From e445af83e913e35f1431a5c4c7a5c74dc0ca0c0e Mon Sep 17 00:00:00 2001
From: Sven <sven.reiche@psi.ch>
Date: Fri, 6 Mar 2026 10:09:14 +0100
Subject: [PATCH] Debug for basic functionality. Use pysdds library to pars
 elegant files.

---
 .idea/workspace.xml   |  88 +++++++++++++++++----------
 ElegantTools.py       |  16 ++++-
 distribution.py       | 137 ++++++++++++++++++++++++------------------
 model.py              |  36 ++++++-----
 plot.py               |   8 +--
 track.py              |  25 ++++----
 ui/ElegantToolsGui.py |  51 +++++++++++-----
 ui/ElegantToolsGui.ui |  69 +++++++++++++++++----
 8 files changed, 283 insertions(+), 147 deletions(-)

diff --git a/.idea/workspace.xml b/.idea/workspace.xml
index 0015300..3f5919a 100644
--- a/.idea/workspace.xml
+++ b/.idea/workspace.xml
@@ -4,7 +4,16 @@
     <option name="autoReloadType" value="SELECTIVE" />
   </component>
   <component name="ChangeListManager">
-    <list default="true" id="0efcf7ff-c00b-4b53-9800-80ad65aeaff9" name="Changes" comment="Fixed to filter for non-existing elements when initializing from a setting file" />
+    <list default="true" id="0efcf7ff-c00b-4b53-9800-80ad65aeaff9" name="Changes" comment="Migrating repo">
+      <change beforePath="$PROJECT_DIR$/.idea/workspace.xml" beforeDir="false" afterPath="$PROJECT_DIR$/.idea/workspace.xml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/ElegantTools.py" beforeDir="false" afterPath="$PROJECT_DIR$/ElegantTools.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/distribution.py" beforeDir="false" afterPath="$PROJECT_DIR$/distribution.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/model.py" beforeDir="false" afterPath="$PROJECT_DIR$/model.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/plot.py" beforeDir="false" afterPath="$PROJECT_DIR$/plot.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/track.py" beforeDir="false" afterPath="$PROJECT_DIR$/track.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/ui/ElegantToolsGui.py" beforeDir="false" afterPath="$PROJECT_DIR$/ui/ElegantToolsGui.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/ui/ElegantToolsGui.ui" beforeDir="false" afterPath="$PROJECT_DIR$/ui/ElegantToolsGui.ui" afterDir="false" />
+    </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
     <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
@@ -18,6 +27,11 @@
     </option>
   </component>
   <component name="Git.Settings">
+    <option name="RECENT_BRANCH_BY_REPOSITORY">
+      <map>
+        <entry key="$PROJECT_DIR$" value="dev" />
+      </map>
+    </option>
     <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
   </component>
   <component name="McpProjectServerCommands">
@@ -32,31 +46,31 @@
     <option name="hideEmptyMiddlePackages" value="true" />
     <option name="showLibraryContents" value="true" />
   </component>
-  <component name="PropertiesComponent"><![CDATA[{
-  "keyToString": {
-    "ModuleVcsDetector.initialDetectionPerformed": "true",
-    "Python.ElegantTools.executor": "Run",
-    "RunOnceActivity.MCP Project settings loaded": "true",
-    "RunOnceActivity.ShowReadmeOnStart": "true",
-    "RunOnceActivity.TerminalTabsStorage.copyFrom.TerminalArrangementManager.252": "true",
-    "RunOnceActivity.git.unshallow": "true",
-    "RunOnceActivity.typescript.service.memoryLimit.init": "true",
-    "SHELLCHECK.PATH": "I do mind",
-    "ai.playground.ignore.import.keys.banner.in.settings": "true",
-    "com.intellij.ml.llm.matterhorn.ej.ui.settings.DefaultModelSelectionForGA.v1": "true",
-    "git-widget-placeholder": "main",
-    "junie.onboarding.icon.badge.shown": "true",
-    "last_opened_file_path": "/home/reiche/Codes/Python/Modelling/ElegantTools",
-    "node.js.detected.package.eslint": "true",
-    "node.js.detected.package.tslint": "true",
-    "node.js.selected.package.eslint": "(autodetect)",
-    "node.js.selected.package.tslint": "(autodetect)",
-    "nodejs_package_manager_path": "npm",
-    "settings.editor.selected.configurable": "com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable",
-    "to.speed.mode.migration.done": "true",
-    "vue.rearranger.settings.migration": "true"
+  <component name="PropertiesComponent">{
+  &quot;keyToString&quot;: {
+    &quot;ModuleVcsDetector.initialDetectionPerformed&quot;: &quot;true&quot;,
+    &quot;Python.ElegantTools.executor&quot;: &quot;Run&quot;,
+    &quot;RunOnceActivity.MCP Project settings loaded&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.ShowReadmeOnStart&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.TerminalTabsStorage.copyFrom.TerminalArrangementManager.252&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.git.unshallow&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.typescript.service.memoryLimit.init&quot;: &quot;true&quot;,
+    &quot;SHELLCHECK.PATH&quot;: &quot;I do mind&quot;,
+    &quot;ai.playground.ignore.import.keys.banner.in.settings&quot;: &quot;true&quot;,
+    &quot;com.intellij.ml.llm.matterhorn.ej.ui.settings.DefaultModelSelectionForGA.v1&quot;: &quot;true&quot;,
+    &quot;git-widget-placeholder&quot;: &quot;main&quot;,
+    &quot;junie.onboarding.icon.badge.shown&quot;: &quot;true&quot;,
+    &quot;last_opened_file_path&quot;: &quot;/home/reiche/Codes/Python/Modelling/ElegantTools&quot;,
+    &quot;node.js.detected.package.eslint&quot;: &quot;true&quot;,
+    &quot;node.js.detected.package.tslint&quot;: &quot;true&quot;,
+    &quot;node.js.selected.package.eslint&quot;: &quot;(autodetect)&quot;,
+    &quot;node.js.selected.package.tslint&quot;: &quot;(autodetect)&quot;,
+    &quot;nodejs_package_manager_path&quot;: &quot;npm&quot;,
+    &quot;settings.editor.selected.configurable&quot;: &quot;com.jetbrains.python.configuration.PyActiveSdkModuleConfigurable&quot;,
+    &quot;to.speed.mode.migration.done&quot;: &quot;true&quot;,
+    &quot;vue.rearranger.settings.migration&quot;: &quot;true&quot;
   }
-}]]></component>
+}</component>
   <component name="RecentsManager">
     <key name="CopyFile.RECENT_KEYS">
       <recent name="$PROJECT_DIR$/Runs" />
@@ -101,8 +115,8 @@
   <component name="SharedIndexes">
     <attachedChunks>
       <set>
-        <option value="bundled-js-predefined-d6986cc7102b-9b0f141eb926-JavaScript-PY-253.29346.308" />
-        <option value="bundled-python-sdk-ca5e2b39c7df-6e1f45a539f7-com.jetbrains.pycharm.pro.sharedIndexes.bundled-PY-253.29346.308" />
+        <option value="bundled-js-predefined-d6986cc7102b-9b0f141eb926-JavaScript-PY-253.31033.139" />
+        <option value="bundled-python-sdk-2653e85de345-6d6dccd035ac-com.jetbrains.pycharm.pro.sharedIndexes.bundled-PY-253.31033.139" />
       </set>
     </attachedChunks>
   </component>
@@ -117,7 +131,10 @@
       <workItem from="1753184384816" duration="49046000" />
       <workItem from="1753433608932" duration="2368000" />
       <workItem from="1753700276583" duration="1239000" />
-      <workItem from="1769421276584" duration="2171000" />
+      <workItem from="1769421276584" duration="3404000" />
+      <workItem from="1772625641497" duration="2357000" />
+      <workItem from="1772704898677" duration="3651000" />
+      <workItem from="1772711572989" duration="8172000" />
     </task>
     <task id="LOCAL-00001" summary="Initial Commit">
       <option name="closed" value="true" />
@@ -191,7 +208,15 @@
       <option name="project" value="LOCAL" />
       <updated>1769421900912</updated>
     </task>
-    <option name="localTasksCounter" value="10" />
+    <task id="LOCAL-00010" summary="Migrating repo">
+      <option name="closed" value="true" />
+      <created>1769423688133</created>
+      <option name="number" value="00010" />
+      <option name="presentableId" value="LOCAL-00010" />
+      <option name="project" value="LOCAL" />
+      <updated>1769423688133</updated>
+    </task>
+    <option name="localTasksCounter" value="11" />
     <servers />
   </component>
   <component name="TypeScriptGeneratedFilesManager">
@@ -213,9 +238,10 @@
     <MESSAGE value="Plotting of elegant results implemented" />
     <MESSAGE value="First release of ElegantTools" />
     <MESSAGE value="Fixed to filter for non-existing elements when initializing from a setting file" />
-    <option name="LAST_COMMIT_MESSAGE" value="Fixed to filter for non-existing elements when initializing from a setting file" />
+    <MESSAGE value="Migrating repo" />
+    <option name="LAST_COMMIT_MESSAGE" value="Migrating repo" />
   </component>
   <component name="com.intellij.coverage.CoverageDataManagerImpl">
-    <SUITE FILE_PATH="coverage/ElegantTools$ElegantTools.coverage" NAME="ElegantTools Coverage Results" MODIFIED="1769421815378" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="false" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+    <SUITE FILE_PATH="coverage/ElegantTools$ElegantTools.coverage" NAME="ElegantTools Coverage Results" MODIFIED="1772718092788" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="false" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
   </component>
 </project>
\ No newline at end of file
diff --git a/ElegantTools.py b/ElegantTools.py
index c058f9d..ad0a6eb 100644
--- a/ElegantTools.py
+++ b/ElegantTools.py
@@ -1,5 +1,5 @@
 import sys
-#import json
+import json
 #import webbrowser
 #import subprocess
 from argparse import ArgumentParser
@@ -38,6 +38,7 @@ class ElegantTools(QtWidgets.QMainWindow, Ui_ElegantGUI):
         self.UIDistCenter.clicked.connect(self.centerDist)
         self.UIDistCut.clicked.connect(self.cutDist)
         self.UIDistInput.clicked.connect(self.setPreferredDist)
+        self.UILoadOpticsSettings.clicked.connect(self.loadOpticsSettings)
         self.UILoadReference.clicked.connect(self.loadLattice)
         self.UISaveReference.clicked.connect(self.saveLattice)
 
@@ -103,6 +104,19 @@ class ElegantTools(QtWidgets.QMainWindow, Ui_ElegantGUI):
             return
         self.model.loadLatticeSettings(fileName)
 
+    def loadOpticsSettings(self):
+        options = QtWidgets.QFileDialog.Options()
+        options |= QtWidgets.QFileDialog.DontUseNativeDialog
+        fileName, _ = QtWidgets.QFileDialog.getOpenFileName(self, "Open Lattice Settings",
+                                                        "LatticeSettings/default.json",
+                                                        "Json Files(*.json)", options=options)
+        if not fileName:
+            return
+        with open(fileName, 'r', encoding='utf-8') as f:
+            settings = json.load(f)
+        self.model.loadSettings(settings)
+
+
     def saveLattice(self):
         options = QtWidgets.QFileDialog.Options()
         options |= QtWidgets.QFileDialog.DontUseNativeDialog
diff --git a/distribution.py b/distribution.py
index 8110bb9..2d273e9 100644
--- a/distribution.py
+++ b/distribution.py
@@ -1,7 +1,8 @@
-import sdds
+import pysdds
 import copy
 import subprocess
 import numpy as np
+import pandas as pd
 
 class Distribution:
     def __init__(self,parent=None,filename=None):
@@ -14,41 +15,56 @@ class Distribution:
         self.loadDist()
 
     def getQ(self):
-        return self.dist.parameterData[self.parameters.index('Charge')][0]
+        return self.Q
 
     def plotLPS(self):
-        x = self.dist.columnData[self.columns.index('t')][0]
-        y = self.dist.columnData[self.columns.index('p')][0]
-        Q = self.dist.parameterData[self.parameters.index('Charge')][0]
-        self.parent.plot.LPS(x,y,Q)
+        self.parent.plot.LPS(self.t,self.p,self.Q)
 
     def loadDist(self):
         if self.filename is None:
             return
-        self.dist = sdds.load(self.filename)
-        self.distcopy = copy.deepcopy(self.dist)
-        self.columns = self.dist.columnName
-        self.parameters =self.dist.parameterName
-        Q = self.dist.parameterData[self.parameters.index('Charge')][0]
-        if Q < 1e-15:
-            Q = float(str(self.parent.UIDistCharge.text()))*1e-12
-        self.dist.setParameterValue('Charge',Q)
-        self.analyseBeam(self.filename,Q)
+        self.dist = pysdds.read(self.filename)
+        self.distCopy = copy.deepcopy(self.dist)
+        self.Q = self.dist.par('Charge').data[0]
+        self.x = self.dist.col('x').data[0]
+        self.xp = self.dist.col('xp').data[0]
+        self.y = self.dist.col('y').data[0]
+        self.yp = self.dist.col('yp').data[0]
+        self.t = self.dist.col('t').data[0]
+        self.p = self.dist.col('p').data[0]
 
+        if self.Q < 1e-15:
+            self.Q = float(str(self.parent.UIDistCharge.text()))*1e-12
         self.plotLPS()
 
+    def getTwiss(self,x,xp,p):
+        x1 = np.mean(x)
+        x2=  np.mean(x*x)
+        xp1 = np.mean(xp)
+        xp2 = np.mean(xp*xp)
+        xxp1 = np.mean(x*xp)
+        g1=np.mean(p)
+        ex = np.sqrt((x2-x1*x1)*(xp2-xp1*xp1)-(xxp1-x1*xp1)**2)*g1
+        bx = (x2-x1*x1)*g1/ex
+        ax = - (xxp1-x1*xp1)*g1/ex
+
+        return bx,ax,ex
 
     def analyseBeamShort(self,filename):
-        output = 'Runs/analysebeam.sdds'
-        subprocess.run(['sddsanalyzebeam', filename, output])
-        fields = ['betax', 'betay', 'alphax', 'alphay', 'pAverage']
-        out = sdds.load(output)
+        dist = pysdds.read(filename)
+        p = dist.col('p').data[0]
+        x = dist.col('x').data[0]
+        xp = dist.col('xp').data[0]
+        y = dist.col('y').data[0]
+        yp = dist.col('yp').data[0]
+        bx, ax, ex = self.getTwiss(x,xp,p)
+        by, ay, ey = self.getTwiss(y,yp,p)
         res={}
-        for i ,field in enumerate(fields):
-            idx = out.columnName.index(field)
-            res[field]=out.columnData[idx][0][0]
-        res['Q']=self.dist.parameterData[self.parameters.index('Charge')][0]
-        del out
+        res['betax']=bx
+        res['alphax']=ax
+        res['betay'] = by
+        res['alphay'] = ay
+        res['pAverage'] = np.mean(p)
         return res
 
     def analyseBeam(self,filename,Q):
@@ -89,53 +105,56 @@ class Distribution:
 
 
     def addBlurr(self):
-        p=self.dist.columnData[self.columns.index('p')][0]
-        ns=len(p)
+        ns=len(self.p)
         blurr = float(str(self.parent.UIDistSpread.text())) / 511.
         dg = np.random.normal(0, blurr, size=ns)
-        self.dist.setColumnValueList('p', [p[i]+dg[i] for i in range(ns)])
+        self.p += dg
         self.plotLPS()
 
     def centerDist(self):
-        Q = float(str(self.parent.UIDistCharge.text()))*1e-12
-        self.dist.setParameterValue('Charge', Q)
+        self.Q = float(str(self.parent.UIDistCharge.text()))*1e-12
         pCenter = float(str(self.parent.UIDistEnergy.text()))/0.511
-        p = self.dist.columnData[self.columns.index('p')][0]
-        p = p - np.mean(p)+pCenter
-        self.dist.columnData[self.columns.index('p')][0] = [p0 for p0 in p]
-        #self.dist.setColumnValueList('p', p)
+        self.p = self.p - np.mean(self.p)+pCenter
         self.plotLPS()
 
+
     def cutDist(self):
-        cut = float(str(self.parent.UIDistLength.text()))
-        t = self.dist.columnData[self.columns.index('t')][0]
-        nti=len(t)
-        t0 = np.mean(t)
-        trms = np.std(t)
-        tmin = t0-cut*trms
-        tmax = t0+cut*trms
-        idx = np.argwhere(np.logical_and(t > tmin,t < tmax))
-        ntf = len(idx)
-        for i, fld in enumerate(self.columns):
-            dat = np.array(self.dist.columnData[i][0])
-            self.dist.setColumnValueList(fld, [d for d in dat[idx].ravel()])
-        Q = self.dist.parameterData[self.parameters.index('Charge')][0]*float(ntf)/float(nti)
-        self.dist.setParameterValue('Charge', Q)
+        sigma = float(str(self.parent.UIDistLength.text()))
+        if sigma <=0:
+            return
+        rmsT=np.std(self.t)
+        idx=np.argwhere(np.abs(self.t)< rmsT*sigma)
+        N0 = float(len(self.t))
+        self.x=self.x[idx]
+        self.y=self.y[idx]
+        self.xp=self.xp[idx]
+        self.yp=self.yp[idx]
+        self.p=self.p[idx]
+        self.t=self.t[idx]
+        N1 = float(len(self.t))
+        self.Q = self.Q*N1/N0
         self.plotLPS()
 
     def revertDist(self):
         self.dist=copy.deepcopy(self.dist)
 
     def saveDist(self,filename):
-        x=sdds.SDDS()
-        x.mode = sdds.SDDS_BINARY
-        x.description[0]="test"
-        x.description[1]="test"
-        x.parameterName=self.dist.parameterName
-        x.parameterData=self.dist.parameterData
-        x.parameterDefinition = self.dist.parameterDefinition
-        x.columnName=self.dist.columnName
-        x.columnData=[self.dist.columnData[i] for i in range(len(self.dist.columnName))]
-        x.columnDefinition=self.dist.columnDefinition
-        x.save(filename)
-        del x
+        if len(self.t.shape) > 1:
+            meas_df = {'t': self.t[:, 0], 'p': self.p[:, 0], 'x': self.x[:, 0], 'xp': self.xp[:, 0],
+                       'y': self.y[:, 0], 'yp': self.yp[:, 0], }
+        else:
+            meas_df = {'t': self.t[:], 'p': self.p[:], 'x': self.x[:], 'xp': self.xp[:],
+                       'y': self.y[:], 'yp': self.yp[:], }
+        df_meas = pd.DataFrame.from_dict(meas_df)
+        parameters = {'Charge': [float(self.Q)]}
+        subprocess.run(['rm', filename])
+        sdds = pysdds.SDDSFile.from_df([df_meas], parameter_dict=parameters, mode='binary')
+        sdds.col('x').nm['units']= 'm'
+        sdds.col('y').nm['units'] = 'm'
+        sdds.col('t').nm['units'] = 's'
+        sdds.col('p').nm['units'] = 'm$be$nc'
+        sdds.par('Charge').nm['units']='C'
+        sdds.validate_data()
+
+        pysdds.write(sdds, filename)
+
diff --git a/model.py b/model.py
index bea84ee..c861c49 100644
--- a/model.py
+++ b/model.py
@@ -77,27 +77,33 @@ class Model:
                     ele.__dict__[field]/=ele.Length
 
     def loadSettings(self,settings):
-        self.loadSettingsGroup(settings['Quadrupole'],['k1'])
+
+        if not 'Phase' in settings.keys():
+            return False
+        if not settings['Phase'] == self.phase:
+            return False
+        self.loadSettingsGroup(settings['Quadrupole'], ['k1'])
         self.loadSettingsGroup(settings['Sextupole'], ['k2'])
         self.loadSettingsGroup(settings['Dipole'], ['angle'])
-        self.loadSettingsGroup(settings['RF'], ['Gradient'],normalized=True)
+        self.loadSettingsGroup(settings['RF'], ['Gradient'], normalized=True)
         self.loadSettingsGroup(settings['RF'], ['Phase'])
-        self.loadSettingsGroup(settings['Undulator'], ['K','kx','ky'])
-        self.loadSettingsGroup(settings['Kicker'], ['cory','design_kick'])
+        self.loadSettingsGroup(settings['Undulator'], ['K', 'kx', 'ky'])
+        self.loadSettingsGroup(settings['Kicker'], ['cory', 'design_kick'])
         E0 = settings['Energy']['energy']
-        if isinstance(E0,list):
-            E0=E0[0]
+        if isinstance(E0, list):
+            E0 = E0[0]
         E0Ref = settings['Energy']['location']
-        if isinstance(E0,list):
-            E0=E0[0]
-        self.initEnergy=E0
-        self.initEnergyRef=E0Ref
-        self.om.forceEnergyAt(E0Ref, E0*1e6)
+        if isinstance(E0, list):
+            E0 = E0[0]
+        self.initEnergy = E0
+        self.initEnergyRef = E0Ref
+        self.om.forceEnergyAt(E0Ref, E0 * 1e6)
         self.startTwiss = settings['InitialCondition']
-        self.parent.UIDistBetax.setText('%7.3f' % self.startTwiss['betax0'])
-        self.parent.UIDistBetay.setText('%7.3f' % self.startTwiss['betay0'])
-        self.parent.UIDistAlphax.setText('%7.3f' % self.startTwiss['alphax0'])
-        self.parent.UIDistAlphay.setText('%7.3f' % self.startTwiss['alphay0'])
+        print('Initial Condition:',self.startTwiss)
+        self.parent.UIDistBetax.setText('%7.3f' % self.startTwiss['betx'])
+        self.parent.UIDistBetay.setText('%7.3f' % self.startTwiss['bety'])
+        self.parent.UIDistAlphax.setText('%7.3f' % self.startTwiss['alfx'])
+        self.parent.UIDistAlphay.setText('%7.3f' % self.startTwiss['alfy'])
         self.parent.UIDistEnergy.setText('%7.3f' % E0)
         self.updateRFTable(settings['RF'])
 
diff --git a/plot.py b/plot.py
index b1b448f..21db889 100644
--- a/plot.py
+++ b/plot.py
@@ -1,5 +1,5 @@
 import sys
-import sdds
+import pysdds
 from PyQt5 import QtWidgets,QtGui
 
 
@@ -118,12 +118,12 @@ class ElegantPlot(QtWidgets.QMainWindow, Ui_ElegantPlotGUI):
         self.UITwissValues.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
 
     def loadDist(self,filename):
-        dist = sdds.load(filename)
+        dist = pysdds.read(filename)
         cols=['t','p','x','xp','y','yp']
         self.dist.clear()
         for col in cols:
-            self.dist[col] = dist.columnData[dist.columnName.index(col)][0]
-        self.Q = dist.parameterData[dist.parameterName.index('Charge')][0]
+            self.dist[col] = dist.col(col)[0]
+        self.Q = dist.par('Charge').data[0]
         return filename
 
 
diff --git a/track.py b/track.py
index cbd0b7f..966255b 100644
--- a/track.py
+++ b/track.py
@@ -2,7 +2,7 @@ from threading import Thread
 import subprocess
 import re
 import os
-import sdds
+import pysdds
 
 from PyQt5 import QtCore
 
@@ -62,7 +62,11 @@ class Track(QtCore.QObject):
         self.parent.preferredDist.saveDist(distfile)
         print('Input distribution copied to',distfile)
         res=self.parent.preferredDist.analyseBeamShort(distfile)
-        inputfile=self.writeInputFile('Runs',project,latfile,distfile,res)
+        print(res)
+        downsample=int(str(self.parent.UISkipParticles.text()))
+        if downsample<1:
+            downsample = 1
+        inputfile=self.writeInputFile('Runs',project,latfile,distfile,res,downsample)
         print('Input file written to',inputfile)
 #        self.cmd=['mpirun','-np','10','Pelegant',inputfile]
         self.cmd=['elegant',inputfile]
@@ -74,6 +78,7 @@ class Track(QtCore.QObject):
     def Telegant(self):
         self.parent.UITrackOutput.appendPlainText('Starting thread to run elegant')
 #        p = subprocess.run(self.cmd)
+        print('Elegant launch:',self.cmd)
         p = subprocess.Popen(self.cmd,stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
         for line in iter(p.stdout.readline, b''):
             self.message.emit(line.decode('utf-8').strip())
@@ -94,18 +99,15 @@ class Track(QtCore.QObject):
         self.loadTracking()
 
     def loadTracking(self):
-        data = sdds.load(self.root+'.cen')
-        columns = data.columnName
+        data = pysdds.read(self.root+'.cen')
         res = {}
         fields = ['s','ElementName','Cx','Cxp','Cy','Cyp','Cdelta','pCentral']
         for field in fields:
-            res[field] = data.columnData[columns.index(field)][0]
-        del data
-        data = sdds.load(self.root + '.sig')
-        columns = data.columnName
+            res[field] = data.col(field)[0]
+        data = pysdds.read(self.root + '.sig')
         fields = ['Sx', 'Sxp', 'Sy', 'Syp', 'Sdelta', 'St','enx','eny','ecnx','ecny','betaxBeam','betayBeam','alphaxBeam','alphayBeam']
         for field in fields:
-            res[field] = data.columnData[columns.index(field)][0]
+            res[field] =  data.col(field)[0]
         del data
         dist = [self.root+'Inputdist.sdds']+self.getDumps()
         self.parent.plot.newData(res,dist)
@@ -126,7 +128,7 @@ class Track(QtCore.QObject):
 #        print(msg)
         self.parent.UITrackOutput.appendPlainText(msg)
 
-    def writeInputFile(self,path,name,latfile,distfile,distinfo):
+    def writeInputFile(self,path,name,latfile,distfile,distinfo,ds):
         filename = '%s/%s.ele' % (path, name)
         with open(filename, 'w') as fid:
             fid.write('&run_setup\n')
@@ -152,7 +154,6 @@ class Track(QtCore.QObject):
             fid.write('\tn_steps\t= 1,\n')
             fid.write('\treset_rf_for_each_step = 1\n')
             fid.write('&end\n\n')
-
             fid.write('&twiss_output\n')
             fid.write('\tfilename\t= %s/%%s.twi,\n' % path)
             fid.write('\tmatched\t\t= 0,\n')
@@ -164,7 +165,7 @@ class Track(QtCore.QObject):
 
             fid.write('&sdds_beam\n')
             fid.write('\tinput_type= "elegant",\n')
-            fid.write('\tsample_interval\t= 1,\n')
+            fid.write('\tsample_interval\t= %d,\n' % ds)
             fid.write('\tinput = %s,\n' % distfile)
             fid.write('\treuse_bunch\t= 0 \n')
             fid.write('&end\n\n')
diff --git a/ui/ElegantToolsGui.py b/ui/ElegantToolsGui.py
index 042cb4b..48ba016 100644
--- a/ui/ElegantToolsGui.py
+++ b/ui/ElegantToolsGui.py
@@ -28,8 +28,8 @@ class Ui_ElegantGUI(object):
         self.TabMaster.setObjectName("TabMaster")
         self.tab_3 = QtWidgets.QWidget()
         self.tab_3.setObjectName("tab_3")
-        self.horizontalLayout = QtWidgets.QHBoxLayout(self.tab_3)
-        self.horizontalLayout.setObjectName("horizontalLayout")
+        self.verticalLayout_7 = QtWidgets.QVBoxLayout(self.tab_3)
+        self.verticalLayout_7.setObjectName("verticalLayout_7")
         self.widget_2 = QtWidgets.QWidget(self.tab_3)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Preferred)
         sizePolicy.setHorizontalStretch(0)
@@ -100,10 +100,26 @@ class Ui_ElegantGUI(object):
         self.label_7 = QtWidgets.QLabel(self.widget_2)
         self.label_7.setObjectName("label_7")
         self.verticalLayout.addWidget(self.label_7)
+        self.horizontalLayout = QtWidgets.QHBoxLayout()
+        self.horizontalLayout.setObjectName("horizontalLayout")
         self.UITrackInput = QtWidgets.QLineEdit(self.widget_2)
         self.UITrackInput.setReadOnly(True)
         self.UITrackInput.setObjectName("UITrackInput")
-        self.verticalLayout.addWidget(self.UITrackInput)
+        self.horizontalLayout.addWidget(self.UITrackInput)
+        spacerItem = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
+        self.horizontalLayout.addItem(spacerItem)
+        self.label_9 = QtWidgets.QLabel(self.widget_2)
+        self.label_9.setObjectName("label_9")
+        self.horizontalLayout.addWidget(self.label_9)
+        self.UISkipParticles = QtWidgets.QLineEdit(self.widget_2)
+        sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Fixed)
+        sizePolicy.setHorizontalStretch(0)
+        sizePolicy.setVerticalStretch(0)
+        sizePolicy.setHeightForWidth(self.UISkipParticles.sizePolicy().hasHeightForWidth())
+        self.UISkipParticles.setSizePolicy(sizePolicy)
+        self.UISkipParticles.setObjectName("UISkipParticles")
+        self.horizontalLayout.addWidget(self.UISkipParticles)
+        self.verticalLayout.addLayout(self.horizontalLayout)
         self.UITrackDoLSC = QtWidgets.QCheckBox(self.widget_2)
         self.UITrackDoLSC.setChecked(True)
         self.UITrackDoLSC.setObjectName("UITrackDoLSC")
@@ -123,7 +139,7 @@ class Ui_ElegantGUI(object):
         self.UITrackOutput = QtWidgets.QPlainTextEdit(self.widget_2)
         self.UITrackOutput.setObjectName("UITrackOutput")
         self.verticalLayout.addWidget(self.UITrackOutput)
-        self.horizontalLayout.addWidget(self.widget_2)
+        self.verticalLayout_7.addWidget(self.widget_2)
         self.TabMaster.addTab(self.tab_3, "")
         self.tab_8 = QtWidgets.QWidget()
         self.tab_8.setObjectName("tab_8")
@@ -147,8 +163,8 @@ class Ui_ElegantGUI(object):
         self.UIDistAnalysis.setReadOnly(True)
         self.UIDistAnalysis.setObjectName("UIDistAnalysis")
         self.verticalLayout_4.addWidget(self.UIDistAnalysis)
-        spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.verticalLayout_4.addItem(spacerItem)
+        spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.verticalLayout_4.addItem(spacerItem1)
         self.UIDistInput = QtWidgets.QPushButton(self.tab_8)
         self.UIDistInput.setObjectName("UIDistInput")
         self.verticalLayout_4.addWidget(self.UIDistInput)
@@ -227,8 +243,8 @@ class Ui_ElegantGUI(object):
         self.UIDistCut = QtWidgets.QPushButton(self.tab_8)
         self.UIDistCut.setObjectName("UIDistCut")
         self.verticalLayout_3.addWidget(self.UIDistCut)
-        spacerItem1 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.verticalLayout_3.addItem(spacerItem1)
+        spacerItem2 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.verticalLayout_3.addItem(spacerItem2)
         self.UIDistSave = QtWidgets.QPushButton(self.tab_8)
         self.UIDistSave.setObjectName("UIDistSave")
         self.verticalLayout_3.addWidget(self.UIDistSave)
@@ -246,6 +262,10 @@ class Ui_ElegantGUI(object):
         self.UISaveReference = QtWidgets.QPushButton(self.tab_2)
         self.UISaveReference.setObjectName("UISaveReference")
         self.verticalLayout_2.addWidget(self.UISaveReference)
+        self.UILoadOpticsSettings = QtWidgets.QPushButton(self.tab_2)
+        self.UILoadOpticsSettings.setStyleSheet("background-color: rgb(255, 255, 127);")
+        self.UILoadOpticsSettings.setObjectName("UILoadOpticsSettings")
+        self.verticalLayout_2.addWidget(self.UILoadOpticsSettings)
         self.label_3 = QtWidgets.QLabel(self.tab_2)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Fixed)
         sizePolicy.setHorizontalStretch(0)
@@ -332,8 +352,8 @@ class Ui_ElegantGUI(object):
         self.UIDeleteDump = QtWidgets.QPushButton(self.tab_2)
         self.UIDeleteDump.setObjectName("UIDeleteDump")
         self.verticalLayout_2.addWidget(self.UIDeleteDump)
-        spacerItem2 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.verticalLayout_2.addItem(spacerItem2)
+        spacerItem3 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.verticalLayout_2.addItem(spacerItem3)
         self.horizontalLayout_2.addLayout(self.verticalLayout_2)
         self.verticalLayout_6 = QtWidgets.QVBoxLayout()
         self.verticalLayout_6.setObjectName("verticalLayout_6")
@@ -377,8 +397,8 @@ class Ui_ElegantGUI(object):
         self.UIAddSectionDump = QtWidgets.QPushButton(self.tab_2)
         self.UIAddSectionDump.setObjectName("UIAddSectionDump")
         self.verticalLayout_6.addWidget(self.UIAddSectionDump)
-        spacerItem3 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.verticalLayout_6.addItem(spacerItem3)
+        spacerItem4 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.verticalLayout_6.addItem(spacerItem4)
         self.horizontalLayout_2.addLayout(self.verticalLayout_6)
         self.TabMaster.addTab(self.tab_2, "")
         self.verticalLayout_5.addWidget(self.TabMaster)
@@ -521,7 +541,7 @@ class Ui_ElegantGUI(object):
         self.menubar.addAction(self.menuHelp.menuAction())
 
         self.retranslateUi(ElegantGUI)
-        self.TabMaster.setCurrentIndex(0)
+        self.TabMaster.setCurrentIndex(2)
         self.actionQuit.triggered.connect(ElegantGUI.close) # type: ignore
         QtCore.QMetaObject.connectSlotsByName(ElegantGUI)
 
@@ -535,9 +555,11 @@ class Ui_ElegantGUI(object):
         self.UITrackStart.setText(_translate("ElegantGUI", "SINLH01"))
         self.label_2.setText(_translate("ElegantGUI", "End-Section"))
         self.label.setText(_translate("ElegantGUI", "Start-Section"))
-        self.UITrackEnd.setText(_translate("ElegantGUI", "SATBD02"))
+        self.UITrackEnd.setText(_translate("ElegantGUI", "SINDI02"))
         self.label_7.setText(_translate("ElegantGUI", "Input Distribution"))
         self.UITrackInput.setText(_translate("ElegantGUI", "not yet defined"))
+        self.label_9.setText(_translate("ElegantGUI", "Skip"))
+        self.UISkipParticles.setText(_translate("ElegantGUI", "10"))
         self.UITrackDoLSC.setText(_translate("ElegantGUI", "Include Longitudinal Space Charge"))
         self.UITrackDoCSR.setText(_translate("ElegantGUI", "Include Coherent Synchrotron Radiation"))
         self.UITrackAutoAlign.setText(_translate("ElegantGUI", "Align Beam After Each Chicane"))
@@ -571,6 +593,7 @@ class Ui_ElegantGUI(object):
         self.TabMaster.setTabText(self.TabMaster.indexOf(self.tab_8), _translate("ElegantGUI", "Distribution"))
         self.UILoadReference.setText(_translate("ElegantGUI", "Load Settings"))
         self.UISaveReference.setText(_translate("ElegantGUI", "Save Settings"))
+        self.UILoadOpticsSettings.setText(_translate("ElegantGUI", "Import OpticsTool Settings"))
         self.label_3.setText(_translate("ElegantGUI", "RF Settings"))
         item = self.UIRFSettings.verticalHeaderItem(0)
         item.setText(_translate("ElegantGUI", "New Row"))
diff --git a/ui/ElegantToolsGui.ui b/ui/ElegantToolsGui.ui
index c4f0fdb..87f0f75 100644
--- a/ui/ElegantToolsGui.ui
+++ b/ui/ElegantToolsGui.ui
@@ -24,13 +24,13 @@
        </sizepolicy>
       </property>
       <property name="currentIndex">
-       <number>0</number>
+       <number>2</number>
       </property>
       <widget class="QWidget" name="tab_3">
        <attribute name="title">
         <string>Track</string>
        </attribute>
-       <layout class="QHBoxLayout" name="horizontalLayout">
+       <layout class="QVBoxLayout" name="verticalLayout_7">
         <item>
          <widget class="QWidget" name="widget_2" native="true">
           <property name="sizePolicy">
@@ -135,7 +135,7 @@
                 </sizepolicy>
                </property>
                <property name="text">
-                <string>SATBD02</string>
+                <string>SINDI02</string>
                </property>
               </widget>
              </item>
@@ -149,14 +149,51 @@
             </widget>
            </item>
            <item>
-            <widget class="QLineEdit" name="UITrackInput">
-             <property name="text">
-              <string>not yet defined</string>
-             </property>
-             <property name="readOnly">
-              <bool>true</bool>
-             </property>
-            </widget>
+            <layout class="QHBoxLayout" name="horizontalLayout">
+             <item>
+              <widget class="QLineEdit" name="UITrackInput">
+               <property name="text">
+                <string>not yet defined</string>
+               </property>
+               <property name="readOnly">
+                <bool>true</bool>
+               </property>
+              </widget>
+             </item>
+             <item>
+              <spacer name="horizontalSpacer">
+               <property name="orientation">
+                <enum>Qt::Horizontal</enum>
+               </property>
+               <property name="sizeHint" stdset="0">
+                <size>
+                 <width>40</width>
+                 <height>20</height>
+                </size>
+               </property>
+              </spacer>
+             </item>
+             <item>
+              <widget class="QLabel" name="label_9">
+               <property name="text">
+                <string>Skip</string>
+               </property>
+              </widget>
+             </item>
+             <item>
+              <widget class="QLineEdit" name="UISkipParticles">
+               <property name="sizePolicy">
+                <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+                 <horstretch>0</horstretch>
+                 <verstretch>0</verstretch>
+                </sizepolicy>
+               </property>
+               <property name="text">
+                <string>10</string>
+               </property>
+              </widget>
+             </item>
+            </layout>
            </item>
            <item>
             <widget class="QCheckBox" name="UITrackDoLSC">
@@ -469,6 +506,16 @@
             </property>
            </widget>
           </item>
+          <item>
+           <widget class="QPushButton" name="UILoadOpticsSettings">
+            <property name="styleSheet">
+             <string notr="true">background-color: rgb(255, 255, 127);</string>
+            </property>
+            <property name="text">
+             <string>Import OpticsTool Settings</string>
+            </property>
+           </widget>
+          </item>
           <item>
            <widget class="QLabel" name="label_3">
             <property name="sizePolicy">