def decodeSQ(raw_attr, level):
result = DTree(name='Sequence', level=level + 1)
for i in _branches_:
result.add_branch(i)
leng_max = getattr(getattr(raw_attr[0], 'metadata'), 'leng')
locator = 0
while locator < leng_max:
_raw_info_locator_ = _read_raw_info_(raw_attr, locator)
raw_info = _raw_info_locator_[0]
locator = _raw_info_locator_[1]
fin_tag = _fine_metadata_(raw_tag)
for i in _branches_:
if i != 'value':
result.add_leaf(branch=i, value=getattr(fine_metadata, i))
raw_attr_sub = _read_raw_sub_attr_(raw_attr, raw_info, locator)
if getattr(raw_tag,
'tag') == 0xfffee000: # To do: add support for itemization
continue
if getattr(raw_tag, 'VR') == 'SQ':
result.append(attribute(fin_tag, decodeSQ(raw_attr_sub)))
locator = locator + getattr(raw_tag, 'leng')
continue
val_sub = readValue(raw_attr_sub, is_sub=True)
result.append(attribute(fin_tag, val_sub))
locator = locator + getattr(raw_tag, 'leng')
if locator != leng_max:
raise InvalidSQError(
'The length of the sequence {} is not equal to the length defined in tag'
.format(str(raw_attr)))
return result
def RF(X_train, y_train):
"""
random forest
"""
trees = []
for i in xrange(300):
d_tree = DTree(0)
bootstrap_X, bootstrap_y = boot_strap(X_train, y_train)
d_tree.fit(bootstrap_X, bootstrap_y)
trees.append(d_tree)
return trees
def RF(X_train, y_train):
"""
random forest
"""
trees = []
for i in xrange(300):
d_tree = DTree(0)
bootstrap_X, bootstrap_y = boot_strap(X_train, y_train)
d_tree.fit(bootstrap_X, bootstrap_y)
trees.append(d_tree)
return trees
def read_item_leng(read, **kwargs):
result = DTree()
for i in _branches_:
result.add_branch(i)
offset = 0
implicity = False
littleEndian = True
encoding = default_encoding
level = 0
for key, value in kwargs.items():
if key == 'implicity':
implicity = value
elif key == 'littleEndian':
littleEndian = value
elif key == 'encoding':
encoding = value
elif key == 'level':
level = value
elif key == 'index':
index = value
result.set_metainfo(name='item' + str(index + 1),
level=level,
index=index + 1)
meta_leng = read_raw_meta_leng(read, **kwargs)
if getattr(meta_leng[0], 'tag') != 0xfffee000:
raise ItemNotFound()
offset = offset + meta_leng[1]
item_max_leng = getattr(meta_leng[0], 'leng')
item_offset = 0
while item_offset < item_max_leng:
attr_leng = read_attribute_leng(read, **kwargs)
offset = offset + attr_leng[1]
item_offset = item_offset + attr_leng[1]
result.add_attribute(attr_leng[0])
return (result, offset)
def read_dataset(read, metainfo):
result = DTree()
if not isinstance(metainfo, DTree):
raise TypeError(
'The metainfo passed to dataset reader is not of the type DTree')
for i in _branches_:
result.add_branch(i)
imp_le = metainfo.get_value('value', tag=0x00020010)
implicity = ('Implicit' in imp_le)
littleEndian = ("Little Endian" in imp_le)
encoding = default_encoding
charset = read_attribute_leng(read,
implicity=implicity,
littleEndian=littleEndian,
encoding=encoding)
if getattr(charset[0], 'tag') != 0x00080005:
raise InvalidDicomError(
'Couldn\'t find the expected (0008,0005) attribute')
encoding = convert_encoding(getattr(charset[0], 'value'), littleEndian)
result.add_attribute(charset[0])
try:
while True:
attr_leng = read_attribute_leng(read,
implicity=implicity,
littleEndian=littleEndian,
encoding=encoding,
level=0)
if not attr_leng:
raise StopIteration
else:
result.add_attribute(attr_leng[0])
except StopIteration:
pass
return result
def dcm_read(filename):
import os
result = DTree(name=os.path.basename(filename), level=0, index=0)
for i in _branches_:
result.add_branch(i)
with open(filename, 'rb') as fp:
read = getattr(fp, 'read')
if not is_dicom(read):
raise InvalidDicomError()
metainfo = read_metainfo(read)
result.merge(metainfo)
dataset = read_dataset(read, metainfo)
result.merge(dataset)
return result
def dcmRead(file_name):
result = DTree(name=file_name.split('.')[0])
for i in _branches_:
result.add_branch(i)
with open(file_name, 'rb') as testFile:
read = getattr(testFile, "read")
__validity__ = isDICOM(read)
if not __validity__:
raise InvalidDicomError()
global meta_length
try:
while True:
raw_gen = genRawAttribute(testFile, read)
raw_attr = next(raw_gen)
"""
with open("write.test",'ab') as fileWrite:
fileWrite.write(str(raw_attr)+'\n')
"""
raw_tag = raw_attr[0]
val = raw_attr[1]
fine_metadata = _fine_metadata_(raw_attr[1])
for i in _branches_:
if i != 'value':
result.add_leaf(branch=i,
value=getattr(fine_metadata, i))
result.add_leaf(branch=_branches_[4],
value=readValue(raw_attr))
if tag == 0x00020000:
meta_length = val + testFile.tell()
"""
with open("write.test",'ab') as fileWrite:
fileWrite.write(str(buf_attr)+'\n')
"""
except StopIteration:
pass
return result
ax.set(xlabel='Number of Samples',
ylabel='Accuracy %',
title='Accuracy with bagging(Base={})'.format(100 *
(1 - base_accuracy)))
ax.legend()
for xy in zip(num_samples, error_rates):
ax.annotate('(%s, %s)' % xy, xy=xy, textcoords='data')
fig.savefig('../data/bagging_accuracy_result.png')
if __name__ == '__main__':
training_data = data_loader.load_diabetes_train_from_file()
testing_data = data_loader.load_diabetes_test_from_file()
# Testing 1 DTree
tree = DTree(sample=False)
tree.train(training_data)
tree.test(testing_data)
print('Error rate for single learner is {}'.format(
100 * (1 - tree.last_error_rate)))
# Testing ensemble
error_rates = []
for num_sample in [1, 3, 5, 10, 20]:
for max_depth in [None, 1, 2, 3, 6]:
bagger = Bagging(num_samples=num_sample, max_depth=max_depth)
bagger.train_ensemble(training_data)
error_rate = bagger.test(testing_data)[0]
if max_depth is None:
error_rates.append(error_rate)
print('Num Samples: {} Depth: {} Accuracy: {}'.format(
def train_ensemble(self, training_data):
for i in range(self._num_samples):
curr_tree = DTree(sample=True, max_depth=self._max_depth)
curr_tree.train(training_data)
self._learners.append(curr_tree)
def read_metainfo(read):
result = DTree(name='metainfo', level=0)
for i in _branches_:
result.add_branch(i)
implicity = False
littleEndian = True
meta_length = 0
locator = 0
encoding = default_encoding
file_meta_leng = read_attribute_leng(read,
implicity=implicity,
littleEndian=littleEndian,
encoding=encoding,
level=0)[0]
if getattr(file_meta_leng, 'tag') != 0x00020000:
raise InvalidDicomError(
'The file is either broken or incomplete. Contact the provider of the file for help'
)
else:
result.add_attribute(file_meta_leng)
meta_length = getattr(file_meta_leng, 'value')
while locator < meta_length:
attr_leng = read_attribute_leng(read)
result.add_attribute(attr_leng[0])
locator = locator + attr_leng[1]
if result.get_value('value', tag=0x00020002) in UID_dictionary:
result.set_value(UID_dictionary[result.get_value('value',
tag=0x00020002)][0],
'value',
tag=0x00020002)
if result.get_value('value', tag=0x00020010) in UID_dictionary:
result.set_value(UID_dictionary[result.get_value('value',
tag=0x00020010)][0],
'value',
tag=0x00020010)
return result