def humanize_address(self, address):
"""
Returns a human-readable string for a particular address.
If ((0, 0), (1, 0)) is passed and no labels are attached to
A1, this will return 'A1:B1'.
For ('label', (1, 0)), it will return the valid label with
the first provided capitalization, for example "LaBeL:B1".
"""
start, end = address
try:
start = normalize_position(start) # Try to convert 'A1'.
# Find a label for that tuple position.
label = self.get_container_label(start)
if label is not None:
start = label
except ValueError:
# If it's not a tuple position, it's a string label.
if start.lower() not in self._container_labels:
raise x.ContainerMissing(
"Invalid container: {}".format(start)
)
start = self._label_case.get(start.lower(), start)
end = humanize_position(end)
return "{}:{}".format(start, end)
def get_coordinates(self, position, axis=None, tool=None):
""" Returns the calibrated coordinates for a position. """
if len(position) == 1:
position = [position[0], (0, 0)]
if tool is not None:
axis = tool.axis
cal = self.get_axis_calibration(axis)
slot, well = position
if slot not in cal:
raise ex.CalibrationMissing(
"No calibration for {} (axis {}).".format(
humanize_position(slot), axis))
defaults = ({'top': 0, 'bottom': 0, 'x': 0, 'y': 0})
output = {}
# Calibration for A1 in this container (x, y, top, bottom).
slot_cal = {}
slot_cal.update(defaults)
slot_cal.update(cal.get((slot), {}))
# Default offset on x, y calculated from container definition.
ox, oy = self._deck.slot(slot).get_child(well).coordinates()
# x, y, top bottom
well_cal = cal.get((slot, well), {})
output.update(well_cal)
# Use calculated offsets if no custom well calibration provided.
if 'x' not in output:
output['x'] = slot_cal['x'] + ox
if 'y' not in output:
output['y'] = slot_cal['y'] + oy
# Merge slot and well calibration
if 'top' not in output:
output['top'] = slot_cal['top']
if 'bottom' not in output:
output['bottom'] = slot_cal['bottom']
return output
def find_well(self, value):
"""
Returns the well position on this plate matching a particular value.
"""
for pos in sorted(self.map.keys()):
if self.map[pos].strip() == value:
return humanize_position(pos)
def find_well(self, value):
"""
Returns the well position on this plate matching a particular value.
"""
for pos in sorted(self.map.keys()):
if self.map[pos].strip() == value:
return humanize_position(pos)
def get_coordinates(self, position, axis=None, tool=None):
""" Returns the calibrated coordinates for a position. """
if len(position) == 1:
position = [position[0], (0, 0)]
if tool is not None:
axis = tool.axis
cal = self.get_axis_calibration(axis)
slot, well = position
if slot not in cal:
raise ex.CalibrationMissing(
"No calibration for {} (axis {}).".
format(humanize_position(slot), axis)
)
defaults = ({'top': 0, 'bottom': 0, 'x': 0, 'y': 0})
output = {}
# Calibration for A1 in this container (x, y, top, bottom).
slot_cal = {}
slot_cal.update(defaults)
slot_cal.update(cal.get((slot), {}))
# Default offset on x, y calculated from container definition.
ox, oy = self._deck.slot(slot).get_child(well).coordinates()
# x, y, top bottom
well_cal = cal.get((slot, well), {})
output.update(well_cal)
# Use calculated offsets if no custom well calibration provided.
if 'x' not in output:
output['x'] = slot_cal['x'] + ox
if 'y' not in output:
output['y'] = slot_cal['y'] + oy
# Merge slot and well calibration
if 'top' not in output:
output['top'] = slot_cal['top']
if 'bottom' not in output:
output['bottom'] = slot_cal['bottom']
return output
def slot(self, position):
pos = self._normalize_position(position)
if pos not in self._children:
raise x.ContainerMissing(
"No deck module at slot {}."
.format(humanize_position(pos))
)
return self._children[pos]
def slot(self, position):
pos = self._normalize_position(position)
if pos not in self._children:
raise KeyError(
"No deck module at slot {}/{}."
.format(humanize_position(pos), pos)
)
return self._children[pos]
def add_module(self, position, mod):
pos = self._normalize_position(position)
if isinstance(mod, str):
mod = load_container(mod)()
if pos not in self._children:
self._children[pos] = mod
mod.position = position
else:
raise x.ContainerConflict(
"Module already allocated to slot: {}.".format(
humanize_position(pos)))
def add_module(self, position, mod):
pos = self._normalize_position(position)
if isinstance(mod, str):
mod = load_container(mod)()
if pos not in self._children:
self._children[pos] = mod
mod.position = position
else:
raise x.ContainerConflict(
"Module already allocated to slot: {}."
.format(humanize_position(pos))
)
def map(self):
"""
Uses the coordinates of label cell to list plate contents by well.
"""
plate_map = {}
for col in range(0, self._cols):
for row in range(0, self._rows):
pos = (col, row)
loc = humanize_position(pos)
data = self.get_well(pos)
if data:
plate_map[loc] = data
return plate_map
def map(self):
"""
Uses the coordinates of label cell to list plate contents by well.
"""
plate_map = {}
for col in range(0, self._cols):
for row in range(0, self._rows):
pos = (col, row)
loc = humanize_position(pos)
data = self.get_well(pos)
if data:
plate_map[loc] = data
return plate_map
def apply_protocol(self, b):
"""
Applies all the operational data from another Protocol to this one.
"""
# Second info supercedes first.
self.set_info(**b.info)
# Add the containers from second.
for slot, name in b._containers.items():
if slot in self._containers and self._containers[slot] != name:
raise x.ContainerConflict(
"Slot {} already allocated to {}".format(slot, name)
)
if slot not in self._containers:
# Add container if it's not there already.
self.add_container(slot, name)
# Add the labels from second.
labels = {v: k for k, v in self._container_labels.items()}
for label, slot in b._container_labels.items():
if slot in labels and labels[slot] != label:
raise x.ContainerConflict(
"Conflicting labels at {}: {} vs {}"
.format(
humanize_position(slot),
labels[slot],
label
)
)
self._container_labels[label] = slot
# Supercede labelcase from second.
for label, case in b._label_case.items():
self._label_case[label] = case
# Add the instruments from second.
for axis, name in b._head.items():
if axis in self._head \
and self._head[axis] != name:
raise x.InstrumentConflict(
"Axis {} already allocated to {}".format(axis, name)
)
self.add_instrument(axis, name)
# Rerun command definitions from second.
for command in b.actions:
c = copy.deepcopy(command)
# Make sure this command runs properly.
self.add_command(c.pop('command'), **c)
self.commands.append(command)
def export(self):
info = OrderedDict()
i = self._protocol.info
order = ['name', 'author', 'description', 'version', 'version_hash',
'created', 'updated']
for key in order:
v = i.pop(key, None)
if v is not None:
info[key] = v
instruments = OrderedDict()
for axis, name in sorted(self._protocol.instruments.items()):
label = "{}_{}".format(name, axis.lower())
instruments[label] = OrderedDict([
('axis', axis),
('name', name)
])
modules = []
for slot, name in sorted(self._protocol._containers.items()):
c = OrderedDict([('name', name)])
label = self._protocol.get_container_label(slot)
if label:
c['label'] = label
if slot:
c['slot'] = humanize_position(slot)
modules.append(c)
instructions = []
for command in self._protocol.commands:
command = self._export_command(command)
instructions.append(command)
out = OrderedDict()
out['info'] = info
out['instruments'] = instruments
out['containers'] = modules
out['instructions'] = instructions
return json.dumps(out, indent=4)
def test_well_offsets(self):
"""
Well offsets.
"""
# We have a plate map listing offset order.
cdir = os.path.dirname(os.path.realpath(__file__))
self.csv_file = os.path.join(
cdir,
'../../fixtures/offset_map.csv'
)
self.plate_map = PlateMap(self.csv_file)
plate = self.plate_map.get_plate('A1', rotated=True)
# Go through every row, col in a standard 96 well plate
# and check against the documented offset order.
n = 0
for col in range(0, 8):
for row in range(0, 12):
c = humanize_position((col, row))
self.assertEqual(int(plate.get_well(c)), n)
n += 1
def test_well_offsets(self):
"""
Well offsets.
"""
# We have a plate map listing offset order.
cdir = os.path.dirname(os.path.realpath(__file__))
self.csv_file = os.path.join(
cdir,
'../../fixtures/offset_map.csv'
)
self.plate_map = PlateMap(self.csv_file)
plate = self.plate_map.get_plate('A1', rotated=True)
# Go through every row, col in a standard 96 well plate
# and check against the documented offset order.
n = 0
for col in range(0, 8):
for row in range(0, 12):
c = humanize_position((col, row))
self.assertEqual(int(plate.get_well(c)), n)
n += 1
def apply_protocol(self, b):
"""
Applies all the operational data from another Protocol to this one.
"""
# Second info supercedes first.
self.set_info(**b.info)
# Add the containers from second.
for slot, name in b._containers.items():
if slot in self._containers and self._containers[slot] != name:
raise x.ContainerConflict(
"Slot {} already allocated to {}".format(slot, name))
if slot not in self._containers:
# Add container if it's not there already.
self.add_container(slot, name)
# Add the labels from second.
labels = {v: k for k, v in self._container_labels.items()}
for label, slot in b._container_labels.items():
if slot in labels and labels[slot] != label:
raise x.ContainerConflict(
"Conflicting labels at {}: {} vs {}".format(
humanize_position(slot), labels[slot], label))
self._container_labels[label] = slot
# Supercede labelcase from second.
for label, case in b._label_case.items():
self._label_case[label] = case
# Add the instruments from second.
for axis, name in b._head.items():
if axis in self._head \
and self._head[axis] != name:
raise x.InstrumentConflict(
"Axis {} already allocated to {}".format(axis, name))
self.add_instrument(axis, name)
# Rerun command definitions from second.
for command in b.actions:
c = copy.deepcopy(command)
# Make sure this command runs properly.
self.add_command(c.pop('command'), **c)
self.commands.append(command)
def export(self):
info = OrderedDict()
i = self._protocol.info
order = [
'name', 'author', 'description', 'version', 'version_hash',
'created', 'updated'
]
for key in order:
v = i.pop(key, None)
if v is not None:
info[key] = v
instruments = OrderedDict()
for axis, name in sorted(self._protocol.instruments.items()):
label = "{}_{}".format(name, axis.lower())
instruments[label] = OrderedDict([('axis', axis), ('name', name)])
modules = []
for slot, name in sorted(self._protocol._containers.items()):
c = OrderedDict([('name', name)])
label = self._protocol.get_container_label(slot)
if label:
c['label'] = label
if slot:
c['slot'] = humanize_position(slot)
modules.append(c)
instructions = []
for command in self._protocol.commands:
command = self._export_command(command)
instructions.append(command)
out = OrderedDict()
out['info'] = info
out['instruments'] = instruments
out['containers'] = modules
out['instructions'] = instructions
return json.dumps(out, indent=4)
def humanize_address(self, address):
"""
Returns a human-readable string for a particular address.
If ((0, 0), (1, 0)) is passed and no labels are attached to
A1, this will return 'A1:B1'.
For ('label', (1, 0)), it will return the valid label with
the first provided capitalization, for example "LaBeL:B1".
"""
start, end = address
try:
start = normalize_position(start) # Try to convert 'A1'.
# Find a label for that tuple position.
label = self.get_container_label(start)
if label is not None:
start = label
except ValueError:
# If it's not a tuple position, it's a string label.
if start.lower() not in self._container_labels:
raise x.ContainerMissing("Invalid container: {}".format(start))
start = self._label_case.get(start.lower(), start)
end = humanize_position(end)
return "{}:{}".format(start, end)
def slot(self, position):
pos = self._normalize_position(position)
if pos not in self._children:
raise x.ContainerMissing("No deck module at slot {}.".format(
humanize_position(pos)))
return self._children[pos]