def test_fromStackToSeriesWithPack(self):
ary = arange(8, dtype=dtypeFunc('int16')).reshape((2, 4))
filename = os.path.join(self.outputdir, "test.stack")
ary.tofile(filename)
image = ImagesLoader(self.sc).fromStack(filename, dims=(4, 2))
strategy = SimpleBlockingStrategy.generateFromBlockSize(image, "150M")
series = image.toBlocks(strategy).toSeries()
seriesVals = series.collect()
seriesAry = series.pack()
# check ordering of keys
assert_equals((0, 0), seriesVals[0][0]) # first key
assert_equals((1, 0), seriesVals[1][0]) # second key
assert_equals((2, 0), seriesVals[2][0])
assert_equals((3, 0), seriesVals[3][0])
assert_equals((0, 1), seriesVals[4][0])
assert_equals((1, 1), seriesVals[5][0])
assert_equals((2, 1), seriesVals[6][0])
assert_equals((3, 1), seriesVals[7][0])
# check dimensions tuple is reversed from numpy shape
assert_equals(ary.shape[::-1], series.dims.count)
# check that values are in original order
collectedVals = array([kv[1] for kv in seriesVals],
dtype=dtypeFunc('int16')).ravel()
assert_true(array_equal(ary.ravel(), collectedVals))
# check that packing returns transpose of original array
assert_true(array_equal(ary.T, seriesAry))
def test_fromStackToSeriesWithPack(self):
ary = arange(8, dtype=dtypeFunc("int16")).reshape((2, 4))
filename = os.path.join(self.outputdir, "test.stack")
ary.tofile(filename)
image = ImagesLoader(self.sc).fromStack(filename, dims=(4, 2))
strategy = SimpleBlockingStrategy.generateFromBlockSize(image, "150M")
series = image.toBlocks(strategy).toSeries()
seriesVals = series.collect()
seriesAry = series.pack()
# check ordering of keys
assert_equals((0, 0), seriesVals[0][0]) # first key
assert_equals((1, 0), seriesVals[1][0]) # second key
assert_equals((2, 0), seriesVals[2][0])
assert_equals((3, 0), seriesVals[3][0])
assert_equals((0, 1), seriesVals[4][0])
assert_equals((1, 1), seriesVals[5][0])
assert_equals((2, 1), seriesVals[6][0])
assert_equals((3, 1), seriesVals[7][0])
# check dimensions tuple is reversed from numpy shape
assert_equals(ary.shape[::-1], series.dims.count)
# check that values are in original order
collectedVals = array([kv[1] for kv in seriesVals], dtype=dtypeFunc("int16")).ravel()
assert_true(array_equal(ary.ravel(), collectedVals))
# check that packing returns transpose of original array
assert_true(array_equal(ary.T, seriesAry))
def test_roundtripConvertToSeries(self):
imagepath = findSourceTreeDir("utils/data/fish/tif-stack")
images = ImagesLoader(self.sc).fromTif(imagepath)
strategy = SimpleBlockingStrategy.generateFromBlockSize(images,
blockSize=76 *
20)
self._run_tst_roundtripConvertToSeries(images, strategy)
def _run_tst_splitCalc(blockSize, image, expectedSplits, expectedSize, testIdx=-1):
strategy = SimpleBlockingStrategy.generateFromBlockSize(image, blockSize)
splits = strategy.splitsPerDim
avgSize = strategy.calcAverageBlockSize()
assert_equals(tuple(expectedSplits), tuple(splits),
msg="Failure in test %i, expected splits %s != actual splits %s" %
(testIdx, tuple(expectedSplits), tuple(splits)))
assert_true(isclose(expectedSize, avgSize, rtol=0.001),
msg="Failure in test %i, expected avg size %g not close to actual size %g" %
(testIdx, expectedSize, avgSize))
def _run_tst_splitCalc(blockSize, image, expectedSplits, expectedSize, testIdx=-1):
strategy = SimpleBlockingStrategy.generateFromBlockSize(image, blockSize)
splits = strategy.splitsPerDim
avgSize = strategy.calcAverageBlockSize()
assert_equals(tuple(expectedSplits), tuple(splits),
msg="Failure in test %i, expected splits %s != actual splits %s" %
(testIdx, tuple(expectedSplits), tuple(splits)))
assert_true(isclose(expectedSize, avgSize, rtol=0.001),
msg="Failure in test %i, expected avg size %g not close to actual size %g" %
(testIdx, expectedSize, avgSize))
def test_roundtripConvertToSeries(self):
imagepath = findSourceTreeDir("utils/data/fish/images")
images = ImagesLoader(self.sc).fromTif(imagepath)
strategy = SimpleBlockingStrategy.generateFromBlockSize(images, blockSize=76 * 20)
self._run_tst_roundtripConvertToSeries(images, strategy)
