Category: Xarray merge two datasets

Xarray merge two datasets

To combine arrays along existing or new dimension into a larger array, you can use concat. In addition to combining along an existing dimension, concat can create a new dimension by stacking lower dimensional arrays together:. If the second argument to concat is a new dimension name, the arrays will be concatenated along that new dimension, which is always inserted as the first dimension:. The second argument to concat can also be an Index or DataArray object as well as a string, in which case it is used to label the values along the new dimension:.

Of course, concat also works on Dataset objects:. With the default parameters, xarray will load some coordinate variables into memory to compare them between datasets. This may be prohibitively expensive if you are manipulating your dataset lazily using Parallel computing with dask. It can merge a list of DatasetDataArray or dictionaries of objects convertible to DataArray objects:. If you merge another dataset or a dictionary including data array objectsby default the resulting dataset will be aligned on the union of all index coordinates:.

This ensures that merge is non-destructive. MergeError is raised if you attempt to merge two variables with the same name but different values:. The same non-destructive merging between DataArray index coordinates is used in the Dataset constructor:.

The resulting coordinates are the union of coordinate labels. Vacant cells as a result of the outer-join are filled with NaN.

For example:. For datasets, ds0. In contrast to mergeupdate modifies a dataset in-place without checking for conflicts, and will overwrite any existing variables with new values:. However, dimensions are still required to be consistent between different Dataset variables, so you cannot change the size of a dimension unless you replace all dataset variables that use it.

Unlike mergeit maintains the alignment of the original array instead of merging indexes:. These methods are used by the optional compat argument on concat and merge. Like pandas objects, two xarray objects are still equal or identical if they have missing values marked by NaN in the same locations.

Note that NaN does not compare equal to NaN in element-wise comparison; you may need to deal with missing values explicitly. In addition to the above comparison methods it allows the merging of xarray objects with locations where either have NaN values.

This can be used to combine data with overlapping coordinates as long as any non-missing values agree or are disjoint:. Note that due to the underlying representation of missing values as floating point numbers NaNvariable data type is not always preserved when merging in this manner.

For combining datasets with different variables, see merge. For combining datasets or data arrays with different indexes or missing values, see combine.

DataArray np. In [6]: xr. In [7]: xr.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Already on GitHub? Sign in to your account. Firstly, I think xarray is great and for the type of physics simulations I run n-dimensional labelled arrays is exactly what I need. I would like to aggregate such DataArrays into a new, single DataArray with nan padding such that:. Here is a quick function I wrote to do such but I would worried about the performance of 'expanding' the new data to the old data's size every iteration i.

Might this be or is this already! I know Datasets have merge and update methods but I couldn't make them work as above. I also notice there are possible plans to introduce a merge function for DataArrays. This is actually closer to the functionality of concat than merge.

Combining Datasets: Merge and Join

Hypothetically, something like the following would do what you want:. In cases where each array does not already have the dimension you want to concat along, this already works fine, because you can simply omit dims in align. I'm having a similar issue, expanding the complexity in that I want to concatenate across multiple dimensions. I'm not sure if that's a cogent way to explain it, but here's an example.

I have:. Note the 'object' type for Dim2 and Dim I think this could make it into merge, which I am in the process of refactoring in The key difference from jcmgray 's implementation that I would want is a check to make sure that the data is all on different domains when using fillna. Something akin to the pandas dataframe update would have value - then you could create an empty array structure and populate it as necessary:. Yes following a similar line of thought to you I recently wrote an 'all missing' dataset constructor rather than 'empty' which I think of as no variables :.

JamesPHoughton jcmgray For empty array creation, take a look at and -- this functionality would certainly be welcome.

xarray merge two datasets

See the big warning here in the docs. But let's open another issue to discuss it. And then fillna to combine variables. Looking now I think this is very similar to what you are suggesting in Fixed by Skip to content. Dismiss Join GitHub today GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Sign up.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. I want to create a new NetCDF file which contains all of these files joined together. So far I have read in the files:. This works, but is clunky and there must be a simpler way to automate this process, as I will be doing this for many different folders full of files.

Is there a more efficient way to do this?

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This is reading only the text of the filename, and not the actual file itself, so it can't merge it. How do I open, store as a variable, then merge without doing it bit by bit? If you are looking for a clean way to get all your datasets merged together, you can use some form of list comprehension and the xarray. The following is an illustration:.

xarray merge two datasets

In response to the out of memory issues you encountered, that is probably because you have more files than the python process can handle. The best fix for that is to use the xarray. This is usually more memory efficient and will often allow you bring your data into python.

The following is equivalent to the previously provided solution, but more memory efficient:. How are we doing? Please help us improve Stack Overflow. Take our short survey. Learn more. Asked 2 years, 5 months ago. Active 2 years, 3 months ago. Viewed 2k times. I have a folder with NetCDF files fromin ten year blocksetc. EDIT: Trying to join these files using glob: for filename in glob.

Pad Pad 4 4 silver badges 26 26 bronze badges. Ok that almost made my computer implode and after un-crashing it said memory error: - this might be due to the size of the files? Perhaps my computer can't handle this? You have more files than your machine's memory capacity can handle.

In this case, you are only processing two files. As for your memory issues, I would advise looking at this. I tried it with less files, it works! Thank you. I will try and sort out memory issues as you suggest also. If you are using xarray. It's already being handled by xarray. Active Oldest Votes. Abdou Abdou 9, 3 3 gold badges 19 19 silver badges 33 33 bronze badges.A dataset resembles an in-memory representation of a NetCDF file, and consists of variables, coordinates and attributes which together form a self describing dataset.

Dataset implements the mapping interface with keys given by variable names and values given by DataArray objects for each variable name. One dimensional variables with name equal to their dimension are index coordinates used for label based indexing. Each dimension must have the same length in all variables in which it appears.

Coordinates values may be given by 1-dimensional arrays or scalars, in which case dims do not need to be supplied: 1D arrays will be assumed to give index values along the dimension with the same name. Backward compatible implementation of map. Assign new data variables to a Dataset, returning a new object with all the original variables in addition to the new ones. Two Datasets are broadcast equal if they are equal after broadcasting all variables against each other.

Return an array whose values are limited to [min, max]. Return a new object with an additional axis or axes inserted at the corresponding position in the array shape. Returns a Dataset with variables that match specific conditions.

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Returns a new dataset with the first n values of each array for the specified dimension s. Like equals, but also checks all dataset attributes and the attributes on all variables and coordinates. Interpolate this object onto the coordinates of another object, filling the out of range values with NaN. Returns a new dataset with the last n values of each array for the specified dimension s.

Returns a new dataset with each array indexed along every n -th value for the specified dimension s. Getting Started Overview: Why xarray? Dataset xarray. Dataset Edit on GitHub. DataFrame into an xarray. Index objects used for label based indexing loc Attribute for location based indexing. Read the Docs v: stable Versions latest stable v0.

Returns a new dataset with dropped labels for missing values along the provided dimension. Two Datasets are equal if they have matching variables and coordinates, all of which are equal.

Returns a new dataset with each array indexed by tick labels along the specified dimension s.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.

Let's say I have two data sets, each containing a different variable of interest and with incomplete but not conflicting indices:. It seems as though the coordinates are being handled like DataArraysin that any non-identical values raise an error. But shouldn't they be handled more like the base coordinates, e.

Or is there another operation I should be doing? In fact, I think it should be safe to merge any non-conflicting values under most circumstances unless the user requests higher scrutiny.

Learn more. How to merge xArray datasets with conflicting coordinates Ask Question. Asked 3 years, 11 months ago. Active 2 years, 4 months ago.

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Viewed 1k times. I'm on python 3. Michael Delgado Michael Delgado 1, 8 8 silver badges 23 23 bronze badges. Active Oldest Votes. This isn't currently easy to achieve in xarray, but it should be! Sign up or log in Sign up using Google.

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I have one dataset of satellite based solar induced fluorescence SIF and one of modeled precipitation. I want to compare precipitation to SIF on a per pixel basis in my study area.

xarray merge two datasets

My two datasets are of the same area, but at slightly different spatial resolutions. The SIF is a little lower resolution than the rainfall. I can successfully plot these values across time and compare against each other when I take the mean for the whole area, but I'm struggling to create a scatter plot of this on a per pixel basis.

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I'm not sure if this is the best way to compare these two values when looking for the impact of precip on SIF so I'm open to ideas of different approaches. As for merging the data currently I'm using xr. I could also do this by converting the netcdfs into geotiffs and then using rasterio to warp them, but that seems like an inefficient way to do this comparison. Here is what I have thus far:.

Currently I'm getting a seemingly unhelpful RecursionError: maximum recursion depth exceeded in comparison on that final line.

xarray merge two datasets

I assumed there was some internal interpolation with this function but it appears not. This documentation from xarray outlines quite simply the solution to the problem. So in this case it is done with. Sign up to join this community. The best answers are voted up and rise to the top.

Home Questions Tags Users Unanswered. Using xarray to resample and merge two datasets Ask Question. Asked 5 months ago. Active 5 months ago. Viewed times. Active Oldest Votes.If you find this content useful, please consider supporting the work by buying the book! One essential feature offered by Pandas is its high-performance, in-memory join and merge operations. If you have ever worked with databases, you should be familiar with this type of data interaction. The main interface for this is the pd.

For convenience, we will start by redefining the display functionality from the previous section:. The behavior implemented in pd. The strength of the relational algebra approach is that it proposes several primitive operations, which become the building blocks of more complicated operations on any dataset. With this lexicon of fundamental operations implemented efficiently in a database or other program, a wide range of fairly complicated composite operations can be performed.

Pandas implements several of these fundamental building-blocks in the pd. As we will see, these let you efficiently link data from different sources. The pd. All three types of joins are accessed via an identical call to the pd. Here we will show simple examples of the three types of merges, and discuss detailed options further below.

As a concrete example, consider the following two DataFrames which contain information on several employees in a company:. To combine this information into a single DataFramewe can use the pd.

The result of the merge is a new DataFrame that combines the information from the two inputs. Notice that the order of entries in each column is not necessarily maintained: in this case, the order of the "employee" column differs between df1 and df2and the pd.

Many-to-one joins are joins in which one of the two key columns contains duplicate entries.

Combining Datasets: Merge and Join

For the many-to-one case, the resulting DataFrame will preserve those duplicate entries as appropriate. Consider the following example of a many-to-one join:.

The resulting DataFrame has an aditional column with the "supervisor" information, where the information is repeated in one or more locations as required by the inputs. Many-to-many joins are a bit confusing conceptually, but are nevertheless well defined. If the key column in both the left and right array contains duplicates, then the result is a many-to-many merge. This will be perhaps most clear with a concrete example.

Consider the following, where we have a DataFrame showing one or more skills associated with a particular group. By performing a many-to-many join, we can recover the skills associated with any individual person:. These three types of joins can be used with other Pandas tools to implement a wide array of functionality.

But in practice, datasets are rarely as clean as the one we're working with here. In the following section we'll consider some of the options provided by pd. We've already seen the default behavior of pd. However, often the column names will not match so nicely, and pd.

Most simply, you can explicitly specify the name of the key column using the on keyword, which takes a column name or a list of column names:. This option works only if both the left and right DataFrame s have the specified column name.

At times you may wish to merge two datasets with different column names; for example, we may have a dataset in which the employee name is labeled as "name" rather than "employee".

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