How to use the tifffile.__version__ function in tifffile

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github ilastik / ilastik / tests / test_lazyflow / test_operators / test_ioOperators / testOpTiffReader.py View on Github external
def test_unknown_axes_tags(self):
        """
        This test is related to https://github.com/ilastik/ilastik/issues/1487

        Here, we generate a 3D tiff file with scikit-learn and try to read it
        """
        import tifffile
        from distutils import version

        # TODO(Dominik) remove version checking once tifffile dependency is fixed
        # ilastik tiffile version >= 2000.0.0
        # latest tifffile version is 0.13.0 right now
        tifffile_version_ilastik_ref = version.StrictVersion("2000.0.0")
        tifffile_version_ref = version.StrictVersion("0.7.0")
        tifffile_version = version.StrictVersion(tifffile.__version__)

        testshapes = [((10, 20), "yx"), ((10, 20, 30), "zyx"), ((10, 20, 30, 3), "zyxc"), ((5, 10, 20, 30, 3), "tzyxc")]

        with tempdir() as d:
            for test_shape, test_axes in testshapes:
                data = numpy.random.randint(0, 256, test_shape).astype(numpy.uint8)
                tiff_path = "{}/myfile_{}.tiff".format(d, test_axes)
                # TODO(Dominik) remove version checking once dependencies for
                # skimage are >= 0.13.0 for all flavours of ilastik
                if (tifffile_version > tifffile_version_ilastik_ref) or (tifffile_version < tifffile_version_ref):
                    tifffile.imsave(tiff_path, data)
                else:
                    tifffile.imsave(tiff_path, data, metadata={"axes": "QQQ"})
                op = OpTiffReader(graph=Graph())
                op.Filepath.setValue(tiff_path)
                assert op.Output.ready()
github ilastik / lazyflow / tests / test_lazyflow / test_operators / test_ioOperators / testOpTiffReader.py View on Github external
def test_unknown_axes_tags(self):
        """
        This test is related to https://github.com/ilastik/ilastik/issues/1487

        Here, we generate a 3D tiff file with scikit-learn and try to read it
        """
        import tifffile
        from distutils import version

        # TODO(Dominik) remove version checking once tifffile dependency is fixed
        # ilastik tiffile version >= 2000.0.0
        # latest tifffile version is 0.13.0 right now
        tifffile_version_ilastik_ref = version.StrictVersion("2000.0.0")
        tifffile_version_ref = version.StrictVersion("0.7.0")
        tifffile_version = version.StrictVersion(tifffile.__version__)

        testshapes = [((10, 20), "yx"), ((10, 20, 30), "zyx"), ((10, 20, 30, 3), "zyxc"), ((5, 10, 20, 30, 3), "tzyxc")]

        with tempdir() as d:
            for test_shape, test_axes in testshapes:
                data = numpy.random.randint(0, 256, test_shape).astype(numpy.uint8)
                tiff_path = "{}/myfile_{}.tiff".format(d, test_axes)
                # TODO(Dominik) remove version checking once dependencies for
                # skimage are >= 0.13.0 for all flavours of ilastik
                if (tifffile_version > tifffile_version_ilastik_ref) or (tifffile_version < tifffile_version_ref):
                    tifffile.imsave(tiff_path, data)
                else:
                    tifffile.imsave(tiff_path, data, metadata={"axes": "QQQ"})
                op = OpTiffReader(graph=Graph())
                op.Filepath.setValue(tiff_path)
                assert op.Output.ready()
github macronucleus / Chromagnon / Chromagnon / imgio / multitifIO.py View on Github external
def openFile(self):
        """
        open a file for reading
        """
        imagej = self.style == 'imagej'
        if int(tifffile.__version__.split('.')[1]) <= 14:
            self.fp = tifffile.TiffWriter(self.fn, software=self.software, imagej=imagej)#, bigtiff=not(imagej))
        else:
            self.fp = tifffile.TiffWriter(self.fn, imagej=imagej)#, bigtiff=not(imagej))

        self.handle = self.fp._fh
        self.dataOffset = self.handle.tell()
github tlambert03 / LLSpy / llspy1 / _llsdir.py View on Github external
def read_tiff_header(self):
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            with tf.TiffFile(self.tiff.raw[0]) as firstTiff:
                self.parameters.shape = firstTiff.series[0].shape
                bitstring = 'bits_per_sample'
                try:
                    if int(tf.__version__.split('.')[1]) >= 13:
                        bitstring = 'bitspersample'
                except Exception:
                    pass
                self.tiff.bit_depth = getattr(firstTiff.pages[0], bitstring)
        self.parameters.nz, self.parameters.ny, self.parameters.nx = self.parameters.shape
github AllenCellModeling / aicsimageio / scripts / benchmark.py View on Github external
"platform_version": platform.version(),
            "architecture": platform.machine(),
            "cpu_total_count": psutil.cpu_count(),
            "cpu_current_utilization": psutil.cpu_percent(),
            "memory_total_gb": psutil.virtual_memory().total / 10e8,
            "memory_available_gb": psutil.virtual_memory().available / 10e8,
        }

        # Store python config
        pyversion = sys.version_info
        _ = {
            "python_version": f"{pyversion.major}.{pyversion.minor}.{pyversion.micro}",
            "aicsimageio": aicsimageio.__version__,
            "czifile": czifile.__version__,
            "imageio": imageio.__version__,
            "tifffile": tifffile.__version__,
        }

        # Run tests
        #######################################################################

        log.info(f"Running tests: no cluster...")
        log.info(f"=" * 80)

        all_results["no-cluster"] = _run_benchmark_suite(resources_dir=resources_dir)

        #######################################################################

        for cluster_config in CLUSTER_CONFIGS:
            total_cores = cluster_config["per_worker_cores"] * cluster_config["workers"]
            log.info(
                f"Running tests: {cluster_config['name']} "