def sample_loader(self,
index,
load_seg=True,
load_pred=False,
backup=False):
# If sample is a backup -> load it from pickle
if backup: return self.load_sample_pickle(index)
# Load the image with the I/O interface
image = self.interface.load_image(index)
# Create a Sample object
sample = MIScnn_sample.Sample(index, image, self.interface.channels,
self.interface.classes)
# IF needed read the provided segmentation for current sample
if load_seg:
segmentation = self.interface.load_segmentation(index)
sample.add_segmentation(segmentation)
# IF needed read the provided prediction for current sample
if load_pred:
prediction = self.interface.load_prediction(
index, self.output_path)
sample.add_prediction(prediction)
# Add optional details to the sample object
sample.add_details(self.interface.load_details(index))
# Return sample object
return sample
def test_IOI_IMAGE_predictionhandling(self):
interface = Image_interface(pattern="image")
sample = MIScnn_sample.Sample("pred.image", self.img[:, :, 0], 1, 2)
sample.add_prediction(self.seg[:, :, 0])
interface.save_prediction(sample, self.tmp_data.name)
pred = interface.load_prediction("pred.image", self.tmp_data.name)
self.assertTrue(np.array_equal(pred, self.seg[:, :, 0]))
def test_IOI_NIFTI_predictionhandling(self):
interface = NIFTI_interface(pattern="nifti")
sample_list = interface.initialize(self.tmp_data.name)
sample = MIScnn_sample.Sample("pred.nifti", np.asarray([0]), interface.channels, interface.classes)
sample.add_prediction(self.seg);
interface.save_prediction(sample, self.tmp_data.name)
pred = interface.load_prediction("pred.nifti", self.tmp_data.name)
self.assertTrue(np.array_equal(pred.reshape(self.seg.shape), self.seg))
def test_IOI_DICTIONARY_predictionhandling(self):
my_dict = dict()
my_dict["dict_sample"] = (self.img, self.seg)
interface = Dictionary_interface(my_dict)
sample_list = interface.initialize("")
sample = MIScnn_sample.Sample("dict_sample", np.asarray([0]), 1, 2)
sample.add_prediction(self.seg);
interface.save_prediction(sample, "")
pred = interface.load_prediction("dict_sample", "")
self.assertTrue(np.array_equal(pred.reshape(self.seg.shape), self.seg))
def test_IOI_NIFTI_loading(self):
interface = NIFTI_interface(pattern="nifti")
sample_list = interface.initialize(self.tmp_data.name)
img, extended = interface.load_image(sample_list[0])
# Create a Sample object
sample = MIScnn_sample.Sample(sample_list[0], img, interface.channels, interface.classes, extended)
seg = interface.load_segmentation(sample_list[0])
self.assertTrue(np.array_equal(img, self.img))
self.assertTrue(np.array_equal(seg, self.seg))