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Tool to draw regions of interest (ROIs)

Project description

[[file:https://travis-ci.org/jdoepfert/roipoly.py.svg?branch=master]]

* roipoly.py

Small python module to select a polygonal region of interest (ROI) in
an image that is stored as a numpy array. The usage is similar to the
[[https://mathworks.com/help/images/ref/roipoly.html][roipoly]]
function present in the image processing toolbox from MATLAB.

[[file:/img/ROIs.PNG]]

** Installation
Either from PyPi: ~pip install roipoly~

Or get the latest version from github: ~pip install git+https://github.com/jdoepfert/roipoly.py~

** Running the examples

Basic usage:
#+begin_SRC shell
python examples/basic_example.py
#+end_SRC

Drawing multiple ROIs:
#+begin_SRC shell
python examples/multi_roi_example.py
#+end_SRC

** Usage
*** Creating a ROI
In your python code, import the roipoly module using
#+begin_SRC python
from roipoly import RoiPoly
#+end_SRC
To draw a ROI within an image present as a numpy array, show it first
using e.g. pylabs's =imshow=:
#+begin_SRC python
from matplotlib import pyplot as plt
plt.imshow(image)
#+end_SRC
Then let the user draw a polygonal ROI within that image:
#+begin_SRC python
my_roi = RoiPoly(color='r') # draw new ROI in red color
#+end_SRC
This lets the user interactively draw a polygon within the image by clicking
with the left mouse button to select the vertices of the polygon. To
close the polygon, click with the right mouse button. After finishing
the ROI, the current figure is closed so that the execution of the code
can continue.


*** Displaying a ROI
To display a created ROI within an image, first display the image as
described above using e.g. =imshow=. Then,
#+begin_SRC python
my_roi.display_roi()
#+end_SRC
shows the created ROI on top of this image.

Display multiple ROIs like so:
#+begin_SRC python
for r in [my_roi1, my_roi2, my_roi3]
r.display_roi()
#+end_SRC

To additionally show the mean pixel grey value inside a ROI in the
image, type
#+begin_SRC python
my_roi.display_mean(image)
#+end_SRC

*** Extracting a binary mask image
The function =get_mask(image)= creates a binary mask for a certain ROI
instance, that is, a 2D numpy array of the size of the image array,
whose elements are =True= if they lie inside the ROI polygon,
and =False= otherwise.
#+begin_SRC python
mask = my_roi.get_mask(image)
plt.imshow(mask) # show the binary signal mask
#+end_SRC

This mask image can be used to e.g. calculate the mean pixel intensity
in an image over that ROI:
#+begin_SRC python
mean = plt.mean(image[mask])
#+end_SRC

*** Drawing multiple ROIs
See =examples/multi_roi_example.py=

** Credits
Based on a code snippet originally posted [[http://matplotlib.1069221.n5.nabble.com/How-to-draw-a-region-of-interest-td4972.html][here]] by Daniel Kornhauser.

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