reverted to only matlab repository

python/BBA/.idea/BBA.iml

-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="projectConfiguration" value="Nosetests" />
-    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
-  </component>
-</module>
\ No newline at end of file

python/BBA/.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7 (BBA)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file

python/BBA/.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/BBA.iml" filepath="$PROJECT_DIR$/.idea/BBA.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

python/BBA/Bumps.py

-
-import scipy.io as sio
-
-class Bumps():
-
-    def __init__(self,debug=True):
-        self._bpms = []
-        self.path = '/mntdirect/_machfs/swhite/Commissioning/BBA/'
-        for i in range(10):
-          self._bpms.append(sio.loadmat(self.path+'bpm'+str(i+1)+'.mat')['bump'])
-
-    def get_bump(self,bpm_nb,plane):
-        bump = self._bpms[bpm_nb-1]
-        if plane =='H':
-            bump = bump[0]
-        elif plane=='V':
-            bump = bump[1]
-        return bump

python/BBA/OrbitController.py

-import tango
-import csv
-import numpy as np
-import os
-from enum import Enum
-
-class EbsMode(Enum):
-    TbT = 0
-    Atlinopt = 1
-    Atx = 2
-    Mixed = 3
-    DetailedAtx = 4
-
-class OrbitController():
-    # Class to get data from BPM
-    # Read/correct/set closed orbit
-    #drive bumps, correctors, quadrupoles
-
-    def __init__(self,debug=True):
-        if debug:
-          os.environ['TANGO_HOST'] = 'ebs-simu:10000'
-          simulator = tango.DeviceProxy('sys/ringsimulator/ebs')
-          simulator.write_attribute('Mode',EbsMode.Atlinopt.value)
-        self._BPMsdev = tango.DeviceProxy('srdiag/beam-position/all')
-        self._Quadsdev = tango.DeviceProxy('srmag/m-q/all')
-        self._corHdev = tango.DeviceProxy('srmag/hst/all')
-        self._corVdev = tango.DeviceProxy('srmag/vst/all')
-        self._autocor = tango.DeviceProxy('sr/beam-orbitcor/svd-auto')
-        self._svd_h = tango.DeviceProxy('sr/beam-orbitcor/svd-h')
-        self._svd_v = tango.DeviceProxy('sr/beam-orbitcor/svd-v')
-
-        self._quad_map = {1:  ['qf1', 'a'],
-                          2:  ['qf4', 'a'],
-                          3:  ['qf4', 'b'],
-                          4:  ['qf6', 'b'],
-                          5:  ['qf8', 'b'],
-                          6:  ['qf8', 'd'],
-                          7:  ['qf6', 'd'],
-                          8:  ['qf4', 'd'],
-                          9:  ['qf4', 'e'],
-                          10: ['qf1', 'e']}
-
-        hmfile = self._svd_h.get_property('SVDFileName')
-        vmfile = self._svd_v.get_property('SVDFileName')
-        hmfile = hmfile['SVDFileName'][0]
-        vmfile = vmfile['SVDFileName'][0]
-        self._hmat = self.load_respmat(hmfile)
-        self._vmat = self.load_respmat(vmfile)
-
-
-    def load_respmat(self, mfile):
-        mat = []
-        f = open(mfile,'r')
-        r = csv.reader(f)
-        for line in r:
-            ld = [float(x) for x in line]
-            mat.append(ld)
-        f.close()
-        return mat
-
-
-    def get_cor_name(self, index, plane):
-        names = []
-        if plane == 'H':
-            names = self._corHdev.read_attribute('CorrectorNames').value
-        elif plane == 'V':
-            names = self._corVdev.read_attribute('CorrectorNames').value
-        elif plane == 'HV':
-            names = [self._corHdev.read_attribute('CorrectorNames').value,
-                     self._corVdev.read_attribute('CorrectorNames').value]
-            return [names[0][index[0]],names[1][index[1]]]
-        else:
-            print 'Plane is H,V or HV'
-        return names[index]
-
-
-    def get_cor_index(self, name):
-        if 'hst' in name:
-            names = self._corHdev.read_attribute('CorrectorNames').value
-        elif 'vst' in name:
-            names = self._corVdev.read_attribute('CorrectorNames').value
-        else:
-            print 'Error Corrector name: '+name
-        return names.index(name)
-
-
-    def get_cor_values(self, plane):
-        values=np.nan
-        if plane == 'H':
-            values = self._corHdev.read_attribute('Strengths').w_value
-        elif plane == 'V':
-            values = self._corVdev.read_attribute('Strengths').w_value
-        elif plane == 'HV':
-            values = [self._corHdev.read_attribute('Strengths').w_value,
-                      self._corVdev.read_attribute('Strengths').w_value]
-        else:
-            print 'Plane is H,V or HV'
-        return values
-
-
-    def set_cor_values(self, plane,values):
-        if 'H' in plane:
-            self._corHdev.write_attribute('Strengths',values)
-        if 'V' in plane:
-            self._corVdev.write_attribute('Strengths',values)
-
-
-    def trim_cor(self,name,value,increment=False):
-        cor = tango.DeviceProxy(name)
-        corval = cor.read_attribute('Strength').w_value
-        if increment:
-            corval = corval + value
-        else:
-            corval = value
-        cor.write_attribute('Strength',corval)
-
-
-    def trim_cor_all(self,name,plane,value,increment=False):
-        cori = self.get_cor_index(name)
-        vals = self.get_cor_values(plane)
-        if increment:
-            vals[cori] = vals[cori]+value
-        else:
-            vals[cori] = value
-        self.set_cor_values(plane,vals)
-
-
-    def get_bpm_name(self, index):
-        return self._BPMsdev.command_inout('GetBPMName',index)
-
-
-    def get_bpm_index(self, name):
-        return self._BPMsdev.command_inout('GetBPMIndex',name)
-
-
-    def get_orbit(self):
-        orbit = [self._BPMsdev.read_attribute('SA_HPositions').value,
-                 self._BPMsdev.read_attribute('SA_VPositions').value]
-        return orbit
-
-    def get_offets(self):
-        offsets = [self._BPMsdev.read_attribute('HOffsets').value,
-                 self._BPMsdev.read_attribute('VOffsets').value]
-        return offsets
-
-    def reset_offets(self):
-        self._BPMsdev.write_attribute('HOffsets',np.zeros(320))
-        self._BPMsdev.write_attribute('VOffsets',np.zeros(320))
-
-    def set_offsets(self,bpmi,values,plane):
-        offsets = self.get_offets()
-        offsets[0][bpmi] += -values[0][0]
-        offsets[1][bpmi] += -values[1][0]
-        if 'H' in plane:
-          self._BPMsdev.write_attribute('HOffsets', offsets[0])
-        if 'V' in plane:
-          self._BPMsdev.write_attribute('VOffsets', offsets[1])
-
-
-    def get_ref_orbit(self,plane):
-        orbit = []
-        if plane == 'H':
-            orbit = self._svd_h.read_attribute('RefOrbit').value
-        elif plane == 'V':
-            orbit = self._svd_v.read_attribute('RefOrbit').value
-        elif plane == 'HV':
-            orbit = [self._svd_h.read_attribute('RefOrbit').value,
-                     self._svd_v.read_attribute('RefOrbit').value]
-        else:
-            print 'Plane is H, V or HV'
-        return orbit
-
-
-    def set_ref_orbit(self,plane,orbit):
-        if 'H' in plane:
-            self._svd_h.write_attribute('RefOrbit',orbit)
-        if 'V' in plane:
-            self._svd_v.write_attribute('RefOrbit',orbit)
-
-    def reset_ref_orbit(self):
-        self.set_ref_orbit('HV',np.zeros((2,320)))
-
-
-    def set_bump(self,plane,bump,bpmi,amp):
-        amp = amp*1.0e3
-        indm = len(bump)/2+1
-        ref_orbit = self.get_ref_orbit(plane)
-        if plane == 'H' or plane == 'V':
-          norm = bump[indm]
-          new_ref = ref_orbit
-          new_ref[bpmi-indm+1:bpmi+indm] = bump[:]*amp/norm
-        elif plane == 'HV':
-          norm = bump[:][indm]
-          new_ref = ref_orbit
-          new_ref[0][bpmi - indm+1:bpmi + indm] = bump[0][:] * amp / norm[0]
-          new_ref[1][bpmi - indm+1:bpmi + indm] = bump[1][:] * amp / norm[1]
-        self.set_ref_orbit(plane,new_ref)
-
-    def get_quad_name(self, index):
-        names = self._Quadsdev.read_attribute('MagnetNames').value
-        return names[index]
-
-
-    def get_quad_index(self, name):
-        names = self._Quadsdev.read_attribute('MagnetNames').value
-        return names.index(name)
-
-
-    def get_quad_values(self):
-        return self._Quadsdev.read_attribute('CorrectionStrengths').w_value
-
-    def get_quad_value(self,name):
-        quad = tango.DeviceProxy(name)
-        quadval = quad.read_attribute('CorrectionStrength').w_value
-        return quadval
-
-
-    def set_quad_values(self,strength):
-        self._Quadsdev.write_attribute('CorrectionStrengths',strength)
-
-
-    def trim_quad_all(self,name,value,increment=False):
-        quadi = self.get_quad_index(name)
-        vals = self.get_quad_values()
-        if increment:
-            vals[quadi] = vals[quadi]+value
-        else:
-            vals[quadi] = value
-        self.set_quad_values(vals)
-
-
-    def trim_quad(self,name,value,increment=False):
-        quad = tango.DeviceProxy(name)
-        quadval = quad.read_attribute('CorrectionStrength').w_value
-        if increment:
-            quadval = quadval + value
-        else:
-            quadval = value
-        quad.write_attribute('CorrectionStrength',quadval)
-
-
-    def get_mec(self, bpm_index,plane):
-        mec=-1
-        if plane == 'H':
-            mec = np.argmax(self._hmat[bpm_index][:])
-        elif plane == 'V':
-            mec = np.argmax(self._vmat[bpm_index][:])
-        elif plane == 'HV':
-            mec = [np.argmax(self._hmat[bpm_index][:]),
-                   np.argmax(self._vmat[bpm_index][:])]
-        else:
-            print 'Plane is H, V or HV'
-        return mec
-
-    def get_bpm_number_cell(self,bpm_name):
-        nsplit = bpm_name.split('/')
-        nsplit = nsplit[2].split('-')
-        cell = nsplit[0]
-        bpm_nb = int(nsplit[1])
-        return bpm_nb,cell
-
-    def get_quad_to_align(self, bpm_name):
-        bpm_nb, cell = self.get_bpm_number_cell(bpm_name)
-        quad_name = 'srmag/m-' + self._quad_map[bpm_nb][0] + \
-                    '/' + cell + '-' + self._quad_map[bpm_nb][1]
-        return quad_name, self.get_quad_index(quad_name)
\ No newline at end of file

python/BBA/Quadrespmat.py

-import numpy as np
-import os
-import OrbitController as oc
-import time
-from scipy.optimize import curve_fit
-from scipy.interpolate import interp1d
-import matplotlib.pyplot as plt
-
-class Quadrespmat():
-
-    def __init__(self,debug=True):
-        if debug:
-          os.environ['TANGO_HOST'] = 'ebs-simu:10000'
-        self.oc = oc.OrbitController()
-        self.dk = 0
-        self.quadi = []
-        self.nbpms=320
-        self.matrix=[]
-
-    def load_settings(self,dk,quadi):
-        self.dk = dk
-        self.quadi = quadi
-        self.matrix = np.zeros((len(quadi),2,self.nbpms))
-
-
-    def run_scan(self,ts):
-        for ind,i in enumerate(self.quadi):
-            name = self.oc.get_quad_name(i)
-            o0 = self.oc.get_orbit()
-            plt.plot(o0[0])
-            print name, self.oc.get_quad_value(name)
-            self.oc.trim_quad(name,self.dk,True)
-            time.sleep(ts)
-            print name, self.oc.get_quad_value(name)
-            op = self.oc.get_orbit()
-            plt.plot(np.subtract(op,o0)[0])
-            self.oc.trim_quad(name,-2*self.dk,True)
-            time.sleep(ts)
-            print name, self.oc.get_quad_value(name)
-            om = self.oc.get_orbit()
-            plt.plot(np.subtract(om, o0)[0])
-            self.oc.trim_quad(name,+self.dk,True)
-            time.sleep(ts)
-            print name, self.oc.get_quad_value(name)
-            orb = np.subtract(op,om)/2.0
-            plt.plot(orb[0])
-            print np.std(orb,1)
-            self.matrix[ind] = orb
-            plt.show()
-

python/BBA/mccExcludedFiles.log

-The List of Excluded Files
-Excluded files	 Exclusion Message ID	 Reason For Exclusion	 Exclusion Rule
-/mntdirect/_sware/com/matlab_2016a/toolbox/local/+matlab/+internal/+toolboxes/addInstalledToolboxesToPath.m	MATLAB:Completion:ExcludedBy	Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler.	/mntdirect/_sware/com/matlab_2016a/toolbox/local/[+]matlab/[+]internal/[+]toolboxes/addInstalledToolboxesToPath[.]m
-/mntdirect/_sware/com/matlab_2016a/toolbox/local/+matlab/+internal/+zipAddOns/addInstalledZipAddOnsToPath.m	MATLAB:Completion:ExcludedBy	Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler.	/mntdirect/_sware/com/matlab_2016a/toolbox/local/[+]matlab/[+]internal/[+]zipAddOns/addInstalledZipAddOnsToPath[.]m
-/mntdirect/_sware/com/matlab_2016a/toolbox/local/pathdef.m	MATLAB:Completion:ExcludedBy	Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler.	/mntdirect/_sware/com/matlab_2016a/toolbox/local/pathdef[.]m
-/mntdirect/_sware/com/matlab_2016a/toolbox/matlab/codetools/initdesktoputils.m	MATLAB:Completion:ExcludedBy	Cannot be packaged for use in the target environment MCR. Removed from the parts list by license Compiler.	/mntdirect/_sware/com/matlab_2016a/toolbox/matlab/codetools

python/BBA/passmethodlist.m

-function passmethodlist()
-%UNTITLED2 Summary of this function goes here
-%   Detailed explanation goes here
-
-AperturePass
-BendLinearPass
-BndMPoleSymplectic4E2Pass
-BndMPoleSymplectic4E2RadPass
-BndMPoleSymplectic4E2QuantPass
-BndMPolePass
-BndMPoleSymplectic4Pass
-BndMPoleSymplectic4KinPass
-BndMPoleSymplectic4FrgFPass
-BndMPoleSymplectic4KinFrgFPass
-BndMPoleSymplectic4ExactPass
-BndMPoleSymplectic4ExactFrgFRadPass
-BndMPoleSymplectic4RadPass
-BndMPoleSymplectic4QuantPass
-BndMPoleSymplectic4KinRadPass
-BndMPoleSymplectic4FrgFRadPass
-BndMPoleSymplectic4FrgFQuantPass
-BndMPoleSymplectic4KinFrgFRadPass
-BndMPoleSymplectic4ExactRadPass
-BndMPoleSymplectic4ExactFrgFRadPass
-BndMPoleSymplecticFringes4Pass
-BndMPoleSymplecticFringesStrMpole4Pass
-BndMPoleSymplecticFringesGeneral4Pass
-CavityPass
-CorrectorPass
-DriftPass
-DriftKinPass
-DriftExactPass
-KinematicPass
-EAperturePass
-IdentityPass
-Matrix66Pass
-QuadLinearPass
-QuadMPoleFringePass
-QuadMPoleFringeRadPass
-QuadMPoleFringeQuantPass
-SolenoidLinearPass
-StrMPolePass
-StrMPoleSymplectic4Pass
-StrMPoleSymplectic4KinPass
-StrMPoleSymplectic4ExactPass
-StrMPoleSymplectic4FrgFPass
-StrMPoleSymplectic4KinFrgFPass
-StrMPoleSymplectic4ExactFrgFPass
-StrMPoleSymplecticFringes4Pass
-StrMPoleSymplecticFringesGeneral4Pass
-StrMPoleSymplectic4RadPass
-StrMPoleSymplectic4KinRadPass
-StrMPoleSymplectic4ExactRadPass
-StrMPoleSymplectic4FrgFRadPass
-StrMPoleSymplectic4KinFrgFRadPass
-StrMPoleSymplectic4ExactFrgFRadPass
-StrMPoleSymplecticFringes4Pass
-StrMPoleSymplecticFringesGeneral4Pass
-ThinMPolePass
-WiggLinearPass
-impedance_RWPass
-impedance_BBRPass
-impedance_BBRZPass
-impedance_LplusRPass
-impedance_tablePass
-DeltaQPass
-SimpleDampingPass
-SimpleNLRFPass
-QuantDiffPass
-NL_kickerPass
-
-end

python/BBA/readme.txt

-Packaging and Deploying test_class
-
-1. Prerequisites for Deployment 
-
-A. If MATLAB Runtime version 9.0.1 (R2016a) has not been installed, install it in one of 
-   these ways:
-
-i. Run the package installer, which will also install the MATLAB Runtime.
-
-ii. Download the Linux 64-bit version of the MATLAB Runtime for R2016a from:
-
-    http://www.mathworks.com/products/compiler/mcr/index.html
-   
-iii. Run the MATLAB Runtime installer provided with MATLAB.
-
-B. Verify that a Linux 64-bit version of Python 2.7, 3.3, and/or 3.4 is installed.
-
-2. Installing the test_class Package
-
-A. Go to the directory that contains the file setup.py and the subdirectory test_class. 
-   If you do not have write permissions, copy all its contents to a temporary location 
-   and go there.
-
-B. Execute the command:
-
-    python setup.py install [options]
-    
-If you have full administrator privileges, and install to the default location, you do 
-   not need to specify any options. Otherwise, use --user to install to your home folder, 
-   or --prefix="installdir" to install to "installdir". In the latter case, add 
-   "installdir" to the PYTHONPATH environment variable. For details, refer to:
-
-    https://docs.python.org/2/install/index.html
-
-C. Copy the following to a text editor:
-
-setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:<MCR_ROOT>/v90/runtime/glnxa64:<MCR_ROOT>/v90/bin/glnxa64:<MCR_ROOT>/v90/sys/os/glnxa64:<MCR_ROOT>/v90/sys/opengl/lib/glnxa64
-setenv XAPPLRESDIR <MCR_ROOT>/v90/X11/app-defaults
-
-Make the following changes:
-- If LD_LIBRARY_PATH is not yet defined, remove the string "${LD_LIBRARY_PATH}:". 
-- Replace "<MCR_ROOT>" with the directory where the MATLAB Runtime is installed.
-- If your shell does not support setenv, use a different command to set the environment 
-   variables.
-
-Finally, execute the commands or add them to your shell initialization file.
-
-3. Using the test_class Package
-
-The test_class package is on your Python path. To import it into a Python script or 
-   session, simply execute:
-
-    import test_class

python/BBA/requiredMCRProducts.txt

-35000	35010	
\ No newline at end of file

python/BBA/setup.py

-# Copyright 2015 The MathWorks, Inc.
-
-from distutils.core import setup
-from distutils.command.clean import clean
-from distutils.command.install import install
-
-class InstallRuntime(install):
-    # Calls the default run command, then deletes the build area 
-    # (equivalent to "setup clean --all").
-    def run(self):
-        install.run(self)
-        c = clean(self.distribution)
-        c.all = True
-        c.finalize_options()
-        c.run()
-
-if __name__ == '__main__':
-
-    setup(
-        name="matlabruntimeforpython",
-        version="R2016a",
-        description='A module to call MATLAB from Python',
-        author='MathWorks',
-        url='http://www.mathworks.com/',
-        platforms=['Linux', 'Windows', 'MacOS'],
-        packages=[
-        'test_class'
-        ],
-        package_data={'test_class': ['*.ctf']},
-        # Executes the custom code above in order to delete the build area.
-        cmdclass={'install': InstallRuntime}
-    )
-

python/BBA/test.py

-import Loops as loops
-import Bumps as bumps
-import OrbitController as oc
-import Quadrespmat as qmat
-import numpy as np
-import time
-
-loops = loops.Loops()
-bumps = bumps.Bumps()
-oc  = oc.OrbitController()
-qmat = qmat.Quadrespmat()
-
-plane='H'
-bpmi = 11