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first attempt of a soleil reader which can read a stack of images.
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| # coding: utf-8 | ||
| # | ||
| # Project: FabIO X-ray image reader | ||
| # | ||
| # Copyright (C) 2010-2016 European Synchrotron Radiation Facility | ||
| # Grenoble, France | ||
| # | ||
| # Copyright (C) 2019 Synchrotron-SOLEIL | ||
| # Gif-sur-Yvette, France | ||
| # | ||
| # Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| # of this software and associated documentation files (the "Software"), to deal | ||
| # in the Software without restriction, including without limitation the rights | ||
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| # copies of the Software, and to permit persons to whom the Software is | ||
| # furnished to do so, subject to the following conditions: | ||
| # | ||
| # The above copyright notice and this permission notice shall be included in | ||
| # all copies or substantial portions of the Software. | ||
| # | ||
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| # THE SOFTWARE. | ||
| # | ||
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| """Soleil HDF5 image for FabIO | ||
| Authors: Jerome Kieffer, Picca Frédéric-Emmanuel | ||
| email: Jerome.Kieffer@terre-adelie.org, picca@synchrotron-soleil.fr | ||
| Specifications: | ||
| input should being the form: | ||
| filename | ||
| Only supports ndim=2 or 3 (exposed as a stack of images) | ||
| """ | ||
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| from __future__ import with_statement, print_function, division | ||
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| __authors__ = ["Jérôme Kieffer", "Picca Frédéric-Emmanuel"] | ||
| __contact__ = "Jerome.Kieffer@terre-adelie.org" | ||
| __license__ = "MIT" | ||
| __copyright__ = "Jérôme Kieffer" | ||
| __date__ = "01/03/2019" | ||
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| import logging | ||
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| logger = logging.getLogger(__name__) | ||
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| from collections import namedtuple | ||
| from functools import partial | ||
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| try: | ||
| import h5py | ||
| from h5py import Dataset, File | ||
| except ImportError: | ||
| h5py = None | ||
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| from fabio.fabioimage import FabioFrame, FabioImage | ||
| from .fabioutils import previous_filename, next_filename | ||
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| # Generic hdf5 access types. | ||
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| DatasetPathContains = namedtuple("DatasetPathContains", "path") | ||
| DatasetPathWithAttribute = namedtuple("DatasetPathWithAttribute", "attribute value") | ||
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| def _v_attrs(attribute, value, _name, obj): | ||
| """extract all the images and accumulate them in the acc variable""" | ||
| if isinstance(obj, Dataset): | ||
| if attribute in obj.attrs and obj.attrs[attribute] == value: | ||
| return obj | ||
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| def _v_item(key, name, obj): | ||
| if key in name: | ||
| return obj | ||
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| def get_dataset(h5file, path): | ||
| res = None | ||
| if isinstance(path, DatasetPathContains): | ||
| res = h5file.visititems(partial(_v_item, path.path)) | ||
| elif isinstance(path, DatasetPathWithAttribute): | ||
| res = h5file.visititems(partial(_v_attrs, | ||
| path.attribute, path.value)) | ||
| return res | ||
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| class SoleilFrame(FabioFrame): | ||
| """Identify a slice of dataset from an HDF5 file""" | ||
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| def __init__(self, soleil_image, frame_num): | ||
| if not isinstance(soleil_image, SoleilImage): | ||
| raise TypeError("Expected class {SoleilImage}".format(SoleilImage)) | ||
| data = soleil_image.dataset[frame_num, :, :] | ||
| super(SoleilFrame, self).__init__(data=data, header=soleil_image.header) | ||
| self.hdf5 = soleil_image.hdf5 | ||
| self.dataset = soleil_image.dataset | ||
| self.filename = soleil_image.filename | ||
| self._nframes = soleil_image.nframes | ||
| self.header = soleil_image.header | ||
| self.currentframe = frame_num | ||
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| class SoleilImage(FabioImage): | ||
| """ | ||
| FabIO image class for Images from an Soleil HDF file | ||
| filename::dataset | ||
| """ | ||
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| DESCRIPTION = "Soleil Hierarchical Data Format HDF5 flat reader" | ||
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| DEFAULT_EXTENSIONS = ["nxs", "h5"] | ||
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| def __init__(self, *arg, **kwargs): | ||
| if not h5py: | ||
| raise RuntimeError("fabio.SoleilImage cannot be used without h5py. Please install h5py and restart") | ||
| super(SoleilImage, self).__init__(*arg, **kwargs) | ||
| self.hdf5 = None | ||
| self.dataset = None | ||
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| def read(self, filename, frame=None): | ||
| """ | ||
| try to read image | ||
| :param fname: filename | ||
| """ | ||
| self.resetvals() | ||
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| path = DatasetPathWithAttribute("interpretation", b"image") | ||
| self.filename = filename | ||
| self.hdf5 = File(self.filename, "r") | ||
| self.dataset = get_dataset(self.hdf5, path) | ||
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| # ndim does not exist for external links ? | ||
| ndim = len(self.dataset.shape) | ||
| if ndim == 3: | ||
| self._nframes = self.dataset.shape[0] | ||
| if frame is not None: | ||
| self.currentframe = int(frame) | ||
| else: | ||
| self.currentframe = 0 | ||
| self.data = self.dataset[self.currentframe, :, :] | ||
| elif ndim == 2: | ||
| self.data = self.dataset[:, :] | ||
| else: | ||
| err = "Only 2D and 3D datasets are supported by FabIO, here %sD" % self.dataset.ndim | ||
| logger.error(err) | ||
| raise RuntimeError(err) | ||
| return self | ||
|
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| def getframe(self, num): | ||
| """ | ||
| Returns a frame as a new FabioImage object | ||
| :param num: frame number | ||
| """ | ||
| if num < 0 or num > self.nframes: | ||
| raise RuntimeError("Requested frame number %i is out of range [0, %i[ " % (num, self.nframes)) | ||
| # Do a deep copy of the header to make a new one | ||
| return SoleilFrame(self, num) | ||
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| def next(self): | ||
| """ | ||
| Get the next image in a series as a fabio image | ||
| """ | ||
| if self.currentframe < (self.nframes - 1): | ||
| return self.getframe(self.currentframe + 1) | ||
| else: | ||
| newobj = SoleilImage() | ||
| newobj.read(next_filename(self.filename)) | ||
| return newobj | ||
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| def previous(self): | ||
| """ | ||
| Get the previous image in a series as a fabio image | ||
| """ | ||
| if self.currentframe > 0: | ||
| return self.getframe(self.currentframe - 1) | ||
| else: | ||
| newobj = SoleilImage() | ||
| newobj.read(previous_filename(self.filename)) | ||
| return newobj | ||
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| def close(self): | ||
| if self.hdf5 is not None: | ||
| self.hdf5.close() | ||
| self.dataset = None |