1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
use crate::{
bindings, errors::OpenSlideError, Address, OpenSlide, Properties, Region, Result, Size,
};
use std::path::Path;
use crate::errors::map_try_error;
#[cfg(feature = "image")]
use image::RgbaImage;
impl Drop for OpenSlide {
fn drop(&mut self) {
bindings::close(*self.osr)
}
}
impl OpenSlide {
pub fn new(path: &Path) -> Result<OpenSlide> {
if !path.exists() {
return Err(OpenSlideError::MissingFile(path.display().to_string()));
}
let filename = path.display().to_string();
let osr = bindings::open(&filename)?;
let property_names = bindings::get_property_names(osr)?;
let property_iter = property_names.into_iter().filter_map(|name| {
if let Ok(value) = bindings::get_property_value(osr, &name) {
Some((name, value))
} else {
None
}
});
let properties = Properties::new(property_iter);
Ok(OpenSlide {
osr: bindings::OpenSlideWrapper(osr),
properties,
})
}
pub fn detect_vendor(path: &Path) -> Result<String> {
if !path.exists() {
return Err(OpenSlideError::MissingFile(path.display().to_string()));
}
let filename = path.display().to_string();
bindings::detect_vendor(&filename)
}
pub fn get_level_count(&self) -> Result<u32> {
let level_count = bindings::get_level_count(*self.osr)?;
let level_count: u32 = level_count.try_into().map_err(map_try_error)?;
Ok(level_count)
}
pub fn get_level0_dimensions(&self) -> Result<Size> {
let (width, height) = bindings::get_level0_dimensions(*self.osr)?;
Ok(Size {
w: width.try_into().map_err(map_try_error)?,
h: height.try_into().map_err(map_try_error)?,
})
}
pub fn get_level_dimensions(&self, level: u32) -> Result<Size> {
let level: i32 = level.try_into().map_err(map_try_error)?;
let (width, height) = bindings::get_level_dimensions(*self.osr, level)?;
Ok(Size {
w: width.try_into().map_err(map_try_error)?,
h: height.try_into().map_err(map_try_error)?,
})
}
pub fn get_all_level_dimensions(&self) -> Result<Vec<Size>> {
let nb_levels = self.get_level_count()?;
let mut res = Vec::with_capacity(nb_levels as usize);
for level in 0..nb_levels {
let level: i32 = level.try_into().map_err(map_try_error)?;
let (width, height) = bindings::get_level_dimensions(*self.osr, level)?;
res.push(Size {
w: width.try_into().map_err(map_try_error)?,
h: height.try_into().map_err(map_try_error)?,
});
}
Ok(res)
}
pub fn get_level_downsample(&self, level: u32) -> Result<f64> {
let level: i32 = level.try_into().map_err(map_try_error)?;
bindings::get_level_downsample(*self.osr, level)
}
pub fn get_all_level_downsample(&self) -> Result<Vec<f64>> {
let nb_levels = self.get_level_count()?;
let mut res = Vec::with_capacity(nb_levels as usize);
for level in 0..nb_levels {
let downsample = bindings::get_level_downsample(*self.osr, level as i32)?;
res.push(downsample);
}
Ok(res)
}
pub fn get_best_level_for_downsample(&self, downsample: f64) -> Result<u32> {
Ok(bindings::get_best_level_for_downsample(*self.osr, downsample)? as u32)
}
pub fn get_property_names(&self) -> Vec<String> {
bindings::get_property_names(*self.osr).unwrap_or_else(|_| vec![])
}
pub fn get_property_value(&self, name: &str) -> Result<String> {
bindings::get_property_value(*self.osr, name)
}
pub fn read_region(&self, region: &Region) -> Result<Vec<u8>> {
bindings::read_region(
*self.osr,
region.address.x as i64,
region.address.y as i64,
region.level.try_into().map_err(map_try_error)?,
region.size.w as i64,
region.size.h as i64,
)
}
pub fn get_associated_image_names(&self) -> Result<Vec<String>> {
bindings::get_associated_image_names(*self.osr)
}
pub fn read_associated_buffer(&self, name: &str) -> Result<(Size, Vec<u8>)> {
let ((width, height), buffer) = bindings::read_associated_image(*self.osr, name)?;
let size = Size {
w: width.try_into().map_err(map_try_error)?,
h: height.try_into().map_err(map_try_error)?,
};
Ok((size, buffer))
}
pub fn get_associated_image_dimensions(&self, name: &str) -> Result<Size> {
let (width, height) = bindings::get_associated_image_dimensions(*self.osr, name)?;
Ok(Size {
w: width.try_into().map_err(map_try_error)?,
h: height.try_into().map_err(map_try_error)?,
})
}
#[cfg(feature = "image")]
pub fn read_associated_image(&self, name: &str) -> Result<RgbaImage> {
let (size, buffer) = self.read_associated_buffer(name)?;
let mut image = RgbaImage::from_vec(size.w, size.h, buffer).unwrap(); _bgra_to_rgba_inplace(&mut image);
Ok(image)
}
#[cfg(feature = "image")]
pub fn read_image(&self, region: &Region) -> Result<RgbaImage> {
let buffer = self.read_region(region)?;
let size = region.size;
let mut image = RgbaImage::from_vec(size.w, size.h, buffer).unwrap(); _bgra_to_rgba_inplace(&mut image);
Ok(image)
}
#[cfg(feature = "image")]
pub fn thumbnail(&self, size: &Size) -> Result<RgbaImage> {
let dimension_level0 = self.get_level0_dimensions()?;
let downsample = (
dimension_level0.w as f64 / size.w as f64,
dimension_level0.h as f64 / size.h as f64,
);
let downsample = f64::max(downsample.0, downsample.1);
let level = self.get_best_level_for_downsample(downsample)?;
let region = Region {
size: self.get_level_dimensions(level)?,
level,
address: Address { x: 0, y: 0 },
};
let image = self.read_image(®ion)?;
let image = image::imageops::thumbnail(&image, size.w, size.h);
Ok(image)
}
}
#[cfg(feature = "image")]
fn _bgra_to_rgba_inplace(image: &mut RgbaImage) {
for pixel in image.pixels_mut() {
let [b, g, r, a] = pixel.0;
pixel.0 = [r, g, b, a];
}
}