def test_get_name(robot):
deck = Deck()
slot = Slot()
c = Container()
deck.add(slot, 'A1', (0, 0, 0))
red = Well(properties={'radius': 5})
blue = Well(properties={'radius': 5})
c.add(red, "Red", (0, 0, 0))
c.add(blue, "Blue", (10, 0, 0))
slot.add(c)
assert red.get_name() == 'Red'
def test_named_well(robot):
deck = Deck()
slot = Slot()
c = Container()
deck.add(slot, 'A1', (0, 0, 0))
red = Well(properties={'radius': 5})
blue = Well(properties={'radius': 5})
c.add(red, "Red", (0, 0, 0))
c.add(blue, "Blue", (10, 0, 0))
slot.add(c)
assert deck['A1'][0]['Red'] == red
def _load_well_object_from_db(db, well_data):
container_name, location, x, y, z, \
depth, volume, diameter, length, width = well_data
props = zip(['depth', 'total-liquid-volume',
'diameter', 'length', 'width'],
[depth, volume, diameter, length, width])
property_dict = {k: v for k, v in props if v}
well = Well(properties=property_dict)
# subtract half the size, because
# Placeable assigns X-Y to bottom-left corner,
# but db assigns X-Y to well center
x -= (well.x_size() / 2)
y -= (well.y_size() / 2)
well_coordinates = (x, y, z)
return (well, location, well_coordinates)
def _parse_well_obj(well: Well):
r_x, r_y, r_z = well._coordinates + well.bottom()[1]
location, depth = well.get_name(), well.z_size()
diameter = well.properties.get('diameter', None)
volume = well.properties.get('total-liquid-volume', None)
width, length = well.properties['width'], well.properties['length']
return {
'location': location,
'x': r_x,
'y': r_y,
'z': r_z,
'depth': depth,
'volume': volume,
'diameter': diameter,
'length': length,
'width': width
}
def _json_to_well(
json_well: dict) -> Tuple[Well, Tuple[Number, Number, Number]]:
well_properties = json_well.copy()
x = well_properties.pop('x')
y = well_properties.pop('y')
z = well_properties.pop('z')
assert isinstance(x, Number)
assert isinstance(y, Number)
assert isinstance(z, Number)
well = Well(properties=well_properties)
well_coordinates = (x, y, z)
return well, well_coordinates
def generate_plate(wells, cols, spacing, offset, radius, height=0):
c = Container()
c.ordering = []
n_rows = int(wells / cols)
for i in range(n_rows):
c.ordering.append([])
for i in range(0, wells):
well = Well(properties={'radius': radius, 'height': height})
row, col = divmod(i, cols)
name = chr(col + ord('A')) + str(1 + row)
c.ordering[row].append(name)
coordinates = (col * spacing[0] + offset[0],
row * spacing[1] + offset[1], 0)
c.add(well, name, coordinates)
return c
def _well_to_json(well: Well) -> dict:
x, y, z = map(lambda num: round(num, 3), well.coordinates())
well_json = {'x': x, 'y': y, 'z': z}
well_json.update(well.properties)
return well_json
def create_container_obj_from_dict(container_data: dict) -> Container:
"""
Example input:
container data for a "24-plate":
{
"origin-offset":{
"x":13.3,
"y":17.5
},
"locations":{
"A1":{
"x":0.0,
"total-liquid-volume":3400,
"y":0.0,
"depth":16.2,
"z":0,
"diameter":15.62
},
"A2":{
"x":0.0,
"total-liquid-volume":3400,
"y":19.3,
"depth":16.2,
"z":0,
"diameter":15.62
}
Exampl input #2:
"trough-12row":
{
"locations":{
"A1":{
"x":0,
"y":0,
"z":0,
"depth":40,
"length":8,
"width":70,
"total-liquid-volume":22000
},
"A2":{
"x":0,
"y":9,
"z":0,
"depth":40,
"length":8,
"width":70,
"total-liquid-volume":22000
},
"A3":{
"x":0,
"y":18,
"z":0,
"depth":40,
"length":8,
"width":70,
"total-liquid-volume":22000
}
"""
container_data = copy.deepcopy(container_data)
origin_offset_x = container_data.get('origin-offset', {}).get('x') or 0
origin_offset_y = container_data.get('origin-offset', {}).get('y') or 0
origin_offset_z = container_data.get('origin-offset', {}).get('z') or 0
container = Container()
locations = container_data['locations']
container._coordinates = Vector(
origin_offset_x,
origin_offset_y,
origin_offset_z
)
for well_name, well_properties in locations.items():
x = well_properties.pop('x')
y = well_properties.pop('y')
z = well_properties.pop('z')
assert isinstance(x, numbers.Number)
assert isinstance(y, numbers.Number)
assert isinstance(z, numbers.Number)
well = Well(properties=well_properties)
# subtract half the size, because
# Placeable assigns X-Y to bottom-left corner, but
# persisted container files assign X-Y to center of each Well
x -= (well.x_size() / 2)
y -= (well.y_size() / 2)
well_coordinates = (x, y, z)
container.add(well, well_name, well_coordinates)
return container
