DobromirN commited on
Commit
154b2e4
·
verified ·
1 Parent(s): 784f256

Update README.md

Browse files
Files changed (1) hide show
  1. README.md +147 -0
README.md CHANGED
@@ -1,3 +1,150 @@
1
  ---
 
 
2
  license: unknown
 
 
 
 
 
3
  ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
  ---
2
+ language:
3
+ - en
4
  license: unknown
5
+ task_categories:
6
+ - image-classification
7
+ pretty_name: DiffraNet
8
+ size_categories:
9
+ - 10K<n<100K
10
  ---
11
+
12
+ # DiffraNet
13
+
14
+ ## Dataset description
15
+
16
+ This repository contains the **DiffraNet** diffraction image dataset introduced by Souza *et al.* in the paper **"DeepFreak: Learning Crystallography Diffraction Patterns with Automated Machine Learning"**. The original dataset consists of **512×512 grayscale diffraction images**, including both synthetic and real experimental data. The synthetic images were generated using the **nanoBragg** simulator, while the real images were collected from serial crystallography experiments. :contentReference[oaicite:0]{index=0}
17
+
18
+ This repository mirrors the original dataset and additionally includes a modified version of the raw real dataset (`real_raw_mod`) for my own purposes.
19
+
20
+ ## Credit
21
+
22
+ The original DiffraNet dataset was created by:
23
+
24
+ - Artur Souza
25
+ - Leonardo B. Oliveira
26
+ - Sabine Hollatz
27
+ - Matt Feldman
28
+ - Kunle Olukotun
29
+ - James M. Holton
30
+ - Aina E. Cohen
31
+ - Luigi Nardi
32
+
33
+ ### Paper
34
+
35
+ > Souza, A. *et al.* **DeepFreak: Learning Crystallography Diffraction Patterns with Automated Machine Learning** (2019)
36
+
37
+ https://arxiv.org/abs/1904.11834
38
+
39
+ ### Original project
40
+
41
+ https://arturluis.github.io/diffranet/
42
+
43
+ All credit for the original dataset belongs to the authors. This repository is intended only as a mirror of the original dataset and includes one additional modified split (`real_raw_mod`) described below.
44
+
45
+ ---
46
+
47
+ # Dataset structure
48
+
49
+ The repository contains four top-level directories:
50
+
51
+ ```text
52
+ synthetic/
53
+ real_raw/
54
+ real_preprocessed/
55
+ real_raw_mod/
56
+ ```
57
+
58
+ Each of the directories represents a different dataset or a different dataset version.
59
+
60
+ The original **DiffraNet** dataset consisted of ```synthetic```, ```real_raw```, ```real_preprocessed```.
61
+
62
+ ```real_raw_mod``` is a modified version of ```real_raw``` for use in transfer learning, and was not a part of the original dataset.
63
+
64
+ The folder hierarchy defines both the **dataset split** and the **class labels**.
65
+
66
+ ## synthetic/
67
+
68
+ Synthetic diffraction images generated with the **nanoBragg** simulator.
69
+
70
+ Dataset splits:
71
+
72
+ - `training`
73
+ - `validation`
74
+ - `test`
75
+
76
+ Classes:
77
+
78
+ 1. blank
79
+ 2. no crystal
80
+ 3. weak diffraction
81
+ 4. good diffraction
82
+ 5. strong diffraction
83
+
84
+ The original dataset contains approximately **25,000 synthetic images**.
85
+
86
+ ## real_raw/
87
+
88
+ Original real diffraction images provided by the DiffraNet authors.
89
+
90
+ Characteristics:
91
+
92
+ - cropped to **512×512**
93
+ - contain the experimental beamstop shadow
94
+
95
+ Dataset splits:
96
+
97
+ - `validation`
98
+ - `test`
99
+
100
+ Classes:
101
+
102
+ 1. no diffraction
103
+ 2. diffraction
104
+
105
+ ## real_preprocessed/
106
+
107
+ Original preprocessed version of the real dataset.
108
+
109
+ The images are identical to `real_raw` except that pixel intensities have been rescaled so that the mean pixel value matches that of the synthetic dataset.
110
+
111
+ The dataset organization is identical to `real_raw`.
112
+
113
+ ## real_raw_mod/
114
+
115
+ Modified version of `real_raw` prepared for supervised learning.
116
+
117
+ The original `validation` split has been subdivided into
118
+
119
+ - `training`
120
+ - `validation`
121
+
122
+ while the original `test` split has been left unchanged.
123
+
124
+
125
+ ---
126
+
127
+ # Dataset statistics
128
+
129
+ | Dataset | Images | Classes |
130
+ |---------|-------:|--------:|
131
+ | Synthetic | ~25,000 | 5 |
132
+ | Real (raw) | 457 | 2 |
133
+ | Real (preprocessed) | 457 | 2 |
134
+
135
+ All images are **512×512 grayscale**.
136
+
137
+ ---
138
+
139
+ # Citation
140
+
141
+ If you use this dataset, please cite the original paper:
142
+
143
+ ```bibtex
144
+ @article{souza2019deepfreak,
145
+ title={DeepFreak: Learning Crystallography Diffraction Patterns with Automated Machine Learning},
146
+ author={Souza, Artur and Oliveira, Leonardo B. and Hollatz, Sabine and Feldman, Matt and Olukotun, Kunle and Holton, James M. and Cohen, Aina E. and Nardi, Luigi},
147
+ journal={arXiv preprint arXiv:1904.11834},
148
+ year={2019}
149
+ }
150
+ ```