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adding tests for processing .cwa blocks with failed checksum
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@l-k-
l-k- committed Dec 5, 2023
1 parent 6ed29a4 commit 6a58d63
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182 changes: 182 additions & 0 deletions tests/testthat/test_readAxivity.R
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,188 @@ test_that("readAxivity reads data from AX3 file correctly", {

})

test_that("readAxivity handles failed checksums correctly", {
# read the blocks 1-11 from the non-corrupt file
cwafile = system.file("testfiles/ax3_testfile.cwa", package = "GGIRread")[1]
AX3 = readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 12)

# From now on we'll be reading a file with corrupt blocks 0, 13, 14, 142, 143 and 144 (which is the last block)
cwafile = system.file("testfiles/ax3_testfile_corrupt_blocks_0_13_14_142_143_144.cwa", package = "GGIRread")[1]

# Since block 0 is corrupt, then if we start reading from that block, it gets skipped, and the results will be
# as if we read starting from block 1. No imputation will be done.
expect_warning(AX3_0_12 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 0, end = 12),
"Skipping corrupt block #0")
expect_equal(AX3_0_12$header$device, "Axivity")
expect_equal(nrow(AX3_0_12$data), nrow(AX3$data))
expect_equal(floor(sum(abs(AX3_0_12$data[,2:4]))), floor(sum(abs(AX3$data[,2:4]))))

expect_false(is.null(AX3_0_12$QClog))
expect_equal(nrow(AX3_0_12$QClog),1)
expect_false(AX3_0_12$QClog$checksum_pass[1])
expect_false(AX3_0_12$QClog$imputed[1])
expect_equal(AX3_0_12$QClog$blockID_current[1], 0)
expect_equal(AX3_0_12$QClog$blockID_next[1], 1)

# if we read blocks 1-11, results should be the same as for the non-corrupt file,
# and there should be nothing in QClog
expect_warning(AX3_1_12 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 12),
"Skipping corrupt block #0") # the warning is there b/c block 0 is always read, and it's corrupt

expect_equal(AX3_1_12$header$device, "Axivity")
expect_equal(nrow(AX3_1_12$data), nrow(AX3$data))
expect_equal(floor(sum(abs(AX3_1_12$data[,2:4]))), floor(sum(abs(AX3$data[,2:4]))))
expect_true(is.null(AX3_1_12$QClog))

# Now read a bigger chunk of the file, so that the corrupt blocks 13-14 fall in the middle
expect_warning(AX3_1_20 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 20),
"Skipping corrupt block #13")
expect_equal(AX3_1_20$header$device, "Axivity")
expect_equal(nrow(AX3_1_20$data), 2306)
expect_equal(ncol(AX3_1_20$data), 7)
expect_equal(floor(sum(abs(AX3_1_20$data[,2:4]))), 3244)

# there should be 3 entries in QClog: one each for blocks 13 and 14 with failed checksums (these initially get skipped, not imputed),
# and one for block 12 that preceeds the corrupt blocks, because data needs to be imputed from block 12 (inclusive) to 15 (exclusive)
expect_false(is.null(AX3_1_20$QClog))
expect_equal(nrow(AX3_1_20$QClog),3)

expect_false(AX3_1_20$QClog$checksum_pass[1])
expect_false(AX3_1_20$QClog$imputed[1])
expect_equal(AX3_1_20$QClog$blockID_current[1], 13)
expect_equal(AX3_1_20$QClog$blockID_next[1], 14)

expect_false(AX3_1_20$QClog$checksum_pass[2])
expect_false(AX3_1_20$QClog$imputed[2])
expect_equal(AX3_1_20$QClog$blockID_current[2], 14)
expect_equal(AX3_1_20$QClog$blockID_next[2], 15)

expect_true(AX3_1_20$QClog$checksum_pass[3])
expect_true(AX3_1_20$QClog$imputed[3])
expect_equal(AX3_1_20$QClog$blockID_current[3], 12) # we finally found the first valid block after #12, so we imputed block #12, up to 15
expect_equal(AX3_1_20$QClog$blockID_next[3], 15) # the first valid block after 12 is 15

# check that data in blocks 12-14 got imputed with the correct values

nrow11 = nrow(AX3_1_12$data)
imputedValues = AX3_1_12$data[nrow11,2:4]
VectorG = sqrt(sum(imputedValues^2))
imputedValues = imputedValues / VectorG

expect_true(all(abs(imputedValues - AX3_1_20$data[nrow11+1,2:4] ) < .0001))
expect_true(all(abs(imputedValues - AX3_1_20$data[nrow11+2,2:4] ) < .0001))
expect_true(all(abs(imputedValues - AX3_1_20$data[nrow11+100,2:4] ) < .0001))
expect_true(all(abs(imputedValues - AX3_1_20$data[nrow11+200,2:4] ) < .0001))
expect_true(all(abs(imputedValues - AX3_1_20$data[nrow11+360,2:4] ) < .0001))
expect_equal(sum(abs(imputedValues)),
sum(abs(AX3_1_20$data[(nrow11+1) : (nrow11+360), 2:4])) / 360,
tolerance = .0001, scale = 1)

# make sure a request for only corrupt blocks returns an error but doesn't crash
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 13, end = 14),
"All requested blocks are corrupt"),
"Skipping corrupt start block #13")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 14, end = 15),
"All requested blocks are corrupt"),
"Skipping corrupt start block #14")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 13, end = 15),
"All requested blocks are corrupt"),
"Skipping corrupt start block #13")

# Now see what happens if the corrupt blocks fall in the very beginning of the requested interval.
# These blocks should be skipped and the file should be read from the first non-corrupt block.
# So reading blocks 13-20 or 14-20 should give the same output as reading blocks 15-20.

expect_warning(AX3_13_20 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 13, end = 20),
"Skipping corrupt start block #13")
expect_warning(AX3_14_20 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 14, end = 20),
"Skipping corrupt start block #14")
expect_warning(AX3_15_20 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 15, end = 20),
"Skipping corrupt block #0") # the warning is there b/c block 0 is always read, and it's corrupt

expect_equal(nrow(AX3_13_20$data), nrow(AX3_15_20$data))
expect_equal(floor(sum(abs(AX3_13_20$data[,2:4]))), floor(sum(abs(AX3_15_20$data[,2:4]))))

expect_equal(nrow(AX3_14_20$data), nrow(AX3_15_20$data))
expect_equal(floor(sum(abs(AX3_14_20$data[,2:4]))), floor(sum(abs(AX3_15_20$data[,2:4]))))

# Now see what happens if the corrupt blocks fall in the very end of the requested interval.
# These blocks should be skipped and the file should be read from the first non-corrupt block.
# So reading blocks 1-13 or 1-14 should give the same output as reading blocks 1-15.

expect_warning(AX3_1_13 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 13),
"Skipping corrupt end block #13")
expect_warning(AX3_1_14 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 14),
"Skipping corrupt end block #14")
expect_warning(AX3_1_15 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 15),
"Skipping corrupt block #13")

expect_equal(nrow(AX3_1_13$data), nrow(AX3_1_15$data))
expect_equal(floor(sum(abs(AX3_1_13$data[,2:4]))), floor(sum(abs(AX3_1_15$data[,2:4]))))

expect_equal(nrow(AX3_1_14$data), nrow(AX3_1_15$data))
expect_equal(floor(sum(abs(AX3_1_14$data[,2:4]))), floor(sum(abs(AX3_1_15$data[,2:4]))))

# Now make sure corrupt blocks at the very end of the file are handled correctly (blocks 142-144).

# make sure a request for only corrupt blocks returns an error but doesn't crash
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 142, end = 143),
"All requested blocks are corrupt"),
"Skipping corrupt end block")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 142, end = 144),
"All requested blocks are corrupt"),
"Skipping corrupt end block")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 142, end = 145),
"All requested blocks are corrupt"),
"Skipping corrupt end block")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 143, end = 144),
"All requested blocks are corrupt"),
"Skipping corrupt end block")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 143, end = 145),
"All requested blocks are corrupt"),
"Skipping corrupt end block")
expect_warning(
expect_error(readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 144, end = 145),
"All requested blocks are corrupt"),
"Skipping corrupt end block")

# If there are corrupt blocks at the very end of the file, then the last non-corrupt block is
# treated as the end block and no imputation is done.
# So in our case, since the end blocks 142-144 are corrupt, they are ignored and the file is
# treated as if it had only 142 blocks (0-141)
expect_warning(AX3_1_141 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 141),
"Skipping corrupt block #0")
expect_warning(AX3_1_142 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 142),
"Skipping corrupt end block")
expect_warning(AX3_1_143 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 143),
"Skipping corrupt block")
expect_warning(AX3_1_144 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 144),
"Skipping corrupt end block")
expect_warning(AX3_1_145 <- readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 145),
"Skipping corrupt end block")

expect_equal(nrow(AX3_1_141$data), nrow(AX3_1_142$data))
expect_equal(floor(sum(abs(AX3_1_141$data[,2:4]))), floor(sum(abs(AX3_1_142$data[,2:4]))))

expect_equal(nrow(AX3_1_141$data), nrow(AX3_1_143$data))
expect_equal(floor(sum(abs(AX3_1_141$data[,2:4]))), floor(sum(abs(AX3_1_143$data[,2:4]))))

expect_equal(nrow(AX3_1_141$data), nrow(AX3_1_144$data))
expect_equal(floor(sum(abs(AX3_1_141$data[,2:4]))), floor(sum(abs(AX3_1_144$data[,2:4]))))

expect_equal(nrow(AX3_1_141$data), nrow(AX3_1_145$data))
expect_equal(floor(sum(abs(AX3_1_141$data[,2:4]))), floor(sum(abs(AX3_1_145$data[,2:4]))))
})


test_that("readAxivity reads data from AX6 file correctly", {
cwafile = system.file("testfiles/ax6_testfile.cwa", package = "GGIRread")[1]
AX6 = readAxivity(filename = cwafile, desiredtz = "Europe/Berlin", start = 1, end = 4)
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