def bias_bySNR_analytic():
'''
Produces the analytic bias as a function of SNR.
ToDo:
Add this to bias_bySNR routine
'''
import src.measure_Bias as mBias
import src.model_Production as modPro
global imageParams
modPro.set_modelParameter(imageParams, fitParamsLabels, fitParamsValues)
handle = intialise_Output(Output+filePrefix+'_AnaBias.dat', mode = 'a')
handle.write('## Recovered statistics as a result of bias run, single fit at a time, done analytically. Output of form [Bias] repeated for all fit quantities \n')
for k in fitParamsLabels:
handle.write('#'+str(k)+' = '+str(fittedParameters[k])+'\n')
S = -1 #Counter
filenames = []
e = 0 ##Loop over this for multiple runs
while True:
print '\n'+400*'-'
S += 1
SNR = SNRRange[0] + S*SNRRange[2]
##Exit Condition
if(SNR > SNRRange[1]):
break
##Set Model
imageParams['SNR'] = SNR
##Produce image to update noise to correct value (THIS IS A HACK AND NEEDS CHANGED) - estimate_Noise works fairly well, but you need to specify the noise correctly
#disc, imageParams = modPro.get_Pixelised_Model(imageParams, noiseType = 'G', outputImage = False)
## Check image to get SNR
imageSB, imageParams = modPro.user_get_Pixelised_Model(imageParams, outputImage = True, sbProfileFunc = SBPro.gaussian_SBProfile_Weave)
imageParams['noise'] = modPro.SNR_Mapping(imageSB, SNR = SNR)
print 'Analytic Bias Check: For SNR', SNR, ' has noise var:', imageParams['noise']
bias = np.array(mBias.analytic_GaussianLikelihood_Bias(fitParamsValues, fitParamsLabels, imageParams, diffType = 'ana'))
#bias = np.array([mBias.analytic_GaussianLikelihood_Bias(fitParamsValues[e], fitParamsLabels[e], imageParams, diffType = 'ana')])
print '\n Analytic Bias for SNR:', SNR, ' is :', bias
print ' '
### different to bias_bySNR
np.savetxt(handle, np.hstack((np.array(SNR).reshape(1,1),bias.reshape(1,bias.shape[0]))))#.reshape(1,bias.shape[1]+1))
handle.close()
def bias_bySNR():
'''
Run multiple realisations and produces SB profile estimates for each run. Set up for measurment of e1, should be generalised.
To Do:
--Generalise to multiple parameters: fitParams and setting defaults for thes fitParams, so that routine does not have any information on these parameters
--Mean output: Header information - fitParams and input value
'''
print 'Producing Bias by SNR ratio'
nRealisation = 10000000 ##This labels the maximum number of iterations
percentError = 1
global imageParams
modPro.set_modelParameter(imageParams, fitParamsLabels, fitParamsValues)
##Get NoiseFree Image
noiseFreeImage, disc = modPro.user_get_Pixelised_Model(imageParams, noiseType = None, sbProfileFunc = SBPro.gaussian_SBProfile_Weave)
modelLookup = None
if(len(fitParamsLabels) <= 2 and useLookup):
modelLookup = modPro.get_Model_Lookup(imageParams, fitParamsLabels, lookupRange, lookupWidth, noiseType = None, sbProfileFunc = SBPro.gaussian_SBProfile_Weave)
print 'Created model lookup table'
print 'Simulating Bias in SNR bins:\n'
S = -1 #Counter
filenames = []; SNRStore = []
while True:
S += 1
SNR = SNRRange[0] + S*SNRRange[2]
##Exit Condition
if(SNR > SNRRange[1]):
break
##Set Model
imageParams['SNR'] = SNR
## Store SNR for output
SNRStore.append(SNR)
##Intialise output and set header
filenames.append(Output+filePrefix+'_SNR'+str(SNR)+'.dat')
handle = intialise_Output(filenames[S], mode = 'a')
##Write Header
handle.write('# Bias Run Output. Following is input image parameters \n')
for k in imageParams.keys():
handle.write('#'+str(k)+' = '+str(imageParams[k])+'\n')
## Output Bias Corrected value
bchandle = None
if(biasCorrect):
bchandle = intialise_Output(Output+filePrefix+'_SNR'+str(SNR)+'_BC.dat', mode = 'a')
bchandle.write('# Bias Corrected Bias Run Output. Following is input image parameters \n')
for k in imageParams.keys():
bchandle.write('#'+str(k)+' = '+str(imageParams[k])+'\n')
MaxL = np.zeros((nRealisation, len(fitParamsLabels))); BCMaxL = np.zeros(MaxL.shape); MaxLErr = np.zeros(MaxL.shape)
for real in range(nRealisation):
## This version uses GALSIM default
#image, imageParams = modPro.get_Pixelised_Model(imageParams, noiseType = 'G')
## GALSIM with user-defined SB Profile
#image, imageParams = modPro.get_Pixelised_Model(imageParams, noiseType = 'G', sbProfileFunc = SBPro.gaussian_SBProfile_Weave)
## SYMPY - Very slow
#modPro.get_Pixelised_Model_wrapFunction(0., imageParams, noiseType = 'G', outputImage = False, sbProfileFunc = SBPro.gaussian_SBProfile_Sympy)
## Entirely user-defined
image, imageParams = modPro.user_get_Pixelised_Model(imageParams, noiseType = 'G', sbProfileFunc = SBPro.gaussian_SBProfile_Weave, inputImage = noiseFreeImage)
#MLEx = ML.find_ML_Estimator(image, modelLookup = None, fitParams = fittedParameters.keys(), outputHandle = None, setParams = imageParams, e1 = 0.35) ##Needs edited to remove information on e1 (passed in for now) - This should only ever be set to the parameters being fit
##Find usign lookup table where appropriate
MLReturn = ML.find_ML_Estimator(image, modelLookup = modelLookup, fitParams = fitParamsLabels, outputHandle = handle, searchMethod = minimiseMethod, preSearchMethod = preSearchMethod, bruteRange = bruteRange, biasCorrect = biasCorrect, bcoutputHandle = bchandle, error = errorType, setParams = imageParams.copy(), **initialGuess)
if(biasCorrect):
MaxL[real,:], BCMaxL[real,:] = MLReturn[0:2]
if(len(MLReturn) == 3): #Erro is output
MaxLErr[real,:] = MLReturn[2]
else:
MaxL[real,:] = MLReturn[0]
if(len(MLReturn) == 2):#Error is output
MaxLErr[real,:] = MLReturn[1]
if(real > 10000 and real%1000 == 0 and percentError > 0.):
Mean = (MaxL[:real,:].mean(axis = 0)-fitParamsValues); Err = MaxL[:real,:].std(axis = 0)/np.sqrt(real)
if((np.absolute(100.*(Err/Mean)) < percentError).sum() == MaxL.shape[1]):
print '\n For SNR:', SNR, ' percentage error was reached in ', real, ' simulated images'
print 'With mean, std, %Err:', Mean, Err, np.absolute(100.*(Err/Mean))
break
#print '----- Realisation:', real, ':: Ex:', MLEx, ' Look:', MLLook, ' :: Ratio:', MLEx/MLLook
#raw_input('Check')
handle.close()
### Construct and output mean, std and error on mean for each fit parameter
handle1 = intialise_Output(Output+filePrefix+'_Statistics.dat', mode = 'a')
handle1.write('## Recovered statistics as a result of bias run. Output of form [Mean, StD, Error on Mean] repeated for all fit quantities \n')
for k in fittedParameters.keys():
handle1.write('#'+str(k)+' = '+str(fittedParameters[k])+'\n')
handle2 = intialise_Output(Output+filePrefix+'_Bias.dat', mode = 'a')
handle2.write('## Recovered statistics as a result of bias run. Output of form [Bias, StD, Error on Bias] repeated for all fit quantities \n')
for k in fittedParameters.keys():
handle2.write('#'+str(k)+' = '+str(fittedParameters[k])+'\n')
##Produce Mean, StD from sampling and output
for f in range(len(filenames)):
Input = np.genfromtxt(filenames[f])
SNR = SNRStore[f]
Mean = Input.mean(axis = 0); StD = Input.std(axis = 0); MeanStD = StD/np.sqrt(Input.shape[0])
if(len(fittedParameters.keys()) == 1):
out = np.array([SNR, Mean, StD, MeanStD])
np.savetxt(handle1, out.reshape(1,out.shape[0]))
out = np.array([SNR, Mean-fittedParameters.values()[0], StD, MeanStD])
np.savetxt(handle2, out.reshape(1,out.shape[0]))
else:
out = np.array([ [SNR, Mean[l], StD[l], MeanStD[l]] for l in range(len(fittedParameters.keys())) ]).flatten()
np.savetxt(handle1, out.reshape(1,out.shape[0]))
out = np.array([ [SNR, Mean[l]-fittedParameters.values()[l], StD[l], MeanStD[l]] for l in range(len(fittedParameters.keys())) ]).flatten()
np.savetxt(handle2, out.reshape(1,out.shape[0]))
print 'Finished SNR Bias loop without incident'