First commit of Alvaro's xtcav code

SConscript

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+#--------------------------------------------------------------------------
+# File and Version Information:
+#  $Id$
+#
+# Description:
+#  SConscript file for package pyimgalgos
+#------------------------------------------------------------------------
+
+# Do not delete following line, it must be present in 
+# SConscript file for any SIT project
+Import('*')
+
+#
+# For the standard SIT packages which build libraries, applications,
+# and Python modules it is usually sufficient to call
+# standardSConscript() function which defines rules for all
+# above targets. Many standard packages do not need any special options, 
+# but those which need can modify standardSConscript() behavior using
+# a number of arguments, here is a complete list:
+#
+#    LIBS - list of additional libraries needed by this package
+#    LIBPATH - list of directories for additional libraries
+#    BINS - dictionary of executables and their corresponding source files
+#    TESTS - dictionary of test applications and their corresponding source files
+#    SCRIPTS - list of scripts in app/ directory
+#    UTESTS - names of the unit tests to run, if not given then all tests are unit tests
+#    PYEXTMOD - name of the Python extension module, package name used by default
+#    CCFLAGS - additional flags passed to C/C++ compilers
+#    NEED_QT - set to True to enable Qt support
+#
+#
+standardSConscript()

app/xtcavDark

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+#!/usr/bin/env python
+
+from xtcav.GenerateDarkBackground import *
+
+GDB=GenerateDarkBackground();
+
+GDB.experiment='amoc8114'
+GDB.runs='85'
+GDB.maxshots=150
+GDB.SetValidityRange(85,109)
+
+GDB.Generate();

app/xtcavLasingOff

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+#!/usr/bin/env python
+
+from xtcav.GenerateLasingOffReference import *
+
+GLOC=GenerateLasingOffReference();
+GLOC.experiment='amoc8114'
+GLOC.runs='86'
+GLOC.maxshots=401
+GLOC.nb=1
+GLOC.groupsize=5
+GLOC.SetValidityRange(86,91)
+
+GLOC.Generate();

doc/ChangeLog

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+#--------------------------------------------------------------------------
+# File and Version Information:
+#  $Id: ChangeLog 8463 2014-06-24 01:53:04Z [email protected] $
+#
+# Description:
+#  ChangeLog file for package xtcav
+#------------------------------------------------------------------------
+
+Package author: Alvaro Sanchez-Gonzalez
+
+Please describe any modifications that you made to the package in the
+reverse time order.
+
+Tag: V00-00-01
+2014-10-24 Christopher O'Grady
+- Initial tag

examples/xtcavShotToShot.py

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+import psana
+from xtcav.ShotToShotCharacterization import *
+
+maxshots=5             #Maximum number of valid shots to process
+experiment='amoc8114'  #Experiment label
+runs='87'              #Runs
+
+#Loading the dataset from the "dark" run, this way of working should be compatible with both xtc and hdf5 files
+dataSource=psana.DataSource("exp=%s:run=%s:idx" % (experiment,runs))
+
+#XTCAV Retrieval (setting the data source is useful to get information such as experiment name)
+XTCAVRetrieval=ShotToShotCharacterization();
+XTCAVRetrieval.SetDataSource(dataSource)
+
+for r,run in enumerate(dataSource.runs()):
+    n_r=0  #Counter for the total number of xtcav images processed within the run       
+    times = run.times()
+    for t in times:
+        evt = run.event(t)
+
+        if not XTCAVRetrieval.SetCurrentEvent(evt):
+            continue
+
+        t,power=XTCAVRetrieval.XRayPower()  
+        agreement=XTCAVRetrieval.ReconstructionAgreement()      
+
+        print "%d/%d" % (n_r,maxshots) #Debugging purposes, will be removed
+        print 'Agreement: %g %% Maximum power: %g GW' %(agreement*100,np.amax(power))
+
+        n_r=n_r+1            
+
+        if n_r>=maxshots: #After a certain number of shots we stop (Ideally this would be an argument, rather than a hardcoded value)
+            break

src/CalibrationPaths.py

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+from psana import *
+from PSCalib.CalibFileFinder import CalibFileFinder
+
+class CalibrationPaths:
+    def __init__(self,datasource):
+        self.ds = datasource
+        self.calibgroup = 'Xtcav::CalibV1'
+        self.src  = 'XrayTransportDiagnostic.0:Opal1000.0'
+        self.cdir = self.ds.env().calibDir()
+
+    def findCalFileName(self,type,rnum):
+        """
+        Returns calibration file name, given run number and type
+        """              
+        cff = CalibFileFinder(self.cdir, self.calibgroup, pbits=0)
+        fname = cff.findCalibFile(self.src, type, rnum)
+        return fname
+
+    def newCalFileName(self,type,runBegin,runEnd='end'):
+        """
+        Returns calibration file name, given run number and type
+        (either 'pedestals' or 'nolasing' for XTCAV.)"
+        """
+
+        path=os.path.join(self.cdir)
+        if not os.path.exists(path): 
+            os.mkdir(path)
+        path=os.path.join(self.cdir,self.calibgroup)
+        if not os.path.exists(path): 
+            os.mkdir(path)
+        path=os.path.join(self.cdir,self.calibgroup,self.src)
+        if not os.path.exists(path): 
+            os.mkdir(path)
+        path=os.path.join(self.cdir,self.calibgroup,self.src,type)
+        if not os.path.exists(path): 
+            os.mkdir(path)
+        return path+'/'+str(runBegin)+'-'+str(runEnd)+'.data'

src/Constants.py

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+import h5py
+import numpy
+import logging
+
+class Empty(object):
+    pass
+
+class ConstantsStore(object):
+    def __init__(self,obj,file):
+        self.f = h5py.File(file,'w')
+        self.cwd = ''
+        for name in obj.__dict__:
+            subobj = getattr(obj,name)
+            self.dispatch(subobj,name)
+        self.f.close()
+    def pushdir(self,dir):
+        '''move down a level and keep track of what hdf directory level we are in'''
+        self.cwd += '/'+dir
+    def popdir(self):
+        '''move up a level and keep track of what hdf directory level we are in'''
+        self.cwd = self.cwd[:self.cwd.rfind('/')]
+    def typeok(self,obj,name):
+        '''check if we support serializing this type to hdf'''
+        allowed = [dict,int,float,str,numpy.ndarray]
+        return type(obj) in allowed
+    def storevalue(self,v,name):
+        '''persist one of the supported types to the hdf file'''
+        self.f[self.cwd+'/'+name] = v
+    def dict(self,d,name):
+        '''called for every dictionary level to create a new hdf group name.
+        it then looks into the dictionary to see if other groups need to
+        be created'''
+        self.f.create_group(name)
+        self.pushdir(name)
+        for k in d.keys():
+            self.dispatch(d[k],k)
+        self.popdir()
+    def dispatch(self,obj,name):
+        '''either persist a supported object, or look into a dictionary
+        to see what objects need to be persisted'''
+        if type(obj) is dict:
+            self.dict(obj,name)
+        else:
+            if self.typeok(obj,name):
+                self.storevalue(obj,name)
+            else:
+                logging.warning('XTCAV Constants.py: variable "'+name+'" of type "'+type(obj).__name__+'" not supported')
+
+class ConstantsLoad(object):
+    def __init__(self,file):
+        self.obj = Empty()
+        self.f = h5py.File(file,'r')
+        self.f.visititems(self.loadCallBack)
+        self.f.close()
+    def setval(self,name,obj):
+        '''see if this hdfname has a / in it.  if so, create the dictionary
+        object.  if not, set our attribute value.  call ourselves
+        recursively to see if other dictionary levels exist.'''
+        if '/' in name:
+            dictname=name[:name.find('/')]
+            remainder=name[name.find('/')+1:]
+            if not hasattr(self.obj,dictname):
+                setattr(obj,dictname,{})
+            self.setval(remainder,getattr(obj,dictname))
+        else:
+            if type(obj) is dict:
+                obj[name]=self.f[self.fullname].value
+            else:
+                setattr(obj,name,self.f[self.fullname].value)
+    def loadCallBack(self,name,obj):
+        '''called back by h5py routine visititems for each
+        item (group/dataset) in the h5 file'''
+        if isinstance(obj,h5py._hl.group.Group):
+            return
+        self.fullname = name
+        self.setval(name,self.obj)
+
+def Load(file):
+    '''takes a string filename, and returns a constants object.'''
+    c = ConstantsLoad(file)
+    return c.obj
+
+def Save(obj,file):
+    '''store a constants object in an hdf5 file.  the object
+    can be a hierarchy (defined by python dictionaries) and
+    hdf5 supported types (int, float, numpy.ndarray, string).
+    the hierarchy can be created by having one value of
+    a dictionary itself be a dictionary.'''
+    c = ConstantsStore(obj,file)
+
+if __name__ == "__main__":
+
+    import cPickle
+    f = open("/reg/d/psdm/amo/amoc8114/calib/XTCAV/XrayTransportDiagnostic.0:Opal1000.0/lasingoffreference/151-159.data")
+    data = cPickle.load(f)
+    Save(data,'junk.h5')
+    data = Load('junk.h5')
+    print data.parameters

src/CustomLoadmat.py

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+#Code extracted from http://stackoverflow.com/questions/7008608/scipy-io-loadmat-nested-structures-i-e-dictionaries
+
+import scipy.io
+
+def customloadmat(filename):
+    '''
+    this function should be called instead of direct spio.loadmat
+    as it cures the problem of not properly recovering python dictionaries
+    from mat files. It calls the function check keys to cure all entries
+    which are still mat-objects
+    '''
+    data = scipy.io.loadmat(filename, struct_as_record=False, squeeze_me=True)
+    return _check_keys(data)
+
+def _check_keys(dict):
+    '''
+    checks if entries in dictionary are mat-objects. If yes
+    todict is called to change them to nested dictionaries
+    '''
+    for key in dict:
+        if isinstance(dict[key], scipy.io.matlab.mio5_params.mat_struct):
+            print key
+            dict[key] = _todict(dict[key])
+    return dict        
+
+def _todict(matobj):
+    '''
+    A recursive function which constructs from matobjects nested dictionaries
+    '''
+    dict = {}
+    for strg in matobj._fieldnames:
+        elem = matobj.__dict__[strg]
+        if isinstance(elem, scipy.io.matlab.mio5_params.mat_struct):
+            dict[strg] = _todict(elem)
+        else:
+            dict[strg] = elem
+    return dict

src/DarkBackground.py

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+
+import scipy.io
+import cPickle
+import numpy
+from xtcav.CustomLoadmat import customloadmat
+from xtcav.Constants import Load as constLoad
+from xtcav.Constants import Save as constSave
+
+class DarkBackground(object):
+    def __init__(self):
+        self.image=[]
+        self.ROI=[]
+        self.runs=numpy.array([],dtype=int)
+        self.n=0
+
+    def Save(self,path):        
+        constSave(self,path)
+
+    @staticmethod    
+    def Load(path):        
+        return constLoad(path)