2. FD curves

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The following code loads an HDF5 file and lists all of the FD curves inside of it:

from lumicks import pylake

file = pylake.File("example.h5")
list(file.fdcurves)  # e.g. shows: "['baseline', '1', '2']"

To visualizes an FD curve, you can use the built-in .plot_scatter() function:

# Pick a single FD curve
fd = file.fdcurves["baseline"]
fd.plot_scatter()

Here, .fdcurves is a standard Python dictionary, so we can do standard dict thing with it. For example, we can iterate over all the FD curve in a file and plot them:

for name, fd in file.fdcurves.items():
    fd.plot_scatter()
    plt.savefig(name)

By default, the FD channel pair is downsampled_force2 and distance1. This assumes that the force extension was done by moving trap 1, which is the most common. In that situation the force measured by trap 2 is more precise because that trap is static. The channels can be switched with the following code:

alt_fd = fd.with_channels(force='1x', distance='2')
alt_fd.plot_scatter()

# or as quick one-liner for plotting
fd.with_channels(force='2y', distance='2').plot_scatter()

The raw data can be accessed as well:

# Access the raw data: default force and distance channels
force = fd.f
distance = fd.d

# Access the raw data: specific channels
force = fd.downsampled_force1y
distance = fd.distance2

# Plot manually: FD curve
plt.scatter(distance.data, force.data)
# Plot manually: force timetrace
plt.plot(force.timestamps, force.data)