How to plot hyperparameter tuning results? - python-3.x

I have the result of a grid search as follows.
"trial","learning_rate","batch_size","accuracy","f1","loss"
1,0.000007,70,0.789,0.862,0.467
2,0.000008,100,0.710,0.822,0.563
3,0.000008,90,0.823,0.874,0.524
4,0.000007,90,0.833,0.878,0.492
5,0.000009,110,0.715,0.825,0.509
6,0.000006,90,0.883,0.885,0.932
7,0.000009,80,0.850,0.895,0.408
8,0.000006,110,0.683,0.812,0.593
9,0.000005,90,0.769,0.848,0.468
10,0.000005,80,0.816,0.868,0.462
11,0.000003,100,0.852,0.901,0.448
12,0.000004,100,0.705,0.818,0.512
13,0.000003,110,0.708,0.818,0.567
14,0.000002,90,0.683,0.812,0.552
15,0.000008,100,0.791,0.857,0.438
16,0.000006,110,0.683,0.812,0.604
17,0.000007,70,0.693,0.816,0.592
18,0.000005,110,0.830,0.883,0.892
19,0.000004,90,0.693,0.816,0.591
20,0.000008,70,0.696,0.818,0.570
I want to create a plot more or less similar to this using matplotlib. I know this is plotted using weights and biases but I cannot use that.
Though I don't care for the inference part. I just want the plot. I've been trying to do this using twinx but have not been successful. This is what I have so far.
from csv import DictReader
import matplotlib.pyplot as plt
trials = list(DictReader(open("hparams_trials.csv")))
trials = {f"trial_{trial['trial']}": [int(trial["batch_size"]),
float(trial["f1"]),
float(trial["loss"]),
float(trial["accuracy"]),
float(trial["learning_rate"])] for trial in trials}
items = ["batch_size", "f1", "loss", "accuracy", "learning_rate"]
host_y_values_index = 0
parts_y_values_indexes = [1, 2, 3, 4]
fig, host = plt.subplots(figsize=(8, 5)) # (width, height) in inches
fig.dpi = 300. # Figure resolution
# Removing extra spines
host.spines.top.set_visible(False)
host.spines.bottom.set_visible(False)
host.spines.right.set_visible(False)
# Creating subplots which share the same x axis.
parts = {index: host.twinx() for index in parts_y_values_indexes}
# Setting the limits of the host plot
host.set_xlim(0, len(trials["trial_1"]))
host.set_ylim(min([i[host_y_values_index] for i in trials.values()]),
max([i[host_y_values_index] for i in trials.values()]))
# Removing the extra spines from the other plots and setting y limits
for part in parts_y_values_indexes:
parts[part].spines.top.set_visible(False)
parts[part].spines.bottom.set_visible(False)
parts[part].set_ylim(min([trial[part] for trial in trials.values()]),
max([trial[part] for trial in trials.values()]))
# Colors of the trials
colors = ["gold", "lightcoral", "maroon", "springgreen", "cyan", "steelblue", "darkmagenta", "fuchsia", "crimson",
"lime", "mediumblue", "cadetblue", "dodgerblue", "olivedrab", "sandybrown", "bisque", "orangered", "black",
"rosybrown", "chocolate"]
# The plots
plots = []
# Plotting the trials. This is where I'm having problems with.
for index, trial in enumerate(trials):
plots.append(host.plot(items, trials[trial], color=colors[index], label=trial)[0])
# Creating the legend
host.legend(handles=plots, fancybox=True, loc='right', facecolor="snow", bbox_to_anchor=(1.02, 0.495), framealpha=1)
# Defining the positions of the spines.
spines_positions = [-104.85 * i for i in parts_y_values_indexes]
# Repositioning the spines
for part in parts_y_values_indexes:
parts[part].spines['right'].set_position(('outward', spines_positions[-part]))
# Adjust spacings around fig
fig.tight_layout()
host.grid(True)
# This is better than the one above but it appears on top of the legend.
# plt.grid(True)
plt.draw()
plt.show()
I'm having several problems with that code. First, I cannot place each value of a single trial based on a different spine and then connect them to one another. What I mean is that each trial has a batch size, an f1, a loss, accuracy and a learning rate. Each of those need to be plotted based on their own spine while connected to each other in that order. However, I cannot plot them based their dedicated spines and then connect them to one another to have a line plot per trial. Accordingly, for now I have placed everything in the host plot but I know that is wrong and have no idea what the correct approach is. Second problem, the ticks of the learning rate change. It gets shown as a range of 2 to 9 and then a 1e-6 appears at the top. I want to keep the original value. Third problem is probably part of the second one. The 1e-6 appears at the top right above the legend rather than above the spine for some reason. I'm struggling with resolving all three of these problems and would appreciate any help anyone can provide. If what I am doing is totally wrong, please help me in finding the correct solution. I'm somewhat going in circles here and haven't been able to find any working solutions so far.

Related

Is it possible to extract the default tick locations from the primary axis and pass it to a secondary access with matplotlib?

When making a plot with with
fig, ax = plt.subplots()
x=[1,2,3,4,5,6,7,8,9,10]
y=[1,2,3,4,5,6,7,8,9,10]
ax.plot(x,y)
plt.show()
matplotlib will determine the tick spacing/location and value of the tick. Is there are way to extract this automatic spacing/location AND the value? I want to do this so i can pass it to
set_xticks()
for my secondary axis (using twiny()) then use set_ticklabels() with a custom label. I realise I could use secondary axes giving both a forward and inverse function however providing an inverse function is not feasible for the goal of my code.
So in the image below, the ticks are only showing at 2,4,6,8,10 rather than all the values of x and I want to somehow extract these values and position so I can pass to set_xticks() and then change the tick labels (on a second x axis created with twiny).
UPDATE
When using the fix suggested it works well for the x axis. However, it does not work well for the y-axis. For the y-axis it seems to take the dataset values for the y ticks only. My code is:
ax4 = ax.twinx()
ax4.yaxis.set_ticks_position('left')
ax4.yaxis.set_label_position('left')
ax4.spines["left"].set_position(("axes", -0.10))
ax4.set_ylabel(self.y_2ndary_label, fontweight = 'bold')
Y = ax.get_yticks()
ax4.yaxis.set_ticks(Y)
ax4.yaxis.set_ticklabels( Y*Y )
ax4.set_ylim(ax.get_ylim())
fig.set_size_inches(8, 8)
plt.show()
but this gives me the following plot. The plot after is the original Y axis. This is not the case when I do this on the x-axis. Any ideas?
# From "get_xticks" Doc: The locations are not clipped to the current axis limits
# and hence may contain locations that are not visible in the output.
current_x_ticks = ax.get_xticks()
current_x_limits = ax.get_xlim()
ax.set_yticks(current_x_ticks) # Use this before "set_ylim"
ax.set_ylim(current_x_limits)
plt.show()

specify the lat/lon label location in cartopy (remove at some sides)

The new capability in Cartopy 0.18.0 to add lat/lon labels for any map projection is excellent. It's a great addition to this package. For some maps, especially in polar regions, the lat/lon labels can be very crowded. Here is an example.
from matplotlib import pyplot as plt
import numpy as np
import cartopy.crs as ccrs
pcproj = ccrs.PlateCarree()
lon0 = -150
mapproj = ccrs.LambertAzimuthalEqualArea(
central_longitude=lon0,central_latitude=75,
)
XLIM = 600e3; YLIM=700e3
dm =5; dp=2
fig = plt.figure(0,(7,7))
ax = fig.add_axes([0.1,0.1,0.85,0.9],projection=mapproj)
ax.set_extent([-XLIM,XLIM,-YLIM,YLIM],crs=mapproj)
ax.coastlines(resolution='50m',color='.5',linewidth=1.5)
lon_grid = np.arange(-180,181,dm)
lat_grid = np.arange(-80,86,dp)
gl = ax.gridlines(draw_labels=True,
xlocs=lon_grid,ylocs=lat_grid,
x_inline=False,y_inline=False,
color='k',linestyle='dotted')
gl.rotate_labels = False
Here is the output plot: I can't embed image yet, so here is the link
What I am looking for is to have lat labels on the left and right sides and lon labels at the bottom, with no labels at the top. This can be easily done in Basemap using a list of flags. I am wondering if this is possible with cartopy now.
Several failed attempts:
I came across a Github open issue for cartopy on a similar topic, but the suggested method does not work for this case. Adding gl.ylocator = mticker.FixedLocator(yticks) does nothing and adding gl.xlocator = mticker.FixedLocator(xticks) gets rid of most of lon labels except the 180 line on left and right sides but all the other lon labels are missing. The 80N lat label is still on the top, see here. After a more careful read of that thread, it seems it is still an ongoing effort for future cartopy releases.
Using gl.top_labels=False does not work either.
Setting y_inline to True makes the lat labels completely gone. I guess this might be because of axes extent I used. The lat labels might be on some longitude lines outside of the box. This is a separate issue, about how to specify the longitude lines/locations of the inline labels.
Right now, I have chosen to turn off the labels. Any suggestions and temporary solutions will be appreciated. At this point, the maps such as the examples above are useful for quicklooks but not ready for any formal use.
UPDATE:
Based on #swatchai 's suggestion, there is a temporary workaround below:
# --- add _labels attribute to gl
plt.draw()
# --- tol is adjusted based on the positions of the labels relative to the borders.
tol = 20
for ea in gl._labels:
pos = ea[2].get_position()
t_label = ea[2].get_text()
# --- remove lon labels on the sides
if abs(abs(pos[0])-XLIM)<tol:
if 'W' in t_label or 'E' in t_label or '180°' in t_label:
print(t_label)
ea[2].set_text('')
# --- remove labels on top
if abs(pos[1]-YLIM)<tol:
ea[2].set_text('')
This is almost what I wanted except that the 74N labels are missing because it is close to the 170W labels on the sides and cartopy chose 170W label instead of 74N. So I need a little more simple tweaks to put it back there.
This could be a workaround for your project until a better solution comes up.
# more code above this line
# this suppresses drawing labels on top edges
# only longitude_labels disappear, some latitude_labels persist
gl.top_labels=False
# workaround here to manipulate the remaining labels
plt.draw() #enable the use of ._lables()
for ea in gl._labels:
#here, ea[2] is a Text object
#print(ea)
if '80°N'==ea[2].get_text():
# set it a blank string
ea[2].set_text("")
ax.set_title("No Labels on Top Edge");
plt.show()
The output plot:

Python visualization - histograms

the following two questions are regarding a histogram I am trying to build.
1) I want the bins to be as follows:
[0-10,10-20,...,580-590, 590-600]. I tried the following code:
bins_range=[]
for i in range(0,610,10):
bins_range.append(i)
plt.hist(df['something'], bins=bins_range, rwidth=0.95)
I expected to see bins as above with their corresponding amount of samples for each bin, but instead I got only 10 bins (as the default parameter).
2) How can I change the y-axis as follows: say my max bin contains 40 samples, so instead of 40 on the y-axis I want it to be 100%, and the others correspondly. I.e., 30 will be 75%, 20 will be 50% and so on.
Your code seems to be working OK. You can even pass the range command directly to the bins parameter of hist.
To get the y-axis as percentages, I think you need two passes: first calculate the bins to know how much the highest bin contains. Then, do the plotting using 1/highest as weights. There is a numpy np.hist that does all the calculations without plotting.
Use the PercentFormatter() to display the axis in percentages. It gets a parameter to tell how many 100% represents. Use PercentFormatter(max(hist)) to get the highest value as 100%. If you just want the total as 100%, just pass PercentFormatter(len(x)), without the need to calculate the histogram twice. As internally the y-axis is still in values, the ticks don't show up at the desired positions. You can use plt.yticks(np.linspace(0, max(hist), 11)) to have ticks for every 10%.
To get nicer separations between the bars, you can set an explicit edge color. Best without the rwidth=0.95
Example code:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import PercentFormatter
x = np.random.rayleigh(200, 50000)
hist, bins = np.histogram(x, bins=range(0, 610, 10))
plt.hist(x, bins=bins, ec='white', fc='darkorange')
plt.gca().yaxis.set_major_formatter(PercentFormatter(max(hist)))
plt.yticks(np.linspace(0, max(hist), 11))
plt.show()
PS: To use matplotlib's standard yticks, and having the y-axis also internally in percentages, you can use the weights parameter of hist. This can be handy when you want to interactively resize or zoom the plot, or need horizontal lines at specific percentages.
plt.hist(x, bins=bins, ec='white', fc='dodgerblue', weights=np.ones_like(x)/max(hist))
plt.gca().yaxis.set_major_formatter(PercentFormatter(1))

How to divide the area between two co-ordinates into blocks and assign some values to those blocks?

Basically I have to create a heatmap of the crowd present in an area.
I have two coordinates. X starts from 0 and maximum is 119994. Y ranges from -14,000 to +27,000. I have to divide these coordinates into as many blocks blocks as I wish, count the number of people in each block and create a heatmap of this whole area.
Basically show the crowdedness of the area divided as blocks.
I have data in the below format:-
Employee_ID X_coord Y_coord_start Y_coord_end
23 1333 0 6000
45 3999 7000 17000
I tried dividing both the coordinate maximums by 100(to make 100 blocks) and tried finding the block coordinates but that was very complex.
As I have to make a heatmap I have to prepare a matrix of values in the form of blocks. Every block will have a count of people which I can count and find out from my data but the problem is how to make these blocks of coordinates?
I have another question regarding scatter plot:-
My data is:-
Batch_ID Pieces_Productivity
181031008780 4.578886
181031008781 2.578886
When I plot it using the following code:-
plt.scatter(list(df_books_location.Batch_ID),list(df_books_location['Pieces_productivity']), s=area, alpha=0.5)
It doesn't give me proper plot. But when I plot with small integers(0-1000) for Batch_ID I get good graph. How to handle large integers for plotting?
I don't know which of both Y_coord_-rows should give the actual Y coordinate, and also don't know whether your plot should be evaluate the data on a strict "grid", or perhaps rather smooth it out; hence I am using both an imshow() and a sns.kdeplot() in the code below:
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
### generate some data
np.random.seed(0)
data = np.random.multivariate_normal([0, 0], [(1, .6), (.6, 1)], 100)
## this would e.g. be X,Y=df['X_coord'], df['Y_coord_start'] :
X,Y=data[:,0],data[:,1]
fig,ax=plt.subplots(nrows=1,ncols=3,figsize=(10,5))
ax[0].scatter(X,Y)
sns.kdeplot(X,Y, shade=True, ax=ax[1],cmap="viridis")
## the X,Y points are binned into 10x10 bins here, you will need
# to adjust the amount of bins so that it looks "nice" for you
heatmap, xedges, yedges = np.histogram2d(X, Y, bins=(10,10))
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]
im=ax[2].imshow(heatmap.T, extent=extent,
origin="lower",aspect="auto",
interpolation="nearest") ## also play with different interpolations
## Loop over heatmap dimensions and create text annotations:
# note that we need to "push" the text from the lower left corner of each pixel
# into the center of each pixel
## also try to choose a text color which is readable on all pixels,
# or e.g. use vmin=… vmax= to adjust the colormap such that the colors
# don't clash with e.g. white text
pixel_center_x=(xedges[1]-xedges[0])/2.
pixel_center_y=(yedges[1]-yedges[0])/2.
for i in range(np.shape(heatmap)[1]):
for j in range(np.shape(heatmap)[0]):
text = ax[2].text(pixel_center_x+xedges[j], pixel_center_y+yedges[i],'{0:0.0f}'.format(heatmap[j, i]),
ha="center", va="center", color="w",fontsize=6)
plt.colorbar(im)
plt.show()
yields:

Distributing plots across a grid of variable axes length in python

I have written a few lines of Python 3 code to assist me in the automated analysis of data generated using a technique called calorimetry (for radiation dosimetry). In the enclosed example, the analysis of the input file returned eighth 'heating regions' (top panel), and in each region a pair of linear regressions (black segment, red segment) were made on portions of data to calculate the magnitude of the 'step', relative to the average value of my quantity of interest (the varying resistance of a thermistor), which is plotted in the bottom panel of the same figure.
automatic identification of 8 heating regions (top panel) and computed relative step magnitude (bottom panel)
Results of this type of analysis are summarized in a data frame (a ndarray from numpy at present) but, ideally, I would hope to produce also a graphical representation with some annotations in each subplot, including information from the corresponding line in the results dataframe:
Step analysis via a pair of linear regressions and further computation
The general output would look something like this last figure, with each subplot including the same essential information from the previous individual plot.
The output is, in this specific case, a grid (2,4) because there were exactly 8 regions to analyse
This was created by hand, without any iteration, using this portion of code in a Jupyter notebook:
%matplotlib inline
results_fig = pyplt.figure(figsize=(20,10))
results_grid = matplotlib.gridspec.GridSpec(2, 4, hspace=0.2, wspace=0.3)
results_fig.suptitle("Faceted presentation of calorimetric runs", fontsize=15)
ax1 = results_fig.add_subplot(results_grid[0,0])
ax1.scatter(time,resistance, marker ='o', s=20, c='blue')
ax1.plot(time[x1[0]:xmid[0]], line_pre[0], color='black', linewidth=3.0)
ax1.plot(time[xmid[0]:x4[0]], line_post[0], color='red', linewidth=3.0)
ax1.set_xlim(xlim1[0],xlim2[0])
ax1.set_ylabel("resistance [Ohm]")
# [... continues for each subplot in the grid ... ]
Given that the number of 'heating regions' may vary considerably from file to file, i.e. I cannot determine it before analyzing each experimental output datafile, here is my pair of questions:
How can I produce a grid of subplots without prior knowledge of how many subplots it will show? One of the dimensions of the grid could be four, as in the example provided here, but the other is unknown. I could iterate over the length of one of the axes of the numpy results array, but then I would need to span over two axes in my plot grid.
Without re-inventing the wheel, is there a python module that can assist in this direction?
Thanks
Here is how you create a grid of n x 4 subplots and iterate over them
numplots = 10 # number of plots to create
m = 4 # number of columns
n = int(np.ceil(numplots/4.)) # number of rows
fig, axes = plt.subplots(nrows=n,ncols=m)
fig.subplots_adjust(hspace=0.2, wspace=0.3)
for data, ax in zip(alldata, axes.flatten()):
ax.plot(data[0],data[1], color='black')
# further plotting, label setting etc.
# optionally, remove empty plots from grid
if n*m > numplots:
for ax in axes.flatten()[numplots:]:
ax.remove()
##or
#ax.set_visible(False)

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