AR D E N B AC H N E R

Niagara College 135 Taylor Road Niagara-on-the-Lake, ON Rm E308

GISC9216 Assignment 2
Due Februrary13, 2013

Principal Component Analysis

GISC9216 - Digital Image Processing

2/13/2013 Niagara College GIS - GM Arden Bachner

AR D E N B AC H N E R
Niagara College 135 Taylor Road Niagara-on-the-Lake, ON Rm E308

GISC9216 Assignment 2
Due Februrary13, 2013

Wednesday February 13, 2013 GISC9216 D2 Mrs. Janet Finlay Niagara College 135 Taylor Road Niagara-on-the-Lake ON L0S 1J0 Re: Submission of GISC9216 Deliverable 2 Dear Mrs. Finlay, Please accept this letter as a formal submission of Deliverable 2 Principal Component Analysis for GISC9216. Attached is the written document for this deliverable. For this assignment we were to perform a PCA and then use that PCA output for an unsupervised classification that we were to compare to the unsupervised classification from Assignment 1. The subset area was the same that we created in Assignment 1. The digital files for this assignment are located under X: GISC9216\Assignment#2 entitled BachnerAGISC9216D2.docx In the event that there is a problem opening or viewing the files please contact me at; ardenbachner@gmail.com. Thank you and I look forward to reading your comments on my assignment. Sincerely,

Joan Arden Bachner

Arden Bachner, H.Ba G.I.S GIS-GM Candidate 2012-2013

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Table of Contents
1.0 2.0 Introduction .................................................................................................................................. - 1 Questions ...................................................................................................................................... - 1 2.1.Principal Components Analysis ............................................................................................... - 1 2.2.Correlation Analysis ................................................................................................................ - 2 2.3.PCA Transformation ................................................................................................................ - 3 2.4.Original Data and PCA Channels ............................................................................................. - 5 2.5.Original Unsupervised and PCA Unsupervised ....................................................................... - 7 3.0 Bibliography ................................................................................................................................ - 10 -

Table of Figures
Figure 1: Correlation Comparison ....................................................................................................................... - 2 Figure 2: Examples of Correlation ....................................................................................................................... - 2 Figure 3: Variance and Covariance of the Original Bands .............................................................................. - 3 Figure 4: PCA Tool ................................................................................................................................................ - 3 Figure 5: PCA Channels ....................................................................................................................................... - 4 Figure 6: Original Subset and PCA Channels Subset ...................................................................................... - 5 Figure 7: Original vs PCA ..................................................................................................................................... - 6 Figure 8: Original vs PCA ..................................................................................................................................... - 6 Figure 9: PCA Unsupervised and Original Unsupervised Outputs ................................................................. - 7 Figure 10: Left - PCA Unsupervised Legend with Class Values ..................................................................... - 7 Figure 11: Unsupervised vs PCA Unsupervised ............................................................................................... - 8 Figure 12: Unsupervised vs PCA Unsupervised ............................................................................................... - 9 -

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

1.0

Introduction

There are multiple ways to project and classify data, for this assignment we will be using PCA or Principal Component Analysis. This analysis takes bands from the original image and condenses them into fewer channels to preform classifications. The PC analysis allows for better distinction between Urban classes and Agricultural, this assignment is to test if the PCA will be able to properly classify Urban and Agricultural areas more accurately then the original unsupervised classification as preformed in assignment 1.

2.0

Questions

2.1. Principal Components Analysis For the area in question, which is around Orillia Ontario, there is very little known about what the physical landscape looks like. The function of Principle Component Analysis can help with this unknown as it is used to describe the data in a different way as it picks out unique information from all of the bands and put that information into fewer, new channels. The new components will have all the data unique from the original bands in the new channels. The Principal Component Analysis has an effect on reducing noise from the 6 bands and compact them into 3 channels, as selected for the study area. For this analysis we only run the PCA analysis once, this single process effectively enhances the topographic features of the data and provides an image with more contrast, almost imitating the image being high-pass filtered. It is important to check how much of the old bands data was transferred to the newly created three channels. When the PC analysis was done the option for saving the Eigenvalues of all the original bands used, the chart below shows the output of these values. The first three rows are the output for the new channels created after the analysis, they are divided by the total for all bands and multiplied by 100, adding them together we get 99.618% which means that over 99 percent of the original data was transformed into the new components.
3206.729889 524.6777816 49.80754616 9.417811676 3.409652839 +1.665451178 3795.708132 84.48304709 13.82292219 + 1.312206957 99.61818%

-1-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

2.2. Correlation Analysis By running the Feature Space Image function in ERDAS all bands are shown in comparison to the others. Below, Figure 1 shows the correlation distinction for each of the comparisons produced.
Viewer # 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Band #s 1 vs 2 1 vs 3 1 vs 4 1 vs 5 1 vs 6 2 vs 3 2 vs 4 2 vs 5 2 vs 6 3 vs 4 3 vs 5 3 vs 6 4 vs 5 4 vs 6 5 vs 6 Correlation Strong/Weak/None Strong Strong Weak Weak Weak Strong Weak Weak Weak None Weak Strong None None Weak

Figure 1: Correlation Comparison

Strong Correlation

Weak Correlation

No Correlation

Band 1 vs Band 2

Band 3 vs Band 4
Figure 2: Examples of Correlation

Band 4 vs Band 6

The Figure 2 scatterplots illustrate the values in one band compared against another. The Colours reflect the density of points, therefore bright tones represent a high density of points and dark tones represent low density. The bands with strong correlations mean that they would be very likely to have point values confused between the two bands. For example band 1 and 6 have a very weak correlation because band 1 is Blue and band 6 is Far IR, whereas band 1 and band 2 (Figure 2) have a strong correlation because they are Blue and Green respectively.
-2-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Band 1 Band 1 Band 2 Band 3 Band 4 Band 5 Band 6

0.049816212 0.117726867 0.161018823 0.734532166 0.571393346 -0.302826369

Band 2
-0.227047768 -0.231147257 -0.417707741 0.601290502 -0.319063642 0.507137678

Band 3
-0.430233601 -0.422990692 -0.472416532 -0.279220163 0.572639852 0.083188004

Band 4
-0.286224744 -0.338369223 0.020837748 0.142184561 -0.485893445 0.739485337

Band 5
0.641517353 0.112489018 -0.701439436 0.012693228 -0.048816136 0.285026826

Band 6
-0.517105005 0.791607664 -0.289765954 -0.023890648 -0.072912148 0.126919135

Figure 3: Variance and Covariance of the Original Bands

Above in Figure 3 is the Variance Matrix that was created when running the PCA. The numbers highlighted are the variance of the band and the white numbers are the covariance between the different bands. This chart correlates to Figure 1 as the number represents the correlation of the bands. If the value is close to 0 then the relation is stronger, if the value is closer to positive or negative 1 then the relation is weaker. For example Band 1vs Band 3 was classified as a strong correlation; the chart above in Figure 3 proves that, as the value is 0.16101.

2.3. PCA Transformation

Figure 4: PCA Tool

To perform the PC analysis the parameters above in Figure 4 need to be set for the study area of Orillia. The Number of Components Desired should be set to three as to combine the original 6 bands into 3 output channels. The boxes for Eigen Matrix and Eigenvalues need to be checked as to give the values used to check the percentage of data successfully transferred as shown in section 3.1. Once the proper settings are chosen the output channels can be projected the same as before by preforming the Feature Space Image.
-3-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Figure 5 shows the channels that were created from the PC analysis created in ERDAS for the study area of Orillia. The three channels that were created have no correlation,

Band 1 vs Band 2

Band 1 vs Band 3

Band 2 vs Band 3

Figure 5: PCA Channels

although band 1 and 3 comparison could be argued to have a weak correlation, which could impact future analysis. The variances of the points are very spread, and do not represent the strong correlation of bands like that in the initial comparison before the PC analysis, they also do not represent the same pixel values as the spread is located higher than the original bands scatterplots. There are also smaller areas of higher concentrations (red and yellow areas). The larger areas of pink points mean that there are fewer areas where points could be confused. If all newly created channels have no correlation then the data is excellent for the use of an unsupervised classification analysis. This is because the data has a lower likelihood of classifying pixels incorrectly.

-4-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

2.4. Original Data and PCA Channels

Figure 6: Original Subset and PCA Channels Subset

There is a visble contrast between the original data, as seen on the left in Figure 6 projected in False Colour IR, and the newly created PCA Chanels on the right. In the full area projection above, the differences between the ground cover is more distinguishable in the PCA Channels. This is because it is not specifically showing the vegetation valuses like that in the IR projection. The spectral reflectancy is shown differently as the Channels are showing all of the 6 bands information into 3 channels. The Bare Earth and Urban areas, which have the highest spectal relfectancy, show up bright red on the PCA Channels and is easily distinguishable. As well the different vegetation types also show well as the different hues of purple and green make it easier on the eyes to distinguish between vegetation. This is not the case in the original data subset as the different varriations of red can be hard to determine.

-5-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Figure 7: Original vs PCA

The PCA Channels also allow for more colour in the water features, as it is not being totally lost to IR bands like that of the original image. Figure 7 highlights the difference in water features as well as urban/bare earth and the difference in vegetation with the purple and green hues. The different hues do not distinguish between forests and crops with textures like the original image. In the bottom of the image there is a grouping of forest located by the water, in the False IR projection the texture of the vegetation comes out, as well as the flat (pink) field to the North West. That same area in the PCA Channels image has lost that texture or definition as it is merged all bands together and are not highlighting one specific class of features like IR does to vegetation.

Figure 8: Original vs PCA

Like highlighted in Figure 7, Figure 8 shows the vegetation in different hues, which allows for easier identification between different class types. The vegetation goes from dark purple (ploughed earth or very minimal vegetation present) to lighter purple to greens indicating forested areas with healthy leaf coverage. This close up also illustrates the confusion even with running PCA on the differences in bare earth and urban uses. The area at the bottom of the original image is most definitely bare earth, as it is not uniform and does not follow the straight lines of the road network that is present beside it. That being said, for both images the spectral reflectance is close to each other, thus in the PCA Channels image both Bare Earth and Urban uses are bright red.
-6-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

2.5. Original Unsupervised and PCA Unsupervised

Figure 9: PCA Unsupervised and Original Unsupervised Outputs

The image on the left in Figure 9 is the PCA Unsupervised classification and on the right is the Original Unsupervised classification from Assignment 1. Both classifications followed the same guidelines, 15 classes, 10 iterations and kept the convergence threshold as default. It can be observed above that there are differences between the two Unsupervised classifications. Typically running an Unsupervised classification on a PCA image helps in better classifying the Urban and Agricultural classes. This can depend on the area that you are classifying and at first look, the PCA did not seem to help with classifying Urban and Agricultural.

Figure 10: Left - PCA Unsupervised Legend with Class Values Right Original Unsupervised Legend with Class Values -7-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Figure 10 shows the different classes through the Unsupervised method. It is interesting to see the different pixel counts for the different classes. For example Urban in the original classification has just under 12,000 pixels, and the PCA classification only has fewer than 1,400 this is clearly observed in Figures 9 as there is very little yellow areas in the PCA unsupervised classification.

Figure 11: Unsupervised vs PCA Unsupervised

Figure 11 shows a comparison between the original unsupervised and the PCA unsupervised, and then for reference, the real colour image of the area. It can be observed that there is very little distinction between the Agricultural and Urban classes in the PCA classification as the road network has been classified as Ploughed Crops. It can be seen in the real colour image that there are areas in the PCA classification that are definitely miss classified as ploughed crops, and is really a part of the road network and even bare earth.

-8-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

Figure 12: Unsupervised vs PCA Unsupervised

For the area illustrated in Figure 12, neither classification has done a great job at classifying. That being said, the original unsupervised classification better classified the forest class, ploughed and crop classes. The PCA classification did not have a great classification of forest area as it just extended over crop classes. There is also very little definition of the road networks that should be running North West as seen in the colour image. For this particular use of PCA Unsupervised classification, the output of classes did not help in the distinction between the Urban/Road Network class and the two Agriculture classes. There was possibly too much variation between the Agriculture classes spectral reflectance to resemble some of that for the Urban/Road Network class.

-9-

AR D E N B AC H N E R

GISC9216 - Assignment 2
Due February 13, 2013

3.0

Bibliography

ERDAS field guide. (2009). Norcross, Ga.: ERDAS. Fanning, D. (2008). Principal Components Analysis in IDL. Coyote's Guide to IDL Programming. Retrieved from http://www.idlcoyote.com/code_tips/pca.html Finlay, J . (2013). GISC9216: Digital Image Proc, Week4-Image Fusion & PCA. [PowerPoint slides]. Retrieved from https://niagara.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_1_1

- 10 -