Athemis/pyDSF
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Coding style

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This commit is contained in:
Alexander Minges 2015-07-07 15:09:14 +02:00
parent a28142fa1e
commit e1f34c094a
1 changed files with 18 additions and 18 deletions
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36
pydsf.py
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@ -57,7 +57,7 @@ class Well:
Apply a filter to the raw data Apply a filter to the raw data
""" """
try: try:
b, a = butter(3, 0.3) b, a = butter(3, 0.3, output='ba')
self.filtered = filtfilt(b, a, self.raw) self.filtered = filtfilt(b, a, self.raw)
except Exception as err: except Exception as err:
print('Filtering of raw data failed!', err) print('Filtering of raw data failed!', err)
@ -95,7 +95,7 @@ class Well:
try: try:
baseline = peakutils.baseline(y) baseline = peakutils.baseline(y)
return baseline return baseline
except: except Exception:
return np.NaN return np.NaN
def calc_tm(self): def calc_tm(self):
@ -152,7 +152,7 @@ class Well:
else: else:
return np.NaN return np.NaN
except: except Exception:
return np.NaN # In case of error, return no peak return np.NaN # In case of error, return no peak
try: try:
@ -165,7 +165,7 @@ class Well:
return tm # and return the Tm return tm # and return the Tm
else: else:
return np.NaN # otherwise, return NaN return np.NaN # otherwise, return NaN
except: except Exception:
return np.NaN # In case of error, return NaN return np.NaN # In case of error, return NaN
def is_denatured(self): def is_denatured(self):
@ -240,7 +240,7 @@ class Well:
class Experiment: class Experiment:
def __init__(self, type, gui=None, files=None, replicates=None, t1=25, def __init__(self, exp_type, gui=None, files=None, replicates=None, t1=25,
t2=95, dt=1, cols=12, rows=8, cutoff_low=None, t2=95, dt=1, cols=12, rows=8, cutoff_low=None,
cutoff_high=None, signal_threshold=None, color_range=None, cutoff_high=None, signal_threshold=None, color_range=None,
baseline_correction=False): baseline_correction=False):
@ -254,7 +254,7 @@ class Experiment:
self.reads = int(round((t2 + 1 - t1) / dt)) self.reads = int(round((t2 + 1 - t1) / dt))
self.wellnum = self.cols * self.rows self.wellnum = self.cols * self.rows
self.files = files self.files = files
self.type = type self.type = exp_type
self.wells = [] self.wells = []
self.max_tm = None self.max_tm = None
self.min_tm = None self.min_tm = None
@ -284,7 +284,7 @@ class Experiment:
# populate self.plates with data in provided files list # populate self.plates with data in provided files list
i = 1 i = 1
for file in files: for file in files:
plate = Plate(type=self.type, owner=self, filename=file, plate = Plate(plate_type=self.type, owner=self, filename=file,
t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols, t1=self.t1, t2=self.t2, dt=self.dt, cols=self.cols,
rows=self.rows, cutoff_low=self.tm_cutoff_low, rows=self.rows, cutoff_low=self.tm_cutoff_low,
cutoff_high=self.tm_cutoff_high, cutoff_high=self.tm_cutoff_high,
@ -296,9 +296,9 @@ class Experiment:
# if more than one file is provied, assume that those are replicates # if more than one file is provied, assume that those are replicates
# and add a special plate representing the average results # and add a special plate representing the average results
if len(files) > 1: if len(files) > 1:
self.avg_plate = Plate(type=self.type, owner=self, filename=None, self.avg_plate = Plate(plate_type=self.type, owner=self,
t1=self.t1, t2=self.t2, dt=self.dt, filename=None, t1=self.t1, t2=self.t2,
cols=self.cols, rows=self.rows, dt=self.dt, cols=self.cols, rows=self.rows,
cutoff_low=self.tm_cutoff_low, cutoff_low=self.tm_cutoff_low,
cutoff_high=self.tm_cutoff_high, cutoff_high=self.tm_cutoff_high,
signal_threshold=self.signal_threshold, signal_threshold=self.signal_threshold,
@ -337,9 +337,10 @@ class Experiment:
class Plate: class Plate:
def __init__(self, type, owner, id=None, filename=None, replicates=None, def __init__(self, plate_type, owner, plate_id=None, filename=None,
t1=None, t2=None, dt=None, cols=12, rows=8, cutoff_low=None, replicates=None, t1=None, t2=None, dt=None, cols=12, rows=8,
cutoff_high=None, signal_threshold=None, color_range=None): cutoff_low=None, cutoff_high=None, signal_threshold=None,
color_range=None):
self.cols = cols self.cols = cols
self.rows = rows self.rows = rows
self.owner = owner self.owner = owner
@ -359,13 +360,13 @@ class Plate:
self.reads = int(round((t2 + 1 - t1) / dt)) self.reads = int(round((t2 + 1 - t1) / dt))
self.wellnum = self.cols * self.rows self.wellnum = self.cols * self.rows
self.filename = filename self.filename = filename
self.type = type self.type = plate_type
self.wells = [] self.wells = []
self.max_tm = None self.max_tm = None
self.min_tm = None self.min_tm = None
self.replicates = None self.replicates = replicates
self.signal_threshold = signal_threshold self.signal_threshold = signal_threshold
self.id = id self.id = plate_id
self.baseline_correction = owner.baseline_correction self.baseline_correction = owner.baseline_correction
if cutoff_low: if cutoff_low:
self.tm_cutoff_low = cutoff_low self.tm_cutoff_low = cutoff_low
@ -401,7 +402,7 @@ class Plate:
if read > 0: if read > 0:
try: try:
temp[read - 1] = row[read] temp[read - 1] = row[read]
except: except Exception:
temp[read - 1] = 0.0 temp[read - 1] = 0.0
elif read == 0: elif read == 0:
self.wells[i].name = row[read] self.wells[i].name = row[read]
@ -413,7 +414,6 @@ class Plate:
# Try to access data file in the given path # Try to access data file in the given path
with open(self.filename) as f: with open(self.filename) as f:
f.close() f.close()
pass
except IOError as e: except IOError as e:
# If the file is not found, or not accessible: abort # If the file is not found, or not accessible: abort
print('Error accessing file: {}'.format(e)) print('Error accessing file: {}'.format(e))