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()