diff options
Diffstat (limited to 'silx/io/fabioh5.py')
| -rw-r--r-- | silx/io/fabioh5.py | 81 |
1 files changed, 56 insertions, 25 deletions
diff --git a/silx/io/fabioh5.py b/silx/io/fabioh5.py index 95eef23..0811ae0 100644 --- a/silx/io/fabioh5.py +++ b/silx/io/fabioh5.py @@ -44,6 +44,7 @@ import numpy from . import commonh5 from silx.third_party import six from silx import version as silx_version +import silx.utils.number try: import h5py @@ -106,11 +107,54 @@ class FrameData(commonh5.LazyLoadableDataset): attrs = {"interpretation": "image"} commonh5.LazyLoadableDataset.__init__(self, name, parent, attrs=attrs) self.__fabio_reader = fabio_reader - + self._shape = None + self._dtype = None def _create_data(self): return self.__fabio_reader.get_data() + def _update_cache(self): + if isinstance(self.__fabio_reader.fabio_file(), + fabio.file_series.file_series): + # Reading all the files is taking too much time + # Reach the information from the only first frame + first_image = self.__fabio_reader.fabio_file().first_image() + self._dtype = first_image.data.dtype + shape0 = self.__fabio_reader.frame_count() + shape1, shape2 = first_image.data.shape + self._shape = shape0, shape1, shape2 + else: + self._dtype = super(commonh5.LazyLoadableDataset, self).dtype + self._shape = super(commonh5.LazyLoadableDataset, self).shape + + @property + def dtype(self): + if self._dtype is None: + self._update_cache() + return self._dtype + + @property + def shape(self): + if self._shape is None: + self._update_cache() + return self._shape + + def __iter__(self): + for frame in self.__fabio_reader.iter_frames(): + yield frame.data + + def __getitem__(self, item): + # optimization for fetching a single frame if data not already loaded + if not self._is_initialized: + if isinstance(item, six.integer_types) and \ + isinstance(self.__fabio_reader.fabio_file(), + fabio.file_series.file_series): + if item < 0: + # negative indexing + item += len(self) + return self.__fabio_reader.fabio_file().jump_image(item).data + return super(FrameData, self).__getitem__(item) + class RawHeaderData(commonh5.LazyLoadableDataset): """Lazy loadable raw header""" @@ -638,30 +682,11 @@ class FabioReader(object): If it is not possible it returns a numpy string. """ try: - value = int(value) - dtype = numpy.min_scalar_type(value) - assert dtype.kind != "O" - return dtype.type(value) + numpy_type = silx.utils.number.min_numerical_convertible_type(value) + converted = numpy_type(value) except ValueError: - try: - # numpy.min_scalar_type is not able to do very well the job - # when there is a lot of digit after the dot - # https://github.com/numpy/numpy/issues/8207 - # Let's count the digit of the string - digits = len(value) - 1 # minus the dot - if digits <= 7: - # A float32 is accurate with about 7 digits - return numpy.float32(value) - elif digits <= 16: - # A float64 is accurate with about 16 digits - return numpy.float64(value) - else: - if hasattr(numpy, "float128"): - return numpy.float128(value) - else: - return numpy.float64(value) - except ValueError: - return numpy.string_(value) + converted = numpy.string_(value) + return converted def _convert_list(self, value): """Convert a string into a typed numpy array. @@ -951,7 +976,13 @@ class File(commonh5.File): if first_file_name is not None: _, ext = os.path.splitext(first_file_name) ext = ext[1:] - use_edf_reader = ext in fabio.edfimage.EdfImage.DEFAULT_EXTENSIONS + edfimage = fabio.edfimage.EdfImage + if hasattr(edfimage, "DEFAULT_EXTENTIONS"): + # Typo on fabio 0.5 + edf_extensions = edfimage.DEFAULT_EXTENTIONS + else: + edf_extensions = edfimage.DEFAULT_EXTENSIONS + use_edf_reader = ext in edf_extensions elif first_image is not None: use_edf_reader = isinstance(first_image, fabio.edfimage.EdfImage) else: |