This tutorial will show you how to use a code to apply QC flags to ECOSTRESS data products. This code shows an example of applying QC flags to Land Surface Temperature (LST) products, but it can be modified for other ECOSTRESS products.
A QC flag is an image used to determine the quality of remotely sensed imagery. QC stands for quality control. In general, most people want to use only good pixels, or sometimes only the very best pixels in their research. ECOSTRESS QC masks have four options:
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0 = Pixel is perfect
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1 = Pixel is nominal quality
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2 = Cloud detected
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3 = Pixel was not produced
This code will help you remove pixels with 2 or 3 as their QC flags, or even 1, 2, and 3 if you want only the highest quality data. This will help improve the accuracy of your data. If you use this code to apply QC, you will not need to apply a cloud mask to your images because the cloud cover detection is accounted for in QC flag 2.
Tip: Make sure you have QC files downloaded in addition to your ECOSTRESS product files. If you do not know how to download these files, see the Downloading from AppEEARS tutorial. Oftentimes, QC files are automatically included in your requested files because they are important for good research.
However, to ensure they will be present in your requested files on AppEEARS, you can add them as a requested layer. Whatever product you are downloading, scroll through the options and look for QC, then press the plus to add it to your requested layers.
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Download the QC_Flag code from https://github.com/ECOSTRESS-Tutorials/ECOSTRESS-QC-Flag.
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Open your finder. Create a project folder to store all the files for this project by right clicking and selecting New Folder. Name your new folder so that you know it is the main project folder.
- Move the downloaded code file into the project folder.
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- Move the folder with your downloaded ECOSTRESS data into the project folder.
- Open the project folder and create a new sub folder to store the completed QCed files. To do this, go inside the project folder, right click, and select New Folder. Then name the folder so that you know it is for the outputs.
- Open Visual Studio Code and use File > Open Folder… to get connected to the main project folder that contains the downloaded ECOSTRESS files, the QC_Flags code, and the output subfolder.
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- In the EXPLORER tab, find the QC_Flags code and click on it to open it.
Tip: If you want to know more about what each line of the code does, read the comments in the code. Comments in the code are identified by #. These comments do not actually change how the code runs, but they can be helpful to put notes on how the code works for yourself or other users. This can also be helpful if you want to customize the code because it will guide you to which parts you may want to change!
Examples of comments (green text following the #):
- Then, find the section of the code titled Set Constants for the Project. Find the variable called input_directory. Change the text that says "Replace_this_text_with_folder_path" to the path of the main folder where your ECOSTRESS files are stored.
- To copy the folder path, use the EXPLORER panel on the left side of Visual Studio Code to find the folder you are interested in. Once you have found it, right click on it and select Copy Path. Now you can paste the path into your code. Make sure it is still wrapped in quotes and has r outside the first quote.
- Then, find the variable called output directory. Change the text that says "Replace_this_text_with_folder_path" to the path of the folder where you want the output files to be stored. Make sure it is still wrapped in quotes and has r outside the first quote.
Example Directory Set-up:
- The last thing you need to set up is how strict of a QC you would like. Under the section of code titled Apply the QC Mask to the LST Image, find the part of the code starting with the green comment # Preprocess the QC File. By default, the code will keep values 0 (pixel is perfect) and 1 (pixel is nominal quality). However, if you would like to filter for just 0 (perfect pixel values) you can do that by commenting out the current line of code, and un-commenting the QC flag for just 0 line of the code. To comment or uncomment a line of code, highlight the line and press Command+/. You will know the line is commented when it has a # in front of it and the text turns green.
| How your code should look if you want 0 (perfect) and 1 (nominal) pixels: | How your code should look if you want just 0 (perfect) pixels: |
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| <img src="Applying_QC_Flags_images/media/image15.png" | |
| style="width:3.00926in;height:0.88895in" | |
| alt="Text Description automatically generated" /> | <img src="Applying_QC_Flags_images/media/image16.png" |
| style="width:3.12312in;height:0.88889in" | |
| alt="Text Description automatically generated" /> |
- Now the code should be set up to be run with your images. Scroll back to the top to the section titled Import the Libraries we Need to Apply the QC Mask. This is the first block of code we want to run. Click into the box with the library importing code and press Shift+Return to run it.
- At the top of the window, a pop up will appear prompting you to select a kernel to run your code with. Click on Python Environments …
- Select the ECOSTRESS environment that you created, or another one if you have a different one you want to use.
Tip: If you do not have an ECOSTRESS environment set up, follow the Creating an Environment tutorial to make one.
- Let the code run for a few seconds. You will see the seconds counting up in the bottom left of the cell. You will know it is done when a green check mark appears.
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Continue this process of running each block of code, in order from top to bottom, by clicking into the module with the code and pressing Shift+Return.
- The Collect File Names section of the code will return a table with the date and time of the image, LST image file path, the associated QC file path, and the output file path that the QCed image will be saved to.
Example:
- The Apply the QC Mask to the LST Image section of the code will return the name of the QCed file and its missing proportion. If the missing proportion is too high, it will give you a message saying “Low quality scene. Skipping this file.” and that file will not be saved to the output folder.
Example:
- Once your code has run, check your outputs folder to make sure the files have been saved there correctly.
Tip: *Read if you do not want to skip files OR you used a polygon shapefile*
If you used a non-rectangular polygon shapefile instead of a rectangle selection or shapefile to download ECOSTRESS data, you will need to adjust your code so that it does not skip all of your images. Part of the code filters for high quality images by skipping files that have more than 50% of the pixels missing. However, when your image is clipped to the shapefile you uploaded, it treats the surrounding area as missing pixels. This will cause your code to flag all of your images as having a high proportion of missing pixels, and thus they will not be saved. Alternatively, you may want to keep all your images, regardless of their missing proportions. To fix this, look in the Apply the QC Mask to the LST Image section, and find this part of the code:
Highlight that section of the code and press Command+/ to comment it out. This means it will be ignored when the rest of the code runs. You will know you have commented it out when it looks like this:
Then you can proceed with the code as normal!
You have now QCed a batch of ECOSTRESS images!