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# Copyright 2014 Diamond Light Source Ltd. |
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# |
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# Licensed under the Apache License, Version 2.0 (the "License"); |
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# you may not use this file except in compliance with the License. |
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# You may obtain a copy of the License at |
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# |
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# http://www.apache.org/licenses/LICENSE-2.0 |
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# |
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# Unless required by applicable law or agreed to in writing, software |
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# distributed under the License is distributed on an "AS IS" BASIS, |
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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# See the License for the specific language governing permissions and |
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# limitations under the License. |
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""" |
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.. module:: temp_loader |
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:platform: Unix |
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:synopsis: A class for loading standard tomography data in a variety of |
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formats. |
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.. moduleauthor:: Nicola Wadeson <[email protected]> |
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""" |
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import os |
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import tempfile |
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import warnings |
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import h5py |
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import numpy as np |
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from savu.data.data_structures.data_types.data_plus_darks_and_flats \ |
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import NoImageKey |
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from savu.data.data_structures.data_types.image_data import ImageData |
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from savu.plugins.loaders.base_loader import BaseLoader |
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from savu.plugins.utils import register_plugin |
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@register_plugin |
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class ImageLoader(BaseLoader): |
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""" |
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Load any FabIO compatible formats (e.g. tiffs) |
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:param dataset_name: The name assigned to the dataset. Default: 'tomo'. |
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:param angles: A python statement to be evaluated \ |
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(e.g np.linspace(0, 180, nAngles)) or a file. Default: None. |
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:param frame_dim: Which dimension requires stitching? Default: 0. |
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:param data_prefix: A file prefix for the data file. Default: None. |
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:param dark_prefix: A file prefix for the dark field files, including the\ |
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folder path if different from the data. Default: None. |
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:param flat_prefix: A file prefix for the flat field files, including the\ |
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folder path if different from the data. Default: None. |
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""" |
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def __init__(self, name='ImageLoader'): |
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super(ImageLoader, self).__init__(name) |
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def setup(self): |
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exp = self.exp |
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data_obj = exp.create_data_object('in_data', |
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self.parameters['dataset_name']) |
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rot = 0 |
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detY = 1 |
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detX = 2 |
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data_obj.set_axis_labels('rotation_angle.degrees', |
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'detector_y.pixel', |
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'detector_x.pixel') |
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data_obj.add_pattern('PROJECTION', core_dims=(detX, detY), |
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slice_dims=(rot,)) |
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data_obj.add_pattern('SINOGRAM', core_dims=(detX, rot), |
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slice_dims=(detY,)) |
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path = os.path.abspath(exp.meta_data.get("data_file")) |
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data_obj.data = self._get_data_type(data_obj, path) |
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self.set_rotation_angles(data_obj) |
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# dummy file |
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filename = path.split(os.sep)[-1] + '.h5' |
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data_obj.backing_file = \ |
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h5py.File(os.path.join(tempfile.mkdtemp(), filename), 'a') |
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data_obj.set_shape(data_obj.data.get_shape()) |
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self.set_data_reduction_params(data_obj) |
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self._set_darks_and_flats(data_obj, path) |
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def _set_darks_and_flats(self, dObj, path): |
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if not self.parameters['flat_prefix']: |
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return |
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dObj.data = NoImageKey(dObj, None, 0) |
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fdim = self.parameters['frame_dim'] |
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# read dark and flat images |
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fpath, ffix = self._get_path(self.parameters['flat_prefix'], path) |
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flat = ImageData(fpath, dObj, [fdim], None, ffix) |
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if self.parameters['dark_prefix']: |
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dpath, dfix = self._get_path(self.parameters['dark_prefix'], path) |
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dark = ImageData(dpath, dObj, [fdim], None, dfix) |
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else: |
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shape = dObj.get_shape() |
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dark = np.zeros([1] + [shape[i] for i in [1, 2]], dtype=flat.dtype) |
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dObj.data._set_dark_path(dark) |
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dObj.data._set_flat_path(flat) |
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dObj.data._set_dark_and_flat() |
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def _get_path(self, param, data): |
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ppath, pfix = os.path.split(param) |
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ppath = \ |
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os.path.join(data, ppath) if not os.path.isabs(ppath) else ppath |
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return ppath, pfix |
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def _get_data_type(self, obj, path): |
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prefix = self.parameters['data_prefix'] |
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return ImageData(path, obj, [self.parameters['frame_dim']], None, prefix) |
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def set_rotation_angles(self, data_obj): |
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angles = self.parameters['angles'] |
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if angles is None: |
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angles = np.linspace(0, 180, data_obj.data.get_shape()[0]) |
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else: |
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try: |
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ldict = {} |
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exec("angles = " + angles,globals(),ldict) |
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angles = ldict['angles'] |
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except Exception as e: |
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warnings.warn("Could not execute statement: {}".format(e)) |
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try: |
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angles = np.loadtxt(angles) |
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except Exception as e: |
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raise Exception('Cannot set angles in loader. Error: {}'.format(e)) |
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n_angles = len(angles) |
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data_angles = data_obj.data.get_shape()[self.parameters['frame_dim']] |
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if data_angles != n_angles: |
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raise Exception("The number of angles %s does not match the data " |
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"dimension length %s", n_angles, data_angles) |
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data_obj.meta_data.set("rotation_angle", angles) |
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DiamondLightSource /
Savu
