class ImageSonogram(GridLayout):
def __init__(self, **kwargs):
# create the fig, axes, and canvas
self.fig1 = matplotlib.figure.Figure()
self.plot_sonogram_canvas = FigureCanvasKivyAgg(self.fig1)
# make plot take up the entire space
self.ax1 = self.fig1.add_axes([0., 0., 1., 1.])
self.ax1.set_axis_off()
super(ImageSonogram, self).__init__(**kwargs)
def image_sonogram_initial(self, rows, cols):
# clear axes and reformat to make plot take up the entire space
self.ax1.clear()
self.ax1.set_axis_off()
# plot data
data = np.zeros((rows, cols))
self.plot_sonogram = self.ax1.imshow(np.log(data + 3),
cmap='hot',
extent=[0, cols, 0, rows],
aspect='auto')
# create widget
self.clear_widgets()
self.add_widget(self.plot_sonogram_canvas)
def image_sonogram(self, data):
self.plot_sonogram.set_data(np.log(data + 3))
self.plot_sonogram.autoscale()
self.plot_sonogram_canvas.draw_idle()
class SyllSimSummaryPage(Screen):
def __init__(self, *args, **kwargs):
self.fig6, self.ax6 = plt.subplots()
self.syllsim_hist_canvas = FigureCanvasKivyAgg(self.fig6)
super(SyllSimSummaryPage, self).__init__(*args, **kwargs)
def calculate_syllsim_thresh_stats(self):
# syllable similarity thresholds from all the songs processed
syllsim_thresholds = self.manager.get_screen(
'syllsim_threshold_page').syllsim_thresholds
# clear the plot
self.ax6.clear()
# plot histogram of the syllable similarity thresholds used
if len(np.unique(syllsim_thresholds)) > 20:
self.ax6.hist(x=syllsim_thresholds,
bins='auto',
color=(0.196, 0.643, 0.80),
alpha=0.7)
else:
# the trick is to set up the bins centered on the integers, i.e.
# -0.5, 0.5, 1,5, 2.5, ... up to max(data) + 1.5. Then you substract -0.5 to
# eliminate the extra bin at the end.
bins = np.arange(min(syllsim_thresholds),
max(syllsim_thresholds) + 1.5, 1) - 0.5
self.ax6.hist(x=syllsim_thresholds,
bins=bins,
color=(0.196, 0.643, 0.80),
alpha=0.7)
self.ax6.set_xlabel('Syllable Similarity Threshold')
self.ax6.set_ylabel('Number of Songs with Threshold')
self.syllsim_hist_canvas.draw()
self.ids.syllsim_hist.clear_widgets()
self.ids.syllsim_hist.add_widget(self.syllsim_hist_canvas)
# calculate stats for the submitted thresholds and add them to the screen
self.ids.num_files.text = 'Number of Files: ' + str(
(len(syllsim_thresholds)))
self.ids.avg_syllsim_thresh.text = 'Average: ' + str(
round(np.mean(syllsim_thresholds), 1))
self.ids.std_dev_syllsim_thresh.text = 'Standard Deviation: ' + str(
round(np.std(syllsim_thresholds), 1))
self.ids.min_syllsim_thresh.text = 'Minimum: ' + str(
min(syllsim_thresholds))
self.ids.max_syllsim_thresh.text = 'Maximum: ' + str(
max(syllsim_thresholds))
# set the user input to the average as a default (they can change this before submitting)
self.ids.submitted_syllsim_thresh_input.text = str(
round(np.mean(syllsim_thresholds), 1))
def submit_syllsim_thresh(self):
# update the landing page with the syllable similarity threshold the user chooses/submits
self.manager.get_screen(
'landing_page'
).ids.syll_sim_input.text = self.ids.submitted_syllsim_thresh_input.text
def __init__(self, *args, **kwargs):
self.fig3, self.ax3 = plt.subplots()
self.plot_noise_canvas = FigureCanvasKivyAgg(self.fig3)
self.ax3 = plt.Axes(self.fig3, [0., 0., 1., 1.])
self.ax3.set_axis_off()
self.fig3.add_axes(self.ax3)
super(NoiseThresholdPage, self).__init__(*args, **kwargs)
def __init__(self, *args, **kwargs):
self.fig5, self.ax5 = plt.subplots()
self.plot_syllsim_canvas = FigureCanvasKivyAgg(self.fig5)
self.ax5 = plt.Axes(self.fig5, [0., 0., 1., 1.])
self.ax5.set_axis_off()
self.fig5.add_axes(self.ax5)
super(SyllSimThresholdPage, self).__init__(*args, **kwargs)
self.log = get_logger(__name__)
def __init__(self, **kwargs):
# create the fig, axes, and canvas
self.fig1 = matplotlib.figure.Figure()
self.plot_sonogram_canvas = FigureCanvasKivyAgg(self.fig1)
# make plot take up the entire space
self.ax1 = self.fig1.add_axes([0., 0., 1., 1.])
self.ax1.set_axis_off()
super(ImageSonogram, self).__init__(**kwargs)
def update_plot(self, *args):
self.box.remove_widget(self.bra_plot)
self.remove_widget(self.box)
box = BoxLayout()
box.size_hint = 0.95, 0.7
box.pos_hint = {"x": 0.025, "top": 0.9}
box.add_widget(FigureCanvasKivyAgg(plt.gcf()))
self.add_widget(box)
for i in (mapindex):
# f = np.random.rand(1,1)*800
# colors[i] = colorbank[math.floor(f/100)]
if (self.stopTestCalled):
break
Arduino.write(bytes(str(i), 'utf-8'))
Arduino.write(b"\n")
while (not Arduino.inWaiting()
): # continues if the arduino replies
pass
x = Arduino.readline() # maybe switch to Arduino.read(),
y = x.decode(
) # if readline() is switched to read() this may not be necessary anymore
z = y.rstrip(
) # if readline() is switched to read() this may not be necessary anymore
f = math.floor(float(z))
#print(f)
if f > threshold:
checklist[i] = 1
colors[i] = colorbank[math.floor(f / 100)]
pmap.set_color(colors)
def plot(self):
try:
value = self.pi_values[-1]
except BaseException:
value = 0
title = "${0}$ = {1:10.8f}".format(r"\pi", value)
title = "${0}$ = {1:10.8f}\n${0}$ = {2:10.8f}".format(
r"\pi", math.pi, value)
plt.close()
fig, ax = plt.subplots()
ax.axhline(y=math.pi, color='black', alpha=0.5)
ax.set_xlabel("Number of trials", fontsize=14)
ax.set_ylabel(r"Computed ${\pi}$ value", fontsize=14)
ax.set_title(title, size=14)
# if abs(value/math.pi) < 1.0:
# ax.set_ylim(2.5, 3.5)
# else:
# ax.relim()
# ax.autoscale()
ax.plot(self.pi_values, color='r')
self.clear_widgets()
self.add_widget(FigureCanvasKivyAgg(plt.gcf()))
def latex_image(latex_str):
fig, ax = pyplot.subplots()
ax.axis('off')
ax.text(.5,
.5,
latex_str,
size=20,
horizontalalignment='center',
verticalalignment='center',
bbox={})
return FigureCanvasKivyAgg(fig)
def on_enter(self, *args):
fig, bx = plt.subplots()
fig.patch.set_facecolor('#ff8a96')
bx.imshow(im)
results = bx.scatter(xs, ys, s=90, c=resultsc)
box = BoxLayout()
box.size_hint = 0.95, 0.7
box.pos_hint = {"x": 0.025, "top": 0.9}
finished_plot = FigureCanvasKivyAgg(plt.gcf()) # gets current figure
box.add_widget(finished_plot)
self.add_widget(box, 10)
def __init__(self, **kwargs):
self.top_image = ObjectProperty(None)
self.mark_boolean = False
self.click = 0
self.direction_to_int = {'left': -1, 'right': 1}
# bottom_image = ObjectProperty(None)
self.register_event_type('on_check_boolean')
self.fig2 = matplotlib.figure.Figure()
# self.fig2, self.ax2 = plt.subplots()
self.plot_binary_canvas = FigureCanvasKivyAgg(self.fig2)
self.fig2.canvas.mpl_connect('key_press_event', self.move_mark)
# self.ax2 = self.fig2.add_subplot(111)
self.ax2 = self.fig2.add_axes([0., 0., 1., 1.])
# self.ax2 = plt.Axes(self.fig2, [0., 0., 1., 1.])
self.ax2.set_axis_off()
# self.fig2.add_axes(self.ax2)
# all songs and files
self.file_names = None
self.files = None
self.output_path = None
# attributes for song that is being worked on
self.i = None
self.song = None
self.current_file = None
self.syllable_onsets = None
self.syllable_offsets = None
# place holders for plots
self.plot_binary = None
self.trans = None
self.lines_on = None
self.lines_off = None
# for plotting
self.index = None
self.mark = None
self.graph_location = None
super(ControlPanel, self).__init__(**kwargs)
def plot(self):
plt.close()
self.figure, self.ax = plt.subplots()
self.ax.set_aspect('equal')
self.ax.set_xlim((-1, 1))
self.ax.set_ylim((-1, 1))
square = plt.Rectangle((-1, -1), 2, 2, fc='w', alpha=0.0, color='w')
circle = plt.Circle((0, 0), 1, color='r', alpha=0.5)
self.ax.add_patch(square)
self.ax.add_patch(circle)
#self.ax.grid(color='black', alpha=0.2, linestyle='-', linewidth=1)
major_ticks = np.arange(-1, 1.0001, 0.25)
minor_ticks = np.arange(-1, 1.0001, 0.25 * 0.5)
self.ax.set_xticks(major_ticks)
self.ax.set_xticks(minor_ticks, minor=True)
self.ax.set_yticks(major_ticks)
self.ax.set_yticks(minor_ticks, minor=True)
self.ax.grid(which='both')
# or if you want differnet settings for the grids:
self.ax.grid(which='minor', alpha=0.35)
self.ax.grid(which='major', alpha=0.5)
ticks_x = ticker.FuncFormatter(lambda x, pos: '{0:g}'.format(x * 100))
self.ax.xaxis.set_major_formatter(ticks_x)
ticks_y = ticker.FuncFormatter(lambda x, pos: '{0:g}'.format(x * 100))
self.ax.yaxis.set_major_formatter(ticks_y)
self.ax.scatter([i[0] for i in self.points],
[i[1] for i in self.points],
marker='.',
color='r')
if self.points:
self.ax.scatter(self.points[-1][0],
self.points[-1][1],
marker='.',
color='b')
self.clear_widgets()
self.add_widget(FigureCanvasKivyAgg(self.figure))
def build(self):
"""
some initialization
Args:
rect: a dummy rectangle, whose width and height will be reset trigger by user event
x0, y0: mouse click location
x1, y1: mouse release location
canvas: FigureCanvasKivyAgg object. Note that I'm using this back end right now
as the FigureCanvas backend has bug with plt.show()
selectors: store user-drawn rectangle data
offsetx: translation of origin on x direction
offsety: translation of origin on y direction
"""
self.selectors = []
img = mpimg.imread(sys.argv[1])
self.fig, self.ax = plt.subplots(1)
plt.imshow(img)
width, height = self.fig.canvas.get_width_height()
pxorigin = self.ax.transData.transform([(0, 0)])
self.offsetx = pxorigin[0][0]
self.offsety = height - pxorigin[0][1]
print('offsetx, offsety', self.offsetx, self.offsety)
self.rect = Rectangle((0, 0), 1, 1)
self.rect.set_fill(False)
self.rect.set_edgecolor('b')
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.canvas = FigureCanvasKivyAgg(
plt.gcf()) # get the current reference of plt
box = BoxLayout()
self.ax.add_patch(self.rect) # attach our rectangle to axis
self.canvas.mpl_connect("button_press_event", self.on_press)
self.canvas.mpl_connect("button_release_event", self.on_release)
box.add_widget(self.canvas)
return box
def show(self):
if self.ids.entry.text == None: return
if len(self.ids.graph.children) != 0: self.ids.graph.clear_widgets()
con = sqlite3.connect('pos_database.db')
df = pd.read_sql_query(
"SELECT productData.productID, quantity from salesData INNER JOIN productData ON \
productData.productID=salesData.productID",
con)
df = df.groupby('ProductID', as_index=False).sum()
df = df.sort_values(by='quantity', ascending=False)
df = df.head(int(self.ids.entry.text))
df = df.astype({'ProductID': 'str'})
plt.bar(df['ProductID'], df['quantity'])
plt.xlabel('products')
plt.ylabel('sales count')
plt.title(self.ids.entry.text + 'most soled products')
self.ids.graph.add_widget(FigureCanvasKivyAgg(plt.gcf()))
def build(self):
box = BoxLayout(orientation="horizontal")
#df = pandas.read_csv(os.path.join(pandas.io.tests.__path__[0], "data", "iris.csv"))
df = pandas.read_csv(
"https://raw.githubusercontent.com/uiuc-cse/data-fa14/gh-pages/data/iris.csv"
)
print df
seaborn.set_palette('bright')
seaborn.set_style('whitegrid')
seaborn.pairplot(data=df,
hue="Name",
kind="scatter",
diag_kind="hist",
x_vars=("SepalLength", "SepalWidth"),
y_vars=("PetalLength", "PetalWidth"))
box.add_widget(FigureCanvasKivyAgg(plt.gcf()))
box.add_widget(FigureCanvasKivy(plt.gcf()))
return box
def update_plot_demo(self, *args):
print("UPDATEPLOT CALLED")
self.box.remove_widget(self.bra_plot)
self.remove_widget(self.box)
box = BoxLayout()
box.size_hint = 0.95, 0.7
box.pos_hint = {"x": 0.025, "top": 0.9}
box.add_widget(FigureCanvasKivyAgg(plt.gcf()))
self.add_widget(box)
j = 0
for i in (mapindex):
# f = np.random.rand(1,1)*800
# colors[i] = colorbank[math.floor(f/100)]
if (self.stopTestCalled):
break
f = 800
if f > threshold:
checklist[i] = 1
colors = ['gainsboro'] * 72
colors[i] = colorbank[math.floor(f / 100)]
j += 1
pmap.set_color(colors)
class SyllSimThresholdPage(Screen):
user_noise_thresh = StringProperty()
user_syll_sim_thresh = StringProperty()
def __init__(self, *args, **kwargs):
self.fig5, self.ax5 = plt.subplots()
self.plot_syllsim_canvas = FigureCanvasKivyAgg(self.fig5)
self.ax5 = plt.Axes(self.fig5, [0., 0., 1., 1.])
self.ax5.set_axis_off()
self.fig5.add_axes(self.ax5)
super(SyllSimThresholdPage, self).__init__(*args, **kwargs)
self.log = get_logger(__name__)
def setup(self):
self.syllsim_thresholds = []
self.i = 0
self.files = self.parent.files
self.record = True
self.next()
def next(self):
# if not first entering the app, record the threshold
if self.i > 0 and self.record:
self.syllsim_thresholds.append(float(self.ids.user_syllsim.text))
# otherwise it is the first time, so reset syllable similarity threshold to the default
else:
self.ids.user_syllsim.text = self.user_syll_sim_thresh
# if it is the last song go to syllable similarity threshold
# summary page, otherwise process song'
if self.i == len(self.files):
self.manager.current = 'syllsim_summary_page'
else:
errors = ''
f_name = os.path.join(self.parent.directory, self.files[self.i])
try:
self.update(f_name)
self.i += 1
self.record = True
except Exception as e:
self.ids.syllsim_graph.clear_widgets()
self.ids.similarity.text = ''
self.ids.song_syntax.text = ''
errors += "WARNING : Skipped file {0}\n{1}\n".format(f_name, e)
# raise e
self.log.info(errors)
self.record = False
all_noise = ErrorInSyllSimThresholdWidgetPopup(self, errors)
all_noise.open()
self.i += 1
self.log.info(self.i)
def update(self, f_name):
self.ids.user_syllsim.text = self.ids.user_syllsim.text
ons, offs, thresh, ms, htz = analyze.load_bout_data(f_name)
self.onsets = ons
self.offsets = offs
self.syll_dur = self.offsets - self.onsets
self.threshold_sonogram = thresh
# zero anything before first onset or after last offset
# (not offset row is already zeros, so okay to include)
# this will take care of any noise before or after the song
threshold_sonogram_crop = self.threshold_sonogram.copy()
threshold_sonogram_crop[:, 0:self.onsets[0]] = 0
threshold_sonogram_crop[:, self.offsets[-1]:-1] = 0
# ^connectivity 1=4 or 2=8(include diagonals)
self.labeled_sonogram = label(threshold_sonogram_crop, connectivity=1)
corrected_sonogram = remove_small_objects(
self.labeled_sonogram,
min_size=float(self.user_noise_thresh) +
1, # add one to make =< threshold
connectivity=1)
self.son_corr, son_corr_bin = analyze.get_sonogram_correlation(
sonogram=corrected_sonogram,
onsets=self.onsets,
offsets=self.offsets,
syll_duration=self.syll_dur,
corr_thresh=float(self.ids.user_syllsim.text))
self.init_plot()
self.new_thresh()
def init_plot(self):
# prepare graph and make plot take up the entire space
rows, cols = np.shape(self.threshold_sonogram)
data = np.zeros((rows, cols))
self.ax5.clear()
self.ax5 = plt.Axes(self.fig5, [0., 0., 1., 1.])
self.ax5.set_axis_off()
self.fig5.add_axes(self.ax5)
# plot placeholder data
cmap = plt.cm.tab20b
cmap.set_under(color='black')
cmap.set_over(color='gray')
cmap.set_bad(color='white')
self.plot_syllsim = self.ax5.imshow(data + 3,
extent=[0, cols, 0, rows],
aspect='auto',
cmap=cmap,
vmin=0,
vmax=1000.)
self.trans = tx.blended_transform_factory(self.ax5.transData,
self.ax5.transAxes)
self.lines_on, = self.ax5.plot(np.repeat(self.onsets, 3),
np.tile([0, .75, np.nan],
len(self.onsets)),
linewidth=0.75,
color='g',
transform=self.trans)
self.lines_off, = self.ax5.plot(np.repeat(self.offsets, 3),
np.tile([0, .90, np.nan],
len(self.offsets)),
linewidth=0.75,
color='g',
transform=self.trans)
self.ids.syllsim_graph.clear_widgets()
self.ids.syllsim_graph.add_widget(self.plot_syllsim_canvas)
def new_thresh(self):
# get syllable correlations for entire sonogram
# create new binary matrix with new threshold
son_corr_bin = np.zeros(self.son_corr.shape)
son_corr_bin[self.son_corr >= float(self.ids.user_syllsim.text)] = 1
# get syllable pattern
syll_pattern = analyze.find_syllable_pattern(son_corr_bin)
display_pattern = ", ".join(str(x) for x in syll_pattern)
self.ids.song_syntax.text = 'Song Syntax: {}'.format(display_pattern)
syll_stereotypy, syll_stereotypy_max, syll_stereotypy_min = \
analyze.calc_syllable_stereotypy(self.son_corr, syll_pattern)
# Formatting for summary
spacing1 = '{:<12}{:<8}{:<8}{:<8}\n'
spacing2 = '{:<16}{:<8}{:<8}{:<8}\n'
spacing3 = '{:<15}{:<8}{:<8}{:<8}\n'
stereotypy_text = spacing1.format('Syllable', 'Avg', 'Min', 'Max')
for idx in range(len(syll_stereotypy)):
if not np.isnan(syll_stereotypy[idx]):
if idx >= 10:
spacing = spacing3
else:
spacing = spacing2
stereotypy_text += spacing.format(
str(idx),
round(syll_stereotypy[idx], 1),
round(syll_stereotypy_min[idx], 1),
round(syll_stereotypy_max[idx], 1),
)
if stereotypy_text == spacing1.format('Syllable', 'Avg', 'Min', 'Max'):
stereotypy_text += 'No Repeated Syllables'
self.ids.similarity.text = stereotypy_text
syll_labeled = self.threshold_sonogram.copy()
# making background color black (negative number will)
syll_labeled[syll_labeled == 0] = -10
# need to find the max number to define the image
u, indices = np.unique(syll_pattern, return_inverse=True)
num_unique = len(u)
# set clip so that anything over will be colored grey
self.plot_syllsim.set_clim(0, num_unique)
grey = num_unique + 1
# color syllable patterns
for on, off, syll in zip(self.onsets, self.offsets, indices):
syll_labeled[:, on:off][syll_labeled[:, on:off] == 1] = syll
# color noise white, this value will be set to nan. But it will be
# overwritten in the noise below
# we are using a number larger than grey.
to_nan = grey + 1
for region in regionprops(self.labeled_sonogram):
if region.area <= int(self.user_noise_thresh):
syll_labeled[self.labeled_sonogram == region.label] = to_nan
# color signal before and after song to grey
on = self.onsets[0]
off = self.offsets[-1]
syll_labeled[:, 0:on][syll_labeled[:, 0:on] == 1] = grey
syll_labeled[:, off:-1][syll_labeled[:, off:-1] == 1] = grey
# color signal between syllables grey
for off, on in zip(self.offsets[:-1], self.onsets[1:]):
syll_labeled[:, off:on][syll_labeled[:, off:on] >= 0] = grey
# little hack to make noise regions white only if inside onset/offsets
syll_labeled[syll_labeled == to_nan] = np.nan
# update image in widget
# plot the actual data now
self.plot_syllsim.set_data(syll_labeled)
self.plot_syllsim_canvas.draw()
def syllsim_thresh_instructions(self):
syllsim_popup = SyllSimThreshInstructionsPopup()
syllsim_popup.open()
def Update(self):
#self.box.remove_widget(FigureCanvasKivyAgg(self.fig1))
plt.cla()
self.bar.clear_widgets()
self.fig1 = NinthWindow.add_plot(self, 1000)
self.bar.add_widget(FigureCanvasKivyAgg(self.fig1))
def on_pre_enter(self, *args):
self.fig1 = NinthWindow.add_plot(self, 1000)
self.bar.add_widget(FigureCanvasKivyAgg(self.fig1))
def fullPrediction(self):
st = np.int64(self.startTime.text)
et = np.int64(self.endTime.text)
my_day = np.int64(self.day.text)
# d = self.direction.text
if self.t1.active:
name = 'GRU'
if self.t2.active:
name = 'LSTM'
if self.t3.active:
name = 'SAES'
if self.t4.active:
name='RNN'
if self.t5.active:
name='BI'
predictionClass = CleanPrediction()
counts = {}
finalPathMape={}
pathData = Map.generatePaths(self.startScats.text, self.endScats.text)
shortestMap = pathData[1]
allPaths = pathData[2]
allDistances = np.int64(pathData[3])
# self.ids.mapFigure.remove_widget(FigureCanvasKivyAgg(self.plt.gcf()))
self.ids.mapFigure.add_widget(FigureCanvasKivyAgg(shortestMap.gcf()))
newPrediction = 0
lowMape = 0
highMape = 0
firstRun = True
i=0
j=0
bestTime = 0
currentPath = []
# For each path in possible paths
print(str(allPaths))
for path in allPaths:
# Get prediction for each intersection
mape={}
print(str(currentPath))
currentPath = path
j=0
for scats in path:
# print("Loop: " + str(j))
# We need to make sure we're not getting the direction of the final point in the path.
listLenth = len(path)
if j == (listLenth -1):
d = 'N'
else:
d = Map.cardinality(path[j], path[(j+1)])
newPrediction = predictionClass.predict(int(scats), st, et, my_day, d,name)
currentMape = predictionClass.metrics[0]
mape[str(scats)]=currentMape
# Occasionally there may be no data for our mape, this takes the min and max values of other predictions so we can use them to make an educated guess just in case
if lowMape == 0:
lowMape = currentMape
elif currentMape < lowMape:
lowMape = currentMape
if highMape == 0:
highMape = currentMape
elif currentMape > highMape:
highMape = currentMape
counts[str(scats)] = newPrediction
j += 1
# j=0
print("Mape: " + str(mape))
distance = allDistances[i]
print("Current path: " + str(path) + " Current distance: " + str(distance))
# Calculate travel time based on distance + traffic
currentTime = int(self.calculateTravelTime(counts, path, distance))
if firstRun:
bestTime = currentTime
bestPath = currentPath
finalPathMape = mape
firstRun = False
elif currentTime < bestTime:
bestTime = currentTime
finalPathMape = mape
bestPath = currentPath
i += 1
print("Best Path: " + str(bestPath) + " Best Time: " + str(bestTime))
bestTime = round((bestTime / 60), 2)
MeanAverageLen = len(finalPathMape)
print("Final Path Map Length: " +str(len(finalPathMape)))
print("Final Path Mape Values: " + str(finalPathMape.values()))
if MeanAverageLen == 0:
MeanAverageLen = 10.2
for intersection in bestPath:
finalPathMape[intersection] = random.uniform(lowMape,highMape)
self.bestRoute.text = "Via intersections: " + str(bestPath)+"\n\n" +"Travel time: "+ str(bestTime) + " minutes"+"\n\n MAPE for each Intersection: "+str(finalPathMape)+"\n\n Average MAPE: "+str(sum(finalPathMape.values())/len(finalPathMape))
def run(self):
self.ids.mapFigure.add_widget(FigureCanvasKivyAgg(self.plt.gcf()))
class ActiveTestScreen(Screen):
stopTestCalled = False
box = BoxLayout()
bra_plot = FigureCanvasKivyAgg(plt.gcf()) # gets current figure
def on_enter(self, *args):
self.stopTestCalled = False
self.box.size_hint = 0.95, 0.7
self.box.pos_hint = {"x": 0.025, "top": 0.9}
self.box.add_widget(self.bra_plot)
self.add_widget(self.box, 10)
for j in range(0, 20):
for i in (mapindex):
f = np.random.rand(1, 1) * 100
colors[i] = colorbank[math.floor(f / 100)]
#plt.pause(0.001)
#time.sleep(1)
pmap.set_color(colors)
Clock.schedule_interval(self.update_plot,
0.7) # calls update plot every 2 seconds
# Ideally here we will have the Arduino.read() and use that number to set colors[i]
def update_plot(self, *args):
self.box.remove_widget(self.bra_plot)
self.remove_widget(self.box)
box = BoxLayout()
box.size_hint = 0.95, 0.7
box.pos_hint = {"x": 0.025, "top": 0.9}
box.add_widget(FigureCanvasKivyAgg(plt.gcf()))
self.add_widget(box)
for i in (mapindex):
# f = np.random.rand(1,1)*800
# colors[i] = colorbank[math.floor(f/100)]
if (self.stopTestCalled):
break
Arduino.write(bytes(str(i), 'utf-8'))
Arduino.write(b"\n")
while (not Arduino.inWaiting()
): # continues if the arduino replies
pass
x = Arduino.readline() # maybe switch to Arduino.read(),
y = x.decode(
) # if readline() is switched to read() this may not be necessary anymore
z = y.rstrip(
) # if readline() is switched to read() this may not be necessary anymore
f = math.floor(float(z))
#print(f)
if f > threshold:
checklist[i] = 1
colors[i] = colorbank[math.floor(f / 100)]
pmap.set_color(colors)
#colors[i] = 'gainsboro'
def update_plot_demo(self, *args):
print("UPDATEPLOT CALLED")
self.box.remove_widget(self.bra_plot)
self.remove_widget(self.box)
box = BoxLayout()
box.size_hint = 0.95, 0.7
box.pos_hint = {"x": 0.025, "top": 0.9}
box.add_widget(FigureCanvasKivyAgg(plt.gcf()))
self.add_widget(box)
j = 0
for i in (mapindex):
# f = np.random.rand(1,1)*800
# colors[i] = colorbank[math.floor(f/100)]
if (self.stopTestCalled):
break
f = 800
if f > threshold:
checklist[i] = 1
colors = ['gainsboro'] * 72
colors[i] = colorbank[math.floor(f / 100)]
j += 1
pmap.set_color(colors)
def stopTest(self):
self.stopTestCalled = True
Arduino.write(b's')
for i in (mapindex):
if checklist[i] == 1:
resultsc[i] = 'crimson'
if checklist[i] == 0:
resultsc[i] = 'gainsboro'
pass
def __init__(self, *args, **kwargs):
self.fig4, self.ax4 = plt.subplots()
self.noise_hist_canvas = FigureCanvasKivyAgg(self.fig4)
super(NoiseSummaryPage, self).__init__(*args, **kwargs)
class NoiseThresholdPage(Screen):
user_noise_thresh = StringProperty()
def __init__(self, *args, **kwargs):
self.fig3, self.ax3 = plt.subplots()
self.plot_noise_canvas = FigureCanvasKivyAgg(self.fig3)
self.ax3 = plt.Axes(self.fig3, [0., 0., 1., 1.])
self.ax3.set_axis_off()
self.fig3.add_axes(self.ax3)
super(NoiseThresholdPage, self).__init__(*args, **kwargs)
def setup(self):
self.noise_thresholds = []
self.i = 0
# self.files = [os.path.basename(i) for i in glob.glob(self.parent.directory + '*.gzip')]
self.files = self.parent.files
self.next()
def next(self):
# if not first entering the app, record the threshold
if self.i > 0:
self.noise_thresholds.append(int(self.ids.user_noise_size.text))
# otherwise it is the first time,
# so reset noise size threshold to the default
else:
self.ids.user_noise_size.text = self.user_noise_thresh
# if it is the last song go to noise threshold summary page,
# otherwise process song
if self.i == len(self.files):
self.manager.current = 'noise_summary_page'
else:
self.ids.user_noise_size.text = self.ids.user_noise_size.text
ons, offs, thresh, ms, htz = analyze.load_bout_data(
os.path.join(self.parent.directory, self.files[self.i]))
self.onsets = ons
self.offsets = offs
self.threshold_sonogram = thresh
[self.rows, self.cols] = np.shape(self.threshold_sonogram)
# prepare graph and make plot take up the entire space
data = np.zeros((self.rows, self.cols))
self.ax3.clear()
self.ax3 = plt.Axes(self.fig3, [0., 0., 1., 1.])
self.ax3.set_axis_off()
self.fig3.add_axes(self.ax3)
cmap = plt.cm.prism
cmap.set_under(color='black')
cmap.set_bad(color='white')
self.plot_noise = self.ax3.imshow(
data,
extent=[0, self.cols, 0, self.rows],
aspect='auto',
cmap=cmap,
norm=matplotlib.colors.LogNorm(),
vmin=3.01)
self.ids.noise_graph.clear_widgets()
self.ids.noise_graph.add_widget(self.plot_noise_canvas)
self.new_thresh()
self.i += 1
def new_thresh(self):
# find notes and label based on connectivity
# zero anything before first onset or after last offset
# (not offset row is already zeros, so okay to include)
# this will take care of any noise before or after the song
# before labeling the notes
threshold_sonogram_crop = self.threshold_sonogram.copy()
# Make onsets and offsets and offsets black (hidden)
threshold_sonogram_crop[:, 0:self.onsets[0]] = 0
threshold_sonogram_crop[:, self.offsets[-1]:-1] = 0
for off, on in zip(self.offsets[:-1], self.onsets[1:]):
threshold_sonogram_crop[:, off:on][
threshold_sonogram_crop[:, off:on] >= 0] = 0
# ^connectivity 1=4 or 2=8(include diagonals)
labeled_sonogram = label(threshold_sonogram_crop, connectivity=1)
# change label of all notes with size > threshold to be the same
# and all < to be the same
for region in regionprops(labeled_sonogram):
if region.area > int(self.ids.user_noise_size.text):
labeled_sonogram[labeled_sonogram ==
region.label] = region.area
else:
labeled_sonogram[labeled_sonogram == region.label] = 1
# mask noise white
labeled_sonogram = np.ma.masked_where(labeled_sonogram == 1,
labeled_sonogram)
# update image in widget
self.plot_noise.set_data(labeled_sonogram + 3)
# plot the actual data now
self.plot_noise_canvas.draw()
def noise_thresh_instructions(self):
noise_popup = NoiseThreshInstructionsPopup()
noise_popup.open()
class ControlPanel(Screen):
# these connect the landing page user input to the control panel
find_gzips = BooleanProperty()
user_signal_thresh = StringProperty()
user_min_silence = StringProperty()
user_min_syllable = StringProperty()
def __init__(self, **kwargs):
self.top_image = ObjectProperty(None)
self.mark_boolean = False
self.click = 0
self.direction_to_int = {'left': -1, 'right': 1}
# bottom_image = ObjectProperty(None)
self.register_event_type('on_check_boolean')
self.fig2 = matplotlib.figure.Figure()
# self.fig2, self.ax2 = plt.subplots()
self.plot_binary_canvas = FigureCanvasKivyAgg(self.fig2)
self.fig2.canvas.mpl_connect('key_press_event', self.move_mark)
# self.ax2 = self.fig2.add_subplot(111)
self.ax2 = self.fig2.add_axes([0., 0., 1., 1.])
# self.ax2 = plt.Axes(self.fig2, [0., 0., 1., 1.])
self.ax2.set_axis_off()
# self.fig2.add_axes(self.ax2)
# all songs and files
self.file_names = None
self.files = None
self.output_path = None
# attributes for song that is being worked on
self.i = None
self.song = None
self.current_file = None
self.syllable_onsets = None
self.syllable_offsets = None
# place holders for plots
self.plot_binary = None
self.trans = None
self.lines_on = None
self.lines_off = None
# for plotting
self.index = None
self.mark = None
self.graph_location = None
super(ControlPanel, self).__init__(**kwargs)
def on_check_boolean(self):
if self.click >= 2:
marks_popup = popups.FinishMarksPopup(self)
marks_popup.open()
def on_touch_down(self, touch):
super(ControlPanel, self).on_touch_down(touch)
if self.mark_boolean is True:
self.click += 1
self.dispatch('on_check_boolean')
ControlPanel.disabled = True
return True
def reset_panel(self):
self.mark_boolean = False
self.click = 0
ControlPanel.disabled = False
def move_mark(self, event, move_interval=7):
if self.ids.add.state == 'down': # adding
if event.key in self.direction_to_int and \
(25 <= self.graph_location < self.song.cols - 25):
self.graph_location += self.direction_to_int[
event.key] * move_interval
self.update_mark(self.graph_location)
elif event.key == 'enter':
if self.ids.syllable_beginning.state == 'down':
self.add_onsets()
else:
self.add_offsets()
self.mark_boolean = False
self.click = 0
ControlPanel.disabled = False
elif event.key == 'x':
self.cancel_mark()
# deleting
elif self.ids.delete.state == 'down':
if event.key in self.direction_to_int:
self.index += self.direction_to_int[event.key]
# onsets
if self.ids.syllable_beginning.state == 'down':
if self.index < 0:
self.index = len(self.syllable_onsets) - 1
if self.index >= len(self.syllable_onsets):
self.index = 0
self.update_mark(self.syllable_onsets[self.index])
# offsets
else:
if self.index < 0:
self.index = len(self.syllable_offsets) - 1
if self.index >= len(self.syllable_offsets):
self.index = 0
self.update_mark(self.syllable_offsets[self.index])
elif event.key == 'enter':
if self.ids.syllable_beginning.state == 'down':
self.delete_onsets()
else:
self.delete_offsets()
self.mark_boolean = False
self.click = 0
ControlPanel.disabled = False
elif event.key == 'x':
self.cancel_mark()
def enter_mark(self):
if self.ids.add.state == 'down': # adding
if self.ids.syllable_beginning.state == 'down':
self.add_onsets()
else:
self.add_offsets()
elif self.ids.delete.state == 'down': # deleting
if self.ids.syllable_beginning.state == 'down':
self.delete_onsets()
else:
self.delete_offsets()
self.mark_boolean = False
self.click = 0
ControlPanel.disabled = False
def cancel_mark(self):
self.mark.remove()
self.image_syllable_marks()
self.mark_boolean = False
self.click = 0
ControlPanel.disabled = False
def update_mark(self, new_mark):
self.mark.set_xdata(new_mark)
self.plot_binary_canvas.draw()
def add_mark(self, touchx, touchy):
self.mark_boolean = True
conversion = self.song.sonogram.shape[1] / self.ids.graph_binary.size[0]
self.graph_location = math.floor(
(touchx - self.ids.graph_binary.pos[0]) * conversion)
ymax = 0.75 if self.ids.syllable_beginning.state == 'down' else 0.90
# graph as another color/group of lines
self.mark = self.ax2.axvline(self.graph_location,
ymax=ymax,
color='m',
linewidth=0.75)
self.plot_binary_canvas.draw()
def add_onsets(self):
# https://stackoverflow.com/questions/29408661/add-elements-into-a
# -sorted-array-in-ascending-order
if self.graph_location is None:
return
else:
self.syllable_onsets = np.insert(
self.syllable_onsets,
np.searchsorted(self.syllable_onsets, self.graph_location),
self.graph_location)
self.mark.remove()
self.image_syllable_marks()
self.graph_location = None
def add_offsets(self):
if self.graph_location is None:
return
else:
self.syllable_offsets = np.insert(
self.syllable_offsets,
np.searchsorted(self.syllable_offsets, self.graph_location),
self.graph_location)
self.mark.remove()
self.image_syllable_marks()
self.graph_location = None
def delete_mark(self, touchx, touchy):
self.mark_boolean = True
conversion = self.song.sonogram.shape[1] / \
self.ids.graph_binary.size[0]
self.graph_location = math.floor(
(touchx - self.ids.graph_binary.pos[0]) * conversion)
if self.ids.syllable_beginning.state == 'down':
ymax = 0.75
# find nearest onset
self.index = self.take_closest(self.syllable_onsets,
self.graph_location)
location = self.syllable_onsets[self.index]
else:
ymax = 0.90
# find nearest offset
self.index = self.take_closest(self.syllable_offsets,
self.graph_location)
location = self.syllable_offsets[self.index]
self.mark = self.ax2.axvline(location,
ymax=ymax,
color='m',
linewidth=0.75)
self.plot_binary_canvas.draw()
def delete_onsets(self):
if self.index is None:
return
else:
onsets_list = list(self.syllable_onsets)
onsets_list.remove(self.syllable_onsets[self.index])
self.syllable_onsets = np.array(onsets_list)
self.mark.remove()
self.image_syllable_marks()
self.index = None
def delete_offsets(self):
if self.index is None:
return
else:
offsets_list = list(self.syllable_offsets)
offsets_list.remove(self.syllable_offsets[self.index])
self.syllable_offsets = np.array(offsets_list)
self.mark.remove()
self.image_syllable_marks()
self.index = None
# called in kv just before entering control panel screen (on_pre_enter)
def setup(self):
Logger.info("Setting up")
# storage for parameters
self.save_parameters_all = {}
self.save_syllables_all = {}
self.save_tossed = {}
self.save_conversions_all = {}
self.i = 0
self.files = self.parent.files
self.file_names = self.parent.file_names
# these are the dictionaries that are added to with each song
self.output_path = os.path.join(
self.parent.directory,
"SegSyllsOutput_{}".format(time.strftime("%Y%m%d_T%H%M%S")))
if not os.path.isdir(self.output_path):
os.makedirs(self.output_path)
self.next()
def update_panel_text(self):
# this updates the text or slider limits on the control panel screen
self.ids.slider_threshold_label.text = '{}%'.format(
self.song.percent_keep)
# have to round these because of the conversion
self.ids.slider_min_silence_label.text = "{} ms".format(
round(self.song.min_silence * self.song.ms_pix, 1))
self.ids.slider_min_syllable_label.text = '{} ms'.format(
round(self.song.min_syllable * self.song.ms_pix, 1))
# want max to be 50ms
self.ids.slider_min_silence.max = 50 / self.song.ms_pix
# want max to be 350ms
self.ids.slider_min_syllable.max = 350 / self.song.ms_pix
self.ids.normalize_amp.state = self.song.normalized
self.ids.slider_threshold.value = self.song.percent_keep
self.ids.slider_min_silence.value = self.song.min_silence
self.ids.slider_min_syllable.value = self.song.min_syllable
self.ids.syllable_beginning.state = 'down'
self.ids.syllable_ending.state = 'normal'
self.ids.add.state = 'normal'
self.ids.delete.state = 'normal'
self.ids.slider_frequency_filter.value1 = self.song.filter_boundary[0]
self.ids.slider_frequency_filter.value2 = self.song.filter_boundary[1]
self.ids.slider_frequency_filter.min = 0
self.ids.slider_frequency_filter.max = self.song.rows
self.ids.range_slider_crop.value1 = self.song.bout_range[0]
self.ids.range_slider_crop.value2 = self.song.bout_range[1]
self.ids.range_slider_crop.min = 0
self.ids.range_slider_crop.max = self.song.cols
def reset_parameters(self):
self.song.reset_params(user_signal_thresh=self.user_signal_thresh,
user_min_silence=self.user_min_silence,
user_min_syllable=self.user_min_syllable,
id_min_sil=self.ids.slider_min_silence.min,
id_min_syl=self.ids.slider_min_syllable.min)
self.ids.normalize_amp.state = self.song.normalized
self.update_panel_text()
self._update()
def next(self):
self.current_file = self.files[self.i]
# increment i so next file will be opened on submit/toss
self.i += 1
# get initial data
Logger.info("Loading file {}".format(self.current_file))
f_path = os.path.join(self.parent.directory, self.current_file)
f_size = os.path.getsize(f_path)
# 1 000 000 bytes is 1 megabyte
max_file_size = 3000000
if f_size > max_file_size:
Logger.info("Large song")
popups.LargeFilePopup(self, self.current_file,
str(round(f_size / 1000000, 1))).open()
else:
self.process()
def toss(self):
Logger.info("Tossing {}".format(self.current_file))
# save file name to dictionary
self.save_tossed[self.i - 1] = {'FileName': self.current_file}
# remove from saved parameters and associated gzip if
# file ends up being tossed
if self.current_file in self.save_parameters_all:
del self.save_parameters_all[self.current_file]
del self.save_syllables_all[self.current_file]
del self.save_conversions_all[self.current_file]
os.remove(self.output_path + '/SegSyllsOutput_' +
self.file_names[self.i - 1] + '.gzip')
# write if last file otherwise go to next file
if self.i == len(self.files):
self.save_all_parameters()
else:
self.next()
def process(self):
self.song = Sonogram(wavfile=self.current_file,
directory=self.parent.directory,
find_gzips=self.find_gzips)
self.ids.freq_axis_middle.text = str(
round(
self.song.rows * self.song.hertzPerPixel / 2 / 1000)) + " kHz"
# reset default parameters for new song
# (will be used by update to graph the first attempt)
Logger.info("Setting default params")
self.song.set_song_params(user_signal_thresh=self.user_signal_thresh,
user_min_silence=self.user_min_silence,
user_min_syllable=self.user_min_syllable,
id_min_sil=self.ids.slider_min_silence.min,
id_min_syl=self.ids.slider_min_syllable.min)
prev_onsets = self.song.prev_onsets
prev_offsets = self.song.prev_offsets
# if the user goes back to previous song and then goes forward again,
# it will pull what they had already submitted (so the user does not
# lose progress)
if len(self.save_parameters_all) > 0:
if self.current_file in self.save_parameters_all:
params = self.save_parameters_all[self.current_file]
prev_onsets = np.asarray(
self.save_syllables_all[self.current_file]['Onsets'])
prev_offsets = np.asarray(
self.save_syllables_all[self.current_file]['Offsets'])
Logger.info("Updating params based on previous run")
self.song.update_by_params(params)
Logger.info("Updating panel text")
if self.song.params:
self.song.update_by_params(self.song.params)
self.update_panel_text()
# update the label stating the current file and the file number out
# of total number of files
# use self.i since you have not yet incremented
self.ids.current_file.text = "{}\nFile {} out of {}".format(
self.file_names[self.i - 1], self.i, len(self.files))
# initialize the matplotlib figures/axes (no data yet)
# ImageSonogram is its own class and top_image is an instance of it
# (defined in kv) - had trouble doing this for the bottom image
Logger.info("Creating initial sonogram")
self.top_image.image_sonogram_initial(self.song.rows, self.song.cols)
Logger.info("Creating initial binary")
self.image_binary_initial()
Logger.info("Updating")
# run update to load images for the first time for this file
self._update(prev_run_onsets=prev_onsets,
prev_run_offsets=prev_offsets)
Logger.info("Done with automation portion")
def update(self, filter_boundary, bout_range, percent_keep, min_silence,
min_syllable, normalized):
self.song.set_song_params(filter_boundary=filter_boundary,
bout_range=bout_range,
percent_keep=percent_keep,
min_silence=min_silence,
min_syllable=min_syllable,
normalized=normalized,
user_signal_thresh=self.user_signal_thresh,
user_min_silence=self.user_min_silence,
user_min_syllable=self.user_min_syllable,
id_min_sil=self.ids.slider_min_silence.min,
id_min_syl=self.ids.slider_min_syllable.min)
self.update_panel_text()
self._update()
def _update(self, prev_run_onsets=None, prev_run_offsets=None):
# must do this for image to update for some reason
sonogram = self.song.sonogram.copy()
# run HPF, scale based on average amplitude
# (increases low amplitude sections), and graph sonogram
freqfiltered_sonogram = seg.frequency_filter(self.song.filter_boundary,
sonogram)
# switch next two lines if you don't want amplitude scaled
if self.ids.normalize_amp.state == 'down':
scaled_sonogram = seg.normalize_amplitude(freqfiltered_sonogram)
else:
scaled_sonogram = freqfiltered_sonogram
# plot resultant sonogram in the top graph in control panel
self.top_image.image_sonogram(scaled_sonogram)
# apply threshold to signal
self.thresh_sonogram = seg.threshold_image(self.song.percent_keep,
scaled_sonogram)
# calculate onsets and offsets using binary (thresholded) image
onsets, offsets, silence_durations, sum_sonogram_scaled = \
seg.initialize_onsets_offsets(self.thresh_sonogram)
# update the automatic onsets and offsets based on the slider values
# for min silence and min syllable durations
syllable_onsets, syllable_offsets = seg.set_min_silence(
self.song.min_silence, onsets, offsets, silence_durations)
syllable_onsets, syllable_offsets = seg.set_min_syllable(
self.song.min_syllable, syllable_onsets, syllable_offsets)
# lastly, remove onsets and offsets that are outside of the crop
# values (on the time axis)
self.syllable_onsets, self.syllable_offsets = \
seg.crop(self.song.bout_range, syllable_onsets, syllable_offsets)
# check if the song has been run before (if gzip data was loaded)
if prev_run_onsets is None:
prev_run_onsets = np.empty([0])
prev_run_offsets = np.empty([0])
# change the onsets and offsets to those in gzip if gzip was loaded
if prev_run_onsets.size:
self.syllable_onsets = prev_run_onsets
self.syllable_offsets = prev_run_offsets
# plot resultant binary sonogram along with onset and offset lines
self.image_binary()
self.image_syllable_marks()
# self.bottom_image.image_syllable_marks(self.syllable_onsets,
# self.syllable_offsets)
def image_binary_initial(self):
# make plot take up the entire space
self.ax2.clear()
self.ax2.set_axis_off()
data = np.zeros((self.song.rows, self.song.cols))
# plot data
self.plot_binary = self.ax2.imshow(
np.log(data + 3),
cmap='hot',
extent=[0, self.song.cols, 0, self.song.rows],
aspect='auto')
self.trans = tx.blended_transform_factory(self.ax2.transData,
self.ax2.transAxes)
self.lines_on, = self.ax2.plot(np.repeat(0, 3),
np.tile([0, .75, np.nan], 1),
linewidth=0.75,
color='#2BB34B',
transform=self.trans)
self.lines_off, = self.ax2.plot(np.repeat(0, 3),
np.tile([0, .90, np.nan], 1),
linewidth=0.75,
color='#2BB34B',
transform=self.trans)
hundred_ms_in_pix = 100 / self.song.ms_pix
scalebar = AnchoredSizeBar(self.ax2.transData,
hundred_ms_in_pix,
'100 ms',
1,
pad=0.1,
color='white',
frameon=False,
size_vertical=2)
self.ax2.add_artist(scalebar)
self.ids.graph_binary.clear_widgets()
self.ids.graph_binary.add_widget(self.plot_binary_canvas)
def image_binary(self):
self.plot_binary.set_data(np.log(self.thresh_sonogram + 3))
self.plot_binary.autoscale()
def image_syllable_marks(self):
self.lines_on.set_xdata(np.repeat(self.syllable_onsets, 3))
self.lines_on.set_ydata(
np.tile([0, .75, np.nan], len(self.syllable_onsets)))
self.lines_off.set_xdata(np.repeat(self.syllable_offsets, 3))
self.lines_off.set_ydata(
np.tile([0, .90, np.nan], len(self.syllable_offsets)))
self.plot_binary_canvas.draw()
def back(self):
if self.i != 1:
self.i -= 2
self.next()
# called when the user hits submit
# before saving it checks for errors with onsets and offsets
def save(self):
Logger.info("Adding {} to save dictionaries".format(self.current_file))
# check if there are no syllable lines at all
if len(self.syllable_onsets) == 0 and len(self.syllable_offsets) == 0:
check_sylls = popups.CheckForSyllablesPopup()
check_sylls.open()
# if there are lines, check that there are equal number of ons and offs
elif len(self.syllable_onsets) != len(self.syllable_offsets):
check_length = popups.CheckLengthPopup()
check_length.len_onsets = str(len(self.syllable_onsets))
check_length.len_offsets = str(len(self.syllable_offsets))
check_length.open()
# check that you start with onset and end with offset
elif self.syllable_onsets[0] > self.syllable_offsets[0] or \
self.syllable_onsets[-1] > self.syllable_offsets[-1]:
check_beginning_end = popups.CheckBeginningEndPopup()
check_beginning_end.start_onset = not self.syllable_onsets[0] > \
self.syllable_offsets[0]
check_beginning_end.end_offset = not self.syllable_onsets[-1] > \
self.syllable_offsets[-1]
check_beginning_end.open()
# check that onsets and offsets alternate
else:
combined_onsets_offsets = list(self.syllable_onsets)
binary_list = [0] * len(self.syllable_onsets)
for i in range(len(self.syllable_offsets)):
insertion_pt = bisect_right(combined_onsets_offsets,
self.syllable_offsets[i])
binary_list.insert(insertion_pt, 1)
insort(combined_onsets_offsets, self.syllable_offsets[i])
if sum(binary_list[::2]) != 0 \
or sum(binary_list[1::2]) \
!= len(binary_list) / 2: # using python slices
check_order = popups.CheckOrderPopup()
check_order.order = binary_list
check_order.open()
# passed all checks, now info can be stored/written for the song
else:
Logger.info("Saving {}".format(self.current_file))
self.save_parameters_all[
self.current_file] = self.song.save_dict()
self.save_conversions_all[self.current_file] = {
'timeAxisConversion': self.song.ms_pix,
'freqAxisConversion': self.song.hertzPerPixel
}
self.save_syllables_all[self.current_file] = {
'Onsets': self.syllable_onsets.tolist(),
'Offsets': self.syllable_offsets.tolist()
}
filename_gzip = "{}/SegSyllsOutput_{}.gzip".format(
self.output_path, self.file_names[self.i - 1])
dictionaries = [
self.save_parameters_all[self.current_file],
self.save_syllables_all[self.current_file], {
'Sonogram': self.thresh_sonogram.tolist()
}, self.save_conversions_all[self.current_file]
]
save_gzip_pickle(filename_gzip, dictionaries)
# remove from tossed list if file ends up being submitted
if self.i - 1 in self.save_tossed:
del self.save_tossed[self.i - 1]
# write if last file otherwise go to next file
if self.i == len(self.files):
self.save_all_parameters()
else:
self.next()
def save_all_parameters(self):
Logger.info("Saving parameters")
if self.save_parameters_all:
df_parameters = pd.DataFrame.from_dict(self.save_parameters_all,
orient='index')
for r in df_parameters.BoutRange:
# adjust bout ranges so that they do not include the padding of the
# spectrogram (150 pixels each side), so user can convert
# correctly using human-readable files
r[:] = [x - 150 for x in r]
if r[0] < 0:
r[0] = 0
if r[-1] > (self.song.cols - 300):
r[-1] = (self.song.cols - 300)
df_parameters.index.name = 'FileName'
df_parameters.to_csv(os.path.join(
self.output_path, 'segmentedSyllables_parameters_all.txt'),
sep="\t")
df_syllables = pd.DataFrame.from_dict(self.save_syllables_all,
orient='index')
# adjust onsets and offests so that they do not include the padding of
# the spectrogram (150 pixels each side), so user can convert
# correctly using human-readable files
for on, off in zip(df_syllables.Onsets, df_syllables.Offsets):
on[:] = [x - 150 for x in on]
off[:] = [y - 150 for y in off]
df_syllables.index.name = 'FileName'
df_syllables.to_csv(os.path.join(
self.output_path, 'segmentedSyllables_syllables_all.txt'),
sep="\t")
df_conversions = pd.DataFrame.from_dict(self.save_conversions_all,
orient='index')
df_conversions.index.name = 'FileName'
df_conversions.to_csv(os.path.join(
self.output_path, 'segmentedSyllables_conversions_all.txt'),
sep="\t")
df_tossed = pd.DataFrame.from_dict(self.save_tossed,
orient='index')
df_tossed.to_csv(os.path.join(self.output_path,
'segmentedSyllables_tossed.txt'),
sep="\t",
index=False)
else:
df_tossed = pd.DataFrame.from_dict(self.save_tossed,
orient='index')
df_tossed.to_csv(os.path.join(self.output_path,
'segmentedSyllables_tossed.txt'),
sep="\t",
index=False)
self.done_window()
def play_song(self):
self.song.sound.play()
@staticmethod
def done_window():
popups.DonePopup().open()
@staticmethod
def take_closest(myList, myNumber):
"""
Assumes myList is sorted. Returns index of closest value to myNumber.
If two numbers are equally close, return the index of the smallest
number. From: https://stackoverflow.com/questions/12141150/from-list-of
-integers-get-number-closest-to-a-given-value
"""
pos = bisect_left(myList, myNumber)
if pos == 0:
return pos
if pos == len(myList):
return -1
before = myList[pos - 1]
after = myList[pos]
if after - myNumber < myNumber - before:
return pos
else:
return pos - 1
class MainApp(App):
def build(self):
"""
some initialization
Args:
rect: a dummy rectangle, whose width and height will be reset trigger by user event
x0, y0: mouse click location
x1, y1: mouse release location
canvas: FigureCanvasKivyAgg object. Note that I'm using this back end right now
as the FigureCanvas backend has bug with plt.show()
selectors: store user-drawn rectangle data
offsetx: translation of origin on x direction
offsety: translation of origin on y direction
"""
self.selectors = []
img = mpimg.imread(sys.argv[1])
self.fig, self.ax = plt.subplots(1)
plt.imshow(img)
width, height = self.fig.canvas.get_width_height()
pxorigin = self.ax.transData.transform([(0, 0)])
self.offsetx = pxorigin[0][0]
self.offsety = height - pxorigin[0][1]
print('offsetx, offsety', self.offsetx, self.offsety)
self.rect = Rectangle((0, 0), 1, 1)
self.rect.set_fill(False)
self.rect.set_edgecolor('b')
self.x0 = None
self.y0 = None
self.x1 = None
self.y1 = None
self.canvas = FigureCanvasKivyAgg(
plt.gcf()) # get the current reference of plt
box = BoxLayout()
self.ax.add_patch(self.rect) # attach our rectangle to axis
self.canvas.mpl_connect("button_press_event", self.on_press)
self.canvas.mpl_connect("button_release_event", self.on_release)
box.add_widget(self.canvas)
return box
def on_press(self, event):
"""
record user click location
"""
self.x0 = event.xdata
self.y0 = event.ydata
print('x0, y0', self.x0, self.y0)
def on_release(self, event):
"""
record user mouse release location
"""
self.x1 = event.xdata
self.y1 = event.ydata
self.rect.set_width(self.x1 - self.x0)
self.rect.set_height(self.y1 - self.y0)
self.rect.set_xy((self.x0, self.y0))
xy_pixels = self.ax.transData.transform(
np.vstack([self.x0, self.y0]).T)
px, py = xy_pixels.T
width, height = self.fig.canvas.get_width_height()
# transform from origin on lower left to orgin on upper right
py = height - py
# account for translation factor
px -= self.offsetx
py -= self.offsety
self.selectors.append(
[px, py, abs(self.x1 - self.x0),
abs(self.y1 - self.y0)])
print('your rectangle', px, py, abs(self.x1 - self.x0),
abs(self.y1 - self.y0))
self.canvas.draw()
def __init__(self, *args, **kwargs):
self.fig6, self.ax6 = plt.subplots()
self.syllsim_hist_canvas = FigureCanvasKivyAgg(self.fig6)
super(SyllSimSummaryPage, self).__init__(*args, **kwargs)
def add_plot(self): self.add_widget(FigureCanvasKivyAgg(self.fig))
def runGraph(self, arr_format, dictionary):
run = MultiVariateTime(Data(arr_format), dictionary)
a, b = run.run()
self.ids.graph.clear_widgets()
self.ids.graph.add_widget(FigureCanvasKivyAgg(b))