diff options
Diffstat (limited to 'silx/io/fabioh5.py')
| -rw-r--r-- | silx/io/fabioh5.py | 57 |
1 files changed, 42 insertions, 15 deletions
diff --git a/silx/io/fabioh5.py b/silx/io/fabioh5.py index 0811ae0..27ef3fd 100644 --- a/silx/io/fabioh5.py +++ b/silx/io/fabioh5.py @@ -40,16 +40,12 @@ import os import fabio.file_series import numpy +import six from . import commonh5 -from silx.third_party import six from silx import version as silx_version import silx.utils.number - -try: - import h5py -except ImportError as e: - h5py = None +import h5py _logger = logging.getLogger(__name__) @@ -197,7 +193,7 @@ class RawHeaderData(commonh5.LazyLoadableDataset): else: dtype = numpy.string_ - if dtype == numpy.unicode_ and h5py is not None: + if dtype == numpy.unicode_: # h5py only support vlen unicode dtype = h5py.special_dtype(vlen=six.text_type) @@ -262,6 +258,30 @@ class ImageGroup(commonh5.LazyLoadableGroup): self.add_node(detector) +class NxDataPreviewGroup(commonh5.LazyLoadableGroup): + """Define the NxData group which is used as the default NXdata to show the + content of the file. + """ + + def __init__(self, name, fabio_reader, parent=None): + if fabio_reader.is_spectrum(): + interpretation = "spectrum" + else: + interpretation = "image" + attrs = { + "NX_class": "NXdata", + "interpretation": interpretation, + "signal": "data", + } + commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) + self.__fabio_reader = fabio_reader + + def _create_child(self): + basepath = self.parent.name + data = commonh5.SoftLink("data", path=basepath + "/instrument/detector_0/data") + self.add_node(data) + + class SampleGroup(commonh5.LazyLoadableGroup): """Define the image group (sub group of measurement) using Fabio data. """ @@ -383,10 +403,11 @@ class FabioReader(object): may fail. """ if self.__must_be_closed: - # It looks like there is no close on FabioImage - # self.__fabio_image.close() - pass - self.__fabio_image = None + # Make sure the API of fabio provide it a 'close' method + # TODO the test can be removed if fabio version >= 0.8 + if hasattr(self.__fabio_file, "close"): + self.__fabio_file.close() + self.__fabio_file = None def fabio_file(self): return self.__fabio_file @@ -917,14 +938,15 @@ class File(commonh5.File): self.__fabio_reader = self.create_fabio_reader(file_name, fabio_image, file_series) if fabio_image is not None: file_name = fabio_image.filename + scan = self.create_scan_group(self.__fabio_reader) attrs = {"NX_class": "NXroot", "file_time": datetime.datetime.now().isoformat(), - "creator": "silx %s" % silx_version} + "creator": "silx %s" % silx_version, + "default": scan.basename} if file_name is not None: attrs["file_name"] = file_name commonh5.File.__init__(self, name=file_name, attrs=attrs) - scan = self.create_scan_group(self.__fabio_reader) self.add_node(scan) def create_scan_group(self, fabio_reader): @@ -934,8 +956,12 @@ class File(commonh5.File): :param FabioReader fabio_reader: A reader for the Fabio image :rtype: commonh5.Group """ - - scan = commonh5.Group("scan_0", attrs={"NX_class": "NXentry"}) + nxdata = NxDataPreviewGroup("image", fabio_reader) + scan_attrs = { + "NX_class": "NXentry", + "default": nxdata.basename, + } + scan = commonh5.Group("scan_0", attrs=scan_attrs) instrument = commonh5.Group("instrument", attrs={"NX_class": "NXinstrument"}) measurement = MeasurementGroup("measurement", fabio_reader, attrs={"NX_class": "NXcollection"}) file_ = commonh5.Group("file", attrs={"NX_class": "NXcollection"}) @@ -949,6 +975,7 @@ class File(commonh5.File): instrument.add_node(detector) file_.add_node(raw_header) scan.add_node(measurement) + scan.add_node(nxdata) if fabio_reader.has_sample_information(): sample = SampleGroup("sample", fabio_reader) |