def loadClassifier(ctb, project):
tidF = WndcharmStorage.getAttachedTableFile(ctb.tcF, project)
tidW = WndcharmStorage.getAttachedTableFile(ctb.tcW, project)
tidL = WndcharmStorage.getAttachedTableFile(ctb.tcL, project)
if tidF is None or tidW is None or tidL is None:
raise Exception("Incomplete set of classifier tables: %s" % (tidF, tidW, tidL))
ctb.openTables(tidF, tidW, tidL)
version = unwrap(ctb.versiontag.getTextValue())
cls = ctb.loadClassifierTables()
# ids,trainClassIds,featureMatrix,featureNames,weights,classIds,classNames
trainFts = wndcharm.FeatureSet.FeatureSet_Discrete()
# if cls['classIds'] != sorted(cls['classIds']):
if cls["classIds"] != range(len(cls["classIds"])):
raise Exception("Incorrectly ordered class IDs")
trainFts.classnames_list = cls["classNames"]
# Objects should be in order of increasing class ID, this makes rebuilding
# data_list much faster
nclasses = len(cls["classNames"])
classCounts = [0] * nclasses
cprev = -1
for c in cls["trainClassIds"]:
if c < cprev:
raise Exception("Incorrectly ordered training class feature data")
cprev = c
classCounts[c] += 1
trainFts.classsizes_list = classCounts
trainFts.feature_vector_version = version
classFts = [[] for n in xrange(len(cls["classNames"]))]
p = 0
for i in xrange(nclasses):
classFts[i] = numpy.array(cls["featureMatrix"][p : (p + classCounts[i])])
p += classCounts[i]
trainFts.data_list = classFts
trainFts.num_images = sum(classCounts)
trainFts.num_features = len(cls["featureNames"])
trainFts.num_classes = nclasses
trainFts.featurenames_list = cls["featureNames"]
trainFts.imagenames_list = [str(i) for i in cls["ids"]]
tmp = trainFts.ContiguousDataMatrix()
weights = wndcharm.FeatureSet.FisherFeatureWeights(
data_dict={"names": cls["featureNames"], "values": cls["weights"]}
)
return (trainFts, weights)
def addToFeatureSet(ftb, ds, fts, classId):
message = ""
tid = WndcharmStorage.getAttachedTableFile(ftb.tc, ds)
if tid:
if not ftb.openTable(tid):
return message + "\nERROR: Table not opened"
version = unwrap(ftb.versiontag.getTextValue())
message += "Opened table id:%d version:%s\n" % (tid, version)
else:
message += "ERROR: Table not found for Dataset id:%d" % ds.getId()
return message
# fts = wndcharm.FeatureSet.FeatureSet_Discrete({'num_images': 0})
for image in ds.listChildren():
imId = image.getId()
message += "\tProcessing features for image id:%d\n" % imId
# message += extractFeatures(tc, d, im = image) + '\n'
sig = wndcharm.FeatureSet.Signatures()
(sig.names, sig.values) = ftb.loadFeatures(imId)
# sig.source_file = image.getName()
sig.source_file = str(imId)
sig.version = version
fts.AddSignature(sig, classId)
fts.classnames_list[classId] = ds.getName()
return message
def addToFeatureSet(ftb, ds, fts, classId, imagesOnly):
message = ''
tid = WndcharmStorage.getAttachedTableFile(ftb.tc, ds)
if tid:
if not ftb.openTable(tid):
return message + '\nERROR: Table not opened'
version = unwrap(ftb.versiontag.getTextValue())
message += 'Opened table id:%d version:%s\n' % (tid, version)
else:
message += 'ERROR: Table not found for Dataset id:%d' % ds.getId()
return message
#fts = wndcharm.FeatureSet.FeatureSet_Discrete({'num_images': 0})
if imagesOnly:
for image in ds.listChildren():
imId = image.getId()
message += '\tProcessing features for image id:%d\n' % imId
sig = wndcharm.FeatureSet.Signatures()
(sig.names, sig.values) = ftb.loadFeatures(imId)
sig.source_file = str(imId)
sig.version = version
fts.AddSignature(sig, classId)
else:
names, values, ids = ftb.bulkLoadFeatures()
message += '\tProcessing all features for dataset id:%d\n' % ds.getId()
for imId, vals in izip(ids, values):
sig = wndcharm.FeatureSet.Signatures()
sig.names = names
sig.values = vals
sig.source_file = str(imId)
sig.version = version
fts.AddSignature(sig, classId)
fts.classnames_list[classId] = ds.getName()
return message
def countCompleted(ftb, ds):
message = ''
tc = ftb.tc
imIds = [im.getId() for im in ds.listChildren()]
tid = WndcharmStorage.getAttachedTableFile(ftb.tc, ds)
if tid is None:
message += 'Image feature status PRESENT:%d ABSENT:%d\n' % \
(0, len(imIds))
return message
if not ftb.openTable(tid):
message += 'ERROR: Table not opened\n'
message += 'Image feature status UNKNOWN:%d\n' % len(imIds)
return message
message += 'Opened table id:%d\n' % tid
d = tc.chunkedRead([0], 0, tc.table.getNumberOfRows(), 100)
ftImIds = d.columns[0].values
matchedIds = set(imIds).intersection(ftImIds)
message += 'Image feature status PRESENT:%d ABSENT:%d\n' % \
(len(matchedIds), len(imIds) - len(matchedIds))
return message
def extractFeatures(ftb, ds, newOnly, chNames, imageId = None, im = None):
message = ''
tc = ftb.tc
# dataset must be explicitly provided because an image can be linked to
# multiple datasets in which case im.getDataset() doesn't work
if not im:
if not imageId:
#raise Exception('No input image')
raise omero.ServerError('No input image')
im = ftb.conn.getObject('Image', imageId)
if not im:
return 'Image id:%d not found\n' % imageId
else:
imageId = im.getId()
tid = WndcharmStorage.getAttachedTableFile(ftb.tc, ds)
if tid:
if not ftb.openTable(tid):
return message + '\nERROR: Table not opened\n'
version = unwrap(ftb.versiontag.getTextValue())
# version seems to be in unicode
message += 'Opened table id:%d version:%s\n' % (tid, str(version))
if newOnly and ftb.tableContainsId(imageId):
return message + 'Image id:%d features already in table' % imageId
# FIXME: default is convert multichannel to greyscale unless user input
# Calculate features for an image channel
# Optionally prepend the channel label to each feature name and combine
ftall = None
for c in xrange( len( chNames ) ):
wndcharm_matrix = PyImageMatrix()
wndcharm_matrix.allocate( im.getSizeX(), im.getSizeY() )
numpy_matrix = wndcharm_matrix.as_ndarray()
numpy_matrix[:] = im.getPrimaryPixels().getPlane(theZ=0,theC=c,theT=0)
feature_plan = wndcharm.StdFeatureComputationPlans.getFeatureSet();
options = "" # This is where you can tell wnd-charm to normalize pixel intensities,
# take ROIs etc. ... leave blank for now.
ft = Signatures.NewFromFeatureComputationPlan( wndcharm_matrix, feature_plan, options )
ft.names = [WndcharmStorage.insert_channel_name(
n, chNames[c]) for n in ft.names]
ft.source_path = im.getName()
if not ftall:
ftall = ft
else:
ftall.names += ft.names
ftall.values += ft.values
# Save the features to a table
if not tid:
ftb.createTable(ftall.names, ft.version)
version = unwrap(ftb.versiontag.getTextValue())
message += 'Created new table id:%d version:%s\n' % (
ftb.tc.tableId, version)
message += WndcharmStorage.addFileAnnotationTo(tc, ds)
if version != ft.version:
return message + 'Incompatible version: Stored=%s Calculated=%s' % (
version, ft.version)
ftb.saveFeatures(imageId, ftall)
return message + 'Extracted features from Image id:%d\n' % imageId
