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Spacetime Documentation

The main objective of the spacetime R package is to make tasks like loading, rescaling, merging, and conducting mathmatical operations on spatiotemporal (or other D-dimensional data sets) easier for the user by providing a set of concise yet powerful functions. Spacetime opperations utilize a cube-like structure for all data sets that makes storing and manipulating large D-dimensional datasets more efficient. For scientists working with spatiotemporal data (such as climate or weather data sets) spacetime is an ideal platform that allows the user to focus on the science rather than the coding. Spacetime is in the beta stage (version number = 0.0.1) and additional functionality will be added on a regular basis. The current functionality of spacetime is below:

Spacetime Objects:

fileObj:

Description: File objects are the output of the read_data() fucntion. They are essentially a list object of all the raster files that were read in. All querrying data stored in a file object will result in a list of outputs (one for each raster in the object). File objects can contain rasters of various scales, time lengths, and sizes. The functions raster_scale() and raster_align() may be used on file objects to return a file object that contains aligned and trimmed rasters. General output: A list of output objects of the length of the list of raster objects loaded by read_data().

• $get_GDAL_data() - Extracts GDAL data object
• $get_epsg_code() - extracts spatial reference system EPSG code
• $get_units() - extracts units of spatial grid
• $get_UL_corner() - Extracts lat and long coords of the upper left corner
• $get_band_number() - Extracts the number of bands
• $get_time() - extracts time values (default = 0-N)
• $get_dims() - Extracts raster x and y dimensions
• $get_nodata_value() - returns no data values
• $get_data() - get full raster data set as numpy array
• $get_bands(min=1, max=2, rasters = [0]) get subset of raster data as numpy array
  • min = (int >= 1) first raster band to extract
  • max = (int <= number of bands) last raster band to extract
  • rasters = (list) list of rasters (0-number of rasters) to pull from
• $get_lat() - get latitude values
• $get_lon() - get longitude values

# extract list of raster data cubes from file object
dataArray <- ds$get_data()

cubeObj:

Description: Cube objects are the main operational unit in the spacetime package. Cube objects are cleaned, aligned D-dimensioal cube-liek datasets that minamally contain a data cube, a time dimension, and latitude and longitude (y, x) dimensions. They are the output of the make_cube() function. Cube objects may be passed to functions like cube_smasher(), cube_plotter() etc. to be opperated on mathmatically or functionally and visulized. General output: The associated value for the cube object as specified by the method.

• $get_GDAL_data() - Extracts orignal data object
• $get_epsg_code() - extracts spatial reference system EPSG code
• $get_units() - extracts units of spatial grid
• $get_UL_corner() - Extracts lat and long coords of the upper left corner
• $get_band_number() - Extracts the number of bands

• $get_time() - extracts time values

• $get_dims() - Extracts raster x and y dimensions
• $get_nodata_value() - returns no data values
• $get_data(variables) - return a full D-dimensional raster data set as an xarray dataArray.
  • variables = selects variables to return if cube was created with the “filestovar” option. Takes a list of character string variable names.
• $get_lat() - get latitude values

• $get_lon() - get longitude values

• $get_var_names() - get the variable names of the cube

# extract latitude dimension from cube object
lat <- ds$get_lat()

spacetime Functions:

Description: spacetime functions conduct scaling, plotting, writing and other tasks on spacetime objects.

read_data(data=None)

• Functionality: Reads in one or multiple raster data files and prepares them for data extraction and/or use with other spacetime functions.
• Input: data = list object containing file names of rasters
• Output: file object
• Additional Arguments: None
• Example function call:

# read in data set from raster files
ds = read_data(data=rasterList)

make_cube(data = None, fileName = None, organizeFiles="filestotime", organizeBands="bandstotime", varNames=None, timeObj=None, inMemory = False)

• Functionality: Writes input objects as a cd4 file to disk and returns a virtualized cube object. Note: for larger datasets, the writing of the cube to disk may take a few minutes
• Input: data = file object or cube object
• Output: cube object
• Additional Arguments:
  • outFile = (char) name of outfile with prefered supported extension.
  • organizeFiles = how files are organized in cube (chr).
    • “filestotime” stacks all files along the time dimension
    • “filestovar” creates a higher dimensional cube where each cube is a different variable and time are bands within each raster. * organizeBands = how bands are treated when assembling the cube (chr).
    • “bandstotime” = bands are a time dimension
    • “bandstovar” = bands are variables
  • varNames = a list of character strings that are the variable names for each file if the “filestovar” option is selected
  • timeObj = A time object created by cube_time() of the desired time length. If not specified, time defaults to integers 0 to length of cube stack.
  • inMemory If False (default), Data arrays are stored as dask array and are lazy loading. If True, data arrays are read into memory when accessed.
• Example function call:

make_cube(data = fileObject, fileName = "test.nc4", organizeFiles = "filestovar", varNames = ["SpA","SpB"], timeObj = years)

raster_align(data=None, resolution=None, SRS=None, noneVal=None, algorithm = "near")

• Functionality: Sets input object to have same spatial reference system and resolution and alignment.
• Input: data = file object as outputted by read_data()
• Output: aligned and rescaled cube or file objects
• Additional Arguments:
  • resolution = (numeric or string) intended pixel size of the outputted data set in either degrees or meters depending on the spatial reference system in use or “min” (the lowest resolution raster’s pixel size) or “max” (the highest resolution raster’s pixel size)
    • Default value: largest resolution in data set in input spacetime object
  • SRS = (int) intended 4-digit spatial reference system code that all data sets in the outputted spacetime object will use.
    • Default value: EPSG of first data set in input object
  • noneVal = (numeric) no data value to be used by all datasets in the outputted spacetime object.
    • Default value: no data value of first data set in input spacetime object
    • algorithm = (character string) The aggregation algorithm method.
    • Default value: “near”
    • Possible values:
      • “near”: nearest neighbour resampling (default, fastest algorithm, worst interpolation quality).
      • “bilinear”: bilinear resampling.
      • “cubic”: cubic resampling.
      • “cubicspline”: cubic spline resampling.
      • “lanczos”: Lanczos windowed sinc resampling.
      • “average”: average resampling, computes the weighted average of all non-NODATA contributing pixels.
      • “rms”: root mean square / quadratic mean of all non-NODATA contributing pixels
      • “mode”: mode resampling, selects the value which appears most often of all the sampled points. In the case of ties, the first value identified as the mode will be selected.
      • “max”: maximum resampling, selects the maximum value from all non-NODATA contributing pixels.
      • “min”: minimum resampling, selects the minimum value from all non-NODATA contributing pixels.
      • “med”: median resampling, selects the median value of all non-NODATA contributing pixels.
      • “q1”: first quartile resampling, selects the first quartile value of all non-NODATA contributing pixels.
      • “q3”: third quartile resampling, selects the third quartile value of all non-NODATA contributing pixels.
      • “sum”: compute the weighted sum of all non-NODATA contributing pixels
• Example function call:

dsAligned = raster_align(data=fileObj, resolution=.08, SRS=4326, noneVal=-9999)

raster_trim(data=None)

• Functionality: Trims datasets in the input object to have the same bounding box (i.e. spatial dimensionality).
• Input: data = aligned file as outputted by data_align()
• Output: file or cube object trimmed to greatest common bounding box
• Additional Arguments: = None
• Example function call:

dsTrimmed = raster_trim(data=cubeObj)

cube_time(start, length, scale)

• Functionality: Creates a time object that is a vector of a desired lenghth of dates or times.
• Inputs:
  • start = starting date (chr)
  • length = length of desired time vector (int)
  • scale = resolution of time vector (chr) options are: “year”, “month”, “day”, “hour”, “minute” or “second”
• Output: file or cube object trimmed to greatest common bounding box
• Additional Arguments: = None
• Example function call:

yearObj = cube_time(start="2000", length=202, scale = "year")

scale_time(cube, scale, method)

• Functionality: Summarizes a cube by some method at a temporal scale of the user’s choosing.
• Inputs:
  • cube = a spacetime cube object
  • scale = the temporal scale the cube is to be summarized upon (“day”, “month”, “year”)
  • method = the summary method options are: “mean”, “max”, “min”, “median”
• Output: a new cube object with rescaled time
• Example function call:

scale_time(cube=ds, scale="month", method="max")

select_time(cube, range="entire", scale = None, element=None)

• Functionality: Select a range and or specific temporal element to extract form a data cube such as speficifc days, months or years.
• Inputs:
  • cube = a spacetime cube object
  • range = (pair of character strings as a list or tuple) the range to be selcted. Either a list of the first and last date to be extracted or the default “entire” argument, which extracts all time points.
  • scale = the temporal scale of the elements to be extracted (“day”, “month”, “year”)
  • element = (int) a numeric year, month or day value
  • Output: a new subsetted cube object
• Example function call:

select_time(cube=cubeObj, range=['2000-02-29', '2000-04-30'], scale = "month", element=4)

expand_time(cube, target_time, starting_scale = "month", target_scale = "day")

• Functionality: Take a cube and expand its time dimension by reapeating layers to match a target cubes time object.
• Inputs:
  • cube = a spacetime cube object
  • target_time = time object from the target cube * starting_scale = the temporal scale of the starting cube (“day”, “month”, “year”)
  • target_scale = the temporal scale of the output cube (“day”, “month”, “year”)
  • Output: a new cube object
• Example function call:

newCube = expand_time(cube = cubeObj, target_time = cube.get_time(), starting_scale = "month", target_scale = "day")

cube_smasher(function = None, eq = None, parentCube = None, **kwarg))

• Functionality: Takes cube objects, arrays or scalar values, and conducts mathmatical and functional opperations on them as specified.
• Input: data = cube objects, numpy arrays or scalar values.
• Output: returns new cube object after opperations are completed
• Additional Arguments:
  • function = name of user specified function to pass to cube_smasher()
  • eq = (string) mathmatical equation to perform on data
  • parentCube = (cube object) The starting cube that the output cube should use as a guide for reconstruction (defaults to first detected cube if multiple are passed)
  • kwarg = additional params to pass for user specified function if not using eq
• Example function call:

# mathmatical operations on two tif files
outputCube = cube_smasher(eq = "a + b ** c", a=cube1, b=cube2, c = 5, parentCube = cube1)


# conduct mathmatical operation on two cube objects
outputCube = cube_smasher(eq = "a + b", a=obj1, b=obj2, parentCube = obj1)

cube_to_dataframe(cube)

• Functionality: Takes a cube object and returns a pandas dataframe that can be used with external plotting functions.
• Input: cube = a cube object of any dimension
• Output: Pandas dataframe with all index variables as columns.
• Additional Arguments: = None
• Example function call:

# convert a cube into a dataframe
df = cube_to_dataframe(cube=cubeObject)

plot_cube(cube, type="space", variable = None, summary="mean", showPlot = True)

• Functionality: Plots data sets as either a heatmap playable over the time dimension if applicable, or a time series plot of a user selected summary statistic.
• Input: data = cube object
• Output: data frame used to make the plot with the figure shown as a side effect
• Additional Arguments:
  • variable = (char) character string of the variable to plot spatialy if their are more than one. If not specified default is the first variable.
  • plot_type = (char) select between spatial (“space”) or temporal (“time_series”).
  • deviation_coefficient Number of standard deviations to show in control chart (default = 1)
  • dataSet = (int) selects data set within object to plot
  • summary = (char) selects intended summary statistic for temporal plot. (“mean”, “max”, “min”, “median”)
  • show_plot = (boolean) turn off plotting and return only the plotting dataframe.
• Example function call:

df = plot_cube(cube=x, variable="B", type="space", summary = "max", showPlot = True)

Example Workflow:

import spacetime as sp

# input file names
file1 = "file1.tif"
file2 = "file2.tif"

data <- list(file1, file2)

# read data from list of files and make a spaceTime file object
ds <- read_data(data)
##########################################################################

# align the rasters to the same epsg codes and grid size
newObj <- raster_align(data=ds)

# trim the rasters to the same greatest common bounding box
trimmed <- raster_trim(newObj)

# create spacetime time object
yearObj <- cube_time(start="2000", length=101, scale = "day")

# make the alinged file object into a cube with a time element (writes the new file to disk)
ds <- make_cube(data = trimmed, fileName = "test.nc4", organizeFiles = "filestovar", timeObj = yearObj)

# scale time does basic temporal summary (here we are doing monthly means)
x <- scale_time(cube=ds, scale="month", method="mean")

# selects ranges of time and/or slices at different scales 
# here we extract aprils between '2000-02-29' and '2000-04-30'
y <- select_time(cube=x, range=c('2000-02-29', '2000-04-30'), scale = "month", element=4)

# cube smasher does mathmatical/function operations on a cube or cubes (times 5)
answer <- cube_smasher(eq = "a * c", a = y, c = 5, parentCube = y)

# convert a cube into a dataframe
df = cube_to_dataframe(cube=x)

# write out our final cube as a .cd4 file
ds <- make_cube(data = x, fileName = "testCube.nc4")