def main():
"""
Imports an XLS file of Victor exported results.
The Experiment ID is determined by the time-stamp of the first measurement.
"""
options = MakeOpts().parse_args()
if options.debug:
db = CreateDummyDB()
else:
db = MySQLDatabase(host=options.host,
user='******',
port=3306,
passwd='a1a1a1',
db='tecan')
if not os.path.exists(options.xls_file):
print "File not found: " + options.xls_file
sys.exit(-1)
print "Importing from file: " + options.xls_file
fp = open(options.xls_file, 'r')
exp_id = VictorParser.ImportFileToDB(fp, db, options.exp_id)
if options.debug:
print "Done, go check out the results at %s" % db.filename
else:
print "Done, go check out the results at http://eladpc1/RoboSite/Exp/%s/0" % exp_id
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys, os
if (not os.path.exists('../res')):
os.mkdir('../res')
vp = VictorParser()
fname = "../data/OD_eGFP_20100711_190.xls"
vp.parse_excel(fname)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
columns = [('4K5', 0, 'y'),\
('GFP-A', 1, 'r'),\
('GFP-B', 2, 'g'),\
('GFP-C', 3, 'c'),\
('GFP-D', 4, 'c:'),\
for vp in vp_vec:
(time, value) = vp.get_data(index, row, col)
time_array = hstack([time_array, time + last_t])
value_array = hstack([value_array, value])
if (len(time_array) > 0):
last_t = time_array.max()
return (time_array, value_array)
if (not os.path.exists('../res')):
os.mkdir('../res')
name = "elad_100903_ace_lux"
vp_vec = []
vp = VictorParser()
vp.parse_excel("../data/%s.xls" % (name))
vp_vec.append(vp)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys, os
if (not os.path.exists('../res')):
os.mkdir('../res')
vp = VictorParser()
name = "RBS-GFP 28-07-10"
fname = "../data/%s.xls" % name
if (not os.path.exists(fname)):
raise Exception("Cannot locate the Excel file: " + fname)
vp.parse_excel(fname)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
plot_types = [(0, "OD", 0.001, 1), (1, "GFP", 1e3, 1e6), ("divide", "GFP/OD", 1e4, 2e6)]
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
import sys
vp = VictorParser()
fname = "../data/victor/Elad's OD600_20100629_186.xls"
vp.parse_excel(fname)
# (t, v) = vp.get_data(0, 0, 0)
# fit_growth(t, v, 1.5, plot_figure=True)
# sys.exit(0)
figure(figsize=(5, 7))
rcParams["text.usetex"] = True
rcParams["legend.fontsize"] = 6
rcParams["font.family"] = "sans-serif"
rcParams["font.size"] = 8
rcParams["lines.linewidth"] = 0.6
rcParams["lines.markersize"] = 2
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
leg = ["SOC+kana", "M9+CAS+Glu+kana", "M9+AA+Nt+Glu+kana", "M9+Glu+kana", "M9+Acetate+kana"]
color = ["g", "r", "b", "m", "c"]
gr_mat = zeros((5, 10))
subplot(2, 1, 1)
for c in range(0, 5):
for r in range(5):
(t, v) = vp.get_data(0, r, c)
plot(t, v - min(v), color[r])
last_t = 0
for vp in vp_vec:
(time, value) = vp.get_data(index, row, col)
time_array = hstack([time_array, time + last_t])
value_array = hstack([value_array, value])
if (len(time_array) > 0):
last_t = time_array.max()
return (time_array, value_array)
if (not os.path.exists('../res')):
os.mkdir('../res')
name = "elad_100903_ace_lux"
vp_vec = []
vp = VictorParser()
vp.parse_excel("../data/%s.xls" % (name))
vp_vec.append(vp)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys, os
if (not os.path.exists('../res')):
os.mkdir('../res')
vp = VictorParser()
name = "d100805_elad_LUX"
fname = "../data/%s.xls" % name
if (not os.path.exists(fname)):
raise Exception("Cannot locate the Excel file: " + fname)
vp.parse_excel(fname)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
plots = [] # (title, victor_index, (t_min, t_max), (y_min, y_max), y_label,
"""
time - a vector of the time of each measurement (in hours)
cell_count - a vector of the cell-count at each time point
window - the size of the window for which to calculate the growth rates (in hours)
start_time - the time point after which the input data can be trusted
Note: the cell_count can be any measure that is proportional to the
number of cells. For example, Optical Density (in OD), or level of
luminescence (in CPS).
"""
from victor_parser import VictorParser
import pylab
if (__name__ == "__main__"):
vp = VictorParser()
fname = "../data/Elad's OD600_20100701_188.xls"
vp.parse_excel(fname)
(time, cell_count) = vp.get_data(0, 3, 0)
pylab.figure()
pylab.subplot(1,2,1)
print "Logistic fit: gr = %.2f" % vp.fit_growth2(time, cell_count, plot_figure=True)
pylab.subplot(1,2,2)
print "linear fit in logscale: gr = %.2f" % vp.fit_growth(time, cell_count, window_size=1.5, start_threshold=0.01, plot_figure=True)
pylab.show()
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys
vp = VictorParser()
fname = "../data/Elad's OD600_20100701_188.xls"
vp.parse_excel(fname)
#(t, v) = vp.get_data(0, 0, 0)
#fit_growth(t, v, 1.5, plot_figure=True)
#sys.exit(0)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 8
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
rows = [('SOC', 0, 'y'),\
('casa', 1, 'r'),\
('DO', 2, 'g'),\
('AA+dntos', 3, 'c'),\
('AA', 4, 'c:'),\
import sys, os
def get_data(index, row, col, vp1, vp2):
(time1, value1) = vp1.get_data(index, row, col)
(time2, value2) = vp2.get_data(index, row, col)
last_t1 = time1.max()
time = array([t for t in time1] + [(t + last_t1) for t in time2])
value = hstack([value1, value2])
return (time, value)
if (not os.path.exists('../res')):
os.mkdir('../res')
vp1 = VictorParser()
vp2 = VictorParser()
name = "d100805_elad_LUX"
vp1.parse_excel("../data/%s_1.xls" % name)
vp2.parse_excel("../data/%s_2.xls" % name)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
"""
time - a vector of the time of each measurement (in hours)
cell_count - a vector of the cell-count at each time point
window - the size of the window for which to calculate the growth rates (in hours)
start_time - the time point after which the input data can be trusted
Note: the cell_count can be any measure that is proportional to the
number of cells. For example, Optical Density (in OD), or level of
luminescence (in CPS).
"""
from victor_parser import VictorParser
import pylab
if (__name__ == "__main__"):
vp = VictorParser()
fname = "../data/Elad's OD600_20100701_188.xls"
vp.parse_excel(fname)
(time, cell_count) = vp.get_data(0, 3, 0)
pylab.figure()
pylab.subplot(1, 2, 1)
print "Logistic fit: gr = %.2f" % vp.fit_growth2(
time, cell_count, plot_figure=True)
pylab.subplot(1, 2, 2)
print "linear fit in logscale: gr = %.2f" % vp.fit_growth(
time,
cell_count,
window_size=1.5,
start_threshold=0.01,
plot_figure=True)
pylab.show()
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys, os
if (not os.path.exists('../res')):
os.mkdir('../res')
vp = VictorParser()
name = "d100721_dor_PRK_IPTG"
fname = "../data/%s.xls" % name
pp = PdfPages('../res/%s.pdf' % name)
vp.parse_excel(fname)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
# 1 2 3 4 5 6 7 8
# B(SN)PRK B(SN)PRK B(SN)PRK B_GFP B_GFP B_GFP NTC NTC
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
import sys
vp = VictorParser()
fname = "../data/victor/Elad's OD600_20100629_186.xls"
vp.parse_excel(fname)
#(t, v) = vp.get_data(0, 0, 0)
#fit_growth(t, v, 1.5, plot_figure=True)
#sys.exit(0)
figure(figsize=(5, 7))
rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 6
rcParams['font.family'] = 'sans-serif'
rcParams['font.size'] = 8
rcParams['lines.linewidth'] = 0.6
rcParams['lines.markersize'] = 2
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
leg = [
'SOC+kana', 'M9+CAS+Glu+kana', 'M9+AA+Nt+Glu+kana', 'M9+Glu+kana',
'M9+Acetate+kana'
]
color = ['g', 'r', 'b', 'm', 'c']
gr_mat = zeros((5, 10))
subplot(2, 1, 1)
for c in range(0, 5):
from victor_parser import VictorParser
from pylab import *
from matplotlib import font_manager
from matplotlib.backends.backend_pdf import PdfPages
import sys, os
if (not os.path.exists('../res')):
os.mkdir('../res')
vp = VictorParser()
name = "d100805_elad_LUX"
fname = "../data/%s.xls" % name
if (not os.path.exists(fname)):
raise Exception("Cannot locate the Excel file: " + fname)
vp.parse_excel(fname)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
fit_window_size = 1.5 # hours
fit_start_threshold = 0.01
plots = [] # (title, victor_index, (t_min, t_max), (y_min, y_max), y_label,
for vp in vp_vec:
(time, value) = vp.get_data(index, row, col)
time_array = hstack([time_array, time + last_t])
value_array = hstack([value_array, value])
if (len(time_array) > 0):
last_t = time_array.max()
return (time_array, value_array)
if (not os.path.exists('../res')):
os.mkdir('../res')
name = "elad_100819_ace_lux"
vp_vec = []
for i in range(1, 3):
vp = VictorParser()
vp.parse_excel("../data/%s_%d.xls" % (name, i))
vp_vec.append(vp)
pp = PdfPages('../res/%s.pdf' % name)
#rcParams['text.usetex'] = True
rcParams['legend.fontsize'] = 12
#rcParams['font.family'] = 'sans-serif'
#rcParams['font.size'] = 8
#rcParams['lines.linewidth'] = 0.3
#rcParams['lines.markersize'] = 2
#rcParams['figure.figsize'] = [5, 10]
#rcParams['figure.subplot.hspace'] = 0.3
#figure()
