All-in-one import function for work loop filesSource:
read_analyze_wl() is an all-in-one function to read in a work loop
file, select cycles, and compute work and power output.
The function returns a
list of class
analyzed_workloopthat provides instantaneous velocity, a smoothed velocity, and computes work,
instantaneous power, and net power from a work loop experiment. All data are
organized by the cycle number and important metadata are stored as
list, each entry is labeled by cycle and includes:
Time, in sec
Length change of the muscle, corrected for gear ratio, in mm
Force, corrected for gear ratio, in mN
When stimulation occurs, on a binary scale
Cycle ID, as a letter
Instantaneous velocity, computed from
Positionchange, reported in meters/sec
Instantaneous velocity, after low-pass filtering, again in meter/sec
Instantaneous power, a product of
Filt_velocity, reported in J
The percent of that particular cycle which has elapsed
In addition, the following information is stored in the
analyzed_workloop object's attributes:
Frequency at which stimulus pulses occurred
Frequency of oscillations (assuming sine wave trajectory)
Total number of oscillatory cycles (assuming sine wave trajectory) that the muscle experienced.
Specifies what part of the cycle is understood as the beginning and end. There are currently three options: 'lo' for L0-to-L0; 'p2p' for peak-to-peak; and 't2t' for trough-to-trough
Amplitude of length change (assuming sine wave trajectory)
Phase of the oscillatory cycle (in percent) at which stimulation occurred. Somewhat experimental, please use with caution
Logical; whether position inversion has been applied)
The units of measurement for each column in the object after running this function. See Warning
Frequency at which samples were collected
Additional information from the header
Units from each Channel of the original ddf file
Protocol in tabular format; taken from the original ddf file
Specific info on stimulus protocol; taken from the original ddf file
Number of sequential pulses within a stimulation train
Timing offset at which stimulus began
Gear ratio applied by this function
Time at which file was last modified
Which cycles were retained, as numerics
Simple table showing work (in J) and net power (in W) for each cycle
As detailed in these three functions, possible arguments include:
cycle_def - used to specify which part of the cycle is understood as
the beginning and end. There are currently three options: 'lo' for L0-to-L0;
'p2p' for peak-to-peak; and 't2t' for trough-to-trough
bworth_order - Filter order for low-pass filtering of
signal::butter prior to finding peak lengths. Default: 2.
bworth_freq - Critical frequency (scalar) for low-pass filtering of
signal::butter prior to finding peak lengths.
keep_cycles - Which cycles should be retained. Default: 4:6.
GR - Gear ratio. Default: 1.
M - Velocity multiplier used to positivize velocity; should be either
-1 or 1. Default: -1.
vel_bf - Critical frequency (scalar) for low-pass filtering of
signal::butter. Default: 0.05.
The gear ratio (GR) and velocity multiplier (M) parameters can help correct
for issues related to the magnitude and sign of data collection. By
default, they are set to apply no gear ratio adjustment and to positivize
velocity. Instantaneous velocity is often noisy and the
parameter allows for low-pass filtering of velocity data. See
signal::filtfilt() for details of how
filtering is achieved.
Most systems we have encountered record Position data in millimeters
and Force in millinewtons, and therefore this function assumes data are
recorded in those units. Through a series of internal conversions, this
function computes velocity in meters/sec, work in Joules, and power in
Watts. If your raw data do not originate in millimeters and millinewtons,
please transform your data accordingly and ignore what you see in the
Josephson RK. 1985. Mechanical Power output from Striated Muscle during Cyclic Contraction. Journal of Experimental Biology 114: 493-512.