Python ImagesLoader.collect方法代码示例

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromMultiTimepointStacks(self):
        ary = arange(16, dtype=dtypeFunc('uint8')).reshape((4, 2, 2))
        ary2 = arange(16, 32, dtype=dtypeFunc('uint8')).reshape((4, 2, 2))
        ary.tofile(os.path.join(self.outputdir, "test01.stack"))
        ary2.tofile(os.path.join(self.outputdir, "test02.stack"))

        image = ImagesLoader(self.sc).fromStack(self.outputdir, dtype="uint8", dims=(2, 2, 4), nplanes=2)
        collectedImage = image.collect()

        # we don't expect to have nrecords cached, since we get an unknown number of images per file
        assert_true(image._nrecords is None)
        assert_equals(4, image.nrecords)
        assert_equals(4, len(collectedImage))
        # check keys:
        assert_equals(0, collectedImage[0][0])
        assert_equals(1, collectedImage[1][0])
        assert_equals(2, collectedImage[2][0])
        assert_equals(3, collectedImage[3][0])
        # check values:
        assert_true(array_equal(ary[:2].T, collectedImage[0][1]))
        assert_true(array_equal(ary[2:].T, collectedImage[1][1]))
        assert_true(array_equal(ary2[:2].T, collectedImage[2][1]))
        assert_true(array_equal(ary2[2:].T, collectedImage[3][1]))

        # 3 planes does not divide 4
        assert_raises(ValueError, ImagesLoader(self.sc).fromStack, self.outputdir, dtype="uint8",
                      dims=(2, 2, 4), nplanes=3)

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def _run_tst_roundtripThroughBlocks(self, strategy):
        imagepath = findSourceTreeDir("utils/data/fish/images")
        images = ImagesLoader(self.sc).fromTif(imagepath)
        blockedimages = images.toBlocks(strategy)
        recombinedimages = blockedimages.toImages()

        collectedimages = images.collect()
        roundtrippedimages = recombinedimages.collect()
        for orig, roundtripped in zip(collectedimages, roundtrippedimages):
            assert_true(array_equal(orig[1], roundtripped[1]))

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromArrays(self):
        ary = arange(8, dtype=dtypeFunc('int16')).reshape((2, 4))

        image = ImagesLoader(self.sc).fromArrays(ary)

        collectedImage = image.collect()
        assert_equals(1, len(collectedImage))
        assert_equals(ary.shape, image.dims.count)
        assert_equals(0, collectedImage[0][0])  # check key
        assert_true(array_equal(ary, collectedImage[0][1]))  # check value

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromStack(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))

        collectedImage = image.collect()
        assert_equals(1, len(collectedImage))
        assert_equals(0, collectedImage[0][0])  # check key
        # assert that image shape *matches* that in image dimensions:
        assert_equals(image.dims.count, collectedImage[0][1].shape)
        assert_true(array_equal(ary.T, collectedImage[0][1]))  # check value

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromStacks(self):
        ary = arange(8, dtype=dtypeFunc('int16')).reshape((2, 4))
        ary2 = arange(8, 16, dtype=dtypeFunc('int16')).reshape((2, 4))
        filename = os.path.join(self.outputdir, "test01.stack")
        ary.tofile(filename)
        filename = os.path.join(self.outputdir, "test02.stack")
        ary2.tofile(filename)

        image = ImagesLoader(self.sc).fromStack(self.outputdir, dims=(4, 2))

        collectedImage = image.collect()
        assert_equals(2, len(collectedImage))
        assert_equals(0, collectedImage[0][0])  # check key
        assert_equals(image.dims.count, collectedImage[0][1].shape)
        assert_true(array_equal(ary.T, collectedImage[0][1]))  # check value
        assert_equals(1, collectedImage[1][0])  # check image 2
        assert_true(array_equal(ary2.T, collectedImage[1][1]))

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromSignedIntTif(self):
        imagePath = os.path.join(self.testResourcesDir, "multilayer_tif", "test_signed.tif")
        tiffImages = ImagesLoader(self.sc).fromTif(imagePath, nplanes=1)
        assert_equals(2, tiffImages.nrecords)
        assert_equals('int16', tiffImages.dtype)

        collectedTiffImages = tiffImages.collect()

        assert_equals(2, len(collectedTiffImages), "Expected 2 images, got %d" % len(collectedTiffImages))
        expectedSums = [1973201, 2254767]
        expectedIdx = 0
        for idx, tiffAry in collectedTiffImages:
            assert_equals((120, 120), tiffAry.shape)
            assert_equals('int16', str(tiffAry.dtype))
            assert_equals(expectedIdx, idx)
            assert_equals(expectedSums[idx], tiffAry.ravel().sum())
            expectedIdx += 1

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromMultiTimepointTif(self):
        imagePath = os.path.join(self.testResourcesDir, "multilayer_tif", "dotdotdot_lzw.tif")
        tiffImages = ImagesLoader(self.sc).fromTif(imagePath, nplanes=1)
        # we don't expect to have nrecords cached, since the driver doesn't know how many images there are per file
        assert_true(tiffImages._nrecords is None)
        assert_equals(3, tiffImages.nrecords)

        collectedTiffImages = tiffImages.collect()

        assert_equals(3, len(collectedTiffImages), "Expected 3 images, got %d" % len(collectedTiffImages))
        expectedSums = [1140006, 1119161, 1098917]
        expectedIdx = 0
        for idx, tiffAry in collectedTiffImages:
            assert_equals((70, 75), tiffAry.shape)
            assert_equals(expectedIdx, idx)
            assert_equals(expectedSums[idx], tiffAry.ravel().sum())
            expectedIdx += 1

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromMultipleMultiTimepointTifs(self):
        imagePath = os.path.join(self.testResourcesDir, "multilayer_tif", "dotdotdot_lzw*.tif")

        tiffImages = ImagesLoader(self.sc).fromTif(imagePath, nplanes=1)
        assert_true(tiffImages._nrecords is None)
        assert_equals(6, tiffImages.nrecords)

        collectedTiffImages = tiffImages.collect()

        assert_equals(6, len(collectedTiffImages), "Expected 6 images, got %d" % len(collectedTiffImages))
        expectedSums = [1140006, 1119161, 1098917, 1140006, 1119161, 1098917]
        expectedIdx = 0
        for idx, tiffAry in collectedTiffImages:
            assert_equals((70, 75), tiffAry.shape)
            assert_equals(expectedIdx, idx)
            assert_equals(expectedSums[idx], tiffAry.ravel().sum())
            expectedIdx += 1

        # 3 pages / file is not evenly divisible by 2 planes
        # note this will still log a big traceback, since the exception is in the executor,
        # not the driver. But this is expected behavior.
        assert_raises(Exception, ImagesLoader(self.sc).fromTif(imagePath, nplanes=2).count)

# 需要导入模块: from thunder.rdds.fileio.imagesloader import ImagesLoader [as 别名]
# 或者: from thunder.rdds.fileio.imagesloader.ImagesLoader import collect [as 别名]
    def test_fromStacksWithConf(self):
        ary = arange(8, dtype=dtypeFunc('int32')).reshape((2, 4))
        ary2 = arange(8, 16, dtype=dtypeFunc('int32')).reshape((2, 4))
        filename = os.path.join(self.outputdir, "test01.stack")
        ary.tofile(filename)
        filename = os.path.join(self.outputdir, "test02.stack")
        ary2.tofile(filename)
        conf = {"dims": [4, 2], "dtype": "int32"}
        with open(os.path.join(self.outputdir, "conf.json"), 'w') as fp:
            json.dump(conf, fp)

        image = ImagesLoader(self.sc).fromStack(self.outputdir)
        assert_equals("int32", image._dtype)
        assert_equals(2, image._nrecords)
        assert_equals((4, 2), image._dims.count)

        collectedImage = image.collect()
        assert_equals(2, len(collectedImage))
        assert_equals(0, collectedImage[0][0])  # check key
        assert_equals(image.dims.count, collectedImage[0][1].shape)
        assert_true(array_equal(ary.T, collectedImage[0][1]))  # check value
        assert_equals(1, collectedImage[1][0])  # check image 2
        assert_true(array_equal(ary2.T, collectedImage[1][1]))