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700 | poppy-project/pypot | pypot/kinematics.py | Link.get_transformation_matrix | def get_transformation_matrix(self, theta):
""" Computes the homogeneous transformation matrix for this link. """
ct = numpy.cos(theta + self.theta)
st = numpy.sin(theta + self.theta)
ca = numpy.cos(self.alpha)
sa = numpy.sin(self.alpha)
return numpy.matrix(((ct, -st * c... | python | def get_transformation_matrix(self, theta):
""" Computes the homogeneous transformation matrix for this link. """
ct = numpy.cos(theta + self.theta)
st = numpy.sin(theta + self.theta)
ca = numpy.cos(self.alpha)
sa = numpy.sin(self.alpha)
return numpy.matrix(((ct, -st * c... | [
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701 | poppy-project/pypot | pypot/kinematics.py | Chain.forward_kinematics | def forward_kinematics(self, q):
""" Computes the homogeneous transformation matrix of the end effector of the chain.
:param vector q: vector of the joint angles (theta 1, theta 2, ..., theta n)
"""
q = numpy.array(q).flatten()
if len(q) != len(self.links):
raise V... | python | def forward_kinematics(self, q):
""" Computes the homogeneous transformation matrix of the end effector of the chain.
:param vector q: vector of the joint angles (theta 1, theta 2, ..., theta n)
"""
q = numpy.array(q).flatten()
if len(q) != len(self.links):
raise V... | [
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702 | poppy-project/pypot | pypot/kinematics.py | Chain.inverse_kinematics | def inverse_kinematics(self, end_effector_transformation,
q=None,
max_iter=1000, tolerance=0.05,
mask=numpy.ones(6),
use_pinv=False):
""" Computes the joint angles corresponding to the end effector transf... | python | def inverse_kinematics(self, end_effector_transformation,
q=None,
max_iter=1000, tolerance=0.05,
mask=numpy.ones(6),
use_pinv=False):
""" Computes the joint angles corresponding to the end effector transf... | [
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:param end_effector_transformation: the end effector homogeneous transformation matrix
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703 | poppy-project/pypot | pypot/dynamixel/__init__.py | _get_available_ports | def _get_available_ports():
""" Tries to find the available serial ports on your system. """
if platform.system() == 'Darwin':
return glob.glob('/dev/tty.usb*')
elif platform.system() == 'Linux':
return glob.glob('/dev/ttyACM*') + glob.glob('/dev/ttyUSB*') + glob.glob('/dev/ttyAMA*')
e... | python | def _get_available_ports():
""" Tries to find the available serial ports on your system. """
if platform.system() == 'Darwin':
return glob.glob('/dev/tty.usb*')
elif platform.system() == 'Linux':
return glob.glob('/dev/ttyACM*') + glob.glob('/dev/ttyUSB*') + glob.glob('/dev/ttyAMA*')
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704 | poppy-project/pypot | pypot/dynamixel/__init__.py | find_port | def find_port(ids, strict=True):
""" Find the port with the specified attached motor ids.
:param list ids: list of motor ids to find
:param bool strict: specify if all ids should be find (when set to False, only half motor must be found)
.. warning:: If two (or more) ports are attached to ... | python | def find_port(ids, strict=True):
""" Find the port with the specified attached motor ids.
:param list ids: list of motor ids to find
:param bool strict: specify if all ids should be find (when set to False, only half motor must be found)
.. warning:: If two (or more) ports are attached to ... | [
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:param list ids: list of motor ids to find
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705 | poppy-project/pypot | pypot/sensor/depth/sonar.py | Sonar._filter | def _filter(self, data):
""" Apply a filter to reduce noisy data.
Return the median value of a heap of data.
"""
filtered_data = []
for queue, data in zip(self._raw_data_queues, data):
queue.append(data)
filtered_data.append(numpy.median(queue))
... | python | def _filter(self, data):
""" Apply a filter to reduce noisy data.
Return the median value of a heap of data.
"""
filtered_data = []
for queue, data in zip(self._raw_data_queues, data):
queue.append(data)
filtered_data.append(numpy.median(queue))
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706 | poppy-project/pypot | pypot/dynamixel/syncloop.py | MetaDxlController.setup | def setup(self):
""" Starts all the synchronization loops. """
[c.start() for c in self.controllers]
[c.wait_to_start() for c in self.controllers] | python | def setup(self):
""" Starts all the synchronization loops. """
[c.start() for c in self.controllers]
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707 | poppy-project/pypot | pypot/creatures/ik.py | IKChain.from_poppy_creature | def from_poppy_creature(cls, poppy, motors, passiv, tip,
reversed_motors=[]):
""" Creates an kinematic chain from motors of a Poppy Creature.
:param poppy: PoppyCreature used
:param list motors: list of all motors that composed the kinematic chain
... | python | def from_poppy_creature(cls, poppy, motors, passiv, tip,
reversed_motors=[]):
""" Creates an kinematic chain from motors of a Poppy Creature.
:param poppy: PoppyCreature used
:param list motors: list of all motors that composed the kinematic chain
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:param poppy: PoppyCreature used
:param list motors: list of all motors that composed the kinematic chain
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708 | poppy-project/pypot | pypot/creatures/ik.py | IKChain.goto | def goto(self, position, duration, wait=False, accurate=False):
""" Goes to a given cartesian position.
:param list position: [x, y, z] representing the target position (in meters)
:param float duration: move duration
:param bool wait: whether to wait for the end of the move... | python | def goto(self, position, duration, wait=False, accurate=False):
""" Goes to a given cartesian position.
:param list position: [x, y, z] representing the target position (in meters)
:param float duration: move duration
:param bool wait: whether to wait for the end of the move... | [
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709 | poppy-project/pypot | pypot/creatures/ik.py | IKChain._goto | def _goto(self, pose, duration, wait, accurate):
""" Goes to a given cartesian pose.
:param matrix pose: homogeneous matrix representing the target position
:param float duration: move duration
:param bool wait: whether to wait for the end of the move
:param bool... | python | def _goto(self, pose, duration, wait, accurate):
""" Goes to a given cartesian pose.
:param matrix pose: homogeneous matrix representing the target position
:param float duration: move duration
:param bool wait: whether to wait for the end of the move
:param bool... | [
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710 | poppy-project/pypot | pypot/creatures/ik.py | IKChain.convert_to_ik_angles | def convert_to_ik_angles(self, joints):
""" Convert from poppy representation to IKPY internal representation. """
if len(joints) != len(self.motors):
raise ValueError('Incompatible data, len(joints) should be {}!'.format(len(self.motors)))
raw_joints = [(j + m.offset) * (1 if m.dir... | python | def convert_to_ik_angles(self, joints):
""" Convert from poppy representation to IKPY internal representation. """
if len(joints) != len(self.motors):
raise ValueError('Incompatible data, len(joints) should be {}!'.format(len(self.motors)))
raw_joints = [(j + m.offset) * (1 if m.dir... | [
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711 | poppy-project/pypot | pypot/creatures/ik.py | IKChain.convert_from_ik_angles | def convert_from_ik_angles(self, joints):
""" Convert from IKPY internal representation to poppy representation. """
if len(joints) != len(self.motors) + 2:
raise ValueError('Incompatible data, len(joints) should be {}!'.format(len(self.motors) + 2))
joints = [rad2deg(j) for j in jo... | python | def convert_from_ik_angles(self, joints):
""" Convert from IKPY internal representation to poppy representation. """
if len(joints) != len(self.motors) + 2:
raise ValueError('Incompatible data, len(joints) should be {}!'.format(len(self.motors) + 2))
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712 | poppy-project/pypot | pypot/dynamixel/io/io_320.py | Dxl320IO.factory_reset | def factory_reset(self, ids, except_ids=False, except_baudrate_and_ids=False):
""" Reset all motors on the bus to their factory default settings. """
mode = (0x02 if except_baudrate_and_ids else
0x01 if except_ids else 0xFF)
for id in ids:
try:
self.... | python | def factory_reset(self, ids, except_ids=False, except_baudrate_and_ids=False):
""" Reset all motors on the bus to their factory default settings. """
mode = (0x02 if except_baudrate_and_ids else
0x01 if except_ids else 0xFF)
for id in ids:
try:
self.... | [
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713 | poppy-project/pypot | pypot/primitive/primitive.py | Primitive.stop | def stop(self, wait=True):
""" Requests the primitive to stop. """
logger.info("Primitive %s stopped.", self)
StoppableThread.stop(self, wait) | python | def stop(self, wait=True):
""" Requests the primitive to stop. """
logger.info("Primitive %s stopped.", self)
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714 | poppy-project/pypot | pypot/primitive/primitive.py | LoopPrimitive.recent_update_frequencies | def recent_update_frequencies(self):
""" Returns the 10 most recent update frequencies.
The given frequencies are computed as short-term frequencies!
The 0th element of the list corresponds to the most recent frequency.
"""
return list(reversed([(1.0 / p) for p in numpy.diff(sel... | python | def recent_update_frequencies(self):
""" Returns the 10 most recent update frequencies.
The given frequencies are computed as short-term frequencies!
The 0th element of the list corresponds to the most recent frequency.
"""
return list(reversed([(1.0 / p) for p in numpy.diff(sel... | [
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715 | poppy-project/pypot | pypot/primitive/primitive.py | MockupMotor.goto_position | def goto_position(self, position, duration, control=None, wait=False):
""" Automatically sets the goal position and the moving speed to reach the desired position within the duration. """
if control is None:
control = self.goto_behavior
if control == 'minjerk':
goto_min... | python | def goto_position(self, position, duration, control=None, wait=False):
""" Automatically sets the goal position and the moving speed to reach the desired position within the duration. """
if control is None:
control = self.goto_behavior
if control == 'minjerk':
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716 | poppy-project/pypot | pypot/primitive/move.py | MoveRecorder.add_tracked_motors | def add_tracked_motors(self, tracked_motors):
"""Add new motors to the recording"""
new_mockup_motors = map(self.get_mockup_motor, tracked_motors)
self.tracked_motors = list(set(self.tracked_motors + new_mockup_motors)) | python | def add_tracked_motors(self, tracked_motors):
"""Add new motors to the recording"""
new_mockup_motors = map(self.get_mockup_motor, tracked_motors)
self.tracked_motors = list(set(self.tracked_motors + new_mockup_motors)) | [
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717 | poppy-project/pypot | pypot/primitive/manager.py | PrimitiveManager.update | def update(self):
""" Combined at a predefined frequency the request orders and affect them to the real motors. """
with self.syncing:
for m in self._motors:
to_set = defaultdict(list)
for p in self._prim:
for key, val in getattr(p.robot, ... | python | def update(self):
""" Combined at a predefined frequency the request orders and affect them to the real motors. """
with self.syncing:
for m in self._motors:
to_set = defaultdict(list)
for p in self._prim:
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718 | poppy-project/pypot | pypot/primitive/manager.py | PrimitiveManager.stop | def stop(self):
""" Stop the primitive manager. """
for p in self.primitives[:]:
p.stop()
StoppableLoopThread.stop(self) | python | def stop(self):
""" Stop the primitive manager. """
for p in self.primitives[:]:
p.stop()
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719 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.load_scene | def load_scene(self, scene_path, start=False):
""" Loads a scene on the V-REP server.
:param str scene_path: path to a V-REP scene file
:param bool start: whether to directly start the simulation after loading the scene
.. note:: It is assumed that the scene file is always available on... | python | def load_scene(self, scene_path, start=False):
""" Loads a scene on the V-REP server.
:param str scene_path: path to a V-REP scene file
:param bool start: whether to directly start the simulation after loading the scene
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720 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.get_motor_position | def get_motor_position(self, motor_name):
""" Gets the motor current position. """
return self.call_remote_api('simxGetJointPosition',
self.get_object_handle(motor_name),
streaming=True) | python | def get_motor_position(self, motor_name):
""" Gets the motor current position. """
return self.call_remote_api('simxGetJointPosition',
self.get_object_handle(motor_name),
streaming=True) | [
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721 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.set_motor_position | def set_motor_position(self, motor_name, position):
""" Sets the motor target position. """
self.call_remote_api('simxSetJointTargetPosition',
self.get_object_handle(motor_name),
position,
sending=True) | python | def set_motor_position(self, motor_name, position):
""" Sets the motor target position. """
self.call_remote_api('simxSetJointTargetPosition',
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722 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.set_motor_force | def set_motor_force(self, motor_name, force):
""" Sets the maximum force or torque that a joint can exert. """
self.call_remote_api('simxSetJointForce',
self.get_object_handle(motor_name),
force,
sending=True) | python | def set_motor_force(self, motor_name, force):
""" Sets the maximum force or torque that a joint can exert. """
self.call_remote_api('simxSetJointForce',
self.get_object_handle(motor_name),
force,
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723 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.get_object_position | def get_object_position(self, object_name, relative_to_object=None):
""" Gets the object position. """
h = self.get_object_handle(object_name)
relative_handle = (-1 if relative_to_object is None
else self.get_object_handle(relative_to_object))
return self.call... | python | def get_object_position(self, object_name, relative_to_object=None):
""" Gets the object position. """
h = self.get_object_handle(object_name)
relative_handle = (-1 if relative_to_object is None
else self.get_object_handle(relative_to_object))
return self.call... | [
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724 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.set_object_position | def set_object_position(self, object_name, position=[0, 0, 0]):
""" Sets the object position. """
h = self.get_object_handle(object_name)
return self.call_remote_api('simxSetObjectPosition',
h, -1, position,
sending=True) | python | def set_object_position(self, object_name, position=[0, 0, 0]):
""" Sets the object position. """
h = self.get_object_handle(object_name)
return self.call_remote_api('simxSetObjectPosition',
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725 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.get_object_handle | def get_object_handle(self, obj):
""" Gets the vrep object handle. """
if obj not in self._object_handles:
self._object_handles[obj] = self._get_object_handle(obj=obj)
return self._object_handles[obj] | python | def get_object_handle(self, obj):
""" Gets the vrep object handle. """
if obj not in self._object_handles:
self._object_handles[obj] = self._get_object_handle(obj=obj)
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726 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.get_collision_state | def get_collision_state(self, collision_name):
""" Gets the collision state. """
return self.call_remote_api('simxReadCollision',
self.get_collision_handle(collision_name),
streaming=True) | python | def get_collision_state(self, collision_name):
""" Gets the collision state. """
return self.call_remote_api('simxReadCollision',
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727 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.get_collision_handle | def get_collision_handle(self, collision):
""" Gets a vrep collisions handle. """
if collision not in self._object_handles:
h = self._get_collision_handle(collision)
self._object_handles[collision] = h
return self._object_handles[collision] | python | def get_collision_handle(self, collision):
""" Gets a vrep collisions handle. """
if collision not in self._object_handles:
h = self._get_collision_handle(collision)
self._object_handles[collision] = h
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728 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.change_object_name | def change_object_name(self, old_name, new_name):
""" Change object name """
h = self._get_object_handle(old_name)
if old_name in self._object_handles:
self._object_handles.pop(old_name)
lua_code = "simSetObjectName({}, '{}')".format(h, new_name)
self._inject_lua_code... | python | def change_object_name(self, old_name, new_name):
""" Change object name """
h = self._get_object_handle(old_name)
if old_name in self._object_handles:
self._object_handles.pop(old_name)
lua_code = "simSetObjectName({}, '{}')".format(h, new_name)
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729 | poppy-project/pypot | pypot/vrep/io.py | VrepIO._create_pure_shape | def _create_pure_shape(self, primitive_type, options, sizes, mass, precision):
""" Create Pure Shape """
lua_code = "simCreatePureShape({}, {}, {{{}, {}, {}}}, {}, {{{}, {}}})".format(
primitive_type, options, sizes[0], sizes[1], sizes[2], mass, precision[0], precision[1])
self._inje... | python | def _create_pure_shape(self, primitive_type, options, sizes, mass, precision):
""" Create Pure Shape """
lua_code = "simCreatePureShape({}, {}, {{{}, {}, {}}}, {}, {{{}, {}}})".format(
primitive_type, options, sizes[0], sizes[1], sizes[2], mass, precision[0], precision[1])
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730 | poppy-project/pypot | pypot/vrep/io.py | VrepIO._inject_lua_code | def _inject_lua_code(self, lua_code):
""" Sends raw lua code and evaluate it wihtout any checking! """
msg = (ctypes.c_ubyte * len(lua_code)).from_buffer_copy(lua_code.encode())
self.call_remote_api('simxWriteStringStream', 'my_lua_code', msg) | python | def _inject_lua_code(self, lua_code):
""" Sends raw lua code and evaluate it wihtout any checking! """
msg = (ctypes.c_ubyte * len(lua_code)).from_buffer_copy(lua_code.encode())
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731 | poppy-project/pypot | pypot/vrep/io.py | VrepIO.call_remote_api | def call_remote_api(self, func_name, *args, **kwargs):
""" Calls any remote API func in a thread_safe way.
:param str func_name: name of the remote API func to call
:param args: args to pass to the remote API call
:param kwargs: args to pass to the remote API call
.. note:: You... | python | def call_remote_api(self, func_name, *args, **kwargs):
""" Calls any remote API func in a thread_safe way.
:param str func_name: name of the remote API func to call
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732 | poppy-project/pypot | pypot/server/httpserver.py | HTTPRobotServer.run | def run(self, **kwargs):
""" Start the tornado server, run forever"""
try:
loop = IOLoop()
app = self.make_app()
app.listen(self.port)
loop.start()
except socket.error as serr:
# Re raise the socket error if not "[Errno 98] Address al... | python | def run(self, **kwargs):
""" Start the tornado server, run forever"""
try:
loop = IOLoop()
app = self.make_app()
app.listen(self.port)
loop.start()
except socket.error as serr:
# Re raise the socket error if not "[Errno 98] Address al... | [
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733 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.close | def close(self, _force_lock=False):
""" Closes the serial communication if opened. """
if not self.closed:
with self.__force_lock(_force_lock) or self._serial_lock:
self._serial.close()
self.__used_ports.remove(self.port)
logger.info("Closing port... | python | def close(self, _force_lock=False):
""" Closes the serial communication if opened. """
if not self.closed:
with self.__force_lock(_force_lock) or self._serial_lock:
self._serial.close()
self.__used_ports.remove(self.port)
logger.info("Closing port... | [
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734 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.ping | def ping(self, id):
""" Pings the motor with the specified id.
.. note:: The motor id should always be included in [0, 253]. 254 is used for broadcast.
"""
pp = self._protocol.DxlPingPacket(id)
try:
self._send_packet(pp, error_handler=None)
retu... | python | def ping(self, id):
""" Pings the motor with the specified id.
.. note:: The motor id should always be included in [0, 253]. 254 is used for broadcast.
"""
pp = self._protocol.DxlPingPacket(id)
try:
self._send_packet(pp, error_handler=None)
retu... | [
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735 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.scan | def scan(self, ids=range(254)):
""" Pings all ids within the specified list, by default it finds all the motors connected to the bus. """
return [id for id in ids if self.ping(id)] | python | def scan(self, ids=range(254)):
""" Pings all ids within the specified list, by default it finds all the motors connected to the bus. """
return [id for id in ids if self.ping(id)] | [
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736 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.get_model | def get_model(self, ids):
""" Gets the model for the specified motors. """
to_get_ids = [i for i in ids if i not in self._known_models]
models = [dxl_to_model(m) for m in self._get_model(to_get_ids, convert=False)]
self._known_models.update(zip(to_get_ids, models))
return tuple(... | python | def get_model(self, ids):
""" Gets the model for the specified motors. """
to_get_ids = [i for i in ids if i not in self._known_models]
models = [dxl_to_model(m) for m in self._get_model(to_get_ids, convert=False)]
self._known_models.update(zip(to_get_ids, models))
return tuple(... | [
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737 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.change_baudrate | def change_baudrate(self, baudrate_for_ids):
""" Changes the baudrate of the specified motors. """
self._change_baudrate(baudrate_for_ids)
for motor_id in baudrate_for_ids:
if motor_id in self._known_models:
del self._known_models[motor_id]
if motor_id in... | python | def change_baudrate(self, baudrate_for_ids):
""" Changes the baudrate of the specified motors. """
self._change_baudrate(baudrate_for_ids)
for motor_id in baudrate_for_ids:
if motor_id in self._known_models:
del self._known_models[motor_id]
if motor_id in... | [
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738 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.get_status_return_level | def get_status_return_level(self, ids, **kwargs):
""" Gets the status level for the specified motors. """
convert = kwargs['convert'] if 'convert' in kwargs else self._convert
srl = []
for id in ids:
try:
srl.extend(self._get_status_return_level((id, ),
... | python | def get_status_return_level(self, ids, **kwargs):
""" Gets the status level for the specified motors. """
convert = kwargs['convert'] if 'convert' in kwargs else self._convert
srl = []
for id in ids:
try:
srl.extend(self._get_status_return_level((id, ),
... | [
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739 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.set_status_return_level | def set_status_return_level(self, srl_for_id, **kwargs):
""" Sets status return level to the specified motors. """
convert = kwargs['convert'] if 'convert' in kwargs else self._convert
if convert:
srl_for_id = dict(zip(srl_for_id.keys(),
[('never', '... | python | def set_status_return_level(self, srl_for_id, **kwargs):
""" Sets status return level to the specified motors. """
convert = kwargs['convert'] if 'convert' in kwargs else self._convert
if convert:
srl_for_id = dict(zip(srl_for_id.keys(),
[('never', '... | [
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740 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.switch_led_on | def switch_led_on(self, ids):
""" Switches on the LED of the motors with the specified ids. """
self._set_LED(dict(zip(ids, itertools.repeat(True)))) | python | def switch_led_on(self, ids):
""" Switches on the LED of the motors with the specified ids. """
self._set_LED(dict(zip(ids, itertools.repeat(True)))) | [
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741 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.switch_led_off | def switch_led_off(self, ids):
""" Switches off the LED of the motors with the specified ids. """
self._set_LED(dict(zip(ids, itertools.repeat(False)))) | python | def switch_led_off(self, ids):
""" Switches off the LED of the motors with the specified ids. """
self._set_LED(dict(zip(ids, itertools.repeat(False)))) | [
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742 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.enable_torque | def enable_torque(self, ids):
""" Enables torque of the motors with the specified ids. """
self._set_torque_enable(dict(zip(ids, itertools.repeat(True)))) | python | def enable_torque(self, ids):
""" Enables torque of the motors with the specified ids. """
self._set_torque_enable(dict(zip(ids, itertools.repeat(True)))) | [
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743 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.disable_torque | def disable_torque(self, ids):
""" Disables torque of the motors with the specified ids. """
self._set_torque_enable(dict(zip(ids, itertools.repeat(False)))) | python | def disable_torque(self, ids):
""" Disables torque of the motors with the specified ids. """
self._set_torque_enable(dict(zip(ids, itertools.repeat(False)))) | [
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744 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.get_pid_gain | def get_pid_gain(self, ids, **kwargs):
""" Gets the pid gain for the specified motors. """
return tuple([tuple(reversed(t)) for t in self._get_pid_gain(ids, **kwargs)]) | python | def get_pid_gain(self, ids, **kwargs):
""" Gets the pid gain for the specified motors. """
return tuple([tuple(reversed(t)) for t in self._get_pid_gain(ids, **kwargs)]) | [
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745 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.set_pid_gain | def set_pid_gain(self, pid_for_id, **kwargs):
""" Sets the pid gain to the specified motors. """
pid_for_id = dict(itertools.izip(pid_for_id.iterkeys(),
[tuple(reversed(t)) for t in pid_for_id.values()]))
self._set_pid_gain(pid_for_id, **kwargs) | python | def set_pid_gain(self, pid_for_id, **kwargs):
""" Sets the pid gain to the specified motors. """
pid_for_id = dict(itertools.izip(pid_for_id.iterkeys(),
[tuple(reversed(t)) for t in pid_for_id.values()]))
self._set_pid_gain(pid_for_id, **kwargs) | [
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746 | poppy-project/pypot | pypot/dynamixel/io/abstract_io.py | AbstractDxlIO.get_control_table | def get_control_table(self, ids, **kwargs):
""" Gets the full control table for the specified motors.
..note:: This function requires the model for each motor to be known. Querring this additional information might add some extra delay.
"""
error_handler = kwargs['error_handler... | python | def get_control_table(self, ids, **kwargs):
""" Gets the full control table for the specified motors.
..note:: This function requires the model for each motor to be known. Querring this additional information might add some extra delay.
"""
error_handler = kwargs['error_handler... | [
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747 | poppy-project/pypot | pypot/robot/config.py | check_motor_eprom_configuration | def check_motor_eprom_configuration(config, dxl_io, motor_names):
""" Change the angles limits depanding on the robot configuration ;
Check if the return delay time is set to 0.
"""
changed_angle_limits = {}
changed_return_delay_time = {}
for name in motor_names:
m = config['motors'... | python | def check_motor_eprom_configuration(config, dxl_io, motor_names):
""" Change the angles limits depanding on the robot configuration ;
Check if the return delay time is set to 0.
"""
changed_angle_limits = {}
changed_return_delay_time = {}
for name in motor_names:
m = config['motors'... | [
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748 | icometrix/dicom2nifti | dicom2nifti/compressed_dicom.py | _get_gdcmconv | def _get_gdcmconv():
"""
Get the full path to gdcmconv.
If not found raise error
"""
gdcmconv_executable = settings.gdcmconv_path
if gdcmconv_executable is None:
gdcmconv_executable = _which('gdcmconv')
if gdcmconv_executable is None:
gdcmconv_executable = _which('gdcmconv.ex... | python | def _get_gdcmconv():
"""
Get the full path to gdcmconv.
If not found raise error
"""
gdcmconv_executable = settings.gdcmconv_path
if gdcmconv_executable is None:
gdcmconv_executable = _which('gdcmconv')
if gdcmconv_executable is None:
gdcmconv_executable = _which('gdcmconv.ex... | [
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749 | icometrix/dicom2nifti | dicom2nifti/compressed_dicom.py | compress_directory | def compress_directory(dicom_directory):
"""
This function can be used to convert a folder of jpeg compressed images to an uncompressed ones
:param dicom_directory: directory of dicom files to compress
"""
if _is_compressed(dicom_directory):
return
logger.info('Compressing dicom files ... | python | def compress_directory(dicom_directory):
"""
This function can be used to convert a folder of jpeg compressed images to an uncompressed ones
:param dicom_directory: directory of dicom files to compress
"""
if _is_compressed(dicom_directory):
return
logger.info('Compressing dicom files ... | [
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750 | icometrix/dicom2nifti | dicom2nifti/compressed_dicom.py | is_dicom_file | def is_dicom_file(filename):
"""
Util function to check if file is a dicom file
the first 128 bytes are preamble
the next 4 bytes should contain DICM otherwise it is not a dicom
:param filename: file to check for the DICM header block
:type filename: six.string_types
:returns: True if it is... | python | def is_dicom_file(filename):
"""
Util function to check if file is a dicom file
the first 128 bytes are preamble
the next 4 bytes should contain DICM otherwise it is not a dicom
:param filename: file to check for the DICM header block
:type filename: six.string_types
:returns: True if it is... | [
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751 | icometrix/dicom2nifti | dicom2nifti/compressed_dicom.py | _is_compressed | def _is_compressed(dicom_file, force=False):
"""
Check if dicoms are compressed or not
"""
header = pydicom.read_file(dicom_file,
defer_size="1 KB",
stop_before_pixels=True,
force=force)
uncompressed_types ... | python | def _is_compressed(dicom_file, force=False):
"""
Check if dicoms are compressed or not
"""
header = pydicom.read_file(dicom_file,
defer_size="1 KB",
stop_before_pixels=True,
force=force)
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752 | icometrix/dicom2nifti | dicom2nifti/compressed_dicom.py | _decompress_dicom | def _decompress_dicom(dicom_file, output_file):
"""
This function can be used to convert a jpeg compressed image to an uncompressed one for further conversion
:param input_file: single dicom file to decompress
"""
gdcmconv_executable = _get_gdcmconv()
subprocess.check_output([gdcmconv_executab... | python | def _decompress_dicom(dicom_file, output_file):
"""
This function can be used to convert a jpeg compressed image to an uncompressed one for further conversion
:param input_file: single dicom file to decompress
"""
gdcmconv_executable = _get_gdcmconv()
subprocess.check_output([gdcmconv_executab... | [
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753 | icometrix/dicom2nifti | scripts/dicomdiff.py | dicom_diff | def dicom_diff(file1, file2):
""" Shows the fields that differ between two DICOM images.
Inspired by https://code.google.com/p/pydicom/source/browse/source/dicom/examples/DicomDiff.py
"""
datasets = compressed_dicom.read_file(file1), compressed_dicom.read_file(file2)
rep = []
for dataset in ... | python | def dicom_diff(file1, file2):
""" Shows the fields that differ between two DICOM images.
Inspired by https://code.google.com/p/pydicom/source/browse/source/dicom/examples/DicomDiff.py
"""
datasets = compressed_dicom.read_file(file1), compressed_dicom.read_file(file2)
rep = []
for dataset in ... | [
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754 | icometrix/dicom2nifti | dicom2nifti/image_volume.py | ImageVolume._get_number_of_slices | def _get_number_of_slices(self, slice_type):
"""
Get the number of slices in a certain direction
"""
if slice_type == SliceType.AXIAL:
return self.dimensions[self.axial_orientation.normal_component]
elif slice_type == SliceType.SAGITTAL:
return self.dimens... | python | def _get_number_of_slices(self, slice_type):
"""
Get the number of slices in a certain direction
"""
if slice_type == SliceType.AXIAL:
return self.dimensions[self.axial_orientation.normal_component]
elif slice_type == SliceType.SAGITTAL:
return self.dimens... | [
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755 | icometrix/dicom2nifti | dicom2nifti/convert_dicom.py | _get_first_header | def _get_first_header(dicom_directory):
"""
Function to get the first dicom file form a directory and return the header
Useful to determine the type of data to convert
:param dicom_directory: directory with dicom files
"""
# looping over all files
for root, _, file_names in os.walk(dicom_di... | python | def _get_first_header(dicom_directory):
"""
Function to get the first dicom file form a directory and return the header
Useful to determine the type of data to convert
:param dicom_directory: directory with dicom files
"""
# looping over all files
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756 | icometrix/dicom2nifti | dicom2nifti/image_reorientation.py | _reorient_3d | def _reorient_3d(image):
"""
Reorganize the data for a 3d nifti
"""
# Create empty array where x,y,z correspond to LR (sagittal), PA (coronal), IS (axial) directions and the size
# of the array in each direction is the same with the corresponding direction of the input image.
new_image = numpy.z... | python | def _reorient_3d(image):
"""
Reorganize the data for a 3d nifti
"""
# Create empty array where x,y,z correspond to LR (sagittal), PA (coronal), IS (axial) directions and the size
# of the array in each direction is the same with the corresponding direction of the input image.
new_image = numpy.z... | [
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757 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for philips images.
As input philips images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the o... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for philips images.
As input philips images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
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758 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _assert_explicit_vr | def _assert_explicit_vr(dicom_input):
"""
Assert that explicit vr is used
"""
if settings.validate_multiframe_implicit:
header = dicom_input[0]
if header.file_meta[0x0002, 0x0010].value == '1.2.840.10008.1.2':
raise ConversionError('IMPLICIT_VR_ENHANCED_DICOM') | python | def _assert_explicit_vr(dicom_input):
"""
Assert that explicit vr is used
"""
if settings.validate_multiframe_implicit:
header = dicom_input[0]
if header.file_meta[0x0002, 0x0010].value == '1.2.840.10008.1.2':
raise ConversionError('IMPLICIT_VR_ENHANCED_DICOM') | [
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759 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _is_multiframe_4d | def _is_multiframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe 4D dataset
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
... | python | def _is_multiframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips multiframe 4D dataset
"""
# check if it is multi frame dicom
if not common.is_multiframe_dicom(dicom_input):
return False
header = dicom_input[0]
# check if there are multiple stacks
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760 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _is_singleframe_4d | def _is_singleframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips singleframe 4D dataset
"""
header = dicom_input[0]
# check if there are stack information
slice_number_mr_tag = Tag(0x2001, 0x100a)
if slice_number_mr_tag not in header:
return False
... | python | def _is_singleframe_4d(dicom_input):
"""
Use this function to detect if a dicom series is a philips singleframe 4D dataset
"""
header = dicom_input[0]
# check if there are stack information
slice_number_mr_tag = Tag(0x2001, 0x100a)
if slice_number_mr_tag not in header:
return False
... | [
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761 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _is_bval_type_a | def _is_bval_type_a(grouped_dicoms):
"""
Check if the bvals are stored in the first of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x2001, 0x1003)
bvec_x_tag = Tag(0x2005, 0x10b0)
bvec_y_tag = Tag(0x2005, 0x10b1)
bvec_z_tag = Tag(0x2005, 0x10b2)
for group in grouped_di... | python | def _is_bval_type_a(grouped_dicoms):
"""
Check if the bvals are stored in the first of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x2001, 0x1003)
bvec_x_tag = Tag(0x2005, 0x10b0)
bvec_y_tag = Tag(0x2005, 0x10b1)
bvec_z_tag = Tag(0x2005, 0x10b2)
for group in grouped_di... | [
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762 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _is_bval_type_b | def _is_bval_type_b(grouped_dicoms):
"""
Check if the bvals are stored in the second of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for group in grouped_dicoms:
if bvec_tag in group[0] and bval_tag in group[0]:
... | python | def _is_bval_type_b(grouped_dicoms):
"""
Check if the bvals are stored in the second of 2 currently known ways for single frame dti
"""
bval_tag = Tag(0x0018, 0x9087)
bvec_tag = Tag(0x0018, 0x9089)
for group in grouped_dicoms:
if bvec_tag in group[0] and bval_tag in group[0]:
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763 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _multiframe_to_nifti | def _multiframe_to_nifti(dicom_input, output_file):
"""
This function will convert philips 4D or anatomical multiframe series to a nifti
"""
# Read the multiframe dicom file
logger.info('Read dicom file')
multiframe_dicom = dicom_input[0]
# Create mosaic block
logger.info('Creating dat... | python | def _multiframe_to_nifti(dicom_input, output_file):
"""
This function will convert philips 4D or anatomical multiframe series to a nifti
"""
# Read the multiframe dicom file
logger.info('Read dicom file')
multiframe_dicom = dicom_input[0]
# Create mosaic block
logger.info('Creating dat... | [
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764 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _singleframe_to_nifti | def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nif... | python | def _singleframe_to_nifti(grouped_dicoms, output_file):
"""
This function will convert a philips singleframe series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _singleframe_to_block(grouped_dicoms)
logger.info('Creating affine')
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765 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _create_affine_multiframe | def _create_affine_multiframe(multiframe_dicom):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4D if in mosaic format
"""
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
last_frame = multiframe_dicom[Tag(0x5200, 0x9230)][-1]
#... | python | def _create_affine_multiframe(multiframe_dicom):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4D if in mosaic format
"""
first_frame = multiframe_dicom[Tag(0x5200, 0x9230)][0]
last_frame = multiframe_dicom[Tag(0x5200, 0x9230)][-1]
#... | [
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766 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _multiframe_to_block | def _multiframe_to_block(multiframe_dicom):
"""
Generate a full datablock containing all stacks
"""
# Calculate the amount of stacks and slices in the stack
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
number_of_stacks = int(int... | python | def _multiframe_to_block(multiframe_dicom):
"""
Generate a full datablock containing all stacks
"""
# Calculate the amount of stacks and slices in the stack
number_of_stack_slices = int(common.get_ss_value(multiframe_dicom[Tag(0x2001, 0x105f)][0][Tag(0x2001, 0x102d)]))
number_of_stacks = int(int... | [
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767 | icometrix/dicom2nifti | dicom2nifti/convert_philips.py | _fix_diffusion_images | def _fix_diffusion_images(bvals, bvecs, nifti, nifti_file):
"""
This function will remove the last timepoint from the nifti, bvals and bvecs if the last vector is 0,0,0
This is sometimes added at the end by philips
"""
# if all zero continue of if the last bvec is not all zero continue
if numpy.... | python | def _fix_diffusion_images(bvals, bvecs, nifti, nifti_file):
"""
This function will remove the last timepoint from the nifti, bvals and bvecs if the last vector is 0,0,0
This is sometimes added at the end by philips
"""
# if all zero continue of if the last bvec is not all zero continue
if numpy.... | [
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768 | icometrix/dicom2nifti | dicom2nifti/convert_generic.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file):
"""
This function will convert an anatomical dicom series to a nifti
Examples: See unit test
:param output_file: filepath to the output nifti
:param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
"""
if... | python | def dicom_to_nifti(dicom_input, output_file):
"""
This function will convert an anatomical dicom series to a nifti
Examples: See unit test
:param output_file: filepath to the output nifti
:param dicom_input: directory with the dicom files for a single scan, or list of read in dicoms
"""
if... | [
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769 | icometrix/dicom2nifti | dicom2nifti/convert_generic.py | _convert_slice_incement_inconsistencies | def _convert_slice_incement_inconsistencies(dicom_input):
"""
If there is slice increment inconsistency detected, for the moment CT images, then split the volumes into subvolumes based on the slice increment and process each volume separately using a space constructed based on the highest resolution increment
... | python | def _convert_slice_incement_inconsistencies(dicom_input):
"""
If there is slice increment inconsistency detected, for the moment CT images, then split the volumes into subvolumes based on the slice increment and process each volume separately using a space constructed based on the highest resolution increment
... | [
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770 | icometrix/dicom2nifti | dicom2nifti/common.py | is_hitachi | def is_hitachi(dicom_input):
"""
Use this function to detect if a dicom series is a hitachi dataset
:param dicom_input: directory with dicom files for 1 scan of a dicom_header
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
... | python | def is_hitachi(dicom_input):
"""
Use this function to detect if a dicom series is a hitachi dataset
:param dicom_input: directory with dicom files for 1 scan of a dicom_header
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
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771 | icometrix/dicom2nifti | dicom2nifti/common.py | is_ge | def is_ge(dicom_input):
"""
Use this function to detect if a dicom series is a GE dataset
:param dicom_input: list with dicom objects
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
return False # we try generic conversi... | python | def is_ge(dicom_input):
"""
Use this function to detect if a dicom series is a GE dataset
:param dicom_input: list with dicom objects
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
return False # we try generic conversi... | [
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772 | icometrix/dicom2nifti | dicom2nifti/common.py | is_philips | def is_philips(dicom_input):
"""
Use this function to detect if a dicom series is a philips dataset
:param dicom_input: directory with dicom files for 1 scan of a dicom_header
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
... | python | def is_philips(dicom_input):
"""
Use this function to detect if a dicom series is a philips dataset
:param dicom_input: directory with dicom files for 1 scan of a dicom_header
"""
# read dicom header
header = dicom_input[0]
if 'Manufacturer' not in header or 'Modality' not in header:
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773 | icometrix/dicom2nifti | dicom2nifti/common.py | is_siemens | def is_siemens(dicom_input):
"""
Use this function to detect if a dicom series is a siemens dataset
:param dicom_input: directory with dicom files for 1 scan
"""
# read dicom header
header = dicom_input[0]
# check if manufacturer is Siemens
if 'Manufacturer' not in header or 'Modality'... | python | def is_siemens(dicom_input):
"""
Use this function to detect if a dicom series is a siemens dataset
:param dicom_input: directory with dicom files for 1 scan
"""
# read dicom header
header = dicom_input[0]
# check if manufacturer is Siemens
if 'Manufacturer' not in header or 'Modality'... | [
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774 | icometrix/dicom2nifti | dicom2nifti/common.py | _get_slice_pixeldata | def _get_slice_pixeldata(dicom_slice):
"""
the slice and intercept calculation can cause the slices to have different dtypes
we should get the correct dtype that can cover all of them
:type dicom_slice: pydicom object
:param dicom_slice: slice to get the pixeldata for
"""
data = dicom_slice... | python | def _get_slice_pixeldata(dicom_slice):
"""
the slice and intercept calculation can cause the slices to have different dtypes
we should get the correct dtype that can cover all of them
:type dicom_slice: pydicom object
:param dicom_slice: slice to get the pixeldata for
"""
data = dicom_slice... | [
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775 | icometrix/dicom2nifti | dicom2nifti/common.py | set_fd_value | def set_fd_value(tag, value):
"""
Setters for data that also work with implicit transfersyntax
:param value: the value to set on the tag
:param tag: the tag to read
"""
if tag.VR == 'OB' or tag.VR == 'UN':
value = struct.pack('d', value)
tag.value = value | python | def set_fd_value(tag, value):
"""
Setters for data that also work with implicit transfersyntax
:param value: the value to set on the tag
:param tag: the tag to read
"""
if tag.VR == 'OB' or tag.VR == 'UN':
value = struct.pack('d', value)
tag.value = value | [
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776 | icometrix/dicom2nifti | dicom2nifti/common.py | set_ss_value | def set_ss_value(tag, value):
"""
Setter for data that also work with implicit transfersyntax
:param value: the value to set on the tag
:param tag: the tag to read
"""
if tag.VR == 'OB' or tag.VR == 'UN':
value = struct.pack('h', value)
tag.value = value | python | def set_ss_value(tag, value):
"""
Setter for data that also work with implicit transfersyntax
:param value: the value to set on the tag
:param tag: the tag to read
"""
if tag.VR == 'OB' or tag.VR == 'UN':
value = struct.pack('h', value)
tag.value = value | [
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777 | icometrix/dicom2nifti | dicom2nifti/common.py | apply_scaling | def apply_scaling(data, dicom_headers):
"""
Rescale the data based on the RescaleSlope and RescaleOffset
Based on the scaling from pydicomseries
:param dicom_headers: dicom headers to use to retreive the scaling factors
:param data: the input data
"""
# Apply the rescaling if needed
pr... | python | def apply_scaling(data, dicom_headers):
"""
Rescale the data based on the RescaleSlope and RescaleOffset
Based on the scaling from pydicomseries
:param dicom_headers: dicom headers to use to retreive the scaling factors
:param data: the input data
"""
# Apply the rescaling if needed
pr... | [
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778 | icometrix/dicom2nifti | dicom2nifti/common.py | write_bvec_file | def write_bvec_file(bvecs, bvec_file):
"""
Write an array of bvecs to a bvec file
:param bvecs: array with the vectors
:param bvec_file: filepath to write to
"""
if bvec_file is None:
return
logger.info('Saving BVEC file: %s' % bvec_file)
with open(bvec_file, 'w') as text_file:
... | python | def write_bvec_file(bvecs, bvec_file):
"""
Write an array of bvecs to a bvec file
:param bvecs: array with the vectors
:param bvec_file: filepath to write to
"""
if bvec_file is None:
return
logger.info('Saving BVEC file: %s' % bvec_file)
with open(bvec_file, 'w') as text_file:
... | [
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779 | icometrix/dicom2nifti | dicom2nifti/common.py | write_bval_file | def write_bval_file(bvals, bval_file):
"""
Write an array of bvals to a bval file
:param bvals: array with the values
:param bval_file: filepath to write to
"""
if bval_file is None:
return
logger.info('Saving BVAL file: %s' % bval_file)
with open(bval_file, 'w') as text_file:
... | python | def write_bval_file(bvals, bval_file):
"""
Write an array of bvals to a bval file
:param bvals: array with the values
:param bval_file: filepath to write to
"""
if bval_file is None:
return
logger.info('Saving BVAL file: %s' % bval_file)
with open(bval_file, 'w') as text_file:
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780 | icometrix/dicom2nifti | dicom2nifti/common.py | sort_dicoms | def sort_dicoms(dicoms):
"""
Sort the dicoms based om the image possition patient
:param dicoms: list of dicoms
"""
# find most significant axis to use during sorting
# the original way of sorting (first x than y than z) does not work in certain border situations
# where for exampe the X wi... | python | def sort_dicoms(dicoms):
"""
Sort the dicoms based om the image possition patient
:param dicoms: list of dicoms
"""
# find most significant axis to use during sorting
# the original way of sorting (first x than y than z) does not work in certain border situations
# where for exampe the X wi... | [
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781 | icometrix/dicom2nifti | dicom2nifti/common.py | validate_orientation | def validate_orientation(dicoms):
"""
Validate that all dicoms have the same orientation
:param dicoms: list of dicoms
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6]
for dicom_ in dicoms... | python | def validate_orientation(dicoms):
"""
Validate that all dicoms have the same orientation
:param dicoms: list of dicoms
"""
first_image_orient1 = numpy.array(dicoms[0].ImageOrientationPatient)[0:3]
first_image_orient2 = numpy.array(dicoms[0].ImageOrientationPatient)[3:6]
for dicom_ in dicoms... | [
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782 | icometrix/dicom2nifti | dicom2nifti/common.py | set_tr_te | def set_tr_te(nifti_image, repetition_time, echo_time):
"""
Set the tr and te in the nifti headers
:param echo_time: echo time
:param repetition_time: repetition time
:param nifti_image: nifti image to set the info to
"""
# set the repetition time in pixdim
nifti_image.header.structarr[... | python | def set_tr_te(nifti_image, repetition_time, echo_time):
"""
Set the tr and te in the nifti headers
:param echo_time: echo time
:param repetition_time: repetition time
:param nifti_image: nifti image to set the info to
"""
# set the repetition time in pixdim
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783 | icometrix/dicom2nifti | dicom2nifti/convert_ge.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: the filepath to the output n... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
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784 | icometrix/dicom2nifti | dicom2nifti/convert_ge.py | _4d_to_nifti | def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
affine, slic... | python | def _4d_to_nifti(grouped_dicoms, output_file):
"""
This function will convert ge 4d series to a nifti
"""
# Create mosaic block
logger.info('Creating data block')
full_block = _get_full_block(grouped_dicoms)
logger.info('Creating affine')
# Create the nifti header info
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785 | icometrix/dicom2nifti | dicom2nifti/convert_hitachi.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for hitachi images.
As input hitachi images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
:param output_file: file path to the o... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion fuction for hitachi images.
As input hitachi images are required. It will then determine the type of images and do the correct conversion
Examples: See unit test
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786 | icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | dicom_to_nifti | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion function for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
:param output_file: filepath to the output nifti
:param dicom_input: dir... | python | def dicom_to_nifti(dicom_input, output_file=None):
"""
This is the main dicom to nifti conversion function for ge images.
As input ge images are required. It will then determine the type of images and do the correct conversion
:param output_file: filepath to the output nifti
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787 | icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _get_sorted_mosaics | def _get_sorted_mosaics(dicom_input):
"""
Search all mosaics in the dicom directory, sort and validate them
"""
# Order all dicom files by acquisition number
sorted_mosaics = sorted(dicom_input, key=lambda x: x.AcquisitionNumber)
for index in range(0, len(sorted_mosaics) - 1):
# Validat... | python | def _get_sorted_mosaics(dicom_input):
"""
Search all mosaics in the dicom directory, sort and validate them
"""
# Order all dicom files by acquisition number
sorted_mosaics = sorted(dicom_input, key=lambda x: x.AcquisitionNumber)
for index in range(0, len(sorted_mosaics) - 1):
# Validat... | [
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788 | icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _mosaic_to_block | def _mosaic_to_block(mosaic):
"""
Convert a mosaic slice to a block of data by reading the headers, splitting the mosaic and appending
"""
# get the mosaic type
mosaic_type = _get_mosaic_type(mosaic)
# get the size of one tile format is 64p*64 or 80*80 or something similar
matches = re.find... | python | def _mosaic_to_block(mosaic):
"""
Convert a mosaic slice to a block of data by reading the headers, splitting the mosaic and appending
"""
# get the mosaic type
mosaic_type = _get_mosaic_type(mosaic)
# get the size of one tile format is 64p*64 or 80*80 or something similar
matches = re.find... | [
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789 | icometrix/dicom2nifti | dicom2nifti/convert_siemens.py | _create_affine_siemens_mosaic | def _create_affine_siemens_mosaic(dicom_input):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4d if in mosaic format
"""
# read dicom series with pds
dicom_header = dicom_input[0]
# Create affine matrix (http://nipy.sourceforge.net/... | python | def _create_affine_siemens_mosaic(dicom_input):
"""
Function to create the affine matrix for a siemens mosaic dataset
This will work for siemens dti and 4d if in mosaic format
"""
# read dicom series with pds
dicom_header = dicom_input[0]
# Create affine matrix (http://nipy.sourceforge.net/... | [
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790 | icometrix/dicom2nifti | dicom2nifti/resample.py | resample_single_nifti | def resample_single_nifti(input_nifti):
"""
Resample a gantry tilted image in place
"""
# read the input image
input_image = nibabel.load(input_nifti)
output_image = resample_nifti_images([input_image])
output_image.to_filename(input_nifti) | python | def resample_single_nifti(input_nifti):
"""
Resample a gantry tilted image in place
"""
# read the input image
input_image = nibabel.load(input_nifti)
output_image = resample_nifti_images([input_image])
output_image.to_filename(input_nifti) | [
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791 | icometrix/dicom2nifti | dicom2nifti/convert_dir.py | convert_directory | def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param ou... | python | def convert_directory(dicom_directory, output_folder, compression=True, reorient=True):
"""
This function will order all dicom files by series and order them one by one
:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param ou... | [
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:param compression: enable or disable gzip compression
:param reorient: reorient the dicoms according to LAS orientation
:param output_folder: folder to write the nifti files to
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792 | aegirhall/console-menu | consolemenu/menu_formatter.py | MenuFormatBuilder.clear_data | def clear_data(self):
"""
Clear menu data from previous menu generation.
"""
self.__header.title = None
self.__header.subtitle = None
self.__prologue.text = None
self.__epilogue.text = None
self.__items_section.items = None | python | def clear_data(self):
"""
Clear menu data from previous menu generation.
"""
self.__header.title = None
self.__header.subtitle = None
self.__prologue.text = None
self.__epilogue.text = None
self.__items_section.items = None | [
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793 | aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.inner_horizontal_border | def inner_horizontal_border(self):
"""
The complete inner horizontal border section, including the left and right border verticals.
Returns:
str: The complete inner horizontal border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
... | python | def inner_horizontal_border(self):
"""
The complete inner horizontal border section, including the left and right border verticals.
Returns:
str: The complete inner horizontal border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
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794 | aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.outer_horizontal_border_bottom | def outer_horizontal_border_bottom(self):
"""
The complete outer bottom horizontal border section, including left and right margins.
Returns:
str: The bottom menu border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
... | python | def outer_horizontal_border_bottom(self):
"""
The complete outer bottom horizontal border section, including left and right margins.
Returns:
str: The bottom menu border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
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795 | aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.outer_horizontal_border_top | def outer_horizontal_border_top(self):
"""
The complete outer top horizontal border section, including left and right margins.
Returns:
str: The top menu border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
... | python | def outer_horizontal_border_top(self):
"""
The complete outer top horizontal border section, including left and right margins.
Returns:
str: The top menu border.
"""
return u"{lm}{lv}{hz}{rv}".format(lm=' ' * self.margins.left,
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796 | aegirhall/console-menu | consolemenu/menu_component.py | MenuComponent.row | def row(self, content='', align='left'):
"""
A row of the menu, which comprises the left and right verticals plus the given content.
Returns:
str: A row of this menu component with the specified content.
"""
return u"{lm}{vert}{cont}{vert}".format(lm=' ' * self.margi... | python | def row(self, content='', align='left'):
"""
A row of the menu, which comprises the left and right verticals plus the given content.
Returns:
str: A row of this menu component with the specified content.
"""
return u"{lm}{vert}{cont}{vert}".format(lm=' ' * self.margi... | [
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797 | aegirhall/console-menu | consolemenu/format/menu_borders.py | MenuBorderStyleFactory.create_border | def create_border(self, border_style_type):
"""
Create a new MenuBorderStyle instance based on the given border style type.
Args:
border_style_type (int): an integer value from :obj:`MenuBorderStyleType`.
Returns:
:obj:`MenuBorderStyle`: a new MenuBorderStyle i... | python | def create_border(self, border_style_type):
"""
Create a new MenuBorderStyle instance based on the given border style type.
Args:
border_style_type (int): an integer value from :obj:`MenuBorderStyleType`.
Returns:
:obj:`MenuBorderStyle`: a new MenuBorderStyle i... | [
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border_style_type (int): an integer value from :obj:`MenuBorderStyleType`.
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:obj:`MenuBorderStyle`: a new MenuBorderStyle instance of the specified style. | [
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798 | aegirhall/console-menu | consolemenu/format/menu_borders.py | MenuBorderStyleFactory.is_win_python35_or_earlier | def is_win_python35_or_earlier():
"""
Convenience method to determine if the current platform is Windows and Python version 3.5 or earlier.
Returns:
bool: True if the current platform is Windows and the Python interpreter is 3.5 or earlier; False otherwise.
"""
retu... | python | def is_win_python35_or_earlier():
"""
Convenience method to determine if the current platform is Windows and Python version 3.5 or earlier.
Returns:
bool: True if the current platform is Windows and the Python interpreter is 3.5 or earlier; False otherwise.
"""
retu... | [
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799 | aegirhall/console-menu | consolemenu/items/submenu_item.py | SubmenuItem.set_menu | def set_menu(self, menu):
"""
Sets the menu of this item.
Should be used instead of directly accessing the menu attribute for this class.
:param ConsoleMenu menu: the menu
"""
self.menu = menu
self.submenu.parent = menu | python | def set_menu(self, menu):
"""
Sets the menu of this item.
Should be used instead of directly accessing the menu attribute for this class.
:param ConsoleMenu menu: the menu
"""
self.menu = menu
self.submenu.parent = menu | [
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Should be used instead of directly accessing the menu attribute for this class.
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