Example #1
0
    def test_splitsAndPix(self):
        def genSlicesForPix(pix, size):
            slices = []
            st = 0
            while st < size:
                en = min(st + pix, size)
                slices.append(slice(st, en, 1))
                st = en
            return slices

        def genSlicesForSplits(splits, size):
            slices = []
            blocksize = size / splits  # integer division
            blockrem = size % splits
            st = 0
            while st < size:
                en = st + blocksize
                if blockrem > 0:
                    en += 1
                    blockrem -= 1
                en = min(en, size)
                slices.append(slice(st, en, 1))
                st = en
            return slices

        Params = namedtuple(
            "Params",
            "unitsPerDim units image padding expPix expSplits expSlices0")
        PARAMS = \
            [Params((5, 5, 1), "pix", MockImage((15, 15, 3), 2, "uint8"), 0, (5, 5, 1), None, genSlicesForPix(5, 15)),
             Params((5, 5, 2), "pix", MockImage((7, 7, 3), 2, "uint8"), 0, (5, 5, 2), None, genSlicesForPix(5, 7)),
             Params((2, 2, 2), "s", MockImage((7, 7, 3), 2, "uint8"), 0, None, (2, 2, 2), genSlicesForSplits(2, 7)),
             Params((5, 5, 1), "pix", MockImage((15, 15, 3), 2, "uint8"), 2, (5, 5, 1), None, genSlicesForPix(5, 15)),
             Params((5, 5, 2), "pix", MockImage((7, 7, 3), 2, "uint8"), 2, (5, 5, 2), None, genSlicesForPix(5, 7)),
             Params((2, 2, 2), "s", MockImage((7, 7, 3), 2, "uint8"), 2, None, (2, 2, 2), genSlicesForSplits(2, 7))]
        for params in PARAMS:
            if params.padding:
                strat = PaddedBlockingStrategy(params.unitsPerDim,
                                               units=params.units,
                                               padding=params.padding)
            else:
                strat = SimpleBlockingStrategy(params.unitsPerDim,
                                               params.units)
            strat.setSource(params.image)
            if params.expPix:
                assert_equals(tuple(params.expPix), tuple(strat._pixPerDim))
            else:
                assert_true(strat._pixPerDim is None)
            if params.expSplits:
                assert_equals(tuple(params.expSplits),
                              tuple(strat._splitsPerDim))
            else:
                assert_true(strat._splitsPerDim is None)
            assert_equals(params.expSlices0, strat._slices[0])
Example #2
0
    def test_paddedBlockExtraction(self):
        for params in TestBlockExtraction.PARAMS:
            strategy = PaddedBlockingStrategy(
                [1] * len(params.aryshape),
                params.padding)  # dummy splits; not used here
            n = reduce(lambda x, y: x * y, params.aryshape)
            ary = arange(n, dtype='int16').reshape(params.aryshape)
            key, val = strategy.extractBlockFromImage(ary, params.blockslices,
                                                      params.timepoint,
                                                      params.ntimepoints)

            expectedSlices = [
                slice(params.timepoint, params.timepoint + 1, 1)
            ] + list(params.blockslices)
            assert_equals(params.timepoint, key.temporalKey)
            assert_equals(params.ntimepoints, key.origShape[0])
            assert_equals(tuple(params.aryshape), tuple(key.origShape[1:]))
            assert_equals(tuple(expectedSlices), tuple(key.imgSlices))

            try:
                _ = len(params.padding)
                padding = list(params.padding)
            except TypeError:
                padding = [params.padding] * ary.ndim

            expectedPaddedSlices = []
            expectedValSlices = []
            for slise, pad, l in zip(params.blockslices, padding, ary.shape):
                paddedStart = max(0, slise.start -
                                  pad) if not (slise.start is None) else 0
                paddedEnd = min(l, slise.stop +
                                pad) if not (slise.stop is None) else l
                actualPadStart = slise.start - paddedStart if not (
                    slise.start is None) else 0
                actualPadEnd = paddedEnd - slise.stop if not (
                    slise.stop is None) else 0
                expectedPaddedSlices.append(slice(paddedStart, paddedEnd, 1))
                expectedValSlices.append(
                    slice(actualPadStart,
                          (paddedEnd - paddedStart) - actualPadEnd, 1))

            expectedAry = expand_dims(ary[expectedPaddedSlices], axis=0)
            expectedPaddedSlices = [
                slice(params.timepoint, params.timepoint + 1, 1)
            ] + expectedPaddedSlices
            expectedValSlices = [slice(0, 1, 1)] + expectedValSlices
            assert_equals(tuple(expectedPaddedSlices), tuple(key.padImgSlices))
            assert_equals(tuple(expectedValSlices), tuple(key.valSlices))
            assert_equals(tuple(expectedAry.shape), tuple(val.shape))
            assert_true(array_equal(expectedAry, val))
    def test_splitsAndPix(self):
        def genSlicesForPix(pix, size):
            slices = []
            st = 0
            while st < size:
                en = min(st + pix, size)
                slices.append(slice(st, en, 1))
                st = en
            return slices

        def genSlicesForSplits(splits, size):
            slices = []
            blocksize = size / splits  # integer division
            blockrem = size % splits
            st = 0
            while st < size:
                en = st + blocksize
                if blockrem > 0:
                    en += 1
                    blockrem -= 1
                en = min(en, size)
                slices.append(slice(st, en, 1))
                st = en
            return slices

        Params = namedtuple("Params", "unitsPerDim units image padding expPix expSplits expSlices0")
        PARAMS = [
            Params((5, 5, 1), "pix", MockImage((15, 15, 3), 2, "uint8"), 0, (5, 5, 1), None, genSlicesForPix(5, 15)),
            Params((5, 5, 2), "pix", MockImage((7, 7, 3), 2, "uint8"), 0, (5, 5, 2), None, genSlicesForPix(5, 7)),
            Params((2, 2, 2), "s", MockImage((7, 7, 3), 2, "uint8"), 0, None, (2, 2, 2), genSlicesForSplits(2, 7)),
            Params((5, 5, 1), "pix", MockImage((15, 15, 3), 2, "uint8"), 2, (5, 5, 1), None, genSlicesForPix(5, 15)),
            Params((5, 5, 2), "pix", MockImage((7, 7, 3), 2, "uint8"), 2, (5, 5, 2), None, genSlicesForPix(5, 7)),
            Params((2, 2, 2), "s", MockImage((7, 7, 3), 2, "uint8"), 2, None, (2, 2, 2), genSlicesForSplits(2, 7)),
        ]
        for params in PARAMS:
            if params.padding:
                strat = PaddedBlockingStrategy(params.unitsPerDim, units=params.units, padding=params.padding)
            else:
                strat = SimpleBlockingStrategy(params.unitsPerDim, params.units)
            strat.setSource(params.image)
            if params.expPix:
                assert_equals(tuple(params.expPix), tuple(strat._pixPerDim))
            else:
                assert_true(strat._pixPerDim is None)
            if params.expSplits:
                assert_equals(tuple(params.expSplits), tuple(strat._splitsPerDim))
            else:
                assert_true(strat._splitsPerDim is None)
            assert_equals(params.expSlices0, strat._slices[0])
    def test_paddedBlockExtraction(self):
        for params in TestBlockExtraction.PARAMS:
            strategy = PaddedBlockingStrategy([1] * len(params.aryshape), params.padding)  # dummy splits; not used here
            n = reduce(lambda x, y: x * y, params.aryshape)
            ary = arange(n, dtype="int16").reshape(params.aryshape)
            key, val = strategy.extractBlockFromImage(ary, params.blockslices, params.timepoint, params.ntimepoints)

            expectedSlices = [slice(params.timepoint, params.timepoint + 1, 1)] + list(params.blockslices)
            assert_equals(params.timepoint, key.temporalKey)
            assert_equals(params.ntimepoints, key.origShape[0])
            assert_equals(tuple(params.aryshape), tuple(key.origShape[1:]))
            assert_equals(tuple(expectedSlices), tuple(key.imgSlices))

            try:
                _ = len(params.padding)
                padding = list(params.padding)
            except TypeError:
                padding = [params.padding] * ary.ndim

            expectedPaddedSlices = []
            expectedValSlices = []
            for slise, pad, l in zip(params.blockslices, padding, ary.shape):
                paddedStart = max(0, slise.start - pad) if not (slise.start is None) else 0
                paddedEnd = min(l, slise.stop + pad) if not (slise.stop is None) else l
                actualPadStart = slise.start - paddedStart if not (slise.start is None) else 0
                actualPadEnd = paddedEnd - slise.stop if not (slise.stop is None) else 0
                expectedPaddedSlices.append(slice(paddedStart, paddedEnd, 1))
                expectedValSlices.append(slice(actualPadStart, (paddedEnd - paddedStart) - actualPadEnd, 1))

            expectedAry = expand_dims(ary[expectedPaddedSlices], axis=0)
            expectedPaddedSlices = [slice(params.timepoint, params.timepoint + 1, 1)] + expectedPaddedSlices
            expectedValSlices = [slice(0, 1, 1)] + expectedValSlices
            assert_equals(tuple(expectedPaddedSlices), tuple(key.padImgSlices))
            assert_equals(tuple(expectedValSlices), tuple(key.valSlices))
            assert_equals(tuple(expectedAry.shape), tuple(val.shape))
            assert_true(array_equal(expectedAry, val))
Example #5
0
 def test_roundtripThroughPaddedBlocks(self):
     strategy = PaddedBlockingStrategy((2, 2, 2), units="s", padding=2)
     self._run_tst_roundtripThroughBlocks(strategy)
Example #6
0
 def test_toSeriesWithPaddedSplitsAndPack(self):
     strategy = PaddedBlockingStrategy((1, 2), units="s", padding=(1, 1))
     self._run_tst_toSeriesWithSplitsAndPack(strategy)