[R-sig-Geo] raster: stackApply problems..

[Leonidas Liakos]

Unfortunately the names are not always in ascending order. This is the
result of my data.

names      : index_4, index_5, index_6, index_7, index_1, index_2, index_3
min values :       3,       3,       3,       3,       3,       3,       3
max values :   307.0,   297.5,   311.0,   313.0,   468.0,   290.0,   302.0

And worst of all, it is not a proper match with indices.

If I run it with clusterR then the result is different:

names      : layer.1, layer.2, layer.3, layer.4, layer.5, layer.6, layer.7
min values :       3,       3,       3,       3,       3,       3,       3
max values :   307.0,   297.5,   311.0,   313.0,   468.0,   290.0,   302.0 


The solution is to reorder the layers of the stack so that the
stackApply indices are in ascending order e.g. 1,1,1,2,2,2,3,3,3 ...

My indices of my data was like that:

4 5 6 7 1 2 3 4 5 6 7 1 2 3 5 6 7

I've reported this behavior here
https://github.com/rspatial/raster/issues/82


On 11/20/19 3:05 PM, Ben Tupper wrote:
> Hi,
>
> That is certainly is unexpected to have two different naming styles.
> It's not really solution to take to the bank, but you could simply
> compose your own names assuming that the layer orders are always
> returned in ascending index order.
> Would that work for you
>
> ### start
> library(raster)
>
> # Compute layer names for stackApply output
> #
> # @param index numeric, 1-based layer indices used for stackApply function
> # @param prefix character, prefix for names
> # @return character layers names in index order
> layer_names <- function(index = c(2,2,3,3,1,1), prefix = c("layer.",
> "index_")[1]){
>   paste0(prefix, sort(unique(index)))
> }
>
> indices <- c(2,2,3,3,1,1)
>
> r <- raster()
> values(r) <- 1
> # simple sequential stack from 1 to 6 in all cells
> s <- stack(r, r*2, r*3, r*4, r*5, r*6)
> s
>
> beginCluster(2)
> res <- clusterR(s, stackApply, args = list(indices=indices, fun = mean))
> raster::endCluster()
> names(res) <- layer_names(indices, prefix = "foobar.")
> res
>
> res2 <- stackApply(s, indices, mean)
> names(res2) <- layer_names(indices, prefix = "foobar.")
> res2
> ### end
>
>
> On Wed, Nov 20, 2019 at 1:36 AM Leonidas Liakos via R-sig-Geo
> <r-sig-geo using r-project.org> wrote:
>> This is not a reasonable solution. It is not efficient to run stackapply
>> twice to get the right names. Each execution can take hours.
>>
>>
>> Στις 20/11/2019 3:30 π.μ., ο Frederico Faleiro έγραψε:
>>> Hi Leonidas,
>>>
>>> both results are in the same order, but the name is different.
>>> You can rename the first as in the second:
>>> names(res) <- names(res2)
>>>
>>> I provided an example to help you understand the logic.
>>>
>>> library(raster)
>>> beginCluster(2)
>>> r <- raster()
>>> values(r) <- 1
>>> # simple sequential stack from 1 to 6 in all cells
>>> s <- stack(r, r*2, r*3, r*4, r*5, r*6)
>>> s
>>> res <- clusterR(s, stackApply, args = list(indices=c(2,2,3,3,1,1), fun =
>>> mean))
>>> res
>>> res2 <- stackApply(s, c(2,2,3,3,1,1), mean)
>>> res2
>>> dif <- res - res2
>>> # exatly the same order because the difference is zero for all layers
>>> dif
>>> # rename
>>> names(res) <- names(res2)
>>>
>>> Best regards,
>>>
>>> Frederico Faleiro
>>>
>>> On Tue, Nov 19, 2019 at 4:15 PM Leonidas Liakos via R-sig-Geo <
>>> r-sig-geo using r-project.org> wrote:
>>>
>>>> I run the example with clusterR:
>>>>
>>>> no_cores <- parallel::detectCores() -1
>>>> raster::beginCluster(no_cores)
>>>> ?????? res <- raster::clusterR(inp, raster::stackApply, args =
>>>> list(indices=c(2,2,3,3,1,1),fun = mean))
>>>> raster::endCluster()
>>>>
>>>> And the result is:
>>>>
>>>>> res
>>>> class?????????? : RasterBrick
>>>> dimensions : 180, 360, 64800, 3?? (nrow, ncol, ncell, nlayers)
>>>> resolution : 1, 1?? (x, y)
>>>> extent???????? : -180, 180, -90, 90?? (xmin, xmax, ymin, ymax)
>>>> crs?????????????? : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
>>>> source???????? : memory
>>>> names?????????? : layer.1, layer.2, layer.3
>>>> min values :???????? 1.5,???????? 3.5,???????? 5.5
>>>> max values :???????? 1.5,???????? 3.5,???????? 5.5??
>>>>
>>>>
>>>> layer.1, layer.2, layer.3 (?)
>>>>
>>>> So what corrensponds to what?
>>>>
>>>>
>>>> If I run:
>>>>
>>>> res2 <- stackApply(inp,c(2,2,3,3,1,1),mean)
>>>>
>>>> The result is:
>>>>
>>>>> res2
>>>> class      : RasterBrick
>>>> dimensions : 180, 360, 64800, 3  (nrow, ncol, ncell, nlayers)
>>>> resolution : 1, 1  (x, y)
>>>> extent     : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
>>>> crs        : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0
>>>> source     : memory
>>>> names      : index_2, index_3, index_1
>>>> min values :     1.5,     3.5,     5.5
>>>> max values :     1.5,     3.5,     5.5
>>>>
>>>> There is no consistency with the names of the output and obscure
>>>> correspondence with the indices in the case of clusterR
>>>>
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
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>>>>
>>
>> --
>> Λιάκος Λεωνίδας, Γεωγράφος
>> https://www.geographer.gr
>> PGP fingerprint: 5237 83F8 E46C D91A 9FBB C7E7 F943 C9B6 8231 0937
>>
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>
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