Athemis/pyKinetics
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improve color handling; fix crash if using log scaled plots and zero values

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This commit is contained in:
Alexander Minges 2016-04-15 15:09:18 +02:00
parent 6d39c4822b
commit 3f5c82e13b
2 changed files with 82 additions and 13 deletions
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43
libkinetics/__init__.py
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@ -64,7 +64,38 @@ class Replicate():
self.x, self.y = xy
self.owner = owner
self.xlim = owner.xlim
self.fitresult = self.fit()
self.conc = '{} {}'.format(self.owner.concentration,
self.owner.concentration_unit)
if not self.owner.owner.end_point:
self.fitresult = self.fit()
else:
self.fitresult = self.end_point_determination()
def end_point_determination(self):
ind_min_max = np.where((self.x >= self.xlim[0]) & (self.x <=
self.xlim[1]))[0]
x_start = self.x[ind_min_max[0]]
x_end = self.x[ind_min_max[-1]]
y_start = self.y[ind_min_max[0]]
y_end = self.y[ind_min_max[-1]]
slope = (y_end - y_start) / (x_end - x_start)
self.logger.info('End point determination for {} #{}:'.format(self.conc, self.num))
self.logger.info(' start x/y: {}/{}'.format(x_start, float(y_start)))
self.logger.info(' end x/y: {}/{}'.format(x_end, float(y_end)))
self.logger.info(' slope: {}'.format(float(slope)))
return {
'slope': slope,
'intercept': None,
'r_value': None,
'r_squared': None,
'p_value': None,
'std_err': None
}
def fit(self):
ind_min_max = np.where((self.x >= self.xlim[0]) & (self.x <=
@ -88,11 +119,8 @@ class Replicate():
# calculcate adjusted R²
adj_r_squared = r_squared - (1 - r_squared) * k/(n - k - 1)
conc = '{} {}'.format(self.owner.concentration,
self.owner.concentration_unit)
self.logger.info('Linear fit for {} #{}:'.format(conc, self.num))
self.logger.info('Linear fit for {} #{}:'.format(self.conc, self.num))
if adj_r_squared < 0.9 and adj_r_squared > 0.7:
msg = ' adjusted R² < 0.9; Check fit manually!'
self.logger.warning(msg.format(round(adj_r_squared, 4)))
@ -232,7 +260,7 @@ class Experiment():
"""
def __init__(self, data_files, xlim, do_hill=False, no_mm=False,
fit_to_replicates=False, logger=None):
fit_to_replicates=False, logger=None, end_point=False):
"""
Inits Experiment class with experimental parameters
@ -267,6 +295,8 @@ class Experiment():
# dictionary to store data for the kinetics calculation
self.raw_kinetic_data = {'x': [], 'y': [], 'yerr': []}
self.xlim = xlim
self.end_point = end_point
# parse data files and generate measurements
for csvfile in data_files:
@ -317,6 +347,7 @@ class Experiment():
self.raw_kinetic_data['x'].append(m.concentration)
self.raw_kinetic_data['y'].append(np.absolute(m.avg_slope))
self.raw_kinetic_data['yerr'].append(m.avg_slope_err)
# calculate kinetics
if not no_mm: