReference(j, i).getImag();             
+            }
+        }
+
+        fft.complexInverse(data, true);
+
+        ComplexMatrix out = new ComplexMatrix(h, w);
+        for (int j=0; j<h; j++) {
+            for (int i=0; i<w; i++) {
+                out.setElement(j, i, data[j][2*i], data[j][2*i+1]);         
+            }
+        }
+
+        return out;
+    }
+    
+    private double[] DFTRegistration(ComplexMatrix ref, ComplexMatrix drifted) {
+        int m = ref.getNrow();
+        int n = ref.getNcol();
+        double[] output = new double[4];
+        
+        // First upsample by a factor of 2 to obtain initial estimate
+            // Embed Fourier data in a 2x larger array
+            int mlarge = m*2;
+            int nlarge = n*2;
+            ComplexMatrix large = new ComplexMatrix(mlarge, nlarge);
+            ComplexMatrix c = fftshift(ElementProduct(ref, drifted.conjugate()));
+
+            for (int j = 0; j < m; j++) {
+                for (int i = 0; i < n; i++) {
+                    large.setElement((int)(j + m - Math.floor(m/2.0)), (int)(i + n - Math.floor(n/2.0)), c.getElementReference(j, i));
+                }
+            }
+  
+            // Compute crosscorrelation and locate the peak
+            ComplexMatrix CC = cifft2(ifftshift(large));
+            double[] peak = cFindPeak(CC); //max, r, c, max_r, max_c
+                
+            // Obtain shift in original pixel grid from the position of the
+            // crosscorrelation peak 
+            if (peak[1] > m) { 
+                peak[1] = peak[1] - mlarge;
+            }
+        if (peak[2] > n) {
+            peak[2] = peak[2] - nlarge;
+        }
+
+            //% If upsampling > 2, then refine estimate with matrix multiply DFT
+            if (this.usfac > 2) {
+                //   %%% DFT computation %%%
+                //   % Initial shift estimate in upsampled grid
+                double row_shift = Math.round(peak[1]/2.0*this.usfac)/this.usfac; 
+                double col_shift = Math.round(peak[2]/2.0*this.usfac)/this.usfac;     
+                int dftshift = (int)Math.floor(Math.ceil(this.usfac*1.5)/2); // Center of output array at dftshift+1
+                //   % Matrix multiply DFT around the current shift estimate
+                ComplexMatrix in = ElementProduct(drifted, ref.conjugate());
+                ComplexMatrix nCC = dftups(in, (int)Math.ceil(this.usfac*1.5), (int)Math.ceil(this.usfac*1.5),
+                        dftshift-row_shift*this.usfac, dftshift-col_shift*this.usfac);
+                    nCC = nCC.times(1.0/(m*n*this.usfac*this.usfac)).conjugate();
+                //   % Locate maximum and map back to original pixel grid 
+                double[] npeak = cFindPeak(nCC); //max_r, max_i, r, c
+    
+            ComplexMatrix mrg00 = dftups(ElementProduct(ref, ref.conjugate()),1,1,0,0);
+            double rg00 = mrg00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+                ComplexMatrix mrf00 = dftups(ElementProduct(drifted, drifted.conjugate()),1,1,0,0);
+                double rf00 = mrf00.getElementReference(0, 0).abs()/(m*n*this.usfac*this.usfac);
+                
+                npeak[1] = npeak[1] - dftshift;
+                npeak[2] = npeak[2] - dftshift;
+                output[0] = Math.sqrt(Math.abs(1.0 - npeak[0]*npeak[0]/(rg00*rf00)));   //error
+            output[1] = Math.atan2(npeak[4], npeak[3]);             //diffphase     
+                output[2] = row_shift + npeak[1]/this.usfac;            //delta row
+                output[3] = col_shift + npeak[2]/this.usfac;            //delta col
+                
+            } else {
+            // % If upsampling = 2, no additional pixel shift refinement
+            double rg00 = SumSquareAbs(ref)/(mlarge*nlarge);
+            double rf00 = SumSquareAbs(drifted)/(mlarge*nlarge);
+            
+            output[0] = Math.sqrt(Math.abs(1.0 - peak[0]*peak[0]/(rg00*rf00))); //error
+            output[1] = Math.atan2(peak[4], peak[3]);               //diffphase     
+            output[2] = peak[1]/2.0;                    //delta row
+                output[3] = peak[2]/2.0;                    //delta col
+            }
+            
+        return output;  
+    }
+
+    private double SumSquareAbs(ComplexMatrix m) {
+        double sum = 0.0;
+
+        for (int j = 0; j < m.getNrow(); j ++){
+            for (int i = 0; i < m.getNcol(); i++) {
+                sum += m.getElementReference(j, i).squareAbs();
+            }
+        }
+
+        return sum;
+    }
+    
+    private double[] cFindPeak(ComplexMatrix m) {
+        double max = 0.0;
+        double realmax = 0.0;
+        double imagmax = 0.0;
+        int cmax = 0, rmax = 0;
+        
+        for (int j = 0; j < m.getNrow(); j ++){
+            for (int i = 0; i < m.getNcol(); i++) {
+                if (m.getElementReference(j, i).abs() > max) {
+                    max = m.getElementReference(j, i).abs();
+                    realmax = m.getElementReference(j, i).getReal();
+                    imagmax = m.getElementReference(j, i).getImag();
+                    rmax = j;
+                    cmax = i;
+                }
+            }
+        }
+
+        double[] res = new double[5];
+        res[0] = Math.sqrt(realmax*realmax+imagmax*imagmax); res[1] = rmax; res[2] = cmax;
+        res[3] = realmax; res[4] = imagmax;
+        return res;
+    }
+    
+    private ComplexMatrix fftshift(ComplexMatrix in) {
+        int nc = in.getNcol();
+        int nr = in.getNrow();
+
+        ComplexMatrix out = new ComplexMatrix (nr, nc);
+        
+        int midi = (int)Math.floor(nc/2.0);
+        int offi = (int)Math.ceil(nc/2.0);
+        int midj = (int)Math.floor(nr/2.0);
+        int offj = (int)Math.ceil(nr/2.0);
+        
+        for (int j = 0; j < nr; j ++){
+            for (int i = 0; i < nc; i++) {
+                if (j < midj) {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElementReference(j+offj, i-midi));       
+                    }
+                } else {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElementReference(j-midj, i-midi));       
+                    }
+                }
+            }
+        }
+
+        return out;
+    }
+
+    private ComplexMatrix ifftshift(ComplexMatrix in) {
+        int nc = in.getNcol();
+        int nr = in.getNrow();
+
+        ComplexMatrix out = new ComplexMatrix (nr, nc);
+        
+        int midi = (int)Math.ceil(nc/2.0);
+        int offi = (int)Math.floor(nc/2.0);
+        int midj = (int)Math.ceil(nr/2.0);
+        int offj = (int)Math.floor(nr/2.0);
+        
+        for (int j = 0; j < nr; j ++){
+            for (int i = 0; i < nc; i++) {
+                if (j < midj) {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElementReference(j+offj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElementReference(j+offj, i-midi));       
+                    }
+                } else {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElementReference(j-midj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElementReference(j-midj, i-midi));       
+                    }
+                }
+            }
+        }
+
+        return out;
+    }
+    
+    private Matrix ifftshift(Matrix in) {
+        int nc = in.getNcol();
+        int nr = in.getNrow();
+
+        Matrix out = new Matrix (nr, nc);
+        
+        int midi = (int)Math.ceil(nc/2.0);
+        int offi = (int)Math.floor(nc/2.0);
+        int midj = (int)Math.ceil(nr/2.0);
+        int offj = (int)Math.floor(nr/2.0);
+        
+        for (int j = 0; j < nr; j ++){
+            for (int i = 0; i < nc; i++) {
+                if (j < midj) {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElement(j+offj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElement(j+offj, i-midi));        
+                    }
+                } else {
+                    if (i < midi) {
+                        out.setElement(j, i, in.getElement(j-midj, i+offi));
+                    } else {
+                        out.setElement(j, i, in.getElement(j-midj, i-midi));        
+                    }
+                }
+            }
+        }
+
+        return out;
+    }
+
+        public Matrix times(Matrix amat, Matrix bmat){
+            
+            if(amat.getNumberOfColumns()!=bmat.getNumberOfRows())throw new IllegalArgumentException("Nonconformable matrices");
+
+            Matrix cmat = new Matrix(amat.getNumberOfRows(), bmat.getNumberOfColumns());
+            double [][] aarray = amat.getArrayReference();
+            double [][] barray = bmat.getArrayReference();
+            double [][] carray = cmat.getArrayReference();
+            double sum = 0.0D;
+
+            for(int i=0; i<amat.getNumberOfRows(); i++){
+                    for(int j=0; j<bmat.getNumberOfColumns(); j++){
+                        sum=0.0D;
+                        for(int k=0; k<amat.getNumberOfColumns(); k++){
+                                sum += aarray[i][k]*barray[k][j];
+                        }
+                        carray[i][j]=sum;
+                    }
+            }
+            return cmat;
+        }   
+    
+    private ComplexMatrix dftups(ComplexMatrix in, int nor, int noc, double roff, double coff) {
+        // function out=dftups(in,nor,noc,usfac,roff,coff);
+        // Upsampled DFT by matrix multiplies, can compute an upsampled DFT in just
+        // a small region.
+        // usfac         Upsampling factor (default usfac = 1)
+        // [nor,noc]     Number of pixels in the output upsampled DFT, in
+        //               units of upsampled pixels (default = size(in))
+        // roff, coff    Row and column offsets, allow to shift the output array to
+        //               a region of interest on the DFT (default = 0)
+        // Recieves DC in upper left corner, image center must be in (1,1)
+        // Loïc Le Guyader - Jun 11, 2011 Java version for ImageJ plugin 
+        // Manuel Guizar - Dec 13, 2007
+        // Modified from dftus, by J.R. Fienup 7/31/06
+
+        // This code is intended to provide the same result as if the following
+        // operations were performed
+        //   - Embed the array "in" in an array that is usfac times larger in each
+        //     dimension. ifftshift to bring the center of the image to (1,1).
+        //   - Take the FFT of the larger array
+        //   - Extract an [nor, noc] region of the result. Starting with the 
+        //     [roff+1 coff+1] element.
+
+        // It achieves this result by computing the DFT in the output array without
+        // the need to zeropad. Much faster and memory efficient than the
+        // zero-padded FFT approach if [nor noc] are much smaller than [nr*usfac nc*usfac]
+
+        int nr = in.getNrow();
+        int nc = in.getNcol();
+        // Compute kernels and obtain DFT by matrix products
+        double amplitude = -2.0*Math.PI/(nc*usfac);
+        
+        Matrix u = new Matrix(nc, 1);
+        for (int i = 0; i < nc; i++) {
+            u.setElement(i, 0, i - Math.floor(nc/2.0));
+        }
+        u = ifftshift(u);
+
+        Matrix v = new Matrix(1, noc);
+        for (int i = 0; i < noc; i++) {
+            v.setElement(0, i, i-coff);
+        }
+        Matrix phase = u.times(v);
+        //Matrix phase = times(u,v);
+      
+        ComplexMatrix kernc = new ComplexMatrix(nc, noc);
+        for (int j = 0; j < nc; j++) {
+            for (int i = 0; i < noc; i++)  {
+                Complex t = new Complex();
+                t.polar(1.0, amplitude*phase.getElement(j, i));
+                kernc.setElement(j, i, t);
+            }       
+        }
+        //ComplexMatrixPrint(kernc);
+        
+        amplitude = -2.0*Math.PI/(nr*usfac);
+        
+        Matrix w = new Matrix(nor, 1); 
+        for (int i = 0; i < nor; i++) {
+            w.setElement(i, 0, i - roff);
+        }
+        
+        Matrix x = new Matrix(1, nr);
+        for (int i = 0; i < nr; i++) {
+            x.setElement(0, i, i - Math.floor(nr/2.0));
+        }
+        x = ifftshift(x);
+
+        Matrix nphase = w.times(x);
+       //Matrix nphase = times(w,x);
+        ComplexMatrix kernr = new ComplexMatrix(nor, nr);
+        for (int j = 0; j < nor; j++) {
+            for (int i = 0; i < nr; i++) {
+                Complex t = new Complex();
+                t.polar(1.0, amplitude*nphase.getElement(j, i));
+                kernr.setElement(j, i, t);
+            }       
+        }
+        //ComplexMatrixPrint(kernr);
+        
+        ComplexMatrix out = kernr.times(in.times(kernc));     
+        return out;
+    }
+    
+    private double[][] CrossCorrelation(ComplexMatrix ref, ComplexMatrix drifted) {
+        int h = ref.getNrow();
+        int w = ref.getNcol();
+        ComplexMatrix b = drifted.conjugate();
+        ComplexMatrix res = ElementProduct(ref, b);
+        
+        double[][] data = ComplexMatrix_to_FFTArray2D(res);
+        DoubleFFT_2D fft = new DoubleFFT_2D(h, w);
+        fft.realInverse(data, true);
+        
+        return data;
+    }
+
+    private ComplexMatrix ElementProduct(ComplexMatrix a, ComplexMatrix b) {
+        int nr = a.getNrow();
+        int nc = a.getNcol();
+        
+        ComplexMatrix res = new ComplexMatrix(nr, nc);
+
+        for(int j = 0; j < nr; j++) {
+            for(int i = 0; i < nc; i++) {
+                res.setElement(j, i, a.getElementReference(j, i).times(b.getElementReference(j, i)));
+            }
+        }
+
+        return res;
+    }
+    
+    private double[][] ImageProcessor_to_FFTArray2D(ImageProcessor ip) {
+
+        float[] pixels = (float[])ip.getPixels();
+        int w = ip.getWidth();
+        int h = ip.getHeight();
+        double[][] data = new double[h][w];
+        
+        for (int j = 0; j < h; j++) { 
+            for (int i = 0; i < w; i++) {
+                data[j][i] = (double)pixels[j*w + i];
+                }
+        }
+
+        return data;
+    }
+    
+    private double[][] ImageProcessor_to_FFTComplexArray2D(ImageProcessor ip_r, ImageProcessor ip_i) {
+
+        float[] pixels_r = (float[])ip_r.getPixels();
+        float[] pixels_i = (float[])ip_i.getPixels();
+        int w = ip_r.getWidth();
+        int h = ip_r.getHeight();
+        double[][] data = new double[h][2*w];
+        
+        for (int j = 0; j < h; j++) { 
+            for (int i = 0; i < w; i++) {
+                data[j][2*i] = (double)pixels_r[j*w + i];
+                data[j][2*i+1] = (double)pixels_i[j*w + i];
+                }
+        }
+
+        return data;
+    }
+    
+    private ComplexMatrix FFTArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+    
+        ComplexMatrix m = new ComplexMatrix(h,w);
+
+        for (int j = 0; j < h; j++) {
+            for (int i = 0; i <= w/2; i++) {
+                if (j > 0 && i > 0 && i < w/2) { 
+                        m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+                        m.setElement(h-j, w-i, new Complex(data[j][2*i], -data[j][2*i+1]));
+                }
+                if (j == 0 && i > 0 && i < w/2) {
+                    m.setElement(0, i, new Complex(data[0][2*i], data[0][2*i+1]));
+                        m.setElement(0, w-i, new Complex(data[0][2*i], -data[0][2*i+1]));
+                }
+                if (i == 0 && j > 0 && j < h/2) {
+                    m.setElement(j,0, new Complex(data[j][0], data[j][1]));
+                        m.setElement(h-j, 0, new Complex(data[j][0], -data[j][1]));
+                        m.setElement(j, w/2, new Complex(data[h-j][1], -data[h-j][0]));
+                        m.setElement(h-j, w/2, new Complex(data[h-j][1], data[h-j][0]));    
+                }
+                if (j == 0 && i == 0) {
+                    m.setElement(0, 0, new Complex(data[0][0], 0));
+                }
+                if (j == 0 && i == w/2) {
+                    m.setElement(0, w/2, new Complex(data[0][1], 0));
+                }
+                if (j == h/2 && i == 0) {
+                    m.setElement(h/2, 0, new Complex(data[h/2][0], 0));
+                }
+                if (j == h/2 && i == w/2) {
+                    m.setElement(h/2, w/2, new Complex(data[h/2][1], 0));
+                }
+            }
+        }
+
+        return m;
+    }
+
+    private ComplexMatrix FFTComplexArray2D_to_ComplexMatrix(double[][] data, int h, int w) {
+    
+        ComplexMatrix m = new ComplexMatrix(h,w);
+
+        for (int j = 0; j < h; j++) {
+            for (int i = 0; i < w; i++) {
+                m.setElement(j,i, new Complex(data[j][2*i], data[j][2*i+1]));
+            }
+        }
+
+        return m;
+    }
+
+    private double[][] ComplexMatrix_to_FFTArray2D(ComplexMatrix m) {
+        int w = m.getNcol();
+        int h = m.getNrow();
+        double[][] data = new double[h][w];
+
+        for (int j = 0; j < h; j++) {
+            for (int i = 0; i <= w/2; i++) {
+                if (j > 0 && i > 0 && i < w/2) {
+                        data[j][2*i] = m.getElementReference(j,i).getReal();
+                        data[j][2*i+1] = m.getElementReference(j,i).getImag();
+                }
+                if (j == 0 && i > 0 && i < w/2) {
+                    data[0][2*i] = m.getElementReference(0,i).getReal();
+                        data[0][2*i+1] = m.getElementReference(0,i).getImag();
+                }
+                if (i == 0 && j > 0 && j < h/2) {
+                    data[j][0] = m.getElementReference(j,0).getReal();
+                        data[j][1] = m.getElementReference(j,0).getImag();
+                        data[h-j][1] = m.getElementReference(j,w/2).getReal();
+                        data[h-j][0] = m.getElementReference(h-j,w/2).getImag();    
+                }
+                if (j == 0 && i == 0) {
+                    data[0][0] = m.getElementReference(0,0).getReal();
+                }
+                if (j == 0 && i == w/2) {
+                    data[0][1] = m.getElementReference(0,w/2).getReal();
+                }
+                if (j == h/2 && i == 0) {
+                    data[h/2][0] = m.getElementReference(h/2,0).getReal();
+                }
+                if (j == h/2 && i == w/2) {
+                    data[h/2][1] = m.getElementReference(h/2,w/2).getReal();
+                }
+            }
+        }
+
+        return data;
+    }
+
+    // convert a Complex Matrix into an 2d real part array data[0][][]
+    // and 2d imaginary part data[1][][]
+    private double[][][] ComplexMatrix_to_RealArray2D(ComplexMatrix m) {
+        int w = m.getNcol();
+        int h = m.getNrow();
+        double[][][] data = new double[2][h][w];
+
+        for (int j = 0; j < h; j++) {
+            for (int i = 0; i < w; i++) {
+                data[0][j][i] = m.getElementReference(j,i).getReal();
+                    data[1][j][i] = m.getElementReference(j,i).getImag();
+            }
+        }
+        
+        return data;
+    }
+}

plugins/Align_TranslationFilter.java

@@ -0,0 +1,115 @@
+import ij.plugin.filter.ExtendedPlugInFilter;
+import ij.plugin.filter.PlugInFilterRunner;
+import ij.plugin.filter.GaussianBlur;
+import ij.*;
+import ij.process.*;
+
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import java.util.ArrayList;
+import java.io.IOException;
+import java.io.File;
+import jmatio.types.*;
+import jmatio.io.*;
+import ij.gui.GenericDialog;
+import ij.IJ;
+import ij.Prefs;
+
+public class Align_TranslationFilter implements ExtendedPlugInFilter {
+     private double[][] shifts;
+     private final int flags = (DOES_ALL-DOES_RGB)|DOES_STACKS|NO_CHANGES|FINAL_PROCESSING;
+     private ImagePlus imp;
+     private ImagePlus registred;
+     private ImageStack translated;
+     private PlugInFilterRunner pifr;
+     private int nbslices = 0;
+     private int processed = 0;  
+
+     public void setShifts(double[][] shifts){
+        this.shifts = shifts;
+     }
+
+     public double[][] getShifts(){
+        return shifts;
+     }
+
+     public ImagePlus getOutput(){
+        return registred;
+     }
+
+     public void  setImp(ImagePlus imp){
+        this.imp = imp;
+     }
+
+     /**
+      * This method is called by ImageJ for initialization.
+      * @param arg Unused here. For plugins in a .jar file this argument string can
+      *            be specified in the plugins.config file of the .jar archive.
+      * @param imp The ImagePlus containing the image (or stack) to process.
+      * @return    The method returns flags (i.e., a bit mask) specifying the
+      *            capabilities (supported formats, etc.) and needs of the filter.
+      *            See PlugInFilter.java and ExtendedPlugInFilter in the ImageJ
+      *            sources for details.
+      */
+     public int setup(String arg, ImagePlus imp) {
+        System.out.println("Setup " + arg);
+         if ("final".equals(arg)) {
+             registred.setStack("REG_" + this.imp.getTitle(), translated);
+            return DONE;
+         } else {
+            if (imp==null ){
+                this.imp = imp;
+            }
+            return flags;
+         }
+     }
+
+    /** Called by ImageJ after setup. */
+    public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
+        pifr = pfr;
+        
+        //ShiftsIO sio = new ShiftsIO();
+        //shifts = sio.load(null, "directshifts");
+        //if (shifts == null) return DONE;
+         
+        //IJ.register(this.getClass());         // protect static class variables (filter parameters) from garbage collection
+        //return IJ.setupDialog(imp, flags);    // ask whether to process all slices of stack (if a stack)
+        return flags;
+    }
+
+     /** Process a FloatProcessor (with the CONVERT_TO_FLOAT flag, ImageJ does the conversion to float).
+      *  Called by ImageJ for each stack slice (when processing a full stack); for RGB also called once for each color. */
+     public void run(ImageProcessor ip) {
+                // translate from shifts
+                if (Thread.currentThread().isInterrupted()) return;
+        
+        int thisone = pifr.getSliceNumber();
+        
+        ImageProcessor nip = ip.duplicate().convertToFloat();
+        nip.setInterpolationMethod(ImageProcessor.BICUBIC);
+        if (shifts.length != nbslices) {
+            nip.translate(shifts[1][3], shifts[1][2]); // translate all the frame by the
+                                // same shifts
+        } else {
+            nip.translate(shifts[thisone-1][3], shifts[thisone-1][2]);
+        }
+        
+        String lbl = imp.getStack().getSliceLabel(thisone);
+        if (lbl != null) {
+            translated.addSlice(lbl, nip, thisone - 1);
+        } else {
+            translated.addSlice("" + thisone, nip, thisone - 1);
+        }
+        translated.deleteSlice(thisone + 1);
+
+        processed++;
+        IJ.showProgress(processed, nbslices);
+    }
+
+     /** Called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar */
+     public void setNPasses(int nPasses) {
+         nbslices = nPasses;
+         registred = imp.createImagePlus();
+         translated = new ImageStack(imp.getWidth(), imp.getHeight(), nbslices);
+     }     
+}

plugins/Eiger.form

@@ -32,8 +32,6 @@
                               <Component id="buttonDone" min="-2" pref="127" max="-2" attributes="0"/>
                               <EmptySpace max="-2" attributes="0"/>
                               <Component id="buttonCloseVG10" min="-2" pref="127" max="-2" attributes="0"/>
-                              <EmptySpace max="-2" attributes="0"/>
-                              <Component id="buttonStopDetector" linkSize="1" max="32767" attributes="0"/>
                           </Group>
                           <Group type="102" alignment="0" attributes="0">
                               <Component id="spinnerExposure" linkSize="1" min="-2" max="-2" attributes="0"/>
@@ -61,11 +59,9 @@
                               <Component id="buttonAquire" min="-2" pref="127" max="-2" attributes="0"/>
                               <EmptySpace max="-2" attributes="0"/>
                               <Component id="buttonOpenVG10" min="-2" pref="127" max="-2" attributes="0"/>
-                              <EmptySpace max="-2" attributes="0"/>
-                              <Component id="buttonStartDetector" linkSize="1" min="-2" max="-2" attributes="0"/>
                           </Group>
                       </Group>
-                      <EmptySpace max="32767" attributes="0"/>
+                      <EmptySpace pref="118" max="32767" attributes="0"/>
                   </Group>
                   <Group type="102" attributes="0">
                       <Component id="renderer" max="32767" attributes="0"/>
@@ -98,7 +94,6 @@
                   <Group type="103" alignment="1" groupAlignment="3" attributes="0">
                       <Component id="buttonAquire" alignment="3" min="-2" pref="35" max="-2" attributes="0"/>
                       <Component id="buttonOpenVG10" alignment="3" min="-2" pref="35" max="-2" attributes="0"/>
-                      <Component id="buttonStartDetector" linkSize="2" alignment="3" min="-2" max="-2" attributes="0"/>
                   </Group>
               </Group>
               <EmptySpace min="-2" max="-2" attributes="0"/>
@@ -109,7 +104,6 @@
                   <Group type="103" alignment="1" groupAlignment="3" attributes="0">
                       <Component id="buttonDone" alignment="3" min="-2" pref="35" max="-2" attributes="0"/>
                       <Component id="buttonCloseVG10" alignment="3" min="-2" pref="35" max="-2" attributes="0"/>
-                      <Component id="buttonStopDetector" linkSize="2" alignment="3" min="-2" max="-2" attributes="0"/>
                   </Group>
               </Group>
               <EmptySpace min="-2" max="-2" attributes="0"/>
@@ -164,11 +158,10 @@
     <Component class="javax.swing.JComboBox" name="comboDepth">
       <Properties>
         <Property name="model" type="javax.swing.ComboBoxModel" editor="org.netbeans.modules.form.editors2.ComboBoxModelEditor">
-          <StringArray count="4">
-            <StringItem index="0" value="4"/>
-            <StringItem index="1" value="8"/>
-            <StringItem index="2" value="16"/>
-            <StringItem index="3" value="32"/>
+          <StringArray count="3">
+            <StringItem index="0" value="8"/>
+            <StringItem index="1" value="16"/>
+            <StringItem index="2" value="32"/>
           </StringArray>
         </Property>
         <Property name="enabled" type="boolean" value="false"/>
@@ -180,14 +173,6 @@
         <AuxValue name="JavaCodeGenerator_TypeParameters" type="java.lang.String" value="&lt;String&gt;"/>
       </AuxValues>
     </Component>
-    <Component class="javax.swing.JButton" name="buttonStartDetector">
-      <Properties>
-        <Property name="text" type="java.lang.String" value="Start EIGER"/>
-      </Properties>
-      <Events>
-        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStartDetectorActionPerformed"/>
-      </Events>
-    </Component>
     <Component class="javax.swing.JLabel" name="jLabel2">
       <Properties>
         <Property name="text" type="java.lang.String" value="Mode:"/>
@@ -241,14 +226,6 @@
         <Property name="deviceName" type="java.lang.String" value="eiger_exposure_rbv"/>
       </Properties>
     </Component>
-    <Component class="javax.swing.JButton" name="buttonStopDetector">
-      <Properties>
-        <Property name="text" type="java.lang.String" value="Stop EIGER"/>
-      </Properties>
-      <Events>
-        <EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="buttonStopDetectorActionPerformed"/>
-      </Events>
-    </Component>
     <Component class="ch.psi.pshell.swing.DeviceValuePanel" name="deviceValuePanel4">
       <Properties>
         <Property name="deviceName" type="java.lang.String" value="eiger_status"/>

plugins/Eiger.java

@@ -92,7 +92,6 @@ public class Eiger extends Panel {
         renderer = new ch.psi.pshell.imaging.Renderer();
         jLabel1 = new javax.swing.JLabel();
         comboDepth = new javax.swing.JComboBox<>();
-        buttonStartDetector = new javax.swing.JButton();
         jLabel2 = new javax.swing.JLabel();
         comboMode = new javax.swing.JComboBox<>();
         jLabel3 = new javax.swing.JLabel();
@@ -100,7 +99,6 @@ public class Eiger extends Panel {
         deviceValuePanel1 = new ch.psi.pshell.swing.DeviceValuePanel();
         deviceValuePanel2 = new ch.psi.pshell.swing.DeviceValuePanel();
         deviceValuePanel3 = new ch.psi.pshell.swing.DeviceValuePanel();
-        buttonStopDetector = new javax.swing.JButton();
         deviceValuePanel4 = new ch.psi.pshell.swing.DeviceValuePanel();
         buttonShowDetectorPanel = new javax.swing.JButton();
         checkMeasurements = new javax.swing.JCheckBox();
@@ -120,7 +118,7 @@ public class Eiger extends Panel {
 
         jLabel1.setText("Bit Depth:");
 
-        comboDepth.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "4", "8", "16", "32" }));
+        comboDepth.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "8", "16", "32" }));
         comboDepth.setEnabled(false);
         comboDepth.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
@@ -128,13 +126,6 @@ public class Eiger extends Panel {
             }
         });
 
-        buttonStartDetector.setText("Start EIGER");
-        buttonStartDetector.addActionListener(new java.awt.event.ActionListener() {
-            public void actionPerformed(java.awt.event.ActionEvent evt) {
-                buttonStartDetectorActionPerformed(evt);
-            }
-        });
-
         jLabel2.setText("Mode:");
 
         comboMode.setModel(new javax.swing.DefaultComboBoxModel<>(new String[] { "Single", "Continuous" }));
@@ -161,13 +152,6 @@ public class Eiger extends Panel {
 
         deviceValuePanel3.setDeviceName("eiger_exposure_rbv");
 
-        buttonStopDetector.setText("Stop EIGER");
-        buttonStopDetector.addActionListener(new java.awt.event.ActionListener() {
-            public void actionPerformed(java.awt.event.ActionEvent evt) {
-                buttonStopDetectorActionPerformed(evt);
-            }
-        });
-
         deviceValuePanel4.setDeviceName("eiger_status");
 
         buttonShowDetectorPanel.setText("Control Panel");
@@ -258,9 +242,7 @@ public class Eiger extends Panel {
                                 .addGap(224, 224, 224)
                                 .addComponent(buttonDone, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                .addComponent(buttonCloseVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                .addComponent(buttonStopDetector, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                                .addComponent(buttonCloseVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE))
                             .addGroup(layout.createSequentialGroup()
                                 .addComponent(spinnerExposure, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
@@ -282,10 +264,8 @@ public class Eiger extends Panel {
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                 .addComponent(buttonAquire, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE)
                                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                .addComponent(buttonOpenVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                .addComponent(buttonStartDetector)))
-                        .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                                .addComponent(buttonOpenVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 127, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                        .addContainerGap(118, Short.MAX_VALUE))
                     .addGroup(layout.createSequentialGroup()
                         .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                         .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
@@ -301,7 +281,7 @@ public class Eiger extends Panel {
                         .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))))
         );
 
-        layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {buttonStartDetector, buttonStopDetector, comboDepth, comboMode, deviceValuePanel1, deviceValuePanel2, deviceValuePanel3, spinnerExposure});
+        layout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {comboDepth, comboMode, deviceValuePanel1, deviceValuePanel2, deviceValuePanel3, spinnerExposure});
 
         layout.setVerticalGroup(
             layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
@@ -313,8 +293,7 @@ public class Eiger extends Panel {
                     .addComponent(deviceValuePanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                     .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                         .addComponent(buttonAquire, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
-                        .addComponent(buttonOpenVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
-                        .addComponent(buttonStartDetector)))
+                        .addComponent(buttonOpenVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)))
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER, false)
                     .addComponent(jLabel1)
@@ -322,8 +301,7 @@ public class Eiger extends Panel {
                     .addComponent(deviceValuePanel2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                     .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
                         .addComponent(buttonDone, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
-                        .addComponent(buttonCloseVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)
-                        .addComponent(buttonStopDetector)))
+                        .addComponent(buttonCloseVG10, javax.swing.GroupLayout.PREFERRED_SIZE, 35, javax.swing.GroupLayout.PREFERRED_SIZE)))
                 .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                 .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
                     .addComponent(jLabel3)
@@ -353,7 +331,7 @@ public class Eiger extends Panel {
                         .addComponent(renderer, javax.swing.GroupLayout.DEFAULT_SIZE, 409, Short.MAX_VALUE))))
         );
 
-        layout.linkSize(javax.swing.SwingConstants.VERTICAL, new java.awt.Component[] {buttonStartDetector, buttonStopDetector, comboDepth, comboMode, deviceValuePanel1, deviceValuePanel2, deviceValuePanel3, deviceValuePanel4, spinnerExposure});
+        layout.linkSize(javax.swing.SwingConstants.VERTICAL, new java.awt.Component[] {comboDepth, comboMode, deviceValuePanel1, deviceValuePanel2, deviceValuePanel3, deviceValuePanel4, spinnerExposure});
 
     }// </editor-fold>//GEN-END:initComponents
 
@@ -365,8 +343,6 @@ public class Eiger extends Panel {
                     buttonDoneActionPerformed(null);
                     eiger.waitState(State.Ready, 10000); //Timeout of 10s
                 }
-                //((ch.psi.pshell.device.Camera) getDevice("eiger")).stop();
-                //TimeUnit.SECONDS.sleep(1);
                 if (comboDepth.getSelectedIndex()!=comboDepth.getItemCount()) {                   
                     Integer value = Integer.valueOf((String)comboDepth.getSelectedItem());
                     bitDepth.write(value);                    
@@ -377,19 +353,6 @@ public class Eiger extends Panel {
         }
     }//GEN-LAST:event_comboDepthActionPerformed
 
-    private void buttonStartDetectorActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStartDetectorActionPerformed
-        try {
-            evalAsync("start_eiger_ioc()").handle((ret,ex)->{
-                if (ex!=null){
-                    showException((Exception)ex);
-                }
-                return ret;
-            });
-        } catch (Exception ex) {
-            showException(ex);
-        }
-    }//GEN-LAST:event_buttonStartDetectorActionPerformed
-
     private void comboModeActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_comboModeActionPerformed
         try{
             if (!updatingControls){
@@ -398,8 +361,6 @@ public class Eiger extends Panel {
                     buttonDoneActionPerformed(null);
                     eiger.waitState(State.Ready, 10000); //Timeout of 10s
                 }
-                //((ch.psi.pshell.device.Camera) getDevice("eiger")).stop();
-                //TimeUnit.SECONDS.sleep(1);
                 Integer value = comboMode.getSelectedIndex();
                 if (value==1){
                     value++;
@@ -428,19 +389,6 @@ public class Eiger extends Panel {
         }
     }//GEN-LAST:event_spinnerExposureStateChanged
 
-    private void buttonStopDetectorActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonStopDetectorActionPerformed
-        try {
-            evalAsync("stop_eiger_ioc()").handle((ret,ex)->{
-                if (ex!=null){
-                    showException((Exception)ex);
-                }
-                return ret;
-            });
-        } catch (Exception ex) {
-            showException(ex);
-        }
-    }//GEN-LAST:event_buttonStopDetectorActionPerformed
-
     private void buttonShowDetectorPanelActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_buttonShowDetectorPanelActionPerformed
         try {
             showDevicePanel("eiger");
@@ -553,8 +501,6 @@ public class Eiger extends Panel {
     private javax.swing.JButton buttonDone;
     private javax.swing.JButton buttonOpenVG10;
     private javax.swing.JButton buttonShowDetectorPanel;
-    private javax.swing.JButton buttonStartDetector;
-    private javax.swing.JButton buttonStopDetector;
     private javax.swing.JCheckBox checkMeasurements;
     private javax.swing.JComboBox<String> comboDepth;
     private javax.swing.JComboBox<String> comboMode;

plugins/ShiftsIO.java

@@ -0,0 +1,109 @@
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import java.util.ArrayList;
+import java.io.IOException;
+import java.io.File;
+import jmatio.types.*;
+import jmatio.io.*;
+import ij.gui.GenericDialog;
+import ij.IJ;
+import ij.Prefs;
+
+public class ShiftsIO {
+    
+    public ShiftsIO () {}
+
+    public double[][] load(String filename, String varname) {
+        if (filename==null){
+                String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+                OpenDialog od = new OpenDialog("Open_shifts .mat file:", analysis_dir, "shifts.mat");
+                String dir = od.getDirectory();
+                if (null == dir) return null; // dialog was canceled
+                if (!dir.endsWith(File.separator)) dir += File.separator;
+                filename = dir + od.getFileName();
+                Prefs.set("peem.analysis_dir", dir);
+            }
+            return low_load(filename, varname);
+    }
+
+       private double[][] low_load(String filename, String varname) {
+        MatFileReader mfr = null;
+        try {
+            mfr = new MatFileReader(filename);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                    + e.getMessage());
+        }
+
+        if (mfr != null) {
+            MLDouble array = (MLDouble)mfr.getMLArray(varname);
+            if (array != null){
+                return array.getArray();
+            } else {
+                return null;
+            }
+        } else {
+            return null;
+        }
+    }
+
+    public void save(String filename, double[][] shifts, String varname) {
+        boolean update = false;
+        if (filename==null){
+        String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+        SaveDialog sd = new SaveDialog("Save_shifts .mat file:", analysis_dir, "shifts.mat", ".mat");
+            String dir = sd.getDirectory();
+            String fname = sd.getFileName();
+            if (null == fname) return; // user canceled dialog
+            if (!dir.endsWith(File.separator)) dir += File.separator;
+            Prefs.set("peem.analysis_dir", dir);       
+        
+            if ((new File(dir + fname)).exists()) { // if file exist, overwrite or update shifts ?
+                GenericDialog gd = new GenericDialog("Update");
+                String[] options = {"overwrite","update"};
+            gd.addChoice("Mode of operation with existing file. You want to: ", options, options[0]);
+            gd.showDialog();
+            if (gd.wasCanceled()) return;
+            if (gd.getNextChoiceIndex() == 1) update = true;
+            }
+            filename = dir + fname;
+        } 
+        double[][] final_shifts;
+            if (update) {
+                double[][] prev_shifts = low_load(filename, "directshifts");
+                if (prev_shifts == null) {
+                    IJ.error("Can't read the direct shifts in this file");
+                    return;
+                }
+
+            if (prev_shifts.length == shifts.length) {
+                    for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[j][3];
+                        prev_shifts[j][4] += shifts[j][4];
+                    }
+            } else if (shifts.length == 2) {// 2 shifts, like between two slices of different
+                            // sequences
+                 for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[1][3];
+                        prev_shifts[j][4] += shifts[1][4];
+                    }
+            } else {
+                IJ.error("Old and new shifts have incompatible length !");
+                return;
+            }
+            final_shifts = prev_shifts;
+            } else {
+            final_shifts = shifts;
+            }
+            
+            MLDouble mlDouble = new MLDouble(varname, final_shifts);
+            ArrayList<MLArray> list = new ArrayList<MLArray>();
+        list.add(mlDouble);
+        try {
+            new MatFileWriter(filename, list);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                            + e.getMessage());
+        }       
+    }
+}

script/Test_Autofocus_Armin.py

@@ -5,7 +5,9 @@ STEP_STIG = 1.0
 UPDATE_POSITION = True
 AVERAGE = 1
 width, height = eiger.getImageSize()
-ROI = Rectangle(width/3, height/3, width/3, height/3,)
+#ROI = Rectangle(width/3, height/3, width/3, height/3,)
+#ROI = Rectangle(0, 0, width, height,)
+ROI = Rectangle(233,30,128,128)
 
 initial_state = objective.read(),obj_stig_a.read(),obj_stig_b.read()    
 print "Initial state:" , initial_state
@@ -15,13 +17,45 @@ def apply_pos(pos):
     obj_stig_a.write(pos[1])
     obj_stig_b.write(pos[2])
 
+def show_roi():
+    global ROI
+    pn=show_panel(image)
+    ov=Overlays.Rect(Pen(Color.BLUE), Point(ROI.x,ROI.y),Dimension(ROI.width,ROI.height))
+    pn.clearOverlays()
+    pn.addOverlay(ov)
+show_roi()
+    
+MAX_SHIFT = 20
+former_data = image.data
+def update_roi():
+    global former_data, ROI
+    cur_data = image.data
+    calc_roi = Roi(ROI.x,ROI.y,ROI.width, ROI.height)
+    try:
+        xoff, yoff, error, diffphase = calculate_shift(former_data,cur_data, calc_roi)
+        print "Calculated shift: ", xoff, yoff, error, diffphase
+        if (0<abs(xoff) < MAX_SHIFT) and (0<abs(yoff) < MAX_SHIFT):
+            x,y=int(ROI.x - xoff), int(ROI.y - yoff)
+            print "Updating ROI location to ", x, y
+            ROI.setLocation(x,y)
+            show_roi()
+    except:
+        print "Error calculating shift: " + str(sys.exc_info()[1])
+    former_data = cur_data
+    
 
 r=scan_focus(objective, RANGE_OBJ, STEP_OBJ, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(obj_stig_a, RANGE_STIG, STEP_STIG, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(obj_stig_b, RANGE_STIG, STEP_STIG, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(objective, RANGE_OBJ, STEP_OBJ, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(obj_stig_a, RANGE_STIG, STEP_STIG, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(obj_stig_b, RANGE_STIG, STEP_STIG, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
+update_roi()
 r=scan_focus(objective, RANGE_OBJ, STEP_OBJ, roi = ROI, average = AVERAGE, update_position = UPDATE_POSITION)
 
 final_state = objective.read(),obj_stig_a.read(),obj_stig_b.read()    

script/Users/Cinthia/2021_june_Energy.py

@@ -0,0 +1,174 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+#Sample M1
+#TRY.write(-1.5)
+#TRZ.write(14)
+
+#time.sleep(30)
+
+#open_vg13()
+#time.sleep(1)
+
+#caput('X11MA-ES3-MAG1:V', 2)
+#time.sleep(15)
+
+#caput('X11MA-KEI10:RANGE', 7)
+#caput('X11MA-KEI11:RANGE', 8)
+#caput('X11MA-KEI12:RANGE', 9)
+#for i in range(2):
+ #   time.sleep(1)
+ # otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M1_Cp')
+ #   otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M1_Cm')    
+ #  otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M1_Cm')
+ #   otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M1_Cp')
+
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M1_LH')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M1_LV')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M1_LV')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M1_LH')
+
+
+#Sample M2
+#TRY.write(-0.9)
+#TRZ.write(22.5)
+
+#time.sleep(30)
+
+#open_vg13()
+#time.sleep(1)
+
+#caput('X11MA-ES3-MAG1:V', 2)
+#time.sleep(15)
+
+#caput('X11MA-KEI10:RANGE', 7)
+#caput('X11MA-KEI11:RANGE', 8)
+#caput('X11MA-KEI12:RANGE', 9)
+#for i in range(2):
+   # time.sleep(1)
+   # otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M2_Cp')
+  #  otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M2_Cm')    
+  #  otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M2_Cm')
+  #  otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M2_Cp')
+
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M2_LH')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M2_LV')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M2_LV')
+#otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M2_LH')
+
+ #Sample M3
+TRY.write(-0.9)
+TRZ.write(30)
+
+time.sleep(30)
+
+open_vg13()
+time.sleep(1)
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)#Changed th gain to 9 due to saturation
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M3_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M3_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M3_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M3_Cp')
+
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M3_LH')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M3_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M3_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M3_LH')
+    
+#Sample M6
+TRY.write(2.0)
+TRZ.write(30.0)
+
+time.sleep(30)
+
+open_vg13()
+time.sleep(1)
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M6_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M6_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M6_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M6_Cp')
+
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M6_LH')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M6_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M6_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M6_LH')
+    
+#Sample M5
+TRY.write(2.0)
+TRZ.write(24.5)
+
+time.sleep(30)
+
+open_vg13()
+time.sleep(1)
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_Cp')
+
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M5_LH')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M5_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M5_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M5_LH')
+
+#Sample M4
+TRY.write(1.0)
+TRZ.write(18)
+
+time.sleep(30)
+
+open_vg13()
+time.sleep(1)
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M4_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M4_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M4_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M4_Cp')
+
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M4_LH')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M4_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 90.0, offset=-1.2, name='Ti_M4_LV')
+otf2(start=450, end=475, time=3.0, delay=10, mode='LINEAR', alpha = 0.0, offset=-1.2, name='Ti_M4_LH')
+        
+           
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/Fe_XMCD.py

@@ -0,0 +1,24 @@
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+sample_name='M4_150'
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    #time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+
+close_vg13()

script/Users/Cinthia/Fe_XMCD_hyst.py

@@ -0,0 +1,763 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+#Sample M5 30V
+'''
+TRY.write(2.0)
+TRZ.write(24.5)
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+
+caput('X11MA-KEI11:VOLTOUT','ON')
+
+
+caput('X11MA-KEI11:SETVOLTAGE',0)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',30)
+time.sleep(10)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_30_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_30_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_30_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_30_Cp')
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_30_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_30_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+#Sample M5 -30
+
+
+
+
+#XMCD
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',0)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-5)
+time.sleep(1)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-30)
+
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-30_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-30_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-30_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-30_Cp')
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_-30_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_-30_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+
+
+
+
+#Sample M5 -50V
+
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',-35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-50)
+time.sleep(10)
+
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-50_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-50_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-50_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-50_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_-50_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_-50_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')    
+
+
+#Sample M5 50V
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',-45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',0)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',50)
+time.sleep(10)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_50_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_50_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_50_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_50_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_50_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_50_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py') 
+
+
+
+#Sample M5 70V
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',70)
+time.sleep(10)
+
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_70_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_70_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_70_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_70_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_70_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_70_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py') 
+
+
+
+#Sample M5 -70V
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',60)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',50)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',0)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-50)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-60)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-70)
+time.sleep(10)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-70_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-70_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-70_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-70_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_-70_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_-70_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')  
+
+
+#Sample M5 -100V
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',-75)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-80)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-85)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-90)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-95)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-100)
+time.sleep(10)
+'''
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-100_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_-100_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_-100_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')      
+
+
+#M5 100V
+
+
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI11:SETVOLTAGE',-95)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-90)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-85)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-80)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-75)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-70)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-60)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-50)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',-5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',0)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',50)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',60)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',70)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',75)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',80)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',85)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',95)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',100)
+time.sleep(10)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_100_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_100_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_100_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_100_Cp')
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_100_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_100_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')   
+
+
+caput('X11MA-KEI11:SETVOLTAGE',95)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',90)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',85)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',80)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',75)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',70)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',65)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',60)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',55)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',50)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',45)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',40)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',35)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',30)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',25)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',0)     
+
+caput('X11MA-KEI11:VOLTOUT','OFF')
+
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/Fe_XMCD_hyst_1.py

@@ -0,0 +1,67 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+#Sample M5
+TRY.write(2.0)
+TRZ.write(24.5)
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+sample_name='M5_100_-20'
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/Fe_XMCD_hyst_1sample_1voltage.py

@@ -0,0 +1,78 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+#Sample M5
+TRY.write(2.0)
+TRZ.write(24.5)
+
+open_vg13()
+time.sleep(1)
+
+#XMCD
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+'''
+caput('X11MA-KEI11:VOLTOUT','ON')
+
+#caput('X11MA-KEI11:VOLTOUT',1)
+caput('X11MA-KEI11:SETVOLTAGE',5)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',10)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',15)
+time.sleep(1)
+caput('X11MA-KEI11:SETVOLTAGE',20)
+'''
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(2):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-20_0_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-20_0_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_M5_-20_0_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_M5_-20_0_Cp')
+
+#HYST
+'''
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="Hyst_M5_-20_0_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="Hyst_M5_-20_0_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+'''
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/Fe_XMCD_hyst_cofield.py

@@ -0,0 +1,613 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+#Sample M6 150
+
+TRY.write(2.0)
+TRZ.write(30.0)
+
+open_vg13()
+time.sleep(1)
+'''
+#XMCD
+sample_name='M6_150'
+
+v_start =0
+v_end = 150
+#run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+#XMCD
+sample_name='M6_150_-20'
+
+v_start =150
+v_end = -20
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 9)
+
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+
+
+
+#XMCD
+#sample_name='M6_-150'
+
+v_start =-20
+v_end = -150
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+sample_name='M6_-150'
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+
+#XMCD
+#sample_name='M6_-150_55'
+
+v_start =-150
+v_end = 55
+
+
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+sample_name='M6_-150_55'
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+
+#XMCD
+#sample_name='M6_150_0'
+
+v_start =55
+v_end = 150
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+v_start =150
+v_end = 0
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+sample_name='M6_150_0'
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+
+#XMCD
+#sample_name='M6_-150_0'
+
+v_start =0
+v_end = -150
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+v_start =-150
+v_end = 0
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+sample_name='M6_-150_0'
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+#XMCD
+#sample_name='M6_150'
+
+v_start =0
+v_end = 150
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+'''
+sample_name='M6_150'
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+#XMCD
+sample_name='M6_150_-20'
+
+v_start =150
+v_end = -20
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+    
+#XMCD
+#sample_name='M6_-150'
+
+v_start =-20
+v_end = -150
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+sample_name='M6_-150'
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+
+
+
+    
+#XMCD
+sample_name='M6_-150_55'
+
+v_start =-150
+v_end = 55
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(15)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+for i in range(1):
+    time.sleep(1)
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')    
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp') 
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC +', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cp')
+    otf2(start=695, end=740, time=3, delay=10, mode='CIRC -', alpha = 0.0, offset=-1.2, name='Fe_'+sample_name + '_Cm')  
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+v_start =55
+v_end = 0
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/apply_voltage.py')
+
+
+caput('X11MA-KEI11:VOLTOUT','OFF')
+
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/Test_alingment.py

@@ -0,0 +1,2 @@
+#otf2(start=703, end=715, time=0.2, delay=5, mode='LINEAR', alpha = 0.0, offset=-1.2, name='test')
+otf2(start=450, end=475, time=3.0, delay=5, mode='CIRC -', alpha = 0.0, offset=-1.2, name='test')

script/Users/Cinthia/apply_voltage.py

@@ -0,0 +1,22 @@
+v_start= -20
+v_end = 0
+
+step_size=5
+n=(v_start - v_end)/step_size
+
+for i in range (int(abs(n))+1):
+    if v_start > v_end:
+        v=v_start - i*step_size
+        #print "reverse"
+        print ("Apply", v," volts")
+        caput('X11MA-KEI11:SETVOLTAGE',v)
+        sleep(0.1)
+    else:
+        v= i*step_size+v_start
+        print "forward"
+        print ("Apply", v," volts")
+        caput('X11MA-KEI11:SETVOLTAGE',v)
+        sleep(0.1)
+sleep(20)
+
+

script/Users/Cinthia/field_sweepID2.py

@@ -0,0 +1,119 @@
+#Parameters
+
+sample_name='M4_120'
+'''
+FILENAME='Hyst_'+ sample_name + '_E2_Cm'
+B1 = 1.0    # starting mag. field in Amps
+B2 = -1.0    # final mag. field in Amps
+BSTEP = 0.5   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+ENERGIES = (707.4) #list of energies in eV
+MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+OFFSET2 = -1.2 #ID2 offset
+FIELD_PRECISION = 0.04 #  
+ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+ACC_TIME = 0.1 # time in 100ms
+'''
+
+
+# List of scans. Each scan is defined as: (start,stop, step)
+# to make a whole loop two scans are needed: [(B1, B2, BSTEP),(B2,B1,-BSTEP)]
+# to make half of a loop one scan is needed: [(B1, B2, BSTEP),]  <- don't forget to put comma before ]
+RANGES = [(B1, B2, -BSTEP),(B2,B1,BSTEP)] 
+set_exec_pars(open=False, tag=FILENAME)
+
+#open_vg13()
+
+#Pre-actions
+# Here polarization and offsets are set
+
+caput ("X11PHS-E:OPT","PGM+ID2")
+print "ID mode set to PGM+ID2"
+#caput(OTF_OFF1,-50) #detune ID1
+caput('X11MA-ID2:ENERGY-OFFS', OFFSET2)
+print "ID offset set to ", OFFSET2
+cawait('X11MA-ID2:DONE',1)
+print "Offset setting done"
+
+
+if MODE is 1 or 2:
+    caput('X11MA-ID2:MODE',MODE)
+    #print "Polarization mode set"
+else:
+    raise Exception("Invalid polarization type: " +  MODE)
+
+cawait('X11MA-ID2:DONE',1)
+print "ID mode setting done"
+
+
+
+
+# setting number of samples to be averaged, which depends on the accumulation time
+avg = ACC_TIME * 10
+caput("X11MA-ES1-10ADC:AVG",avg)
+
+# Generating a list of mag. fields (setpoints) needed for the loop
+setpoints = []
+for r in RANGES:
+    setpoints = setpoints + frange(r[0], r[1], r[2], True)
+
+# plot properties
+set_preference(Preference.ENABLED_PLOTS,  ['field', 'tey_norm'])
+set_preference(Preference.PLOT_TYPES, {'tey_norm':1})
+
+#scan = ManualScan(['field', 'Energy'], ['TEY', 'I0', 'polarization', 'temperature', 'RingCurrent', 'tey_norm'] , [min(setpoints), min(ENERGIES)], [max(setpoints), max(ENERGIES)], [len(setpoints)-1, len(ENERGIES)-1])
+scan = ManualScan(['field', 'Energy'], ['I0', 'TEY', 'TFY', 'polarization', 'temperature', 'RingCurrent', 'tey_norm','tfy_norm'] , [min(setpoints), min(ENERGIES)], [max(setpoints), max(ENERGIES)], [len(setpoints)-1, len(ENERGIES)-1])
+scan.start()
+
+# Main loop
+for B in setpoints:
+    print "Setting field = ", B
+    caput("X11MA-XMCD:I-SETraw",B)
+    time.sleep( FIELD_CHANGE_SLEEP )     # Settling time
+
+    #readback1 = caget("X11MA-XMCD:Ireadout")
+    readback1 = field.read()    
+
+    while abs(readback1-B) > FIELD_PRECISION:
+        #readback1 = caget("X11MA-XMCD:Ireadout")
+        readback1 = field.read() 
+        time.sleep(0.1)
+
+    for E in ENERGIES:
+        print "Setting energy = ", E
+        #caput('X11PHS-E:GO.A', E)
+        energy.write(E)
+        time.sleep (0.1)
+        print "Energy set"
+        cawait('X11PHS:alldone', 1)
+        print "done"
+
+        readback2  = energy.read()
+        if abs(readback2 - E) > 0.1 : # TODO: Check accuracy
+            raise Exception('Energy could not be set to the value ' + str(E))
+        sleep( ENERGY_CHANGE_SLEEP ) # Settling time
+
+        detector1 = keithley_1a.read() #Keithley1
+        detector2 = keithley_2a.read() #Keithley2
+        detector3 = keithley_3a.read() #Keithley3
+        detector4 = caget('X11MA-ID2:MODE')   #polarization in ID2
+        #detector5 = caget("X11MA-ID2:ALPHA-READ") # polAngle in ID2
+        detector6 = caget('X11MA-ES3-LSCI:TEMP_RBV') #temperature.get() 
+        detector7 = caget("ARIDI-PCT:CURRENT")
+        #detector8 = signal_field_analog_x.read() # fieldAnalogX.get() 
+
+        tey_norm = detector2/detector1     
+        tfy_norm = detector3/detector1
+
+        #converting polarization strings to integer numbers: C+ -> 1 and C- -> 2
+        if detector4 == 'CIRC +': detector4 = 1
+        elif detector4 == 'CIRC -': detector4 = 2
+        else: detector4 = 0
+        #print "step 7"
+        #scan.append ([B, E], [readback1, readback2], [detector1, detector2, detector4, detector6, detector7, tey_norm])
+        scan.append ([B, E], [readback1, readback2], [detector1, detector2, detector3, detector4, detector6, detector7, tey_norm, tfy_norm])
+
+scan.end()
+caput("X11MA-ES1-10ADC:AVG",1) 
+
+#close_vg13()

script/Users/Cinthia/hyst_ID2_Fe.py

@@ -0,0 +1,48 @@
+
+open_vg13()
+
+
+sample_name='M4_120'
+
+
+#HYST
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+
+for i in range(1):
+    FILENAME='Hyst_'+ sample_name + '_Cm'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME='Hyst_'+ sample_name + '_Cp'
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+close_vg13()
+
+
+
+
+
+
+

script/Users/Cinthia/hyst_ID2_Fe_all_samples.py

@@ -0,0 +1,238 @@
+
+time.sleep(1)
+open_vg13()
+open_vg13()
+'''
+
+#Sample M1
+TRY.write(-1.5)
+TRZ.write(14)
+
+time.sleep(30)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.04   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.03 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.04   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.03 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+#Sample M2
+TRY.write(-0.9)
+TRZ.write(22.5)
+
+
+
+time.sleep(30)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.04   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.03 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="M2_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.04   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.03 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+    #Sample M3
+TRY.write(-0.9)
+TRZ.write(30)
+
+time.sleep(30)
+
+FILENAME="M3"
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 8)
+
+for i in range(1):
+    FILENAME="M3_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="M3_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+'''
+
+    #Sample M4
+TRY.write(1.0)
+TRZ.write(18)
+
+
+
+time.sleep(30)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+
+for i in range(1):
+    FILENAME="M4_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="M4_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+    #Sample M5
+TRY.write(2.0)
+TRZ.write(24.5)
+
+time.sleep(30)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+
+
+for i in range(1):
+    FILENAME="M5_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="M5_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+    #Sample M6
+TRY.write(2.0)
+TRZ.write(30)
+
+time.sleep(30)
+
+caput('X11MA-KEI10:RANGE', 7)
+caput('X11MA-KEI11:RANGE', 7)
+caput('X11MA-KEI12:RANGE', 9)
+
+
+for i in range(1):
+    FILENAME="M6_Cm"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 2  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+    
+    FILENAME="M6_Cp"
+    B1 = 2.0    # starting mag. field in Amps
+    B2 = -2.0    # final mag. field in Amps
+    BSTEP = 0.05   # step size mag. field in Amps. in Amps (1mT ~0.25A)
+    ENERGIES = (700,707.4) #list of energies in eV
+    MODE = 1  #polarization (CIRC+ -> 1 or CIRC- -> 2)
+    OFFSET2 = -1.2 #ID2 offset
+    FIELD_PRECISION = 0.04 #  
+    ENERGY_CHANGE_SLEEP = 0.5 # put the Enerrgy settling time if needed
+    FIELD_CHANGE_SLEEP =  0.5 # put the Field   settling time if needed
+    ACC_TIME = 0.1 #I think this number x 10 is in seconds
+    run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/field_sweepID2.py')
+
+close_vg13()

script/Users/Cinthia/night.py

@@ -0,0 +1,2 @@
+#run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/2021_june_Energy.py')#there was a timeout in the second script, but this one was complete, so I re start from the second one
+run('/sls/X11MA/data/X11MA/pshell/home/script/Users/Cinthia/hyst_ID2_Fe_all_samples.py')

script/Users/Cinthia/troubleshooting.py

@@ -0,0 +1,3 @@
+#energy.write(710)
+#time.sleep (2)
+cawait('X11PHS:alldone', 0, timeout=5)

script/Users/Sridhar/Test.py

@@ -0,0 +1 @@
+otf2(start=703, end=715, time=0.2, delay=5, mode='LINEAR', alpha = 0.0, offset=-1.2, name='test')

script/Users/federico/2021_may_beamtime.py

@@ -1,11 +1,7 @@
 #otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
 
 
-#Sample Na
-set_exec_pars(path="/sls/X11MA/data/X11MA/Data1/XAS/210512/LMO/")
-nr_loops=2
-
-TRY.write(21.0)
+TRY.write()
 TRZ.write(8.2)
 
 time.sleep(30)

script/Users/federico/test.py

@@ -0,0 +1,24 @@
+#otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST')
+
+
+#Sample Na
+set_exec_pars(path="/sls/X11MA/data/X11MA/Data1/XAS/2021/2021_05/")
+nr_loops=1
+
+time.sleep(10)
+
+open_vg13()
+time.sleep(1)
+
+caput('X11MA-ES3-MAG1:V', 2)
+time.sleep(5)
+caput('X11MA-ES3-MAG1:V', 1)
+time.sleep(2)
+
+
+time.sleep(1)
+caput('X11MA-KEI10:RANGE', 6)
+caput('X11MA-KEI11:RANGE', 8)
+caput('X11MA-KEI12:RANGE', 10)
+otf2(start=520, end=570, time=2.5, delay=10, mode='LINEAR', alpha = 90.0, offset=0.0, name='test1052_', folder='/sls/X11MA/data/X11MA/Data1/XAS/2021/2021_05/')
+

script/imaging/shifts.py

@@ -0,0 +1,642 @@
+from ijutils import *
+import java.lang.reflect
+import flanagan.complex.ComplexMatrix as ComplexMatrix
+import flanagan.math.Matrix as Matrix
+import flanagan.complex.Complex as Complex
+import org.jtransforms.fft.DoubleFFT_2D as DoubleFFT_2D
+import math
+from startup import ScriptUtils
+import ij.plugin.filter.PlugInFilterRunner as PlugInFilterRunner
+import ij.plugin.filter.ExtendedPlugInFilter as ExtendedPlugInFilter
+import ij.plugin.filter.ExtendedPlugInFilter as ExtendedPlugInFilter
+import java.lang.Thread as Thread
+
+
+def new_array(type, *dimensions):
+    return java.lang.reflect.Array.newInstance(ScriptUtils.getPrimitiveType(type), *dimensions)
+
+def load_stack(title, file_list, show=False):
+    ip_list = []
+    for f in file_list:
+        ip_list.append(open_image(expand_path(f)))
+    stack = create_stack(ip_list, title=title)
+    if show:
+        stack.show()
+    return stack
+
+def load_test_stack(title="Test", show=False, size=9):
+    file_list = []
+    for index in range(40, 40+size):
+        file_list.append("{images}/TestObjAligner/i210517_0" + str(index) + "#001.tif")
+    return load_stack(title, file_list, show)
+
+def load_corr_stack(title="Corr", show=False):
+    file_list = []
+    for index in range(40, 49):
+        file_list.append("{images}/TestObjAligner_corr/i210517_0" + str(index) + "#001.tif")
+    return load_stack(title, file_list, show)
+
+def complex_edge_filtering(imp, complex=True, g_sigma=3.0, g_resolution=1e-4, show=False, java_code=False):
+    if java_code:
+        get_context().getPluginManager().loadInitializePlugin("Align_ComplexEdgeFiltering.java")
+        complex_edge_filter = get_context().getClassByName("Align_ComplexEdgeFiltering").newInstance()
+        complex_edge_filter.setup(str(g_sigma)+","+str(complex)+","+str(show), imp)   #Gaussian blur radius, Complex (True) or Real (False), show dialog = False
+        complex_edge_filter.run(imp.getProcessor())
+        return complex_edge_filter.output
+        
+    gb = GaussianBlur()
+    sobel_r = [1, 0, -1, 2, 0, -2, 1, 0, -1]
+    sobel_i = [1, 2, 1, 0, 0, 0, -1, -2, -1]
+
+    imp_r = imp.createImagePlus()
+    stack_r = ImageStack(imp.getWidth(), imp.getHeight())
+
+    if (complex):
+        imp_i = imp.createImagePlus()
+        stack_i = ImageStack(imp.getWidth(), imp.getHeight())
+        for i in range(1, imp.getImageStackSize() + 1):
+            ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat()
+            # Gaussian blurring
+            gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution)
+            ip_i = ip_r.duplicate()
+            # Sobel edge filtering
+            ip_r.convolve3x3(sobel_r)
+            ip_i.convolve3x3(sobel_i)
+
+            stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r)
+            stack_i.addSlice(imp.getStack().getSliceLabel(i), ip_i)
+            IJ.showProgress(i, imp.getImageStackSize())
+
+        # imag
+        imp_i.setStack("EdgeImag_" + imp.getTitle(), stack_i);
+        imp_i.resetDisplayRange()
+        if show:
+            imp_i.show()
+            imp_i.updateAndDraw()
+    else:
+        imp_i = None
+        for i in range(1, imp.getImageStackSize() + 1):
+            ip_r = imp.getStack().getProcessor(i).duplicate().convertToFloat()
+            # Gaussian blurring
+            gb.blurGaussian(ip_r, g_sigma, g_sigma, g_resolution)
+            # Sobel edge filtering
+            ip_r.filter(ImageProcessor.FIND_EDGES)
+            stack_r.addSlice(imp.getStack().getSliceLabel(i), ip_r)
+            IJ.showProgress(i, imp.getImageStackSize())
+
+    # real
+    imp_r.setStack("EdgeReal_" + imp.getTitle(), stack_r)
+    imp_r.resetDisplayRange()
+    if show:
+        imp_r.show()
+        imp_r.updateAndDraw()
+    return [imp_r, imp_i]
+
+class TranslationFilter(ExtendedPlugInFilter):
+    def __init__(self):
+         self.shifts=None
+         self.flags = (self.DOES_ALL-self.DOES_RGB)|self.DOES_STACKS|self.NO_CHANGES|self.FINAL_PROCESSING
+         self.imp=None
+         self.output = None
+         self.translated = None
+         self.pifr = None
+         self.nbslices = 0
+         self.processed = 0
+              
+    def setup(self, arg, imp):
+         if "final"==arg:
+             self.output.setStack("REG_" + self.imp.getTitle(), self.translated)
+             return self.DONE
+         else:
+            if self.imp is None:
+                self.imp = imp;
+            return self.flags;
+            
+    def showDialog(self,imp, command, pfr):
+        self.pifr = pfr
+        return flags
+
+    # Called by ImageJ to set the number of calls to run(ip) corresponding to 100% of the progress bar 
+    def setNPasses(self, nPasses):
+         self.nbslices = nPasses;
+         self.output = self.imp.createImagePlus();
+         self.translated = ImageStack(self.imp.getWidth(), self.imp.getHeight(), self.nbslices)
+
+    #Process a FloatProcessor (with the CONVERT_TO_FLOAT flag, ImageJ does the conversion to float).
+    #  Called by ImageJ for each stack slice (when processing a full stack); for RGB also called once for each color. */
+    def run(self, ip):
+        if Thread.currentThread().isInterrupted():
+            return
+        thisone = self.pifr.getSliceNumber()
+        
+        nip = ip.duplicate().convertToFloat()
+        nip.setInterpolationMethod(ImageProcessor.BICUBIC)
+        if len(self.shifts) != self.nbslices:
+            xoff, yoff = self.shifts[1][3], self.shifts[1][2]  # translate all the frame by the same shifts
+        else:
+            xoff, yoff =  self.shifts[thisone-1][3], self.shifts[thisone-1][2]
+        nip.translate(xoff, yoff)
+     
+        lbl = self.imp.getStack().getSliceLabel(thisone)
+        if lbl != None:
+            self.translated.addSlice(lbl, nip, thisone - 1)
+        else:
+            self.translated.addSlice(str(thisone), nip, thisone - 1)
+       
+        self.translated.deleteSlice(thisone + 1)
+
+        self.processed+=1
+        IJ.showProgress(self.processed, self.nbslices);     
+
+def translate(stack, shifts, show=False, java_code=False):
+    WindowManager.setTempCurrentImage(stack)
+    if java_code:
+        get_context().getPluginManager().loadInitializePlugin("Align_TranslationFilter.java")
+        translation_filter = get_context().getClassByName("Align_TranslationFilter").newInstance()
+        translation_filter.imp = imp
+        translation_filter.shifts = shifts
+        pfr = PlugInFilterRunner(translation_filter, "", "" )
+        ret = translation_filter.output
+    else:
+        translation_filter = TranslationFilter()
+        translation_filter.shifts = shifts
+        translation_filter.imp = stack
+        pfr = PlugInFilterRunner(translation_filter, "", "" )
+        ret = translation_filter.output     
+    if show:
+        ret.show()
+        ret.updateAndDraw()
+    return ret
+
+
+def load_shifts(filename):
+    get_context().getPluginManager().loadInitializePlugin("ShiftsIO.java")
+    sio = get_context().getClassByName("ShiftsIO").newInstance()
+    return sio.load(expand_path(filename), "directshifts")
+
+def save_shifts(filename, shifts):
+    get_context().getPluginManager().loadInitializePlugin("ShiftsIO.java")
+    sio = get_context().getClassByName("ShiftsIO").newInstance()
+    sio.save(expand_path(filename), shifts, "directshifts")
+
+
+def ip_to_fft_array_2d(ip):
+    pixels = ip.getPixels()
+    w = ip.getWidth()
+    h = ip.getHeight()
+    data = new_array('d', h, w)  # new double[h][w]
+    for j in range(h):  # (int j = 0; j < h; j++)
+        for i in range(w):  # for (int i = 0; i < w; i++)
+            data[j][i] = pixels[j * w + i]
+    return data
+
+
+def ip_to_fft_complex_array_2d(ip_r, ip_i):
+    pixels_r = ip_r.getPixels()
+    pixels_i = ip_i.getPixels()
+    w = ip_r.getWidth()
+    h = ip_r.getHeight()
+    data = new_array('d', h, 2 * w)  # new double[h][2*w];
+    for j in range(h):  # (int j = 0; j < h; j++)
+        for i in range(w):  # for (int i = 0; i < w; i++)
+            data[j][2 * i] = pixels_r[j * w + i]
+            data[j][2 * i + 1] = pixels_i[j * w + i];
+    return data
+
+def fft_array_2d_to_complex_matrix(data, h, w):
+    m = ComplexMatrix(h,w)
+    for j in range(h): #for (int j = 0; j < h; j++) {
+        for i in range(w/2): # for (int i = 0; i <= w/2; i++) {
+            if (j > 0) and (i > 0) and (i < w/2): 
+                    m.setElement(j, i, Complex(data[j][2*i], data[j][2*i+1]))
+                    m.setElement(h-j, w-i, Complex(data[j][2*i], -data[j][2*i+1]))
+            if (j == 0) and (i > 0) and (i < w/2):
+                m.setElement(0, i, Complex(data[0][2*i], data[0][2*i+1]))
+                m.setElement(0, w-i, Complex(data[0][2*i], -data[0][2*i+1]))
+            if (i == 0) and (j > 0) and (j < h/2):
+                m.setElement(j,0, Complex(data[j][0], data[j][1]))
+                m.setElement(h-j, 0, Complex(data[j][0], -data[j][1]))
+                m.setElement(j, w/2, Complex(data[h-j][1], -data[h-j][0]))
+                m.setElement(h-j, w/2, Complex(data[h-j][1], data[h-j][0]))
+            if (j == 0) and (i == 0):
+                m.setElement(0, 0, Complex(data[0][0], 0));
+            if (j == 0) and (i == w/2):
+                m.setElement(0, w/2, Complex(data[0][1], 0));
+            if (j == h/2) and (i == 0):
+                m.setElement(h/2, 0, Complex(data[h/2][0], 0));
+            if (j == h/2) and (i == w/2):
+                m.setElement(h/2, w/2, Complex(data[h/2][1], 0));
+    return m
+
+
+def fft_complex_array_2d_to_complex_matrix(data, h, w):
+    m = ComplexMatrix(h,w);
+    for j in range(h): #for (int j = 0; j < h; j++) {
+        for i in range(w): # for (int i = 0; i < w; i++) {
+            m.setElement(j,i, Complex(data[j][2*i], data[j][2*i+1]))
+    return m
+
+def complex_matrix_to_fft_array_2d(m):
+    w = m.getNcol()
+    h = m.getNrow()
+    data = new_array('d', h,w) #new double[h][w];
+    for j in range(h): #for (int j = 0; j < h; j++) {
+        for i in range(w): #for (int i = 0; i <= w/2; i++) {
+            if (j > 0) and (i > 0) and (i < w/2):
+                    data[j][2*i] = m.getElementReference(j,i).getReal()
+                    data[j][2*i+1] = m.getElementReference(j,i).getImag()
+            if (j == 0) and (i > 0) and (i < w/2):
+                data[0][2*i] = m.getElementReference(0,i).getReal()
+                data[0][2*i+1] = m.getEementReference(0,i).getImag()
+            if (i == 0) and (j > 0) and (j < h/2):
+                data[j][0] = m.getElementReference(j,0).getReal()
+                data[j][1] = m.getElementReference(j,0).getImag()
+                data[h-j][1] = m.getElementReference(j,w/2).getReal()
+                data[h-j][0] = m.getElementReference(h-j,w/2).getImag()    
+            if (j == 0) and (i == 0):
+                data[0][0] = m.getElementReference(0,0).getReal()
+            if (j == 0) and (i == w/2):
+                data[0][1] = m.getElementReference(0,w/2).getReal()
+            if (j == h/2) and (i == 0):
+                data[h/2][0] = m.getElementReference(h/2,0).getReal()
+            if (j == h/2) and ( i == w/2):
+                data[h/2][1] = m.getElementReference(h/2,w/2).getReal()
+    return data
+
+
+# convert a Complex Matrix into an 2d real part array data[0][][] and 2d imaginary part data[1][][]
+def complex_matrix_to_real_array_2d(m):
+    w = m.getNcol()
+    h = m.getNrow()
+    data = new_array('d', 2,h,w) #new double[2][h][w];
+    for j in range(h): #for (int j = 0; j < h; j++) {
+        for i in range(w): #for (int i = 0; i < w; i++) {
+            data[0][j][i] = m.getElementReference(j,i).getReal()
+            data[1][j][i] = m.getElementReference(j,i).getImag()
+    return data;
+
+
+def compute_fft(imp_r, imp_i, roi):
+    slices = imp_r.getStackSize()
+    ffts = java.lang.reflect.Array.newInstance(ComplexMatrix, slices)  # new ComplexMatrix[slices]
+    for i in range(1, slices + 1):
+        if imp_i is None:
+            ip = imp_r.getStack().getProcessor(i)
+            ip.setRoi(roi)
+            curr = ip.crop().convertToFloat();
+            data = ip_to_fft_array_2d(curr)
+            ffts[i - 1] = fft2(data)
+        else:
+            ip1 = imp_r.getStack().getProcessor(i)
+            ip1.setRoi(roi)
+            curr_r = ip1.crop().convertToFloat()
+            ip2 = imp_i.getStack().getProcessor(i)
+            ip2.setRoi(roi)
+            curr_i = ip2.crop().convertToFloat()
+            data = ip_to_fft_complex_array_2d(curr_r, curr_i)
+            ffts[i - 1] = cfft2(data)
+        IJ.showProgress(i, slices)
+    return ffts
+
+
+def element_product(a, b):
+    nr = a.getNrow()
+    nc = a.getNcol()
+    res = ComplexMatrix(nr, nc)
+    for j in range(nr):  # (int j = 0; j < nr; j++) {
+        for i in range(nc):  # (int i = 0; i < nc; i++) {
+            res.setElement(j, i, a.getElementReference(j, i).times(b.getElementReference(j, i)))
+    return res;
+
+
+def fft_shift(complex_matrix):
+    nc = complex_matrix.getNcol()
+    nr = complex_matrix.getNrow()
+    out = ComplexMatrix(nr, nc)
+    midi = int(math.floor(nc / 2.0))
+    offi = int(math.ceil(nc / 2.0))
+    midj = int(math.floor(nr / 2.0))
+    offj = int(math.ceil(nr / 2.0))
+    for j in range(nr):  # for (int j = 0; j < nr; j ++){
+        for i in range(nc):  # for (int i = 0; i < nc; i++) {
+            if j < midj:
+                if i < midi:
+                    out.setElement(j, i, complex_matrix.getElementReference(j + offj, i + offi))
+                else:
+                    out.setElement(j, i, complex_matrix.getElementReference(j + offj, i - midi))
+            else:
+                if i < midi:
+                    out.setElement(j, i, complex_matrix.getElementReference(j - midj, i + offi))
+                else:
+                    out.setElement(j, i, complex_matrix.getElementReference(j - midj, i - midi))
+    return out
+
+
+def ifft_shift(complex_matrix):
+    nc = complex_matrix.getNcol()
+    nr = complex_matrix.getNrow()
+    out = ComplexMatrix(nr, nc)
+    midi = int(math.ceil(nc / 2.0))
+    offi = int(math.floor(nc / 2.0))
+    midj = int(math.ceil(nr / 2.0))
+    offj = int(math.floor(nr / 2.0))
+
+    for j in range(nr):  # (int j = 0; j < nr; j ++){
+        for i in range(nc):  # for (int i = 0; i < nc; i++) {
+            if j < midj:
+                if i < midi:
+                    out.setElement(j, i, complex_matrix.getElementReference(j + offj, i + offi))
+                else:
+                    out.setElement(j, i, complex_matrix.getElementReference(j + offj, i - midi))
+            else:
+                if i < midi:
+                    out.setElement(j, i, complex_matrix.getElementReference(j - midj, i + offi))
+                else:
+                    out.setElement(j, i, complex_matrix.getElementReference(j - midj, i - midi))
+    return out;
+
+
+def ifft_shift_real(matrix):
+    nc = matrix.getNcol()
+    nr = matrix.getNrow()
+    out = Matrix (nr, nc)
+
+    midi = int(math.ceil(nc/2.0))
+    offi = int(math.floor(nc/2.0))
+    midj = int(math.ceil(nr/2.0))
+    offj = int(math.floor(nr/2.0))
+    
+    for j in range(nr):  # for (int j = 0; j < nr; j ++){
+        for i in range(nc): #for (int i = 0; i < nc; i++) {
+            if j < midj:
+                if i < midi:
+                    out.setElement(j, i, matrix.getElement(j+offj, i+offi))
+                else:
+                    out.setElement(j, i, matrix.getElement(j+offj, i-midi))       
+            else:
+                if i < midi:
+                    out.setElement(j, i, matrix.getElement(j-midj, i+offi))
+                else:
+                    out.setElement(j, i, matrix.getElement(j-midj, i-midi))        
+    return out
+
+
+
+# compute 2D fft from an image
+def fft2(data):
+    h =len(data)
+    w = len(data[0])
+    fft = DoubleFFT_2D(h, w)
+    fft.realForward(data)
+    return fft_array_2d_to_complex_matrix(data, h, w)
+
+# compute complex 2D fft from an image
+def cfft2(data):
+    h = len(data)
+    w = len(data[0])
+    fft = DoubleFFT_2D(h, w/2)
+    fft.complexForward(data)
+    return fft_complex_array_2d_to_complex_matrix(data, h, w/2)
+# compute inverse 2D fft from a complex matrix
+def ifft2(m):
+    w = m.getNcol()
+    h = m.getNrow()
+    fft = DoubleFFT_2D(h, w)
+    data = complex_matrix_to_fft_array_2d(m)
+    fft.realInverse(data, True)
+    return data
+    
+# compute complex inverse 2D fft from a complex matrix
+def cifft2(m):
+    w = m.getNcol()
+    h = m.getNrow()
+    fft = DoubleFFT_2D(h, w)
+    data = new_array('d', h, 2 * w)  # new double[h][2*w];
+    for j in range(h):  # for (int j=0; j<h; j++):
+        for i in range(w):  # for (int i=0; i<w; i++) {
+            data[j][2 * i] = m.getElementReference(j, i).getReal()
+            data[j][2 * i + 1] = m.getElementReference(j, i).getImag()
+    fft.complexInverse(data, True)
+    out = ComplexMatrix(h, w)
+    for j in range(h):  # (int j=0; j<h; j++) {
+        for i in range(w):  # (int i=0; i<w; i++) {
+            out.setElement(j, i, data[j][2 * i], data[j][2 * i + 1])
+    return out;
+
+
+def c_find_peak(m):
+    max = 0.0
+    realmax = 0.0
+    imagmax = 0.0
+    cmax = 0
+    rmax = 0
+    for j in range(m.getNrow()):  # (int j = 0; j < m.getNrow(); j ++){
+        for i in range(m.getNcol()):  # for (int i = 0; i < m.getNcol(); i++) {
+            if m.getElementReference(j, i).abs() > max:
+                max = m.getElementReference(j, i).abs()
+                realmax = m.getElementReference(j, i).getReal()
+                imagmax = m.getElementReference(j, i).getImag()
+                rmax = j
+                cmax = i
+    res = new_array("d", 5)
+    res[0] = math.sqrt(realmax * realmax + imagmax * imagmax)
+    res[1] = rmax
+    res[2] = cmax
+    res[3] = realmax
+    res[4] = imagmax
+    return res;
+
+
+def sum_square_abs(m):
+    s = 0.0
+    for j in range(m.getNrow()):  # (int j = 0; j < m.getNrow(); j ++):
+        for i in range(m.getNcol()):  # for (int i = 0; i < m.getNcol(); i++):
+            s += m.getElementReference(j, i).squareAbs();
+    return s;
+
+
+def dftups(complex_matrix, nor, noc, roff, coff, usfac):
+    # function out=dftups(in,nor,noc,usfac,roff,coff);
+    # Upsampled DFT by matrix multiplies, can compute an upsampled DFT in justa small region.
+    # usfac         Upsampling factor (default usfac = 1)
+    # [nor,noc]     Number of pixels in the output upsampled DFT, in
+    #               units of upsampled pixels (default = size(in))
+    # roff, coff    Row and column offsets, allow to shift the output array to
+    #               a region of interest on the DFT (default = 0)
+    # Recieves DC in upper left corner, image center must be in (1,1)
+    # Loic Le Guyader - Jun 11, 2011 Java version for ImageJ plugin
+    # Manuel Guizar - Dec 13, 2007
+    # Modified from dftus, by J.R. Fienup 7/31/06
+
+    # This code is intended to provide the same result as if the following
+    # operations were performed
+    #   - Embed the array "in" in an array that is usfac times larger in each
+    #     dimension. ifftshift to bring the center of the image to (1,1).
+    #   - Take the FFT of the larger array
+    #   - Extract an [nor, noc] region of the result. Starting with the
+    #     [roff+1 coff+1] element.
+
+    # It achieves this result by computing the DFT in the output array without
+    # the need to zeropad. Much faster and memory efficient than the
+    # zero-padded FFT approach if [nor noc] are much smaller than [nr*usfac nc*usfac]
+
+    nr = complex_matrix.getNrow()
+    nc = complex_matrix.getNcol()
+    # Compute kernels and obtain DFT by matrix products
+    amplitude = -2.0 * math.pi / (nc * usfac)
+    nor,noc=int(nor),int(noc)
+    u = Matrix(nc, 1)
+    for i in range(nc):  # (int i = 0; i < nc; i++) {
+        u.setElement(i, 0, i - math.floor(nc / 2.0))
+    u = ifft_shift_real(u)
+
+    v = Matrix(1, noc)
+    for i in range(noc):  # for (int i = 0; i < noc; i++) {
+        v.setElement(0, i, i - coff)
+
+    phase = u.times(v)
+    kernc = ComplexMatrix(nc, noc)
+    for j in range(nc):  # for (int j = 0; j < nc; j++) {
+        for i in range(noc):  # for (int i = 0; i < noc; i++)  {
+            t = Complex()
+            t.polar(1.0, amplitude * phase.getElement(j, i));
+            kernc.setElement(j, i, t)
+
+    # ComplexMatrixPrint(kernc)
+    amplitude = -2.0 * math.pi / (nr * usfac)
+
+    w = Matrix(nor, 1)
+    for i in range(nor):  # for (int i = 0; i < nor; i++) {
+        w.setElement(i, 0, i - roff)
+
+    x = Matrix(1, nr)
+    for i in range(nr):  # for (int i = 0; i < nr; i++) {
+        x.setElement(0, i, i - math.floor(nr / 2.0))
+    x = ifft_shift_real(x)
+
+    nphase = w.times(x);
+    kernr = ComplexMatrix(nor, nr)
+    for j in range(nor):  # for (int j = 0; j < nor; j++) {
+        for i in range(nr):  # for (int i = 0; i < nr; i++) {
+            t = Complex();
+            t.polar(1.0, amplitude * nphase.getElement(j, i))
+            kernr.setElement(j, i, t)
+    # ComplexMatrixPrint(kernr);
+    return kernr.times(complex_matrix.times(kernc))
+    
+def dft_registration(ref, drifted, usfac):
+    m = ref.getNrow()
+    n = ref.getNcol()
+    output = new_array('d', 4)  # new double[4]
+
+    # First upsample by a factor of 2 to obtain initial estimate
+    # Embed Fourier data in a 2x larger array
+    mlarge = m * 2
+    nlarge = n * 2
+    large = ComplexMatrix(mlarge, nlarge)
+    c = fft_shift(element_product(ref, drifted.conjugate()))
+
+    for j in range(m):  # (int j = 0; j < m; j++):
+        for i in range(n):  # (int i = 0; i < n; i++):
+            large.setElement(int(j + m - math.floor(m / 2.0)), int(i + n - math.floor(n / 2.0)), c.getElementReference(j, i))
+
+    # Compute crosscorrelation and locate the peak
+    CC = cifft2(ifft_shift(large));
+    peak = c_find_peak(CC);  # max, r, c, max_r, max_c 
+    # Obtain shift in original pixel grid from the position of the
+    # crosscorrelation peak
+    if peak[1] > m:
+        peak[1] = peak[1] - mlarge;
+    if peak[2] > n:
+        peak[2] = peak[2] - nlarge; 
+        # If upsampling > 2, then refine estimate with matrix multiply DFT
+    if usfac > 2:
+        # DFT computation
+        # Initial shift estimate in upsampled grid
+        row_shift = round(peak[1] / 2.0 * usfac) / usfac
+        col_shift = round(peak[2] / 2.0 * usfac) / usfac
+        dftshift = math.floor(math.ceil(usfac * 1.5) / 2)  # Center of output array at dftshift+1
+        # Matrix multiply DFT around the current shift estimate
+        cm = element_product(drifted, ref.conjugate())
+        nCC = dftups(cm, math.ceil(usfac * 1.5), math.ceil(usfac * 1.5), \
+                     dftshift - row_shift * usfac, dftshift - col_shift * usfac, usfac)
+        nCC = nCC.times(1.0 / (m * n * usfac * usfac)).conjugate()
+        # Locate maximum and map back to original pixel grid
+        npeak = c_find_peak(nCC)  # max_r, max_i, r, c
+        mrg00 = dftups(element_product(ref, ref.conjugate()), 1, 1, 0, 0, usfac)
+        rg00 = mrg00.getElementReference(0, 0).abs() / (m * n * usfac * usfac)
+        mrf00 = dftups(element_product(drifted, drifted.conjugate()), 1, 1, 0, 0, usfac)
+        rf00 = mrf00.getElementReference(0, 0).abs() / (m * n * usfac * usfac)
+        npeak[1] = npeak[1] - dftshift
+        npeak[2] = npeak[2] - dftshift
+        output[0] = math.sqrt(abs(1.0 - npeak[0] * npeak[0] / (rg00 * rf00)))  # error
+        output[1] = math.atan2(npeak[4], npeak[3])  # diffphase
+        output[2] = row_shift + npeak[1] / usfac  # delta row
+        output[3] = col_shift + npeak[2] / usfac  # delta col
+    else:
+        # If upsampling = 2, no additional pixel shift refinement
+        rg00 = sum_square_abs(ref) / (mlarge * nlarge)
+        rf00 = sum_square_abs(drifted) / (mlarge * nlarge)
+        output[0] = math.sqrt(abs(1.0 - peak[0] * peak[0] / (rg00 * rf00)))  # error
+        output[1] = math.atan2(peak[4], peak[3])  # diffphase
+        output[2] = peak[1] / 2.0  # delta row
+        output[3] = peak[2] / 2.0  # delta col
+    return output
+
+    
+def calculate_shifts(imp_r, imp_i, roi, upscale_factor=100, reference_slide=1, java_code=False):
+    if roi is None or roi.bounds.minX <0 or roi.bounds.minY<0 or roi.bounds.maxX>=imp_r.width or roi.bounds.maxY>=imp_r.height:
+        raise Exception("Invalid roi: " + str(roi))
+    if java_code:
+        get_context().getPluginManager().loadInitializePlugin("Align_ComputeShifts.java")
+        compute_shifts_filter = get_context().getClassByName("Align_ComputeShifts").newInstance()
+        compute_shifts_filter.setup(upscale_factor, False, imp_r, imp_i, 1, roi)
+        compute_shifts_filter.run(None)
+        return compute_shifts_filter.shifts
+    
+    IJ.showStatus("1/2 Perform FFT of each slice")
+    ffts = compute_fft(imp_r, imp_i, roi)
+
+    # calculate shifts
+    IJ.showStatus("2/2 Calculate shifts between slices")
+
+    shifts = new_array('d', len(ffts), 6)  # new double[ffts.length][6];
+    for i in range(len(ffts)):  # (int i = 0; i < ffts.length; i++):        
+        shifts[i][0] = reference_slide
+        shifts[i][1] = i + 1
+        temp = dft_registration(ffts[reference_slide - 1], ffts[i], upscale_factor)        
+        shifts[i][2] = temp[2]
+        shifts[i][3] = temp[3]
+        shifts[i][4] = temp[0]
+        shifts[i][5] = temp[1]
+        IJ.showProgress(i + 1, len(ffts))\   
+    return shifts  # [ref, drifted, dr, dc, error, diffphase]
+
+def to_ip(obj):
+    if is_string(obj):
+        try:
+            obj = open_image(obj)
+        except: 
+            obj = load_image(obj)
+    else:
+        if type(obj) == Data:
+            obj = obj.toBufferedImage(False)
+        if type(obj) == BufferedImage:
+            obj = load_image(obj)
+    return obj
+
+#TODO: Check maximum error and phase diff values
+def calculate_shift(ref,img, roi, g_sigma=3.0, upscale_factor=100, max_error=2.0, max_diffphase=0.1):
+    ref = to_ip(ref)
+    img = to_ip(img)      
+    stack = create_stack([ref,img])
+    ipr, ipi = complex_edge_filtering(stack, g_sigma=g_sigma, show=False) 
+    shifts = calculate_shifts(ipr, ipi, roi, upscale_factor=upscale_factor, java_code=True)
+    xoff, yoff =  shifts[1][3], shifts[1][2]
+    error, diffphase =  shifts[1][4], shifts[1][5]
+    if math.isnan(error) or abs(error)> max_error:
+        raise Exception("Bad image registration error: " + str(error))
+    if math.isnan(diffphase) or abs(diffphase)> max_diffphase:
+        raise Exception("Bad image registration phase difference: " + str(diffphase))
+    return xoff, yoff, error, diffphase
+

script/local.py

@@ -8,6 +8,7 @@ from mathutils import estimate_peak_indexes, fit_gaussians, create_fit_point_lis
 from mathutils import fit_polynomial,fit_gaussian, fit_harmonic, calculate_peaks
 from mathutils import PolynomialFunction, Gaussian, HarmonicOscillator
 from collections import OrderedDict
+run ("imaging/shifts")
 
 ProviderCSV.setDefaultItemSeparator(", ")
 get_context().dataManager.createLogs=False
@@ -48,6 +49,14 @@ TIME_DELAY_COMPLETE = "X11MA-ES2-scan1.SMSG"
 TBT_MAG = "X11MA-LSCI632:MFIELD"
 "
 """
+
+
+#Device initialization
+keithley_1a.setForcedRead(False)
+keithley_2a.setForcedRead(False)
+keithley_3a.setForcedRead(False)
+
+
 def get_next_fid(folder, prefix):
     try:
         import glob   
@@ -240,10 +249,8 @@ def otf(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None,
 def otf2(start, end, time, delay = 0.0, mode = None, offset = None, alpha = None, name = None, folder = 'TEST'):
     """
     """    
-    if name is None:
-        name = get_exec_pars().name
     #folder = get_context().setup.expandPath("{year}_{month}/{date}");    
-    run("templates/EnergyScan_v2", {"E1":start, "E2":end, "TIME":time, "DELAY":float(delay), "MODE":mode, "OFFSET":(offset), "FOLDER":folder, "FILE":name, "ALPHA":float(alpha) if alpha is not None else None})    
+    run("templates/EnergyScan_v2", {"E1":start, "E2":end, "TIME":time, "DELAY":float(delay), "MODE":mode, "OFFSET":(offset), "FOLDER":folder, "FILE":name, "TAG":name, "ALPHA":float(alpha) if alpha is not None else None})    
 
 
 def two_pol(switching="Tune_Detune", sequence="A", measurements=1, exposure=1.0, average=1, name = None):
@@ -738,7 +745,10 @@ def fit(ydata, xdata = None, limit_to_range=False):
         if limit_to_range:
             print "Max -> " +  str(max_x)
             p.addMarker(max_x, None, "Max="+str(round(max_x,2)), Color.MAGENTA.darker())
-            return (None , max_x, None)        
+            return (None , max_x, None)     
+        else:
+            print "Fit error"
+            return (None, None, None)                 
     (norm, mean, sigma) = gaussians[0]
     print " mean:" + str(mean)    
     fitted_gaussian_function = Gaussian(norm, mean, sigma)

script/old_scripts/EnergyScanID2only_juraj.py

@@ -1,185 +0,0 @@
-import os
-import traceback
-import thread
-
-###############################################################################
-# Plotting
-###############################################################################
-
-task = None
-running = False
-
-
-def _startPlot(type):
-    global running
-    print "Starting plot: type " + str(type)
-    running = True
-    p = plot(None,name="Energy")[0]
-    s = p.getSeries(0)
-    cur = 0
-    time.sleep(3.0)
-    while running: 
-        try:
-            if  otf_start.read() == 0:
-                break
-            e = energy.read()
-            if (abs(e-cur)) > 0.1:            
-                v = abs((keithley_2a.read() / ((keithley_1a if (type==1) else keithley_3a).read() )))
-                s.appendData(e,v)    
-                cur = e                                  
-            time.sleep(0.2)
-        except:
-            pass
-    print "Done Plotting"
-  
-def startPlot(type = 1):
-    global task
-    task = fork((_startPlot,(type,)),)        
-
-def stopPlot():
-    global task, running
-    running = False
-    ret = join(task)
-
-###############################################################################
-# Parameters
-###############################################################################
-
-
-E1 = 634
-E2 = 660
-TIME = 4.0 #min
-DELAY = 1.0 #s
-#PREFIX = 'Data'
-RUNTYPE = "+/-"
-ROUNDS = 1
-OFFSETp = -1.9
-OFFSETm = -1.9
-PLOT_TYPE = 1
-
-caput ("X11PHS-E:OPT","PGM+ID2")
-
-print "\nStarting energy scan - Parameters: ",
-print E1,E2,TIME,DELAY,RUNTYPE
-
-file_prefix = time.strftime("%y%m%d")
-#input_path =  "/sls/X11MA/data/X11MA/fechner_beamtime/"+file_prefix+"/"
-input_path =  "/sls/X11MA/data/X11MA/pshell/home/data/2017_12/juraj/"
-output_path = input_path #+file_prefix+"/" #"/sls/X/pshell/home/data/2017_12/juraj11MA/Data1/public/e10989/"+file_prefix+"/"
-pol_str = None
-mag_str = None
-fid = get_next_fid(input_path, "o" + file_prefix)
-number_of_scans = 1
-
-    
-wait_channel(OTF_DONE, 1, type = 'i')
-
-
-###############################################################################
-#Prepare scan for PGM+ID2
-###############################################################################
-
-caput ("X11PHS-E:OPT","PGM+ID2")
-#caput(OTF_OFF1,-40) #detune ID2
-#wait_channel(OTF_DONE, 1, type = 'i')/sls/X11MA/datmokuser/
-
-if RUNTYPE in ["+/-", "+", "-"]:
-    if RUNTYPE == "+":
-        caput(OTF_MODE2,1) # circ+ in ID2
-        caput(OTF_OFF2,OFFSETp)
-        number_of_scans = ROUNDS
-    elif RUNTYPE == "-":
-        caput(OTF_MODE2,2) # circ- in ID2
-        caput(OTF_OFF2,OFFSETm)
-        number_of_scans = ROUNDS
-    elif RUNTYPE == "+/-":
-        caput(OTF_MODE2,1) # circ+ in ID2
-        caput(OTF_OFF2,OFFSETp)
-        number_of_scans = 2 * ROUNDS
-    wait_channel(OTF_DONE, 1, type = 'i')
-
-elif RUNTYPE in ["LH/LV", "LH", "LV"]:
-    print "Wrong polarization selected!"
-    
-
-else:
-    raise Exception("Invalid run type: " +  RUNTYPE)
-
-#open_vg10()
-#time.sleep(0.5)
-#open_vg11()
-#time.sleep(0.5)
-#open_vg12()
-#time.sleep(0.5)
-open_vg13()
-
-###############################################################################
-#Main scan loop
-###############################################################################
-
-for scan_no  in range(number_of_scans):
-    suffix = ("%03d" % fid)
-    input_file = input_path + "o" + file_prefix + "_" + suffix + ".dat" 
-
-    caput(OTF_E1, E1)
-    caput(OTF_E2, E2)
-    caput(OTF_TIME, TIME)
-    caput(OTF_FTS,file_prefix)
-    caput(OTF_FID,fid)
-    time.sleep(2.0) 
-    caput(OTF_ESET, E1)
-    wait_channel(OTF_DONE, 1, type = 'i')
-    time.sleep(DELAY)    
-    time.sleep(2.0)
-
-    startPlot(PLOT_TYPE)
-    otf_start.write(1) #Start the OTF scan
-    time.sleep(3.0)
-    print "Running scan " + str(scan_no+1) + " out of " + str(number_of_scans)
-    try:
-        #wait_channel(OTF_START, 'STOP', timeout = int(TIME*60), type = 's')
-        otf_start.waitValue(0, (15 + int(TIME*60)) *1000)        
-    except:
-        print "********    OTF STOP TIMEOUT   **********"
-        otf_start.write(0)    
-    finally:
-        stopPlot()
-    
-    time.sleep(5.0)
-    #TODO: wait for file instead of sleep
-    #Convert file
-    output_file = output_path + "os" + file_prefix + "_" + suffix + ".dat"
-
-   
-    
-    if RUNTYPE in ["+/-"]:
-        pol_str = caget(OTF_MODE2)
-        if pol_str == "CIRC +":
-           caput(OTF_MODE2,2) # circ- in ID2
-           caput(OTF_OFF2,OFFSETm)
-        elif pol_str == "CIRC -":
-            caput(OTF_MODE2,1) # circ+ in ID2
-            caput(OTF_OFF2,OFFSETp)
-        else: print "Check pol. change"
-        wait_channel(OTF_DONE, 1, type = 'i')
-    else:
-        print "running in one polarization mode, no switching"
-        pol_str = caget(OTF_MODE2)
-
-    print("Converting data file: " + output_file);     
-    mag_str = caget(MAG)          
-    #convert_file(input_file, output_file, mag_str, pol_str)
-    convert_file(input_file, output_file, mag_str, pol_str) #  tey and tfy saved - not normalized
-    plot_file(output_file, file_prefix+"_" + suffix) #"Scan " + str(scan_no+1))
-    print "Finished scan " + str(scan_no+1) + " out of " + str(number_of_scans)
-        
-    time.sleep(3.0)
-    fid = fid + 1
-   
-caput(OTF_ESET, E1) 
-#close_vg13()
-
-print "Finished Energy scan"
-
-print("Success") 
-       

script/templates/EnergyScan_v2.py

@@ -9,6 +9,7 @@ OFFSET = 0.0
 FOLDER = 'XAS/2020/11/SL-IN/'
 FILE = 'test'
 ALPHA=0.0
+TAG=None
 """
 
 print "\nStart energy scan..."
@@ -19,7 +20,11 @@ else:
     print E1,"eV ->",E2,"eV,",TIME,"min duration,",DELAY,"sec delay,",str(MODE)
 
 folder = os.path.expanduser("~/Data1/") + FOLDER + "/";
-set_exec_pars(name= FILE)
+
+if TAG is not None:
+    TAG = ("%03d" % (get_exec_pars().index,)) + "_" + TAG
+#set_exec_pars(name= FILE)
+
 
 #Pre-actions
 #if NO_BEAM_CHECK == False:  
@@ -84,7 +89,7 @@ try:
     
     print "Scanning...",               
     try:    
-        mscan(Ecrbk, sensors, -1, None, range="auto", domain_axis="Ecrbk", enabled_plots = ["NORMtey", "NORMdiode", CADC1,CADC3, CADC2], )
+        mscan(Ecrbk, sensors, -1, None, range="auto", domain_axis="Ecrbk", enabled_plots = ["NORMtey", "NORMdiode", CADC1,CADC3, CADC2], tag=TAG)
     finally:        
         ret[0].cancel(True)        
     print "Finished Energy scan."    

script/test/ExitSlitCalib.py

@@ -0,0 +1,83 @@
+################################################################################################### 
+# Function fitting and peak search with mathutils.py
+################################################################################################### 
+
+from mathutils import fit_polynomial
+from mathutils import PolynomialFunction
+
+# Input parameters
+Slit = exit_slit
+Slit_offset = exit_slit_offset
+
+start = 30.0
+end = -20.0
+step_size = 1.0
+settling_time= 1.0 #Slits need 1s to accept next command
+final_pos = 20.0
+
+#setting parameters
+caput('X11MA-KEI10:RANGE', 6) # 6 --> 200 nA
+Slit.move(start)
+#Slit.
+
+if(Slit==exit_slit):
+    speed = Slit.getSpeed()
+    min_speed=Slit.getMinSpeed() 
+    Slit.setSpeed(min_speed)
+
+time.sleep(1)
+
+# Execute the scan
+result=cscan(Slit, keithley_1a, start, end, float(step_size))
+
+readable_ = result[keithley_1a]
+positions_ = result[Slit]
+print positions_
+readable=[]
+positions=[]
+
+# execute the fit
+fit_threshold=readable_[0]*0.05
+
+#filter the positions with analog values above the threshold
+for i in range(8,len(positions_),1):
+    if(readable_[i]>fit_threshold):
+        readable.append(readable_[i])
+        positions.append(positions_[i])
+
+
+
+pars_polynomial = (a0, a1) = fit_polynomial(readable, positions,1)
+fitted_polynomial_function = PolynomialFunction(pars_polynomial)
+print pars_polynomial
+
+
+resolution = step_size/100
+fit_polinomial = []
+
+# from the fit function calculate the values at the positions
+for x in frange(end,start,resolution, True):
+    fit_polinomial.append(fitted_polynomial_function.value(x))
+x = frange(end, start+resolution, resolution)
+
+# crate plots
+plots = plot([readable_, fit_polinomial] , ["data", "polinomial"], xdata = [positions_,x], title="Data")
+p = plot(None,name="Data 1")[0]
+p.addSeries(LinePlotSeries("Data2"))
+p.getSeries(0).setData(positions_, readable_)
+p.getSeries(1).setData(x, fit_polinomial)
+
+#calculate the position where the line crosses zero
+k=-pars_polynomial[0]/pars_polynomial[1]
+print k
+
+#change the offset
+offset=Slit_offset.read()
+Slit_offset.write(offset+k)
+
+#resetting parameters
+caput('X11MA-KEI10:RANGE', 0) # 0--> AUTO
+if(Slit == exit_slit):
+    Slit.setSpeed(speed)
+Slit.write(final_pos)
+

script/test/LEEM_example_scans.py

@@ -1,19 +1,38 @@
 #ascan ([manip_x,manip_y],machine_cur, [-950,900], [-960,910], [5.0,5.0], latency=1.0,zigzag=True, save=False)
 
-RANGE_V = [-2000, 2000]
-RANGE_H = [-2000, 2000]
-STEP_V = 500.0
-STEP_H = 500.0
+RANGE_V = [-500, 500]
+RANGE_H = [-500, 500]
+STEP_V = 100.0
+STEP_H = 100.0
 SETTLING_TIME = 1.0
 
+
+class LeemRoiIntensity (ImageMeasurement):
+    def __init__(self, x,y,w,h):
+        ImageMeasurement.__init__(self, image2,  "roi"+ str([x,y,w,h]))
+        self.x, self.y, self.w, self.h, =  x,y,w,h
+    def calc(self, data):
+        return data.getRoi(Rectangle(self.x, self.y, self.w, self.h)).integrate(False)
+       
+
+microscope.move_timeout=240000
+
 #We start at 0,0 absolute position
 tilt_vertical.initialize()
 tilt_horizontal.initialize()
 
+roi_intensity = LeemRoiIntensity(550,420, 150, 150)
+set_device_alias(image2.intensity, "CameraIntensity")    
+set_device_alias(roi_intensity, "ROI_Intensity")    
+sensors = [machine_cur, image2.intensity, roi_intensity]
+
+def before_read(pos,scan):
+    image2.update()
+    
 try:
-    ascan ( [tilt_horizontal, tilt_vertical], machine_cur, \
+    ascan ( [tilt_horizontal, tilt_vertical], sensors, \
             [RANGE_H[0], RANGE_V[0]], [RANGE_H[1], RANGE_V[1]], [float(STEP_H), float(STEP_V)], \
-            latency=SETTLING_TIME,zigzag=True, save=True)
+            latency=SETTLING_TIME,zigzag=True, save=True, before_read=before_read)
 
 finally:
     tilt_vertical.write(0)

script/test/TestBasler.py

@@ -0,0 +1,33 @@
+class BaslerRoiIntensity (ImageMeasurement):
+    def __init__(self, x,y,w,h):
+        ImageMeasurement.__init__(self, image2,  "roi"+ str([x,y,w,h]))
+        self.x, self.y, self.w, self.h, =  x,y,w,h
+    def calc(self, data):
+        return data.getRoi(Rectangle(self.x, self.y, self.w, self.h)).integrate(False)
+       
+class Profile(ReadableArray):
+    def read(self):
+        return image2.data.integrateHorizontally(False)        
+    def getSize(self):
+        return image2.data.getWidth() 
+        
+def before_read(pos, scan):
+    cam2.start();
+    image2.waitNext(3000)
+
+EXPOSITION = [0.001, 0.002, 0.005, 0.01 , 0.025, 0.05, 0.1, 0.25, 0.5, 1.0]
+def before_pass(pass_id, scan):
+    #exposure = (0.005) * (pass_ids)
+    exposure = EXPOSITION[pass_id-1]
+    while cam2.exposure != exposure:
+        cam2.setExposure(exposure)
+        time.sleep(0.5)
+    print "Exposure = ", exposure
+
+set_device_alias(image2.intensity, "Intensity")    
+p=Profile()
+set_device_alias(p, "Profile_1d")   
+sensors = [image2.intensity, Profile(),p,BaslerRoiIntensity(10,10,20,20)]    
+tscan(sensors, 10, 1.0, passes = 10, \
+    before_read=before_read, before_pass=before_pass, \ 
+    save=False, line_plots=[p])

script/test/TestMscan.py

@@ -0,0 +1,23 @@
+import ch.psi.pshell.scan.ScanAbortedException as ScanAbortedException
+
+
+start = 1
+end = 5
+fe_slit_V_size.move(float(start))
+
+
+fe_slit_V_size.moveAsync(float(end))
+
+readback=fe_slit_V_size.getReadback()
+#Execute the scan: sample undefined number of samples until a condition is met, with auto range
+scan_completed=False
+def after_read(record, scan):
+    global scan_completed
+    if abs(readback.take()-end) < 0.1:
+        print "Stopping"
+        scan_completed=True
+        scan.abort()
+try:
+    r5 = mscan(readback, keithley_1a, -1, after_read=after_read, range="auto")
+except ScanAbortedException as ex:
+    if not scan_completed: raise

script/test/TestShifts.py

@@ -0,0 +1,90 @@
+from ijutils import Roi
+#from sim import *
+import traceback
+run ("imaging/shifts")
+"""
+roi=Roi(256,0,128,128)
+stack = load_test_stack(show=False, size=9)
+ipr, ipi = complex_edge_filtering(stack, show=False) 
+shifts = calculate_shifts(ipr, ipi, roi,  java_code=True)
+#shifts= load_shifts("{images}/TestObjAligner/shifts.mat")
+#stack = load_test_stack(show=True)
+r=translate(stack, shifts, show=True)
+
+ref = "{images}/TestObjAligner/i210517_040#001.tif"
+img = "{images}/TestObjAligner/i210517_041#001.tif"
+#ref = stack.getStack().getProcessor(1)
+#img = stack.getStack().getProcessor(2)
+#roi=Roi(0,0,32, 32)
+#ref=image2.data.getRoi(Rectangle(Point(0,0),image.data.getSize(False)))
+#time.sleep(0.2)
+#img =image.data
+"""
+
+
+def eval_shift(roi, obj=None, stiga=None, stigb=None, wait=3.0):
+    ref = image.data
+    if obj is not None:
+        objective.write(obj)
+    if  stiga is not None:
+        obj_stig_a.write(stiga)
+    if  stigb is not None:
+        obj_stig_b.write(stigb)
+    time.sleep(wait)
+    image.waitNext(10000)
+    img = image.data
+    xoff, yoff, error, diffphase = calculate_shift(ref,img, roi)
+    print "xoff: ", xoff
+    print "yoff: ", yoff
+    print "error: ", error
+    print "diffphase: ", diffphase
+"""    
+roi=Roi(300,240,64,64)
+eval_shift(roi, obj=1493.5)
+eval_shift(roi, obj=1494.8)    
+"""
+
+    
+def eval_shift_obj(roi, obj1, obj2, wait=3.0):
+    cur = objective.read()
+    if abs(obj1-cur) > 0.001:
+        objective.write(obj1)
+        time.sleep(wait)
+        image.waitNext(10000)    
+    ref = image.data
+    objective.write(obj2)
+    time.sleep(wait)
+    image.waitNext(10000)
+    img = image.data
+    xoff, yoff, error, diffphase = calculate_shift(ref,img, roi)
+    print "Ref obj: ", obj1, " img obj: ", obj2
+    print "xoff: ", xoff
+    print "yoff: ", yoff
+    print "error: ", error
+    print "diffphase: ", diffphase
+
+
+def get_roi_overlay():
+    pn=show_panel(image)
+    for ov in pn.overlays:
+        if type(ov) is Overlays.Rect:
+            return ov
+    return None
+
+def get_roi():    
+    #return Roi(300,240,64,64)
+    roi_ov=get_roi_overlay(); 
+    return  Roi(roi_ov.position.x, roi_ov.position.y, roi_ov.width, roi_ov.height)
+     
+def set_roi_size(size):
+    pn=show_panel(image)
+    roi = get_roi_overlay()
+    if roi is None:
+        raise Exception("No ROI defined")
+    roi.width = size
+    roi.height = size
+    pn.refresh()
+    
+#set_roi_size(128)
+eval_shift_obj(get_roi(), 1494.8, 1493.5)
+eval_shift_obj(get_roi(), 1493.5, 1494.8)