# -*- coding:utf-8 -*-
__author__ = "Heather"
try:
import xml.etree.cElementTree as ET
except ImportError:
import xml.etree.cElementTree as ET
if __name__ == '__main__':
print("解析本地data_demo.xml文档")
# 加载url
tree = ET.parse("data_demo.xml")
# 获取根节点，并打印节点文本：data
root = tree.getroot()
print(root.tag)
# 遍历输出country及其name属性
for child in root:
print(child.tag, "name:", child.attrib["name"])
# 遍历rank节点
# 我们借助iter迭代器来进行全迭代查找感兴趣的节点
# 输出节点tag及其文本
print("使用iter迭代器查找目标节点")
for rank in root.iter("rank"):
print(rank.tag, "-", rank.text)
# 换一种方式来遍历rank节点
# 我们借助findall和find方法来查找感兴趣的节点
# 输出节点tag及其文本
# 注意：findall只能查找从当前节点的子节点查找目标节点
print("使用findall查找目标节点")
# 使用findall查找所有country节点，用于遍历
price_out = max(price, rprice)
return str(price_out)
# Save XML settings
form = cgi.FieldStorage()
erc.save_xml_set(form)
erc.save()
filename = 'erc.xml'
download_patch = '/var/www/parse_erc/download_file/'
fileXML = download_patch + filename
dt = time.strftime("%Y-%m-%d %H:%M", time.localtime())
elem = ET.parse(fileXML)
root = elem.getroot()
doc = minidom.Document()
price = doc.createElement('price')
doc.appendChild(price)
price.setAttribute('date', time.strftime("%Y-%m-%d %H:%M", time.localtime()))
name = doc.createElement('name')
price.appendChild(name)
text = doc.createTextNode('Интернет-магазин')
name.appendChild(text)
currencies = doc.createElement('currencies')
price.appendChild(currencies)
def spliting(name_list, addr):
Modality = ('flair', 't1', 't1ce', 't2')
for i_mol in Modality:
# NumofSubject = 49
split_addr = addr + i_mol + '/ImageSets/Main/'
annotation_addr = addr + i_mol + '/Annotations/'
# We ensure i_mol folder exists
if not os.path.exists(split_addr):
os.mkdir(addr + i_mol + '/ImageSets/')
os.mkdir(split_addr)
cv = KFold(10)
# filename tumour
fn_tumour_train = []
fn_tumour_trainval = []
fn_tumour_val = []
fn_tumour_test = []
# filename core
fn_core_train = []
fn_core_trainval = []
fn_core_val = []
fn_core_test = []
# filename necrosis
fn_necrosis_train = []
fn_necrosis_trainval = []
fn_necrosis_val = []
fn_necrosis_test = []
# filename whole0
fn_whole0_train = []
fn_whole0_trainval = []
fn_whole0_val = []
fn_whole0_test = []
# filename whole1
fn_whole1_train = []
fn_whole1_trainval = []
fn_whole1_val = []
fn_whole1_test = []
# filename whole2
fn_whole2_train = []
fn_whole2_trainval = []
fn_whole2_val = []
fn_whole2_test = []
#
fn_train = []
fn_test = []
fn_trainval = []
fn_val = []
FD = 0
in_FD = 0
for trainval, test in cv.split(name_list):
# filename tumour
fn_tumour_trainval.append(split_addr + 'cv' + str(FD) +
'_tumour_trainval.txt')
fn_tumour_test.append(split_addr + 'cv' + str(FD) +
'_tumour_test.txt')
fn_tumour_train.append(split_addr + 'cv' + str(FD) +
'_tumour_train.txt')
fn_tumour_val.append(split_addr + 'cv' + str(FD) +
'_tumour_val.txt')
# filename core
fn_core_trainval.append(split_addr + 'cv' + str(FD) +
'_core_trainval.txt')
fn_core_test.append(split_addr + 'cv' + str(FD) + '_core_test.txt')
fn_core_train.append(split_addr + 'cv' + str(FD) +
'_core_train.txt')
fn_core_val.append(split_addr + 'cv' + str(FD) + '_core_val.txt')
# filename necrosis
fn_necrosis_trainval.append(split_addr + 'cv' + str(FD) +
'_necrosis_trainval.txt')
fn_necrosis_test.append(split_addr + 'cv' + str(FD) +
'_necrosis_test.txt')
fn_necrosis_train.append(split_addr + 'cv' + str(FD) +
'_necrosis_train.txt')
fn_necrosis_val.append(split_addr + 'cv' + str(FD) +
'_necrosis_val.txt')
# filename whole0
fn_whole0_trainval.append(split_addr + 'cv' + str(FD) +
'_whole0_trainval.txt')
fn_whole0_test.append(split_addr + 'cv' + str(FD) +
'_whole0_test.txt')
fn_whole0_train.append(split_addr + 'cv' + str(FD) +
'_whole0_train.txt')
fn_whole0_val.append(split_addr + 'cv' + str(FD) +
'_whole0_val.txt')
# filename whole1
fn_whole1_trainval.append(split_addr + 'cv' + str(FD) +
'_whole1_trainval.txt')
fn_whole1_test.append(split_addr + 'cv' + str(FD) +
'_whole1_test.txt')
fn_whole1_train.append(split_addr + 'cv' + str(FD) +
'_whole1_train.txt')
fn_whole1_val.append(split_addr + 'cv' + str(FD) +
'_whole1_val.txt')
# filename whole2
fn_whole2_trainval.append(split_addr + 'cv' + str(FD) +
'_whole2_trainval.txt')
fn_whole2_test.append(split_addr + 'cv' + str(FD) +
'_whole2_test.txt')
fn_whole2_train.append(split_addr + 'cv' + str(FD) +
'_whole2_train.txt')
fn_whole2_val.append(split_addr + 'cv' + str(FD) +
'_whole2_val.txt')
#
fn_trainval.append(split_addr + 'cv' + str(FD) + '_trainval.txt')
fn_test.append(split_addr + 'cv' + str(FD) + '_test.txt')
fn_train.append(split_addr + 'cv' + str(FD) + '_train.txt')
fn_val.append(split_addr + 'cv' + str(FD) + '_val.txt')
# writing files
trainval_list = np.array(name_list)[trainval]
test_list = np.array(name_list)[test]
# writing files for trainval set
for i_train_val_sub in trainval_list:
fn_trval_sub, slt_trval_sub = select_from_start(
annotation_addr, i_train_val_sub)
#print(i_train_val_sub)
for i_slice_fn in fn_trval_sub:
i_slice_addr_fn = annotation_addr + i_slice_fn
#print(i_slice_addr_fn)
tree = et.parse(i_slice_addr_fn)
root = tree.getroot()
filename = root.find('filename').text
#print(filename)
have_tumour = -1
have_core = -1
have_necrosis = -1
have_whole0 = -1
have_whole1 = -1
have_whole2 = -1
for obj in root.findall('object'):
name = obj.find('name').text
if name == 'tumour':
have_tumour = 1
if name == 'core':
have_core = 1
if name == 'necrosis':
have_necrosis = 1
if name == 'whole0':
have_whole0 = 1
if name == 'whole1':
have_whole1 = 1
if name == 'whole2':
have_whole2 = 1
with open(fn_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + '\n')
with open(fn_tumour_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_tumour) +
'\n')
with open(fn_core_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_core) + '\n')
with open(fn_necrosis_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_necrosis) +
'\n')
with open(fn_whole0_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole0) +
'\n')
with open(fn_whole1_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole1) +
'\n')
with open(fn_whole2_trainval[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole2) +
'\n')
# writing files for testing set
for i_test_sub in test_list:
fn_test_sub, slt_test_sub = select_from_start(
annotation_addr, i_test_sub)
for i_slice_fn in fn_test_sub:
i_slice_addr_fn = annotation_addr + i_slice_fn
tree = et.parse(i_slice_addr_fn)
root = tree.getroot()
filename = root.find('filename').text
#print(filename)
have_tumour = -1
have_core = -1
have_necrosis = -1
have_whole0 = -1
have_whole1 = -1
have_whole2 = -1
for obj in root.findall('object'):
name = obj.find('name').text
if name == 'tumour':
have_tumour = 1
if name == 'core':
have_core = 1
if name == 'necrosis':
have_necrosis = 1
if name == 'whole0':
have_whole0 = 1
if name == 'whole1':
have_whole1 = 1
if name == 'whole2':
have_whole2 = 1
with open(fn_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + '\n')
with open(fn_tumour_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_tumour) +
'\n')
with open(fn_core_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_core) + '\n')
with open(fn_necrosis_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_necrosis) +
'\n')
with open(fn_whole0_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole0) +
'\n')
with open(fn_whole1_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole1) +
'\n')
with open(fn_whole2_test[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole2) +
'\n')
for A in range(1):
train_and_val = train_test_split(range(len(trainval)),
test_size=0.1)
train_list = np.array(trainval_list)[train_and_val[0]]
val_list = np.array(trainval_list)[train_and_val[1]]
# writing files for training set
for i_train_sub in train_list:
fn_tr_sub, slt_tr_sub = select_from_start(
annotation_addr, i_train_sub)
#print(fn_tr_sub)
for i_slice_fn in fn_tr_sub:
i_slice_addr_fn = annotation_addr + i_slice_fn
tree = et.parse(i_slice_addr_fn)
root = tree.getroot()
filename = root.find('filename').text
#print(filename)
have_tumour = -1
have_core = -1
have_necrosis = -1
have_whole0 = -1
have_whole1 = -1
have_whole2 = -1
for obj in root.findall('object'):
name = obj.find('name').text
if name == 'tumour':
have_tumour = 1
if name == 'core':
have_core = 1
if name == 'necrosis':
have_necrosis = 1
if name == 'whole0':
have_whole0 = 1
if name == 'whole1':
have_whole1 = 1
if name == 'whole2':
have_whole2 = 1
with open(fn_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + '\n')
with open(fn_tumour_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_tumour) +
'\n')
with open(fn_core_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_core) +
'\n')
with open(fn_necrosis_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' +
str(have_necrosis) + '\n')
with open(fn_whole0_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole0) +
'\n')
with open(fn_whole1_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole1) +
'\n')
with open(fn_whole2_train[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole2) +
'\n')
# writing files for val set
for i_val_sub in val_list:
fn_val_sub, slt_val_sub = select_from_start(
annotation_addr, i_val_sub)
for i_slice_fn in fn_val_sub:
i_slice_addr_fn = annotation_addr + i_slice_fn
tree = et.parse(i_slice_addr_fn)
root = tree.getroot()
filename = root.find('filename').text
#print(filename)
have_tumour = -1
have_core = -1
have_necrosis = -1
have_whole0 = -1
have_whole1 = -1
have_whole2 = -1
for obj in root.findall('object'):
name = obj.find('name').text
if name == 'tumour':
have_tumour = 1
if name == 'core':
have_core = 1
if name == 'necrosis':
have_necrosis = 1
if name == 'whole0':
have_whole0 = 1
if name == 'whole1':
have_whole1 = 1
if name == 'whole2':
have_whole2 = 1
with open(fn_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + '\n')
with open(fn_tumour_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_tumour) +
'\n')
with open(fn_core_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_core) +
'\n')
with open(fn_necrosis_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' +
str(have_necrosis) + '\n')
with open(fn_whole0_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole0) +
'\n')
with open(fn_whole1_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole1) +
'\n')
with open(fn_whole2_val[FD], 'a') as f:
f.write(i_slice_fn[:-4] + ' ' + str(have_whole2) +
'\n')
FD += 1
return
dir_dic = {}
#make the corresponding to training and xml directory
for i in os.listdir(imgpath):
dir_dic[i.split('_')[-1]] = i
if __name__ == '__main__':
xmlpath = os.path.join(root_dir, 'DETRAC-Train-Annotations-XML')
annopath = os.path.join(root_dir, 'anno')
for i in os.listdir(xmlpath):
annofile = os.path.join(annopath,
dir_dic[i.split('.')[0].split('_')[-1]])
xmlfile = os.path.join(xmlpath, i)
os.mkdir(annofile)
tree = ET.parse(xmlfile)
root = tree.getroot() #sequence
#ignore region
for ignore in root.findall('ignored_region'):
ignorefile = os.path.join(annofile, 'ignored_region')
fi = open(ignorefile, 'w')
fi.write('ignored_region\n')
fi.write(str(len(ignore.findall('box'))) + '\n')
for box in ignore.findall('box'):
str1 = box.get('left') + ' ' + box.get('top') + ' ' + box.get(
'width') + ' ' + box.get('height') + '\n'
fi.write(str1)
fi.close()
#each frame generate an annotation file
for frame in root.findall('frame'):
framefile = os.path.join(annofile,
def obfuscate(self, obfuscation_info: Obfuscation):
self.logger.info('Running "{0}" obfuscator'.format(self.__class__.__name__))
try:
Xml.register_namespace(
"android", "http://schemas.android.com/apk/res/android"
)
xml_parser = Xml.XMLParser(encoding="utf-8")
manifest_tree = Xml.parse(
obfuscation_info.get_manifest_file(), parser=xml_parser
)
manifest_root = manifest_tree.getroot()
self.package_name = manifest_root.get("package")
if not self.package_name:
raise Exception(
"Unable to extract package name from application manifest"
)
# Get a mapping between class name and smali file path.
for smali_file in util.show_list_progress(
obfuscation_info.get_smali_files(),
interactive=obfuscation_info.interactive,
description="Class name to smali file mapping",
):
with open(smali_file, "r", encoding="utf-8") as current_file:
class_name = None
for line in current_file:
if not class_name:
# Every smali file contains a class.
class_match = util.class_pattern.match(line)
if class_match:
self.class_name_to_smali_file[
class_match.group("class_name")
] = smali_file
break
self.transform_package_name(manifest_root)
# Write the changes into the manifest file.
manifest_tree.write(obfuscation_info.get_manifest_file(), encoding="utf-8")
xml_files: Set[str] = set(
os.path.join(root, file_name)
for root, dir_names, file_names in os.walk(
obfuscation_info.get_resource_directory()
)
for file_name in file_names
if file_name.endswith(".xml")
and (
"layout" in root or "xml" in root
) # Only res/layout-*/ and res/xml-*/ folders.
)
xml_files.add(obfuscation_info.get_manifest_file())
# TODO: use the following code to rename only the classes declared in
# application's package.
# package_smali_files: Set[str] = set(
# smali_file
# for class_name, smali_file in self.class_name_to_smali_file.items()
# if class_name[1:].startswith(self.package_name.replace(".", "/"))
# )
#
# # Rename the classes declared in the application's package.
# class_rename_transformations = self.rename_class_declarations(
# list(package_smali_files), obfuscation_info.interactive
# )
# Get user defined ignore package list.
self.ignore_package_names = obfuscation_info.get_ignore_package_names()
# Rename all classes declared in smali files.
class_rename_transformations = self.rename_class_declarations(
obfuscation_info.get_smali_files(), obfuscation_info.interactive
)
# Update renamed classes through all the smali files.
self.rename_class_usages_in_smali(
obfuscation_info.get_smali_files(),
class_rename_transformations,
obfuscation_info.interactive,
)
# Update renamed classes through all the xml files.
self.rename_class_usages_in_xml(
list(xml_files),
class_rename_transformations,
obfuscation_info.interactive,
)
except Exception as e:
self.logger.error(
'Error during execution of "{0}" obfuscator: {1}'.format(
self.__class__.__name__, e
)
)
raise
finally:
obfuscation_info.used_obfuscators.append(self.__class__.__name__)
def load_fig_option(path_prj, name_prj):
"""
This function loads the figure option saved in the xml file and create a dictionnary will be given to the functions
which create the figures to know the different options chosen by the user. If the options are not written, this
function uses data by default which are in the fonction create_default_fig_options().
:param path_prj: the path to the xml project file
:param name_prj: the name to this file
:return: the dictionary containing the figure options
"""
fig_dict = create_default_figoption()
fname = os.path.join(path_prj, name_prj + '.xml')
if not os.path.isfile(fname) and name_prj != '': # no project exists
pass
elif name_prj == '':
pass
elif not os.path.isfile(fname): # the project is not found
print('Warning: No project file (.xml) found.\n')
else:
doc = ET.parse(fname)
root = doc.getroot()
child1 = root.find(".//Figure_Option")
if child1 is not None: # modify existing option
width1 = root.find(".//Width")
height1 = root.find(".//Height")
colormap1 = root.find(".//ColorMap1")
colormap2 = root.find(".//ColorMap2")
fontsize1 = root.find(".//FontSize")
linewidth1 = root.find(".//LineWidth")
grid1 = root.find(".//Grid")
time1 = root.find(".//TimeStep")
raw1 = root.find(".//PlotRawData")
format1 = root.find(".//Format")
marker1 = root.find(".//Marker")
reso1 = root.find(".//Resolution")
fish1 = root.find(".//FishNameType")
text1 = root.find(".//TextOutput")
shape1 = root.find(".//ShapeOutput")
para1 = root.find(".//ParaviewOutput")
langfig1 = root.find(".//LangFig")
hopt1 = root.find(".//MinHeight")
fishinfo1 = root.find(".//FishInfo")
erase1 = root.find(".//EraseId")
try:
if width1 is not None:
fig_dict['width'] = float(width1.text)
if height1 is not None:
fig_dict['height'] = float(height1.text)
if colormap1 is not None:
fig_dict['color_map1'] = colormap1.text
if colormap2 is not None:
fig_dict['color_map2'] = colormap2.text
if fontsize1 is not None:
fig_dict['font_size'] = int(fontsize1.text)
if linewidth1 is not None:
fig_dict['line_width'] = int(linewidth1.text)
if grid1 is not None:
fig_dict['grid'] = grid1.text
if time1 is not None:
fig_dict['time_step'] = time1.text # -99 is all
if raw1 is not None:
fig_dict['raw_data'] = raw1.text
if format1 is not None:
fig_dict['format'] = format1.text
if marker1 is not None:
fig_dict['marker'] = marker1.text
if reso1 is not None:
fig_dict['resolution'] = int(reso1.text)
if fish1 is not None:
fig_dict['fish_name_type'] = fish1.text
if text1 is not None:
fig_dict['text_output'] = text1.text
if shape1 is not None:
fig_dict['shape_output'] = shape1.text
if para1 is not None:
fig_dict['paraview'] = para1.text
if langfig1 is not None:
fig_dict['language'] = int(langfig1.text)
if hopt1 is not None:
fig_dict['min_height_hyd'] = float(hopt1.text)
if fish1 is not None:
fig_dict['fish_info'] = fishinfo1.text
if erase1 is not None:
fig_dict['erase_id'] = erase1.text
except ValueError:
print('Error: Figure Options are not of the right type.\n')
fig_dict['time_step'] = fig_dict['time_step'].split(',')
try:
fig_dict['time_step'] = list(map(int, fig_dict['time_step']))
except ValueError:
print('Error: Time step could not be read in the options'
) # sendLog not read yet
return fig_dict
def count_tags(filename):
# YOUR CODE HERE
tree = ET.parse(filename)
root = tree.getroot()
tags = childTags(root)
return tags
node_count = 800
interval = 0.05
total_count = node_count * interval
sumo_path = 'F:/sumo-win32-0.24.0/sumo-0.24.0/'
os.popen(sumo_path + 'bin/netconvert --osm-files target.osm -o input_net.net.xml')
print sumo_path + 'bin/netconvert --osm-files target.osm -o input_net.net.xml'
node = dict()
while len(node) < node_count :
print(len(node))
os.popen('python ' + sumo_path + '/tools/randomTrips.py -n input_net.net.xml -e ' + str(total_count) + ' -p ' + str(interval))
os.popen(sumo_path + 'bin/duarouter.exe --trip-files=trips.trips.xml --net-file=input_net.net.xml --output-file=routes.rou.xml')
tree = ET.parse('routes.rou.xml') # 载入数据
root = tree.getroot() # 获取根节点
for child in root:
# print child.tag, child.attrib # vehicle {'depart': '0.00', 'id': '0'}
idx = int(child.attrib['id'])
if idx in node:
continue
node[idx] = dict()
for subchild in child:
# print subchild.tag, subchild.attrib # route {'edges': '29141670#0
node[idx]['route_str'] = subchild.attrib['edges']
node[idx]['route'] = subchild.attrib['edges'].split(' ')
node[idx]['from'] = node[idx]['route'][0]
node[idx]['to'] = node[idx]['route'][len(node[idx]['route']) - 1]
print len(node)
def load_hoomdxml(filename, top=None):
"""Load a single conformation from an HOOMD-Blue XML file.
For more information on this file format, see:
http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
Notably, all node names and attributes are in all lower case.
HOOMD-Blue does not contain residue and chain information explicitly.
For this reason, chains will be found by looping over all the bonds and
finding what is bonded to what.
Each chain consisists of exactly one residue.
Parameters
----------
filename : string
The path on disk to the XML file
top : None
This argumet is ignored
Returns
-------
trajectory : md.Trajectory
The resulting trajectory, as an md.Trajectory object, with corresponding
Topology.
Notes
-----
This function requires the NetworkX python package.
"""
from mdtraj.core.trajectory import Trajectory
from mdtraj.core.topology import Topology
topology = Topology()
tree = cElementTree.parse(filename)
config = tree.getroot().find('configuration')
position = config.find('position')
bond = config.find('bond')
atom_type = config.find('type') # MDTraj calls this "name"
box = config.find('box')
box.attrib = dict((key.lower(), val) for key, val in box.attrib.items())
# be generous for case of box attributes
lx = float(box.attrib['lx'])
ly = float(box.attrib['ly'])
lz = float(box.attrib['lz'])
try:
xy = float(box.attrib['xy'])
xz = float(box.attrib['xz'])
yz = float(box.attrib['yz'])
except (ValueError, KeyError):
xy = 0.0
xz = 0.0
yz = 0.0
unitcell_vectors = np.array([[[lx, xy*ly, xz*lz],
[0.0, ly, yz*lz],
[0.0, 0.0, lz ]]])
positions, types = [], {}
for pos in position.text.splitlines()[1:]:
positions.append((float(pos.split()[0]),
float(pos.split()[1]),
float(pos.split()[2])))
for idx, atom_name in enumerate(atom_type.text.splitlines()[1:]):
types[idx] = str(atom_name.split()[0])
if len(types) != len(positions):
raise ValueError('Different number of types and positions in xml file')
# ignore the bond type
bonds = [(int(b.split()[1]), int(b.split()[2])) for b in bond.text.splitlines()[1:]]
chains = _find_chains(bonds)
ions = [i for i in range(len(types)) if not _in_chain(chains, i)]
# add chains, bonds and ions (each chain = 1 residue)
for chain in chains:
t_chain = topology.add_chain()
t_residue = topology.add_residue('A', t_chain)
for atom in chain:
topology.add_atom(types[atom], 'U', t_residue)
for ion in ions:
t_chain = topology.add_chain()
t_residue = topology.add_residue('A', t_chain)
topology.add_atom(types[ion], 'U', t_residue)
for bond in bonds:
atom1, atom2 = bond[0], bond[1]
topology.add_bond(topology.atom(atom1), topology.atom(atom2))
traj = Trajectory(xyz=np.array(positions), topology=topology)
traj.unitcell_vectors = unitcell_vectors
return traj
# 添加文件到目录路径
xmlrealpath = os.path.join(xmlsplit[0], "changzhainengli.xml")
print(xmlrealpath)
# 遍历xml
def traverseXml(element):
if (len(element)) > 0:
for child in element:
print("child tag", "------", child)
traverseXml(child)
if __name__ == '__main__':
try:
tree = ET.parse(xmlrealpath)
print("tree type:", type(tree))
# 获取根节点
root = tree.getroot()
# print("根节点:", root, root.attrib)
# for child in root:
# print("child tag", "------", type(child.attrib), child.attrib)
# print(traverseXml(root))
for child in root:
print(child)
for children in child:
print(children.tag, children.attrib)
childlist = root[0].findall("personDebtPayingAbilityEvaluate")
print(childlist)
#!/usr/bin/env python3
# by ysan
import xml.etree.cElementTree as ET
tree = ET.parse('xml_test.xml')
root = tree.getroot()
print(root, root.tag)
# 遍历xml文档
for child in root:
print(child.tag, child.attrib)
for i in child:
print(i.tag, i.text)
# 只遍历year 节点
for node in root.iter('year'):
print(node.tag, node.text)
# 修改
for node in root.iter('year'):
new_year = int(node.text) + 1
node.text = str(new_year)
node.set('update', 'yes')
tree.write('xml_test.xml')
# 删除
for country in root.iter('country'):
rank = int(country.find('rank').text)
if rank > 40:
def XML_PMS2aTV(PMS_baseURL, path, options):
# double check aTV UDID, redo from client IP if needed/possible
if not 'PlexConnectUDID' in options:
UDID = getATVFromIP(options['aTVAddress'])
if UDID:
options['PlexConnectUDID'] = UDID
else:
declareATV(options['PlexConnectUDID'],
options['aTVAddress']) # update with latest info
# check cmd to work on
cmd = ''
if 'PlexConnect' in options:
cmd = options['PlexConnect']
dprint(__name__, 1, "PlexConnect Cmd: " + cmd)
# check aTV language setting
if not 'aTVLanguage' in options:
dprint(__name__, 1, "no aTVLanguage - pick en")
options['aTVLanguage'] = 'en'
# XML Template selector
# - PlexConnect command
# - path
# - PMS ViewGroup
XMLtemplate = ''
PMS = None
PMSroot = None
# XML direct request or
# XMLtemplate defined by solely PlexConnect Cmd
if path.endswith(".xml"):
XMLtemplate = path.lstrip('/')
path = '' # clear path - we don't need PMS-XML
elif cmd == 'Play':
XMLtemplate = 'PlayVideo.xml'
elif cmd == 'PlayVideo_ChannelsV1':
dprint(__name__, 1, "playing Channels XML Version 1: {0}".format(path))
UDID = options['PlexConnectUDID']
PMS_uuid = PlexAPI.getPMSFromAddress(UDID, PMS_baseURL)
auth_token = PlexAPI.getPMSProperty(UDID, PMS_uuid, 'accesstoken')
path = PlexAPI.getDirectVideoPath(path, auth_token)
return XML_PlayVideo_ChannelsV1(
PMS_baseURL, path) # direct link, no PMS XML available
elif cmd == 'PlayTrailer':
trailerID = options['PlexConnectTrailerID']
info = urllib2.urlopen("http://youtube.com/get_video_info?video_id=" +
trailerID).read()
parsed = urlparse.parse_qs(info)
key = 'url_encoded_fmt_stream_map'
if not key in parsed:
return XML_Error('PlexConnect',
'Youtube: No Trailer Info available')
streams = parsed[key][0].split(',')
url = ''
for i in range(len(streams)):
stream = urlparse.parse_qs(streams[i])
if stream['itag'][0] == '18':
url = stream['url'][0] + '&signature=' + stream['sig'][0]
if url == '':
return XML_Error('PlexConnect',
'Youtube: ATV compatible Trailer not available')
return XML_PlayVideo_ChannelsV1('', url.replace('&', '&'))
elif cmd == 'ScrobbleMenu':
XMLtemplate = 'ScrobbleMenu.xml'
elif cmd == 'ScrobbleMenuVideo':
XMLtemplate = 'ScrobbleMenuVideo.xml'
elif cmd == 'ScrobbleMenuTVOnDeck':
XMLtemplate = 'ScrobbleMenuTVOnDeck.xml'
elif cmd == 'ChangeShowArtwork':
XMLtemplate = 'ChangeShowArtwork.xml'
elif cmd == 'ChangeSingleArtwork':
XMLtemplate = 'ChangeSingleArtwork.xml'
elif cmd == 'ChangeSingleArtworkVideo':
XMLtemplate = 'ChangeSingleArtworkVideo.xml'
elif cmd == 'PhotoBrowser':
XMLtemplate = 'Photo_Browser.xml'
elif cmd == 'MoviePreview':
XMLtemplate = 'MoviePreview.xml'
elif cmd == 'HomeVideoPrePlay':
XMLtemplate = 'HomeVideoPrePlay.xml'
elif cmd == 'MoviePrePlay':
XMLtemplate = 'MoviePrePlay.xml'
elif cmd == 'EpisodePrePlay':
XMLtemplate = 'EpisodePrePlay.xml'
elif cmd == 'ChannelPrePlay':
XMLtemplate = 'ChannelPrePlay.xml'
elif cmd == 'ChannelsVideo':
XMLtemplate = 'ChannelsVideo.xml'
elif cmd == 'ByFolder':
XMLtemplate = 'ByFolder.xml'
elif cmd == 'HomeVideoByFolder':
XMLtemplate = 'HomeVideoByFolder.xml'
elif cmd == 'HomeVideoDirectory':
XMLtemplate = 'HomeVideoDirectory.xml'
elif cmd == 'MovieByFolder':
XMLtemplate = 'MovieByFolder.xml'
elif cmd == 'MovieDirectory':
XMLtemplate = 'MovieDirectory.xml'
elif cmd == 'MovieSection':
XMLtemplate = 'MovieSection.xml'
elif cmd == 'HomeVideoSection':
XMLtemplate = 'HomeVideoSection.xml'
elif cmd == 'TVSection':
XMLtemplate = 'TVSection.xml'
elif cmd.find('SectionPreview') != -1:
XMLtemplate = cmd + '.xml'
elif cmd == 'AllMovies':
XMLtemplate = 'Movie_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'movieview').replace(' ', '') + '.xml'
elif cmd == 'AllHomeVideos':
XMLtemplate = 'HomeVideo_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'homevideoview').replace(' ',
'') + '.xml'
elif cmd == 'MovieSecondary':
XMLtemplate = 'MovieSecondary.xml'
elif cmd == 'AllShows':
XMLtemplate = 'Show_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'showview') + '.xml'
elif cmd == 'TVSecondary':
XMLtemplate = 'TVSecondary.xml'
elif cmd == 'PhotoSecondary':
XMLtemplate = 'PhotoSecondary.xml'
elif cmd == 'Directory':
XMLtemplate = 'Directory.xml'
elif cmd == 'DirectoryWithPreview':
XMLtemplate = 'DirectoryWithPreview.xml'
elif cmd == 'DirectoryWithPreviewActors':
XMLtemplate = 'DirectoryWithPreviewActors.xml'
elif cmd == 'Settings':
XMLtemplate = 'Settings.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'SettingsVideoOSD':
XMLtemplate = 'Settings_VideoOSD.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'SettingsMovies':
XMLtemplate = 'Settings_Movies.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'SettingsTVShows':
XMLtemplate = 'Settings_TVShows.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'SettingsHomeVideos':
XMLtemplate = 'Settings_HomeVideos.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'SettingsChannels':
XMLtemplate = 'Settings_Channels.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd.startswith('SettingsToggle:'):
opt = cmd[len('SettingsToggle:'):] # cut command:
parts = opt.split('+')
g_ATVSettings.toggleSetting(options['PlexConnectUDID'],
parts[0].lower())
XMLtemplate = parts[1] + ".xml"
dprint(__name__, 2, "ATVSettings->Toggle: {0} in template: {1}",
parts[0], parts[1])
path = '' # clear path - we don't need PMS-XML
elif cmd == ('MyPlexLogin'):
dprint(__name__, 2, "MyPlex->Logging In...")
if not 'PlexConnectCredentials' in options:
return XML_Error('PlexConnect',
'MyPlex Sign In called without Credentials.')
parts = options['PlexConnectCredentials'].split(':', 1)
(username, auth_token) = PlexAPI.MyPlexSignIn(parts[0], parts[1],
options)
UDID = options['PlexConnectUDID']
g_ATVSettings.setSetting(UDID, 'myplex_user', username)
g_ATVSettings.setSetting(UDID, 'myplex_auth', auth_token)
XMLtemplate = 'Settings.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd == 'MyPlexLogout':
dprint(__name__, 2, "MyPlex->Logging Out...")
UDID = options['PlexConnectUDID']
auth_token = g_ATVSettings.getSetting(UDID, 'myplex_auth')
PlexAPI.MyPlexSignOut(auth_token)
g_ATVSettings.setSetting(UDID, 'myplex_user', '')
g_ATVSettings.setSetting(UDID, 'myplex_auth', '')
XMLtemplate = 'Settings.xml'
path = '' # clear path - we don't need PMS-XML
elif cmd.startswith('Discover'):
UDID = options['PlexConnectUDID']
auth_token = g_ATVSettings.getSetting(UDID, 'myplex_auth')
PlexAPI.discoverPMS(UDID, g_param['CSettings'], auth_token)
return XML_Error(
'PlexConnect',
'Discover!') # not an error - but aTV won't care anyways.
elif path.startswith('/search?'):
XMLtemplate = 'Search_Results.xml'
elif path == '/library/sections': # from PlexConnect.xml -> for //local, //myplex
XMLtemplate = 'Library.xml'
elif path == '/channels/all':
XMLtemplate = 'Channel_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'channelview') + '.xml'
path = ''
# request PMS XML
if not path == '':
if 'PlexConnectUDID' in options:
UDID = options['PlexConnectUDID']
PMS_uuid = PlexAPI.getPMSFromAddress(UDID, PMS_baseURL)
auth_token = PlexAPI.getPMSProperty(UDID, PMS_uuid, 'accesstoken')
else:
auth_token = ''
if PMS_baseURL.startswith('//'): # //local, //myplex
UDID = options['PlexConnectUDID']
type = PMS_baseURL[2:]
PMS = PlexAPI.getXMLFromMultiplePMS(UDID, path, type, options)
else:
PMS = PlexAPI.getXMLFromPMS(PMS_baseURL,
path,
options,
authtoken=auth_token)
if PMS == False:
return XML_Error('PlexConnect',
'No Response from Plex Media Server')
PMSroot = PMS.getroot()
dprint(__name__, 1, "viewGroup: " + PMSroot.get('viewGroup', 'None'))
# XMLtemplate defined by PMS XML content
if path == '':
pass # nothing to load
elif not XMLtemplate == '':
pass # template already selected
elif PMSroot.get('viewGroup', '') == "secondary" and (
PMSroot.get('art', '').find('video') != -1
or PMSroot.get('thumb', '').find('video') != -1):
XMLtemplate = 'HomeVideoSectionTopLevel.xml'
elif PMSroot.get('viewGroup', '') == "secondary" and (
PMSroot.get('art', '').find('movie') != -1
or PMSroot.get('thumb', '').find('movie') != -1):
XMLtemplate = 'MovieSectionTopLevel.xml'
elif PMSroot.get('viewGroup', '') == "secondary" and (
PMSroot.get('art', '').find('show') != -1
or PMSroot.get('thumb', '').find('show') != -1):
XMLtemplate = 'TVSectionTopLevel.xml'
elif PMSroot.get('viewGroup', '') == "secondary" and (
PMSroot.get('art', '').find('photo') != -1
or PMSroot.get('thumb', '').find('photo') != -1):
XMLtemplate = 'PhotoSectionTopLevel.xml'
elif PMSroot.get('viewGroup', '') == "secondary":
XMLtemplate = 'Directory.xml'
elif PMSroot.get('viewGroup', '') == 'show':
if PMSroot.get('title2') == 'By Folder':
# By Folder View
XMLtemplate = 'ByFolder.xml'
else:
# TV Show grid view
XMLtemplate = 'Show_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'showview') + '.xml'
elif PMSroot.get('viewGroup', '') == 'season':
# TV Season view
XMLtemplate = 'Season_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'seasonview') + '.xml'
elif PMSroot.get(
'viewGroup',
'') == 'movie' and PMSroot.get('thumb', '').find('video') != -1:
if PMSroot.get('title2') == 'By Folder':
# By Folder View
XMLtemplate = 'HomeVideoByFolder.xml'
else:
# Home Video listing
XMLtemplate = 'HomeVideo_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'homevideoview').replace(
' ', '') + '.xml'
elif PMSroot.get(
'viewGroup',
'') == 'movie' and PMSroot.get('thumb', '').find('movie') != -1:
if PMSroot.get('title2') == 'By Folder':
# By Folder View
XMLtemplate = 'MovieByFolder.xml'
else:
# Movie listing
XMLtemplate = 'Movie_' + g_ATVSettings.getSetting(
options['PlexConnectUDID'], 'homevideoview').replace(
' ', '') + '.xml'
elif PMSroot.get('viewGroup', '') == 'track':
XMLtemplate = 'Music_Track.xml'
elif PMSroot.get('viewGroup', '') == 'episode':
if PMSroot.get('title2')=='On Deck' or \
PMSroot.get('title2')=='Recently Viewed Episodes' or \
PMSroot.get('title2')=='Recently Aired' or \
PMSroot.get('title2')=='Recently Added':
# TV On Deck View
XMLtemplate = 'TV_OnDeck.xml'
else:
# TV Episode view
XMLtemplate = 'Episode.xml'
elif PMSroot.get('viewGroup', '') == 'photo':
# Photo listing
XMLtemplate = 'Photo.xml'
else:
XMLtemplate = 'Directory.xml'
dprint(__name__, 1, "XMLTemplate: " + XMLtemplate)
# get XMLtemplate
aTVTree = etree.parse(sys.path[0] + '/assets/templates/' + XMLtemplate)
aTVroot = aTVTree.getroot()
# convert PMS XML to aTV XML using provided XMLtemplate
global g_CommandCollection
g_CommandCollection = CCommandCollection(options, PMSroot, PMS_baseURL,
path)
XML_ExpandTree(aTVroot, PMSroot, 'main')
XML_ExpandAllAttrib(aTVroot, PMSroot, 'main')
del g_CommandCollection
dprint(__name__, 1, "====== generated aTV-XML ======")
dprint(__name__, 1, prettyXML(aTVTree))
dprint(__name__, 1, "====== aTV-XML finished ======")
return etree.tostring(aTVroot)
def get_elements(filename):
tree = ET.parse(filename)
root = tree.getroot()
elements = [c for c in root]
return elements
def read(self):
tree = ElementTree.parse(self.gccxml_file)
saxifier = etree_saxifier_t(tree, self)
saxifier.saxify()
def filter_meme_results(meme_dir: str, promoter_sets: List[Motif],
anchor: str) -> List[Motif]:
"""Analyse and filter MEME results"""
def fetch_node_text(root: ElementTree.Element, search_string: str) -> str:
""" Finds the text of a node with the given search string label """
node = root.find(search_string)
if node is None or not hasattr(node, "text") or node.text is None:
raise ValueError("unknown MEME output format")
return node.text
for motif in promoter_sets:
xml_file = os.path.join(meme_dir, motif.pairing_string, "meme.xml")
root = ElementTree.parse(xml_file).getroot()
reason = fetch_node_text(root, "model/reason_for_stopping")
anchor_seq_id = ""
# no motif found for given e-value cutoff :-(
if "Stopped because motif E-value > " in reason:
if cassis.VERBOSE_DEBUG:
logging.debug("MEME: motif %s; e-value exceeds cutoff",
motif.pairing_string)
# motif(s) found :-)
elif "Stopped because requested number of motifs (1) found" in reason:
# find anchor genes' sequence_id
training_set = root.findall(
"training_set/sequence"
) # all promoter sequences passed to MEME
for element in training_set:
if "__ANCHOR" in element.attrib["name"]:
anchor_seq_id = element.attrib["id"] # e.g. id=sequence_1
# only accept motifs which occur in the anchor genes promoter
# sequences which contributed to the motif
contributing_sites = root.findall(
"motifs/motif/contributing_sites/contributing_site")
if anchor_seq_id in map(lambda site: site.attrib["sequence_id"],
contributing_sites):
# save motif score
node = root.find("motifs/motif")
if not node:
raise ValueError("unknown MEME output format")
motif.score = float(node.attrib["e_value"]
) # one motif, didn't ask MEME for more
# save sequence sites which represent the motif
motif.seqs = [
"".join(
map(lambda letter: letter.attrib["letter_id"],
site.findall("site/letter_ref")))
for site in contributing_sites
]
# write sites to fasta file
with open(
os.path.join(meme_dir, str(motif),
"binding_sites.fasta"), "w") as handle:
handle.write(">{}__{}\n".format(anchor, str(motif)))
handle.write("\n".join(motif.seqs))
if cassis.VERBOSE_DEBUG:
logging.debug("MEME: motif %s; e-value = %s", motif,
motif.score)
else:
if cassis.VERBOSE_DEBUG:
logging.debug(
"MEME: motif %s; does not occur in anchor gene promoter",
motif)
# unexpected reason, don't know why MEME stopped :-$
else:
logging.error("MEME stopped unexpectedly (reason: %s)", reason)
return [motif for motif in promoter_sets if motif.score is not None]
#用来进行albumentations增强，主要解决了拷贝多个的问题
def save_option_fig(self):
"""
A function which save the options for the figures in the xlm project file. The options for the figures are
contained in a dictionnary. The idea is to give this dictinnory in argument to all the fonction which create
figures. In the xml project file, the options for the figures are saved under the attribute "Figure_Option".
If you change things here, it is necessary to start a new project as the old projects will not be compatible.
For the new version of HABBY, it will be necessary to insure compatibility by adding xml attribute.
"""
# get default option
fig_dict = create_default_figoption()
# get the data and check validity
# fig_size
fig_size = self.fig1.text()
if fig_size:
fig_size = fig_size.split(',')
try:
fig_dict['width'] = np.float(fig_size[0])
fig_dict['height'] = np.float(fig_size[1])
except IndexError:
self.send_log.emit(
'Error: The size of the figure should be in the format: num1,num2.\n'
)
except ValueError:
self.send_log.emit(
'Error: The size of the figure should be in the format: num1,num2.\n'
)
# color map
c1 = str(self.fig2.currentText())
if c1:
fig_dict['color_map1'] = c1
c2 = str(self.fig3.currentText())
if c2:
fig_dict['color_map2'] = c2
# font size
font_size = self.fig5.text()
if font_size:
try:
fig_dict['font_size'] = int(font_size)
except ValueError:
self.send_log.emit('Error: Font size should be an integer. \n')
# line width
line_width = self.fig6.text()
if line_width:
try:
fig_dict['line_width'] = int(line_width)
except ValueError:
self.send_log.emit(
'Error: Line width should be an integer. \n')
# grid
if self.fig7a.isChecked() and self.fig7b.isChecked():
self.send_log.emit(
'Error: Grid cannot be on and off at the same time. \n')
if self.fig7a.isChecked():
fig_dict['grid'] = True
elif self.fig7b.isChecked():
fig_dict['grid'] = False
# time step
fig_dict['time_step'] = str(self.fig8.text())
# raw data
if self.fig9a.isChecked() and self.fig9b.isChecked():
self.send_log.emit(
'Error: The option to plot raw output cannot be on and off at the same time. \n'
)
if self.fig9a.isChecked():
fig_dict['raw_data'] = True
elif self.fig9b.isChecked():
fig_dict['raw_data'] = False
# format
fig_dict['format'] = str(self.fig10.currentIndex())
# resolution
try:
fig_dict['resolution'] = int(self.fig11.text())
except ValueError:
self.send_log.emit(
'Error: the resolution should be an integer. \n')
if fig_dict['resolution'] < 0:
self.send_log.emit(
'Error: The resolution should be higher than zero \n')
return
if fig_dict['resolution'] > 2000:
self.send_log.emit(
'Warning: The resolution is higher than 2000 dpi. Figures might be very large.\n'
)
# fish name type
fig_dict['fish_name_type'] = int(self.fig12.currentIndex())
# marker
if self.out9a.isChecked():
fig_dict['marker'] = True
elif self.out9b.isChecked():
fig_dict['marker'] = False
# outputs
if self.out1a.isChecked() and self.out1b.isChecked():
self.send_log.emit(
'Error: Text Output cannot be on and off at the same time. \n')
if self.out1a.isChecked():
fig_dict['text_output'] = True
elif self.out1b.isChecked():
fig_dict['text_output'] = False
if self.out2a.isChecked() and self.out2b.isChecked():
self.send_log.emit(
'Error: Shapefile output cannot be on and off at the same time. \n'
)
if self.out2a.isChecked():
fig_dict['shape_output'] = True
elif self.out2b.isChecked():
fig_dict['shape_output'] = False
if self.out3a.isChecked() and self.out3b.isChecked():
self.send_log.emit(
'Error: Paraview cannot be on and off at the same time. \n')
if self.out3a.isChecked():
fig_dict['paraview'] = True
elif self.out3b.isChecked():
fig_dict['paraview'] = False
if self.out4a.isChecked():
fig_dict['fish_info'] = True
elif self.out4b.isChecked():
fig_dict['fish_info'] = False
# other option
try:
fig_dict['min_height_hyd'] = float(self.hopt.text())
except ValueError:
self.send_log.emit('Error: Minimum Height should be a number')
if self.out5a.isChecked():
fig_dict['erase_id'] = True
elif self.out5b.isChecked():
fig_dict['erase_id'] = False
# save the data in the xml file
# open the xml project file
fname = os.path.join(self.path_prj, self.name_prj + '.xml')
# save the name and the path in the xml .prj file
if not os.path.isfile(fname):
self.msg2.setIcon(QMessageBox.Warning)
self.msg2.setWindowTitle(self.tr("Image Options Not Saved"))
self.msg2.setText(
self.
tr("The project is not saved. Save the project in the General tab before saving data."
))
self.msg2.setStandardButtons(QMessageBox.Ok)
self.msg2.show()
else:
doc = ET.parse(fname)
root = doc.getroot()
child1 = root.find(".//Figure_Option")
if child1 is not None: # modify existing option
width1 = root.find(".//Width")
height1 = root.find(".//Height")
colormap1 = root.find(".//ColorMap1")
colormap2 = root.find(".//ColorMap2")
fontsize1 = root.find(".//FontSize")
linewidth1 = root.find(".//LineWidth")
grid1 = root.find(".//Grid")
time1 = root.find(".//TimeStep")
raw1 = root.find(".//PlotRawData")
format1 = root.find(".//Format")
reso1 = root.find(".//Resolution")
fish1 = root.find(".//FishNameType")
marker1 = root.find(".//Marker")
text1 = root.find(".//TextOutput")
shape1 = root.find(".//ShapeOutput")
para1 = root.find(".//ParaviewOutput")
langfig1 = root.find(".//LangFig")
hopt1 = root.find(".//MinHeight")
fishinfo1 = root.find(".//FishInfo")
erase1 = root.find(".//EraseId")
else: # save in case no fig option exist
child1 = ET.SubElement(root, 'Figure_Option')
width1 = ET.SubElement(child1, 'Width')
height1 = ET.SubElement(child1, 'Height')
colormap1 = ET.SubElement(child1, 'ColorMap1')
colormap2 = ET.SubElement(child1, 'ColorMap2')
fontsize1 = ET.SubElement(child1, 'FontSize')
linewidth1 = ET.SubElement(child1, 'LineWidth')
grid1 = ET.SubElement(child1, 'Grid')
time1 = ET.SubElement(child1, 'TimeStep')
raw1 = ET.SubElement(child1, "PlotRawData")
format1 = ET.SubElement(child1, "Format")
reso1 = ET.SubElement(child1, "Resolution")
fish1 = ET.SubElement(child1, "FishNameType")
marker1 = ET.SubElement(child1, "Marker")
text1 = ET.SubElement(child1, "TextOutput")
shape1 = ET.SubElement(child1, "ShapeOutput")
para1 = ET.SubElement(child1, "ParaviewOutput")
langfig1 = ET.SubElement(child1, "LangFig")
hopt1 = ET.SubElement(child1, "MinHeight")
fishinfo1 = ET.SubElement(child1, "FishInfo")
erase1 = ET.SubElement(child1, "EraseId")
width1.text = str(fig_dict['width'])
height1.text = str(fig_dict['height'])
colormap1.text = fig_dict['color_map1']
colormap2.text = fig_dict['color_map2']
fontsize1.text = str(fig_dict['font_size'])
linewidth1.text = str(fig_dict['line_width'])
grid1.text = str(fig_dict['grid'])
time1.text = str(fig_dict['time_step']) # -99 is all time steps
raw1.text = str(fig_dict['raw_data'])
format1.text = str(fig_dict['format'])
reso1.text = str(fig_dict['resolution'])
# usually not useful, but should be added to new options for comptability with older project
if fish1 is None:
fish1 = ET.SubElement(child1, "FishNameType")
fish1.text = str(fig_dict['fish_name_type'])
marker1.text = str(fig_dict['marker'])
if langfig1 is None:
langfig1 = ET.SubElement(child1, "LangFig")
langfig1.text = str(fig_dict['language'])
text1.text = str(fig_dict['text_output'])
shape1.text = str(fig_dict['shape_output'])
para1.text = str(fig_dict['paraview'])
hopt1.text = str(fig_dict['min_height_hyd'])
fishinfo1.text = str(fig_dict['fish_info'])
erase1.text = str(fig_dict['erase_id'])
doc.write(fname)
self.send_log.emit('The new options for the figures are saved. \n')
self.send_log.emit('# Modifications of figure options. \n')
# #################################################################################################
# Author: Talal Najam
# Date : 21/12/2018
# Github: https://github.com/mistat44
# #################################################################################################
import os
from xml.etree import cElementTree
from nltk.tokenize import word_tokenize, sent_tokenize
# from sentiment_shifter import should_invert
file_name = 'en-sentiment.xml'
full_file = os.path.abspath(os.path.join('data', file_name))
xml = cElementTree.parse(full_file)
xml = xml.getroot()
def sentiment_score(tweet):
words = word_tokenize(tweet)
print(words)
acum_score = 0
for word in words:
for w in xml.findall('word'):
w, pos, p = (w.attrib.get("form"), w.attrib.get("pos"),
w.attrib.get("polarity", 0.0))
if word == str(w):
acum_score += float(p)
def read(filepath):
"""Read the MMM File from disc and sets keyframes."""
start = bpy.context.scene.frame_current
fps = bpy.context.scene.render.fps
scale_factor = 0.001
doc = etree.parse(filepath)
root = doc.getroot()
tolower(root)
names = [
e.get("name").replace('_joint', '')
for e in root.findall(".//jointorder/joint")
]
missing = []
for i in names:
if i not in bpy.context.object.data.bones.keys():
print("Could not find joint: {}".format(i))
names.remove(i)
missing.append(i)
print(missing)
timestamps = [
float(e.text.strip())
for e in root.findall(".//motionframes/motionframe/timestep")
]
root_positions = [[
float(i) * scale_factor for i in e.text.strip().split()
] for e in root.findall(".//motionframes/motionframe/rootposition")]
root_rotations = [[
float(i) for i in e.text.strip().split()
] for e in root.findall(".//motionframes/motionframe/rootrotation")]
joint_positions = [[
float(i) for i in e.text.strip().split()
] for e in root.findall(".//motionframes/motionframe/jointposition")]
print(len(root_positions), len(root_rotations))
bpy.ops.object.mode_set(mode='OBJECT')
# lastFrame = start -20
counter = 3 # frame counter for skipping frames, value of 3 ensures that first frame is used
frameCounter = start # count the current frame in blender
# disable kinematic updates for import
bpy.context.scene.RobotDesigner.doKinematicUpdate = False
for [i, [timestamp, root_position, root_rotation,
joint_position]] in enumerate(
itertools.zip_longest(timestamps,
root_positions,
root_rotations,
joint_positions,
fillvalue=[])):
counter += 1 # increase counter
if counter != 4: # process frame only if counter equals 4 => use every 4th frame
# print('Skipping') # inform that we're skipping
continue # skip frame
counter = 0 # reset counter
# bpy.context.scene.frame_current = start + timestamp * fps * 10
bpy.context.scene.frame_current = frameCounter # set current frame in blender
frameCounter += 1 # increase frameCounter for next frame
# if bpy.context.scene.frame_current - lastFrame < 12: #or bpy.context.scene.frame_current > 100:
# print('Skipping')
# continue
# lastFrame = bpy.context.scene.frame_current
print("Frame number: ", bpy.context.scene.frame_current, " of ",
len(root_positions) / 4 - 1)
armName = bpy.context.active_object.name
segment_name = bpy.context.active_object.data.bones[0].name
bpy.context.active_object.location = Vector(root_position)
bpy.context.active_object.rotation_euler = Euler(root_rotation, "XYZ")
bpy.ops.anim.keyframe_insert(type="Location")
bpy.ops.anim.keyframe_insert(type="Rotation")
# bpy.context.active_object.location = Vector(root_position)
# bpy.context.active_object.rotation_euler = Euler(root_rotation, "XYZ")
for [x, value] in enumerate(joint_position):
if x < len(names):
bpy.ops.RobotDesigner.select_segment(segment_name=names[x])
try:
bpy.context.active_bone.RobotDesigner.theta.value = value / pi * 180.0
except KeyError:
print("Error updating {}".format(s))
# print(names[x], value/pi*180, bpy.context.active_bone.RobotDesigner.theta.value)
bpy.ops.object.mode_set(mode='POSE')
bpy.ops.pose.select_all(action='SELECT')
armatures.updateKinematics(armName, segment_name)
bpy.ops.anim.keyframe_insert(type='Rotation')
bpy.ops.object.mode_set(mode='OBJECT')
# armatures.updateKinematics(armName,segment_name)
bpy.context.scene.RobotDesigner.doKinematicUpdate = True
def main():
sys.path.append(sys.argv[1])
sys.argv.remove(sys.argv[1])
#Now we can import all the stuff..
from sonLib.bioio import getBasicOptionParser
from sonLib.bioio import parseBasicOptions
from sonLib.bioio import logger
from sonLib.bioio import addLoggingFileHandler, redirectLoggerStreamHandlers
from sonLib.bioio import setLogLevel
from sonLib.bioio import getTotalCpuTime, getTotalCpuTimeAndMemoryUsage
from sonLib.bioio import getTempDirectory
from sonLib.bioio import makeSubDir
from jobTree.src.job import Job
from jobTree.src.master import getEnvironmentFileName, getConfigFileName, listChildDirs, getTempStatsFile, setupJobAfterFailure
from sonLib.bioio import system
##########################################
#Input args
##########################################
jobTreePath = sys.argv[1]
jobFile = sys.argv[2]
##########################################
#Load the environment for the job
##########################################
#First load the environment for the job.
fileHandle = open(getEnvironmentFileName(jobTreePath), 'r')
environment = cPickle.load(fileHandle)
fileHandle.close()
for i in environment:
if i not in ("TMPDIR", "TMP", "HOSTNAME", "HOSTTYPE"):
os.environ[i] = environment[i]
# sys.path is used by __import__ to find modules
if "PYTHONPATH" in environment:
for e in environment["PYTHONPATH"].split(':'):
if e != '':
sys.path.append(e)
#os.environ = environment
#os.putenv(key, value)
##########################################
#Setup the temporary directories.
##########################################
#Dir to put all the temp files in.
localSlaveTempDir = getTempDirectory()
localTempDir = makeSubDir(os.path.join(localSlaveTempDir, "localTempDir"))
##########################################
#Setup the logging
##########################################
#Setup the logging. This is mildly tricky because we don't just want to
#redirect stdout and stderr for this Python process; we want to redirect it
#for this process and all children. Consequently, we can't just replace
#sys.stdout and sys.stderr; we need to mess with the underlying OS-level
#file descriptors. See <http://stackoverflow.com/a/11632982/402891>
#When we start, standard input is file descriptor 0, standard output is
#file descriptor 1, and standard error is file descriptor 2.
#What file do we want to point FDs 1 and 2 to?
tempSlaveLogFile = os.path.join(localSlaveTempDir, "slave_log.txt")
#Save the original stdout and stderr (by opening new file descriptors to the
#same files)
origStdOut = os.dup(1)
origStdErr = os.dup(2)
#Open the file to send stdout/stderr to.
logDescriptor = os.open(tempSlaveLogFile, os.O_WRONLY | os.O_CREAT | os.O_APPEND)
#Replace standard output with a descriptor for the log file
os.dup2(logDescriptor, 1)
#Replace standard error with a descriptor for the log file
os.dup2(logDescriptor, 2)
#Since we only opened the file once, all the descriptors duped from the
#original will share offset information, and won't clobber each others'
#writes. See <http://stackoverflow.com/a/5284108/402891>. This shouldn't
#matter, since O_APPEND seeks to the end of the file before every write, but
#maybe there's something odd going on...
#Close the descriptor we used to open the file
os.close(logDescriptor)
for handler in list(logger.handlers): #Remove old handlers
logger.removeHandler(handler)
#Add the new handler. The sys.stderr stream has been redirected by swapping
#the file descriptor out from under it.
logger.addHandler(logging.StreamHandler(sys.stderr))
#Put a message at the top of the log, just to make sure it's working.
print "---JOBTREE SLAVE OUTPUT LOG---"
sys.stdout.flush()
#Log the number of open file descriptors so we can tell if we're leaking
#them.
logger.debug("Next available file descriptor: {}".format(
nextOpenDescriptor()))
##########################################
#Parse input files
##########################################
config = ET.parse(getConfigFileName(jobTreePath)).getroot()
setLogLevel(config.attrib["log_level"])
job = Job.read(jobFile)
job.messages = [] #This is the only way to stop messages logging twice, as are read only in the master
job.children = [] #Similarly, this is where old children are flushed out.
job.write() #Update status, to avoid reissuing children after running a follow on below.
if os.path.exists(job.getLogFileName()): #This cleans the old log file
os.remove(job.getLogFileName())
logger.info("Parsed arguments and set up logging")
#Try loop for slave logging
##########################################
#Setup the stats, if requested
##########################################
if config.attrib.has_key("stats"):
startTime = time.time()
startClock = getTotalCpuTime()
stats = ET.Element("slave")
else:
stats = None
##########################################
#The max time
##########################################
maxTime = float(config.attrib["job_time"])
assert maxTime > 0.0
assert maxTime < sys.maxint
##########################################
#Slave log file trapped from here on in
##########################################
slaveFailed = False
try:
##########################################
#The next job
##########################################
def globalTempDirName(job, depth):
return job.getGlobalTempDirName() + str(depth)
command, memoryAvailable, cpuAvailable, depth = job.followOnCommands[-1]
defaultMemory = int(config.attrib["default_memory"])
defaultCpu = int(config.attrib["default_cpu"])
assert len(job.children) == 0
startTime = time.time()
while True:
job.followOnCommands.pop()
##########################################
#Global temp dir
##########################################
globalTempDir = makeSubDir(globalTempDirName(job, depth))
i = 1
while os.path.isdir(globalTempDirName(job, depth+i)):
system("rm -rf %s" % globalTempDirName(job, depth+i))
i += 1
##########################################
#Old children, not yet deleted
#
#These may exist because of the lazy cleanup
#we do
##########################################
for childDir in listChildDirs(job.jobDir):
logger.debug("Cleaning up old child %s" % childDir)
system("rm -rf %s" % childDir)
##########################################
#Run the job
##########################################
if command != "": #Not a stub
if command[:11] == "scriptTree ":
##########################################
#Run the target
##########################################
loadStack(command).execute(job=job, stats=stats,
localTempDir=localTempDir, globalTempDir=globalTempDir,
memoryAvailable=memoryAvailable, cpuAvailable=cpuAvailable,
defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
else: #Is another command
system(command)
##########################################
#Cleanup/reset a successful job/checkpoint
##########################################
job.remainingRetryCount = int(config.attrib["try_count"])
system("rm -rf %s/*" % (localTempDir))
job.update(depth=depth, tryCount=job.remainingRetryCount)
##########################################
#Establish if we can run another job
##########################################
if time.time() - startTime > maxTime:
logger.info("We are breaking because the maximum time the job should run for has been exceeded")
break
#Deal with children
if len(job.children) >= 1: #We are going to have to return to the parent
logger.info("No more jobs can run in series by this slave, its got %i children" % len(job.children))
break
if len(job.followOnCommands) == 0:
logger.info("No more jobs can run by this slave as we have exhausted the follow ons")
break
#Get the next job and see if we have enough cpu and memory to run it..
command, memory, cpu, depth = job.followOnCommands[-1]
if memory > memoryAvailable:
logger.info("We need more memory for the next job, so finishing")
break
if cpu > cpuAvailable:
logger.info("We need more cpus for the next job, so finishing")
break
logger.info("Starting the next job")
##########################################
#Finish up the stats
##########################################
if stats != None:
totalCpuTime, totalMemoryUsage = getTotalCpuTimeAndMemoryUsage()
stats.attrib["time"] = str(time.time() - startTime)
stats.attrib["clock"] = str(totalCpuTime - startClock)
stats.attrib["memory"] = str(totalMemoryUsage)
tempStatsFile = getTempStatsFile(jobTreePath)
fileHandle = open(tempStatsFile + ".new", "w")
ET.ElementTree(stats).write(fileHandle)
fileHandle.close()
os.rename(tempStatsFile + ".new", tempStatsFile) #This operation is atomic
logger.info("Finished running the chain of jobs on this node, we ran for a total of %f seconds" % (time.time() - startTime))
##########################################
#Where slave goes wrong
##########################################
except: #Case that something goes wrong in slave
traceback.print_exc()
logger.critical("Exiting the slave because of a failed job on host %s", socket.gethostname())
job = Job.read(jobFile)
setupJobAfterFailure(job, config)
job.write()
slaveFailed = True
##########################################
#Cleanup
##########################################
#Close the slave logging
#Flush at the Python level
sys.stdout.flush()
sys.stderr.flush()
#Flush at the OS level
os.fsync(1)
os.fsync(2)
#Close redirected stdout and replace with the original standard output.
os.dup2(origStdOut, 1)
#Close redirected stderr and replace with the original standard error.
os.dup2(origStdOut, 2)
#sys.stdout and sys.stderr don't need to be modified at all. We don't need
#to call redirectLoggerStreamHandlers since they still log to sys.stderr
#Close our extra handles to the original standard output and standard error
#streams, so we don't leak file handles.
os.close(origStdOut)
os.close(origStdErr)
#Now our file handles are in exactly the state they were in before.
#Copy back the log file to the global dir, if needed
if slaveFailed:
truncateFile(tempSlaveLogFile)
system("mv %s %s" % (tempSlaveLogFile, job.getLogFileName()))
#Remove the temp dir
system("rm -rf %s" % localSlaveTempDir)
#This must happen after the log file is done with, else there is no place to put the log
if (not slaveFailed) and len(job.followOnCommands) == 0 and len(job.children) == 0 and len(job.messages) == 0:
##########################################
#Cleanup global files at the end of the chain
##########################################
job.delete()
def edit_bbox(obj_to_edit, action):
''' action = `delete`
`change_class:new_class_index`
`resize_bbox:new_x_left:new_y_top:new_x_right:new_y_bottom`
'''
if 'change_class' in action:
new_class_index = int(action.split(':')[1])
elif 'resize_bbox' in action:
new_x_left = max(0, int(action.split(':')[1]))
new_y_top = max(0, int(action.split(':')[2]))
new_x_right = min(width, int(action.split(':')[3]))
new_y_bottom = min(height, int(action.split(':')[4]))
# 1. initialize bboxes_to_edit_dict
# (we use a dict since a single label can be associated with multiple ones in videos)
bboxes_to_edit_dict = {}
current_img_path = IMAGE_PATH_LIST[img_index]
bboxes_to_edit_dict[current_img_path] = obj_to_edit
# 2. add elements to bboxes_to_edit_dict
'''
If the bbox is in the json file then it was used by the video Tracker, hence,
we must also edit the next predicted bboxes associated to the same `anchor_id`.
'''
# if `current_img_path` is a frame from a video
is_from_video, video_name = is_frame_from_video(current_img_path)
if is_from_video:
# get json file corresponding to that video
json_file_path = '{}.json'.format(os.path.join(TRACKER_DIR,
video_name))
file_exists, json_file_data = get_json_file_data(json_file_path)
# if json file exists
if file_exists:
# match obj_to_edit with the corresponding json object
frame_data_dict = json_file_data['frame_data_dict']
json_object_list = get_json_file_object_list(
current_img_path, frame_data_dict)
obj_matched = get_json_object_dict(obj_to_edit, json_object_list)
# if match found
if obj_matched is not None:
# get this object's anchor_id
anchor_id = obj_matched['anchor_id']
frame_path_list = get_next_frame_path_list(
video_name, current_img_path)
frame_path_list.insert(0, current_img_path)
if 'change_class' in action:
# add also the previous frames
prev_path_list = get_prev_frame_path_list(
video_name, current_img_path)
frame_path_list = prev_path_list + frame_path_list
# update json file if contain the same anchor_id
for frame_path in frame_path_list:
json_object_list = get_json_file_object_list(
frame_path, frame_data_dict)
json_obj = get_json_file_object_by_id(
json_object_list, anchor_id)
if json_obj is not None:
bboxes_to_edit_dict[frame_path] = [
json_obj['class_index'], json_obj['bbox']['xmin'],
json_obj['bbox']['ymin'], json_obj['bbox']['xmax'],
json_obj['bbox']['ymax']
]
# edit json file
if 'delete' in action:
json_object_list.remove(json_obj)
elif 'change_class' in action:
json_obj['class_index'] = new_class_index
elif 'resize_bbox' in action:
json_obj['bbox']['xmin'] = new_x_left
json_obj['bbox']['ymin'] = new_y_top
json_obj['bbox']['xmax'] = new_x_right
json_obj['bbox']['ymax'] = new_y_bottom
else:
break
# save the edited data
with open(json_file_path, 'w') as outfile:
json.dump(json_file_data,
outfile,
sort_keys=True,
indent=4)
# 3. loop through bboxes_to_edit_dict and edit the corresponding annotation files
for path in bboxes_to_edit_dict:
obj_to_edit = bboxes_to_edit_dict[path]
class_index, xmin, ymin, xmax, ymax = map(int, obj_to_edit)
for ann_path in get_annotation_paths(path, annotation_formats):
if '.txt' in ann_path:
# edit YOLO file
with open(ann_path, 'r') as old_file:
lines = old_file.readlines()
yolo_line = yolo_format(
class_index, (xmin, ymin), (xmax, ymax), width,
height) # TODO: height and width ought to be stored
with open(ann_path, 'w') as new_file:
for line in lines:
if line != yolo_line + '\n':
new_file.write(line)
elif 'change_class' in action:
new_yolo_line = yolo_format(
new_class_index, (xmin, ymin), (xmax, ymax),
width, height)
new_file.write(new_yolo_line + '\n')
elif 'resize_bbox' in action:
new_yolo_line = yolo_format(
class_index, (new_x_left, new_y_top),
(new_x_right, new_y_bottom), width, height)
new_file.write(new_yolo_line + '\n')
elif '.xml' in ann_path:
# edit PASCAL VOC file
tree = ET.parse(ann_path)
annotation = tree.getroot()
for obj in annotation.findall('object'):
class_name_xml, class_index_xml, xmin_xml, ymin_xml, xmax_xml, ymax_xml = get_xml_object_data(
obj)
if (class_index == class_index_xml and xmin == xmin_xml
and ymin == ymin_xml and xmax == xmax_xml
and ymax == ymax_xml):
if 'delete' in action:
annotation.remove(obj)
elif 'change_class' in action:
# edit object class name
object_class = obj.find('name')
object_class.text = CLASS_LIST[new_class_index]
elif 'resize_bbox' in action:
object_bbox = obj.find('bndbox')
object_bbox.find('xmin').text = str(new_x_left)
object_bbox.find('ymin').text = str(new_y_top)
object_bbox.find('xmax').text = str(new_x_right)
object_bbox.find('ymax').text = str(new_y_bottom)
break
xml_str = ET.tostring(annotation)
write_xml(xml_str, ann_path)
# import xml.etree.ElementTree as ET
import xml.etree.cElementTree as ET
tree = ET.parse("country.xml") #<xml.etree.ElementTree.ElementTree object at 0x0029FD10>
print(tree)
root = tree.getroot()
print(root)
print(root.tag, ":", root.attrib)
# 遍历xml文档的第二层
for child in root:
# 第二层节点的标签名称和属性
print(child.tag,":", child.attrib)
# 遍历xml文档的第三层
for children in child:
# 第三层节点的标签名称和属性
print(children.tag, ":", children.attrib)
print(root[0][1].text)
# 过滤出所有neighbor标签
for neighbor in root.iter("neighbor"):
print(neighbor.tag, ":", neighbor.attrib)
# 遍历所有的counry标签
for country in root.findall("country"):
# 查找country标签下的第一个rank标签
rank = country.find("rank").text
# 获取country标签的name属性
def parse(file):
tree = ET.parse(file)
return XMLTree(tree.getroot())
def update_library(self,
ep_obj=None,
host=None,
username=None,
password=None,
plex_server_token=None,
force=True):
"""Handles updating the Plex Media Server host via HTTP API
Plex Media Server currently only supports updating the whole video library and not a specific path.
Returns:
Returns None for no issue, else a string of host with connection issues
"""
if sickbeard.USE_PLEX and sickbeard.PLEX_UPDATE_LIBRARY:
if not sickbeard.PLEX_SERVER_HOST:
logger.log(
u'PLEX: No Plex Media Server host specified, check your settings',
logger.DEBUG)
return False
if not host:
host = sickbeard.PLEX_SERVER_HOST
if not username:
username = sickbeard.PLEX_USERNAME
if not password:
password = sickbeard.PLEX_PASSWORD
if not plex_server_token:
plex_server_token = sickbeard.PLEX_SERVER_TOKEN
# if username and password were provided, fetch the auth token from plex.tv
token_arg = ''
if plex_server_token:
token_arg = '?X-Plex-Token=' + plex_server_token
elif username and password:
logger.log(
u'PLEX: fetching plex.tv credentials for user: '******'https://plex.tv/users/sign_in.xml',
data='')
authheader = 'Basic %s' % base64.encodestring(
'%s:%s' % (username, password))[:-1]
req.add_header('Authorization', authheader)
req.add_header('X-Plex-Device-Name', 'SickRage')
req.add_header('X-Plex-Product', 'SickRage Notifier')
req.add_header('X-Plex-Client-Identifier',
sickbeard.common.USER_AGENT)
req.add_header('X-Plex-Version', '1.0')
try:
response = urllib2.urlopen(req)
auth_tree = etree.parse(response)
token = auth_tree.findall(
'.//authentication-token')[0].text
token_arg = '?X-Plex-Token=' + token
except urllib2.URLError as e:
logger.log(
u'PLEX: Error fetching credentials from from plex.tv for user %s: %s'
% (username, ex(e)), logger.DEBUG)
except (ValueError, IndexError) as e:
logger.log(
u'PLEX: Error parsing plex.tv response: ' + ex(e),
logger.DEBUG)
file_location = '' if None is ep_obj else ep_obj.location
host_list = [x.strip() for x in host.split(',')]
hosts_all = {}
hosts_match = {}
hosts_failed = []
for cur_host in host_list:
url = 'http://%s/library/sections%s' % (cur_host, token_arg)
try:
xml_tree = etree.parse(urllib.urlopen(url))
media_container = xml_tree.getroot()
except IOError, e:
logger.log(
u'PLEX: Error while trying to contact Plex Media Server: '
+ ex(e), logger.WARNING)
hosts_failed.append(cur_host)
continue
except Exception as e:
if 'invalid token' in str(e):
logger.log(
u'PLEX: Please set TOKEN in Plex settings: ',
logger.ERROR)
else:
logger.log(
u'PLEX: Error while trying to contact Plex Media Server: '
+ ex(e), logger.ERROR)
continue
sections = media_container.findall('.//Directory')
if not sections:
logger.log(
u'PLEX: Plex Media Server not running on: ' + cur_host,
logger.DEBUG)
hosts_failed.append(cur_host)
continue
for section in sections:
if 'show' == section.attrib['type']:
keyed_host = [(str(section.attrib['key']), cur_host)]
hosts_all.update(keyed_host)
if not file_location:
continue
for section_location in section.findall('.//Location'):
section_path = re.sub(
r'[/\\]+', '/',
section_location.attrib['path'].lower())
section_path = re.sub(r'^(.{,2})[/\\]', '',
section_path)
location_path = re.sub(r'[/\\]+', '/',
file_location.lower())
location_path = re.sub(r'^(.{,2})[/\\]', '',
location_path)
if section_path in location_path:
hosts_match.update(keyed_host)
def main():
logging.basicConfig(format='%(levelname)s:%(message)s',
level=logging.DEBUG)
if len(sys.argv) < 4:
sys.stderr.write("transform_benchmark_to_pcidss.py PCI_DSS.json "
"SOURCE_XCCDF DESTINATION_XCCDF\n")
sys.exit(1)
id_tree = None
with open(sys.argv[1], "r") as f:
id_tree = json.load(f)
benchmark = ElementTree.parse(sys.argv[2])
rules = []
for rule in \
benchmark.findall(".//{%s}Rule" % (XCCDF_NAMESPACE)):
rules.append(rule)
rule_usage_map = {}
# only PCI-DSS related rules in that list, to speed-up processing
filtered_rules = []
for rule in rules:
for ref in rule.findall("./{%s}reference" % (XCCDF_NAMESPACE)):
if ref.get("href") == REMOTE_URL:
filtered_rules.append(rule)
break
values = []
for value in \
benchmark.findall(".//{%s}Value" % (XCCDF_NAMESPACE)):
values.append(value)
parent_map = dict((c, p) for p in benchmark.getiterator() for c in p)
for rule in \
benchmark.findall(".//{%s}Rule" % (XCCDF_NAMESPACE)):
parent_map[rule].remove(rule)
for value in \
benchmark.findall(".//{%s}Value" % (XCCDF_NAMESPACE)):
parent_map[value].remove(value)
for group in \
benchmark.findall(".//{%s}Group" % (XCCDF_NAMESPACE)):
parent_map[group].remove(group)
root_element = benchmark.getroot()
for id_, desc, children in id_tree:
element = \
construct_xccdf_group(id_, desc, children,
filtered_rules, rule_usage_map)
root_element.append(element)
if len(values) > 0:
group = ElementTree.Element("{%s}Group" % (XCCDF_NAMESPACE))
group.set("id", "xccdf_org.ssgproject.content_group_values")
group.set("selected", "true")
title = ElementTree.Element("{%s}title" % (XCCDF_NAMESPACE))
title.text = "Values"
group.append(title)
description = ElementTree.Element("{%s}description" %
(XCCDF_NAMESPACE))
description.text = "Group of values used in PCI-DSS profile"
group.append(description)
for value in values:
copied_value = copy.deepcopy(value)
group.append(copied_value)
root_element.append(group)
unused_rules = []
for rule in rules:
if rule.get("id") not in rule_usage_map:
# this rule wasn't added yet, it would be lost unless we added it
# to a special non-PCI-DSS group
unused_rules.append(rule)
for ref in rule.findall("./{%s}reference" % (XCCDF_NAMESPACE)):
if ref.get("href") == REMOTE_URL:
logging.error(
"Rule '%s' references PCI-DSS '%s' but doesn't match "
"any Group ID in our requirement tree. Perhaps it's "
"referencing something we don't consider applicable on "
"the Operating System level?", rule.get("id"),
ref.text)
if len(unused_rules) > 0:
logging.warning("%i rules don't reference PCI-DSS!" %
(len(unused_rules)))
group = ElementTree.Element("{%s}Group" % (XCCDF_NAMESPACE))
group.set("id", "xccdf_org.ssgproject.content_group_non-pci-dss")
group.set("selected", "true")
title = ElementTree.Element("{%s}title" % (XCCDF_NAMESPACE))
title.text = "Non PCI-DSS"
group.append(title)
description = ElementTree.Element("{%s}description" %
(XCCDF_NAMESPACE))
description.text = "Rules that are not part of PCI-DSS"
group.append(description)
for rule in unused_rules:
copied_rule = copy.deepcopy(rule)
group.append(copied_rule)
root_element.append(group)
# change the Benchmark ID to avoid validation issues
root_element.set(
"id",
root_element.get("id").replace("_benchmark_", "_benchmark_PCIDSS-"))
for title_element in \
root_element.findall("./{%s}title" % (XCCDF_NAMESPACE)):
title_element.text += " (PCI-DSS centric)"
# filter out all profiles except PCI-DSS
for profile in \
benchmark.findall("./{%s}Profile" % (XCCDF_NAMESPACE)):
if profile.get("id").endswith("pci-dss"):
# change the profile ID to avoid validation issues
profile.set(
"id",
profile.get("id").replace("pci-dss", "pci-dss_centric"))
else:
root_element.remove(profile)
continue
# filter out old group selectors from the PCI-DSS profile
for select in profile.findall("./{%s}select" % (XCCDF_NAMESPACE)):
if select.get("idref").startswith(
"xccdf_org.ssgproject.content_group_"):
# we will remove all group selectors, all PCI-DSS groups are
# selected by default so we don't need any in the final
# PCI-DSS Benchmark
profile.remove(select)
benchmark.write(sys.argv[3])
dict = {
"Traffic Light": "0",
"Red": "1",
"Green": "2",
"Yellow": "3",
"Straight": "4",
"Right": "5",
"Left": "6"
}
files = listdir(path_root)
inputtxt = open("test.txt", 'r')
for i in files:
# print(i[0:-4])
# print(lines)
# print(lines[-2][0:-4])
tree = ET.parse(path_root + i[0:-4] + '.xml')
root = tree.getroot()
save = open(txt_path + i[0:-4] + ".txt", 'w')
line = ''
for child in root.findall('object'):
name = child.find('name').text
bndbox = child.find('bndbox')
xmin = (bndbox.find('xmin').text)
ymin = (bndbox.find('ymin').text)
xmax = (bndbox.find('xmax').text)
ymax = (bndbox.find('ymax').text)
if int(ymax) - int(ymin) <= 5:
continue
line += dict[
name] + ' ' + xmin + ' ' + ymin + ' ' + xmax + ' ' + ymax + '\n'
for child2 in child.findall('status'):
renamed 'bikeStations.xml'. That database table should be empty (to
avoid an exception due to inserting row with duplicate key).
"""
import logging
logging.basicConfig(level=logging.DEBUG, format='%(levelname)s - %(message)s')
import psycopg2
import sys
conn = psycopg2.connect(dbname='gisdb', user='******', password='******')
cur = conn.cursor()
import xml.etree.cElementTree as ET
tree = ET.parse('bikeStations.xml')
# These are the children of interest
childTags = ['name', 'terminalName', 'lat', 'long', 'nbBikes', 'nbEmptyDocks']
falseStatusTags = ['locked', 'temporary']
trueStatusTags = ['installed', 'public']
stations = tree.findall('station')
for station in stations:
print("STATION")
stationName = station.find('name').text
stationId = station.find('terminalName').text
lat = station.find('lat').text
lon = station.find('long').text
fullDocks = station.find('nbBikes').text
emptyDocks = station.find('nbEmptyDocks').text
dockQty = int(fullDocks) + int(emptyDocks)
def parse_abstracts_xml(abstracts_xmlfilename, csv_file):
""" Method for getting structured list containing all the abstracts from XML.
Every abstract in the list is an object of Abstract class.
It contains 4 main components:
1. Track of abstract
2. Title
3. List of authors. Every author is an object of Person class
4. Abstract itself (content)
"""
tree_abstracts = ET.parse(abstracts_xmlfilename)
root_abstracts = tree_abstracts.getroot()
doc_abstracts = LXML_ET.parse(abstracts_xmlfilename)
count_abstracts = doc_abstracts.xpath('count(//abstract)')
track = ""
title = ""
content = ""
flag = False
authors = []
abstracts_list = []
unknown_affiliations = []
affiliation_standarts = create_dict_standarts(csv_file)
print("1. Parsing all abstracts from XML")
for i in range(1, int(count_abstracts) + 1):
for child in root_abstracts[i]:
if child.tag == "Title":
title = child.text.strip()
continue
if child.tag == "Content":
content = child.text.strip()
continue
if child.tag == "PrimaryAuthor" or child.tag == "Co-Author":
# Bringing different affiliations to the same standard
affiliation = str(child[3].text).strip()
# If affiliation is in standards - bring affiliation to standard
if affiliation in affiliation_standarts:
affiliation = affiliation_standarts[affiliation]
else:
unknown_affiliations.append(affiliation)
primary_author = Person(first_name=str(child[0].text),
family_name=str(child[1].text),
email=str(child[2].text),
affiliation=affiliation,
is_primary_author=True if child.tag == "PrimaryAuthor" else False)
authors.append(primary_author)
continue
if child.tag == "Track" and not flag:
track = child.text
flag = True
continue
abstract = Abstract(title, content, authors, track)
abstracts_list.append(abstract)
authors = []
flag = False
# Print unknown affiliations
unknown_affiliations = list(set(unknown_affiliations))
print("2. The following affiliations are unknown. Please add them to CSV file with standards.")
for affiliation in unknown_affiliations:
print(affiliation)
print("==============================================")
return abstracts_list
def execute(self, context):
zip_name = self.filepath
#file paths ans zip extraction dirs
zip_path = os.path.abspath(zip_name)
zip_dir = os.path.dirname(zip_path)
html_path = os.path.join(zip_dir, 'html')
xml_path = os.path.join(html_path, 'xml')
zip2_path = os.path.join(html_path, os.path.basename(zip_path))
#remove old files
shutil.rmtree(xml_path, True)
#unzip files
with ZipFile(zip_path, 'r') as zip_file:
zip_file.extractall(html_path)
with ZipFile(zip2_path, 'r') as zip_file:
zip_file.extractall(xml_path)
#clear scene
bpy.data.scenes["Scene"].unit_settings.scale_length = 1.0
bpy.ops.object.mode_set(mode='OBJECT')
bpy.ops.object.select_all(action='SELECT')
bpy.ops.object.delete(use_global=False)
#clear images
imgs = bpy.data.images
for image in imgs:
image.user_clear()
#clear materials
for material in bpy.data.materials:
material.user_clear()
bpy.data.materials.remove(material)
#clear textures
textures = bpy.data.textures
for tex in textures:
tex.user_clear()
bpy.data.textures.remove(tex)
#read xml and files
xmlPath = os.path.join(xml_path, 'Home.xml')
xmlRoot = ElementTree.parse(xmlPath).getroot()
#read house
filename = os.path.join(xml_path, xmlRoot.get('structure'))
bpy.ops.import_scene.obj(filepath=filename)
obs = bpy.context.selected_editable_objects[:]
bpy.context.scene.objects.active = obs[0]
bpy.ops.object.join()
obs[0].name = xmlRoot.get('name')
obs[0].dimensions = obs[0].dimensions * scale
obs[0].location = (0.0, 0.0, 0.0)
bpy.ops.object.shade_flat()
bpy.context.active_object.layers[0] = True
bpy.context.active_object.layers[1] = False
bpy.context.active_object.layers[2] = False
bpy.context.active_object.layers[3] = False
Level = namedtuple("Level", "id elev ft")
levels = []
for element in xmlRoot:
objectName = element.tag
if objectName == 'level':
levels.append(
Level(id=element.get('id'),
elev=float(element.get('elevation')),
ft=float(element.get('floorThickness'))))
if objectName == 'furnitureGroup':
for furniture in element:
xmlRoot.append(furniture)
#if objectName in ('doorOrWindow','pieceOfFurniture'):
if 'model' in element.keys():
print(objectName)
filename = os.path.join(xml_path,
unquote(element.get('model')))
dimX = float(element.get('width'))
dimY = float(element.get('height'))
dimZ = float(element.get('depth'))
locX = float(element.get('x')) * scale
locY = -float(element.get('y')) * scale
lve = 0.0
if 'level' in element.keys():
for lv in levels:
if lv.id == element.get('level'):
lve = (lv.elev) * scale
if 'elevation' in element.keys():
locZ = (dimY * scale / 2.0) + (
float(element.get('elevation')) * scale) + lve
else:
locZ = (dimY * scale / 2.0) + lve
bpy.ops.import_scene.obj(filepath=filename)
obs = bpy.context.selected_editable_objects[:]
bpy.context.scene.objects.active = obs[0]
bpy.ops.object.join()
obs[0].name = element.get('name')
bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY',
center='BOUNDS')
if objectName in ('doorOrWindow'):
bpy.context.active_object.layers[1] = True
bpy.context.active_object.layers[2] = False
else:
bpy.context.active_object.layers[2] = True
bpy.context.active_object.layers[1] = False
bpy.context.active_object.layers[0] = False
bpy.context.active_object.layers[3] = False
if 'modelMirrored' in element.keys():
if element.get('modelMirrored') == 'true':
bpy.ops.transform.mirror(
constraint_axis=(True, False, False),
constraint_orientation='GLOBAL',
proportional='DISABLED')
if 'modelRotation' in element.keys():
value = element.get('modelRotation')
va = value.split()
mat_rot = mathutils.Matrix()
mat_rot[0][0] = float(va[0])
mat_rot[0][1] = float(va[1])
mat_rot[0][2] = float(va[2])
mat_rot[1][0] = float(va[3])
mat_rot[1][1] = float(va[4])
mat_rot[1][2] = float(va[5])
mat_rot[2][0] = float(va[6])
mat_rot[2][1] = float(va[7])
mat_rot[2][2] = float(va[8])
ob = bpy.context.object
ob.matrix_world = mat_rot
bpy.ops.object.transform_apply(location=False,
rotation=True,
scale=False)
ob.rotation_euler = (math.pi / 2, 0.0, 0.0)
#if 'backFaceShown' in element.keys():
#TODO
#object position and rotation
obs[0].dimensions = (dimX * scale, dimY * scale, dimZ * scale)
bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY',
center='BOUNDS')
obs[0].location = (locX, locY, locZ)
bpy.ops.object.transform_apply(location=False,
rotation=True,
scale=True)
if 'angle' in element.keys():
angle = element.get('angle')
obs[0].rotation_euler[2] = -float(angle)
if 'color' in element.keys():
color = element.get('color')
r = int(color[2:4], 16) / 255.0
g = int(color[4:6], 16) / 255.0
b = int(color[6:8], 16) / 255.0
bcolor = [r, g, b]
for material in bpy.context.active_object.data.materials:
material.diffuse_color = bcolor
#search for texture or materials
for prop in element:
if prop.tag == 'texture':
image = prop.get('image')
for material in bpy.context.active_object.data.materials:
img = bpy.data.images.load(
os.path.join(xml_path, image))
tex = bpy.data.textures.new(image, type='IMAGE')
tex.image = img
mtex = material.texture_slots.add()
mtex.texture = tex
if prop.tag == 'material':
mname = prop.get('name')
if 'color' in prop.keys():
color = prop.get('color')
r = int(color[2:4], 16) / 255.0
g = int(color[4:6], 16) / 255.0
b = int(color[6:8], 16) / 255.0
bcolor = [r, g, b]
for material in bpy.context.active_object.data.materials:
if mname in material.name:
material.diffuse_color = bcolor
#face texture of material
for texture in prop:
if texture.tag == 'texture':
image = texture.get('image')
for material in bpy.context.active_object.data.materials:
if mname in material.name:
img = bpy.data.images.load(
os.path.join(xml_path, image))
tex = bpy.data.textures.new(
image, type='IMAGE')
tex.image = img
mtex = material.texture_slots.add()
mtex.texture = tex
if objectName in ('light'):
owner = bpy.context.active_object
bpy.ops.object.lamp_add(type='POINT', location=(0.0, 0.0, 0.0))
bpy.context.active_object.data.energy = 200.0 * scale
bpy.context.active_object.data.shadow_method = 'RAY_SHADOW'
bpy.context.active_object.data.color = (0.9, 0.9, 0.9)
bpy.context.active_object.parent = owner
bpy.context.active_object.layers[3] = True
bpy.context.active_object.layers[0] = False
bpy.context.active_object.layers[1] = False
bpy.context.active_object.layers[2] = False
#insert camera
if objectName in ('observerCamera'):
if element.get('attribute') == 'observerCamera':
locX = float(element.get('x')) * scale
locY = -float(element.get('y')) * scale
locZ = float(element.get('z')) * scale
yaw = float(element.get('yaw'))
pitch = float(element.get('pitch'))
bpy.ops.object.camera_add(
location=(locX, locY, locZ),
rotation=((-pitch / 8.0) + (-math.pi / 2.0), math.pi,
0))
bpy.ops.mesh.primitive_cube_add(
location=(locX, locY, locZ - (170.0 * scale / 2.0)),
rotation=(0.0, 0.0, -yaw))
obs = bpy.context.selected_editable_objects[:]
bpy.context.scene.objects.active = obs[0]
obs[0].name = 'player'
obs[0].dimensions = (40 * scale, 20 * scale, 170.0 * scale)
bpy.data.objects["Camera"].parent = bpy.data.objects[
"player"]
bpy.data.objects["Camera"].location = (0.0, -30.0 * scale,
22 * scale)
bpy.data.objects["player"].game.physics_type = 'CHARACTER'
bpy.data.objects["player"].game.use_collision_bounds = True
bpy.data.objects["player"].game.step_height = 0.8
#add logic blocks
obj = bpy.data.objects["player"]
cam = bpy.data.objects["Camera"]
#foward
bpy.ops.logic.sensor_add(type="KEYBOARD", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOTION", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].name = "w"
obj.game.sensors[-1].key = "W"
obj.game.actuators[-1].offset_location[1] = -speed
#backward
bpy.ops.logic.sensor_add(type="KEYBOARD", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOTION", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].name = "s"
obj.game.sensors[-1].key = "S"
obj.game.actuators[-1].offset_location[1] = speed
#left
bpy.ops.logic.sensor_add(type="KEYBOARD", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOTION", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].name = "a"
obj.game.sensors[-1].key = "A"
obj.game.actuators[-1].offset_location[0] = speed
#right
bpy.ops.logic.sensor_add(type="KEYBOARD", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOTION", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].name = "d"
obj.game.sensors[-1].key = "D"
obj.game.actuators[-1].offset_location[0] = -speed
#jump
bpy.ops.logic.sensor_add(type="KEYBOARD", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOTION", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].name = "space"
obj.game.sensors[-1].key = "SPACE"
obj.game.actuators[-1].mode = 'OBJECT_CHARACTER'
obj.game.actuators[-1].use_character_jump = True
#mouse view
bpy.ops.logic.sensor_add(type="MOUSE", object="player")
bpy.ops.logic.controller_add(type="LOGIC_AND",
object="player")
bpy.ops.logic.actuator_add(type="MOUSE", object="player")
obj.game.sensors[-1].link(obj.game.controllers[-1])
obj.game.actuators[-1].link(obj.game.controllers[-1])
obj.game.sensors[-1].mouse_event = 'MOVEMENT'
obj.game.actuators[-1].mode = 'LOOK'
obj.game.actuators[-1].sensitivity_y = 0.0
bpy.ops.logic.actuator_add(type="MOUSE", object="Camera")
cam.game.actuators[-1].link(obj.game.controllers[-1])
cam.game.actuators[-1].mode = 'LOOK'
cam.game.actuators[-1].sensitivity_x = 0.0
#Iterate over all members of the material struct and disable apha (to solve texture errors in blender game engine)
for item in bpy.data.materials:
if item.alpha == 1.0:
item.use_transparency = False
item.use_transparent_shadows = True
else:
item.raytrace_mirror.use = True
item.raytrace_mirror.reflect_factor = 0.1
item.diffuse_intensity = 0.01
#better collision detection
bpy.data.scenes["Scene"].game_settings.physics_step_sub = 5.0
#world settings
bpy.data.worlds["World"].light_settings.use_ambient_occlusion = True
bpy.data.worlds["World"].light_settings.ao_factor = 0.01
bpy.data.worlds["World"].light_settings.use_environment_light = True
bpy.data.worlds["World"].light_settings.environment_energy = 0.01
bpy.data.scenes["Scene"].unit_settings.system = 'METRIC'
bpy.data.scenes["Scene"].unit_settings.scale_length = 0.01 / scale
bpy.data.scenes["Scene"].layers[0] = True
bpy.data.scenes["Scene"].layers[1] = True
bpy.data.scenes["Scene"].layers[2] = True
bpy.data.scenes["Scene"].layers[3] = True
return {'FINISHED'}
def loadVSS(fn):
'''Decode a Vicon Skeleton file (VST format). VSK is labeling skeleton. VSS is solving skeleton.'''
import xml.etree.cElementTree as ET
import numpy as np
dom = ET.parse(fn)
parameters = dom.findall('Parameters')[0]
params = dict([(p.get('NAME'),p.get('VALUE')) for p in parameters])
sticks = dom.findall('MarkerSet')[0].find('Sticks')
sticksPairs = [(x.get('MARKER1'),x.get('MARKER2')) for x in sticks]
sticksColour= [np.fromstring(x.get('RGB1', '255 255 255'), dtype=np.uint8, sep=' ') for x in sticks]
hasTargetSet = True
try: markers = dom.findall('TargetSet')[0].find('Targets')
except: markers = dom.findall('MarkerSet')[0].find('Markers'); hasTargetSet = False
markerOffsets = [x.get('POSITION').split() for x in markers]
def ev(x,params):
for k,v in params.items(): x = x.replace(k,v)
return float(x) # eval(x)
markerOffsets = [[ev(x,params) for x in mp] for mp in markerOffsets]
markerColour= [np.fromstring(col, dtype=np.uint8, sep=' ') for col in \
[x.get('MARKER', x.get('RGB')) for x in dom.findall('MarkerSet')[0].find('Markers')]]
colouredMarkers = [x.get('MARKER', x.get('NAME')) for x in dom.findall('MarkerSet')[0].find('Markers')]
markerNames = [x.get('MARKER', x.get('NAME')) for x in markers]
markerWeights = [float(x.get('WEIGHT')) if hasTargetSet else 1.0 for x in markers]
markerParents = [x.get('SEGMENT') for x in markers]
skeleton = dom.findall('Skeleton')[0]
# skeleton is defined as a tree of Segments
# Segment contains Joint and Segment
# Joint is JointDummy(0)/JointHinge(1)/JointHardySpicer(2)/JointBall(3)/JointFree(6), containing JointTemplate
def ap(skeleton, parent, skel):
for seg in skeleton:
if seg.tag == 'Segment':
skel.append([seg.get('NAME'),parent,seg.attrib])
ap(seg, len(skel)-1, skel)
else:
skel[parent].extend([seg.tag,seg.attrib,{} if len(seg) == 0 else seg[0].attrib])
return skel
# recursively parse the skeleton
root = ap(skeleton, -1, [])
assert(len(markerParents) == len(markerOffsets))
def cqToR(rs, R):
'''Given a compressed quaternion, form a 3x3 rotation matrix.'''
angle = np.dot(rs,rs)**0.5
scale = (np.sin(angle*0.5)/angle if angle > 1e-8 else 0.5)
q = np.array([rs[0]*scale,rs[1]*scale,rs[2]*scale,np.cos(angle*0.5)], dtype=np.float32)
q = np.outer(q, q)*2
R[:3,:3] = [
[1.0-q[1, 1]-q[2, 2], q[0, 1]-q[2, 3], q[0, 2]+q[1, 3]],
[ q[0, 1]+q[2, 3], 1.0-q[0, 0]-q[2, 2], q[1, 2]-q[0, 3]],
[ q[0, 2]-q[1, 3], q[1, 2]+q[0, 3], 1.0-q[0, 0]-q[1, 1]]]
def float3(x): return np.array(map(lambda x:ev(x,params), x.split()),dtype=np.float32)
def mats(x):
preT = x.get('PRE-POSITION', '0 0 0')
postT = x.get('POST-POSITION', '0 0 0')
preR = x.get('PRE-ORIENTATION', '0 0 0')
postR = x.get('POST-ORIENTATION', '0 0 0')
pre = np.zeros((3,4),dtype=np.float32)
post = np.zeros((3,4),dtype=np.float32)
pre[:,3] = float3(preT)
post[:,3] = float3(postT)
cqToR(float3(preR), pre[:3,:3])
cqToR(float3(postR), post[:3,:3])
return pre,post
name = fn.rpartition('/')[2].partition('.')[0]
numBones = len(root)
jointNames = [r[0] for r in root]
markerParents = np.array([jointNames.index(mp) for mp in markerParents],dtype=np.int32)
jointNames[0] = 'root' # !!!! WARNING !!!!
jointParents = [r[1] for r in root]
jointData = [mats(r[4]) for r in root]
jointTypes = [r[3] for r in root] # JointDummy(0)/JointHinge(1)/JointHardySpicer(2)/JointBall(3)/JointFree(6)
#jointTemplates = [mats(r[5]) for r in root] # JointTemplate ... contains the same data as jointTypes
jointAxes = [r[4].get('AXIS',r[4].get('AXIS-PAIR',r[4].get('EULER-ORDER','XYZ'))) for r in root] # order
jointTs = [r[4].get('T',None) for r in root]
Gs = np.zeros((numBones,3,4),dtype=np.float32) # GLOBAL mats
Ls = np.zeros((numBones,3,4),dtype=np.float32) # LOCAL mats
Bs = np.zeros((numBones,3),dtype=np.float32) # BONES
for ji,pi in enumerate(jointParents):
if pi == -1: Ls[ji] = jointData[ji][0]
else: np.dot(jointData[pi][1][:,:3],jointData[ji][0],out=Ls[ji]); Ls[ji,:,3] += jointData[pi][1][:,3]
dofNames = []
jointChans = [] # tx=0,ty,tz,rx,ry,rz
jointChanSplits = [0]
# TODO: locked channels
for ji,(jt,T) in enumerate(zip(jointTypes,jointTs)):
jointChanSplits.append(len(jointChans))
if jt == 'JointDummy': assert(T is None)
elif jt == 'JointHinge':
assert(T == '* ')
jointChans.append(jointAxes[ji].split().index('1')+3)
elif jt == 'JointHardySpicer':
assert(T == '* * ')
ja = jointAxes[ji].split()
jointChans.append(ja.index('1',3))
jointChans.append(ja.index('1')+3)
elif jt == 'JointBall':
assert(T == '* * * ')
ja = jointAxes[ji]
jointChans.append(ord(ja[0])-ord('X')+3)
jointChans.append(ord(ja[1])-ord('X')+3)
jointChans.append(ord(ja[2])-ord('X')+3)
elif jt == 'JointFree':
assert(T == '* * * * * * ' or T is None) # version 1 of the file apparently doesn't fill this!
ja = jointAxes[ji]
jointChans.append(0)
jointChans.append(1)
jointChans.append(2)
jointChanSplits[-1] = len(jointChans)
jointChans.append(ord(ja[0])-ord('X')+3)
jointChans.append(ord(ja[1])-ord('X')+3)
jointChans.append(ord(ja[2])-ord('X')+3)
for jc in jointChans[jointChanSplits[-2]:]:
dofNames.append(jointNames[ji]+':'+'tx ty tz rx ry rz'.split()[jc])
jointChanSplits.append(len(jointChans))
numDofs = len(dofNames)
# fill Gs
chanValues = np.zeros(numDofs,dtype=np.float32)
rootMat = np.eye(3, 4, dtype=np.float32)
# fill Bs; TODO add dummy joints to store the extra bones (where multiple joints have the same parent)
for ji,pi in enumerate(jointParents):
if pi != -1: Bs[pi] = Ls[ji,:,3]
Bs[np.where(Bs*Bs<0.01)] = 0 # zero out bones < 0.1mm
# TODO: compare skeleton with ASF exported version
skel_dict = {
'markerOffsets' : np.array(markerOffsets, dtype=np.float32),
'markerParents' : markerParents,
'markerNames' : markerNames,
'markerNamesUnq' : colouredMarkers,
'markerColour' : markerColour,
'markerWeights' : np.array(markerWeights,dtype=np.float32),
'numMarkers' : len(markerNames),
'sticks' : sticksPairs,
'sticksColour' : sticksColour,
'name' : str(name),
'numJoints' : int(numBones),
'jointNames' : jointNames, # list of strings
'jointIndex' : dict([(k,v) for v,k in enumerate(jointNames)]), # dict of string:int
'jointParents' : np.array(jointParents,dtype=np.int32),
'jointChans' : np.array(jointChans,dtype=np.int32), # 0 to 5 : tx,ty,tz,rx,ry,rz
'jointChanSplits': np.array(jointChanSplits,dtype=np.int32),
'chanNames' : dofNames, # list of strings
'chanValues' : np.zeros(numDofs,dtype=np.float32),
'numChans' : int(numDofs),
'Bs' : np.array(Bs, dtype=np.float32),
'Ls' : np.array(Ls, dtype=np.float32),
'Gs' : np.array(Gs, dtype=np.float32),
'rootMat' : rootMat,
}
Character.pose_skeleton(skel_dict['Gs'], skel_dict)
return skel_dict