def do(board):
dev = surf.Surf()
print 'identify:'
dev.identify()
print 'path:', dev.path
dev.labc.run_mode(0)
dev.labc.testpattern_mode(0)
dev.labc.reset_fifo()
dev.labc.reset_ramp()
dev.labc.dll(15) #disable DLL
time.sleep(1)
dev.i2c.default_config()
dev.clock(dev.internalClock)
dev.labc.default() #send default values to LAB registers
dev.set_phase(2)
dev.labc.automatch_phab(15)
if not surf_cal.check_board(board, dev.dna()):
print 'adding board to calibration json file..'
surf_cal.add_board(board, dev.dna())
else:
print 'cal file entry already exists for board: ', board
#
# if surf_cal.read_vadjn(dev.dna()) == None:
# print 'scanning for Vadjn..'
# vadjn = []
# for i in range(12):
# vadjn.append(dev.labc.autotune_vadjn(i))
#
# surf_cal.save_vadjn(dev.dna(), vadjn)
#
if surf_cal.read_vadjp(dev.dna()) == None:
print 'scanning for Vadjp..'
vadjp = []
for i in range(12):
vadjp.append(dev.labc.autotune_vadjp(i))
surf_cal.save_vadjp(dev.dna(), vadjp)
##turn on the DLL
time.sleep(1)
dev.labc.dll(15, mode=True)
##show the board status
dev.status()
return dev
def __init__(self):
self.dev = surf.Surf()
self.pedestals = np.zeros(((lab4d_storage_cells, surf_channels)),
dtype=np.int)
self.lab_lut = np.zeros((2**LAB_ADC_BITS, 12), dtype=float)
def run(self):
self.game.display.blit(self.background, (0, 0))
self.pressed = self.game.get_pressed()
# shadow text
name = self.font.render(self.UNIVERSITIES[self.index], 0,
(153, 132, 0))
text_rect = name.get_rect(
center=(pygame.display.Info().current_w / 2 + 5,
pygame.display.Info().current_h / 2 + 5))
self.game.display.blit(name, text_rect)
# main text
name = self.font.render(self.UNIVERSITIES[self.index], 0,
(255, 255, 0))
text_rect = name.get_rect(center=(pygame.display.Info().current_w / 2,
pygame.display.Info().current_h / 2))
self.game.display.blit(name, text_rect)
if self.pressed[0] and not self.bounce and not self.ready:
self.bounce = True
self.bounce_time = pygame.time.get_ticks()
self.index -= 1
if self.pressed[1] and not self.bounce and not self.ready:
self.bounce = True
self.bounce_time = pygame.time.get_ticks()
self.index += 1
if self.pressed[3] and not self.ready:
self.ready = True
self.ready_time = pygame.time.get_ticks()
elif not self.pressed[3]:
self.ready = False
self.index = self.index % len(self.UNIVERSITIES)
if pygame.time.get_ticks() - self.bounce_time > 1000:
self.bounce = False
if self.ready:
remaining = 5 - int(
(pygame.time.get_ticks() - self.ready_time) / 1000.0)
if remaining <= -1:
self.game.university = self.UNIVERSITIES[self.index]
if pygame.key.get_pressed(
)[pygame.K_KP_PERIOD] and pygame.key.get_pressed(
)[pygame.K_KP1] and pygame.key.get_pressed()[pygame.K_KP3]:
self.game.titi = True
self.game.university = 'TITI'
self.game.state = surf.Surf(self.game)
return
pygame.draw.rect(
self.game.display, (0, 255, 0),
(pygame.display.Info().current_w / 2 - 500 / 2,
pygame.display.Info().current_h / 2 - 200 / 2, 500, 200))
name = self.font.render("READY " + str(remaining), 0, (0, 0, 0))
text_rect = name.get_rect(
center=(pygame.display.Info().current_w / 2,
pygame.display.Info().current_h / 2))
self.game.display.blit(name, text_rect)
codon_colour = {
"M": "r",
"V": "b",
}
with os.scandir(basepath) as entries:
for entry in entries:
try:
assert (entry.is_file())
files.append(entry.name)
except:
print(entry.name, " is apparently a problem file.")
for file in files:
print(file)
f68 = sf.Surf("F-68", 1800, 8350, 80)
f127 = sf.Surf("F-127", 3600, 12600, 70)
f38 = sf.Surf("F-38", 900, 5000, 80)
f108 = sf.Surf("F-108", 3000, 14000, 80)
p84 = sf.Surf("P-84", 2250, 3750, 80)
##plotting strip plots
exp5 = [f127, files[20], [0, 0.0001, 0.0005, 0.001, 0.0011, 0.1]]
exp6 = [f68, files[21], [0, 0.0001, 0.0005, 0.001, 0.0011, 0.1]]
exp7 = [
f127, files[22], [0, 0.000033, 0.000066, 0.0001, 0.00016, 0.00033, 0.0005]
]
exp8 = [f68, files[23], [0, 0.0001, 0.0005, 0.001, 0.0011, 0.1]]
e = plotsurf.PlotSurf(
f68,
ex9.get_mastermixes()
##print(ex10)
##ex10.get_mastermixes()
##set up datfram for adding data
df_blank = ex9.getPlate()
##obtain and analyse data
df_data = rd.RTQuICData_feat(files[24], numCycles = 200).get_df()
##print(df_data)
##join above two dataframas
df_labelled_data = pd.concat([df_blank, df_data], axis = 1)
##plot the data
params = ["Lag Time"]
surfs = sf.Surf("F-108", 3000, 14000, 80), sf.Surf("P-84", 2250, 3750, 80)
for surf in surfs:
df_surf = df_labelled_data[df_labelled_data["Add"] == surf.get_name()]
groups = df_surf.groupby("Seed")
for param in params:
for name, group in groups:
x_, y_ = group["Conc"], group[param]
print(x_)
print(type(surf.get_mw()))
print(type(x_))
plt.scatter(x = x_.astype(float),y = y_, label = name)
plt.title("Effect of "+ surf.get_name()+ \
" on RTQuIC "+param)
plt.xlabel("Conc %")
plt.xscale("log")
plt.xlim(0.00001,0.001)