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Pill Detection & Prescription Analysis

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Abstract and Figures

The main objective of this research was to apply computer vision and artificial intelligence techniques to identify pills and extract information from the labels on pill bottles. This project began with an app we created earlier that sorts and organizes an individual’s medical files. Given the data, it also creates reminders to take medicines on time, with a description of the medicine and how it should be taken. However, a major flaw in the app’s design was that users would have to manually enter data from a prescription into a form. Hence, we decided to write a program that extracts information from a prescription (typically found on pill bottles) in a useful format. Additionally, given that we wanted to increase people’s organization with respect to their medical lives, we decided to design an algorithm to identify pills based on their shapes, colors, and imprints.
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Research Report
Pill Detection &
Prescription Analysis
Gitika Bose (gb2606)
Tejit Pabari (tvp2107)
May 10, 2019
Table of Contents
Table of Contents 1
Introduction 3
Pill Recognition 5
Introduction 5
Collecting Data 6
Shape 7
Opencv’s Grabcut 8
K-Means Clustering 9
Contour Detection 11
Template Matching 13
Color 15
Imprint 21
Initial Attempts 21
Google Vision Model 23
Integration 26
Text Extraction from Labels 27
Introduction 27
Text Detection 28
Natural Language Processing 29
Extensions 33
Pill Recognition 33
Text Extraction 35
Citations 36
Appendix 37
Introduction
The main objective of this research was to apply computer vision and artificial
intelligence techniques to identify pills and extract information from the labels on pill bottles.
This project began with an app we created earlier that sorts and organizes an individual’s
medical files. Given the data, it also creates reminders to take medicines on time, with a
description of the medicine and how it should be taken. However, a major flaw in the app’s
design was that users would have to manually enter data from a prescription into a form. Hence,
we decided to write a program that extracts information from a prescription (typically found on
pill bottles) in a useful format. Additionally, given that we wanted to increase people’s
organization with respect to their medical lives, we decided to design an algorithm to identify
pills based on their shapes, colors, and imprints.
In this report, we first discuss our approach to identifying pills using primarily opencv
algorithms. Given the shape, color, and imprint of a pill, we were able to query an FDA
approved database. To determine the shape of a pill, we first use various preprocessing
algorithms such as grabcut and k-means clustering to remove the background. Then, we apply
the the findContours() function built into the opencv framework to get contours surrounding the
pill. Since we had images of pills from the database, we created templates for each shape so that
we can perform template matching against the pill contour to determine the closest shape. For the
color, the image is again preprocessed with grabcut. To identify the colors, we perform k-means
clustering and isolated three cluster centers, one of which is always black and thus removed from
consideration. To determine the name of the corresponding colors, we used k-nearest neighbours
by comparing the distance between the cluster centers and every RGB value observed for each
color and choosing the majority of the 5 closest colors.
Finally, we had to determine the imprint on a pill from a given picture. This proved to be
one of the most challenging and important parts of pill identification. Ultimately, we used
Google Vision to train using dataset from the database. Through this method, we are able to
recognize most letters and numbers that appear on pills without much preprocessing. This
method and all other algorithms discussed here are explained in detail throughout the report.
For the next part of this report, we discuss our approach to text detection and extraction
from pill labels. To recognize the text, we used the Google Vision OCR algorithm, which was
very successful. To extract relevant information from this text, we combined our knowledge of
the structure of prescriptions on pill bottles and Natural Language Processing techniques. For
example, to determine the name of the medicine, we first query the database for every every
word identified in the label. From this, we make a list of potential names and compare them to
standard drug nomenclature to determine which one is a medicine name. If we are not able to
narrow down one choice for the medicine name, we choose the largest word of all potential
medicine names. With similar techniques, we are able to isolate the pharmacy name, dosage and
form of medication, and how and when to take it. This completes the prescription and can be
easily integrated into our app.
Finally, we highlight areas of improvements and potential extensions to this research. For
example, it would be useful to integrate our pill identification and prescription analysis
algorithms to our app. Other improvements include training a model with more samples, using
multiple databases to check for medicine names, and performing post processing of text using
other NLP algorithms.
Pill Recognition
Introduction
Our first objective was to recognize a pill given a picture. We did this by extracting
features from that picture that uniquely identify it.
Our first step was to gather an understanding of the problem at hand. After going through
standardized pill databases, we found that each pill can be recognized by the combination of
three main features: color, shape and imprint.
To elaborate on these three features:
1. Shape: The database classifies the pills into 15 shapes, including some common ones
such as square and pentagon, alongside obscure ones such as freeform. To identify the
shape of the pill in the picture, we use opencv’s grabcut-algorithm to obtain the outline of
the pill, then passed it through K-Means and processed it to clear up the background, and
then used grabcut again to get the contours of the pill. We compared the contours against
templates of differently shaped pills that we extracted earlier. This gives us the number of
pixels in the image not matching the templates’, which when passed through a threshold
function, gives us the top shape possible for that pill image.
2. Color: Based on our observation, a pill can have one or two colors in itself. To identify
the color of the pill, we use K-Means clustering with k
= 3 (1 for the background) and
check the hex values of the resultant clusters. If any two hex values are within the
threshold set by us, then we consider them as one (the pill is only single colored).
3. Imprint: Every pill that requires a prescription is mandated to have an imprint on it. An
imprint can be formed of any letter, upper or lower, or number. To identify imprint, we
trained a neural network for letters and numbers and processed the result to get individual
imprint and group imprints.
Collecting Data
To collect data, we used the rx-API. We considered this amongst other APIs because of
three major reasons:
1. It was easier to use and query as compared to other APIs/websites. Often we had to deal
with websites and that required parsing through HTML code to get the desired
information. Hence we chose the most convenient option available.
2. It was updated and had concise information, information that we needed. Other API’s
were not updated according to the latest FDA standards.
3. It had clear images that we could use to develop our algorithms and models. Other
API’s/websites had images missing for some medicines, while some weren’t clear.
After selecting the API, we parsed through all different categorizations we can use to
group the pills in the database. We used shape and color to group the pills, since we have to
cover all shapes and color for the shape and color algorithm. We downloaded all images by the
category for further use.
We also downloaded data from the database, to make a mini database of our own, with
data for each pill including their names, urls, imprints, colors and shapes. We made dictionaries
for all single word imprint in the database (A-Z,a-z,0-9), storing each imprint letter with the pills
that have the letter. These are used later to shorten the list of pills and identify pills quickly. This
helps as the database allow querying of a single letter imprint, which may be possible in several
scenarios. We made similar dictionaries for color and shape.
 
Shape
The pill database gives us a total of 15 shapes used to classify pills. Some of these shapes
have a significantly high number of pills (with round as the highest at 2000+ images), while
some have very few (with freeform, octagon as the lowest with 3 images each). Some shapes
occur commonly, while others are obscure.
Figure 1: Pills of Different Shapes
1
We researched multiple algorithms to extract the shape of the pill and even developed our
own. One significant algorithm that we developed, but did not end up using, was to extract pixels
in a 5 × 5 box, from the corners of the pill image and consider them as the background. Any
pixel in the picture that comes in the set of background pixels is changed to (0,0,0) i.e. black,
which gave us the foreground. This was a good method, however, it didn’t work on images with
multicolored and patterned background, since the pixels in the corners do not necessarily
represent the background of the whole picture in such cases. Out final method of choice was
opencv’s grabcut-algorithm.
Applying Grabcut to a pill gives us:
Figure 2: Pill Before Grabcut (left). Pill After Grabcut (right)
1 https://rxnav.nlm.nih.gov/RxImageAPIs.html#
Opencv’s Grabcut
The grabcut algorithm works in the following way:
1. The user of the algorithmselects a rectangle that highlights the foreground of the image.
All pixels outside the rectangle are classified as definite background - called known
pixels, while images inside the rectangle can be potential background, hence called
unknown pixels.
2. The foreground and background are modeled as Gaussian Mixture Models (GMMs).
3. The Foreground GMM and the Background GMM assign a label to each pixel (the most
potential gaussian component for that pixel). New GMMs are learned from this.
4. A graph of the pixels is made and Graph Cut is used to find a new classification of the
foreground and background pixels.
5. Steps 3-4 are repeated as defined by the user or until convergence is reached.
Code for Grabcut Algorithm:
# Create a mask of the image, similar to the image. This is where the algorithm marks pixels
as foreground or background
mask = np.zeros(img.shape[:2],np.uint8)
# Define the Foreground and Background Models - arrays used by the algorithm internally
bgdModel = np.zeros((1,65),np.float64)
fgdModel = np.zeros((1,65),np.float64)
# Define the Rectangular Foreground. Everything outside the box is considered a definite
background
rect = (5,5,img.shape[1]-5,img.shape[0]-5)
# Run the algorithm, with 5 iterations in this case. cv2.GC_INIT_WITH_RECT is used because
the rectangle mode is used.
cv2.grabCut(img,mask,rect,bgdModel,fgdModel,5,cv2.GC_INIT_WITH_RECT)
# The mask has four labels. All pixels labelled 0 and 2 are converted to background (black)
and all pixels labelled 1,3 are kept as foreground.
mask2 = np.where((mask==2)|(mask==0),0,1).astype('uint8')
# The mask is multiplied with the input image to give the new image.
img = img*mask2[:,:,np.newaxis]
Amongst all the algorithms we tried, grabcut gave the best result since it uses the most
sophisticated and precise way to segment the foreground and the background. However, it
sometimes leaves some part of the background out, such as:
Figure 3: Faulty Grabcut - Pill Before Grabcut (left). Pill After Grabcut (right)
In the above image, grabcut does not crop the pixels near the border, as they are too near
to the pill and hence, grabcut groups them with the pill. To resolve the issue, we use K-Means.
Also, at this point, the image is passed on to the Color algorithm.
K-Means Clustering
K-means Clustering takes the pixels of the image and clusters them in k parts. It starts
with k random points as cluster, classifying each pixel to a cluster center and then recalculates
the cluster centers as the mean of each cluster. It continues this process until convergence is
reached and all the points are classified. A full explanation and a detailed implementation of the
algorithm is given in the next section (Color), since it is used primarily to identify the color.
We use a clustering of 4, i.e. 4 cluster centers are made. After K-Means, the image looks like:
Figure 4: Before K-Means Clustering (left) After K-Means clustering(right)
We decided to use k
=4 since we assumed that, in worse case scenario, there is some
background left after the grabcut and that the pill in the picture has the maximum colors it can
have i.e. 2. Summing them up gives me 3, plus one for the black, which leads to 4 clusters.
In case of this picture, clustering doesn’t help because the pill is single colored and so is
the background. Hence, it classifies the pink of the pill using two clusters, the background as the
third cluster and black as the fourth. Hence, we post process the image after K-Means.
In post processing, we consider 5 pixels from all the edges of the picture as background.
We then make a set of the pixels and remove those which have a count less than 500, since it is
possible that there were a few pixels in the background with the same color as the pill, pixels left
out by grabcut, that we can’t see with our naked eye because of the black. This results in a set of
pictures forming only the background, pixels that can be deleted from the picture to give the
foreground. The algorithm for post processing is as follows:
# 5 pixels from the edges as background
edge_pixels = {}
w_in = [x for x in range(5,w-5)]
h_in = [x for x in range(5,h-5)]
# parse through the image and count all the pixels in the selection above
for i in range(h):
for j in range(w):
if i not in h_in:
if tuple(new_img[i][j]) not in edge_pixels: edge_pixels[tuple(new_img[i][j])] = 0
edge_pixels[tuple(new_img[i][j])] += 1
if j not in w_in:
if tuple(new_img[i][j]) not in edge_pixels: edge_pixels[tuple(new_img[i][j])] = 0
edge_pixels[tuple(new_img[i][j])] += 1
# remove pixels with count less than 500
to_delete = [e for e in edge_pixels if edge_pixels[e]<500]
for t in to_delete: del edge_pixels[t]
# parse through the image and set all the remaining background pixels to (0,0,0) i.e. black
edge_pixels = set(edge_pixels.keys())
for i in range(h):
for j in range(w):
if tuple(new_img[i][j]) in edge_pixels:
new_img[i][j] = [0,0,0]
After post-processing the image becomes:
Figure 4: Image before post-processing (left) Image post-processing (right)
As seen above, post processing effectively removes the grey background.
Contour Detection
We finally have a picture of the foreground with a black background. To get the shape of
the pill, we extract the contours from this image. Contours are curves joining all continuous
points along the boundary that have the same color or intensity . Before getting the contours, we
2
process the image by converting the non-black pixels of the images to white. Next we blur it,
using the GaussianBlur method, which is the blurring of an image by a Gaussian Function. Then
we convert the image to black and white using cv2’s COLOR_BGR2GRAY function and
threshold it by passing it through cv2’s Otsu’s Threshold, which makes all non black pixels
white, converting the image to a pure binary image. All this processing helps with contour
detection.
We then pass this new image through cv2’s findContour function. The findContour
function a list of contours; oftentimes, there are more than one, however all are insignificant
except the the one outlining the shape. Post finding the largest contour, we make a blank image
such that the contour lies exactly on the edge of the image, and then draw the contours out on a
new image using cv2’s drawContour function.
2 OpenCV: Contours
: Getting Started
. https://docs.opencv.org/3.4/d4/d73/tutorial_py_contours_begin.html.
Accessed 9 May 2019.
Figure 5: Image with Contours (left) Outline of the pill made from the largest contour (right)
The algorithm for finding contours is:
# Changing all non-black pixels to white to ready the image for find-contour
img[np.where((img!=[0,0,0]).all(axis=2))] = [255,255,255]
# Blurr, Gray and Thresholding to ready the image for find-contour
blurred = cv2.GaussianBlur(img, (5, 5), 0)
gray = cv2.cvtColor(blurred, cv2.COLOR_BGR2GRAY)
thresh = cv2.threshold(gray,0,255,cv2.THRESH_OTSU)[1]
# Finding contours using cv2's findContours
cnts = cv2.findContours(thresh.copy(), cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
cnts = imutils.grab_contours(cnts)
# Calculating the largest contour
final = []
for c in cnts:
if len(final)==0:
final = c
elif len(c) > len(final):
final = c
# Making a blank image of the size of the contour, with 5 pixels as leeway.
# cv2's boundingRect returns a rectangle around the contour.
# x_n and y_n arrays shift the contour to the edge of the image
# Draw contour draws the contour on the new image
x, y, w, h = cv2.boundingRect(final)
white = np.zeros((h+5,w+5),np.uint8)
white[white == 0] = 255
x_n = [c[0][0]-x+3 for c in final]
y_n = [c[0][1]-y+3 for c in final]
arr = [[x_n[i], y_n[i]] for i in range(len(x_n))]
ctr = np.array(arr).reshape((-1,1,2)).astype(np.int32)
cv2.drawContours(white, [ctr], -1, (0, 0, 0), 8)
Template Matching
We now have the outline for the pill-image, next comes finding what the shape actually
is. To do so, we use a modified version of template matching. Template matching is a technique
used to find parts of an image that match the given template. It slides the template over the image
and compares the template and patch of input image under the template . In our case, we have
3
pre-extracted outlines for each shape, which we use as templates, while the outline of the
pill-image forms the image the template is compared against. We resize these two images to the
same width and compare them using the mean square error function. This function finds the
difference between each pixel, squares it, sums this for all pixels and divides that by the product
of number of pixels in both images, giving the mean of the squared error. The lower the error,
the better the images match each other. The Mean Square error function is:
def mse(imageA, imageB):
# convert pixel values to float, find the difference and square it.
# Sum the error for each pixel and divide by product of total pixels to obtain the mean
err = np.sum((imageA.astype("float") - imageB.astype("float")) ** 2)
err /= float(imageA.shape[0] * imageA.shape[1])
return err
We calculate the Mean Square error of the picture with all the templates and take the
lowest one as our first shape. We don’t consider it as the final shape, since we found that often
shapes are closer to each other and the first shape might not be the one that the pill refers to.
Even though the template comparison shows otherwise, pills can still vary by a bit and the
shapes can look like one another.
To counter this, we group together similar looking shapes, such as oval and diamond:
Figure 6: Diamond (left) and Oval (right)
3 Template Matching — OpenCV-Python Tutorials 1 Documentation
.
https://opencv-python-tutroals.readthedocs.io/en/latest/py_tutorials/py_imgproc/py_template_matching/py_template
_matching.html. Accessed 9 May 2019.
We find the group the first shape belongs to and multiply the mean square error for each shape in
that group by the probability of not finding that shape amongst all pills. We do this since we are
comparing lower numbers, i.e. if the probability of finding a shape is high, probability of not
finding it is low and hence multiplying it by the mean square error error will decrease the mean
square error more than that of a shape which has a low probability of being found and hence a
high probability of not finding. For instance, say the mean square errors for oval and diamond
are 16000 and 14000 respectively. The probability for not finding oval and diamond is 0.665 and
0.996 respectively. Multiplying them gives 10640 and 13944 for oval and diamond respectively.
Here oval is much lesser than diamond, even though initially it was much larger. Thus, oval is
selected since it has a higher chance of occuring.
The code for the algorithm is:
for shape in shapes:
temp = cv2.imread(template_folder+shape+'.png')
template = temp.copy()
h_t, w_t = template.shape[:2]
# If the height of image is >= half of the template or vice versa, don't compare them
if h >= h_t*2 or h_t >= h*2: compare.append((99999999,shape))
else:
w_i, h_i = min(w, w_t), min(h, h_t)
# finding the mean square error
result = mse(img[:h_i,:w_i],template[:h_i,:w_i])
compare.append((result, shape))
compare_dict[shape] = result
# remove all not-compared shapes and sort them by the mean square errors
compare = [x for x in compare if x[0]!=99999999]
compare.sort(key=lambda x:x[0])
# take the first shape
ans = compare[0][1]
for g in groups:
if ans in g:
# for all shape in that group, multiply them by the probability of not being found.
for gg in g:
if gg in compare_dict:
result = compare_dict[gg] * (1-probability[gg]/4400)
compare2.append((result,gg))
compare2.sort(key=lambda x:x[0])
The element with the lowest error is our shape. Running the shape algorithm takes 5.7 seconds.
Color
Color is another distinguishing feature of a pill. Based on the database used, there are a
total of 12 possible colors for a pill with white being the most common. Initially, we calculated
the mean of pixels in different parts of the pill. Then, we chose the color (from the 12 identified
colors) with the minimum euclidean distance to the mean. The first major problem with this
method was that it was not reliable. While the pills came in a variety of shades, this algorithm
was based on choosing an arbitrary shade for each color. This is especially problematic if the
RGB value of the pixels in the image were between two of the given colors. For example, it
identified the color of the pill below, shown on the left in Figure 2, as “gray” even though the
label given in the database was “white”. Secondly, we could not predict whether the pill
consisted of one or two colors. Hence, we were not sure which regions we should use in
detecting the “mean” color of the pill. The image below shows an example of a capsule with two
colors (on the right).
Figure 7: White pill easily mistaken for gray (left) and pill with two colors (right)
K-Means Clustering
A more suitable alternative was to use k-means clustering to divide the colors in the pill
and background clearly. K-means clustering typically chooses k
cluster centers arbitrarily and
changes them until the data is divided into k
clusters such that each center is the mean of all
values in one of the clusters. The data is fully divided once all values in a cluster are closest to
their cluster center. We decided to set k = 3
for all images to account for pills consisting of two
colors. To perform k-means clustering, we used the library “scikit-learn” as follows:
# Opens image using PIL and gets all pixels in a list
im = Image.open(input_file)
pixels = list(im.getdata())
# Converts the pixels from RGB values to uint8
pixels = [(x/255, y/255, z/255) for (x,y,z) in pixels]
# Clusters the data using c as the number of clusters
c = 3
cluster = KMeans(n_clusters=c).fit(pixels)
# Makes a list of the cluster centers (dominant colors)
colors = cluster.cluster_centers_
color_rgb = [(x*255, y*255, z*255) for [x,y,z] in colors]
This algorithm was advantageous because we no longer had to choose regions in advance
to study as the algorithm adapts well to new images. To ensure that there was less disturbance
from the background, we used the grabcut algorithm (introduced above with the section
regarding Shape) on every image before attempting to decide its color. Since the algorithm is
designed to make the background black, we made an assumption that one of one of the cluster
centers would be black and could be removed from consideration. Figure 8 below shows the
effect of using grabcut and k-means clustering on two images of pills.
Figure 8: Grabcut and k-means clustering on a white pill (left) and a two color pill
According to these images, this algorithm is successful in dividing the pill and
background into its respective colors. The pill on the left in Figure 8 highlights a caveat of using
k-means algorithm with k = 3
. It returned two cluster centers for the pill, one of which evaluated
to white while the other was gray. To isolate white, we compared the predictions for all the
pixels in the image. We found that while approximately 160000 pixels were white, only 4000
were gray. Given that this is not close to an equal division of the two colors we decided, it is
obvious that white is the only color for the pill. Generalizing this idea to all pills, we decided that
if two different colors are returned by the algorithm, we will check if the pixels of one color are
more that double the number of pixels of the other color. If this is the case, we return only the
more frequent one. If not, both colors are returned as if the pill consists of 2 colors (shown on the
right in Figure 8).
K-Nearest Neighbours
While k-means clustering is effective in isolating the correct RGB values for the pill, this
method did not solve our first major problem of colors existing in many shades instead of the one
arbitrary shade. To account for this, we extracted all the RGB values for every color that
appeared in the database (for only single colored pills) using k-means with k
= 2 and saved these
values to text files. The images below shows 3D visualizations (using matplotlib) of the range of
colors present for various pills. On the left we show a plot consisting of all RGB values for
yellow and green, while the right shows all RGB values for blue and brown. The points are
marked by their respective colors.
Figure 9: Visualization of RGB values for various colors in the database
After performing k-means clustering on a new image, we used k-nearest neighbours
with the dataset described above to classify the RGB value as one of the 12 colors. Since there
were less than 4000 unique colors to compare with, we realized that a brute force implementation
of KNN would be appropriate in this case.
# Loop through the cluster centers
for c in color_rgb:
# Creates list of tuples of euclidean distances and the color names
all = []
for color in colors:
for i in color_values[color]:
if i:
d = dist.euclidean(c, i)
all.append((d,color))
# Sorts the list and selected the top k (in this case, k=5) values
all.sort(key=lambda x: x[0])
all = all[:5]
Hence, we compared the new cluster centers with each RGB value for each color using
Euclidean distance and performed majority voting on the k
nearest values. After some trial and
error, we chose k
= 5 as it often led to the correct answer and seems to be a fair number in this
case. In the case of a tie, we decided to choose the set of neighbours whose total distance from
the point was least. The 3D plots in Figure 9 indicate how a point is classified based on the
region in which it falls on the graph. While this model worked well with most pill images, it was
faulty in some instances. For example, the image below (left) shows a pink pill which the
algorithm identifies as white.
Figure 10: Misclassified image (left) and visualization of pink and white RGB values along with
misclassified color (right)
The image on the right in Figure 10 is the 3D visualization of all white and pink RGB
values with the cluster center for the pill, returned by the k-means algorithm. According to this
plot, the B value was so high that it was categorized as white. To understand why this occurred,
we found the database image for the pill and compared this processed image to the database one.
When the algorithm is run on the database pill, it returns “pink”. The images are shown below.
Figure 11: Processed misclassified pill (left) and pill from database (right)
This highlights the effect of lighting and quality of picture taken as there is significant
difference between the picture we took and the actual pill. However, another issue is that even
though we used 5 nearest neighbours, there was significant overlap between some RGB values
which could potentially distort the color returned. Consider the example shown below.
Figure 12: Classified pill (left) and visualization of yellow and green RGB values along with the cluster
center for yellow from the pill (right)
The image on the right in Figure 12 is once again the 3D visualization of all green and
yellow RGB values. However, this time we are focusing on the point (129, 153, 119) which was
the cluster center for the green side of the pill, returned by the k-means algorithm. Clearly, it falls
in a region between yellow and green where there is significant overlap. Personally, I had trouble
deciding between the two colors and was leaning towards yellow before I checked the database.
Similarly, the algorithm could have misclassified it as yellow, instead of green. While there were
no issues in this case, this error is difficult to eradicate and hence the algorithm is only mostly
effective. However, in an attempt to reduce the likelihood of such an error, we decided to clean
up the data collected for the various RGB values. To do this, we calculated the mean and
standard of the data for each color. Then, using their z
-scores, we checked that each value was
within 3 standard deviations of the mean. The code snippet below shows how we did this:
def outliers(data):
# Creates a list of outliers to be removed later
outliers = []
# Calculates mean and standard deviation
mean = np.mean(data)
std =np.std(data)
for v in data:
# Checks if z score is less than 3 standard deviations
z_score= (v - mean)/std
if np.abs(z_score) > 3:
outliers.append(v)
return outliers
Finally, after removing outliers, we used images of pills taken by us and found that
k-means clustering with k-nearest neighbours for classification of colors was accurate in most
cases.
Running the Color algorithm takes a total of 3.8 seconds, however, it shares 1 second
with the grabcut used for shape as well.
 
Imprint
Initial Attempts
Given that the imprint is one of the most important ways to uniquely identify a pill,
recognizing imprints was arguably the most challenging aspect of identifying pills. To get
started, we used Tesseract OCR and Google Vision in an attempt to extract text from the pill.
However, we quickly noticed that these algorithms were not suited for unusual fonts such as the
the one shown below in Figure 13 (leftmost image). A better alternative, we thought, was
handwriting recognition algorithms. However, as seen in Figure 13 (middle) it was also
unsuccessful because because the font is unlike any handwriting and the text is usually engraved
into the pill making it difficult to discern, sometimes even for the human eye. The images below
shows two pills in which the imprint is unclear for these reasons.
Figure 13: Pills with imprints that are unclear due to unusual fonts (left) and faint engravings (right)
To rectify these issues, we decided to focus on the preprocessing of the image. Initially,
we performed Adaptive Gaussian thresholding, in an attempt to make the image black and white
with clear text. However, we found that it did not affect the image significantly. Instead, we used
our own algorithm for which we decided a fixed threshold. Any pixel whose RGB value was
below than the threshold was immediately classified as black. The intent of this algorithm was to
highlight the text, which is typically darker than the rest of the pill. The result of the algorithm is
shown below in Figure 14.
Figure 14: Pill with WC after preprocessing with algorithm
As seen above in Figure 14, the main issue with this algorithm is that the letters were not
complete even though there are other regions of the pill that also turned black and gray colored.
We also tried to apply k-means clustering since it was successful in determining shape and color.
The results are shown below.
Figure 15: Pills after k-means clustering
Evidently, the pill on the left in Figure 15 was made clear as the imprint was classified
immediately as black while the pill itself was a lighter color. The image on the right, however,
was affected even less than the algorithm we wrote. Most of the pill is divided into different
shades of gray but there are no discernable letters. Finally, we attempted to make the image
clearer using simple techniques like increasing the contrast and sharpness. However, ultimately
we found that none of these techniques were effective. Hence, we decided to train a model.
Google Vision Model
To train our model we chose Google Vision, since we found that it a better text
recognition algorithm, in general with an easy interface for training. Before training we
assimilated the data for all the letters and numbers separately and labelled them such that there
was a max of 2.5 to 1 ratio between the number of pictures labelled for each letter (so that, for
instance if J is 40, we labelled about 100 A’s). We did so because this ensured seamless training
of the model and prohibited skewing of the data. We chose to train the number and letters model
separately since there were many more images for each number than there were for each letter.
To label the images, we used a software called RectLabel. It gave us the xml files for
each labelled image, from which we extracted the labels and the coordinates for bounding boxes
into a csv file. We then uploaded it to google vision ML training, which gave us a model.
Post labelling, we called our model to get predictions. We used the following function:
def get_prediction(content, project_id, model_id):
prediction_client = automl_v1beta1.PredictionServiceClient()
name = 'projects/{}/locations/us-central1/models/{}'.format(project_id, model_id)
payload = {'image': {'image_bytes': content }}
params = {}
request = prediction_client.predict(name, payload, params)
return request
The function returns predictions to us. The prediction look something like this:
Figure 16: Image (left) and Prediction (right)
The prediction contains the display name, the threshold score for that label and the
bounding boxes.
Next, we resolve these bounding boxes in the y and x direction. In resolving them, we
identify groupings of the letters and numbers, based on bounding boxes.
Figure 17: Sample pill for imprint recognition
For instance, for this pill, we get the labels ['5', '5', '5', '0', '0', '0'] from the model.
Querying 5 and 0 separately (since we don’t know the order) in the API gives us 100s of images.
To remove the incorrect ones, we have to get the right grouping of the imprints, such that we get
['50', '50', '50'].
To do so, we first resolve the imprints in y
direction. We check each y
coordinate of the
labels and group together labels that share 75% of the same area. This gives us seperate lines of
imprints in the pill. The code is as follows:
# Parse through all the bounding labels
for r in res:
ytop,ybot = r[2],r[4]
check = True
for b in bounds:
# Calculating 75% of the y for the bounds
s5 = 75*(b[1]-b[0])/100
# Checks for checking if the label falls under already defined bounds.
if b[0] <= ybot <= b[1] and b[0] <= ytop <= b[1] and (ybot-ytop) >= s5: ...
elif ybot >= b[1] and b[0] >= ytop and (ybot-ytop) >= s5: ...
elif b[0] <= ybot <= b[1] and (ybot-b[0]) >= s5: ...
elif b[0] <= ytop <= b[1] and (b[1]-ytop) >= s5: ...
# If it doesn't fall under defined bounds add to bounds
if check:
bounds.append([ytop, ybot, count])
return [sorted(v,key=lambda x:x[1]) for k,v in result.items()]
We do similar bound checking for x as well, grouping together labels that are near each
other, as compared to the threshold (0.3). The code is:
for rr in res:
bounds = []
for r in rr:
n, x1, x2 = r[0], r[1], r[3]
check = True
for b in bounds:
b_n, b_x1, b_x2 = b[0], b[1], b[2]
# If the two labels are less than 0.03 far, then consider them in a group
if abs(x1-b_x2) <= 0.03:
b[0] += n
b[2] = x2
check=False
break
# If it doesn't fall in any bound, add new bounds
if check:
bounds.append([r[0],r[1],r[3]])
for b in bounds: result.append(b[0])
return result
Our final step includes making a set of all pills that have the imprint, the color and the
shape. We intersect these three to get set of pills. If we get a return value from the resolved
imprints, we parse through the set of pills we have and find which pill has the resolved imprints.
If not, we just output the set of pills.
The final output of our Pill-Detection Algorithm Looks like this:
Color: ['white']
Shape: ['trapezoid']
Imprint1: ['5', '5', '5', '0', '0', '0']
Imprint2: ['50', '50', '50']
Pill: 0001trapezoid, url:
https://rxpillimage.nlm.nih.gov/RxImage/image/images/gallery/original/50111-0441-02_RXNAVIMA
GE10_CB1265D3.jpg
We provide a pill name, which is how we have stored basic information about the pill in
our database. We also give a URL to the picture and information of the pill in the actual
database.
The imprint algorithm takes 2.3 seconds.
Integration
Our algorithm runs in 11 seconds. Below is the final design, shown using the pill “pantoprazol”:
 
Text Extraction from Labels
Introduction
Our second objective involves extracting information from prescriptions found as labels
on pill bottles. The image below shows an example of such a label, found on CVS bottles.
Figure 18: An example of a typical label found on CVS pill bottles
4
The process of extracting relevant information from labels can be divided into the
following steps:
1. The first step in our research was recognizing the text shown in sample labels. To ensure
the text would be accurate, we first researched on techniques to preprocess the image so
that it is readable. Then, we focused on choosing a seemingly reliable algorithm that
worked consistently for various labels. Ultimately, we applied adaptive gaussian
thresholding on the image and converted to a grayscale image, which is preferred by
Google Cloud Vision, the text detection framework that was finally used.
2. The next step was to apply Natural Language Processing to extract relevant information
such as the name of the medicine, patient name, pharmacy, and other such details related
to the medication.
4 “ScriptPath Prescription Labels Help Make Adherence Easier.” CVS Health Payor Solutions
,
https://payorsolutions.cvshealth.com/insights/scriptpath-prescription-labels-help-make-adherence-easier. Accessed
10 May 2019.
Text Detection
Initial research on optical character recognition (OCR) showed that Tesseract OCR was
commonly used for text detection. While this algorithm was occasionally effective, it was highly
dependent on the image itself. With further exploration, we discovered that an ideal image would
have black text on a white background with minimal noise. To do this, we first attempted to
create our own image thresholding algorithm that used the RGB of each pixel to determine
whether it was closer to black or white, classifying it accordingly. This is shown in the image
below in Figure 19. Later, we tried a number of thresholding algorithms, which we compared
until we decided to use Adaptive Gaussian thresholding to create the most clear black and
white image. The advantage of this thresholding is that the algorithm determines the threshold
for a pixel based on a small region around it. Hence, we can get different thresholds throughout
the same image leading to better results, especially when there is varying illumination.
Figure 19: Standard CVS prescription after thresholding
We were easily able to read such an image after thresholding. However, our first major
caveat was using real pictures taken in imperfect conditions. These pictures are affected more
severely by lighting and many of them tend to be curved or rotated given that most of them can
be found on pill bottles. The set of images below in Figure 18 are pictures taken by us that show
a complete prescription on an actual pill bottle.
Figure 20: Set of images describing a prescription for Atorvastatin
As seen above, the leftmost and rightmost image in Figure 18 appear especially curved
while the others are not too clear as the paper is not of perfect quality. Hence, to improve the
quality of recognition of text, we switched to Google Vision. This accounted for rotation and
proved more accurate in reading all kinds of text.
Natural Language Processing
Once we had the text, the challenging part was extracting the relevant information for it
and building a electronic prescription for the user. Since the medicine name is the most essential
part of a prescription, we decided to extract that first. To do this, we recognized three
distinguishing facts about how the medicine name is typically presented. Firstly, it follows drug
nomenclature in that it satisfies one of many possible prefixes and suffixes. Secondly, it
generally has the generic name of the drug somewhere on the cover meaning that it would be
present in the database used for pill identification. Lastly, a pill name would normally be one of
the largest words on the prescription. All these are obvious from the four pill bottle images
shown above in Figure 18. Since the name would be in the database, first we queried every word
to see if there is a match in the database. The code snippet below shows how this is done.
URL = "https://rximage.nlm.nih.gov/api/rximage/1/rxnav?name=" + t
r = requests.get(url = URL)
r = r.json()
if r['replyStatus']['imageCount'] != 0:
potential.append((t, i))
We found that while we could identify the pill name through this method, there were
often other words such as tablet and drug that also appeared in the database. At first, we
considered ignoring words like tablets and drug when we encountered them as they are common
on pill bottles but insignificant. However, the database also had results for chemicals like
“calcium” and brand names like “Lipitor” which appeared in some of the prescriptions we
considered. Hence, we decided that we would also incorporate drug nomenclature to isolate only
valid names. The code snippet below shows the list of prefixes, suffixes and word fragments that
appear in medicines. It also shows how we compare the suffix of each potential medicine name
with the list of suffixes. The same is done for the prefixes and fragments.
prefixes = ['ceph', 'tretin', 'pred', 'sulfa', 'cef']
suffixes = ['setron', 'cycline', 'pramine', 'trel', 'asone', 'vir', 'tyline', 'zolam',
'profen', 'zepam', 'onide', 'tretin', 'nacin', 'gliptin', 'cillin', 'dronate', 'phylline',
'zosin', 'parin', 'glitazone', 'lamide', 'mab', 'oprazole', 'semide', 'sartan', 'dazole',
'bital', 'zodone', 'eprazole', 'tinib', 'statin', 'fenac', 'afil', 'caine', 'terol',
'floxacin', 'nazole', 'tadine', 'mustine', 'vudine', 'iramine', 'triptan', 'mycin',
'dipine', 'bicin', 'pril', 'ridone', 'olone', 'thiazide', 'olol']
middles = ['cort', 'tretin', 'pred', 'parin', 'vir']
med_names = set()
if len(potential) > 1:
for s in suffixes:
l = len(s)
for p in potential:
m = p[0]
if m[len(m)-l:len(m)].lower() == s.lower():
med_names.add(p)
This method was successful for all medicines that we tried except “Aspirin”. This is
because Aspirin is a common brand name and hence does not need to follow drug nomenclature.
Hence, as a last resort, if drug nomenclature is not able to isolate one name or the medicine does
not satisfy these naming rules, we incorporate the size of each potential medicine name. The
code below was used to extract the bounding boxes for every word and find the area associated
with each of them. Then, I chose the largest medicine name from the list of potential ones.
boxes = [b.bounding_poly.vertices for i, b in enumerate(text_response.text_annotations) if i
!= 0]
box_sizes =
[((i[1].x-i[0].x)**2+(i[1].y-i[0].y)**2)**(0.5)*((i[2].x-i[1].x)**2+(i[2].y-i[1].y)**2)**(0.
5) for i in boxes]
Another important aspect of a prescription is how and when the patient is supposed to
take the medicine. After viewing numerous pill labels, we concluded that this direction usually
begins with “take” and continues for 2 consecutive lines. Since Google Vision provides the
bounding boxes of every word identified, we were able to isolate these two lines to process
further. Using regex, we broke down these two lines and extracted all the schedule related
information. For example, the following code snippet shows how we extracted the number of
tablets from the line. Similarly, we extracted whether it was taken by mouth, the timing in
relation to meals, and which times of the day.
if "tablet" in schedule:
reg = '(\w+)\s+tablet'
m = re.search(reg, schedule)
m2 = words_in_sched.index(m.group(1))
words_in_sched[m2] = ""
words_in_sched[m2+1] = ""
sched['No. of tablets'] = m.group(1)
While looping through the rest of the text in the prescription, we were able to extract
more information using the following heuristics:
1. If a word matched any word in the list of pharmacies in the United States, it was chosen
as the pharmacy name
2. If it was equivalent to “mcg” or “mg”, we used regex to find the preceding word and
treated it as the dosage of the medicine
3. If the word contains “tablet” or “capsule” it is classified accordingly under “type” of pill
4. If it matches one of the patients names (stored in the app)
Figure 19 shows two images from pill bottles that contain a majority of the information
discussed above. The first label is for the drug Atorvastatin. The dosage is 80 mg and it comes in
tablet form. In terms of schedule, it directs the patient to take it once a day by mouth at bedtime.
The second label is for Aspirin. The dosage is 81 mg in tablet form. It was prescribed once a day
with meals, also by mouth. As we extracted information from the label, we added it to a
dictionary that is included below the images.
Figure 21: Pill labels for Atorvastatin and Aspirin
The dictionaries embedded below are samples of the output for two different pills shown
in Figure 19 and described above.
{'Dosage': '80 MG', 'type': 'Tablet', 'Schedule': {'How': 'by mouth', 'No. of tablets': '1',
'When': 'daily at bedtime'}, 'medicine_name': 'ATORVASTATIN'}
{'Dosage': '81 MG', 'type': 'Tablet', 'Schedule': {'How': 'by mouth', 'No. of tablets': '1',
'Meals': 'wih meals', 'When': 'once daily'}, 'medicine_name': 'ASPIRIN'}
Hence, we are able to extract all the necessary information almost perfectly using various
heuristics based on our knowledge of pill labels and drug nomenclature.
Extensions
Overall, we hope to extend the pill identification and prescription analysis algorithms by
integrating them into the app such that we can input images of pills and bottle labels in a user
friendly interface. Aside from this, we had some improvements that we would like to match to
each project.
Pill Recognition
The first improvement could have been to the kind and quantity of data used to train the
model for imprint detection. There are a number of other accessible databases that we could have
used to supplement us with more data regarding medicines and their features. This would ensure
that we are covering almost all potential pills, including over the counter and prescription drugs.
Additionally, while the images from the database were effective in training the model, a better
alternative would be images clicked by people that are more affected by lighting, different
angles, and noisy backgrounds. As the dataset increases, precision also generally increases. Since
this dataset is not easily available, we could possibly collect the data from users on the app who
upload pictures of pills they want identified.
Another issue with imprint detection was that we were unable to account for pills that had
curved text, as shown in the example below. This is because we could not include labels of
letters that appeared both sideways and straight it would confuse the model. To fix this in the
future we could rotate the image and read text at 30° angles until a full rotation is achieved.
Figure 22: Image with rotated text that says “PLIVA” and “468”
Additionally, since the two models were trained separately (for numbers and letters), it
was possible that the models could identify the same engraving differently. For example, an “I”
could be mistaken for a “1” and thus be recognized differently in both models. To handle this
error, we would have to compare the bounding boxes returned by each model. If there is an
overlap of 75% or greater between the two bounding boxes, we would choose the model that
returned a higher probability. Another improvement that we can do is based on an observation
we made that letters and numbers are mostly followed by letters and numbers respectively (in
case of grouped imprints). Hence, if we see an ‘I’ preceded or followed by numbers, we can
safely assume it is ‘1’ and vice versa. This is important since there are a significant number of
pairs that can be mistaken by the model, since our letter and number models are seperate) and
applying this would improve the model accuracy. Another possible solution for this would be to
train a model for each conflicting pair. This would give us a sure result between the conflicting
labels.
Figure 22: ‘1’ recognized as ‘I’ by the algorithm. Based on the context, we can guess 1
Lastly, we can improve the shape and color algorithm. To improve the shape algorithm
we can make more templates of the pills and then use K-Nearest neighbours to identify what
shape does the pill belong to. This improves the accuracy by allowing us to consider different
templates for the same image (such as oval, which has different types of templates since it is so
diverse). We could also train a model to recognize shapes. To improve the color algorithm, we
can find the cluster centers for all pill-images ourselves, get their color names and then make a
database of our own, classifying pills by color. This would help since the colors given by the
database are often labelled wrong. Hence, classifying them ourselves would greatly improve our
output.
Text Extraction
The first improvement we intend to do with text extraction is spell checking and common
word removal. Spell checking is necessary as our algorithm hunts for specific terms in the text.
Since there is no way to predict what Google Vision will read and output, we need to get the
spellings right for the words for our queries to work smoothly. Alongside this, sometimes names
of pills have common words in them, such as patient or drugs. We would improve in the
algorithm to remove such common words from the text or at-least not count them while querying
the database for the pill name and information.
Another improvement to this algorithm is to make add code to return information about
the pill. This is important as the user can then directly access information about the drug he/she
is taking. Also, since pill-label extraction is going to be added to our app, providing users
information about the pill they are taking increases convenience for them and also allows them to
understand what medicines they are taking and what their side effects are.
 
Citations
1. “ScriptPath Prescription Labels Help Make Adherence Easier.” CVS Health Payor Solutions,
https://payorsolutions.cvshealth.com/insights/scriptpath-prescription-labels-help-make-adherence
-easier. Accessed 10 May 2019.
2. Template Matching — OpenCV-Python Tutorials 1 Documentation.
https://opencv-python-tutroals.readthedocs.io/en/latest/py_tutorials/py_imgproc/py_template_mat
ching/py_template_matching.html. Accessed 9 May 2019.
3. OpenCV: Contours: Getting Started.
https://docs.opencv.org/3.4/d4/d73/tutorial_py_contours_begin.html. Accessed 9 May 2019.
4. RxImage API. https://rxnav.nlm.nih.gov/RxImageAPIs.html#. Accessed 10 May 2019.
 
Appendix
Gaussian Mixture Model(GMM):
A gaussian mixture model is a probabilistic model that assumes that all data points are generated
from a mixture of a finite number of Gaussian distributions with unknown parameters. In a way,
it is like generalizing K-Means Clustering, incorporating information about the covariance of the
structure of the data.
5
Graph Cut:
In context of the grabcut algorithm, the graph cut algorithm works by generating a graph using
the foreground and background pixels as nodes. Two more nodes are added, the source node, to
which all foreground nodes are connected, and the sink node, to which all the background pixels
are connected. The edges for the foreground and background node have weights defined by the
probability of a pixel being in the foreground or background respectively. The algorithm then
segments the graph into two, separating source and sink node using a cost function calculated by
the sum of all weights of the edges. Post segmentation, the pixels connected to the source node
are labelled as foreground and those connected to sink node are labelled as background. The
process is repeated as specified by the user.
6
5 2.1. Gaussian Mixture Models — Scikit-Learn 0.20.3 Documentation
.
https://scikit-learn.org/stable/modules/mixture.html. Accessed 8 May 2019.
6 “Python | Foreground Extraction in an Image Using Grabcut Algorithm.” GeeksforGeeks
, 28 Dec. 2018,
https://www.geeksforgeeks.org/python-foreground-extraction-in-an-image-using-grabcut-algorithm/.
... With this they were able to figure out the shape of the image. To determine the name of the corresponding colors, k-nearest neighbors was employed by comparing the distance between the cluster centers and every RGB value observed for each color and choosing the majority of the 5 closest colors (2) . According to Tanjina piash Proma et al, data sets are divided based on the amount of colors and imprinted texts on the pills. ...
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Full-text available
Objectives: To create a tablet recognition system that recognizes and gives an audio output of the name of the tablet so that the visually impaired person may recognize it. Methods: In this, to create a user friendly system, such that a blind person does not require the help of another person to use it. These systems give medical assistive instrument to take the drug at the accurate time as per the doctor prescription and removes dependency on others for the visually challenged people. Various models were technologically advanced to compact with misidentification of remedies but are incompetent of formative exact pill picked by the person. Findings: The name of the medicine is obtained from the image. Then the name of the medicine is converted from text to speech using Google text to speech (gTTS). The proposed system will be helpful for visually challenged people, SQLite Database management system has been used along with Scale Invariant Feature Transform algorithm (SIFT) to identify and pronounce local features in the image. The image of the medicine given by the user is matched with the images in the database. Novelty: Developed a user-friendly voice based tablet recognition system for visually impaired people and this system is fast and accurate.
ScriptPath Prescription Labels Help Make Adherence Easier
"ScriptPath Prescription Labels Help Make Adherence Easier." CVS Health Payor Solutions, https://payorsolutions.cvshealth.com/insights/scriptpath-prescription-labels-help-make-adherence -easier. Accessed 10 May 2019.