wsi-rs 0.5.2

wsi-rs whole-slide image reader
Documentation
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
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
use super::*;
use std::io::{Read, Seek, SeekFrom};

const SEGMENT_HEADER_BYTES: u64 = 32;
const FILE_HEADER_DATA_BYTES: u64 = 512;
const DIRECTORY_FIXED_BYTES: u64 = 128;
const METADATA_FIXED_BYTES: u64 = 256;
const ATTACHMENT_DIRECTORY_FIXED_BYTES: u64 = 256;
const ATTACHMENT_DIRECTORY_ENTRY_BYTES: u64 = 128;
const MIN_DIRECTORY_ENTRY_BYTES: u64 = 32;
const SUBBLOCK_FIXED_BYTES: u64 = 256;
const SUBBLOCK_METADATA_BYTES: u64 = 16 * 1024 * 1024;
const SUBBLOCK_ATTACHMENT_BYTES: u64 = 16 * 1024 * 1024;
const DIRECTORY_MAGIC: &[u8; 16] = b"ZISRAWDIRECTORY\0";
const METADATA_MAGIC: &[u8; 16] = b"ZISRAWMETADATA\0\0";
const ATTACHMENT_DIRECTORY_MAGIC: &[u8; 16] = b"ZISRAWATTDIR\0\0\0\0";
const SUBBLOCK_MAGIC: &[u8; 16] = b"ZISRAWSUBBLOCK\0\0";

pub(super) fn preflight_czi_file(path: &Path) -> Result<(), WsiError> {
    let mut file = File::open(path).map_err(|source| WsiError::IoWithPath {
        source: Arc::new(source),
        path: path.to_path_buf(),
    })?;
    let file_len = file.metadata()?.len();
    preflight_czi_reader(&mut file, file_len).map_err(|error| WsiError::InvalidSlide {
        path: path.to_path_buf(),
        message: error.to_string(),
    })
}

pub(super) fn preflight_czi_subblock(path: &Path, offset: u64) -> Result<(), WsiError> {
    let mut file = File::open(path).map_err(|source| WsiError::IoWithPath {
        source: Arc::new(source),
        path: path.to_path_buf(),
    })?;
    let file_len = file.metadata()?.len();
    preflight_czi_subblock_reader(&mut file, file_len, offset).map_err(|error| {
        WsiError::InvalidSlide {
            path: path.to_path_buf(),
            message: error.to_string(),
        }
    })
}

fn preflight_czi_reader(reader: &mut (impl Read + Seek), file_len: u64) -> Result<(), WsiError> {
    let file_header_size = read_segment_header(
        reader,
        file_len,
        0,
        FILE_MAGIC,
        FILE_HEADER_DATA_BYTES,
        "file header",
    )?;
    if file_header_size < FILE_HEADER_DATA_BYTES {
        return Err(preflight_error("CZI file header is too short"));
    }
    let file_header = read_exact_at(
        reader,
        file_len,
        SEGMENT_HEADER_BYTES,
        FILE_HEADER_DATA_BYTES as usize,
        "file header",
    )?;
    let directory_offset = read_u64(&file_header, 52, "subblock directory offset")?;
    let metadata_offset = read_u64(&file_header, 60, "metadata offset")?;
    let attachment_directory_offset = read_u64(&file_header, 72, "attachment directory offset")?;

    preflight_directory(reader, file_len, directory_offset)?;
    if metadata_offset != 0 {
        preflight_metadata(reader, file_len, metadata_offset)?;
    }
    if attachment_directory_offset != 0 {
        preflight_attachment_directory(reader, file_len, attachment_directory_offset)?;
    }
    Ok(())
}

fn preflight_directory(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
) -> Result<(), WsiError> {
    let effective_size = read_segment_header(
        reader,
        file_len,
        offset,
        DIRECTORY_MAGIC,
        DIRECTORY_FIXED_BYTES,
        "subblock directory",
    )?;
    let payload_bytes = effective_size - DIRECTORY_FIXED_BYTES;
    if payload_bytes > MAX_CZI_DIRECTORY_BYTES {
        return Err(preflight_error(format!(
            "CZI subblock directory declares {payload_bytes} bytes, exceeding the {MAX_CZI_DIRECTORY_BYTES}-byte safety limit"
        )));
    }
    let fixed = read_exact_at(
        reader,
        file_len,
        checked_add(offset, SEGMENT_HEADER_BYTES, "directory header")?,
        DIRECTORY_FIXED_BYTES as usize,
        "subblock directory header",
    )?;
    let entry_count = read_i32(&fixed, 0, "subblock count")?;
    if entry_count < 0 {
        return Err(preflight_error("CZI subblock count is negative"));
    }
    let entry_count = entry_count as usize;
    if entry_count > MAX_CZI_SUBBLOCKS {
        return Err(preflight_error(format!(
            "CZI subblock count {entry_count} exceeds the {MAX_CZI_SUBBLOCKS}-entry safety limit"
        )));
    }
    let minimum_payload = u64::try_from(entry_count)
        .ok()
        .and_then(|count| count.checked_mul(MIN_DIRECTORY_ENTRY_BYTES))
        .ok_or_else(|| preflight_error("CZI subblock directory size overflows"))?;
    if minimum_payload > payload_bytes {
        return Err(preflight_error(format!(
            "CZI subblock directory is too short for {entry_count} entries"
        )));
    }
    Ok(())
}

fn preflight_metadata(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
) -> Result<(), WsiError> {
    let effective_size = read_segment_header(
        reader,
        file_len,
        offset,
        METADATA_MAGIC,
        METADATA_FIXED_BYTES,
        "metadata",
    )?;
    let fixed = read_exact_at(
        reader,
        file_len,
        checked_add(offset, SEGMENT_HEADER_BYTES, "metadata header")?,
        METADATA_FIXED_BYTES as usize,
        "metadata header",
    )?;
    let xml_bytes = u64::from(read_u32(&fixed, 0, "metadata length")?);
    if xml_bytes > MAX_CZI_METADATA_BYTES {
        return Err(preflight_error(format!(
            "CZI metadata declares {xml_bytes} bytes, exceeding the {MAX_CZI_METADATA_BYTES}-byte safety limit"
        )));
    }
    if xml_bytes > effective_size - METADATA_FIXED_BYTES {
        return Err(preflight_error(
            "CZI metadata payload exceeds its declared segment size",
        ));
    }
    Ok(())
}

fn preflight_attachment_directory(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
) -> Result<(), WsiError> {
    let effective_size = read_segment_header(
        reader,
        file_len,
        offset,
        ATTACHMENT_DIRECTORY_MAGIC,
        ATTACHMENT_DIRECTORY_FIXED_BYTES,
        "attachment directory",
    )?;
    let fixed = read_exact_at(
        reader,
        file_len,
        checked_add(offset, SEGMENT_HEADER_BYTES, "attachment directory header")?,
        ATTACHMENT_DIRECTORY_FIXED_BYTES as usize,
        "attachment directory header",
    )?;
    let entry_count = read_i32(&fixed, 0, "attachment count")?;
    if entry_count <= 0 {
        return Ok(());
    }
    let entry_count = entry_count as usize;
    if entry_count > MAX_CZI_ATTACHMENTS {
        return Err(preflight_error(format!(
            "CZI attachment count {entry_count} exceeds the {MAX_CZI_ATTACHMENTS}-entry safety limit"
        )));
    }
    let entries_bytes = u64::try_from(entry_count)
        .ok()
        .and_then(|count| count.checked_mul(ATTACHMENT_DIRECTORY_ENTRY_BYTES))
        .ok_or_else(|| preflight_error("CZI attachment directory size overflows"))?;
    if entries_bytes > effective_size - ATTACHMENT_DIRECTORY_FIXED_BYTES {
        return Err(preflight_error(
            "CZI attachment directory payload exceeds its declared segment size",
        ));
    }
    Ok(())
}

fn preflight_czi_subblock_reader(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
) -> Result<(), WsiError> {
    let effective_size = read_segment_header(
        reader,
        file_len,
        offset,
        SUBBLOCK_MAGIC,
        SUBBLOCK_FIXED_BYTES,
        "subblock",
    )?;
    let fixed = read_exact_at(
        reader,
        file_len,
        checked_add(offset, SEGMENT_HEADER_BYTES, "subblock header")?,
        SUBBLOCK_FIXED_BYTES as usize,
        "subblock header",
    )?;
    let metadata_bytes = u64::from(read_u32(&fixed, 0, "subblock metadata length")?);
    let attachment_bytes = u64::from(read_u32(&fixed, 4, "subblock attachment length")?);
    let data_bytes = read_u64(&fixed, 8, "subblock data length")?;
    if metadata_bytes > SUBBLOCK_METADATA_BYTES {
        return Err(preflight_error(format!(
            "CZI subblock metadata declares {metadata_bytes} bytes, exceeding the {SUBBLOCK_METADATA_BYTES}-byte safety limit"
        )));
    }
    if attachment_bytes > SUBBLOCK_ATTACHMENT_BYTES {
        return Err(preflight_error(format!(
            "CZI subblock attachment declares {attachment_bytes} bytes, exceeding the {SUBBLOCK_ATTACHMENT_BYTES}-byte safety limit"
        )));
    }
    if data_bytes > crate::core::limits::MAX_COMPRESSED_INPUT_BYTES {
        return Err(preflight_error(format!(
            "CZI subblock data declares {data_bytes} bytes, exceeding the {}-byte safety limit",
            crate::core::limits::MAX_COMPRESSED_INPUT_BYTES
        )));
    }
    if fixed.get(16..18) != Some(b"DV".as_slice()) {
        return Err(preflight_error("unsupported CZI subblock schema"));
    }
    let dimension_count = u64::from(read_u32(&fixed, 44, "subblock dimension count")?);
    if dimension_count > 1_024 {
        return Err(preflight_error(format!(
            "CZI subblock dimension count {dimension_count} exceeds the 1024-dimension safety limit"
        )));
    }
    let dynamic_header_bytes = 16_u64
        .checked_add(32)
        .and_then(|value| value.checked_add(dimension_count.checked_mul(20)?))
        .ok_or_else(|| preflight_error("CZI subblock header size overflows"))?;
    let actual_bytes = dynamic_header_bytes
        .max(SUBBLOCK_FIXED_BYTES)
        .checked_add(metadata_bytes)
        .and_then(|value| value.checked_add(data_bytes))
        .and_then(|value| value.checked_add(attachment_bytes))
        .ok_or_else(|| preflight_error("CZI subblock total size overflows"))?;
    if actual_bytes > effective_size {
        return Err(preflight_error(format!(
            "CZI subblock requires {actual_bytes} bytes, exceeding its {effective_size}-byte segment"
        )));
    }
    Ok(())
}

fn read_segment_header(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
    expected_magic: &[u8; 16],
    minimum_size: u64,
    label: &str,
) -> Result<u64, WsiError> {
    let header = read_exact_at(
        reader,
        file_len,
        offset,
        SEGMENT_HEADER_BYTES as usize,
        label,
    )?;
    if &header[..16] != expected_magic {
        return Err(preflight_error(format!("invalid CZI {label} magic")));
    }
    let allocated_size = read_u64(&header, 16, "allocated segment size")?;
    let used_size = read_u64(&header, 24, "used segment size")?;
    let effective_size = if used_size == 0 {
        allocated_size
    } else {
        used_size
    };
    if effective_size < minimum_size {
        return Err(preflight_error(format!(
            "CZI {label} declares {effective_size} bytes, smaller than the {minimum_size}-byte header"
        )));
    }
    let end = offset
        .checked_add(SEGMENT_HEADER_BYTES)
        .and_then(|value| value.checked_add(effective_size))
        .ok_or_else(|| preflight_error(format!("CZI {label} range overflows")))?;
    if end > file_len {
        return Err(preflight_error(format!(
            "CZI {label} range ends at {end}, beyond file length {file_len}"
        )));
    }
    Ok(effective_size)
}

fn read_exact_at(
    reader: &mut (impl Read + Seek),
    file_len: u64,
    offset: u64,
    len: usize,
    label: &str,
) -> Result<Vec<u8>, WsiError> {
    let end = offset
        .checked_add(u64::try_from(len).unwrap_or(u64::MAX))
        .ok_or_else(|| preflight_error(format!("CZI {label} range overflows")))?;
    if end > file_len {
        return Err(preflight_error(format!(
            "CZI {label} is truncated at file offset {offset}"
        )));
    }
    reader.seek(SeekFrom::Start(offset))?;
    let mut bytes = vec![0; len];
    reader.read_exact(&mut bytes)?;
    Ok(bytes)
}

fn checked_add(left: u64, right: u64, label: &str) -> Result<u64, WsiError> {
    left.checked_add(right)
        .ok_or_else(|| preflight_error(format!("CZI {label} offset overflows")))
}

fn read_u32(bytes: &[u8], offset: usize, label: &str) -> Result<u32, WsiError> {
    let value = bytes
        .get(offset..offset + 4)
        .ok_or_else(|| preflight_error(format!("CZI {label} is truncated")))?;
    Ok(u32::from_le_bytes(value.try_into().map_err(|_| {
        preflight_error(format!("CZI {label} is malformed"))
    })?))
}

fn read_i32(bytes: &[u8], offset: usize, label: &str) -> Result<i32, WsiError> {
    read_u32(bytes, offset, label).map(|value| i32::from_le_bytes(value.to_le_bytes()))
}

fn read_u64(bytes: &[u8], offset: usize, label: &str) -> Result<u64, WsiError> {
    let value = bytes
        .get(offset..offset + 8)
        .ok_or_else(|| preflight_error(format!("CZI {label} is truncated")))?;
    Ok(u64::from_le_bytes(value.try_into().map_err(|_| {
        preflight_error(format!("CZI {label} is malformed"))
    })?))
}

fn preflight_error(message: impl Into<String>) -> WsiError {
    WsiError::DisplayConversion(message.into())
}

#[cfg(test)]
mod tests {
    use super::*;
    use std::io::Cursor;

    const FILE_HEADER_BYTES: usize = 32 + 512;
    const DIRECTORY_OFFSET: usize = FILE_HEADER_BYTES;

    fn write_u32(bytes: &mut [u8], offset: usize, value: u32) {
        bytes[offset..offset + 4].copy_from_slice(&value.to_le_bytes());
    }

    fn write_u64(bytes: &mut [u8], offset: usize, value: u64) {
        bytes[offset..offset + 8].copy_from_slice(&value.to_le_bytes());
    }

    fn base_czi(metadata_offset: u64) -> Vec<u8> {
        let mut bytes = vec![0; DIRECTORY_OFFSET + 32 + 128];
        bytes[..16].copy_from_slice(b"ZISRAWFILE\0\0\0\0\0\0");
        write_u64(&mut bytes, 16, 512);
        write_u64(&mut bytes, 24, 512);
        write_u64(&mut bytes, 32 + 52, DIRECTORY_OFFSET as u64);
        write_u64(&mut bytes, 32 + 60, metadata_offset);
        bytes[DIRECTORY_OFFSET..DIRECTORY_OFFSET + 16].copy_from_slice(b"ZISRAWDIRECTORY\0");
        write_u64(&mut bytes, DIRECTORY_OFFSET + 16, 128);
        write_u64(&mut bytes, DIRECTORY_OFFSET + 24, 128);
        bytes
    }

    #[test]
    fn czi_preflight_rejects_excessive_directory_entry_count() {
        let mut bytes = base_czi(0);
        write_u32(&mut bytes, DIRECTORY_OFFSET + 32, (1_000_000_u32) + 1);
        let mut cursor = Cursor::new(bytes.clone());
        let error = preflight_czi_reader(&mut cursor, bytes.len() as u64)
            .expect_err("excessive CZI directory must be rejected");
        assert!(error.to_string().contains("subblock count"), "{error}");
    }

    #[test]
    fn czi_preflight_rejects_oversized_metadata_declaration() {
        let metadata_offset = (DIRECTORY_OFFSET + 32 + 128) as u64;
        let mut bytes = base_czi(metadata_offset);
        bytes.resize(metadata_offset as usize + 32 + 256, 0);
        let offset = metadata_offset as usize;
        bytes[offset..offset + 16].copy_from_slice(b"ZISRAWMETADATA\0\0");
        write_u64(&mut bytes, offset + 16, 256);
        write_u64(&mut bytes, offset + 24, 256);
        write_u32(&mut bytes, offset + 32, (32 * 1024 * 1024) + 1);

        let mut cursor = Cursor::new(bytes.clone());
        let error = preflight_czi_reader(&mut cursor, bytes.len() as u64)
            .expect_err("oversized CZI metadata must be rejected");
        assert!(error.to_string().contains("metadata"), "{error}");
    }

    #[test]
    fn czi_subblock_preflight_rejects_oversized_payload_declaration() {
        let mut bytes = vec![0; 32 + 256];
        bytes[..16].copy_from_slice(b"ZISRAWSUBBLOCK\0\0");
        write_u64(&mut bytes, 16, 256);
        write_u64(&mut bytes, 24, 256);
        write_u64(
            &mut bytes,
            32 + 8,
            crate::core::limits::MAX_COMPRESSED_INPUT_BYTES + 1,
        );
        bytes[32 + 16..32 + 18].copy_from_slice(b"DV");

        let mut cursor = Cursor::new(bytes.clone());
        let error = preflight_czi_subblock_reader(&mut cursor, bytes.len() as u64, 0)
            .expect_err("oversized CZI subblock must be rejected");
        assert!(error.to_string().contains("subblock data"), "{error}");
    }
}