def getSample(wellx,welly,rack,grid,pos):
plate=Plate.lookup(grid,pos)
if plate==None:
plate=Plate(rack,grid,pos)
wellname="%c%d"%(ord('A')+welly-1,wellx)
well=plate.wellnumber(wellname)
sample=Sample.lookupByWell(plate,well)
if sample==None:
sample=Sample("%s.%d.%d.%d"%(rack,grid,pos,well),plate,well)
if grid==3:
sample.volume=20000 # Troughs
else:
sample.volume=0
return sample
def add_message():
content = request.get_json()
new_plate = Plate(content['serial'])
plates_list.append(new_plate)
return "Plate registered"
def __init__(self, plate, gap, direction=1, dielectric=None):
"""
plate: the plate to start from. a copy will be made of plate offset from it
gap > 0: the distance between the plates (in meters)
direction: 1 or -1: direction is assumed to be along the shortest dimension of the plate
"""
self.plate1 = plate
self.resistivity = plate.resistivity
offset = direction * (gap + plate.thickness)
self.plate2 = Plate(plate.vertex1 + offset,
plate.vertex2 + offset,
resistivity=self.resistivity)
def load_random_level(path, pos):
with open(path, 'r') as f:
levels = json.load(f)
r = random.randrange(len(levels))
lvl_obj = levels[r]
raw_plates = np.array(lvl_obj['plates'])
start = tuple(lvl_obj['start'])
end = tuple(lvl_obj['end'])
plates = np.empty((raw_plates.shape[1], raw_plates.shape[0]),
dtype=Plate)
y = 0
for row in raw_plates:
for x in range(len(row)):
plate_type = row[x]
t = Plate.ROCK if plate_type == 0 else Plate.YELLOW
plates[x, y] = Plate(
(x * Plate.SIZE[0] + pos[0], y * Plate.SIZE[1] + pos[1]),
type=t)
y += 1
return {"plates": plates, "start": start, "end": end}
# Use dimensional data from Robot/Calibration/20150302-LiquidHeights
#REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=24.45,gemArea=51.61,gemHOffset=-7.15,gemShape='v-shaped')
#REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=13.83,gemArea=51.84,gemHOffset=0,gemShape='v-shaped')
REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=9.59,gemArea=43.03,gemHOffset=0,gemShape='v-shaped')
MAGPLATELOC=Plate("MagPlate",18,2,12,8,False,unusableVolume=9,maxVolume=200,zmax=1459,angle=17.5,r1=2.80,h1=10.04,v0=10.8) # HSP9601 on magnetic plate (Use same well dimensions as SAMPLE)
hspmaxspeeds={200:1400,150:1600,100:1850,50:2000,20:2200} # From shaketest experiment
grenmaxspeeds={150:1750,125:1900,100:1950,75:2200,50:2200} # From shaketest experiment
eppmaxspeeds={195:1600,150:1800,125:1900,100:1950,75:2050,50:2150,25:2150,0:2150} # From shaketest experiment 5/17/16
#eppdilmaxspeeds={195:1400,150:1600,125:1700,100:1750,75:1850,50:1950,25:1950,0:1950} # Decrease by 200 RPM 7/7/16 to avoid spilling
#eppmaxspeeds={195:0,150:1150,138:1250,100:1350,75:1850,50:1950,25:1950,0:1950} # Decrease based on 9/23/16 testing with MTaq
eppglycerolmaxspeeds={195:0,150:1150,138:1250,100:1350,90:1450,80:1500,70:1550,60:1650,50:1750,40:1950,20:2000,0:2000} # Decrease based on 10/21/16 testing with MTaq (with Glycerol @ 0.5%)
eppminspeeds={20:1900,32:1800,64:1700,96:1400,150:1100} # 1100@150ul untested
SAMPLEPLATE=Plate("Samples",4,3,12,8,False,unusableVolume=15,maxVolume=200,
zmax=1033,angle=17.5,r1=2.698,h1=9.31,v0=17.21,slopex=0.000,slopey=0.000,
gemDepth=2.81,gemArea=16.41,
gemShape='v-shaped',vectorName="Microplate Landscape",maxspeeds=eppmaxspeeds,minspeeds=eppminspeeds,glycerolmaxspeeds=eppglycerolmaxspeeds,glycerol=0.005) # EppLoBind
SAMPLEPLATE.wells=SAMPLEPLATE.wells[1:-1] # Skip A1 and H12 due to leakage
SHAKERPLATELOC=Plate("Shaker",9,0,1,1)
QPCRPLATE=Plate("qPCR",QPCRLOC.grid,QPCRLOC.pos,12,8,False,unusableVolume=15,maxVolume=200,
zmax=996,angle=17.5,r1=2.704,h1=10.89,v0=0.44,slopex=0.000,slopey=0.000,gemDepth=3.17,gemArea=14.33,
gemShape='v-shaped')
# If changing location of QPCRPLATE, also update QPCRLOC in worklist.py
DILPLATE=Plate("Dilutions",4,2,12,8,False,unusableVolume=15,maxVolume=200,
zmax=1033,angle=17.5,r1=2.705,h1=9.13,v0=13.14,slopex=0.000,slopey=0.000,gemDepth=2.81,gemArea=16.41,
gemShape='v-shaped',vectorName="Microplate Landscape",maxspeeds=eppmaxspeeds,minspeeds=eppminspeeds,glycerolmaxspeeds=eppglycerolmaxspeeds,glycerol=0.005) # EppLoBind
SSDDILLOC=Plate("SSDDil",3,1,1,4,False,100,100000,zmax=1367,gemDepth=0,gemArea=1232,gemShape='flat')
WATERLOC=Plate("Water",3,2,1,4,False,100,100000,zmax=1367,gemDepth=0,gemArea=1232,gemShape='flat')
BLEACHLOC=Plate("Bleach",3,3,1,4,False,0,100000,zmax=1367,gemDepth=0,gemArea=1232,gemShape='flat')
PTCPOS=Plate("PTC",25,1,1,1)
def __init__(self, *args, **kwargs):
super(ParametricStudy, self).__init__(*args, **kwargs)
if 'plate' not in kwargs.keys():
self.plate = Plate()
self.plate.pstudy = self
class ParametricStudy(YLPATreeNode):
def __init__(self, *args, **kwargs):
super(ParametricStudy, self).__init__(*args, **kwargs)
if 'plate' not in kwargs.keys():
self.plate = Plate()
self.plate.pstudy = self
plate = Instance(Plate)
def _plate_changed(self):
self.plate.pstudyref = self
def __getstate__ (self):
'''Overriding __getstate__ because of
'''
state = super(ParametricStudy, self).__getstate__()
return state
plate_changed = Event
params_changed = Event
node_params = List(Instance(Parameter), [])
'''A list of tuples (base_value, (min, max))
'''
plate_params = List(Instance(Parameter), [])
'''A list of tuples (base_value, (min, max))
'''
param_nodes = List(Instance(ParamNode), [])
'''A list of tuples (node, trait_name, param_no, multiplier, base_value)
'''
param_plate = List(Instance(ParamPlate), [])
'''A list of tuples (trait_name, param_no, multiplier, base_value)
'''
optimization_constrain_value = Float(0.01)
def get_unit_work_ratio(self, vals):
nds = self.plate.nodes_with_ref
for pn in self.param_nodes_with_ref:
val = pn.base_value + pn.multiplier * vals[pn.param_no - 1]
setattr(nds[pn.node_no - 1], pn.trait_name, val)
return self.plate.unit_work_ratio
def get_unit_work_ratio_neg(self, vals):
vals2 = [par[0] for par in self.node_params_with_ref]
bds2 = [par[1] for par in self.node_params_with_ref]
for pp in self.param_plate_with_ref:
val = pp.base_value + pp.multiplier * vals[pp.param_no - 1]
setattr(self.plate.reinf_dict[pp.reinf_layout_name], pp.trait_name, val)
if len(vals2) > 0:
res = minimize(fun=self.get_unit_work_ratio, x0=vals2, bounds=bds2, method=METHOD)
return -self.plate.unit_work_ratio
min_work_ratio = Property(depends_on='node_params,plate_params,param_nodes,param_plate,params_changed,plate_changed')
@cached_property
def _get_min_work_ratio(self):
print 'Commencing optimization...'
start = time.clock()
vals = [par[0] for par in self.plate_params_with_ref]
bds = [par[1] for par in self.plate_params_with_ref]
if len(vals) > 0:
res = minimize(fun=self.get_unit_work_ratio_neg, x0=vals, bounds=bds, constraints={'type':'eq', 'fun':self.constrain_function}, method='SLSQP')
else:
vals2 = [par[0] for par in self.node_params_with_ref]
bds2 = [par[1] for par in self.node_params_with_ref]
res = minimize(fun=self.get_unit_work_ratio, x0=vals2, bounds=bds2, method=METHOD)
end = time.clock()
print 'Optimization finished in', str(end - start), 'seconds'
print res
return self.plate.unit_work_ratio
def constrain_function(self, *args):
cns = 0.
for i in range(len(args[0])):
cns += args[0][i] * self.plate_params_with_ref[i].optimization_constrain_multiplier
return cns - self.optimization_constrain_value
def plot_plate(self):
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.7, 0.7])
self.plate.plot(ax)
plt.show()
def plot(self, fig):
self.plate.plot(fig)
def calculate(self, fig):
'''Calculate the optimized limit load factor and plot geometry.
'''
try:
print 'Optimized load factor: %f' % self.min_work_ratio
except:
print 'Optimization failed. Check input.'
self.plate.plot(fig)
return
node_name = Str('Parametric study')
tree_node_list = Property(depends_on='plate')
@cached_property
def _get_tree_node_list(self):
return [self.plate]
node_params_with_ref = Property(List(Instance(Parameter)), depends_on='node_params')
def _get_node_params_with_ref(self):
for i in range(len(self.node_params)):
self.node_params[i].node_name = 'Parameter ' + str(i + 1)
self.node_params[i].pstudyref = self
return self.node_params
plate_params_with_ref = Property(List(Instance(Parameter)), depends_on='plate_params')
def _get_plate_params_with_ref(self):
for i in range(len(self.plate_params)):
self.plate_params[i].node_name = 'Parameter ' + str(i + 1)
self.plate_params[i].pstudyref = self
return self.plate_params
param_nodes_with_ref = Property(List(Instance(ParamNode)), depends_on='param_nodes')
def _get_param_nodes_with_ref(self):
for i in range(len(self.param_nodes)):
self.param_nodes[i].node_name = 'Node data ' + str(i + 1)
self.param_nodes[i].pstudyref = self
return self.param_nodes
param_plate_with_ref = Property(List(Instance(ParamPlate)), depends_on='param_plate')
def _get_param_plate_with_ref(self):
for i in range(len(self.param_plate)):
self.param_plate[i].node_name = 'Plate data ' + str(i + 1)
self.param_plate[i].pstudyref = self
return self.param_plate
tree_view = View(HGroup(VGroup(
Group(Item('node_params_with_ref', editor=TableEditor(columns=[ObjectColumn(name='node_name', label='Name', editable=False),
ObjectColumn(name='base_value', label='Default value'),
ObjectColumn(name='minimum', label='Minimum'),
ObjectColumn(name='maximum', label='Maximum'),
],
row_factory=Parameter,
show_toolbar=True,
deletable=True,
auto_size=False,
auto_add=True,
),
show_label=False,
), label='Node parameters:', springy=True),
Group(Item('param_nodes_with_ref', editor=TableEditor(columns=[ObjectColumn(name='node_name', label='Name', editable=False),
ObjectColumn(name='node_no', label='Node Number'),
ObjectColumn(name='trait_name', label='Unknown value name'),
ObjectColumn(name='param_no', label='Parameter'),
ObjectColumn(name='multiplier', label='Multiplier'),
ObjectColumn(name='base_value', label='Default value'),
],
row_factory=ParamNode,
show_toolbar=True,
deletable=True,
auto_size=False,
auto_add=True,
),
show_label=False,
), label='Node optimization data:', springy=True)),
VGroup(
Group(Item('optimization_constrain_value', show_label=False), label='Optimization constrain value:', springy=True),
Group(Item('plate_params_with_ref', editor=TableEditor(columns=[ObjectColumn(name='node_name', label='Name', editable=False),
ObjectColumn(name='base_value', label='Default value'),
ObjectColumn(name='minimum', label='Minimum'),
ObjectColumn(name='maximum', label='Maximum'),
ObjectColumn(name='optimization_constrain_multiplier', label='Constrain multiplier'),
],
row_factory=Parameter,
show_toolbar=True,
deletable=True,
auto_size=False,
auto_add=True,
),
show_label=False,
), label='Plate parameters:', springy=True),
Group(Item('param_plate_with_ref', editor=TableEditor(columns=[ObjectColumn(name='node_name', label='Name', editable=False),
ObjectColumn(name='reinf_layout_name', label='Reinf. layout name'),
ObjectColumn(name='trait_name', label='Unknown value name'),
ObjectColumn(name='param_no', label='Parameter'),
ObjectColumn(name='multiplier', label='Multiplier'),
ObjectColumn(name='base_value', label='Default value'),
],
row_factory=ParamPlate,
show_toolbar=True,
deletable=True,
auto_size=False,
auto_add=True,
),
show_label=False,
), label='Plate optimization data:', springy=True),)
)
)
db = sqlite3.connect('/path/to/db')
db.row_factory = dict_factory
cur = db.cursor()
cur.execute("SELECT * FROM plates")
dbplates = cur.fetchall()
db.close()
plates = []
for dbplate in dbplates:
print(dbplate['plate'])
plate = Plate(dbplate['plate'], dbplate['entrance_time'],
dbplate['confidence'], dbplate['location'],
json.loads(dbplate['candidates']),
dbplate['processing_time'], dbplate['plate_processing'])
plates.append(plate)
prev = None
first = None
newplates = []
for each in plates:
if prev is None:
first = each
prev = each
else:
if float(prev.entrance_time) + float(prev.plate_processing) + float(
prev.processing_time) >= float(each.entrance_time):
print(each.entrance_time)
"Module for generating a worklist from a set of commands"
import math
import string
import shutil
from zlib import crc32
from plate import Plate
import clock
import logging
WASHLOC = Plate(
"Wash", 1, 2, 1, 8, False, 0
) # Duplicate of what's in decklayout.py -- but don't want to include all those dependencies...
QPCRLOC = Plate(
"qPCR", 4, 1, 12, 8, False, 0
) # Duplicate of what's in decklayout.py -- but don't want to include all those dependencies...
DITI200 = 0
DITI10 = 2
OPEN = 0
CLOSE = 1
DONOTMOVE = 2
SAFETOEND = 0
ENDTOSAFE = 1
lnum = 0
debug = False
wlist = []
volumes = {}
diticnt = [0, 0, 0, 0] # Indexed by DiTi Type
delayEnabled = False
def create3DBeamWebBeamWeb(self):
'''self,uiObj,resultObj,dictbeamdata,dictcoldata):
creating 3d cad model with beam web beam web
'''
##### PRIMARY BEAM PARAMETERS #####
pBeam_D = int(self.dictcoldata[QString("D")])
pBeam_B = int(self.dictcoldata[QString("B")])
pBeam_tw = float(self.dictcoldata[QString("tw")])
pBeam_T = float(self.dictcoldata[QString("T")])
pBeam_alpha = float(self.dictcoldata[QString("FlangeSlope")])
pBeam_R1 = float(self.dictcoldata[QString("R1")])
pBeam_R2 = float(self.dictcoldata[QString("R2")])
pBeam_length = 800.0 # This parameter as per view of 3D cad model
# beam = ISectionold(B = 140, T = 16,D = 400,t = 8.9, R1 = 14, R2 = 7, alpha = 98,length = 500)
column = ISection(B=pBeam_B,
T=pBeam_T,
D=pBeam_D,
t=pBeam_tw,
R1=pBeam_R1,
R2=pBeam_R2,
alpha=pBeam_alpha,
length=pBeam_length,
notchObj=None)
##### SECONDARY BEAM PARAMETERS ######
sBeam_D = int(self.dictbeamdata[QString("D")])
sBeam_B = int(self.dictbeamdata[QString("B")])
sBeam_tw = float(self.dictbeamdata[QString("tw")])
sBeam_T = float(self.dictbeamdata[QString("T")])
sBeam_alpha = float(self.dictbeamdata[QString("FlangeSlope")])
sBeam_R1 = float(self.dictbeamdata[QString("R1")])
sBeam_R2 = float(self.dictbeamdata[QString("R2")])
# --Notch dimensions
notchObj = Notch(R1=pBeam_R1,
height=(pBeam_T + pBeam_R1),
width=((pBeam_B - (pBeam_tw + 40)) / 2.0 + 10),
length=sBeam_B)
# column = ISectionold(B = 83, T = 14.1, D = 250, t = 11, R1 = 12, R2 = 3.2, alpha = 98, length = 1000)
beam = ISection(B=sBeam_B,
T=sBeam_T,
D=sBeam_D,
t=sBeam_tw,
R1=sBeam_R1,
R2=sBeam_R2,
alpha=sBeam_alpha,
length=500,
notchObj=notchObj)
#### WELD,PLATE,BOLT AND NUT PARAMETERS #####
fillet_length = self.resultObj['Plate']['height']
fillet_thickness = self.resultObj['Weld']['thickness']
plate_width = self.resultObj['Plate']['width']
plate_thick = self.uiObj['Plate']['Thickness (mm)']
bolt_dia = self.uiObj["Bolt"]["Diameter (mm)"]
bolt_r = bolt_dia / 2
bolt_R = self.bolt_R
nut_R = bolt_R
bolt_T = self.bolt_T
bolt_Ht = self.bolt_Ht
nut_T = self.nut_T
nut_Ht = 12.2 # 150
# plate = Plate(L= 300,W =100, T = 10)
plate = Plate(L=fillet_length, W=plate_width, T=plate_thick)
# Fweld1 = FilletWeld(L= 300,b = 6, h = 6)
Fweld1 = FilletWeld(L=fillet_length,
b=fillet_thickness,
h=fillet_thickness)
# bolt = Bolt(R = bolt_R,T = bolt_T, H = 38.0, r = 4.0 )
bolt = Bolt(R=bolt_R, T=bolt_T, H=bolt_Ht, r=bolt_r)
# nut =Nut(R = bolt_R, T = 10.0, H = 11, innerR1 = 4.0, outerR2 = 8.3)
nut = Nut(R=bolt_R, T=nut_T, H=nut_Ht, innerR1=bolt_r)
gap = sBeam_tw + plate_thick + nut_T
nutBoltArray = NutBoltArray(self.resultObj, nut, bolt, gap)
beamwebconn = BeamWebBeamWeb(column, beam, notchObj, plate, Fweld1,
nutBoltArray)
beamwebconn.create_3dmodel()
return beamwebconn
def create3DColFlangeBeamWeb(self):
'''
Creating 3d cad model with column flange beam web connection
'''
# self.dictbeamdata = self.fetchBeamPara()
# self.resultObj = self.call_finCalculation()
fillet_length = self.resultObj['Plate']['height']
fillet_thickness = self.resultObj['Weld']['thickness']
plate_width = self.resultObj['Plate']['width']
plate_thick = self.uiObj['Plate']['Thickness (mm)']
##### BEAM PARAMETERS #####
beam_D = int(self.dictbeamdata[QString("D")])
beam_B = int(self.dictbeamdata[QString("B")])
beam_tw = float(self.dictbeamdata[QString("tw")])
beam_T = float(self.dictbeamdata[QString("T")])
beam_alpha = float(self.dictbeamdata[QString("FlangeSlope")])
beam_R1 = float(self.dictbeamdata[QString("R1")])
beam_R2 = float(self.dictbeamdata[QString("R2")])
beam_length = 500.0 # This parameter as per view of 3D cad model
# beam = ISectionold(B = 140, T = 16,D = 400,t = 8.9, R1 = 14, R2 = 7, alpha = 98,length = 500)
beam = ISection(B=beam_B,
T=beam_T,
D=beam_D,
t=beam_tw,
R1=beam_R1,
R2=beam_R2,
alpha=beam_alpha,
length=beam_length,
notchObj=None)
##### COLUMN PARAMETERS ######
column_D = int(self.dictcoldata[QString("D")])
column_B = int(self.dictcoldata[QString("B")])
column_tw = float(self.dictcoldata[QString("tw")])
column_T = float(self.dictcoldata[QString("T")])
column_alpha = float(self.dictcoldata[QString("FlangeSlope")])
column_R1 = float(self.dictcoldata[QString("R1")])
column_R2 = float(self.dictcoldata[QString("R2")])
# column = ISectionold(B = 83, T = 14.1, D = 250, t = 11, R1 = 12, R2 = 3.2, alpha = 98, length = 1000)
column = ISection(B=column_B,
T=column_T,
D=column_D,
t=column_tw,
R1=column_R1,
R2=column_R2,
alpha=column_alpha,
length=1000,
notchObj=None)
#### WELD,PLATE,BOLT AND NUT PARAMETERS #####
fillet_length = self.resultObj['Plate']['height']
fillet_thickness = self.resultObj['Weld']['thickness']
plate_width = self.resultObj['Plate']['width']
plate_thick = self.uiObj['Plate']['Thickness (mm)']
bolt_dia = self.uiObj["Bolt"]["Diameter (mm)"]
bolt_r = bolt_dia / 2
# bolt_R = self.boltHeadDia_Calculation(bolt_dia) /2
bolt_R = self.bolt_R
# bolt_R = bolt_r + 7
nut_R = bolt_R
# bolt_T = self.boltHeadThick_Calculation(bolt_dia)
bolt_T = self.bolt_T
# bolt_T = 10.0 # minimum bolt thickness As per Indian Standard
# bolt_Ht = self.boltLength_Calculation(bolt_dia)
bolt_Ht = self.bolt_Ht
# bolt_Ht =100.0 # minimum bolt length as per Indian Standard
# nut_T = self.nutThick_Calculation(bolt_dia)# bolt_dia = nut_dia
nut_T = self.nut_T
# nut_T = 12.0 # minimum nut thickness As per Indian Standard
nut_Ht = 12.2 #
# plate = Plate(L= 300,W =100, T = 10)
plate = Plate(L=fillet_length, W=plate_width, T=plate_thick)
# Fweld1 = FilletWeld(L= 300,b = 6, h = 6)
Fweld1 = FilletWeld(L=fillet_length,
b=fillet_thickness,
h=fillet_thickness)
# bolt = Bolt(R = bolt_R,T = bolt_T, H = 38.0, r = 4.0 )
bolt = Bolt(R=bolt_R, T=bolt_T, H=bolt_Ht, r=bolt_r)
# nut =Nut(R = bolt_R, T = 10.0, H = 11, innerR1 = 4.0, outerR2 = 8.3)
nut = Nut(R=bolt_R, T=nut_T, H=nut_Ht, innerR1=bolt_r)
gap = beam_tw + plate_thick + nut_T
nutBoltArray = NutBoltArray(self.resultObj, nut, bolt, gap)
colflangeconn = ColFlangeBeamWeb(column, beam, Fweld1, plate,
nutBoltArray)
colflangeconn.create_3dmodel()
return colflangeconn
from plate import Plate
from pyrogram.types import InlineKeyboardMarkup, InlineKeyboardButton
from util import config
plate = Plate(root=config.LANGUAGES_DIR)
def get_message(message_name: str, language_name: str = 'en_US', **kwargs):
try:
return plate(message_name, language_name, **kwargs)
except ValueError:
return plate(message_name, 'en_US', **kwargs)
def create_keyboard(is_group: bool,
back: InlineKeyboardButton,
settings=None) -> InlineKeyboardMarkup:
keyboard = [[]]
for lang in plate.locales:
if len(keyboard[-1]) >= 3:
keyboard.append([])
flag = plate('flag', lang)
keyboard[-1].append(
InlineKeyboardButton(
flag,
callback_data=
f'language_{f"g_{settings.id}" if is_group else "p"}_{lang}'))
LOCAL.FLOOD_PERCENTAGE = anti_flood_wait_config.getint("flood_percentage")
LOCAL.BAN_TIME = anti_flood_wait_config.getint("ban_time")
LOCAL.DELETE_MESSAGES = anti_flood_wait_config.getboolean("delete_messages")
LOCAL.FLOOD_NOTICE = anti_flood_wait_config.get("flood_notice")
LOCAL.PURGE_POLLING_RATE = anti_flood_wait_config.getint("purge_polling_rate")
LOCAL.INACTIVE_THRESHOLD = anti_flood_wait_config.getint("inactive_threshold")
LOCAL.FLOOD_WAITED = filters.user()
LOCAL.OWNER_ID = bot_config.getint("owner_id")
LOCAL.DB_URI = database_config.get("db_uri")
LOCAL.DB_POOL_SIZE = (database_config.getint("min_pool_size"),
database_config.getint("max_pool_size"))
logging.basicConfig(format=logging_config.get("format"),
datefmt=logging_config.get("date_format"))
LOCAL.LOGGER = logging.getLogger("Kanri")
LOCAL.LOGGER.setLevel(logging_config.getint("level"))
LOCAL.PLATE = Plate()
LOCAL.HTTP_SESSION = aiohttp.ClientSession()
# TODO: move this to the database for per-user translations.
LOCAL.DEFAULT_LANG = lang_config.get("default")
LOCAL.APP = Client(":memory:", config_file="config.ini")
async def set_bot():
"""
Sets the bot's own username and ID
in the thread-local storage space
"""
self = await LOCAL.APP.get_me()
LOCAL.bot_id = self.id
LOCAL.bot_name = self.first_name
import os
from plate import Plate
from sample import Sample
from liquidclass import LCBleachMix
from worklist import WASHLOC, QPCRLOC
############ Plates and plate locations #############
#WASHLOC=Plate("Wash",1,2,1,8,False,0) # Defined in worklist
# Use dimensional data from Robot/Calibration/20150302-LiquidHeights
#REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=24.45,gemArea=51.61,gemHOffset=-7.15,gemShape='v-shaped')
#REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=13.83,gemArea=51.84,gemHOffset=0,gemShape='v-shaped')
REAGENTPLATE=Plate("Reagents",18,1,6,5,False,unusableVolume=20,maxVolume=1700,zmax=569,angle=17.5,r1=4.062,h1=17.75,v0=13.7,slopex=-0.022,slopey=-0.038,gemDepth=9.59,gemArea=43.03,gemHOffset=0,gemShape='v-shaped')
MAGPLATELOC=Plate("MagPlate",18,2,12,8,False,unusableVolume=9,maxVolume=200,zmax=1459,angle=17.5,r1=2.80,h1=10.04,v0=10.8) # HSP9601 on magnetic plate (Use same well dimensions as SAMPLE)
hspmaxspeeds={200:1400,150:1600,100:1850,50:2000,20:2200} # From shaketest experiment
grenmaxspeeds={150:1750,125:1900,100:1950,75:2200,50:2200} # From shaketest experiment
eppmaxspeeds={195:1600,150:1800,125:1900,100:1950,75:2050,50:2150,25:2150,0:2150} # From shaketest experiment 5/17/16
#eppdilmaxspeeds={195:1400,150:1600,125:1700,100:1750,75:1850,50:1950,25:1950,0:1950} # Decrease by 200 RPM 7/7/16 to avoid spilling
#eppmaxspeeds={195:0,150:1150,138:1250,100:1350,75:1850,50:1950,25:1950,0:1950} # Decrease based on 9/23/16 testing with MTaq
eppglycerolmaxspeeds={195:0,150:1150,138:1250,100:1350,90:1450,80:1500,70:1550,60:1650,50:1750,40:1950,20:2000,0:2000} # Decrease based on 10/21/16 testing with MTaq (with Glycerol @ 0.5%)
eppminspeeds={20:1900,32:1800,64:1700,96:1400,150:1100} # 1100@150ul untested
SAMPLEPLATE=Plate("Samples",4,3,12,8,False,unusableVolume=15,maxVolume=200,
zmax=1033,angle=17.5,r1=2.698,h1=9.31,v0=17.21,slopex=0.000,slopey=0.000,
gemDepth=2.81,gemArea=16.41,
gemShape='v-shaped',vectorName="Microplate Landscape",maxspeeds=eppmaxspeeds,minspeeds=eppminspeeds,glycerolmaxspeeds=eppglycerolmaxspeeds,glycerol=0.005) # EppLoBind
SAMPLEPLATE.wells=SAMPLEPLATE.wells[1:-1] # Skip A1 and H12 due to leakage
SHAKERPLATELOC=Plate("Shaker",9,0,1,1)
QPCRPLATE=Plate("qPCR",QPCRLOC.grid,QPCRLOC.pos,12,8,False,unusableVolume=15,maxVolume=200,
zmax=996,angle=17.5,r1=2.704,h1=10.89,v0=0.44,slopex=0.000,slopey=0.000,gemDepth=3.17,gemArea=14.33,
gemShape='v-shaped')
SYSTEM_VERSION = "1.1a"
# Host OS version, can be the same as VERSION - also useless for a Bot
LANG_CODE = "en_US"
# Session lang_code
bot = Client(
api_id=API_ID,
api_hash=API_HASH,
bot_token=BOT_TOKEN,
plugins=PLUGINS_ROOT,
session_name=SESSION_NAME,
workers=WORKERS_NUM,
device_model=DEVICE_MODEL,
system_version=SYSTEM_VERSION,
lang_code=LANG_CODE,
)
plate = Plate(root="BotBase/locales")
# endregion
# region Logging configuration
# To know more about what these options mean, check https://docs.python.org/3/library/logging.html
LOGGING_FORMAT = (
"[%(levelname)s %(asctime)s] In thread '%(threadName)s', "
f"module %(module)s, function %(funcName)s at line %(lineno)d -> [{SESSION_NAME}] %(message)s"
)
DATE_FORMAT = "%d/%m/%Y %H:%M:%S %p"
LOGGING_LEVEL = 30
# endregion
# region Start module
# P.S.: {mention} in the GREET message will be replaced with a mention to the user, same applies for {id} and {username}
def make_plate(params, inducer_conc):
amount = inducer_conc * 1e-6 #milli moles
agar_thickness = 3.12 # mm
init_conc = amount / (w**2 * agar_thickness) #mol/mm^3
init_conc *= 1e6 # mM
A_0 = init_conc
D_N, mu_max, K_mu, gamma, D_A, \
alpha_T, beta_T, K_IT, n_IT, K_lacT, T7_0, \
alpha_R, beta_R, K_IR, n_IR, K_lacR, R_0, \
alpha_G, beta_G, n_A, K_A, n_R, K_R, X_0, G_s = params
## Create our environment
plate = Plate(environment_size)
dist = 4.5 # mm
centre = plate_width / 2
receiver_radius = 2
receiver_pos = [[centre - i * dist, centre] for i in range(1, 4)]
receiver_pos.extend([[centre + i * dist, centre] for i in range(1, 4)])
receiver_pos.extend([[centre, centre + i * dist] for i in range(1, 4)])
receiver_pos.extend([[centre, centre - i * dist] for i in range(1, 4)])
receiver_coordinates = get_node_coordinates(receiver_pos, receiver_radius,
environment_size[0],
environment_size[1], w)
rows = receiver_coordinates[:, 0]
cols = receiver_coordinates[:, 1]
receiver_flags = np.zeros(environment_size)
receiver_flags[rows, cols] = 1
## add nutrient to the plate
U_N = np.ones(environment_size) * N_0
N = Species("N", U_N)
def N_behaviour(t, species, params):
## unpack params
D_N, mu_max, K_mu, gamma, D_A, \
alpha_T, beta_T, K_IT, n_IT, K_lacT, T7_0, \
alpha_R, beta_R, K_IR, n_IR, K_lacR, R_0, \
alpha_G, beta_G, n_A, K_A, n_R, K_R, X_0, G_s = params
#mu = mu_max * np.maximum(0, species['N']) / (K_mu + np.maximum(0,species['N'])) * np.maximum(0,species['X'])
#print(np.max(mu))
mu = dx(t, species) * receiver_flags
#print('mu', mu)
n = D_N * hf.ficks(np.maximum(0, species['N']), w) - mu / gamma
return n
N.set_behaviour(N_behaviour)
plate.add_species(N)
## add one strain to the plate
U_X = np.zeros(environment_size)
U_X[rows, cols] = X_0
strain = Species("X", U_X)
def X_behaviour(t, species, params):
## unpack params
#mu = mu_max * np.maximum(0, species['N']) / (K_mu + np.maximum(0, species['N'])) * np.maximum(0,species['X'])
mu = dx(t, species) * receiver_flags
return mu
strain.set_behaviour(X_behaviour)
plate.add_species(strain)
## add IPTG to plate
#inducer_position = [[int(j * (4.5/w)) for j in i] for i in inducer_positions # convert position to specified dims
U_A = np.zeros(environment_size)
U_A[inducer_position[0], inducer_position[1]] = A_0
A = Species("A", U_A)
def A_behaviour(t, species, params):
## unpack params
D_N, mu_max, K_mu, gamma, D_A, \
alpha_T, beta_T, K_IT, n_IT, K_lacT, T7_0, \
alpha_R, beta_R, K_IR, n_IR, K_lacR, R_0, \
alpha_G, beta_G, n_A, K_A, n_R, K_R, X_0, G_s = params
a = D_A * hf.ficks(np.maximum(0, species['A']), w)
return a
A.set_behaviour(A_behaviour)
plate.add_species(A)
#add T7 to the plate
U_T7 = np.ones(environment_size) * T7_0
T7 = Species("T7", U_T7)
def T7_behaviour(t, species, params):
D_N, mu_max, K_mu, gamma, D_A, \
alpha_T, beta_T, K_IT, n_IT, K_lacT, T7_0, \
alpha_R, beta_R, K_IR, n_IR, K_lacR, R_0, \
alpha_G, beta_G, n_A, K_A, n_R, K_R, X_0, G_s = params
mu = dx(t, species) * receiver_flags
dT7 = (alpha_T * mu *
(1 + (np.maximum(0, species['A']) / K_IT)**n_IT)) / (
1 + (np.maximum(0, species['A']) / K_IT)**n_IT +
K_lacT) + beta_T * mu - mu * np.maximum(0, species['T7'])
return dT7
T7.set_behaviour(T7_behaviour)
plate.add_species(T7)
## add GFP to plate
U_G = np.ones(environment_size) * GFP_0
G = Species("G", U_G)
def G_behaviour(t, species, params):
## unpack params
D_N, mu_max, K_mu, gamma, D_A, \
alpha_T, beta_T, K_IT, n_IT, K_lacT, T7_0, \
alpha_R, beta_R, K_IR, n_IR, K_lacR, R_0,\
alpha_G, beta_G, n_A, K_A, n_R, K_R, X_0, G_s = params
#mu = mu_max * np.maximum(0, species['N']) / (K_mu + np.maximum(0, species['N'])) * np.maximum(0,species['X'])
mu = dx(t, species) * receiver_flags
#T7 = alpha_T + beta_T - alpha_T * K_lacT / (1 + (np.maximum(0, species['A']) / K_IT)**n_IT + K_lacT) + T7_0 * np.exp(-mu * t)
#T7 = alpha_T + beta_T - alpha_T * K_lacT / (1 + (np.maximum(0, species['A']) / K_IT)**n_IT + K_lacT) + T7_0 * np.exp(-mu * t) #rescaled
T7 = np.maximum(0, species['T7'])
#print(np.max(T7))
#R = alpha_R + beta_R - alpha_R * K_lacR / (1 + (np.maximum(0, species['A']) / K_IR)**n_IR + K_lacR) + R_0 * np.exp(-mu * t)
#R = alpha_R + beta_R - alpha_R * K_lacR / (1 + (np.maximum(0, species['A']) / K_IR)**n_IR + K_lacR) + R_0 * np.exp(-mu * 1e8 * t) #rescaled
R = 0 # produces treshold
T7**n_A / (K_A**n_A + T7**n_A)
K_R**n_R / (K_R**n_R + R**n_R)
#dGFP = alpha_G * mu * T7**n_A / (K_A**n_A + T7**n_A) * K_R**n_R / (K_R**n_R + R**n_R) + beta_G * mu - np.maximum(0, species['G']) * mu*G_s
dGFP = alpha_G * mu * T7**n_A / (K_A**n_A +
T7**n_A) + beta_G * mu - np.maximum(
0, species['G']) * mu * G_s
return dGFP
G.set_behaviour(G_behaviour)
plate.add_species(G)
return plate