def find_lowest(self):
self.__get_data__()
min_distance = 0
min_path = None
min_mid = None
candidates = get_molecules.get_mid_list(conn)
i = 0
for mid in candidates:
if mid is 144:
continue
if mid in [3,4,94,35,34,49, 38, 37,36, 39, 92]:
continue
#if mid in [3, 1, 29, 48, 22, 76, 125, 24, 83, 46, 80, 82, 44]:
# continue
#print mid
frequencies, intensities = get_peaks.get_frequency_intensity_list(conn, mid)#,
#max=self.max_frequency,
#min=0)
#frequencies, intensities = get_peaks.get_frequency_intensity_list(conn, mid)
distance, path = fastdtw(self.efreqlist, frequencies, dist=euclidean)
if min_path is None:
min_path = path
min_distance = distance
min_mid = mid
elif distance < min_distance:
min_distance = distance
min_path = path
min_mid = mid
print min_distance
print min_mid
print get_molecules.getName(conn, min_mid)
def __get_data__(self):
# Get Experiment Frequencies
self.efreqlist, self.eintelist = \
get_peaks.get_frequency_intensity_list(conn, self.mid)
# Get MAX and MIN
self.max_frequency = get_peaks.get_max_frequency(conn, self.mid)
self.min_frequency = get_peaks.get_min_frequency(conn, self.mid)
# Get Candidates
#self.candidates = get_molecules.get_mid_list(conn)
self.get_candidates()
print "Candidates: "
print self.candidates
print "\n"
def __get_data__(self):
# Get Experiment Frequencies
self.efreqlist, self.eintelist = \
get_peaks.get_frequency_intensity_list(conn, self.mid)
# Get MAX and MIN
self.max_frequency = get_peaks.get_max_frequency(conn, self.mid)
self.min_frequency = get_peaks.get_min_frequency(conn, self.mid)
# Get Candidates
self.candidates = get_molecules.get_mid_list(conn)
#self.get_candidates()
print "Candidates: "
print self.candidates
print "\n"
def find_lowest(self):
self.__get_data__()
min_distance = 0
min_path = None
min_mid = None
candidates = get_molecules.get_mid_list(conn)
i = 0
for mid in candidates:
if mid is 144:
continue
if mid in [3, 4, 94, 35, 34, 49, 38, 37, 36, 39, 92]:
continue
#if mid in [3, 1, 29, 48, 22, 76, 125, 24, 83, 46, 80, 82, 44]:
# continue
#print mid
frequencies, intensities = get_peaks.get_frequency_intensity_list(
conn, mid) #,
#max=self.max_frequency,
#min=0)
#frequencies, intensities = get_peaks.get_frequency_intensity_list(conn, mid)
distance, path = fastdtw(self.efreqlist,
frequencies,
dist=euclidean)
if min_path is None:
min_path = path
min_distance = distance
min_mid = mid
elif distance < min_distance:
min_distance = distance
min_path = path
min_mid = mid
print min_distance
print min_mid
print get_molecules.getName(conn, min_mid)
def find_lowest(self):
"""
:return: mid, distance, path
"""
min_distance = 0
min_path = None
min_mid = None
candidates = self.candidates #get_molecules.get_mid_list(conn)
i = 0
for mid in candidates:
frequencies, intensities = get_peaks.get_frequency_intensity_list(
conn, mid, max=self.max_frequency, min=0) # ,
try:
distance, path = fastdtw(self.efreqlist,
frequencies,
dist=euclidean)
except IndexError:
continue
if min_path is None:
min_path = path
min_distance = distance
min_mid = mid
elif distance < min_distance:
min_distance = distance
min_path = path
min_mid = mid
print min_distance
print min_mid
print get_molecules.getName(conn, min_mid)
return min_mid, min_distance, min_path
def find_lowest(self):
"""
:return: mid, distance, path
"""
min_distance = 0
min_path = None
min_mid = None
candidates = self.candidates #get_molecules.get_mid_list(conn)
i = 0
for mid in candidates:
frequencies, intensities = get_peaks.get_frequency_intensity_list(conn,
mid,
max=self.max_frequency,
min=0) # ,
try:
distance, path = fastdtw(self.efreqlist, frequencies, dist=euclidean)
except IndexError:
continue
if min_path is None:
min_path = path
min_distance = distance
min_mid = mid
elif distance < min_distance:
min_distance = distance
min_path = path
min_mid = mid
print min_distance
print min_mid
print get_molecules.getName(conn, min_mid)
return min_mid, min_distance, min_path
'blue',
'yellow',
'#ff6500',
'cyan',
'magenta',
'#008B8B',
'#8B0000',
'#FA8072',
'#FF69B4',
'#BDB76B',
'#663399',
'#7cfc00',
]
color_index = 0
experiment_peaks, experiment_intensities = get_peaks.get_frequency_intensity_list(
conn, experiment_mid)
# Determine Axes
# Axes are determined my maximum values of experiment freq/inte values
x_axis = get_peaks.get_max_frequency(conn, experiment_mid)
y_axis = get_peaks.get_max_intensity(conn, experiment_mid)
f, axarr = plt.subplots(2, sharex=True) # Create subplot
#plt.axis(x_axis,y_axis)
#plt.axis([0, x_axis,0, y_axis]) # set axis
plt.xlabel("Frequency")
plt.ylabel("Intensity")
# Plot experiment
axarr[0].set_title('Experiment Peaks')
axarr[0].bar(experiment_peaks, experiment_intensities, edgecolor='black')
# jasmine Oliveira
# Date: 09/20/2016
import matplotlib.pyplot as plot
from temp.get import get_peaks
from config import conn
print "Enter first __setup_graph MID:"
mid1 = raw_input()
print "Enter second __setup_graph MID:"
mid2 = raw_input()
print "Graphing..."
freq1, inte1 = get_peaks.get_frequency_intensity_list(conn, mid1)
freq2, inte2 = get_peaks.get_frequency_intensity_list(conn, mid2)
subplot2 = plot.subplot(212)
subplot1 = plot.subplot(211, sharex=subplot2)
subplot1.bar(freq1, inte1)
subplot2.bar(freq2, inte2)
# Set Labels
rects = subplot2.patches
labels = ["%d" % i for i in xrange(len(rects))]
for rect, label in zip(rects, labels):
height = rect.get_height()
subplot2.text(rect.get_x() + rect.get_width() / 2,
# Store new assignments in database
remove_assignments.remove_all(conn, experiment_mid) # Remove all existing assignments
for key, value in experiment.molecule_matches.iteritems():
for match in value.matches:
entry_assignments.add_assignment(conn, match.exp_pid, experiment_mid, match.mid, match.pid) # add new assigments
# Graph Results
#assigned_mids = experiment.get_assigned_mids() # GET ASSIGNED MIDS
#for assigned_mid in assigned_mids:
# graph_peaks.graph_experiment_and_assignment(conn, experiment_mid, assigned_mid, subplot=True, show_exp_peaks=False,show_assigned_lines=True)
lower_limit = 0.2
colors = ['green', 'blue', 'yellow', '#ff6500', 'cyan', 'magenta', '#008B8B', '#8B0000','#FA8072', '#FF69B4','#BDB76B', '#663399','#7cfc00', ]
color_index = 0
experiment_peaks, experiment_intensities = get_peaks.get_frequency_intensity_list(conn, experiment_mid)
# Determine Axes
# Axes are determined my maximum values of experiment freq/inte values
x_axis = get_peaks.get_max_frequency(conn, experiment_mid)
y_axis = get_peaks.get_max_intensity(conn, experiment_mid)
f, axarr = plt.subplots(2, sharex=True) # Create subplot
#plt.axis(x_axis,y_axis)
#plt.axis([0, x_axis,0, y_axis]) # set axis
plt.xlabel("Frequency")
plt.ylabel("Intensity")
# Plot experiment
axarr[0].set_title('Experiment Peaks')
axarr[0].bar(experiment_peaks, experiment_intensities, edgecolor='black')
# jasmine Oliveira
# Date: 09/20/2016
import matplotlib.pyplot as plot
from temp.get import get_peaks
from config import conn
print "Enter first __setup_graph MID:"
mid1 = raw_input()
print "Enter second __setup_graph MID:"
mid2 = raw_input()
print "Graphing..."
freq1, inte1 = get_peaks.get_frequency_intensity_list(conn, mid1)
freq2, inte2 = get_peaks.get_frequency_intensity_list(conn, mid2)
subplot2 = plot.subplot(212)
subplot1 = plot.subplot(211, sharex=subplot2)
subplot1.bar(freq1, inte1)
subplot2.bar(freq2, inte2)
# Set Labels
rects = subplot2.patches
labels = ["%d" % i for i in xrange(len(rects))]
for rect, label in zip(rects, labels):
height = rect.get_height()
from temp.get import get_peaks
from config import conn
# Get data from file
frequencies = []
intensities = []
with open("/home/joli/PycharmProjects/SPECData/data/experiments/145.sp") as f:
for line in f:
point = str.split((line.strip()))
frequencies.append(float(point[0])) # get frequency
intensities.append(float(point[1])) # get actual intensity (logx ^ x)
print "Got Experiment Data: " + str(len(frequencies))
# Determine Peaks
#frequencies, intensities = peak_finder.peak_finder(frequencies, intensities, 0.2)
frequencies, intensities = get_peaks.get_frequency_intensity_list(conn, 145)
print " .....determined peaks."
all = get_peaks.get_all_known_frequencies(conn)
mids, all = get_peaks.get_all_known_freqencies_with_mids(conn)
print "Got Known Data: " + str(len(all))
#x = np.array([0, 0, 1, 1, 2, 4, 2, 1, 2, 0]).reshape(-1, 1)
#y = np.array([1, 1, 1, 2, 2, 2, 2, 3, 2, 0]).reshape(-1, 1)
#x = frequencies
#y = all
x = np.array(frequencies)
from temp.get import get_peaks
from config import conn
# Get data from file
frequencies = []
intensities = []
with open("/home/joli/PycharmProjects/SPECData/data/experiments/145.sp") as f:
for line in f:
point = str.split((line.strip()))
frequencies.append(float(point[0])) # get frequency
intensities.append(float(point[1])) # get actual intensity (logx ^ x)
print "Got Experiment Data: " + str(len(frequencies))
# Determine Peaks
#frequencies, intensities = peak_finder.peak_finder(frequencies, intensities, 0.2)
frequencies, intensities = get_peaks.get_frequency_intensity_list(conn, 145)
print " .....determined peaks."
all = get_peaks.get_all_known_frequencies(conn)
mids, all = get_peaks.get_all_known_freqencies_with_mids(conn)
print "Got Known Data: " + str(len(all))
#x = np.array([0, 0, 1, 1, 2, 4, 2, 1, 2, 0]).reshape(-1, 1)
#y = np.array([1, 1, 1, 2, 2, 2, 2, 3, 2, 0]).reshape(-1, 1)
#x = frequencies
#y = all
x = np.array(frequencies)
y = np.array(all)