Athemis/pyKinetics
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More work on documentation

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This commit is contained in:
Alexander Minges 2015-09-01 16:02:30 +02:00
parent c7a8525410
commit 19c97dc6f2
2 changed files with 30 additions and 3 deletions
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4
analyze-cli.py
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@ -141,8 +141,8 @@ class ExperimentHelper():
writer.writerow([]) writer.writerow([])
writer.writerow(['HILL KINETICS']) writer.writerow(['HILL KINETICS'])
writer.writerow(['', 'value', 'std']) writer.writerow(['', 'value', 'std'])
writer.writerow(['vmax', exp.hill['vmax'], writer.writerow(['vmax', exp.hill['vmax'], exp.hill['vmax_err']
exp.hill['vmax_err']]) ])
writer.writerow(['Kprime', exp.hill['Kprime'], writer.writerow(['Kprime', exp.hill['Kprime'],
exp.hill['Kprime_err']]) exp.hill['Kprime_err']])
writer.writerow(['h', exp.hill['h'], exp.hill['h_err']]) writer.writerow(['h', exp.hill['h'], exp.hill['h_err']])

29
libkinetics/__init__.py
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@ -49,6 +49,16 @@ class Replicate():
""" """
def __init__(self, num, xy, owner): def __init__(self, num, xy, owner):
"""
Inits Replicate class with provided data.
Args:
logger: logging.Logger instance inherited by the owning Experiment.
xy: tuple of floats
time and signal to be analysed.
owner: object
measurement this measurement belongs to
"""
self.logger = owner.logger self.logger = owner.logger
self.num = num + 1 self.num = num + 1
self.x, self.y = xy self.x, self.y = xy
@ -57,7 +67,8 @@ class Replicate():
self.fitresult = self.fit() self.fitresult = self.fit()
def fit(self): def fit(self):
ind_min_max = np.where((self.x >= self.xlim[0]) & (self.x <= self.xlim[1])) ind_min_max = np.where((self.x >= self.xlim[0]) & (self.x <=
self.xlim[1]))
x_for_fit = np.take(self.x, ind_min_max) x_for_fit = np.take(self.x, ind_min_max)
y_for_fit = np.take(self.y, ind_min_max) y_for_fit = np.take(self.y, ind_min_max)
@ -126,6 +137,22 @@ class Measurement():
""" """
def __init__(self, xy, conc, conc_unit, owner): def __init__(self, xy, conc, conc_unit, owner):
"""
Inits Measurement class with provided data.
This is usually called from within an Experiment object.
Args:
logger: logging.Logger instance inherited by the owning Experiment.
concentration: float
substrate concentration associated with the measurement.
concentration_unit: string
unit of the concentration; only used for labeling plots/tables.
xy: tuple of floats
time and signal to be analysed.
owner: object
experiment this measurement belongs to
"""
self.logger = owner.logger self.logger = owner.logger
self.concentration = float(conc) self.concentration = float(conc)
self.concentration_unit = conc_unit self.concentration_unit = conc_unit