def _migrate_container(container_name):
print('migrating {} from json to database'.format(container_name))
container = get_persisted_container(container_name)
container = rotate_container_for_alpha(container)
print("CONTAINER: {}, {}".format(container_name, container._coordinates))
database.save_new_container(container, container_name)
def _setup_container(container_name):
try:
container = database.load_container(container_name)
# Database.load_container throws ValueError when a container name is not
# found.
except ValueError:
# First must populate "get persisted container" list
old_container_loading.load_all_containers_from_disk()
# Load container from old json file
container = old_container_loading.get_persisted_container(
container_name)
# Rotate coordinates to fit the new deck map
rotated_container = database_migration.rotate_container_for_alpha(
container)
# Save to the new database
database.save_new_container(rotated_container, container_name)
container.properties['type'] = container_name
container_x, container_y, container_z = container._coordinates
if not fflags.split_labware_definitions():
# infer z from height
if container_z == 0 and 'height' in container[0].properties:
container_z = container[0].properties['height']
from opentrons.util.vector import Vector
container._coordinates = Vector(container_x, container_y, container_z)
return container
def calibrate_container_with_delta(pose_tree,
container,
delta_x,
delta_y,
delta_z,
save,
new_container_name=None):
delta = Point(delta_x, delta_y, delta_z)
new_coordinates = change_base(
pose_tree, src=container, dst=container.parent) + delta
pose_tree = update(pose_tree, container, new_coordinates)
if ff.split_labware_definitions():
for well in container.wells():
well._coordinates = well._coordinates + delta
else:
container._coordinates = container._coordinates + delta
if save and new_container_name:
database.save_new_container(container, new_container_name)
elif save:
database.overwrite_container(container)
return pose_tree
def _load_weird_container(container_name):
""" Load a container from persisted containers, whatever that is """
# First must populate "get persisted container" list
old_container_loading.load_all_containers_from_disk()
# Load container from old json file
container = old_container_loading.get_persisted_container(container_name)
# Rotate coordinates to fit the new deck map
rotated_container = database_migration.rotate_container_for_alpha(
container)
# Save to the new database
database.save_new_container(rotated_container, container_name)
return container
def migrate_containers_and_wells():
print("Loading json containers...")
load_all_containers_from_disk()
print("Json container file load complete.")
print("Starting migration...")
for container_name in list_container_names():
print('migrating {} from json to database'.format(container_name))
container = get_persisted_container(container_name)
container = rotate_container_for_alpha(container)
print("CONTAINER: {}, {}".format(container_name,
container._coordinates))
database.save_new_container(container, container_name)
print("Database migration complete!")
def _calibrate_container_with_delta(pose_tree,
container,
delta_x,
delta_y,
delta_z,
save,
new_container_name=None):
delta = pose_tracker.Point(delta_x, delta_y, delta_z)
# Note: pose tree is updated here, in order to update in-memory state.
# Separately from that, on-disk state is updated. This is a point of
# possible dis-unity. Would probably work better to un-load the labware
# after calibration, and then reload it (would have to figure out where
# in the call-stack this could be done without raising exceptions due
# to trying to access old references).
# Have to update all of the things in the pose tree that have the same
# load name, otherwise you end up getting the calibration values
# added together in the on-disk representation
target_name = container.get_name()
matching_entries = [
x for x in list(pose_tree.keys())
if type(x) == Container and x.get_name() == target_name
]
for entry in matching_entries:
old_coordinates = pose_tracker.change_base(pose_tree,
src=entry,
dst=entry.parent)
new_coordinates = old_coordinates + delta
pose_tree = pose_tracker.update(pose_tree, entry, new_coordinates)
entry._coordinates = entry._coordinates + delta
if save and container.properties.get('labware_hash'):
save_new_offsets(container.properties['labware_hash'], delta,
container.properties['definition'])
elif save and new_container_name:
database.save_new_container(container, new_container_name)
elif save:
database.overwrite_container(container)
return pose_tree
def create(name, grid, spacing, diameter, depth, volume=0):
"""
Creates a labware definition based on a rectangular gird, depth, diameter,
and spacing. Note that this function can only create labware with regularly
spaced wells in a rectangular format, of equal height, depth, and radius.
Irregular labware defintions will have to be made in other ways or modified
using a regular definition as a starting point. Also, upon creation a
definition always has its lower-left well at (0, 0, 0), such that this
labware _must_ be calibrated before use.
:param name: the name of the labware to be used with `labware.load`
:param grid: a 2-tuple of integers representing (<n_columns>, <n_rows>)
:param spacing: a 2-tuple of floats representing
(<col_spacing, <row_spacing)
:param diameter: a float representing the internal diameter of each well
:param depth: a float representing the distance from the top of each well
to the internal bottom of the same well
:param volume: [optional] the maximum volume of each well
:return: the labware object created by this function
"""
columns, rows = grid
col_spacing, row_spacing = spacing
custom_container = Container()
properties = {
'type': 'custom',
'diameter': diameter,
'height': depth,
'total-liquid-volume': volume
}
for r in range(rows):
for c in range(columns):
well = Well(properties=properties)
well_name = chr(r + ord('A')) + str(1 + c)
coordinates = (c * col_spacing, (rows - r - 1) * row_spacing, 0)
custom_container.add(well, well_name, coordinates)
database.save_new_container(custom_container, name)
return database.load_container(name)
def _calibrate_container_with_delta(pose_tree,
container,
delta_x,
delta_y,
delta_z,
save,
new_container_name=None):
delta = pose_tracker.Point(delta_x, delta_y, delta_z)
new_coordinates = pose_tracker.change_base(
pose_tree, src=container, dst=container.parent) + delta
pose_tree = pose_tracker.update(pose_tree, container, new_coordinates)
container._coordinates = container._coordinates + delta
if save and container.properties.get('labware_hash'):
save_new_offsets(container.properties['labware_hash'], delta)
elif save and new_container_name:
database.save_new_container(container, new_container_name)
elif save:
database.overwrite_container(container)
return pose_tree
