def classProportions( labs ):
res = np.histogram( labs, bins=range(pomio.getNumClasses()+1) )[0].astype(float)
s = res.sum()
if s>0:
prop = res / s
else:
prop = np.zeros( (pomio.getNumClasses(),), dtype=float )
return prop, res
def classProportions(labs):
res = np.histogram(labs,
bins=range(pomio.getNumClasses() + 1))[0].astype(float)
s = res.sum()
if s > 0:
prop = res / s
else:
prop = np.zeros((pomio.getNumClasses(), ), dtype=float)
return prop, res
def reportAccuracy( exptName, labs, predlabs ):
print exptName, ' accuracy (frac correct) = ', np.mean(predlabs==labs)
apc = accuracyPerClass( labs, predlabs )
print ' - average accuracy per class = ', apc.mean()
for i in range(pomio.getNumClasses()):
print ' %s: %f' %( pomio.getClasses()[i], apc[i] )
clp, clnum = classProportions( labs )
print ' - class proportions in %s:' % exptName
for i in range(pomio.getNumClasses()):
print ' %15s: %.6f (%6d examples)' %( pomio.getClasses()[i], clp[i], clnum[i] )
def reportAccuracy(exptName, labs, predlabs):
print exptName, ' accuracy (frac correct) = ', np.mean(predlabs == labs)
apc = accuracyPerClass(labs, predlabs)
print ' - average accuracy per class = ', apc.mean()
for i in range(pomio.getNumClasses()):
print ' %s: %f' % (pomio.getClasses()[i], apc[i])
clp, clnum = classProportions(labs)
print ' - class proportions in %s:' % exptName
for i in range(pomio.getNumClasses()):
print ' %15s: %.6f (%6d examples)' % (pomio.getClasses()[i],
clp[i], clnum[i])
def classifyFeatures( features, classifier, requireAllClasses=True ):
if requireAllClasses:
assert classifier.classes_ == np.arange( pomio.getNumClasses() ), \
'Error: given classifier only has %d classes - %s' % \
( len(classifier.classes_), str(classifier.classes_) )
c = classifier.predict( features )
return c
def classifyFeatures(features, classifier, requireAllClasses=True):
if requireAllClasses:
assert classifier.classes_ == np.arange( pomio.getNumClasses() ), \
'Error: given classifier only has %d classes - %s' % \
( len(classifier.classes_), str(classifier.classes_) )
c = classifier.predict(features)
return c
def trainLogisticRegressionModel(
featureData, labels, Cvalue, outputClassifierFile, scaleData=True, requireAllClasses=True
):
# See [http://scikit-learn.org/dev/modules/generated/sklearn.linear_model.LogisticRegression.html]
# Features are numPixel x numFeature np arrays, labels are numPixel np array
numTrainDataPoints = np.shape(featureData)[0]
numDataLabels = np.size(labels)
assert ( np.size( np.shape(labels) ) == 1) , ("Labels should be a 1d array. Shape of labels = " + str(np.shape(labels)))
assert ( numTrainDataPoints == numDataLabels) , ("The length of the feature and label data arrays must be equal. Num data points=" + str(numTrainDataPoints) + ", labels=" + str(numDataLabels) )
classLabels = np.unique(labels)
assert not requireAllClasses or \
( np.size(classLabels) == pomio.getNumClasses() or np.size(classLabels) == pomio.getNumLabels() ), \
"Training data does not contains all classes::\n\t" + str(classLabels)
if scaleData == True:
featureData = preprocessing.scale(featureData)
# sklearn.linear_model.LogisticRegression(penalty='l2', dual=False, tol=0.0001, C=1.0, fit_intercept=True, intercept_scaling=1, class_weight=None, random_state=None)
lrc = LogisticRegression(penalty='l1' , dual=False, tol=0.0001, C=Cvalue, fit_intercept=True, intercept_scaling=1)
lrc.fit(featureData, labels)
pickleObject(lrc, outputClassifierFile)
print "LogisticRegression classifier saved to " + str(outputClassifierFile)
return lrc
def accuracyPerClass(labsGT, labsPred):
n = pomio.getNumClasses()
correct = (labsGT == labsPred)
res = np.zeros((n, ), dtype=float)
for i in range(n):
msk = labsGT == i
if np.any(msk):
res[i] = np.mean(correct[labsGT == i])
return res
def accuracyPerClass( labsGT, labsPred ):
n = pomio.getNumClasses()
correct = (labsGT == labsPred)
res = np.zeros( (n,), dtype=float )
for i in range(n):
msk = labsGT == i
if np.any(msk):
res[i] = np.mean( correct[ labsGT == i ] )
return res
def classProbsOfFeatures( features, classifier, requireAllClasses=True ):
if requireAllClasses:
assert classifier.classes_ == np.arange( pomio.getNumClasses() ), \
'Error: given classifier only has %d classes - %s' % \
( len(classifier.classes_), str(classifier.classes_) )
probs = classifier.predict_proba( features )
if len(classifier.classes_) != pomio.getNumClasses():
# Transform class probs to the correct sized matrix.
nbClasses = pomio.getNumClasses()
n = probs.shape[0]
cpnew = np.zeros( (n, nbClasses) )
for i in range( probs.shape[1] ):
# stuff this set of probs to new label
cpnew[:,classifier.classes_[i]-1] = probs[:,i]
probs = cpnew
del cpnew
assert probs.shape[1] == pomio.getNumClasses()
return probs
def classProbsOfFeatures(features, classifier, requireAllClasses=True):
if requireAllClasses:
assert classifier.classes_ == np.arange( pomio.getNumClasses() ), \
'Error: given classifier only has %d classes - %s' % \
( len(classifier.classes_), str(classifier.classes_) )
probs = classifier.predict_proba(features)
if len(classifier.classes_) != pomio.getNumClasses():
# Transform class probs to the correct sized matrix.
nbClasses = pomio.getNumClasses()
n = probs.shape[0]
cpnew = np.zeros((n, nbClasses))
for i in range(probs.shape[1]):
# stuff this set of probs to new label
cpnew[:, classifier.classes_[i] - 1] = probs[:, i]
probs = cpnew
del cpnew
assert probs.shape[1] == pomio.getNumClasses()
return probs
def classProbsOfFeatures( features, classifier ):
assert np.all( classifier.classes_ == np.arange( pomio.getNumClasses() ) ), \
'Error: given classifier has %d classes, expecting %d - %s' % \
( len(classifier.classes_), pomio.getNumClasses(), str(classifier.classes_) )
probs = classifier.predict_proba( features )
# Can't happen now due to above assertion
# if len(classifier.classes_) != pomio.getNumClasses():
# # Transform class probs to the correct sized matrix.
# nbClasses = pomio.getNumClasses()
# n = probs.shape[0]
# cpnew = np.zeros( (n, nbClasses) )
# for i in range( probs.shape[1] ):
# # stuff this set of probs to new label
# cpnew[:,classifier.classes_[i]] = probs[:,i]
# probs = cpnew
# del cpnew
assert probs.shape[1] == pomio.getNumClasses()
assert probs.shape[0] == features.shape[0]
return probs
def generateImagePredictionClassDist(rgbImage,
classifier,
requireAllClasses=True):
"""This image takes an RGB image as an (i,j,3) numpy array, a scikit-learn classifier and produces probability distribution over each pixel and class.
Returns an (i,j,N) numpy array where N= total number of classes for use in subsequent modelling."""
# TODO Broaden to cope with more classifiers :)
#assert (str(type(classifier)) == "<class 'sklearn.linear_model.logistic.LogisticRegression'>") , "Check classifier type value:: " + str(type(classifier))
testClassifier = None
imageDimensions = rgbImage[:, :, 0].shape
nbCols = imageDimensions[1]
nbRows = imageDimensions[0]
#params = classifier.get_params(deep=True)
#print "Classifier paras::" , params
# Take image, generate features, use classifier to predict labels, ensure normalised dist and shape to (i,j,N) np.array
# generate predictions for the image
# todo: replace with features.computePixelFeatures JRS
imagePixelFeatures = FeatureGenerator.generatePixelFeaturesForImage(
rgbImage)
#print imagePixelFeatures
predictedPixelLabels = classifier.predict(imagePixelFeatures)
predictionProbs = classifier.predict_proba(imagePixelFeatures)
print "\nShape of predicted labels::", np.shape(predictedPixelLabels)
print "\nShape of prediction probs::", np.shape(predictionProbs)
numClasses = pomio.getNumClasses()
assert not requireAllClasses or \
(np.shape(predictionProbs)[1] == numClasses or \
np.shape(predictionProbs)[1] == numClasses+1) , \
"Classifer prediction does not match all classes (23 or 24):: " + \
str(np.shape(predictionProbs)[1])
print predictionProbs
#!!predictionProbs = np.reshape(predictionProbs, (nbCols, nbRows, numClasses ))
print 'reshaping to ', (nbCols, nbRows, predictionProbs.shape[1])
predictionProbs = np.reshape(predictionProbs,
(nbRows, nbCols, predictionProbs.shape[1]))
return predictionProbs
def evaluateConfusionMatrix(predictedImg, gtImg):
assert np.shape(predictedImg) == np.shape(
gtImg), "Predict image and ground truth image are not the same size..."
numClasses = pomio.getNumClasses()
confusionMatrix = np.zeros([numClasses, numClasses], int)
# rows are actual, cols are predicted
for cl in range(numClasses):
clMask = (gtImg == cl)
# It's easy, just histogram those values
vals = predictedImg[clMask]
assert np.all(np.logical_and(0 <= vals, vals < numClasses)), vals.max()
confusionMatrix[cl, :] = np.histogram(vals, range(numClasses + 1))[0]
assert confusionMatrix.sum() == np.count_nonzero(
gtImg != pomio.getVoidIdx())
return confusionMatrix
def generateImagePredictionClassDist(rgbImage, classifier, requireAllClasses=True):
"""This image takes an RGB image as an (i,j,3) numpy array, a scikit-learn classifier and produces probability distribution over each pixel and class.
Returns an (i,j,N) numpy array where N= total number of classes for use in subsequent modelling."""
# TODO Broaden to cope with more classifiers :)
#assert (str(type(classifier)) == "<class 'sklearn.linear_model.logistic.LogisticRegression'>") , "Check classifier type value:: " + str(type(classifier))
testClassifier = None
imageDimensions = rgbImage[:,:,0].shape
nbCols = imageDimensions[1]
nbRows = imageDimensions[0]
#params = classifier.get_params(deep=True)
#print "Classifier paras::" , params
# Take image, generate features, use classifier to predict labels, ensure normalised dist and shape to (i,j,N) np.array
# generate predictions for the image
# todo: replace with features.computePixelFeatures JRS
imagePixelFeatures = FeatureGenerator.generatePixelFeaturesForImage(rgbImage)
#print imagePixelFeatures
predictedPixelLabels = classifier.predict(imagePixelFeatures)
predictionProbs = classifier.predict_proba(imagePixelFeatures)
print "\nShape of predicted labels::" , np.shape(predictedPixelLabels)
print "\nShape of prediction probs::" , np.shape(predictionProbs)
numClasses = pomio.getNumClasses()
assert not requireAllClasses or \
(np.shape(predictionProbs)[1] == numClasses or \
np.shape(predictionProbs)[1] == numClasses+1) , \
"Classifer prediction does not match all classes (23 or 24):: " + \
str(np.shape(predictionProbs)[1])
print predictionProbs
#!!predictionProbs = np.reshape(predictionProbs, (nbCols, nbRows, numClasses ))
print 'reshaping to ', (nbCols, nbRows, predictionProbs.shape[1] )
predictionProbs = np.reshape(predictionProbs, (nbRows, nbCols, predictionProbs.shape[1] ))
return predictionProbs
def trainLogisticRegressionModel(featureData,
labels,
Cvalue,
outputClassifierFile,
scaleData=True,
requireAllClasses=True):
# See [http://scikit-learn.org/dev/modules/generated/sklearn.linear_model.LogisticRegression.html]
# Features are numPixel x numFeature np arrays, labels are numPixel np array
numTrainDataPoints = np.shape(featureData)[0]
numDataLabels = np.size(labels)
assert (np.size(np.shape(labels)) == 1), (
"Labels should be a 1d array. Shape of labels = " +
str(np.shape(labels)))
assert (numTrainDataPoints == numDataLabels), (
"The length of the feature and label data arrays must be equal. Num data points="
+ str(numTrainDataPoints) + ", labels=" + str(numDataLabels))
classLabels = np.unique(labels)
assert not requireAllClasses or \
( np.size(classLabels) == pomio.getNumClasses() or np.size(classLabels) == pomio.getNumLabels() ), \
"Training data does not contains all classes::\n\t" + str(classLabels)
if scaleData == True:
featureData = preprocessing.scale(featureData)
# sklearn.linear_model.LogisticRegression(penalty='l2', dual=False, tol=0.0001, C=1.0, fit_intercept=True, intercept_scaling=1, class_weight=None, random_state=None)
lrc = LogisticRegression(penalty='l1',
dual=False,
tol=0.0001,
C=Cvalue,
fit_intercept=True,
intercept_scaling=1)
lrc.fit(featureData, labels)
pickleObject(lrc, outputClassifierFile)
print "LogisticRegression classifier saved to " + str(outputClassifierFile)
return lrc
if 0:
# logistic regression
# Use fixed C
C = 0.5
classifier = trainLogisticRegressionModel(
trainingData[0][subset,:], trainingData[1][subset], C, classifierBaseFilename, \
scaleData=True, \
requireAllClasses=False
)
elif 0:
# Neural Network
# Construct nn dataset
datmat = trainingData[0][subset, :]
labvec = trainingData[1][subset]
nbFeatures = datmat.shape[1]
nbClasses = pomio.getNumClasses()
nbHidden = 100
maxIter = 200
classifier = NeuralNet.NNet(nbFeatures, nbClasses, nbHidden)
nnds = classifier.createTrainingSetFromMatrix(datmat, labvec)
classifier.trainNetworkBackprop(nnds, maxIter)
else:
#classifier = None
# Random forest
datmat = trainingData[0][subset, :]
labvec = trainingData[1][subset]
print '**Training a random forest on %d examples...' % len(labvec)
print 'Labels represented: ', np.unique(labvec)
classifier = sklearn.ensemble.RandomForestClassifier(\
n_estimators=100)
classifier = classifier.fit(datmat, labvec)
def getSuperPixelData(msrcImages, numberSuperPixels, superPixelCompactness):
# Should probably make this a call to pomio in case the ordering changes in the future...
voidClassLabel = pomio.getVoidIdx()
numberImages = len(msrcImages)
# for each image:
# determine superpixel label (discard if void)
# compute superpixel features of valid superpixels
# append features to cumulative array of all super pixel features
# append label to array of all labels
superPixelFeatures = None
superPixelLabels = np.array([], int) # used for superpixel labels
numberVoidSuperPixels = 0 # keep track of void superpixels
nbClasses = pomio.getNumClasses()
classAdjCounts = np.zeros((nbClasses, nbClasses))
adjCountsTotal = 0
adjVoidCountsTotal = 0
for imgIdx in range(0, numberImages):
superPixelIgnoreList = np.array(
[], int
) # this is used to skip over the superpixel in feature processing
print "\n**Processing Image#", (imgIdx + 1), " of", numberImages
# get raw image and ground truth labels
img = msrcImages[imgIdx].m_img
imgPixelLabels = msrcImages[imgIdx].m_gt
# create superpixel map and graph for image
spgraph = SuperPixels.computeSuperPixelGraph(
img, 'slic', [numberSuperPixels, superPixelCompactness])
imgSuperPixelMask = spgraph.m_labels
imgSuperPixels = spgraph.m_nodes
numberImgSuperPixels = spgraph.getNumSuperPixels()
# create superpixel exclude list & superpixel label array
allSPClassLabels = []
for spIdx in range(0, numberImgSuperPixels):
superPixelValue = imgSuperPixels[spIdx]
#print "\tINFO: Processing superpixel =", superPixelValue , " of" , numberImgSuperPixels, " in image"
# Assume superpixel labels are sequence of integers
superPixelValueMask = (
imgSuperPixelMask == superPixelValue
) # Boolean array for indexing superpixel-pixels
superPixelLabel = assignClassLabelToSuperPixel(
superPixelValueMask, imgPixelLabels)
allSPClassLabels.append(superPixelLabel)
if (superPixelLabel == voidClassLabel):
# add to ignore list, increment void count & do not add to superpixel label array
superPixelIgnoreList = np.append(superPixelIgnoreList,
superPixelValue)
numberVoidSuperPixels = numberVoidSuperPixels + 1
else:
superPixelLabels = np.append(superPixelLabels, superPixelLabel)
assert len(allSPClassLabels) == numberImgSuperPixels
(theseClassAdjCounts, adjVoidCount,
adjCount) = spgraph.countClassAdjacencies(nbClasses, allSPClassLabels)
classAdjCounts += theseClassAdjCounts
adjCountsTotal += adjCount
adjVoidCountsTotal += adjVoidCount
# Now we have the superpixel labels, and an ignore list of void superpixels - time to get the features!
imgSuperPixelFeatures = FeatureGenerator.generateSuperPixelFeatures(
img, imgSuperPixelMask, excludeSuperPixelList=superPixelIgnoreList)
if superPixelFeatures == None:
superPixelFeatures = imgSuperPixelFeatures
else:
# stack the superpixel features into a single list
superPixelFeatures = np.vstack(
[superPixelFeatures, imgSuperPixelFeatures])
assert np.shape(superPixelFeatures)[0] == np.shape(
superPixelFeatures)[0], "Number of samples != number labels"
print "\n**Processed total of", numberImages, "images"
print " %d out of %d adjacencies were ignored due to void (%.2f %%)" % \
(adjVoidCountsTotal, adjCountsTotal, \
100.0*adjVoidCountsTotal/adjCountsTotal)
# Now return the results
return [superPixelFeatures, superPixelLabels, classAdjCounts]
import numpy as np
"""
Neural Network Classifier
"""
#from amb.seg import pomio, FeatureGenerator
import pomio
import FeatureGenerator
from pybrain.tools.shortcuts import buildNetwork
from pybrain.supervised import BackpropTrainer
from pybrain.datasets.classification import ClassificationDataSet
numFeatures = 86
numClasses = pomio.getNumClasses() # no void class
voidClass = 13
class NNet:
def __init__(self, numFeatures, numClasses, nbHidden=None):
if nbHidden == None:
nbHidden = np.round((numFeatures + numClasses) / 2,
0).astype('int')
self.net = buildNetwork(numFeatures, nbHidden, numClasses, bias=True)
self.nbFeatures = numFeatures
self.nbClasses = numClasses
print "\tNetwork creation complete:"
print "\t\tinputLayer=", self.net['in']
print "\t\thiddenLayer=", self.net['hidden0']
print "\t\toutputLayer=", self.net['out']
import numpy as np
#from amb.seg import pomio, FeatureGenerator
import pomio
import FeatureGenerator
from pybrain.tools.shortcuts import buildNetwork
from pybrain.supervised import BackpropTrainer
from pybrain.datasets.classification import ClassificationDataSet
numFeatures = 86
numClasses = pomio.getNumClasses() # no void class
voidClass = 13
class NNet:
def __init__(self, numFeatures, numClasses, nbHidden = None):
if nbHidden == None:
nbHidden = np.round( (numFeatures + numClasses) / 2 , 0 ).astype('int')
self.net = buildNetwork(numFeatures, nbHidden, numClasses, bias=True)
self.nbFeatures = numFeatures
self.nbClasses = numClasses
print "\tNetwork creation complete:"
print "\t\tinputLayer=" , self.net['in']
print "\t\thiddenLayer=" , self.net['hidden0']
print "\t\toutputLayer=" , self.net['out']
print "\tb\tiasLayer=" , self.net['bias']
D = ftrs.shape[1]
print '%d feature vectors of dimensionality = %d' % (N,D)
if args.labs == None:
labs = None
else:
if args.labs.endswith('.pkl'):
labs = pomio.unpickleObject( args.labs )
else:
labs = pomio.readMatFromCSV( args.labs ).astype(np.int32)
# show labels
if labs != None:
plt.figure()
plt.hist( labs, pomio.getNumClasses() )
plt.title('Class counts')
plt.xticks( range(pomio.getNumClasses()),
pomio.getClasses()[:pomio.getNumClasses()],
size='small' )
# show at most 9 features at once
fstarts = range( args.nstart, D, args.nshow )
plt.figure()
for fs in fstarts:
fend = min(D-1,fs+args.nshow-1)
print ' Displaying features %d-%d:' % (fs, fend)
rng = range( fs, fend+1 )
fnames = [ 'F%d' % x for x in rng ]
if 0:
# logistic regression
# Use fixed C
C = 0.5
classifier = trainLogisticRegressionModel(
trainingData[0][subset,:], trainingData[1][subset], C, classifierBaseFilename, \
scaleData=True, \
requireAllClasses=False
)
elif 0:
# Neural Network
# Construct nn dataset
datmat = trainingData[0][subset,:]
labvec = trainingData[1][subset]
nbFeatures = datmat.shape[1]
nbClasses = pomio.getNumClasses()
nbHidden = 100
maxIter = 200
classifier = NeuralNet.NNet(nbFeatures, nbClasses, nbHidden)
nnds = classifier.createTrainingSetFromMatrix( datmat, labvec )
classifier.trainNetworkBackprop(nnds,maxIter)
else:
#classifier = None
# Random forest
datmat = trainingData[0][subset,:]
labvec = trainingData[1][subset]
print '**Training a random forest on %d examples...' % len(labvec)
print 'Labels represented: ', np.unique( labvec )
classifier = sklearn.ensemble.RandomForestClassifier(\
n_estimators=100)
classifier = classifier.fit( datmat, labvec )
def getSuperPixelData(msrcImages,numberSuperPixels, superPixelCompactness):
# Should probably make this a call to pomio in case the ordering changes in the future...
voidClassLabel = pomio.getVoidIdx()
numberImages = len(msrcImages)
# for each image:
# determine superpixel label (discard if void)
# compute superpixel features of valid superpixels
# append features to cumulative array of all super pixel features
# append label to array of all labels
superPixelFeatures = None
superPixelLabels = np.array([], int) # used for superpixel labels
numberVoidSuperPixels = 0 # keep track of void superpixels
nbClasses = pomio.getNumClasses()
classAdjCounts = np.zeros( (nbClasses, nbClasses) )
adjCountsTotal = 0
adjVoidCountsTotal = 0
for imgIdx in range(0, numberImages):
superPixelIgnoreList = np.array([], int) # this is used to skip over the superpixel in feature processing
print "\n**Processing Image#" , (imgIdx + 1) , " of" , numberImages
# get raw image and ground truth labels
img = msrcImages[imgIdx].m_img
imgPixelLabels = msrcImages[imgIdx].m_gt
# create superpixel map and graph for image
spgraph = SuperPixels.computeSuperPixelGraph( img, 'slic', [numberSuperPixels, superPixelCompactness] )
imgSuperPixelMask = spgraph.m_labels
imgSuperPixels = spgraph.m_nodes
numberImgSuperPixels = spgraph.getNumSuperPixels()
# create superpixel exclude list & superpixel label array
allSPClassLabels = []
for spIdx in range(0, numberImgSuperPixels):
superPixelValue = imgSuperPixels[spIdx]
#print "\tINFO: Processing superpixel =", superPixelValue , " of" , numberImgSuperPixels, " in image"
# Assume superpixel labels are sequence of integers
superPixelValueMask = (imgSuperPixelMask == superPixelValue ) # Boolean array for indexing superpixel-pixels
superPixelLabel = assignClassLabelToSuperPixel(superPixelValueMask, imgPixelLabels)
allSPClassLabels.append( superPixelLabel)
if(superPixelLabel == voidClassLabel):
# add to ignore list, increment void count & do not add to superpixel label array
superPixelIgnoreList = np.append(superPixelIgnoreList, superPixelValue)
numberVoidSuperPixels = numberVoidSuperPixels + 1
else:
superPixelLabels = np.append(superPixelLabels, superPixelLabel)
assert len(allSPClassLabels) == numberImgSuperPixels
(theseClassAdjCounts,adjVoidCount,adjCount) = spgraph.countClassAdjacencies( nbClasses, allSPClassLabels )
classAdjCounts += theseClassAdjCounts
adjCountsTotal += adjCount
adjVoidCountsTotal += adjVoidCount
# Now we have the superpixel labels, and an ignore list of void superpixels - time to get the features!
imgSuperPixelFeatures = FeatureGenerator.generateSuperPixelFeatures(img, imgSuperPixelMask, excludeSuperPixelList=superPixelIgnoreList)
if superPixelFeatures == None:
superPixelFeatures = imgSuperPixelFeatures;
else:
# stack the superpixel features into a single list
superPixelFeatures = np.vstack( [ superPixelFeatures, imgSuperPixelFeatures ] )
assert np.shape(superPixelFeatures)[0] == np.shape(superPixelFeatures)[0] , "Number of samples != number labels"
print "\n**Processed total of" , numberImages, "images"
print " %d out of %d adjacencies were ignored due to void (%.2f %%)" % \
(adjVoidCountsTotal, adjCountsTotal, \
100.0*adjVoidCountsTotal/adjCountsTotal)
# Now return the results
return [ superPixelFeatures, superPixelLabels, classAdjCounts ]
N = ftrs.shape[0]
D = ftrs.shape[1]
print '%d feature vectors of dimensionality = %d' % (N, D)
if args.labs == None:
labs = None
else:
if args.labs.endswith('.pkl'):
labs = pomio.unpickleObject(args.labs)
else:
labs = pomio.readMatFromCSV(args.labs).astype(np.int32)
# show labels
if labs != None:
plt.figure()
plt.hist(labs, pomio.getNumClasses())
plt.title('Class counts')
plt.xticks(range(pomio.getNumClasses()),
pomio.getClasses()[:pomio.getNumClasses()],
size='small')
# show at most 9 features at once
fstarts = range(args.nstart, D, args.nshow)
plt.figure()
for fs in fstarts:
fend = min(D - 1, fs + args.nshow - 1)
print ' Displaying features %d-%d:' % (fs, fend)
rng = range(fs, fend + 1)
fnames = ['F%d' % x for x in rng]
amntools.gplotmatrix(ftrs[:, rng], labs, featureNames=fnames)
