Plot 2d gaussian python

This chapter of the tutorial will give a brief introduction to some of the tools in seaborn for examining univariate and bivariate distributions. You may also want to look at the categorical plots chapter for examples of functions that make it easy to compare the distribution of a variable across levels of other variables. The most convenient way to take a quick look at a univariate distribution in seaborn is the distplot function. By default, this will draw a histogram and fit a kernel density estimate KDE.

Histograms are likely familiar, and a hist function already exists in matplotlib. A histogram represents the distribution of data by forming bins along the range of the data and then drawing bars to show the number of observations that fall in each bin.

plot 2d gaussian python

You can make the rug plot itself with the rugplot function, but it is also available in distplot :. When drawing histograms, the main choice you have is the number of bins to use and where to place them. The kernel density estimate may be less familiar, but it can be a useful tool for plotting the shape of a distribution. Like the histogram, the KDE plots encode the density of observations on one axis with height along the other axis:. Drawing a KDE is more computationally involved than drawing a histogram.

What happens is that each observation is first replaced with a normal Gaussian curve centered at that value:. Next, these curves are summed to compute the value of the density at each point in the support grid. The resulting curve is then normalized so that the area under it is equal to We can see that if we use the kdeplot function in seaborn, we get the same curve.

This function is used by distplotbut it provides a more direct interface with easier access to other options when you just want the density estimate:. The bandwidth bw parameter of the KDE controls how tightly the estimation is fit to the data, much like the bin size in a histogram. It corresponds to the width of the kernels we plotted above. The default behavior tries to guess a good value using a common reference rule, but it may be helpful to try larger or smaller values:. As you can see above, the nature of the Gaussian KDE process means that estimation extends past the largest and smallest values in the dataset.

You can also use distplot to fit a parametric distribution to a dataset and visually evaluate how closely it corresponds to the observed data:. It can also be useful to visualize a bivariate distribution of two variables.

The easiest way to do this in seaborn is to just use the jointplot function, which creates a multi-panel figure that shows both the bivariate or joint relationship between two variables along with the univariate or marginal distribution of each on separate axes. The most familiar way to visualize a bivariate distribution is a scatterplot, where each observation is shown with point at the x and y values.

This is analogous to a rug plot on two dimensions. You can draw a scatterplot with scatterplotand it is also the default kind of plot shown by the jointplot function:.

This plot works best with relatively large datasets. It looks best with a white background:. It is also possible to use the kernel density estimation procedure described above to visualize a bivariate distribution. In seaborn, this kind of plot is shown with a contour plot and is available as a style in jointplot :.

You can also draw a two-dimensional kernel density plot with the kdeplot function. This allows you to draw this kind of plot onto a specific and possibly already existing matplotlib axes, whereas the jointplot function manages its own figure:. If you wish to show the bivariate density more continuously, you can simply increase the number of contour levels:.

The jointplot function uses a JointGrid to manage the figure. For more flexibility, you may want to draw your figure by using JointGrid directly. To plot multiple pairwise bivariate distributions in a dataset, you can use the pairplot function. This creates a matrix of axes and shows the relationship for each pair of columns in a DataFrame.

By default, it also draws the univariate distribution of each variable on the diagonal Axes:. Specifying the hue parameter automatically changes the histograms to KDE plots to facilitate comparisons between multiple distributions. Much like the relationship between jointplot and JointGridthe pairplot function is built on top of a PairGrid object, which can be used directly for more flexibility:.In statistics, kernel density estimation KDE is a non-parametric way to estimate the probability density function PDF of a random variable.

This function uses Gaussian kernels and includes automatic bandwidth determination. The method used to calculate the estimator bandwidth. See scipy. Evaluation points for the estimated PDF.

If None defaultequally spaced points are used. If ind is an integer, ind number of equally spaced points are used. Additional keyword arguments are documented in pandas. Representation of a kernel-density estimate using Gaussian kernels.

This is the function used internally to estimate the PDF. Given a Series of points randomly sampled from an unknown distribution, estimate its PDF using KDE with automatic bandwidth determination and plot the results, evaluating them at equally spaced points default :. A scalar bandwidth can be specified.

Using a small bandwidth value can lead to over-fitting, while using a large bandwidth value may result in under-fitting:. Finally, the ind parameter determines the evaluation points for the plot of the estimated PDF:.

Home What's New in 1. DataFrame pandas. T pandas. Returns matplotlib. Axes or numpy.This post will show you how to:. For fitting the gaussian kernel, we specify a meshgrid which will use points interpolation on each axis e. The matplotlib object doing the entire magic is called QuadContour set cset in the code.

We can programatically access the contour lines by iterating through allsegs object. The calculated labels are accessible from labelTexts. We can plot the density as a surface:. Representation using 2D histograms. Another way to present the same information is by using 2D histograms. The entire code is available on Github. Sign in. Simple example of 2D density plots in python.

How to visualize joint distributions. Madalina Ciortan Follow. Towards Data Science A Medium publication sharing concepts, ideas, and codes. Computer science engineer, bioinformatician, researcher in data science. Towards Data Science Follow. A Medium publication sharing concepts, ideas, and codes. Write the first response. More From Medium.

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Clustering with Gaussian Mixture Models

Become a member.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. The dark mode beta is finally here. Change your preferences any time. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. You are missing a parantheses in the denominator of your gaussian function.

But that is not true and as you can see of your plots the greater variance the more narrow the gaussian is - which is wrong, it should be opposit. In addition to previous answers, I recommend to first calculate the ratio in the exponent, then taking the square:. Learn more. Plotting of 1-dimensional Gaussian distribution function Ask Question.

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Asked 7 years, 1 month ago. Active 2 months ago.

plot 2d gaussian python

Viewed k times. I'm new to programming, using Python. Thank you in advance! Active Oldest Votes. With the excellent matplotlib and numpy packages from matplotlib import pyplot as mp import numpy as np def gaussian x, mu, sig : return np.

plot 2d gaussian python

The old X values where counters, not the values of X ie a mistake. XValidated XValidated 7 7 silver badges 11 11 bronze badges. The correct form, based on the original syntax, and correctly normalized is: def gaussian x, mu, sig : return 1. Adrian Tompkins 2, 1 1 gold badge 11 11 silver badges 42 42 bronze badges. This is the only answer with normalization that matches scipy. So just change the gaussian function to: def gaussian x, mu, sig : return np. In addition to previous answers, I recommend to first calculate the ratio in the exponent, then taking the square: def gaussian x,x0,sigma : return np.

That way, you can also calculate the gaussian of very small or very large numbers: In: gaussian 1e,5e,3e Out: 0. PhMota 3 2 2 bronze badges. Felix Felix 2 2 gold badges 7 7 silver badges 20 20 bronze badges. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password.

Post as a guest Name. Email Required, but never shown. The Overflow Blog.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. Cross Validated is a question and answer site for people interested in statistics, machine learning, data analysis, data mining, and data visualization.

It only takes a minute to sign up. I am trying to plot a histogram of my data, and I seem to be a little confused here. I am using matplotlib in Python. Here is the code from their website:. I am confused as to what the x -axis should be for my use. I have calculated the standard deviation and the mean, but I am uncertain if I should replace the np.

It sounds like what you want to do is completely replace x in the plotting function with your data, so what you should get looks like this:. Also, if you aren't planning on using nbinsor patches you can discard them by just running:. The code you proposed for generating random numbers will not generate a distribution centered on mean and with a standard deviation sigmaas your variable names suggest.

Note that if you calculate using. To generate a vector with 10 numbers following a gaussian distribution of parameters mu and sigma use. Then you can feed your x vector to the histogram plotting routine, that will calculate the histogram of a vector for plotting. Sign up to join this community. The best answers are voted up and rise to the top. Home Questions Tags Users Unanswered.

Plotting a Gaussian in Python Ask Question. Asked 5 years, 8 months ago. Active 5 years, 8 months ago. Viewed 10k times. Nick Stauner Active Oldest Votes. Henry Hammond Henry Hammond 81 3 3 bronze badges. Just one last question, when I plot this, what will go on the y-axis? It looks like it may be what portion of my data a certain bin will fall in. If you want the counts for each bin you can simply remove the whole normed argument.

My data is just looking odd. Note that if you calculate using np. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name.You will find many algorithms using it before actually processing the image. The size of the kernel and the standard deviation.

Create a vector of equally spaced number using the size argument passed. We will see the function definition later. In order to set the sigma automatically, we will use following equation: This will work for our purpose, where filter size is between :. As you are seeing the sigma value was automatically set, which worked nicely.

This simple trick will save you time to find the sigma for different settings. Here is the dorm function. Just calculated the density using the formula of Univariate Normal Distribution. We will create the convolution function in a generic way so that we can use it for other operations.

This is not the most efficient way of writing a convolution function, you can always replace with one provided by a library. However the main objective is to perform all the basic operations from scratch. I am not going to go detail on the Convolution or Cross-Correlation operation, since there are many fantastic tutorials available already.

Here we will only focus on the implementation. The function has the image and kernel as the required parameters and we will also pass average as the 3rd argument.

The average argument will be used only for smoothing filter. Since our convolution function only works on image with single channel, we will convert the image to gray scale in case we find the image has 3 channels Color Image. Then plot the gray scale image using matplotlib. We want the output image to have the same dimension as the input image.

Intro to Data Analysis / Visualization with Python, Matplotlib and Pandas - Matplotlib Tutorial

In order to do so we need to pad the image. Here we will use zero paddingwe will talk about other types of padding later in the tutorial. In the the last two lines, we are basically creating an empty numpy 2D array and then copying the image to the proper location so that we can have the padding applied in the final output.

In the below image we have applied a padding of 7, hence you can see the black border. This will be done only if the value of average is set True. This is because we have used zero padding and the color of zero is black. You can implement two different strategies in order to avoid this.

Your email address will not be published. Save my name, email, and website in this browser for the next time I comment. This site uses Akismet to reduce spam.In the previous postwe calculated the area under the standard normal curve using Python and the erf function from the math module in Python's Standard Library.

In this post, we will construct a plot that illustrates the standard normal curve and the area we calculated. To build the Gaussian normal curve, we are going to use Python, Matplotlib, and a module called SciPy. Calculating the probability under a normal curve is useful for engineers. This type of calculation can be helpful to predict the likely hood of a part coming off an assembly line being within a given specification when the statistical properties of all the parts that have come of the assembly line previously are known.

In this post, we will calculate the probability under the normal curve to answer a question like the one below:. The resistor's resistances are measured and recorded. A mean resistance of Show the probability that a resistor picked off the production line is within spec on a plot. To build the plot, we will use Python and a plotting package called Matplotlib. We will also use the norm function from SciPy's stats library.

Both Matplotlib and SciPy come included when you install Anaconda. If you do not have Anaconda installed, Matplotlib and SciPy can be installed from the command line with pip. Before we build the plot, let's take a look at a gaussin curve. The shape of a gaussin curve is sometimes referred to as a "bell curve. Next, we need to define the constants given in the problem. The mean is The lower bound is and the upper bound is Next, we calculate the Z-transform of the lower and upper bound using the mean and standard deviation defined above.

After the Z-transform of the lower and upper bounds are calculated, we calculate the probability with SciPy's scipy. Finally, we build the plot. Note how Matplotlib's ax. The finished plot is below. Notice how the area corresponding to resistors in the given specification between the upper and lower bounds is shaded.

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