示例#1
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    def test_9_TestView(self):
        """
        Load some of the dataset again; this time with an offset view.
        Note: The original blockwise fileset must be closed before this test starts.
        """
        # Create a copy of the original description, but specify a translated (and smaller) view
        desc = BlockwiseFileset.readDescription(self.description_path)
        desc.view_origin = [0, 300, 200, 100, 0]
        desc.view_shape = [1, 50, 50, 50, 1]
        offsetConfigPath = self.description_path + "_offset"
        BlockwiseFileset.writeDescription(offsetConfigPath, desc)

        # Open the fileset using the special description file
        bfs = BlockwiseFileset(offsetConfigPath, "r")
        try:
            assert (bfs.description.view_origin == desc.view_origin).all()
            assert (bfs.description.view_shape == desc.view_shape).all()

            # Read some data
            logger.debug("Reading data...")
            disk_slicing = numpy.s_[:, 300:350, 200:250, 100:150, :]
            view_slicing = numpy.s_[:, 0:50, 0:50, 0:50, :]
            roi = sliceToRoi(view_slicing, self.dataShape)
            roiShape = roi[1] - roi[0]
            read_data = numpy.zeros(tuple(roiShape), dtype=numpy.uint8)

            bfs.readData(roi, read_data)

            # The data we read should match the correct part of the original dataset.
            logger.debug("Checking data...")
            assert self.data[disk_slicing].shape == read_data.shape
            assert (self.data[disk_slicing] == read_data).all(), "Data didn't match."

        finally:
            bfs.close()
示例#2
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class OpBlockwiseFilesetReader(Operator):
    """
    Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
    """

    name = "OpBlockwiseFilesetReader"

    DescriptionFilePath = InputSlot(stype="filestring")
    Output = OutputSlot()

    class MissingDatasetError(Exception):
        pass

    def __init__(self, *args, **kwargs):
        super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
        self._blockwiseFileset = None
        self._opDummyData = OpDummyData(parent=self)

    def setupOutputs(self):
        if not os.path.exists(self.DescriptionFilePath.value):
            raise OpBlockwiseFilesetReader.MissingDatasetError(
                "Dataset description not found: {}".format(
                    self.DescriptionFilePath.value))

        # Load up the class that does the real work
        self._blockwiseFileset = BlockwiseFileset(
            self.DescriptionFilePath.value)

        # Check for errors in the description file
        descriptionFields = self._blockwiseFileset.description
        axes = descriptionFields.axes
        assert False not in [
            a in "txyzc" for a in axes
        ], "Unknown axis type.  Known axes: txyzc  Your axes:".format(axes)

        self.Output.meta.shape = tuple(descriptionFields.view_shape)
        self.Output.meta.dtype = descriptionFields.dtype
        self.Output.meta.axistags = vigra.defaultAxistags(
            str(descriptionFields.axes))
        drange = descriptionFields.drange
        if drange is not None:
            self.Output.meta.drange = drange

    def execute(self, slot, subindex, roi, result):
        assert slot == self.Output, "Unknown output slot"
        try:
            self._blockwiseFileset.readData((roi.start, roi.stop), result)
        except BlockwiseFileset.BlockNotReadyError:
            result[:] = self._opDummyData.execute(slot, subindex, roi, result)
        return result

    def propagateDirty(self, slot, subindex, roi):
        assert slot == self.DescriptionFilePath, "Unknown input slot."
        self.Output.setDirty(slice(None))

    def cleanUp(self):
        if self._blockwiseFileset is not None:
            self._blockwiseFileset.close()
        super(OpBlockwiseFilesetReader, self).cleanUp()
class OpBlockwiseFilesetReader(Operator):
    """
    Adapter that provides an operator interface to the BlockwiseFileset class for reading ONLY.
    """

    name = "OpBlockwiseFilesetReader"

    DescriptionFilePath = InputSlot(stype="filestring")
    Output = OutputSlot()

    class MissingDatasetError(Exception):
        pass

    def __init__(self, *args, **kwargs):
        super(OpBlockwiseFilesetReader, self).__init__(*args, **kwargs)
        self._blockwiseFileset = None
        self._opDummyData = OpDummyData(parent=self)

    def setupOutputs(self):
        if not os.path.exists(self.DescriptionFilePath.value):
            raise OpBlockwiseFilesetReader.MissingDatasetError(
                "Dataset description not found: {}".format(self.DescriptionFilePath.value)
            )

        # Load up the class that does the real work
        self._blockwiseFileset = BlockwiseFileset(self.DescriptionFilePath.value)

        # Check for errors in the description file
        descriptionFields = self._blockwiseFileset.description
        axes = descriptionFields.axes
        assert False not in [a in "txyzc" for a in axes], "Unknown axis type.  Known axes: txyzc  Your axes:".format(
            axes
        )

        self.Output.meta.shape = tuple(descriptionFields.view_shape)
        self.Output.meta.dtype = descriptionFields.dtype
        self.Output.meta.axistags = vigra.defaultAxistags(str(descriptionFields.axes))
        drange = descriptionFields.drange
        if drange is not None:
            self.Output.meta.drange = drange

    def execute(self, slot, subindex, roi, result):
        assert slot == self.Output, "Unknown output slot"
        try:
            self._blockwiseFileset.readData((roi.start, roi.stop), result)
        except BlockwiseFileset.BlockNotReadyError:
            result[:] = self._opDummyData.execute(slot, subindex, roi, result)
        return result

    def propagateDirty(self, slot, subindex, roi):
        assert slot == self.DescriptionFilePath, "Unknown input slot."
        self.Output.setDirty(slice(None))

    def cleanUp(self):
        if self._blockwiseFileset is not None:
            self._blockwiseFileset.close()
        super(OpBlockwiseFilesetReader, self).cleanUp()
示例#4
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    def test_9_TestView(self):
        """
        Load some of the dataset again; this time with an offset view.
        Note: The original blockwise fileset must be closed before this test starts.
        """
        # Create a copy of the original description, but specify a translated (and smaller) view
        desc = BlockwiseFileset.readDescription(self.description_path)
        desc.view_origin = [0, 300, 200, 100, 0]
        desc.view_shape = [1, 50, 50, 50, 1]
        offsetConfigPath = self.description_path + "_offset"
        BlockwiseFileset.writeDescription(offsetConfigPath, desc)

        # Open the fileset using the special description file
        bfs = BlockwiseFileset(offsetConfigPath, "r")
        try:
            assert (bfs.description.view_origin == desc.view_origin).all()
            assert (bfs.description.view_shape == desc.view_shape).all()

            # Read some data
            logger.debug("Reading data...")
            disk_slicing = numpy.s_[:, 300:350, 200:250, 100:150, :]
            view_slicing = numpy.s_[:, 0:50, 0:50, 0:50, :]
            roi = sliceToRoi(view_slicing, self.dataShape)
            roiShape = roi[1] - roi[0]
            read_data = numpy.zeros(tuple(roiShape), dtype=numpy.uint8)

            bfs.readData(roi, read_data)

            # The data we read should match the correct part of the original dataset.
            logger.debug("Checking data...")
            assert self.data[disk_slicing].shape == read_data.shape
            assert (self.data[disk_slicing] == read_data
                    ).all(), "Data didn't match."

        finally:
            bfs.close()
示例#5
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    def test_6_TestExportSubset(self):
        roi = ((0, 0, 50, 100, 0), (1, 100, 200, 200, 1))
        exportDir = tempfile.mkdtemp()
        self.bfs.close()
        self.bfs.reopen("r")
        exported_description_path = self.bfs.exportSubset(roi, exportDir)

        try:
            exported_bfs = BlockwiseFileset(exported_description_path, "r")
            assert os.path.exists(exported_description_path), "Couldn't even find the exported description file."

            read_data = exported_bfs.readData(roi)
            expected_data = self.data[roiToSlice(*roi)]

            assert read_data.shape == expected_data.shape, "Exported data had wrong shape"
            assert read_data.dtype == expected_data.dtype, "Exported data had wrong dtype"
            assert (read_data == expected_data).all(), "Exported data did not match expected data"

        finally:
            shutil.rmtree(exportDir)
示例#6
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    def test_6_TestExportSubset(self):
        roi = ((0, 0, 50, 100, 0), (1, 100, 200, 200, 1))
        exportDir = tempfile.mkdtemp()
        self.bfs.close()
        self.bfs.reopen("r")
        exported_description_path = self.bfs.exportSubset(roi, exportDir)

        try:
            exported_bfs = BlockwiseFileset(exported_description_path, "r")
            assert os.path.exists(
                exported_description_path
            ), "Couldn't even find the exported description file."

            read_data = exported_bfs.readData(roi)
            expected_data = self.data[roiToSlice(*roi)]

            assert read_data.shape == expected_data.shape, "Exported data had wrong shape"
            assert read_data.dtype == expected_data.dtype, "Exported data had wrong dtype"
            assert (read_data == expected_data
                    ).all(), "Exported data did not match expected data"

        finally:
            shutil.rmtree(exportDir)