Crop raster r

This tutorial explains how to crop a raster using the extent of a vector shapefile. We will also cover how to extract values from a raster that occur within a set of polygons, or in a buffer surrounding region around a set of points. You will need the most current version of R and, preferably, RStudio loaded on your computer to complete this tutorial. Download Dataset. Set Working Directory: This lesson assumes that you have set your working directory to the location of the downloaded and unzipped data subsets.

An overview of setting the working directory in R can be found here. If available, the code for challenge solutions is found in the downloadable R script of the entire lesson, available in the footer of each lesson page. The graphic below illustrates the extent of several of the spatial layers that we have worked with in this vector data tutorial series:.

Sometimes we have a raster file that is much larger than our study area or area of interest. It is often most efficient to crop the raster to the extent of our study area to keep reduce file sizes as we process our data. Cropping a raster can also be useful when creating pretty maps so that the raster layer matches the extent of the desired vector layers. These data can be used to create maps that characterize our study location.

If you have completed the Vector tutorials in this Introduction to Working with Vector Data in R series, you can skip this code as you have already created these object. We can use the crop function to crop a raster to the extent of another spatial object. To do this, we need to specify the raster to be cropped and the spatial object that will be used to crop the raster.

R will use the extent of the spatial object as the cropping boundary. We can see from the plot above that the full CHM extent plotted in green is much larger than the resulting cropped raster. Which object has the largest extent? Our plot location extent is not the largest but is larger than the AOI Boundary. It would be nice to see our vegetation plot locations with the Canopy Height Model information.

If you completed the. In the plot above, created in the challenge, all the vegetation plot locations blue appear on the Canopy Height Model raster layer except for one. One is situated on the white space.

A modification of the first figure in this tutorial is below, showing the relative extents of all the spatial objects. Notice that the extent for our vegetation plot layer black extends further west than the extent of our CHM raster bright green. The crop function will make a raster extent smaller, it will not expand the extent in areas where there are no data. Thus, extent of our vegetation plot layer will still extend further west than the extent of our cropped raster data dark green.

We can also use an extent method to define an extent to be used as a cropping boundary. This creates an object of class extent. Notice that our manual new. See the documentation for the extent function for more ways to create an extent object:?? Often we want to extract values from a raster layer for particular locations - for example, plot locations that we are sampling on the ground.

To do this in R, we use the extract function.

crop raster r

The extract function requires:. We will begin by extracting all canopy height pixel values located within our aoiBoundary polygon which surrounds the tower located at the NEON Harvard Forest field site.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. It only takes a minute to sign up.

I am trying to crop a raster by a polygon in R to the state of Sergipe-Brazil. My raster is a raster brick criated by 7. Here is the script:. I've changed the CRS os the shapefile to let both rasterbrick and shapefile in the same coordinate system.

BUT, when I run it:. It looks like you have a single point in the shapefile you are trying to crop to and the error message isn't exactly right. Lets' try and simulate that with a reproducible example:. Perhaps the crop algorithm is computing the area of overlap, getting zero, and assuming the areas don't overlap. Anyway, its a minor bug in cropI'd say.

To check, lets just make sure it works with a larger extent:. Of course we can't be sure this is your situation without your data, but it looks like it. Track back your SE. Sign up to join this community. The best answers are voted up and rise to the top. Home Questions Tags Users Unanswered. Asked 4 years ago. Active 4 years ago. Viewed 5k times. Isis Dias Isis Dias 13 1 1 silver badge 3 3 bronze badges. Active Oldest Votes. Spacedman Spacedman Sign up or log in Sign up using Google.

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Email Required, but never shown. The Overflow Blog. Featured on Meta. Community and Moderator guidelines for escalating issues via new response…. Feedback on Q2 Community Roadmap. Related 1. Hot Network Questions. Question feed.Areas included in y but outside the extent of x are ignored see extend if you want a larger area. You can check this with the extent function.

New Extent objects can be also be created with function extent and drawExtent by clicking twice on a plot. To crop by row and column numbers you can create an extent like this for Raster xrow 5 to 10, column 7 to 12 crop x, extent x, 5, 10, 7, For more information on customizing the embed code, read Embedding Snippets. Man pages API Source code S4 method for signature 'Spatial' crop xyRelated to crop in raster Package overview Introduction to the raster package.

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crop raster r

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Change your preferences any time. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. However, I need the output in the exact same geometry of the shapefile. Any tips? Learn more. Clipping raster using shapefile in R, but keeping the geometry of the shapefile Ask Question.

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Viewed 22k times. Meyer ALS. Meyer 1 1 gold badge 2 2 silver badges 6 6 bronze badges. Active Oldest Votes. Worked perfectly! Thank you. Meyer Apr 16 '14 at You need to mask first and then crop it to remove NA's not the other way around. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password.

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crop raster r

Technical site integration observational experiment live on Stack Overflow. Dark Mode Beta - help us root out low-contrast and un-converted bits. Linked 2. Related 0. Hot Network Questions. Question feed. Stack Overflow works best with JavaScript enabled.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service.

The dark mode beta is finally here. Change your preferences any time. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. Learn more. Asked 4 years, 2 months ago. Active 4 years, 2 months ago. Viewed 1k times. How can I crop right raster to extent of left raster below? Thanks for suggesting a work around. See here: gis. Active Oldest Votes.

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I am new to R and using the raster package. I have a problem extracting polygons from an existing raster file. If I use. After reading a bit more I think the crop function is what I really need. But when I try to use this function. Can you tell me what could be wrong here? Is it even right that the crop function creates another raster and not a list? EDIT : The extent function does not work for me. I still get the same error. But I am sure the 2 datasets overlap! With the. I get the right data from it.

Just as a list and not as a raster like I want to have it. I just loaded the datasets in ArcGIS before and they fit very well so I did not check the projection. Now I tried. The extract function seems to be able to automatically transform the files in the right way. I know that because I did the following:. The 2 have the exact same result so I guess the conclusion should be that the extract function did work correct.

Now I have 2 options I guess:. The extract function is behaving exactly as it should. You can force the crop function to use the extent of the polygon and then mask the object to return the exact raster representing the polygon area.

Load raster and polygon data

If you continue to receive the error it means that your data, in fact, does not overlap. Please keep in mind that R does not perform "on the fly" projection so, check your projections. You can check if your extents overlap using the "extent " function.In this chapter general aspects of the design of the raster package are discussed, notably the structure of the main classes, and what they represent.

The use of the package is illustrated in subsequent sections. See the help files of the package for more information on individual functions and help "raster-package" for an index of functions by topic. A RasterLayer can easily be created from scratch using the function raster. You can also change these parameters after creating the object. If you set the projection, this is only to properly define it, not to change it. To transform a RasterLayer to another coordinate reference system projection you can use the function 1projectRaster1.

Setting and accessing values is illustrated below. In some cases, for example when you change the number of columns or rows, you will lose the values associated with the RasterLayer if there were any or the link to a file if there was one.

The same applies, in most cases, if you change the resolution directly as this can affect the number of rows or columns. Values are not lost when changing the extent as this change adjusts the resolution, but does not change the number of rows or columns. It is more common, however, to create a RasterLayer object from a file. Most formats supported for reading can also be written to. A notable feature of the raster package is that it can work with raster datasets that are stored on disk and are too large to be loaded into memory RAM.

The package can work with large files because the objects it creates from these files only contain information about the structure of the data, such as the number of rows and columns, the spatial extent, and the filename, but it does not attempt to read all the cell values in memory.

In computations with these objects, data is processed in chunks. If no output filename is specified to a function, and the output raster is too large to keep in memory, the results are written to a temporary file. For this example, we first we get the name of an example file installed with the package. Do not use this system. Multi-layer objects can be created in memory from RasterLayer objects or from files. In these functions you can mix raster objects with numbers, as long as the first argument is a raster object.

If you use multiple Raster objects in functions where this is relevant, such as rangethese must have the same resolution and origin. The origin of a Raster object is the point closest to 0, 0 that you could get if you moved from a corners of a Raster object toward that point in steps of the x and y resolution. Normally these objects would also have the same extent, but if they do not, the returned object covers the spatial intersection of the objects used.

For example, if you multiply a 4-layer object a1, a2, a3, a4 with a 2-layer object b1, b2the result is a four-layer object a1b1, a2b2, a3b1, a3b2. Summary functions min, max, mean, prod, sum, Median, cv, range, any, all always return a RasterLayer object. Perhaps this is not obvious when using functions like minsum or mean.

Use cellStats if instead of a RasterLayer you want a single number summarizing the cell values of each layer.


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