MODIS data in R - fire remote sensing

Welcome to Week 7!

Welcome to week 7 of Earth Analytics! This week we will dive deeper into working with remote sensing data surrounding the Cold Springs fire. Specifically, we will learn how to

  • Download data from Earth Explorer
  • Deal with cloud shadows and cloud coverage
  • Deal with scale factors and no data values

Download Week 6/7 Data (~500 MB)

TimeTopicSpeaker
3:00 - 3:15Questions 
3:15 - 3:40Addititive light models - interactive experiment 
3:45 - 4:15Dealing with clouds & cloud masks in R 
4:30 - 5:00Group activity: Get data from Earth Explorer 
5:00 - 5:30MODIS data in R - NA values & scale factors - Coding Session 
5:30 - 5:50Group project / Home work time 

1a. Remote sensing readings

There are no new readings for this week.

2. Complete the assignment below (10 points)

Homework Submission

Produce a .pdf report

Create a new R markdown document. Name it: lastName-firstInitial-week7.Rmd Within your .Rmd document, include the plots listed below. When you are done with your report, use knitr to convert it to PDF format. Submit both the .Rmd file and the .pdf file. Be sure to name your files as instructed above!

Use knitr code chunk arguments

In your final report, use the following knitr code chunk arguments to hide messages and warnings and code as you see fit.

  • message=F, warning=F Hide warnings and messages in a code chunk
  • echo=F Hide code and just show code output
  • results='hide' Hide the verbose output from some functions like readOGR().

Answer the following questions below in your report

  1. What is the spatial resolution of NAIP, Landsat & MODIS data in meters? Are these data types different in terms of resolution? How could this resolution difference impact analysis using these data? Use plot 1 BELOW to visually show the difference.
  2. Calculate the area of “high severity” and the area of “moderate severity” burn in meters using the post-fire data for both Landsat and MODIS. State what the area in meters is for each data type (Landsat and MODIS) in your answer. Are the area values different calculated from MODIS vs Landsat? Why / why not? Use plots 4 and 5 to discuss any differences you notice.
  3. Describe 3 potential impacts of cloud cover on remote sensing imagery analysis. What are 2 ways that we can deal with clouds when we encounter them in our work? Refer to plots 2 & 3 in your homework to answer this question.

Include the plots below.

For all plots:

  1. Be sure to describe what each plot shows in your final report using a figure caption argument in your code chunks: fig.cap="caption here.
  2. Add appropriate titles that tells someone reading your report what the map shows
  3. Use clear legends as appropriate - especially for the classified data plots!

Plot 1 - Grid of plots: NAIP, Landsat and MODIS

Use the plotRGB() function to create color infrared (also called false color) images of NAIP, Landsat and MODIS in one figure. It doesn’t matter whether you use pre-post fire data. However you might want to use pre-fire data for NAIP (that is all that you have). And then cloud free data for landsat and MODIS which may be post fire. For each map be sure to:

  • Overlay the fire boundary layer (vector_layers/fire-boundary-geomac/co_cold_springs_20160711_2200_dd83.shp)
  • Use the band combination r = infrared band, g= green band, b=blue band. You can use mfrow=c(rows, columns)
  • Render the map to the extent of the fire boundary layer using the ext=extent() plot argument.
  • Be sure to label each plot with the data type (NAIP vs. Landsat vs. MODIS) and spatial resolution.

Use this figure to help answer question 1 above. An example of what this plot should look like (without all of the labels that you need to add), is here at the bottom of the page.

Plot 2 - Pre-fire NBR using landsat data

Create a MAP of the classified pre-burn NBR using the landsat scene that you downloaded from Earth Explorer this week. Overlay the fire extent layer vector_layers/fire-boundary-geomac/co_cold_springs_20160711_2200_dd83.shp on top of the NBR map. Add a legend. This file should not have a cloud in the middle of the burn area! You can use Earth Explorer to download the data. Use the classes that you used in your homework from week 6 to classify the data.

Plot 3 - Pre-fire NBR using landsat data with cloud mask

Create a MAP of the classified pre-burn NBR using the Landsat data file that was provided to you in your data download data/week06/landsat/LC80340322016189-SC20170128091153/crop. Be sure to mask the clouds from your analysis. Overlay the fire extent layer vector_layers/fire-boundary-geomac/co_cold_springs_20160711_2200_dd83.shp on top of the NBR map. Add a legend that clearly explains what each class represents (ie high severity, moderate etc.).

Plot 4 - Post-fire NBR using landsat data

Create a MAP of post fire classified NBR using Landsat data. Note: you did this for your homework last week, re-use the code. However this time, use a cloud mask to remove any clouds in your data. Then, overlay the fire extent layer (vector_layers/fire-boundary-geomac/co_cold_springs_20160711_2200_dd83.shp) on top of the NBR map. Add a legend that shows each NBR class and that clearly explains what each class represents (ie high severity, moderate etc.).

Plot 5 - Post-fire NBR MODIS

Create a classified map of post fire NBR using MODIS data. Be sure to mask the data using a cloud mask. Ideally you’ll do this BEFORE you calculate NBR and classify it. Add a legend that shows each NBR class and that clearly explains what each class represents (i.e. high severity, moderate etc.).

SEVERITY LEVELdNBR RANGE
Enhanced Regrowth<= -100
Unburned-100 to +100
Low Severity+100 to +270
Moderate Severity+270 to +660
High Severity>= 660

Homework due: Friday March 10, 2017 @ NOON.

Submit your report in both .Rmd and .PDF format to the D2l dropbox.

Grading

.Pdf Report structure & code: 10%

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
PDF and RMD submitted Only one of the 2 files are submitted No files submitted
Code is written using “clean” code practices following the Hadley Wickham style guideSpaces are placed after all # comment tags, variable names do not use periods, or function names.Clean coding is used in some of the code but spaces or variable names are incorrect 2-4 times Clean coding is not implemented consistently throughout the report.
Code chunk contains code and runsAll code runs in the documentThere are 1-2 errors in the code in the document that make it not run The are more than 3 code errors in the document
All required R packages are listed at the top of the document in a code chunk. Some packages are listed at the top of the document and some are lower down.  
Lines of code are broken up at commas to make the code more readable    

Knitr pdf output: 10%

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
Code chunk arguments are used to hide warnings    
Code chunk arguments are used to hide code and just show output    
PDf report emphasizes the write up and the code outputs rather than showing each step of the code    

Report questions: 40%

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
1. What is the spatial resolution for NAIP, Landsat & MODIS data in meters?    
1. Are these data types different in terms of resolution?    
1. How could this resolution difference impact analysis using these data? Use plot 1 BELOW to visually show the difference.    
2. Calculate the area of “high severity” and the area of “moderate severity” burn in meters using the post-fire data for both Landsat and MODIS. State what the area in meters is for each data type (Landsat and MODIS) in your answer.    
2. Are the values different? Why / why not? Use plots 4 and 5 to discuss any differences you notice.    
3. Describe 3 potential impacts of cloud cover on remote sensing imagery analysis. What are 2 ways that we can deal with clouds when we encounter them in our work? Refer to plot 2 in your homework to answer this question.    
3. What are 2 ways that we can deal with clouds when we encounter them in our work? Refer to plot 2 in your homework to answer this question.    

Plots are worth 40% of the assignment grade

Plot 1 - Grid of NAIP, Landsat and MODIS

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
All three plots are correct (color infrared with NIR light on the red band.)    
Plots are stacked vertically (or horizontally) and render properly on the pdf.    
Plot contains a meaningful title.    
Plot has a 2-3 sentence figure caption that clearly describes plot contents.    

Plot 2 - Pre-fire NBR using landsat data

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
A new landsat image has been downloaded to use for this plot.    
The landsat image is largely (< 20% clouds) cloud free over the study area.    
If there are clouds in the scene, a cloud mask has been applied.    
Plot renders on the pdf.    
Plot has been classified according to burn severity classes specified in the assignment.    
Plot contains a meaningful title.    
Plot has a 2-3 sentence figure caption that clearly describes plot contents.    
Plot includes a clear legend with each “level” of burn severity labeled clearly.    
Fire boundary exent has been overlayed on top of the plot    

Plot 3 - Pre-fire NBR using landsat data - with cloud mask

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
Plot renders on the pdf.    
Plot has been classified according to burn severity classes specified in the assignment.    
If there are clouds in the scene, a cloud mask has been applied.    
Plot has a clear title that describes the data being shown.    
Plot has a 2-3 sentence figure caption that clearly describes plot contents.    
Plot includes a clear legend with each “level” of burn severity labeled clearly.    
Fire boundary exent has been overlayed on top of the plot    

Plot 4 - Post-fire NBR using landsat data

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
Plot renders on the pdf.    
Plot has been classified according to burn severity classes specified in the assignment.    
If there are clouds in the scene, a cloud mask has been applied.    
Plot has a clear title that describes the data being shown.    
Plot has a 2-3 sentence figure caption that clearly describes plot contents.    
Plot includes a clear legend with each “level” of burn severity labeled clearly.    
Fire boundary exent has been overlayed on top of the plot    

Plot 5 - Post-fire NBR MODIS

Full CreditPartial Credit ~BPartial Credit ~CPartial Credit ~DNo Credit
Plot renders on the pdf.    
Plot has been classified according to burn severity classes specified in the assignment.    
If there are clouds in the scene, a cloud mask has been applied.    
Plot has a clear title that describes the data being shown.    
Plot has a 2-3 sentence figure caption that clearly describes plot contents.    
Plot includes a clear legend with each “level” of burn severity labeled clearly.    
Fire boundary exent has been overlayed on top of the plot    
Data have been scaled using the scale factor & the no data value has been applied for values outside of the range of acceptable values for MODIS reflectance.    

Updated: