def test_carina():
# Load the data.
carina_location = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/carina.tiff')
image_data = Data(location=carina_location,
radec=(10.7502222, -59.8677778),
meta={},
processing=[])
image_data.get_data()
# Add to the data collection
dc = DataCollection()
dc.add(image_data)
assert len(dc) == 1
#
# Create the cutouts with a processing step applied
#
sliding_window_cutouts = BasicCutoutGenerator(output_size=224,
step_size=550)
cc = CutoutCollection()
for cutout in sliding_window_cutouts.create_cutouts(image_data):
cc.add(cutout)
assert len(cc) == 35
cmp_arr = np.array(
[[[51, 66, 69], [50, 70, 78]], [[48, 66, 72], [49, 65, 72]]],
dtype=np.uint8)
assert np.allclose(cc[0].get_data()[:2, :2], cmp_arr)
#
# Compute the fingerprints for each cutout
#
fc = FingerprintCollection()
fc_save = FingerprintCalculatorResnet().save()
for fingerprint in fingerprint_calculate(cc, fc_save):
fc.add(fingerprint)
assert [x[1] for x in fc[0].predictions[:3]
] == ['hammerhead', 'stingray', 'binder']
#
# Compute the similarity metrics
#
similarity_tsne = similarity_calculate(fc, 'tsne')
assert True
def test_end2end():
# Load the data.
carina_location = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/carina.tiff')
image_data = Data(location=carina_location,
radec=(10.7502222, -59.8677778),
meta={},
processing=[])
image_data.get_data()
# Add to the data collection
dc = DataCollection()
dc.add(image_data)
#
# Create the cutouts with a processing step applied
#
sliding_window_cutouts = BasicCutoutGenerator(output_size=224,
step_size=550)
cc = CutoutCollection()
for cutout in sliding_window_cutouts.create_cutouts(image_data):
cc.add(cutout)
#
# Compute the fingerprints for each cutout
#
fc = FingerprintCollection()
fc_save = FingerprintCalculatorResnet().save()
for fingerprint in fingerprint_calculate(cc, fc_save):
fc.add(fingerprint)
#
# Compute the similarity metrics
#
similarity_tsne = similarity_calculate(fc, 'tsne')
new_similarity_tsne = Similarity.factory(similarity_tsne.save())
assert json.dumps(new_similarity_tsne.save(),
sort_keys=True) == json.dumps(similarity_tsne.save(),
sort_keys=True)
def load(self, thedict):
log.info('Loading cutout')
self._uuid = thedict['uuid']
self._data = Data.factory(thedict['data'])
self._generator_parameters = thedict['generator_parameters']
self._bounding_box = BoundingBox.load(thedict['bounding_box'])
self._base_cutout_uuid = thedict['base_cutout_uuid']
self._cutout_processing = [
ImageProcessing.load(x) for x in thedict['cutout_processing']
]
# Add to the cutout collection
CutoutCollection._add(self)
from transfer_learning.cutout import CutoutCollection
from transfer_learning.cutout.generators import BasicCutoutGenerator
config = ConfigParser()
config.read('config.ini')
#
# Load the data
#
print('Going to load the HST Heritage data')
data = DataCollection()
for filename in glob.glob('../../data/heritage/*.???'):
print(' adding data {}'.format(filename))
image_data = Data(location=filename, radec=(-32, 12), meta={})
data.add(image_data)
#
# Create the cutout generator.
#
print('Going to calculate the sliding window cutouts')
sliding_window_cutouts = BasicCutoutGenerator(output_size=224, step_size=112)
#
# Create the cutouts
#
cutouts = sliding_window_cutouts.create_cutouts(data)
#
# Setup an image processing step on the data. This will convert
# any data that is not gray scale into gray scal.
#
gray_scale = image_processing.GrayScale()
#
# Now create teh actual data and add to the data collection.
#
print('Setting up the data structure required')
data_collection = DataCollection()
np.random.seed(12)
for fileinfo in np.random.choice(processing_dict, 200, replace=False):
im = Data(location=fileinfo['location'],
radec=fileinfo['radec'],
meta=fileinfo['meta'])
im.add_processing(gray_scale)
# Add to the data collection
data_collection.add(im)
#
# Create cutout pre-processing steps, which for this,
# is just crop and resize.
#
cutout_crop = image_processing.Crop([15, -15, 15, -15])
cutout_resize = image_processing.Resize([224, 224])
#
#
# Create the data pre-processing.
#
resize_224 = Resize(output_size=(224, 224))
#
# Create the datasets
#
print('Creating data objects')
data = DataCollection()
for fileinfo in processing_dict[:20]:
im = Data(location=fileinfo['location'],
radec=fileinfo['radec'],
meta=fileinfo['meta'])
im.add_processing(resize_224)
data.append(im)
#
# Create cutout generator
#
print('Creating the cutout generator')
full_cutout = FullImageCutoutGenerator(output_size=(224, 224))
#
# Create the cutouts.
#
from transfer_learning.cutout import CutoutCollection
from transfer_learning.fingerprint import FingerprintCollection
from transfer_learning.cutout.generators import BasicCutoutGenerator
fc_save = FingerprintCalculatorResnet().save()
config = ConfigParser()
config.read('config.ini')
#
# Load the data
#
print('Going to load the carina data')
image_data = Data(location='../../data/carina.tiff',
radec=(10.7502222, -59.8677778),
meta={},
processing=[])
image_data.get_data()
#
# Add to the data collection
#
dc = DataCollection()
dc.add(image_data)
#
# Create the sliding window cutout generator.
#
print('Creating cutout generator')