def test_rotation(subject, subjects_file):
subject = int(subject)
import pickle
# subjects = pickle.load(open(subjects_file, 'rb'))
# s2 = subjects._sample_s(10)
# cr = CameraRotate('.')
# cr.data
# subjects = []
# i = 0
# for s in s2.list():
# s.id = i
# subjects.append(s)
# for n in range(6):
# a = cr.rotate(s.charge, n)
# subjects.append(Subject(i + n, None, a))
# i += 6
cr = CameraRotate('.')
cr.data
subject = Subject(0, None, np.array(range(499)))
_s = [subject]
for i in range(1, 6):
a = cr.rotate(subject.charge, i)
_s.append(Subject(i, None, a))
Subjects(_s).plot_subjects(w=6)
plt.show()
interact(locals())
def run(path, components, mle, plot, save, all):
if len(path) == 0:
print('No data files provided')
return
# swap.config.logger.init()
subjects = Subjects.from_data(path)
logger.info('Done loading subjects')
if mle:
cluster = Cluster.create(subjects, 'mle')
if all:
cluster = Cluster.create(subjects, None)
else:
cluster = Cluster.create(subjects, components)
logger.info('Done creating cluster')
if plot:
try:
cluster.plot()
except Exception:
pass
if save:
pickle.dump(cluster, open(save, 'wb'))
interact(locals())
def subject_rotation(subject, subjects_file):
subject = int(subject)
import pickle
subjects = pickle.load(open(subjects_file, 'rb'))
s2 = subjects._sample_s(10)
cr = CameraRotate('.')
cr.data
subjects = []
i = 0
for s in s2.list():
s.id = i
subjects.append(s)
for n in range(1, 6):
a = cr.rotate(s.charge, n)
subjects.append(Subject(i + n, None, a))
i += 6
Subjects(subjects).plot_subjects(w=6)
plt.show()
interact(locals())
def subject_images(self, subjects, size=None):
"""
Get list of scikit-image objects of subject images from panoptes
subjects: list of subject ids
size: select random sample from list of subjects
"""
print(len(subjects), size)
if size is not None and size < len(subjects):
subjects = random.sample(subjects, size)
print(len(subjects))
subjects = [self.subjects[s] for s in subjects]
return Subjects(subjects).load_images()
def download_subjects(self, subjects, size=None, prefix='', dir_=None):
"""
Download subject images from panoptes
subjects: list of subject ids
size: select random sample from list of subjects
"""
print(len(subjects), size)
if size is not None and size < len(subjects):
subjects = random.sample(subjects, size)
print(len(subjects))
subjects = [self.subjects[s] for s in subjects]
Subjects(subjects).download_images(prefix, dir_)
def visualize(path):
subjects = Subjects.from_data(path)
cluster = Cluster.create(subjects)
cluster.visualize()
def save(fname, data):
subjects = Subjects.from_data(data)
pickle.dump(subjects, open(fname, 'wb'))
def charge_array(subjects):
return Subjects(subjects).get_charge_array()