def run(self, imagename=None):
if imagename is not None:
self.load_image(imagename)
if self.image is None:
raise ImportError('Image cannot be loaded')
# Create ilastik dataMgr
dataMgr = DataMgr()
di = DataItemImage('')
di.setDataVol(DataAccessor(self.image))
dataMgr.append(di, alreadyLoaded=True)
dataMgr.module["Classification"][
"classificationMgr"].classifiers = self.classifiers
# Create FeatureMgr
fm = FeatureMgr(dataMgr, self.features)
fm.prepareCompute(dataMgr)
fm.triggerCompute()
fm.joinCompute(dataMgr)
# Predict with loaded classifier
classificationPredict = ClassifierPredictThread(dataMgr)
classificationPredict.start()
classificationPredict.wait()
#del dataMgr
return classificationPredict._prediction[0]
def run(self, workspace):
# get input image
image = workspace.image_set.get_image(self.image_name.value,
must_be_color=False)
# recover raw image domain
image_ = image.pixel_data * image.get_scale()
#
# Apply a rescaling that's done similarly in ilastik's dataImpex
#
image_max = np.max(image_)
if (image_max > 255) and (image_max < 4096):
image_ = image_ / 4095. * 255.0
# Create ilastik dataMgr
dataMgr = DataMgr()
# Transform input image to ilastik convention s
# 3D = (time,x,y,z,channel)
# 2D = (time,1,x,y,channel)
# Note, this work for 2D images right now. Is there a need for 3D
image_.shape = (1, 1) + image_.shape
# Check if image_ has channels, if not add singelton dimension
if len(image_.shape) == 4:
image_.shape = image_.shape + (1, )
# Add data item di to dataMgr
di = DataItemImage('')
di.setDataVol(DataAccessor(image_))
dataMgr.append(di, alreadyLoaded=True)
dataMgr.module["Classification"]["classificationMgr"].classifiers =\
self.get_classifiers(workspace)
# Create FeatureMgr
fm = FeatureMgr(dataMgr, self.get_feature_items(workspace))
# Compute features
fm.prepareCompute(dataMgr)
fm.triggerCompute()
fm.joinCompute(dataMgr)
# Predict with loaded classifier
classificationPredict = ClassifierPredictThread(dataMgr)
classificationPredict.start()
classificationPredict.wait()
workspace.display_data.source_image = image.pixel_data
workspace.display_data.dest_images = []
for group in self.probability_maps:
# Produce output image and select the probability map
probMap = classificationPredict._prediction[0][
0, 0, :, :, int(group.class_sel.value)]
temp_image = cpi.Image(probMap, parent_image=image)
workspace.image_set.add(group.output_image.value, temp_image)
workspace.display_data.dest_images.append(probMap)
def run(self, imagename=None):
if imagename is not None:
self.load_image(imagename)
if self.image is None:
raise ImportError("Image cannot be loaded")
# Create ilastik dataMgr
dataMgr = DataMgr()
di = DataItemImage("")
di.setDataVol(DataAccessor(self.image))
dataMgr.append(di, alreadyLoaded=True)
dataMgr.module["Classification"]["classificationMgr"].classifiers = self.classifiers
# Create FeatureMgr
fm = FeatureMgr(dataMgr, self.features)
fm.prepareCompute(dataMgr)
fm.triggerCompute()
fm.joinCompute(dataMgr)
# Predict with loaded classifier
classificationPredict = ClassifierPredictThread(dataMgr)
classificationPredict.start()
classificationPredict.wait()
# del dataMgr
return classificationPredict._prediction[0]
def run(self, workspace):
# get input image
image = workspace.image_set.get_image(self.image_name.value, must_be_color=False)
# recover raw image domain
image_ = image.pixel_data
if image.get_scale() is not None:
image_ = image_ * image.get_scale()
else:
# Best guess for derived images
image_ = image_ * 255.0
#
# Apply a rescaling that's done similarly in ilastik's dataImpex
#
image_max = np.max(image_)
if (image_max > 255) and (image_max < 4096):
image_ = image_ / 4095.0 * 255.0
# Create ilastik dataMgr
dataMgr = DataMgr()
# Transform input image to ilastik convention s
# 3D = (time,x,y,z,channel)
# 2D = (time,1,x,y,channel)
# Note, this work for 2D images right now. Is there a need for 3D
image_.shape = (1, 1) + image_.shape
# Check if image_ has channels, if not add singelton dimension
if len(image_.shape) == 4:
image_.shape = image_.shape + (1,)
# Add data item di to dataMgr
di = DataItemImage("")
di.setDataVol(DataAccessor(image_))
dataMgr.append(di, alreadyLoaded=True)
dataMgr.module["Classification"]["classificationMgr"].classifiers = self.get_classifiers(workspace)
# Create FeatureMgr
fm = FeatureMgr(dataMgr, self.get_feature_items(workspace))
# Compute features
fm.prepareCompute(dataMgr)
fm.triggerCompute()
fm.joinCompute(dataMgr)
# Predict with loaded classifier
classificationPredict = ClassifierPredictThread(dataMgr)
classificationPredict.start()
classificationPredict.wait()
workspace.display_data.source_image = image.pixel_data
workspace.display_data.dest_images = []
for group in self.probability_maps:
# Produce output image and select the probability map
probMap = classificationPredict._prediction[0][0, 0, :, :, int(group.class_sel.value)]
temp_image = cpi.Image(probMap, parent_image=image)
workspace.image_set.add(group.output_image.value, temp_image)
workspace.display_data.dest_images.append(probMap)
def setFeaturesAndClassifier(self, classifiers=None, featureList=None):
# get Classifers
if classifiers is None:
self.classifiers = ClassificationModuleMgr.importClassifiers(self.classifierFile)
else:
self.classifiers = classifiers
if featureList is None:
self.featureList = FeatureMgr.loadFeatureItemsFromFile(self.classifierFile)
else:
self.featureList = featureList
self.isReady = True
def _predict_image_with_ilastik(self, image_):
import ilastik
from ilastik.core.dataMgr import DataMgr, DataItemImage
from ilastik.modules.classification.core.featureMgr import FeatureMgr
from ilastik.modules.classification.core.classificationMgr import ClassificationMgr
from ilastik.modules.classification.core.features.featureBase import FeatureBase
from ilastik.modules.classification.core.classifiers.classifierRandomForest import ClassifierRandomForest
from ilastik.modules.classification.core.classificationMgr import ClassifierPredictThread
from ilastik.core.volume import DataAccessor
import numpy, h5py
dataMgr = DataMgr()
# Transform input image to ilastik convention s
# 3D = (time,x,y,z,channel)
# 2D = (time,1,x,y,channel)
# Note, this work for 2D images right now. Is there a need for 3D
image_.shape = (1,1) + image_.shape
# Check if image_ has channels, if not add singelton dimension
if len(image_.shape) == 4:
image_.shape = image_.shape + (1,)
# Add data item di to dataMgr
di = DataItemImage('')
di.setDataVol(DataAccessor(image_))
dataMgr.append(di, alreadyLoaded=True)
fileName = self.params["ilastik_classifier"]
ilastik_class = self.params["ilastik_class_selector"]
hf = h5py.File(fileName,'r')
temp = hf['classifiers'].keys()
# If hf is not closed this leads to an error in win64 and mac os x
hf.close()
del hf
classifiers = []
for cid in temp:
cidpath = 'classifiers/' + cid
classifiers.append(ClassifierRandomForest.loadRFfromFile(fileName, str(cidpath)))
dataMgr.module["Classification"]["classificationMgr"].classifiers = classifiers
# Restore user selection of feature items from hdf5
featureItems = []
f = h5py.File(fileName,'r')
for fgrp in f['features'].values():
featureItems.append(FeatureBase.deserialize(fgrp))
f.close()
del f
fm = FeatureMgr(dataMgr, featureItems)
# Create FeatureMgr
# Compute features
fm.prepareCompute(dataMgr)
fm.triggerCompute()
fm.joinCompute(dataMgr)
# Predict with loaded classifier
classificationPredict = ClassifierPredictThread(dataMgr)
classificationPredict.start()
classificationPredict.wait()
if ilastik_class >= classificationPredict._prediction[0].shape[-1]:
raise RuntimeError('ilastik output class not valid...')
# Produce output image and select the probability map
probMap = (classificationPredict._prediction[0][0,0,:,:, ilastik_class] * 255).astype(numpy.uint8)
img_out = ccore.numpy_to_image(probMap, True)
return img_out