Load Volumes

Load based on volume ID

The volume ID is it's number from the beginning of the recording (volume IDs start at 0!).

You can use list_volumes method to get a list of all available volume IDs. You will see ID -1 if there is a non-full volume at the beginning of the recording, and -2 for the non-full volume at the end of the recording.

import vodex as vx
experiment = vx.Experiment.load("test.db")
experiment.list_volumes()

array([-2,  0,  1,  2,  3])

Here's how you can load some volumes:

# so we have 4 full volumes : 0,1,2,3 and some extra frames at the end (-2)
# let's load two full volumes , 0 and 2:
vol02 = experiment.load_volumes([0,2])
print(vol02.shape)

(2, 10, 200, 200)

We loaded two volumes, each has 10 slices and each frame is 200 by 200 pixels.

If you want to have a look at the fames at the end of the recording that do not form a full volume, you can do so by asking for the volume ID -2:

volm2 = experiment.load_volumes([-2])
print(volm2.shape)

((1, 2, 200, 200))

Notice how this volume only has 2 frames!

Load based on experimental conditions

You will use to method choose_volumes to get the IDs of the volumes that correspond to certain conditions and then load_volumes to actually load the volumes.

You can choose volumes based on any annotation. Let's see what volumes correspond to light "off":

light_off_ids = experiment.choose_volumes([("light","off")])
light_off_ids

[0, 3]

Volumes 0 and 3 have light off for every frame. Use load_volumes to load these volumes:

vol_light_off = experiment.load_volumes(light_off_ids)

You can also combine the conditions with a logical and or logical or. You can go and experiment with this: what volumes correspond to the times when the light is off or the c label is c2 ?

light_off_ids = experiment.choose_volumes([("light","off"),("c label","c2")], logic="or")
light_off_ids

[0, 1, 3]

How about such volumes that the light is "off" and "on"

light_off_ids = experiment.choose_volumes([("light","off"),("light","on")], logic="and")
light_off_ids

[]

We got an empty list : no such volumes, since the light can't be on and off at the same time. What if we had an or?

light_off_ids = experiment.choose_volumes([("light","off"),("light","on")], logic="or")
light_off_ids

[0, 1, 2, 3]

on or off returns all full volumes, since for every frame the light was either on or off.