def processOneProjection(listOfDictionnaries, projectionNumber):
print('------------------------------------------------------')
print('processOneProjection')
projectionFiles = []
referencesFiles = []
darkFieldFiles = []
for dict in listOfDictionnaries:
projectionFiles.append(dict['projections'][projectionNumber])
referencesFiles.append(dict['references'][0])
darkFieldFiles.append(dict['darkField'])
print(projectionFiles)
Is = spytIO.openSeq(projectionFiles)
print(Is.shape)
Ir = spytIO.openSeq(referencesFiles)
print(Ir.shape)
df = spytIO.openSeq(darkFieldFiles)
print(df.shape)
#Is,Ir=corr.registerImagesBetweenThemselves(Is,Ir)
spytIO.save3D_Edf(
Is,
'/Volumes/ID17/speckle/md1097/id17/Phantoms/ThreeDimensionalPhantom/OpticalFlowMultiTomo/Is/Is_'
)
spytIO.save3D_Edf(
Ir,
'/Volumes/ID17/speckle/md1097/id17/Phantoms/ThreeDimensionalPhantom/OpticalFlowMultiTomo/Ir/Ir_'
)
toReturn = OpticalFlow.processProjectionSetWithDarkFields(Is, Ir, df)
return toReturn
def run(self):
for numeroProjection in self.listOfProjection:
numeroProjection=int(numeroProjection)
print('Processing '+str(numeroProjection))
projectionFiles = []
referencesFiles = []
darkFieldFiles = []
for dict in self.listOfDictionnaries:
projectionFiles.append(dict['projections'][numeroProjection])
referencesFiles.append(dict['references'][0])
darkFieldFiles.append(dict['darkField'])
print(projectionFiles)
Is = spytIO.openSeq(projectionFiles)
Ir = spytIO.openSeq(referencesFiles)
df = spytIO.openSeq(darkFieldFiles)
#Is, Ir = corr.registerImagesBetweenThemselves(Is, Ir)
result = OpticalFlow.processProjectionSetWithDarkFields(Is, Ir, df)
dx = result['dx']
dy = result['dy']
phi = result['phi']
phi2 = result['phi2']
phi3 = result['phi3']
textProj='%4.4d'%numeroProjection
spytIO.saveEdf(dx.real, self.dxFolder + '/dx' + textProj + '.edf')
spytIO.saveEdf(dy.real, self.dyFolder + '/dy' + textProj + '.edf')
spytIO.saveEdf(phi.real, self.phiFolder + '/phi' + textProj + '.edf')
spytIO.saveEdf(phi2.real, self.phi2Folder + '/phi2' + textProj + '.edf')
spytIO.saveEdf(phi3.real, self.phi3Folder + '/phi3' + textProj + '.edf')
def processOneProjection(listOfDictionnaries,projectionNumber):
print('------------------------------------------------------')
print('processOneProjection')
projectionFiles=[]
referencesFiles=[]
darkFieldFiles=[]
for dict in listOfDictionnaries :
projectionFiles.append(dict['projections'][projectionNumber])
referencesFiles.append(dict['references'][0])
darkFieldFiles.append(dict['darkField'])
print(projectionFiles)
Is=spytIO.openSeq(projectionFiles)
print(Is.shape)
Ir=spytIO.openSeq(referencesFiles)
print(Ir.shape)
df=spytIO.openSeq(darkFieldFiles)
print(df.shape)
#Is,Ir=corr.registerImagesBetweenThemselves(Is,Ir)
toReturn=OpticalFlow.processProjectionSetWithDarkFields(Is,Ir,df)
return toReturn
phi = result['phi']
phi2 = result['phi2']
phi3 = result['phi3']
gradientNorm = result['gradientNorm']
spytIO.saveEdf(dx, 'output/dx' + txtNbPoint + '.edf')
spytIO.saveEdf(dy.real, 'output/dy' + txtNbPoint + '.edf')
spytIO.saveEdf(phi.real, 'output/phi' + txtNbPoint + '.edf')
spytIO.saveEdf(phi2.real, 'output/phiLarkinson' + txtNbPoint + '.edf')
spytIO.saveEdf(phi3.real, 'output/phiKottler' + txtNbPoint + '.edf')
spytIO.saveEdf(gradientNorm, 'output/gradientNorm' + txtNbPoint + '.edf')
if __name__ == "__main__":
IrNames = glob.glob(
'/Users/embrun/Codes/specklematching/Experiments/MoucheSimapAout2017/ref/*.tif'
)
IsNames = glob.glob(
'/Users/embrun/Codes/specklematching/Experiments/MoucheSimapAout2017/sample/*.tif'
)
Ir = spytIO.openSeq(IrNames)
Is = spytIO.openSeq(IsNames)
nbPointsTotal = len(Is)
for nbPoints in range(1, nbPointsTotal + 1):
pointsToTake = generateArrayOfRandomNumbers(nbPoints, 0,
nbPointsTotal - 1)
IrToTake = Ir[pointsToTake]
IsToTake = Is[pointsToTake]
result = processProjectionSet(IsToTake, IrToTake)
saveresults(result, nbPoints)
Ir = spytIO.openImage(str(referenceFiles[0]))
Is = spytIO.openImage(str(sampleFiles[0]))
result = processOneProjection(Is, Ir)
dx = result['dx']
dy = result['dy']
phi = result['phi']
phi2 = result['phi2']
phi3 = result['phi3']
spytIO.saveEdf(dx, saveFolder + '/dx.edf')
spytIO.saveEdf(dy.real, saveFolder + '/dy.edf')
spytIO.saveEdf(phi.real, saveFolder + '/phi.edf')
spytIO.saveEdf(phi2.real, saveFolder + '/phi2.edf')
spytIO.saveEdf(phi3.real, saveFolder + '/phi3.edf')
Ir3D = spytIO.openSeq(referenceFiles)
Is3D = spytIO.openSeq(sampleFiles)
result = processProjectionSet(Is3D, Ir3D)
dx = result['dx']
dy = result['dy']
phi = result['phi']
phi2 = result['phi2']
phi3 = result['phi3']
spytIO.saveEdf(dx, saveFolder + '/dxAllFiles.edf')
spytIO.saveEdf(dy.real, saveFolder + '/dyAllFiles.edf')
spytIO.saveEdf(phi.real, saveFolder + '/phiAllFiles.edf')
spytIO.saveEdf(phi2.real, saveFolder + '/phi2AllFiles.edf')
spytIO.saveEdf(phi3.real, saveFolder + '/phi3AllFiles.edf')
#offsett=corr.registerRefAndSample(Ir,Is,1000)