def _run_fromFishTif(self, blocksize="150M"):
imagepath = TestSeriesLoader._findSourceTreeDir("utils/data/fish/tif-stack")
series = SeriesLoader(self.sc).fromMultipageTif(imagepath, blockSize=blocksize)
series_ary = series.pack()
series_ary_xpose = series.pack(transpose=True)
assert_equals((76, 87, 2), series.dims.count)
assert_equals((20, 76, 87, 2), series_ary.shape)
assert_equals((20, 2, 87, 76), series_ary_xpose.shape)
def _run_fromFishTif(self, blocksize):
imagepath = TestSeriesLoader._findSourceTreeDir("utils/data/fish/images")
series = SeriesLoader(self.sc).fromTif(imagepath, blockSize=blocksize)
assert_equals('float16', series._dtype)
seriesAry = series.pack()
seriesAry_xpose = series.pack(transpose=True)
assert_equals('float16', str(seriesAry.dtype))
assert_equals((76, 87, 2), series.dims.count)
assert_equals((20, 76, 87, 2), seriesAry.shape)
assert_equals((20, 2, 87, 76), seriesAry_xpose.shape)
def _run_fromFishTif(self, blocksize):
imagepath = TestSeriesLoader._findSourceTreeDir(
"utils/data/fish/tif-stack")
series = SeriesLoader(self.sc).fromTif(imagepath, blockSize=blocksize)
assert_equals('float16', series._dtype)
seriesAry = series.pack()
seriesAry_xpose = series.pack(transpose=True)
assert_equals('float16', str(seriesAry.dtype))
assert_equals((76, 87, 2), series.dims.count)
assert_equals((20, 76, 87, 2), seriesAry.shape)
assert_equals((20, 2, 87, 76), seriesAry_xpose.shape)
def test_fromMultipleArrays(self):
ary = arange(8, dtype=dtype('int16')).reshape((2, 4))
ary2 = arange(8, 16, dtype=dtype('int16')).reshape((2, 4))
series = SeriesLoader(self.sc).fromArrays([ary, ary2])
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((3, 0), seriesvals[3][0])
assert_equals((0, 1), seriesvals[4][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, with subsequent point concatenated in values
collectedvals = array([kv[1] for kv in seriesvals], dtype=dtype('int16'))
assert_true(array_equal(ary.ravel(), collectedvals[:, 0]))
assert_true(array_equal(ary2.ravel(), collectedvals[:, 1]))
# check that packing returns concatenation of input arrays, with time as first dimension
assert_true(array_equal(ary.T, seriesary[0]))
assert_true(array_equal(ary2.T, seriesary[1]))
def test_fromArrays(self):
ary = arange(8, dtype=dtype('int16')).reshape((2, 4))
series = SeriesLoader(self.sc).fromArrays(ary)
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=dtype('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_fromMultipleArrays(self):
ary = arange(8, dtype=dtypeFunc('int16')).reshape((2, 4))
ary2 = arange(8, 16, dtype=dtypeFunc('int16')).reshape((2, 4))
series = SeriesLoader(self.sc).fromArraysAsImages([ary, ary2])
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((3, 0), seriesVals[3][0])
assert_equals((0, 1), seriesVals[4][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, with subsequent point concatenated in values
collectedVals = array([kv[1] for kv in seriesVals],
dtype=dtypeFunc('int16'))
assert_true(array_equal(ary.ravel(), collectedVals[:, 0]))
assert_true(array_equal(ary2.ravel(), collectedVals[:, 1]))
# check that packing returns concatenation of input arrays, with time as first dimension
assert_true(array_equal(ary.T, seriesAry[0]))
assert_true(array_equal(ary2.T, seriesAry[1]))
def test_fromArrays(self):
ary = arange(8, dtype=dtypeFunc('int16')).reshape((2, 4))
series = SeriesLoader(self.sc).fromArraysAsImages(ary)
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_loadStacksAsSeries(self):
rangeary = arange(64*128, dtype=dtype('int16'))
rangeary.shape = (64, 128)
filepath = os.path.join(self.outputdir, "rangeary.stack")
rangeary.tofile(filepath)
series = SeriesLoader(self.sc).fromStack(filepath, dims=(128, 64))
series_ary = series.pack()
assert_equals((128, 64), series.dims.count)
assert_equals((128, 64), series_ary.shape)
assert_true(array_equal(rangeary.T, series_ary))
def test_loadStacksAsSeries(self):
rangeary = arange(64 * 128, dtype=dtype('int16'))
rangeary.shape = (64, 128)
filepath = os.path.join(self.outputdir, "rangeary.stack")
rangeary.tofile(filepath)
series = SeriesLoader(self.sc).fromStack(filepath, dims=(128, 64))
series_ary = series.pack()
assert_equals((128, 64), series.dims.count)
assert_equals((128, 64), series_ary.shape)
assert_true(array_equal(rangeary.T, series_ary))
def _run_tst_roundtripConvertToSeries(self, images, strategy):
outdir = os.path.join(self.outputdir, "fish-series-dir")
partitionedimages = images.toBlocks(strategy)
series = partitionedimages.toSeries()
series_ary = series.pack()
partitionedimages.saveAsBinarySeries(outdir)
converted_series = SeriesLoader(self.sc).fromBinary(outdir)
converted_series_ary = converted_series.pack()
assert_equals(images.dims.count, series.dims.count)
expected_shape = tuple([images.nimages] + list(images.dims.count))
assert_equals(expected_shape, series_ary.shape)
assert_true(array_equal(series_ary, converted_series_ary))
def _run_tst_roundtripConvertToSeries(self, images, strategy):
outdir = os.path.join(self.outputdir, "fish-series-dir")
partitionedimages = images.toBlocks(strategy)
series = partitionedimages.toSeries()
series_ary = series.pack()
partitionedimages.saveAsBinarySeries(outdir)
converted_series = SeriesLoader(self.sc).fromBinary(outdir)
converted_series_ary = converted_series.pack()
assert_equals(images.dims.count, series.dims.count)
expected_shape = tuple([images.nrecords] + list(images.dims.count))
assert_equals(expected_shape, series_ary.shape)
assert_true(array_equal(series_ary, converted_series_ary))
def test_roundtripConvertToSeries(self):
imagepath = TestImagesUsingOutputDir._findSourceTreeDir("utils/data/fish/tif-stack")
outdir = os.path.join(self.outputdir, "fish-series-dir")
images = ImagesLoader(self.sc).fromMultipageTif(imagepath)
series = images.toSeries(blockSize=76*20)
series_ary = series.pack()
images.saveAsBinarySeries(outdir, blockSize=76*20)
converted_series = SeriesLoader(self.sc).fromBinary(outdir)
converted_series_ary = converted_series.pack()
assert_equals((76, 87, 2), series.dims.count)
assert_equals((20, 76, 87, 2), series_ary.shape)
assert_true(array_equal(series_ary, converted_series_ary))
def test_roundtripConvertToSeries(self):
imagepath = TestImagesUsingOutputDir._findSourceTreeDir(
"utils/data/fish/tif-stack")
outdir = os.path.join(self.outputdir, "fish-series-dir")
images = ImagesLoader(self.sc).fromMultipageTif(imagepath)
series = images.toSeries(blockSize=76 * 20)
series_ary = series.pack()
images.saveAsBinarySeries(outdir, blockSize=76 * 20)
converted_series = SeriesLoader(self.sc).fromBinary(outdir)
converted_series_ary = converted_series.pack()
assert_equals((76, 87, 2), series.dims.count)
assert_equals((20, 76, 87, 2), series_ary.shape)
assert_true(array_equal(series_ary, converted_series_ary))
def test_fromMultipageTif(self):
testresourcesdir = TestSeriesLoader._findTestResourcesDir()
imagepath = os.path.join(testresourcesdir, "multilayer_tif", "dotdotdot_lzw.tif")
testimg_pil = Image.open(imagepath)
testimg_arys = list()
testimg_arys.append(pil_to_array(testimg_pil))
testimg_pil.seek(1)
testimg_arys.append(pil_to_array(testimg_pil))
testimg_pil.seek(2)
testimg_arys.append(pil_to_array(testimg_pil))
series = SeriesLoader(self.sc).fromMultipageTif(imagepath)
series_ary = series.pack()
assert_equals((70, 75, 3), series.dims.count)
assert_equals((70, 75, 3), series_ary.shape)
assert_true(array_equal(testimg_arys[0], series_ary[:, :, 0]))
assert_true(array_equal(testimg_arys[1], series_ary[:, :, 1]))
assert_true(array_equal(testimg_arys[2], series_ary[:, :, 2]))
def test_fromMultipageTif(self):
testresourcesdir = TestSeriesLoader._findTestResourcesDir()
imagepath = os.path.join(testresourcesdir, "multilayer_tif",
"dotdotdot_lzw.tif")
testimg_pil = Image.open(imagepath)
testimg_arys = list()
testimg_arys.append(pil_to_array(testimg_pil))
testimg_pil.seek(1)
testimg_arys.append(pil_to_array(testimg_pil))
testimg_pil.seek(2)
testimg_arys.append(pil_to_array(testimg_pil))
series = SeriesLoader(self.sc).fromMultipageTif(imagepath)
assert_equals('float16', series._dtype)
series_ary = series.pack()
assert_equals((70, 75, 3), series.dims.count)
assert_equals((70, 75, 3), series_ary.shape)
assert_true(array_equal(testimg_arys[0], series_ary[:, :, 0]))
assert_true(array_equal(testimg_arys[1], series_ary[:, :, 1]))
assert_true(array_equal(testimg_arys[2], series_ary[:, :, 2]))
