|
1
|
|
|
# Copyright 2014 Diamond Light Source Ltd. |
|
2
|
|
|
# |
|
3
|
|
|
# Licensed under the Apache License, Version 2.0 (the "License"); |
|
4
|
|
|
# you may not use this file except in compliance with the License. |
|
5
|
|
|
# You may obtain a copy of the License at |
|
6
|
|
|
# |
|
7
|
|
|
# http://www.apache.org/licenses/LICENSE-2.0 |
|
8
|
|
|
# |
|
9
|
|
|
# Unless required by applicable law or agreed to in writing, software |
|
10
|
|
|
# distributed under the License is distributed on an "AS IS" BASIS, |
|
11
|
|
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
|
12
|
|
|
# See the License for the specific language governing permissions and |
|
13
|
|
|
# limitations under the License. |
|
14
|
|
|
|
|
15
|
|
|
""" |
|
16
|
|
|
.. module:: lfov_loader |
|
17
|
|
|
:platform: Unix |
|
18
|
|
|
:synopsis: Large field-of-view loader. A class for loading 2 standard |
|
19
|
|
|
tomography scans. |
|
20
|
|
|
.. moduleauthor:: Nicola Wadeson <[email protected]> |
|
21
|
|
|
|
|
22
|
|
|
""" |
|
23
|
|
|
|
|
24
|
|
|
import os |
|
25
|
|
|
import copy |
|
26
|
|
|
import numpy as np |
|
27
|
|
|
import glob |
|
28
|
|
|
|
|
29
|
|
|
import savu.test.test_utils as tu |
|
30
|
|
|
from savu.plugins.utils import register_plugin |
|
31
|
|
|
from savu.plugins.loaders.full_field_loaders.multi_nxtomo_loader import \ |
|
32
|
|
|
MultiNxtomoLoader |
|
33
|
|
|
|
|
34
|
|
|
|
|
35
|
|
|
@register_plugin |
|
36
|
|
|
class LfovLoader(MultiNxtomoLoader): |
|
37
|
|
|
|
|
38
|
|
|
def __init__(self, name='LfovLoader'): |
|
39
|
|
|
super(LfovLoader, self).__init__(name) |
|
40
|
|
|
|
|
41
|
|
|
def _update_preview(self, preview, offset): |
|
42
|
|
|
""" |
|
43
|
|
|
Add extra sinograms to the preview if there are not enough to stitch |
|
44
|
|
|
at least one frame after taking into account the offset between images. |
|
45
|
|
|
|
|
46
|
|
|
Parameters |
|
47
|
|
|
---------- |
|
48
|
|
|
preview : list |
|
49
|
|
|
A Savu preview data list. |
|
50
|
|
|
|
|
51
|
|
|
Returns |
|
52
|
|
|
------- |
|
53
|
|
|
None. |
|
54
|
|
|
|
|
55
|
|
|
""" |
|
56
|
|
|
if not offset or not preview: |
|
57
|
|
|
return preview |
|
58
|
|
|
dObj = self.exp.index['in_data']['tomo'] |
|
59
|
|
|
|
|
60
|
|
|
# Revert the data shape to before previewing was applied |
|
61
|
|
|
dObj.set_shape(dObj.get_original_shape()) |
|
62
|
|
|
preview = dObj.get_preview().get_integer_entries(preview) |
|
63
|
|
|
sino_slice_dim = dObj.get_data_dimension_by_axis_label("detector_y") |
|
64
|
|
|
max_sino_idx = dObj.data.shape[sino_slice_dim] |
|
65
|
|
|
sl = list(map(int, preview[sino_slice_dim].split(":"))) |
|
66
|
|
|
sl_0 = sl[0] + offset |
|
67
|
|
|
sl_1 = sl[1] + offset |
|
68
|
|
|
if (max_sino_idx >= sl_0 >= 0) and (max_sino_idx >= sl_1 >= 0): |
|
69
|
|
|
sl[0] = sl_0 |
|
70
|
|
|
sl[1] = sl_1 |
|
71
|
|
|
preview[sino_slice_dim] = ":".join(map(str, sl)) |
|
72
|
|
|
self.parameters['preview'][sino_slice_dim] = preview[sino_slice_dim] |
|
73
|
|
|
return preview |
|
74
|
|
|
|
|
75
|
|
|
def _get_order_list(self): |
|
76
|
|
|
order = self.parameters['order'] |
|
77
|
|
|
if order[0] < order[-1]: |
|
78
|
|
|
order_list = np.arange(order[0], order[1] + 1) |
|
79
|
|
|
else: |
|
80
|
|
|
order_list = np.arange(order[0], order[1] - 1, -1) |
|
81
|
|
|
return order_list |
|
82
|
|
|
|
|
83
|
|
|
def _get_file_list(self, order_list): |
|
84
|
|
|
shared_name = self.parameters["file_name"] |
|
85
|
|
|
file_path = copy.copy(self.exp.meta_data.get('data_file')) |
|
86
|
|
|
self.exp.meta_data.set('data_file', file_path) |
|
87
|
|
|
|
|
88
|
|
|
if shared_name is None: |
|
89
|
|
|
file_list = self._find_files(file_path, "/*.hdf") |
|
90
|
|
|
if len(file_list) == 0: |
|
91
|
|
|
file_list = self._find_files(file_path, "/*.nxs") |
|
92
|
|
|
else: |
|
93
|
|
|
file_list = self._find_files(file_path, "/*" + shared_name + "*") |
|
94
|
|
|
|
|
95
|
|
|
if len(order_list) != len(file_list): |
|
96
|
|
|
raise ValueError( |
|
97
|
|
|
"Number of files found in the folder is not the same as the" |
|
98
|
|
|
" requested number") |
|
99
|
|
|
return file_list |
|
100
|
|
|
|
|
101
|
|
|
def _find_files(self, base, name): |
|
102
|
|
|
return sorted(glob.glob(base + name)) if base else [] |
|
103
|
|
|
|
|
104
|
|
|
def _get_data_objects(self, nxtomo): |
|
105
|
|
|
order_list = self._get_order_list() |
|
106
|
|
|
file_list = self._get_file_list(order_list) |
|
107
|
|
|
dark_folder, dark_key, dark_scale = self.parameters['dark'] |
|
108
|
|
|
flat_folder, flat_key, flat_scale = self.parameters['flat'] |
|
109
|
|
|
dark_folder = self.get_conf_path(dark_folder) |
|
110
|
|
|
flat_folder = self.get_conf_path(flat_folder) |
|
111
|
|
|
dark_list = self._find_files(dark_folder, "/*dark*") |
|
112
|
|
|
flat_list = self._find_files(flat_folder, "/*flat*") |
|
113
|
|
|
offset = self.parameters['row_offset'] |
|
114
|
|
|
data_obj_list = [] |
|
115
|
|
|
for i in order_list: |
|
116
|
|
|
self.exp.meta_data.set('data_file', file_list[i]) |
|
117
|
|
|
# update darks and flats |
|
118
|
|
|
if dark_folder is not None: |
|
119
|
|
|
nxtomo.parameters['dark'] = [ |
|
120
|
|
|
dark_list[i], dark_key, dark_scale] |
|
121
|
|
|
if flat_folder is not None: |
|
122
|
|
|
nxtomo.parameters['flat'] = [ |
|
123
|
|
|
flat_list[i], flat_key, flat_scale] |
|
124
|
|
|
|
|
125
|
|
|
nxtomo.setup() |
|
126
|
|
|
# update preview |
|
127
|
|
|
if offset[i] != 0: |
|
128
|
|
|
nxtomo.parameters['preview'] = \ |
|
129
|
|
|
self._update_preview(nxtomo.parameters['preview'], offset[i]) |
|
130
|
|
|
data_obj_list.append(self.exp.index['in_data']['tomo']) |
|
131
|
|
|
self.exp.index['in_data'] = {} |
|
132
|
|
|
return data_obj_list |
|
133
|
|
|
|
|
134
|
|
|
def get_conf_path(self, path): |
|
135
|
|
|
# For Savu tests |
|
136
|
|
|
if path.split(os.sep)[0] == 'Savu': |
|
137
|
|
|
path = tu.get_test_data_path(path.split('/test_data/data/')[1]) |
|
138
|
|
|
return path |
|
139
|
|
|
|
DiamondLightSource /
Savu
