matplotlib x-axis ticks dates formatting and locations - matplotlib

I've tried to duplicate plotted graphs originally created with flotr2 for pdf output with matplotlib. I must say that flotr is way easyer to use... but that aside - im currently stuck at trying to format the dates /times on x-axis to desired format, which is hours:minutes with interval of every 2 hours, if period on x-axis is less than one day and year-month-day format if period is longer than 1 day with interval of one day.
I've read through numerous examples and tried to copy them, but outcome remains the same which is hours:minutes:seconds with 1 to 3 hour interval based on how long is the period.
My code:
colorMap = {
'speed': '#3388ff',
'fuel': '#ffaa33',
'din1': '#3bb200',
'din2': '#ff3333',
'satellites': '#bfbfff'
}
otherColors = ['#00A8F0','#C0D800','#CB4B4B','#4DA74D','#9440ED','#800080','#737CA1','#E4317F','#7D0541','#4EE2EC','#6698FF','#437C17','#7FE817','#FBB117']
plotMap = {}
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.dates as dates
fig = plt.figure(figsize=(22, 5), dpi = 300, edgecolor='k')
ax1 = fig.add_subplot(111)
realdata = data['data']
keys = realdata.keys()
if 'speed' in keys:
speed_index = keys.index('speed')
keys.pop(speed_index)
keys.insert(0, 'speed')
i = 0
for key in keys:
if key not in colorMap.keys():
color = otherColors[i]
otherColors.pop(i)
colorMap[key] = color
i += 1
label = u'%s' % realdata[keys[0]]['name']
ax1.set_ylabel(label)
plotMap[keys[0]] = {}
plotMap[keys[0]]['label'] = label
first_dates = [ r[0] for r in realdata[keys[0]]['data']]
date_range = first_dates[-1] - first_dates[0]
ax1.xaxis.reset_ticks()
if date_range > datetime.timedelta(days = 1):
ax1.xaxis.set_major_locator(dates.WeekdayLocator(byweekday = 1, interval=1))
ax1.xaxis.set_major_formatter(dates.DateFormatter('%Y-%m-%d'))
else:
ax1.xaxis.set_major_locator(dates.HourLocator(byhour=range(24), interval=2))
ax1.xaxis.set_major_formatter(dates.DateFormatter('%H:%M'))
ax1.xaxis.grid(True)
plotMap[keys[0]]['plot'] = ax1.plot_date(
dates.date2num(first_dates),
[r[1] for r in realdata[keys[0]]['data']], colorMap[keys[0]], xdate=True)
if len(keys) > 1:
first = True
for key in keys[1:]:
if first:
ax2 = ax1.twinx()
ax2.set_ylabel(u'%s' % realdata[key]['name'])
first = False
plotMap[key] = {}
plotMap[key]['label'] = u'%s' % realdata[key]['name']
plotMap[key]['plot'] = ax2.plot_date(
dates.date2num([ r[0] for r in realdata[key]['data']]),
[r[1] for r in realdata[key]['data']], colorMap[key], xdate=True)
plt.legend([value['plot'] for key, value in plotMap.iteritems()], [value['label'] for key, value in plotMap.iteritems()], loc = 2)
plt.savefig(path +"node.png", dpi = 300, bbox_inches='tight')
could someone point out why im not getting desired results, please?
Edit1:
I moved the formatting block after the plotting and seem to be getting better results now. They are still now desired results though. If period is less than day then i get ticks after every 2 hours (interval=2), but i wish i could get those ticks at even hours not uneven hours. Is that possible?
if date_range > datetime.timedelta(days = 1):
xax.set_major_locator(dates.DayLocator(bymonthday=range(1,32), interval=1))
xax.set_major_formatter(dates.DateFormatter('%Y-%m-%d'))
else:
xax.set_major_locator(dates.HourLocator(byhour=range(24), interval=2))
xax.set_major_formatter(dates.DateFormatter('%H:%M'))
Edit2:
This seemed to give me what i wanted:
if date_range > datetime.timedelta(days = 1):
xax.set_major_locator(dates.DayLocator(bymonthday=range(1,32), interval=1))
xax.set_major_formatter(dates.DateFormatter('%Y-%m-%d'))
else:
xax.set_major_locator(dates.HourLocator(byhour=range(0,24,2)))
xax.set_major_formatter(dates.DateFormatter('%H:%M'))
Alan

You are making this way harder on your self than you need to. matplotlib can directly plot against datetime objects. I suspect your problem is you are setting up the locators, then plotting, and the plotting is replacing your locators/formatters with the default auto versions. Try moving that block of logic about the locators to below the plotting loop.
I think that this could replace a fair chunk of your code:
d = datetime.timedelta(minutes=2)
now = datetime.datetime.now()
times = [now + d * j for j in range(500)]
ax = plt.gca() # get the current axes
ax.plot(times, range(500))
xax = ax.get_xaxis() # get the x-axis
adf = xax.get_major_formatter() # the the auto-formatter
adf.scaled[1./24] = '%H:%M' # set the < 1d scale to H:M
adf.scaled[1.0] = '%Y-%m-%d' # set the > 1d < 1m scale to Y-m-d
adf.scaled[30.] = '%Y-%m' # set the > 1m < 1Y scale to Y-m
adf.scaled[365.] = '%Y' # set the > 1y scale to Y
plt.draw()
doc for AutoDateFormatter

I achieved what i wanted by doing this:
if date_range > datetime.timedelta(days = 1):
xax.set_major_locator(dates.DayLocator(bymonthday=range(1,32), interval=1))
xax.set_major_formatter(dates.DateFormatter('%Y-%m-%d'))
else:
xax.set_major_locator(dates.HourLocator(byhour=range(0,24,2)))
xax.set_major_formatter(dates.DateFormatter('%H:%M'))

Related

Csv file search speedup

I need to build a relief profile graph by coordinates, I have a csv file with 12,000,000 lines. searching through a csv file of the same height takes about 2 - 2.5 seconds. I rewrote the csv to parquet and it helped me save some time, it takes about 1.7 - 1 second to find one height. However, I need to build a profile for 500 - 2000 values, which makes the time very long. In the future, you may have to increase the base of the csv file, which will slow down this process even more. In this regard, my question is, is it possible to somehow reduce the processing time of values?
Code example:
import dask.dataframe as dk
import numpy as np
import pandas as pd
import time
filename = 'n46_e032_1arc_v3.csv'
df = dk.read_csv(filename)
df.to_parquet('n46_e032_1arc_v3_parquet')
Latitude1y, Longitude1x = 46.6276, 32.5942
Latitude2y, Longitude2x = 46.6451, 32.6781
sec, steps, k = 0.00027778, 1, 11.73
Latitude, Longitude = [Latitude1y], [Longitude1x]
sin, cos = Latitude2y - Latitude1y, Longitude2x - Longitude1x
y, x = Latitude1y, Longitude1x
while Latitude[-1] < Latitude2y and Longitude[-1] < Longitude2x:
y, x, steps = y + sec * k * sin, x + sec * k * cos, steps + 1
Latitude.append(y)
Longitude.append(x)
time_start = time.time()
long, elevation_data = [], []
df2 = dk.read_parquet('n46_e032_1arc_v3_parquet')
for i in range(steps + 1):
elevation_line = df2[(Longitude[i] <= df2['x']) & (df2['x'] <= Longitude[i] + sec) &
(Latitude[i] <= df2['y']) & (df2['y'] <= Latitude[i] + sec)].compute()
elevation = np.asarray(elevation_line.z.tolist())
if elevation[-1] < 0:
elevation_data.append(0)
else:
elevation_data.append(elevation[-1])
long.append(30 * i)
plt.bar(long, elevation_data, width = 30)
plt.show()
print(time.time() - time_start)
Here's one way to solve this problem using KD trees. A KD tree is a data structure for doing fast nearest-neighbor searches.
import scipy.spatial
tree = scipy.spatial.KDTree(df[['x', 'y']].values)
elevations = df['z'].values
long, elevation_data = [], []
for i in range(steps):
lon, lat = Longitude[i], Latitude[i]
dist, idx = tree.query([lon, lat])
elevation = elevations[idx]
if elevation < 0:
elevation = 0
elevation_data.append(elevation)
long.append(30 * i)
Note: if you can make assumptions about the data, like "all of the points in the CSV are equally spaced," faster algorithms are possible.
It looks like your data might be on a regular grid. If (and only if) every combination of x and y exist in your data, then it probably makes sense to turn this into a labeled 2D array of points, after which querying the correct position will be very fast.
For this, I'll use xarray, which is essentially pandas for N-dimensional data, and integrates well with dask:
# bring the dataframe into memory
df = dk.read('n46_e032_1arc_v3_parquet').compute()
da = df.set_index(["y", "x"]).z.to_xarray()
# now you can query the nearest points:
desired_lats = xr.DataArray([46.6276, 46.6451], dims=["point"])
desired_lons = xr.DataArray([32.5942, 32.6781], dims=["point"])
subset = da.sel(y=desired_lats, x=desired_lons, method="nearest")
# if you'd like, you can return to pandas:
subset_s = subset.to_series()
# you could do this only once, and save the reshaped array as a zarr store:
ds = da.to_dataset(name="elevation")
ds.to_zarr("n46_e032_1arc_v3.zarr")

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In my program, im using mplcursors on a matplotlib graph so I can identify certain points precisely.
mplcursors.cursor(multiple=True).connect("add", lambda sel: sel.annotation.draggable(False))
Now I made a complex graph with multiple axis:
first = 1
offset = 60
for x in range(len(cat_list)):
if "Time" not in cat_list[x]:
if first and not cat_list[x].startswith("EngineSpeed"):
parasites[x] = ParasiteAxes(host, sharex = host)
host.parasites.append(parasites[x])
parasites[x].axis["right"].set_visible(True)
parasites[x].set_ylabel(cat_list[x])
parasites[x].axis["right"].major_ticklabels.set_visible(True)
parasites[x].axis["right"].label.set_visible(True)
p_plot, = parasites[x].plot(t, t_num_list[x], label = cat_list[x])
#parasites[x].axis["right"+str(x+1)].label.set_color(p_plot.get_color())
parasites[x].axis["right"].label.set_color(p_plot.get_color())
first = 0
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parasites[x] = ParasiteAxes(host, sharex = host)
host.parasites.append(parasites[x])
parasites[x].set_ylabel(cat_list[x])
new_axisline = parasites[x].get_grid_helper().new_fixed_axis
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plt.show()
This code results in the following graph:
https://i.stack.imgur.com/Wl7yC.png
Now I have to somehow be able to select certain points by selecting which axis im using. How do I make a selection menu for choosing an active axis and how do I then use mplcursors to select my points?
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Ziga

Pandas Timeseries: Total duration meeting a specific condition

I have a timeseries
ts = pd.Series(data=[0,1,2,3,4],index=[pd.Timestamp('1991-01-01'),pd.Timestamp('1995-01-01'),pd.Timestamp('1996-01-01'),pd.Timestamp('2010-01-01'),pd.Timestamp('2011-01-01')])
Whats the fastest, most readable, way to get the total duration in which the value is below 2, assuming the values are valid until the next time-step indicates otherwise (no linear interpolation). I imagine there probably is a pandas function for this
This seems to be working quite well, however I am still baffled that there does not seem to be a pandas function for this!
import pandas as pd
import numpy as np
ts = pd.Series(data=[0,1,2,3,4],index=[pd.Timestamp('1991-01-01'),pd.Timestamp('1995-01-01'),pd.Timestamp('1996-01-01'),pd.Timestamp('2010-01-01'),pd.Timestamp('2011-01-01')])
# making the timeseries binary. 1 = meets condition, 0 = does not
ts = ts.where(ts>=2,other=1)
ts = ts.where(ts<2,other=0)
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time_above_2 = np.sum(delta_time[(ts.values[:-1])]).total_seconds()
The above function seems to break for certain timeframes. This option is slower, but did not break in any of my tests:
def get_total_duration_above_and_below_value(value,ts):
# making the timeseries binary. 1 = above value, 0 = below value
ts = ts.where(ts >= value, other=1)
ts = ts.where(ts < value, other=0)
time_above_value = 0
time_below_value = 0
for i in range(ts.size - 1):
if ts[i] == 1:
time_above_value += abs(pd.Timedelta(
ts.index[i] - ts.index[i + 1]).total_seconds()) / 3600
else:
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ts.index[i] - ts.index[i + 1]).total_seconds()) / 3600
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Matplotlib Stopping an Animation

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def animate(frame):
eq_num = frame % len(X)
i = frame % len(P)
P['colour'][:,3] = np.maximum(0, P['colour'][:,3] - 1.0/len(P))
P['size'] += P['growth']
magnitude = X['magnitude'][eq_num]
P['epicentre'][i] = m(*X['epicentre'][eq_num])
P['size'][i] = 5
P['growth'][i]= np.exp(magnitude) * 0.1
if magnitude < 4:
P['colour'][i] = 0,0,1,1
else:
P['colour'][i] = 1,0,0,1
scatter.set_edgecolors(P['colour'])
scatter.set_facecolors(P['colour']*(1,1,1,0.25))
scatter.set_sizes(P['size'])
scatter.set_offsets(P['epicentre'])
return scatter,
ani = FuncAnimation(fig,animate,frames=62,interval=1000,blit=False)
ani.save('animation.gif', writer='imagemagick', fps=100)
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Plot random points a specified distance apart

I'm trying to come up with a function that plots n points inside the unit circle, but I need them to be sufficiently spread out.
ie. something that looks like this:
Is it possible to write a function with two parameters, n (number of points) and min_d (minimum distance apart) such that the points are:
a) equidistant
b) no pairwise distance exceeds a given min_d
The problem with sampling from a uniform distribution is that it could happen that two points are almost on top of each other, which I do not want to happen. I need this kind of input for a network diagram representing node clusters.
EDIT: I have found an answer to a) here: Generator of evenly spaced points in a circle in python, but b) still eludes me.
At the time this answer was provided, the question asked for random numbers. This answer thus gives a solution drawing random numbers. It ignores any edits made to the question afterwards.
On may simply draw random points and for each one check if the condition of the minimum distance is fulfilled. If not, the point can be discarded. This can be done until a list is filled with enough points or some break condition is met.
import numpy as np
import matplotlib.pyplot as plt
class Points():
def __init__(self,n=10, r=1, center=(0,0), mindist=0.2, maxtrials=1000 ) :
self.success = False
self.n = n
self.r = r
self.center=np.array(center)
self.d = mindist
self.points = np.ones((self.n,2))*10*r+self.center
self.c = 0
self.trials = 0
self.maxtrials = maxtrials
self.tx = "rad: {}, center: {}, min. dist: {} ".format(self.r, center, self.d)
self.fill()
def dist(self, p, x):
if len(p.shape) >1:
return np.sqrt(np.sum((p-x)**2, axis=1))
else:
return np.sqrt(np.sum((p-x)**2))
def newpoint(self):
x = (np.random.rand(2)-0.5)*2
x = x*self.r-self.center
if self.dist(self.center, x) < self.r:
self.trials += 1
if np.all(self.dist(self.points, x) > self.d):
self.points[self.c,:] = x
self.c += 1
def fill(self):
while self.trials < self.maxtrials and self.c < self.n:
self.newpoint()
self.points = self.points[self.dist(self.points,self.center) < self.r,:]
if len(self.points) == self.n:
self.success = True
self.tx +="\n{} of {} found ({} trials)".format(len(self.points),self.n,self.trials)
def __repr__(self):
return self.tx
center =(0,0)
radius = 1
p = Points(n=40,r=radius, center=center)
fig, ax = plt.subplots()
x,y = p.points[:,0], p.points[:,1]
plt.scatter(x,y)
ax.add_patch(plt.Circle(center, radius, fill=False))
ax.set_title(p)
ax.relim()
ax.autoscale_view()
ax.set_aspect("equal")
plt.show()
If the number of points should be fixed, you may try to run find this number of points for decreasing distances until the desired number of points are found.
In the following case, we are looking for 60 points and start with a minimum distance of 0.6 which we decrease stepwise by 0.05 until there is a solution found. Note that this will not necessarily be the optimum solution, as there is only maxtrials of retries in each step. Increasing maxtrials will of course bring us closer to the optimum but requires more runtime.
center =(0,0)
radius = 1
mindist = 0.6
step = 0.05
success = False
while not success:
mindist -= step
p = Points(n=60,r=radius, center=center, mindist=mindist)
print p
if p.success:
break
fig, ax = plt.subplots()
x,y = p.points[:,0], p.points[:,1]
plt.scatter(x,y)
ax.add_patch(plt.Circle(center, radius, fill=False))
ax.set_title(p)
ax.relim()
ax.autoscale_view()
ax.set_aspect("equal")
plt.show()
Here the solution is found for a minimum distance of 0.15.