raster: stackApply problems..

Thank you for your help!

I tried to fix stackApply according to your instructions.

Now the indices of names are the same and consistent with indices
enumeration (gist for validation and tests:
https://gist.github.com/kokkytos/93f315a5ecf59c0b183f9788754bc170).

I've attached a patch file here:

https://gist.github.com/kokkytos/ca2c319134677b19900579665267a7a7

stackapply_mean

class????? : RasterBrick
dimensions : 300, 300, 90000, 7? (nrow, ncol, ncell, nlayers)
resolution : 500, 500? (x, y)
extent???? : 0, 150000, 0, 150000? (xmin, xmax, ymin, ymax)
crs??????? : NA
source???? : /tmp/Rtmp9W8UNc/raster/r_tmp_2019-11-27_191205_2929_20324.grd
names????? :? index_5,? index_6,? index_7,? index_1,? index_2,?
index_3,? index_4
min values : 444.6946, 440.2028, 429.6900, 442.7436, 440.0467, 444.9182,
437.1589
max values : 565.8671, 560.1375, 561.7972, 556.2471, 563.8341, 561.7687,
560.4509

ver_mean

class????? : RasterStack
dimensions : 300, 300, 90000, 7? (nrow, ncol, ncell, nlayers)
resolution : 500, 500? (x, y)
extent???? : 0, 150000, 0, 150000? (xmin, xmax, ymin, ymax)
crs??????? : NA
names????? :? layer.1,? layer.2,? layer.3,? layer.4,? layer.5,?
layer.6,? layer.7
min values : 442.7436, 440.0467, 444.9182, 437.1589, 444.6946, 440.2028,
429.6900
max values : 556.2471, 563.8341, 561.7687, 560.4509, 565.8671, 560.1375,
561.7972





On 11/26/19 10:58 PM, Vijay Lulla wrote:

Hmm...it appears that stackApply is using different conditions which
might be causing this problem. Below is the snippet of the code which
I think might be the problem.

## For canProcessInMemory
if (rowcalc) {
? v <- lapply(uin, function(i) fun(x[, ind == i, drop = FALSE], na.rm
= na.rm))
}
else {
? v <- lapply(uin, function(i, ...) apply(x[, ind == i, drop = FALSE],
1, fun, na.rm = na.rm))
}


## If canProcessInMemory is not TRUE
if (rowcalc) {
? v <- lapply(uin, function(i) fun(a[, ind == uin[i], drop = FALSE],
na.rm = na.rm))
}
else {
? v <- lapply(uin, function(i, ...) apply(a[, ind == uin[i], drop =
FALSE], 1, fun, na.rm = na.rm))
}

I think they should both be same but it appears that they aren't and
that's what you've discovered.? Maybe you can try fix(stackApply) to
see if it really is the problem and can tell us what you find.?
Anyways, good catch...and...sorry for wasting your time.
Cordially,
Vijay.

On Tue, Nov 26, 2019 at 2:53 PM Leonidas Liakos
<leonidas_liakos at yahoo.gr <mailto:leonidas_liakos at yahoo.gr>> wrote:

? ? Thank you!
? ? The problem is not with the resulting values but with the index
? ? mapping. Values are correct in all three cases.

? ? As I wrote in a previous post in the thread
? ? (https://stat.ethz.ch/pipermail/r-sig-geo/2019-November/027821.html)
? ? , stackApply behaves inconsistently depending on whether the
? ? exported stack will remain in memory or it will be stored, due to
? ? its large size, on the hard disk.

? ? In the first case the indices are identical to my function
? ? (ver_mean) and the lubridate::wday indexing system (and are
? ? correct) while in the second they are shuffled.

? ? So, while Sunday has index 1 and while in the first case (when the
? ? result is in memory) stackApply returns the correct index, in the
? ? second case (when the result is stored on the hard disk) it
? ? returns index_4! So how can one be sure if index_1 corresponds to
? ? Sunday or another day using stackApply since it sometimes
? ? enumerates it with index_1 and sometimes index_4?


? ? Try to run this example (when the resulting stack remains in
? ? memory) to see that the indexes are identical (stackApply =
? ? ver_median = lubridate::wday)
? ? https://gist.github.com/kokkytos/5d554b5a725bb48d2189e2d1fa0e2206

? ? Thank you again

? ? On 11/26/19 9:00 PM, Vijay Lulla wrote:

? ? I'm sorry for the miscommunication.? What I meant to say is that
? ? the output from stackApply and zApply are the same (because
? ? zApply uses stackApply internally) except the names.? The
? ? behavior of stackApply makes sense because AFAIUI R doesn't
? ? automatically reorder vectors/indices that it receives.? Your
? ? observation about inconsistent result with ver_mean is very valid
? ? though!? And, that's what I meant with my comment that using
? ? sapply with the explicit ordering that you want is the best way
? ? to control what raster package will output.? In R the input order
? ? should be maintained (this is the prime difference between SQL
? ? and R) but packages/tools do not always adhere to this...so it's
? ? never clear how the output will be ordered.? Sorry for the confusion.


? ? On Tue, Nov 26, 2019 at 12:22 PM Leonidas Liakos
? ? <leonidas_liakos at yahoo.gr <mailto:leonidas_liakos at yahoo.gr>> wrote:

? ? ? ? Why do they seem logical since they do not match?

? ? ? ? Check for example index 1 (Sunday). The results are different
? ? ? ? for the three processes

? ? ? ? > stackapply_mean
? ? ? ? class????? : RasterBrick
? ? ? ? dimensions : 300, 300, 90000, 7? (nrow, ncol, ncell, nlayers)
? ? ? ? resolution : 500, 500? (x, y)
? ? ? ? extent???? : 0, 150000, 0, 150000? (xmin, xmax, ymin, ymax)
? ? ? ? crs??????? : NA
? ? ? ? source???? :
? ? ? ? /tmp/RtmpkRMXLb/raster/r_tmp_2019-11-26_191359_7710_20324.grd
? ? ? ? names????? :? index_5,? index_6,? index_7,? index_1,?
? ? ? ? index_2,? index_3,? index_4
? ? ? ? min values : 440.0467, 444.9182, 437.1589, 444.6946,
? ? ? ? 440.2028, 429.6900, 442.7436
? ? ? ? max values : 563.8341, 561.7687, 560.4509, 565.8671,
? ? ? ? 560.1375, 561.7972, 556.2471


? ? ? ? > ver_mean
? ? ? ? class????? : RasterStack
? ? ? ? dimensions : 300, 300, 90000, 7? (nrow, ncol, ncell, nlayers)
? ? ? ? resolution : 500, 500? (x, y)
? ? ? ? extent???? : 0, 150000, 0, 150000? (xmin, xmax, ymin, ymax)
? ? ? ? crs??????? : NA
? ? ? ? names????? :? layer.1,? layer.2,? layer.3,? layer.4,?
? ? ? ? layer.5,? layer.6,? layer.7
? ? ? ? min values : 442.7436, 440.0467, 444.9182, 437.1589,
? ? ? ? 444.6946, 440.2028, 429.6900
? ? ? ? max values : 556.2471, 563.8341, 561.7687, 560.4509,
? ? ? ? 565.8671, 560.1375, 561.7972


? ? ? ? > z
? ? ? ? class????? : RasterBrick
? ? ? ? dimensions : 300, 300, 90000, 7? (nrow, ncol, ncell, nlayers)
? ? ? ? resolution : 500, 500? (x, y)
? ? ? ? extent???? : 0, 150000, 0, 150000? (xmin, xmax, ymin, ymax)
? ? ? ? crs??????? : NA
? ? ? ? source???? :
? ? ? ? /tmp/RtmpkRMXLb/raster/r_tmp_2019-11-26_191439_7710_04780.grd
? ? ? ? names????? :?????? X1,?????? X2,?????? X3,?????? X4,??????
? ? ? ? X5,?????? X6,?????? X7
? ? ? ? min values : 440.0467, 444.9182, 437.1589, 444.6946,
? ? ? ? 440.2028, 429.6900, 442.7436
? ? ? ? max values : 563.8341, 561.7687, 560.4509, 565.8671,
? ? ? ? 560.1375, 561.7972, 556.2471
? ? ? ? ?????????? : 1, 2, 3, 4, 5, 6, 7


? ? ? ? On 11/26/19 7:03 PM, Vijay Lulla wrote:

? ? ? ? If you read the code/help for `stackApply` and `zApply`
? ? ? ? you'll see that the results that you obtain make sense (at
? ? ? ? least they seem sensible/reasonable to me).? IMO, if you
? ? ? ? want to control the ordering of your layers then just use
? ? ? ? sapply, like how you've used for ver_mean.? IMO, this is the
? ? ? ? only reliable (safe?), and quite a readable, way to
? ? ? ? accomplish what you're trying to do.
? ? ? ? Just my 2 cents.
? ? ? ? -- Vijay.

? ? ? ? On Tue, Nov 26, 2019 at 11:19 AM Leonidas Liakos via
? ? ? ? R-sig-Geo <r-sig-geo at r-project.org
? ? ? ? <mailto:r-sig-geo at r-project.org>> wrote:

? ? ? ? ? ? I added raster::zApply in my tests to validate the
? ? ? ? ? ? results. However, the
? ? ? ? ? ? indices of the names of the results are different now.
? ? ? ? ? ? Recall that the
? ? ? ? ? ? goal is to calculate from a raster stack time series the
? ? ? ? ? ? mean per day of
? ? ? ? ? ? the week. And that problem I have is that stackApply,
? ? ? ? ? ? zApply and
? ? ? ? ? ? calc/sapply return different indices in the result
? ? ? ? ? ? names. New code is
? ? ? ? ? ? available here:
? ? ? ? ? ? https://gist.github.com/kokkytos/93f315a5ecf59c0b183f9788754bc170
? ? ? ? ? ? I'm really curious about missing something.


? ? ? ? ? ? On 11/20/19 3:30 AM, Frederico Faleiro wrote:
? ? ? ? ? ? > 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 at r-project.org
? ? ? ? ? ? <mailto:r-sig-geo at r-project.org>
? ? ? ? ? ? <mailto:r-sig-geo at r-project.org
? ? ? ? ? ? <mailto:r-sig-geo at 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
? ? ? ? ? ? >
? ? ? ? ? ? >
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? ? ? ? ? ? >
? ? ? ? ? ? >? ? ?_______________________________________________
? ? ? ? ? ? >? ? ?R-sig-Geo mailing list
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? ? ? ? ? ? <mailto:R-sig-Geo at r-project.org>
? ? ? ? ? ? <mailto:R-sig-Geo at r-project.org
? ? ? ? ? ? <mailto:R-sig-Geo at r-project.org>>
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? ? ? ? ? ? >

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