Update documentation.md

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Clears the socket buffer if the robot is in tracking mode and do_clear_buffer is True.
### MecaRobotForDosimetry
This class inherits from the MecaRobot class and adapts it for scintillation dosimetry. It reads the signal of scintillators using a NIDAQ device, while keeping track of each scintillators' position. For each scintillator, two files will be created : one containing the scintillator's position relative to the source (scintillator_x_position_relative_to_source.txt) and one containing the scintillator's absolute distance to the source (scintillator_x_distance_to_source.txt). A file containing the signal read on the NIDAQ device (scintillators_signal.txt) will be created, as well as a file containing the time (time.txt).
This class inherits from the MecaRobot class and adapts it for scintillation dosimetry. It reads the signal of scintillators from a signal queue, while keeping track of each scintillators' position. The lowest scintillator is set as the tool reference frame (TRF), which means that the movement commands will send the lowest scintillator to the specified position. For each scintillator, two files will be created : one containing the scintillator's position relative to the source (scintillator_x_position_relative_to_source.txt) and one containing the scintillator's absolute distance to the source (scintillator_x_distance_to_source.txt). A file containing the scintillators' signal (scintillators_signal.txt) will be created, as well as a file containing the time (time.txt).
**MecaRobotForDosimetry**(*ip="192.168.0.100", port=10000, simulation_mode=False, enable_log=False, scintillators_positions=np.array([0]), source_position=np.array([0,0,0]), measure_with_nidaq=False, daq_path_number=None, analog_input_channel=None, analog_output_channel=None*)
**MecaRobotForDosimetry**(*ip="192.168.0.100", port=10000, simulation_mode=False, enable_log=False, scintillators_positions=np.array([0]), source_position=np.array([0,0,0]), water_level=-np.inf, scintillators_signal_queue=None*)
Connects to the robot. The robot is then activated, homed and sent to its initial position (every joint at 0°). Connects to the NI DAQ device and activates it.
Connects to the robot. The robot is then activated, homed and sent to its initial position (every joint at 0°).
Parameters:
- **ip : *str***
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- **source_position : *np.ndarray***
Position (x, y, z) of the source (in mm) in relation to the base of the robot (world reference frame).
- **measure_with_nidaq : *bool***
- **water_level : *float***
Enables tracking with NI data acquisition device.
- **daq_path_number : *int***
Height of the water in relation to the base of the robot (WRF). If specified, this will make sure that the robot never touches the water during sequences.
- **scintillators_signal_queue : *queue.Queue***
Number of the daq board path (i.e. 1 for Dev1, 2 for Dev2)
- **analog_input_channel : *tuple***
Analog input channels for the scintillators' signal.
- **analog_output_channel : *tuple***
Analog output channels to use. A constant 1V output is sent on every output channel. This parameter is used to set the gain for the [Hamamatsu H10722-01 photomultiplier tubes](https://www.hamamatsu.com/jp/en/product/type/H10722-01/index.html).
Queue object containing the scintillators' signal. Should be a LIFO queue (last in, first out).
**MecaRobotForDosimetry.start_tracking**()
......@@ -249,7 +243,7 @@ Stops tracking and closes all the files.
**MecaRobotForDosimetry.get_scintillators_signal**()
Reads one sample of the NI DAQ board to get the scintillators' signal.
Reads the last sample in the scintillator signal queue.
Return:
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Array of the scintillators' position relative to source.
**MecaRobotForDosimetry.set_source_position**(*source_position_relative_to_TRF*)
Sets the source position.
Parameters:
- **source_position_relative_to_TRF : *np.ndarray***
Current source position relative to the tool reference frame (TRF), which is the lowest scintillator by default (in mm).
**MecaRobotForDosimetry.find_source_position**()
Automatically finds the source's position by moving along every axis near the source until we get the maximum signal. This assumes that an estimate of the source position as already been set, as it will move around this point to find the maximum. An example of the robot movements during the calibration procedure is shown [here](https://www.youtube.com/watch?v=5iPs_rH62hA).
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