Install Miniconda on Mac

This post introduces how to install Miniconda on Mac.

(For installing Miniconda on Linux OS, check out this post.)

(For commonly used conda commands check this post.)

(For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.)

Step 1: download  Miniconda (bash installer) from

https://docs.conda.io/en/latest/miniconda.html 

see the highlighted in the pic below.

A file called Miniconda3-latest-MacOSX-x86_64.sh will be shown in your Downloads folder.

Step 2: Open a Terminal window.

(If you don’t know how to open a terminal window,  through lauchpad type in Terminal, you will see the application.)

In the terminal window, type in

$ cd Downloads

Step 3: run the bash “shell” script to install Miniconda

In the terminal window, type in the following.

$ bash Miniconda3-latest-MacOSX-x86_64.sh

Scroll through the license (press the Space bar or Enter to move through quickly), type ‘yes’ to approve the terms, and then accept all the installation defaults.

Step 4: Close the Terminal window, and open a new Terminal window.

in the newly opened Terminal window.

Type the following:

$ conda -V

If you see something like the following, it means you have successfully installed conda via miniconda on your Mac.

conda 4.5.11

Step 5: Uninstalling Miniconda

To uninstall Python Anconda/Miniconda, we just simply remove the installation folder and remove the environment variables set in the hidden file .bash_profile in your home directory. For my installation, it will be just like this.

$ rm -rf /users/my-user-name/miniconda/
$ rm -rf /users/my-user-name/anaconda/

Then, you can edit the .bash_profile file and remove the following entries added for Anaconda/Miniconda directory from your PATH environment variable.

# added by Miniconda3 installer
$ export PATH="/Users/my-user-name/miniconda3/bin:$PATH"
# added by Anaconda3 installer
$ export PATH="/Users/my-user-name/anaconda3/bin:$PATH"

If you do not know where the hidden .bash_profile is located and how to edit it, see below for detailed instructions.

(1) Open a new terminal and go to your home directory. You can do this by using the command below.

$ cd

(2) use the following command to list all files, including hidden files in your home directory.

$ ls -a 
# you should see there is a file called .bash_profile.

(3) Use the cat command to see the contents of the hidden file .bash_profile. Type the following command into your terminal.

$ cat .bash_profile

You will see something like the following (depends on what you installed, if you installed Miniconda3, you will only see the first two lines. If you installed Anaconda3, you will see the bottom two lines.

# added by Miniconda3 installer 
$ export PATH="/Users/my-user-name/miniconda3/bin:$PATH" 

# added by Anaconda3 installer 
$ export PATH="/Users/my-user-name/anaconda3/bin:$PATH"

(4) To remove installed Miniconda/Anaconda from your .bash_profile use the command below to edit the file using the nano editor.

$ nano .bash_profile

Remove the Miniconda /Anoconda path in your .bash_profile hidden file.

Then Type control + X to exit out of nano

Save changes by typing Y.

Close the terminal, and now Miniconda/Anaconda should be successfully uninstalled from your Mac.

 

(Tested on macOS Mojave. Note that you can install Miniconda onto your Mac even when you are not an admin user.)

For commonly used conda commands check this post.

For the comparison among Anaconda, Miniconda, and Virtualenv with pip, check this post.

 

 

 

 

 

 

Anaconda vs. Miniconda vs. Virtualenv

This post briefly introduces which to choose among Anaconda, Miniconda, and Virtualenv.

If you have used pip and virtualenv in the past, you can use conda to perform all of the same operations. Pip is a package manager, and virtualenv is an environment manager; and conda is both.

Specifically, conda is a packaging tool and installer that aims to do more than what pip does; it handles library dependencies outside of the Python packages as well as the Python packages themselves. Conda also creates a virtual environment, like virtualenv does.

Both Anaconda and Miniconda uses Conda as the package manager. The difference among Anaconda and Miniconda is that Miniconda only comes the package management system. So when you install it, there is just the management system and not coming with a bundle of pre-installed packages like Anaconda does. Once Conda is installed, you can then install whatever package you need from scratch along with any desired version of Python.

Choose Anaconda if you:

  • Are new to conda or Python
  • Prefer having Python and 720+ open source certified packages automatically installed at once
  • Have the time and disk space (a few minutes and 3 GB), and/or
  • Don’t want to install each of the packages you want to use individually.

Choose Miniconda if you:

  • Know what package(s) you need to install
  • Do not have time or disk space (about 3 GB) to install over 720+ packages (many of the packages are never used and could be easily installed when needed), and/or
  • Just want fast access to Python and the conda commands, and prefer to sorting out the other packages later.

Choose Virtualenv only when you have sudo access to the machine you are working on. It is much easier to setup conda rather than virtualenv for a regular (i.e., non sudo/root) user on a linux/Mac machine.

I use Miniconda myself (because it is much more light weight than Anaconda) when I need to setup python programming environment and when I do not have sudo privilege, and I use Virtualenv when I have sudo access on the machine.

(Thanks to  Dr. Brendt Wohlberg  for introducing Miniconda — Miniconda makes me switching from pip & virtualenv to conda.)

References

 

Install OpenCV3 into virtualenv on Mac

This post introduces how to install OpenCV3 into a virtualenv on Mac.

If you have not setup virtualenv on your mac, check my post here to do that before you proceed the tutorial in this post.

Let us get started.

Step 1: Activate your virtualenv in your terminal

for example:

$ source ~/ipy-jupyter-venv3/bin/activate  

(ipy-jupyter-venv3)$  # Your prompt should change

Step 2: Install OpenCV (modules) according to your needs

  1. If you need only main modules, in your activated virtualenv in your terminal, run the following
(ipy-jupyter-venv3)$ pip3 install opencv-python 

2. If you need both main and contrib modules (check extra modules listing from OpenCV documentation),  in your activated virtualenv in your terminal, run the following

(ipy-jupyter-venv3)$ pip3 install opencv-contrib-python 

Step 3: Test whether openCV is installed correctly

To test whether OpenCV installed correctly into your virtualenv, in your terminal type in those command below in bold.

(ipy-jupyter-venv3) liping$ python3.6

Python 3.6.5 (default, Mar 30 2018, 06:41:53)

[GCC 4.2.1 Compatible Apple LLVM 9.0.0 (clang-900.0.39.2)] on darwin

Type “help”, “copyright”, “credits” or “license” for more information.

>>> import cv2

>>> cv2.__version__

‘3.4.3’

>>

Step 4 (optional): To uninstall opencv inside virtualenv, following the command below according to how you installed it.

(ipy-jupyter-venv3) Liping:~$ pip3 uninstall opencv-python 

or

(ipy-jupyter-venv3) Liping:~$ pip3 uninstall opencv-contrib-python

 

Summary:

In this post, you learned how to install and uninstall OpenCV into your virtualenv.

Setting up Python and Jupyter Notebook on Mac

This page provides the instructions for how to install and run IPython and  Jupyter Notebook in a virtualenv  on Mac.

Most probably your Mac has already come with Python installed (see step 1 and step 2 below to check whether Python and Python 3 is installed on your mac, because my Mac book air has both Python and Python3.6 installed, I will go ahead to step 3 to install virtualenv).  

Open a terminal on your mac and type in Python and Python3 to see whether Python and Python3 installed on your mac. See below for example.

Follow the steps below for detailed instructions.

Step 1: Check whether Python is installed on your Mac

To test whether your Mac has Python 2.x or 3.x, look at the instructions below.

Open a terminal  (in your launchpad, type in terminal, and then click and open it.)

Type in python, if you see similar thing as the pic shown below, it means python 2.7 was installed on your Mac

type exit() to exit from the Python 2.7 environment

Type python3 in your terminal, if you see similar warning as the pic shown below, it means you will need to install Python 3 (see the steps below for installation). If you see older version (< 3.5) of python 3 installed on your mac, follow step 2 to install Python 3.5

Step 2: Install Python 3.5

I recommend you download Python 3.5.4 from here, if you do not have Python 3.x pre-installed on your mac.

https://www.python.org/downloads/mac-osx/ 

Click the installer and install it following the wizard.

When you finish the installation, type python3 in your terminal, if you see similar stuff in the pic below, Python 3.5 is installed successfully and you are ready to proceed to step 3.

Step 3: Install virtualenv 

Note: the command text in blue is the exact command you should type into your terminal, the same through this whole instruction.

Lipings-MacBook-Pro:~ Liping$ pip3 install virtualenv

Step 4: Setup virtualenv environment

Issue the command below to set up a virtualenv environment that we will use later, using the vitualenvwe installed in step 3 above.

$ virtualenv --system-site-packages -p python3 ~/ipy-jupyter-venv3

Step 5: Install IPython

Before installing IPython and Jupyter Notebook, be sure to activate your python virtual environment first.

$ source ~/ipy-jupyter-venv3/bin/activate 
(ipy-jupyter-venv3)$  # Your prompt should change

Type the following command to install IPython

(ipy-jupyter-venv3) liping:~pip3 install ipython

Step 6: Install Jupyter Notebook

Use the following command to install Jupyter Notebook

(ipy-jupyter-venv3) liping:~$ pip3 install jupyter

Step 7: Test jupypter notebook installation

(ipy-jupyter-venv3) liping:~$ which python3

/Users/Liping/ipy-jupyter-venv3/bin/python3
#for python 3.x
(ipy-jupyter-venv3) liping:~$ which ipython3

/Users/Liping/ipy-jupyter-venv3/bin/ipython3
#for python 3.x
(ipy-jupyter-venv3) liping:~$ which jupyter-notebook

/Users/Liping/ipy-jupyter-venv3/bin/jupyter-notebook

Step 8: Add Kernel

The Jupyter Notebook and other frontends automatically ensure that the IPython kernel is available. However, if you want to use a kernel with a different version of Python, or in a virtualenv environment, you’ll need to install that manually. 

We are using virutalenv, so we need to install IPython kernel in the virtualenv we created in Step 4 above.

(ipy-jupyter-venv3) liping:~$  python3 -m ipykernel install --user --name myipy_jupter_env3 --display-name "ipy-jupyter-venv3"

Installed kernelspec myipy_jupter_env3 in /Users/Liping/Library/Jupyter/kernels/myipy_jupter_env3

 

Step 9: Before we are running our jupyter Notebook, let us create a folder from which we will start our jupyter notebook.

The following command will change our directory to Desktop (cd refers to change directory)

(ipy-jupyter-venv3) Lipings-MacBook-Pro:~ Liping$ cd Desktop 

the following command will help us create a folder named Geog597_ML_session under our Desktop folder

(ipy-jupyter-venv3) Lipings-MacBook-Pro:Desktop Liping$ mkdir test_jupyter

the following command will change our directory into the folder we just created.

(ipy-jupyter-venv3) Lipings-MacBook-Pro:Desktop Liping$ cd test_jupyter/

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ 

Step 10: Run Jupyter Notebook

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ jupyter-notebook

Then your default browser should automatically open a web page similar to the one shown below.

If the web page does not show up automatically, just type localhost:8888 into your browser, you should see the page shown above.

 

Step 11: Testing and Using Jupyter Notebook

By this point you should have Jupyter Notebook running, and you should be connected to it using a web browser. Jupyter Notebook is very powerful and has many features. Below I will outline a few of the basic features to get you started using the notebook. Automatically, Jupyter Notebook will show all of the files and folders in the directory it is run from (for our case, it is empty now, because we have not put anything in that folder Desktop/test_jupyter we just created in step 9 ).

To create a new notebook file, select New > ipy-jupyter-venv3 from the top right pull-down menu (Note: this is the so called kernel we installed in Step 8 above):

This will open a notebook. We can now run Python code in the cell or change the cell to markdown (markdown is for note, not for code). For example, change the first cell to accept Markdown by clicking Cell > Cell Type > Markdown from the top navigation bar, or by click the Markdown shown in the pic below. We can now write notes using Markdown,  for example, type the following into the cell after changing it to markdown:

# Testing

Hit Ctrl + Enter, you will see it the text changed into heading style.

          Then insert one cell by the menu shown below (insert Cell Below).

type in the following

a = 5
b = 10
print (a+b)

and then hit Ctrl + Enter.  You should see the following.

Step 12: Stop jupyter Notebook.

To stop the Jupyter Notebook process, press CTRL+C,

type Y, and hit ENTER to confirm. The following will be displayed:

Step 13: Exit virtualenv environment

Once you are done, remember to exit your virtualenv using the following command:

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$

deactivate

Note that your prompt changes back (see the pic below)

Step 14: Instructions for using Jupyter Notebook next time

Next time when you need to use you jupyther notebook, following the steps summarized below.

Lipings-MacBook-Pro:~ Liping$ source ~/ipy-jupyter-venv3/bin/activate  

(ipy-jupyter-venv3)$  # Your prompt should change

Change directory to where you would like to start your jupyter-notebook

(ipy-jupyter-venv3) Lipings-MacBook-Pro:~ Liping$ cd Desktop/test_jupyter

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ 

Run jupyter notebook:

(ipy-jupyter-venv3) Lipings-MacBook-Pro:test_jupyter Liping$ jupyter-notebook

 

Congratulations, you have now set up ipython and jupyter notebook on your mac!

Cool Python Tricks

This post provides some cool python tricks.

(Stay tuned, as I may update the tricks while I plow in my deep learning garden)

With increase in popularity of python, more and more features are becoming available for python coding. Using this features makes writing the code in fewer lines and cleaner. In this article we will see 10 such python tricks which are very frequently used and most useful.

Reversing a List

We can simply reverse a given list by using a reverse() function. It handles both numeric and string data types present in the list.

Example

List = ["Shriya", "Lavina","Sampreeti" ]
List.reverse()
print(List)

Output

Running the above code gives us the following result −

['Sampreeti', 'Lavina', 'Shriya']

Print list elements in any order

If you need to print the values of a list in different orders, you can assign the list to a series of variables and programmatically decide the order in which you want to print the list.

Example

List = [1,2,3]
w, v, t = List
print(v, w, t )
print(t, v, w )

Output

Running the above code gives us the following result −

(2, 1, 3)
(3, 2, 1)

Using Generators Inside Functions

We can use generators directly inside a function to writer shorter and cleaner code. In the below example we find the sum using a generator directly as an argument to the sum function.

Example

sum(i for i in range(10) )

Output

Running the above code gives us the following result −

45

*Using the zip() function

When we need to join many iterator objects like lists to get a single list we can use the zip function. The result shows each item to be grouped with their respective items from the other lists.

Example

Year = (1999, 2003, 2011, 2017)
Month = ("Mar", "Jun", "Jan", "Dec")
Day = (11,21,13,5)
print zip(Year,Month,Day)

Output

Running the above code gives us the following result −

[(1999, 'Mar', 11), (2003, 'Jun', 21), (2011, 'Jan', 13), (2017, 'Dec', 5)]

Swap two numbers using a single line of code

Swapping of numbers usually requires storing of values in temporary variables. But with this python trick we can do that using one line of code and without using any temporary variables.

Example

x,y = 11, 34
print x
print y
x,y = y,x
print x
print y

Output

Running the above code gives us the following result −

11
34
34
11

Transpose a Matrix

Transposing a matrix involves converting columns into rows. In python we can achieve it by designing some loop structure to iterate through the elements in the matrix and change their places or we can use the following script involving zip function in conjunction with the * operator to unzip a list which becomes a transpose of the given matrix.

Example

x = [[31,17],
[40 ,51],
[13 ,12]]
print (zip(*x))

Output

Running the above code gives us the following result −

[(31, 40, 13), (17, 51, 12)]

*Print a string N Times

The usual approach in any programming language to print a string multiple times is to design a loop. But python has a simple trick involving a string and a number inside the print function.

Example

str ="Point";
print(str * 3);

Output

Running the above code gives us the following result −

PointPointPoint

*Reversing List Elements Using List Slicing

List slicing is a very powerful technique in python which can also be used to reverse the order of elements in a list.

Example

#Reversing Strings
list1 = ["a","b","c","d"]
print list1[::-1]

# Reversing Numbers
list2 = [1,3,6,4,2]
print list2[::-1]

Output

Running the above code gives us the following result −

['d', 'c', 'b', 'a']
[2, 4, 6, 3, 1]

Find the Factors of a Number

When we are need of the factors of a number, required for some calculation or analysis, we can design a small loop which will check the divisibility of that number with the iteration index.

Example

f = 32
print "The factors of",x,"are:"
for i in range(1, f + 1):
   if f % i == 0:
print(i)

Output

Running the above code gives us the following result −

The factors of 32 are:
1
2
4
8
16
32

*Checking the Usage of Memory

We can check the amount of memory consumed by each variable that we declare by using the getsizeof() function. As you can see below, different string lengths will consume different amount of memory.

Example

import sys
a, b, c,d = "abcde" ,"xy", 2, 15.06
print(sys.getsizeof(a))
print(sys.getsizeof(b))
print(sys.getsizeof(c))
print(sys.getsizeof(d))

Output

Running the above code gives us the following result −

38
35
24
24

 

 

References:

https://www.tutorialspoint.com/10-interesting-python-cool-tricks (Pradeep Elance Published on 08-Aug-2019 10:22:06)

https://www.tutorialspoint.com/questions/category/Python

Timing how long a python script runs

This post introduces several ways to find out how long a python script takes to complete its execution.

  • If you are using Linux or Mac OS, in your terminal
$ time ./your_script.py
  • Several ways to do the task by adding a few lines of code in your py script.
import time
startTime = time.time()

your_func() #python3: print ("It took", time.time() - startTime, "seconds.")

See the following for an example in python 3. 

import time
import functools

startTime = time.time()

print(functools.reduce(lambda x,y: x+y, [47,11,42,13]))

#python3:
print ("It took", time.time() - startTime, "seconds.")

Another way to do the same thing:

from datetime import datetime
startTime = datetime.now()

#do something

#Python 2: 
print datetime.now() - startTime 

#Python 3: 
print(datetime.now() - startTime)

One more way to do the same thing with a nicely formatted output.

import sys
import timeit

startTime = timeit.default_timer()

#do some nice things...

stopTime = timeit.default_timer()
totalRunningTime = stopTime - startTime

# output running time in a nice format.
mins, secs = divmod(totalRunningTime, 60)
hours, mins = divmod(mins, 60)

sys.stdout.write("Total running time: %d:%d:%d.\n" % (hours, mins, secs))

If you want to compare two blocks of code / functions quickly you can do the following:

import timeit

startTime = timeit.default_timer()
your_func1()
#python3
print(timeit.default_timer() - startTime)

startTime2 = timeit.default_timer()
your_func2()
#python3
print(timeit.default_timer() - starTime2)

[django] Sending matplotlib generated figure(s) to django web app

This post introduces how to serve the figures generated by matplotlib to django web app without saving on the server.

In your django views py file, import the following libraries

import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt

from io import BytesIO
import base64

Note: the two lines of code above in blue need to be placed at the very beginning of the py script; otherwise, you would meet the following error: _tkinter.TclError: no display name and no $DISPLAY environment variable.

In the views py file, in the function that you defined to pass the image data to the front end template file, add the following code:

buf = BytesIO()
plt.savefig(buf, format='png', dpi=300)
image_base64 = base64.b64encode(buf.getvalue()).decode('utf-8').replace('\n', '')
buf.close()

Note: in the function that you defined to pass the image data to the front end template file in your views py file, remember to send the value of the variable image_base64 via, for example, json.

Now, in your front end template file, you can add the following image tag.

<img src="data:image/png;base64,{{image_base64}}" alt="some text to display to your users when the image does not show correctly" width=500 height=auto />

You now should be able to see the figure displayed on your web app page:)

For more details about using data url to pass image data to front end html file, check here (pdf).

 

 

Tips about Jupyter Notebook

This post provides some tips about Jupyter Notebook.

  • When you open a pdf file in a browser via your running Jupyter Notebook.

You may encounter some error similar to this “Error! (file) is not UTF-8 encoded”,

the solution:

check the address in your browser, for example, for the following case,

http://localhost:8000/edit/confusionmatrix.pdf

if I change the edit in the url address given above to  view

http://localhost:8000/view/confusionmatrix.pdf

You will see your beautiful fig or document in pdf format.

  • Another similar situation:

When you open a html file in your browser via your running Jupyter Notebook, and you would like to edit the html file, instead of seeing its display,

the solution:

change view to edit in the url address of the file, see the following for an example, then you should be able to edit your html file.

http://localhost:8000/view/index.html 

to

http://localhost:8000/edit/index.html

Happy Jupyter Notebooking!

How to Deploy a Django Application on a Server Running Ubuntu

This post provides tutorials on how to deploy a Django application on a server running Ubuntu.

Softwares needed to set up a server for Django application:

  • Virtualenv & Virtualenvwrapper / Conda
  • Django
  • Gunicorn
  • Nginx
  • Supervisor

Concept

Nginx will face the outside world. It will serve media files (images, CSS, etc.) directly from the file system. However, it can’t talk directly to Django applications; it needs something that will run the application, feed it requests from the web, and return responses.

That’s Gunicorn‘s job. Gunicorn will create a Unix socket, and serve responses to Nginx via the wsgi protocol – the socket passes data in both directions:

The outside world <-> Nginx <-> The socket <-> Gunicorn

All this family will live into a Virtualenv. Already wondered why Virtualenv is so useful when you develop Pythons’s applications? Continue to read and you will understand.

Before you start

References

I assume you have a server available on which you have root privileges. I am using a server running Debian 7, so everything here should also work on an Ubuntu server or other Debian-based distribution. If you’re using an RPM-based distro (such as CentOS), you will need to replace the aptitude commands by their yum counterparts and if you’re using FreeBSD you can install the components from ports.