alex-feeel commited on
Commit
8a3d8ea
·
verified ·
1 Parent(s): 0247e20

Re-upload current cxr_auditor package with salvage parsing (robustness fix)

Browse files
cxr_auditor/inference.py CHANGED
@@ -18,9 +18,18 @@ the grounding turn). That same ``generate_fn`` shape is exactly what
18
  its documented injected-callable contract rather than re-implemented here, and the
19
  whole orchestration is testable with a fake ``generate_fn`` and no model.
20
 
21
- A retry-on-invalid-JSON loop (``run_with_retry``) wraps each generation so a
22
- single malformed completion is re-attempted (a fresh generation) before failing;
23
- the final ``SchemaParseError`` carries the last raw text for inspection.
 
 
 
 
 
 
 
 
 
24
 
25
  The heavy stack (torch, transformers) is imported lazily via ``importlib`` inside
26
  ``load_model`` and ``_generate_text`` so importing this module on a pure-logic
@@ -41,6 +50,8 @@ safe to call from a GPU worker.
41
  from __future__ import annotations
42
 
43
  import importlib
 
 
44
  from collections.abc import Callable
45
  from dataclasses import dataclass
46
  from typing import TYPE_CHECKING, Any
@@ -75,6 +86,99 @@ DEFAULT_MAX_NEW_TOKENS: int = 512
75
  # this many additional re-generations.
76
  DEFAULT_MAX_RETRIES: int = 2
77
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
78
 
79
  @dataclass(frozen=True, slots=True)
80
  class AuditOutcome:
@@ -89,10 +193,14 @@ class AuditOutcome:
89
  result: The canonical ``AuditResult`` (image findings, draft findings,
90
  label-only audit, disclaimer, box format).
91
  comparison: The per-item comparator detail (boxes, urgency, draft spans).
 
 
 
92
  """
93
 
94
  result: AuditResult
95
  comparison: ComparisonReport
 
96
 
97
 
98
  def grounded_dicts_to_image_findings(grounded: list[dict[str, Any]]) -> list[ImageFinding]:
@@ -186,29 +294,34 @@ def _coerce_confidence(raw: Any) -> float | None:
186
 
187
 
188
  def run_with_retry(
189
- generate_fn: GenerateFn,
190
  prompt: str,
191
  parse_fn: Callable[[str], list[Any]],
192
  max_retries: int = DEFAULT_MAX_RETRIES,
 
 
193
  ) -> list[Any]:
194
- """Generate then parse, retrying when the parse fails on invalid JSON.
195
 
196
  The model occasionally emits prose, a truncated array, or otherwise
197
- unparseable text. This re-invokes ``generate_fn`` with the same prompt up to
198
- ``max_retries`` additional times, returning the first successful parse. If
199
- every attempt fails, the last ``SchemaParseError`` is raised so its
200
- ``raw_text`` (the final raw completion) is available to the caller.
201
-
202
- The retry is a plain re-generation: a fresh model call is the cheapest
203
- effective repair for transient malformed output. Callers wanting a stricter
204
- repair can wrap ``generate_fn`` to append a corrective instruction on retry.
205
 
206
  Args:
207
- generate_fn: Callable mapping the prompt to the model's raw completion.
208
- prompt: The rendered prompt to send on every attempt.
 
 
209
  parse_fn: A tolerant parser turning raw text into a list (raises
210
  ``SchemaParseError`` on unparseable text).
211
  max_retries: Number of additional attempts after the first. Must be >= 0.
 
212
 
213
  Returns:
214
  The first successfully parsed list.
@@ -221,42 +334,75 @@ def run_with_retry(
221
  raise ValueError(f"max_retries must be non-negative, got {max_retries}")
222
 
223
  last_error: SchemaParseError | None = None
224
- for _attempt in range(max_retries + 1):
225
- raw_text = generate_fn(prompt)
 
 
 
226
  try:
227
  return parse_fn(raw_text)
228
  except SchemaParseError as exc:
229
  last_error = exc
 
230
  assert last_error is not None # loop runs at least once, so an error was set
231
  raise last_error
232
 
233
 
234
- def make_generate_fn(model: Any, processor: Any, image: Image.Image) -> GenerateFn:
 
 
 
 
 
235
  """Build an image-bound ``generate_fn`` over a loaded model and processor.
236
 
237
- The returned closure captures the model, processor, and image, exposing the
238
- text-in/text-out ``GenerateFn`` shape that the grounding path, the retry loop,
239
- and ``cxr_auditor.parser.parse_draft`` all consume. Binding the image into the
240
- closure lets the draft parser - which only knows about a text-prompt
241
- ``generate_fn`` - reuse the same single-turn multimodal model the grounding
242
- step uses, satisfying the Gate C decision to parse the draft with the SAME
243
- model.
244
 
245
  Args:
246
  model: A loaded vision-language model exposing ``generate``.
247
  processor: The matching transformers processor.
248
  image: The chest X-ray bound to every generation through this closure.
 
 
249
 
250
  Returns:
251
  A ``GenerateFn`` mapping a rendered prompt to the model's raw completion.
252
  """
253
 
254
  def _generate(prompt: str) -> str:
255
- return _generate_text(model, processor, prompt, image)
256
 
257
  return _generate
258
 
259
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
260
  def generate_findings(
261
  image: Image.Image,
262
  *,
@@ -266,8 +412,8 @@ def generate_findings(
266
  ) -> list[ImageFinding]:
267
  """Ground an image into validated ``ImageFinding`` objects.
268
 
269
- Builds the pinned image-grounding prompt, generates through the invalid-JSON
270
- retry loop, and assembles validated findings. This is the image-side entry
271
  point the app uses when it wants only the grounded findings (for example to
272
  draw boxes before a draft is supplied).
273
 
@@ -275,7 +421,7 @@ def generate_findings(
275
  image: The chest X-ray as a PIL image.
276
  model: A loaded vision-language model (keyword-only).
277
  processor: The matching transformers processor (keyword-only).
278
- max_retries: Retry budget for the invalid-JSON loop (keyword-only).
279
 
280
  Returns:
281
  The image-grounded findings with bounding-box evidence.
@@ -283,8 +429,13 @@ def generate_findings(
283
  Raises:
284
  SchemaParseError: If grounding output cannot be parsed after all retries.
285
  """
286
- generate_fn = make_generate_fn(model, processor, image)
287
- grounded = run_with_retry(generate_fn, build_image_grounding_prompt(), extract_finding_list, max_retries=max_retries)
 
 
 
 
 
288
  return grounded_dicts_to_image_findings(grounded)
289
 
290
 
@@ -300,10 +451,13 @@ def run_audit(
300
 
301
  Steps:
302
  1. Ground the image into validated ``ImageFinding`` objects
303
- (``generate_findings``), through the invalid-JSON retry loop.
304
  2. If a non-blank draft is supplied, parse it into the same label space via
305
  ``cxr_auditor.parser.parse_draft``, driven by an image-bound
306
- ``generate_fn`` and wrapped in the same retry loop.
 
 
 
307
  3. Run the deterministic comparator (``cxr_auditor.comparator.compare``) and
308
  bundle everything into an ``AuditOutcome``.
309
 
@@ -318,15 +472,17 @@ def run_audit(
318
  image-side findings (and urgent flags).
319
  model: A loaded vision-language model exposing ``generate`` (keyword-only).
320
  processor: The matching transformers processor (keyword-only).
321
- max_retries: Retry budget for both invalid-JSON loops (keyword-only).
 
 
322
 
323
  Returns:
324
- An ``AuditOutcome`` carrying the canonical ``AuditResult`` and the per-item
325
- ``ComparisonReport``.
326
 
327
  Raises:
328
  ValueError: If ``model`` or ``processor`` is not supplied.
329
- SchemaParseError: If the model emits text that cannot be parsed into a
330
  finding list after all retries.
331
  """
332
  if model is None or processor is None:
@@ -335,10 +491,16 @@ def run_audit(
335
  image_findings = generate_findings(image, model=model, processor=processor, max_retries=max_retries)
336
 
337
  draft_findings: list[DraftFinding] = []
 
338
  cleaned_draft = (draft_text or "").strip()
339
  if cleaned_draft:
340
- generate_fn = make_generate_fn(model, processor, image)
341
- draft_findings = _parse_draft_with_retry(cleaned_draft, generate_fn, max_retries=max_retries)
 
 
 
 
 
342
 
343
  comparison = compare(image_findings, draft_findings)
344
  result = AuditResult(
@@ -346,24 +508,46 @@ def run_audit(
346
  draft_findings=draft_findings,
347
  audit=comparison.audit,
348
  )
349
- return AuditOutcome(result=result, comparison=comparison)
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
350
 
351
 
352
  def _parse_draft_with_retry(
353
  draft_text: str,
354
- generate_fn: GenerateFn,
355
- max_retries: int = DEFAULT_MAX_RETRIES,
356
  ) -> list[DraftFinding]:
357
- """Parse a draft through ``parser.parse_draft`` with invalid-JSON retries.
358
 
359
- Wraps the draft parser's injected-callable contract in the same
360
- re-generation retry policy the grounding path uses: each attempt re-runs the
361
- full ``parse_draft`` (build prompt, generate, validate); the first successful
362
- parse wins, and the final ``SchemaParseError`` propagates if all attempts fail.
 
363
 
364
  Args:
365
  draft_text: The non-empty draft impression to parse.
366
- generate_fn: The image-bound ``generate_fn`` driving the parser.
 
367
  max_retries: Number of additional attempts after the first. Must be >= 0.
368
 
369
  Returns:
@@ -377,11 +561,16 @@ def _parse_draft_with_retry(
377
  raise ValueError(f"max_retries must be non-negative, got {max_retries}")
378
 
379
  last_error: SchemaParseError | None = None
380
- for _attempt in range(max_retries + 1):
 
 
 
 
381
  try:
382
  return parse_draft(draft_text, generate_fn)
383
  except SchemaParseError as exc:
384
  last_error = exc
 
385
  assert last_error is not None
386
  raise last_error
387
 
@@ -451,15 +640,23 @@ def load_model(model_id: str = DEFAULT_MODEL_ID) -> tuple[Any, Any]:
451
  return model, processor
452
 
453
 
454
- def _generate_text(model: Any, processor: Any, prompt: str, image: Image.Image) -> str:
 
 
 
 
 
 
455
  """Run one single-turn multimodal generation and return the decoded reply.
456
 
457
  This is the only function that touches the model at inference time, and the
458
  single seam tests patch to drive the orchestration without a real model. It
459
  builds a single-turn chat message with the image and the prompt text, applies
460
- the processor's chat template, generates greedily, and decodes only the newly
461
- generated tokens (slicing off the prompt) so the returned text is just the
462
- model's reply (a plain ``str``, never a tensor across a worker boundary).
 
 
463
 
464
  Heavy imports are local to keep module import free of the vision stack. The
465
  chat-message construction follows the transformers image-text-to-text
@@ -471,6 +668,7 @@ def _generate_text(model: Any, processor: Any, prompt: str, image: Image.Image)
471
  processor: The matching processor.
472
  prompt: The fully rendered text prompt.
473
  image: The chest X-ray as a PIL image.
 
474
 
475
  Returns:
476
  The model's decoded reply text (prompt tokens stripped).
@@ -494,19 +692,135 @@ def _generate_text(model: Any, processor: Any, prompt: str, image: Image.Image)
494
  return_tensors="pt",
495
  ).to(model.device)
496
 
 
 
 
 
 
 
 
 
 
 
 
 
 
497
  input_len = inputs["input_ids"].shape[-1]
498
  with torch.inference_mode():
499
- generated = model.generate(**inputs, max_new_tokens=DEFAULT_MAX_NEW_TOKENS, do_sample=False)
500
  new_tokens = generated[0][input_len:]
501
  return processor.decode(new_tokens, skip_special_tokens=True)
502
 
503
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
504
  __all__ = [
505
  "DEFAULT_MAX_NEW_TOKENS",
506
  "DEFAULT_MAX_RETRIES",
507
  "DEFAULT_MODEL_ID",
 
 
 
 
 
508
  "AuditOutcome",
 
 
509
  "audit",
 
510
  "generate_findings",
511
  "grounded_dicts_to_image_findings",
512
  "load_model",
 
18
  its documented injected-callable contract rather than re-implemented here, and the
19
  whole orchestration is testable with a fake ``generate_fn`` and no model.
20
 
21
+ A retry-on-invalid-JSON ladder (``run_with_retry``) wraps each generation. Each
22
+ attempt changes the conditions so a deterministic failure mode cannot simply
23
+ repeat: attempt one decodes greedily with the base prompt, attempt two appends a
24
+ corrective instruction (``RETRY_CORRECTIVE_SUFFIX``), and attempt three switches
25
+ to sampling (``RETRY_SAMPLING_SETTINGS``). Every parse failure is logged to
26
+ stdout with its full traceback and the offending raw model text, and the final
27
+ ``SchemaParseError`` carries the last raw text for inspection. Draft parsing
28
+ degrades gracefully: when the draft cannot be parsed after its retries, the audit
29
+ proceeds image-only and records ``AuditOutcome.draft_parse_note`` so the user
30
+ interface can say so prominently. ``categorize_serving_error`` maps the
31
+ exceptions an audit call can surface (including the string-transported ZeroGPU
32
+ platform errors) to honest, user-facing messages.
33
 
34
  The heavy stack (torch, transformers) is imported lazily via ``importlib`` inside
35
  ``load_model`` and ``_generate_text`` so importing this module on a pure-logic
 
50
  from __future__ import annotations
51
 
52
  import importlib
53
+ import sys
54
+ import traceback
55
  from collections.abc import Callable
56
  from dataclasses import dataclass
57
  from typing import TYPE_CHECKING, Any
 
86
  # this many additional re-generations.
87
  DEFAULT_MAX_RETRIES: int = 2
88
 
89
+ # Draft-parsing retry budget: one initial attempt plus this many retries. Smaller
90
+ # than the grounding budget because draft parsing degrades gracefully (the audit
91
+ # proceeds image-only), and the combined worst case of grounding plus draft
92
+ # attempts must stay inside the GPU duration the serving app declares.
93
+ DRAFT_MAX_RETRIES: int = 1
94
+
95
+ # User-facing note recorded on the outcome when a supplied draft could not be
96
+ # parsed after all retries and the audit proceeded image-only.
97
+ DRAFT_PARSE_FAILURE_NOTE: str = "The draft text could not be parsed; results show image findings only."
98
+
99
+ # Corrective instruction appended to the prompt on retry attempts, so a retry
100
+ # never repeats the exact conditions that already failed deterministically.
101
+ RETRY_CORRECTIVE_SUFFIX: str = (
102
+ "\nIMPORTANT: your previous reply was not one valid JSON array. "
103
+ "Reply with ONE complete JSON array, starting with '[' and ending with ']'. "
104
+ "Do not repeat elements. No prose."
105
+ )
106
+
107
+ # Truncation bound for raw model text echoed into stdout logs on parse failures.
108
+ _RAW_TEXT_LOG_LIMIT: int = 2000
109
+
110
+
111
+ @dataclass(frozen=True, slots=True)
112
+ class GenerationSettings:
113
+ """Decoding settings for one model generation.
114
+
115
+ Attributes:
116
+ do_sample: Whether to sample instead of decoding greedily.
117
+ temperature: Sampling temperature; only forwarded when ``do_sample``.
118
+ top_p: Nucleus-sampling probability mass; only forwarded when
119
+ ``do_sample``.
120
+ """
121
+
122
+ do_sample: bool = False
123
+ temperature: float | None = None
124
+ top_p: float | None = None
125
+
126
+
127
+ # Deterministic greedy decoding: the default for every first attempt.
128
+ GREEDY_SETTINGS: GenerationSettings = GenerationSettings()
129
+
130
+ # Mild sampling for the final retry attempt: enough randomness to escape a
131
+ # deterministic degenerate completion while keeping the constrained JSON shape
132
+ # likely.
133
+ RETRY_SAMPLING_SETTINGS: GenerationSettings = GenerationSettings(do_sample=True, temperature=0.4, top_p=0.9)
134
+
135
+ # A factory producing a ``GenerateFn`` bound to specific decoding settings. The
136
+ # retry ladder requests a fresh ``GenerateFn`` per attempt so attempt three can
137
+ # switch from greedy decoding to sampling.
138
+ type GenerateFnFactory = Callable[[GenerationSettings], GenerateFn]
139
+
140
+
141
+ def _attempt_settings(attempt: int) -> tuple[GenerationSettings, bool]:
142
+ """Return the decoding plan for a 1-based retry-ladder attempt.
143
+
144
+ Attempt 1 decodes greedily with the base prompt; attempt 2 keeps greedy
145
+ decoding but appends the corrective suffix; attempt 3 and beyond switch to
146
+ sampling (still with the suffix) so a deterministic failure cannot repeat
147
+ verbatim.
148
+
149
+ Args:
150
+ attempt: The 1-based attempt number.
151
+
152
+ Returns:
153
+ A ``(settings, append_corrective_suffix)`` pair.
154
+ """
155
+ if attempt == 1:
156
+ return GREEDY_SETTINGS, False
157
+ if attempt == 2:
158
+ return GREEDY_SETTINGS, True
159
+ return RETRY_SAMPLING_SETTINGS, True
160
+
161
+
162
+ def _log_parse_failure(stage: str, attempt: int, error: SchemaParseError) -> None:
163
+ """Print a parse failure's traceback and raw model text to stdout.
164
+
165
+ Worker stdout reaches the serving platform's run logs, so this is the durable
166
+ diagnostic channel for malformed model output: the full traceback shows where
167
+ parsing failed and the delimited block shows exactly what the model emitted
168
+ (truncated to ``_RAW_TEXT_LOG_LIMIT`` characters to keep log entries bounded).
169
+
170
+ Args:
171
+ stage: The pipeline stage that failed (for example ``"image_grounding"``).
172
+ attempt: The 1-based attempt number that produced the failure.
173
+ error: The parse error carrying the offending raw model text.
174
+ """
175
+ print(f"[cxr-auditor] parse failure: stage={stage} attempt={attempt}", flush=True)
176
+ traceback.print_exception(error, file=sys.stdout)
177
+ raw = error.raw_text
178
+ if len(raw) > _RAW_TEXT_LOG_LIMIT:
179
+ raw = f"{raw[:_RAW_TEXT_LOG_LIMIT]} ...[truncated]"
180
+ print(f"[cxr-auditor] raw model text (stage={stage} attempt={attempt}) >>>\n{raw}\n<<<", flush=True)
181
+
182
 
183
  @dataclass(frozen=True, slots=True)
184
  class AuditOutcome:
 
193
  result: The canonical ``AuditResult`` (image findings, draft findings,
194
  label-only audit, disclaimer, box format).
195
  comparison: The per-item comparator detail (boxes, urgency, draft spans).
196
+ draft_parse_note: A user-facing note set when a supplied draft could not
197
+ be parsed after all retries, so the audit proceeded image-only.
198
+ ``None`` when no draft was supplied or the draft parsed.
199
  """
200
 
201
  result: AuditResult
202
  comparison: ComparisonReport
203
+ draft_parse_note: str | None = None
204
 
205
 
206
  def grounded_dicts_to_image_findings(grounded: list[dict[str, Any]]) -> list[ImageFinding]:
 
294
 
295
 
296
  def run_with_retry(
297
+ generate_fn_factory: GenerateFnFactory,
298
  prompt: str,
299
  parse_fn: Callable[[str], list[Any]],
300
  max_retries: int = DEFAULT_MAX_RETRIES,
301
+ *,
302
+ stage: str = "generation",
303
  ) -> list[Any]:
304
+ """Generate then parse, escalating the retry conditions on each failure.
305
 
306
  The model occasionally emits prose, a truncated array, or otherwise
307
+ unparseable text - and a greedy decode of the same prompt fails the same way
308
+ every time. Each attempt therefore changes the conditions per
309
+ ``_attempt_settings``: attempt 1 is greedy with the base prompt, attempt 2 is
310
+ greedy with ``RETRY_CORRECTIVE_SUFFIX`` appended, and attempt 3 onward samples
311
+ (``RETRY_SAMPLING_SETTINGS``) with the suffix. Every failed attempt is logged
312
+ to stdout with its traceback and raw model text. If every attempt fails, the
313
+ last ``SchemaParseError`` is raised so its ``raw_text`` (the final raw
314
+ completion) is available to the caller.
315
 
316
  Args:
317
+ generate_fn_factory: Factory returning a ``GenerateFn`` for the decoding
318
+ settings of each attempt.
319
+ prompt: The rendered base prompt (the corrective suffix is appended to it
320
+ on retry attempts).
321
  parse_fn: A tolerant parser turning raw text into a list (raises
322
  ``SchemaParseError`` on unparseable text).
323
  max_retries: Number of additional attempts after the first. Must be >= 0.
324
+ stage: Stage label used in failure logs (keyword-only).
325
 
326
  Returns:
327
  The first successfully parsed list.
 
334
  raise ValueError(f"max_retries must be non-negative, got {max_retries}")
335
 
336
  last_error: SchemaParseError | None = None
337
+ for attempt in range(1, max_retries + 2):
338
+ settings, corrective = _attempt_settings(attempt)
339
+ generate_fn = generate_fn_factory(settings)
340
+ attempt_prompt = prompt + RETRY_CORRECTIVE_SUFFIX if corrective else prompt
341
+ raw_text = generate_fn(attempt_prompt)
342
  try:
343
  return parse_fn(raw_text)
344
  except SchemaParseError as exc:
345
  last_error = exc
346
+ _log_parse_failure(stage, attempt, exc)
347
  assert last_error is not None # loop runs at least once, so an error was set
348
  raise last_error
349
 
350
 
351
+ def make_generate_fn(
352
+ model: Any,
353
+ processor: Any,
354
+ image: Image.Image,
355
+ settings: GenerationSettings = GREEDY_SETTINGS,
356
+ ) -> GenerateFn:
357
  """Build an image-bound ``generate_fn`` over a loaded model and processor.
358
 
359
+ The returned closure captures the model, processor, image, and decoding
360
+ settings, exposing the text-in/text-out ``GenerateFn`` shape that the
361
+ grounding path, the retry ladder, and ``cxr_auditor.parser.parse_draft`` all
362
+ consume. Binding the image into the closure lets the draft parser - which
363
+ only knows about a text-prompt ``generate_fn`` - reuse the same single-turn
364
+ multimodal model the grounding step uses, so the draft is parsed with the
365
+ SAME model rather than a separate text-only stack.
366
 
367
  Args:
368
  model: A loaded vision-language model exposing ``generate``.
369
  processor: The matching transformers processor.
370
  image: The chest X-ray bound to every generation through this closure.
371
+ settings: Decoding settings bound to every generation through this
372
+ closure.
373
 
374
  Returns:
375
  A ``GenerateFn`` mapping a rendered prompt to the model's raw completion.
376
  """
377
 
378
  def _generate(prompt: str) -> str:
379
+ return _generate_text(model, processor, prompt, image, settings=settings)
380
 
381
  return _generate
382
 
383
 
384
+ def _generate_fn_factory(model: Any, processor: Any, image: Image.Image) -> GenerateFnFactory:
385
+ """Build a settings-to-``GenerateFn`` factory bound to one model and image.
386
+
387
+ This is the shape the retry ladder consumes: each attempt requests a
388
+ ``GenerateFn`` for its own decoding settings while the model, processor, and
389
+ image stay fixed.
390
+
391
+ Args:
392
+ model: A loaded vision-language model exposing ``generate``.
393
+ processor: The matching transformers processor.
394
+ image: The chest X-ray bound to every generation.
395
+
396
+ Returns:
397
+ A factory mapping ``GenerationSettings`` to an image-bound ``GenerateFn``.
398
+ """
399
+
400
+ def _factory(settings: GenerationSettings) -> GenerateFn:
401
+ return make_generate_fn(model, processor, image, settings=settings)
402
+
403
+ return _factory
404
+
405
+
406
  def generate_findings(
407
  image: Image.Image,
408
  *,
 
412
  ) -> list[ImageFinding]:
413
  """Ground an image into validated ``ImageFinding`` objects.
414
 
415
+ Builds the pinned image-grounding prompt, generates through the escalating
416
+ retry ladder, and assembles validated findings. This is the image-side entry
417
  point the app uses when it wants only the grounded findings (for example to
418
  draw boxes before a draft is supplied).
419
 
 
421
  image: The chest X-ray as a PIL image.
422
  model: A loaded vision-language model (keyword-only).
423
  processor: The matching transformers processor (keyword-only).
424
+ max_retries: Retry budget for the invalid-JSON ladder (keyword-only).
425
 
426
  Returns:
427
  The image-grounded findings with bounding-box evidence.
 
429
  Raises:
430
  SchemaParseError: If grounding output cannot be parsed after all retries.
431
  """
432
+ grounded = run_with_retry(
433
+ _generate_fn_factory(model, processor, image),
434
+ build_image_grounding_prompt(),
435
+ extract_finding_list,
436
+ max_retries=max_retries,
437
+ stage="image_grounding",
438
+ )
439
  return grounded_dicts_to_image_findings(grounded)
440
 
441
 
 
451
 
452
  Steps:
453
  1. Ground the image into validated ``ImageFinding`` objects
454
+ (``generate_findings``), through the escalating retry ladder.
455
  2. If a non-blank draft is supplied, parse it into the same label space via
456
  ``cxr_auditor.parser.parse_draft``, driven by an image-bound
457
+ ``generate_fn`` through the same ladder (with the ``DRAFT_MAX_RETRIES``
458
+ budget). A draft that still cannot be parsed never fails the audit: the
459
+ audit proceeds image-only and ``AuditOutcome.draft_parse_note`` records
460
+ the degradation for the user interface.
461
  3. Run the deterministic comparator (``cxr_auditor.comparator.compare``) and
462
  bundle everything into an ``AuditOutcome``.
463
 
 
472
  image-side findings (and urgent flags).
473
  model: A loaded vision-language model exposing ``generate`` (keyword-only).
474
  processor: The matching transformers processor (keyword-only).
475
+ max_retries: Retry budget for the image-grounding ladder (keyword-only).
476
+ Draft parsing uses the fixed ``DRAFT_MAX_RETRIES`` budget because it
477
+ degrades gracefully instead of failing.
478
 
479
  Returns:
480
+ An ``AuditOutcome`` carrying the canonical ``AuditResult``, the per-item
481
+ ``ComparisonReport``, and the draft-degradation note when it applies.
482
 
483
  Raises:
484
  ValueError: If ``model`` or ``processor`` is not supplied.
485
+ SchemaParseError: If the image-grounding output cannot be parsed into a
486
  finding list after all retries.
487
  """
488
  if model is None or processor is None:
 
491
  image_findings = generate_findings(image, model=model, processor=processor, max_retries=max_retries)
492
 
493
  draft_findings: list[DraftFinding] = []
494
+ draft_parse_note: str | None = None
495
  cleaned_draft = (draft_text or "").strip()
496
  if cleaned_draft:
497
+ try:
498
+ draft_findings = _parse_draft_with_retry(cleaned_draft, _generate_fn_factory(model, processor, image))
499
+ except SchemaParseError:
500
+ # Per-attempt details are already logged by _log_parse_failure; the
501
+ # audit degrades to image-only rather than failing on the draft.
502
+ print("[cxr-auditor] draft parsing failed after all retries; auditing image only", flush=True)
503
+ draft_parse_note = DRAFT_PARSE_FAILURE_NOTE
504
 
505
  comparison = compare(image_findings, draft_findings)
506
  result = AuditResult(
 
508
  draft_findings=draft_findings,
509
  audit=comparison.audit,
510
  )
511
+ return AuditOutcome(result=result, comparison=comparison, draft_parse_note=draft_parse_note)
512
+
513
+
514
+ def _with_corrective_suffix(generate_fn: GenerateFn) -> GenerateFn:
515
+ """Wrap a ``GenerateFn`` so every prompt carries the corrective suffix.
516
+
517
+ ``parser.parse_draft`` builds its prompt internally, so retry attempts inject
518
+ ``RETRY_CORRECTIVE_SUFFIX`` by wrapping the callable rather than editing the
519
+ prompt directly.
520
+
521
+ Args:
522
+ generate_fn: The inner ``GenerateFn`` to wrap.
523
+
524
+ Returns:
525
+ A ``GenerateFn`` that appends the corrective suffix to every prompt.
526
+ """
527
+
528
+ def _generate(prompt: str) -> str:
529
+ return generate_fn(prompt + RETRY_CORRECTIVE_SUFFIX)
530
+
531
+ return _generate
532
 
533
 
534
  def _parse_draft_with_retry(
535
  draft_text: str,
536
+ generate_fn_factory: GenerateFnFactory,
537
+ max_retries: int = DRAFT_MAX_RETRIES,
538
  ) -> list[DraftFinding]:
539
+ """Parse a draft through ``parser.parse_draft`` with the escalating ladder.
540
 
541
+ Wraps the draft parser's injected-callable contract in the same attempt plan
542
+ the grounding path uses (``_attempt_settings``): each attempt re-runs the full
543
+ ``parse_draft`` (build prompt, generate, validate), retry attempts append the
544
+ corrective suffix via a wrapped ``GenerateFn``, the first successful parse
545
+ wins, and the final ``SchemaParseError`` propagates if all attempts fail.
546
 
547
  Args:
548
  draft_text: The non-empty draft impression to parse.
549
+ generate_fn_factory: Factory returning an image-bound ``GenerateFn`` for
550
+ each attempt's decoding settings.
551
  max_retries: Number of additional attempts after the first. Must be >= 0.
552
 
553
  Returns:
 
561
  raise ValueError(f"max_retries must be non-negative, got {max_retries}")
562
 
563
  last_error: SchemaParseError | None = None
564
+ for attempt in range(1, max_retries + 2):
565
+ settings, corrective = _attempt_settings(attempt)
566
+ generate_fn = generate_fn_factory(settings)
567
+ if corrective:
568
+ generate_fn = _with_corrective_suffix(generate_fn)
569
  try:
570
  return parse_draft(draft_text, generate_fn)
571
  except SchemaParseError as exc:
572
  last_error = exc
573
+ _log_parse_failure("draft_parsing", attempt, exc)
574
  assert last_error is not None
575
  raise last_error
576
 
 
640
  return model, processor
641
 
642
 
643
+ def _generate_text(
644
+ model: Any,
645
+ processor: Any,
646
+ prompt: str,
647
+ image: Image.Image,
648
+ settings: GenerationSettings = GREEDY_SETTINGS,
649
+ ) -> str:
650
  """Run one single-turn multimodal generation and return the decoded reply.
651
 
652
  This is the only function that touches the model at inference time, and the
653
  single seam tests patch to drive the orchestration without a real model. It
654
  builds a single-turn chat message with the image and the prompt text, applies
655
+ the processor's chat template, generates with the supplied decoding settings,
656
+ and decodes only the newly generated tokens (slicing off the prompt) so the
657
+ returned text is just the model's reply (a plain ``str``, never a tensor
658
+ across a worker boundary). ``pad_token_id`` is pinned to the tokenizer's
659
+ end-of-sequence token so generation runs without a pad-token warning.
660
 
661
  Heavy imports are local to keep module import free of the vision stack. The
662
  chat-message construction follows the transformers image-text-to-text
 
668
  processor: The matching processor.
669
  prompt: The fully rendered text prompt.
670
  image: The chest X-ray as a PIL image.
671
+ settings: Decoding settings for this generation.
672
 
673
  Returns:
674
  The model's decoded reply text (prompt tokens stripped).
 
692
  return_tensors="pt",
693
  ).to(model.device)
694
 
695
+ generate_kwargs: dict[str, Any] = {
696
+ "max_new_tokens": DEFAULT_MAX_NEW_TOKENS,
697
+ "do_sample": settings.do_sample,
698
+ "pad_token_id": processor.tokenizer.eos_token_id,
699
+ }
700
+ # Sampling knobs are forwarded only when sampling; transformers warns when
701
+ # they accompany greedy decoding.
702
+ if settings.do_sample:
703
+ if settings.temperature is not None:
704
+ generate_kwargs["temperature"] = settings.temperature
705
+ if settings.top_p is not None:
706
+ generate_kwargs["top_p"] = settings.top_p
707
+
708
  input_len = inputs["input_ids"].shape[-1]
709
  with torch.inference_mode():
710
+ generated = model.generate(**inputs, **generate_kwargs)
711
  new_tokens = generated[0][input_len:]
712
  return processor.decode(new_tokens, skip_special_tokens=True)
713
 
714
 
715
+ # Titles the ZeroGPU scheduler attaches to the quota and scheduling errors it
716
+ # raises in the serving app's main process. These failures are platform-side: the
717
+ # uploaded image is never the cause, so the user message must not blame it.
718
+ _GPU_SCHEDULING_ERROR_TITLES: frozenset[str] = frozenset(
719
+ {
720
+ "ZeroGPU quota exceeded",
721
+ "ZeroGPU illegal duration",
722
+ "ZeroGPU pending credits exceeded",
723
+ "ZeroGPU queue timeout",
724
+ "ZeroGPU client error",
725
+ }
726
+ )
727
+
728
+ # Title the ZeroGPU platform attaches when a worker exception was converted to a
729
+ # string-transported error whose message body is the worker exception class name.
730
+ _WORKER_ERROR_TITLE: str = "ZeroGPU worker error"
731
+
732
+ # Worker exception class names that mean "the model output could not be parsed".
733
+ _PARSE_ERROR_CLASS_NAMES: frozenset[str] = frozenset({"SchemaParseError"})
734
+
735
+ # Message body the ZeroGPU platform uses when it cuts a GPU task short.
736
+ _GPU_TASK_ABORTED_BODY: str = "GPU task aborted"
737
+
738
+ _GPU_QUOTA_MESSAGE: str = (
739
+ "**GPU quota reached.** Free ZeroGPU time is temporarily exhausted, so this audit could not get a "
740
+ "GPU slot - the image is not the problem. Wait a few minutes and press Run audit again."
741
+ )
742
+
743
+ _GPU_INTERRUPTED_MESSAGE: str = (
744
+ "**GPU task was interrupted.** The platform cut the GPU run short before the audit finished. "
745
+ "Please press Run audit again."
746
+ )
747
+
748
+
749
+ def _parse_failure_message(class_name: str) -> str:
750
+ """Return the user-facing message for an unparseable-model-output failure."""
751
+ return (
752
+ f"**Could not analyze this image.** The model returned output that could not be parsed ({class_name}). "
753
+ "Please try again, or use a clearer frontal chest X-ray."
754
+ )
755
+
756
+
757
+ def _generic_failure_message(detail: str) -> str:
758
+ """Return the user-facing message for an uncategorized failure."""
759
+ return (
760
+ f"**Audit failed.** An unexpected error occurred ({detail}). "
761
+ "Please try again; if this keeps happening, check the Space logs."
762
+ )
763
+
764
+
765
+ def categorize_serving_error(error: Exception) -> str:
766
+ """Map an audit-time exception to an honest, user-facing Markdown message.
767
+
768
+ The ZeroGPU platform never pickles worker exceptions across the process
769
+ boundary: it transports the worker exception's class name as the message body
770
+ of a gradio error object whose own class ``__name__`` is literally ``"Error"``
771
+ and whose ``title`` attribute names the failure source. This categorizer
772
+ therefore classifies on the exception's class name, ``title`` attribute, and
773
+ message body - never on ``isinstance`` against gradio types - so it stays
774
+ importable and unit-testable without gradio installed.
775
+
776
+ Categories:
777
+ - Quota and scheduling errors (a title in the known ZeroGPU set, or any
778
+ title or body mentioning "quota") produce a GPU-quota message that
779
+ never blames the image.
780
+ - An aborted GPU task (body ``"GPU task aborted"``) produces a transient
781
+ interrupted-please-retry message.
782
+ - A worker error whose body names a parse-failure class, or a directly
783
+ raised ``SchemaParseError``, produces the could-not-parse message
784
+ naming the real exception class.
785
+ - Anything else produces a generic failure message naming the true type.
786
+
787
+ Args:
788
+ error: The exception caught around the GPU audit call.
789
+
790
+ Returns:
791
+ A Markdown message suitable for the audit panel.
792
+ """
793
+ if isinstance(error, SchemaParseError):
794
+ return _parse_failure_message(type(error).__name__)
795
+
796
+ body = str(error)
797
+ if type(error).__name__ == "Error":
798
+ title = str(getattr(error, "title", ""))
799
+ if title in _GPU_SCHEDULING_ERROR_TITLES or "quota" in title.lower() or "quota" in body.lower():
800
+ return _GPU_QUOTA_MESSAGE
801
+ if _GPU_TASK_ABORTED_BODY in body:
802
+ return _GPU_INTERRUPTED_MESSAGE
803
+ if title == _WORKER_ERROR_TITLE:
804
+ if body in _PARSE_ERROR_CLASS_NAMES:
805
+ return _parse_failure_message(body)
806
+ return _generic_failure_message(body or type(error).__name__)
807
+ return _generic_failure_message(type(error).__name__)
808
+
809
+
810
  __all__ = [
811
  "DEFAULT_MAX_NEW_TOKENS",
812
  "DEFAULT_MAX_RETRIES",
813
  "DEFAULT_MODEL_ID",
814
+ "DRAFT_MAX_RETRIES",
815
+ "DRAFT_PARSE_FAILURE_NOTE",
816
+ "GREEDY_SETTINGS",
817
+ "RETRY_CORRECTIVE_SUFFIX",
818
+ "RETRY_SAMPLING_SETTINGS",
819
  "AuditOutcome",
820
+ "GenerateFnFactory",
821
+ "GenerationSettings",
822
  "audit",
823
+ "categorize_serving_error",
824
  "generate_findings",
825
  "grounded_dicts_to_image_findings",
826
  "load_model",
cxr_auditor/parser.py CHANGED
@@ -1,7 +1,7 @@
1
  """
2
  Draft-report parser: map a draft impression into the canonical label space.
3
 
4
- This is Gate C's PRIMARY parser. It prompts the same MedGemma model (via the
5
  pinned draft-parsing prompt) to extract which canonical findings a draft
6
  impression asserts present and which it explicitly denies, then validates the
7
  model's JSON list into ``DraftFinding`` objects.
 
1
  """
2
  Draft-report parser: map a draft impression into the canonical label space.
3
 
4
+ This is the PRIMARY draft parser. It prompts the same MedGemma model (via the
5
  pinned draft-parsing prompt) to extract which canonical findings a draft
6
  impression asserts present and which it explicitly denies, then validates the
7
  model's JSON list into ``DraftFinding`` objects.
cxr_auditor/render.py CHANGED
@@ -32,12 +32,22 @@ the others. ``cluster_overlay_boxes`` merges spatially-overlapping boxes into on
32
  is drawn exactly once with the correct, order-independent color and a single
33
  combined label.
34
 
 
 
 
 
 
 
 
 
 
35
  Unsupported claims are draft-only and have no image box, so they appear in the
36
  table and the audit panel rather than as overlay boxes.
37
  """
38
 
39
  from __future__ import annotations
40
 
 
41
  from dataclasses import dataclass
42
  from enum import Enum
43
 
@@ -64,6 +74,13 @@ _MAX_OVERLAY_LONG_SIDE = 1280
64
  _MIN_LABEL_FONT_SIZE = 14
65
  _MAX_LABEL_FONT_SIZE = 28
66
 
 
 
 
 
 
 
 
67
  # RGB colors for each evidence category. Chosen for contrast on a grayscale X-ray.
68
  _SUPPORTED_COLOR = (46, 204, 113)
69
  _MISSING_COLOR = (243, 156, 18)
@@ -317,6 +334,64 @@ def _combined_label(cluster: OverlayBox) -> str:
317
  return text
318
 
319
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
320
  def _draw_label(
321
  draw: ImageDraw.ImageDraw,
322
  box_xyxy: XYXYBox,
@@ -325,14 +400,17 @@ def _draw_label(
325
  color: tuple[int, int, int],
326
  font: LoadedFont,
327
  image_size: tuple[int, int],
328
- ) -> None:
 
329
  """Draw a filled, high-contrast label band anchored to a box, clamped on-image.
330
 
331
  The label sits just above the box top by default, but flips to just below the
332
  box top when there is no room above (the box touches the top edge), and its
333
  left edge is clamped so the band never runs off the right side of the image.
334
- The band is filled with ``color`` and the text is drawn in a contrasting ink so
335
- it is legible over a grayscale X-ray.
 
 
336
 
337
  Args:
338
  draw: The active drawing context.
@@ -341,6 +419,11 @@ def _draw_label(
341
  color: The band fill color (the cluster's status color).
342
  font: The scaled font to measure and render with.
343
  image_size: ``(width, height)`` of the canvas, for on-image clamping.
 
 
 
 
 
344
  """
345
  image_width, image_height = image_size
346
  x_min, y_min, _x_max, _y_max = box_xyxy
@@ -361,11 +444,12 @@ def _draw_label(
361
  band_left = max(0, image_width - band_width)
362
  band_top = max(0, min(band_top, image_height - band_height))
363
 
364
- draw.rectangle(
365
- (band_left, band_top, band_left + band_width, band_top + band_height),
366
- fill=color,
367
- )
368
- draw.text((band_left + pad, band_top + pad), text, fill=_contrast_ink(color), font=font)
 
369
 
370
 
371
  def _contrast_ink(color: tuple[int, int, int]) -> tuple[int, int, int]:
@@ -390,7 +474,9 @@ def annotate_evidence(image: Image.Image, outcome: AuditOutcome) -> Image.Image:
390
  (see ``cluster_overlay_boxes``) so each region is drawn exactly once, colored by
391
  audit status (see the module color legend). Urgent regions are drawn in red with
392
  a doubled, thicker border and an "(URGENT)" tag so they stand out. Every label
393
- uses the human-readable display name. Findings without a localizable box
 
 
394
  contribute no drawing (they still appear in the table and panel).
395
 
396
  Args:
@@ -414,6 +500,8 @@ def annotate_evidence(image: Image.Image, outcome: AuditOutcome) -> Image.Image:
414
  # stay proportionate on both tiny test fixtures and canvas-capped X-rays.
415
  base_width = max(2, round(max(width, height) / 320))
416
 
 
 
417
  for cluster in cluster_overlay_boxes(categorize_image_findings(outcome)):
418
  box_xyxy = normalized_to_xyxy_abs(cluster.box, width, height)
419
  x_min, y_min, x_max, y_max = box_xyxy
@@ -428,7 +516,17 @@ def annotate_evidence(image: Image.Image, outcome: AuditOutcome) -> Image.Image:
428
  outline=color,
429
  width=max(1, base_width),
430
  )
431
- _draw_label(draw, box_xyxy, _combined_label(cluster), color=color, font=font, image_size=(width, height))
 
 
 
 
 
 
 
 
 
 
432
 
433
  return canvas
434
 
@@ -495,11 +593,13 @@ def _status_word(status: FindingStatus) -> str:
495
  def audit_panel_markdown(outcome: AuditOutcome) -> str:
496
  """Render the audit verdict as a plain-English Markdown panel.
497
 
498
- Leads with a short "How to read this" orientation line, then lists urgent
499
- flags first (most important), then missing findings, then unsupported claims,
500
- with per-item detail (draft spans for unsupported claims). Every finding is
501
- shown by its human-readable display name. When nothing is flagged, reports
502
- agreement.
 
 
503
 
504
  Args:
505
  outcome: The audit outcome.
@@ -508,11 +608,22 @@ def audit_panel_markdown(outcome: AuditOutcome) -> str:
508
  A Markdown string.
509
  """
510
  audit = outcome.result.audit
511
- lines: list[str] = [
512
- "**How to read this:** this panel compares what the AI sees in the image against the draft text. "
513
- "It is a research aid, not a diagnosis - always confirm with a qualified radiologist.",
514
- "",
515
- ]
 
 
 
 
 
 
 
 
 
 
 
516
 
517
  if audit.urgent_review_flags:
518
  lines.append("### URGENT - needs radiologist review")
 
32
  is drawn exactly once with the correct, order-independent color and a single
33
  combined label.
34
 
35
+ Label collision avoidance
36
+ -------------------------
37
+ Distinct regions can still carry long labels at nearly the same height (for
38
+ example bilateral opacities over the two lung fields), where independently
39
+ placed label bands would overlap and clip each other. Each band is therefore
40
+ checked against the bands already drawn on the canvas and nudged vertically
41
+ (below its own box first) until it overlaps none of them, always staying
42
+ clamped on-image; a lone label keeps its exact anchored position.
43
+
44
  Unsupported claims are draft-only and have no image box, so they appear in the
45
  table and the audit panel rather than as overlay boxes.
46
  """
47
 
48
  from __future__ import annotations
49
 
50
+ from collections.abc import Sequence
51
  from dataclasses import dataclass
52
  from enum import Enum
53
 
 
74
  _MIN_LABEL_FONT_SIZE = 14
75
  _MAX_LABEL_FONT_SIZE = 28
76
 
77
+ # Vertical search budget for nudging a colliding label band: this many
78
+ # band-height steps downward and again upward. At the tallest band a capped
79
+ # canvas produces (about 37 px) eight steps sweep roughly 300 px each way -
80
+ # ample clearance for the handful of labels one audit draws - while keeping
81
+ # the candidate count, and therefore the worst-case drawing work, bounded.
82
+ _LABEL_NUDGE_ATTEMPTS = 8
83
+
84
  # RGB colors for each evidence category. Chosen for contrast on a grayscale X-ray.
85
  _SUPPORTED_COLOR = (46, 204, 113)
86
  _MISSING_COLOR = (243, 156, 18)
 
334
  return text
335
 
336
 
337
+ def _rects_overlap(a: XYXYBox, b: XYXYBox) -> bool:
338
+ """Return whether two pixel rectangles share interior area.
339
+
340
+ Rectangles are ``(left, top, right, bottom)``. Edge-touching rectangles do
341
+ not count as overlapping, so nudged label bands may sit flush against one
342
+ another without triggering a further nudge.
343
+ """
344
+ a_left, a_top, a_right, a_bottom = a
345
+ b_left, b_top, b_right, b_bottom = b
346
+ return a_left < b_right and b_left < a_right and a_top < b_bottom and b_top < a_bottom
347
+
348
+
349
+ def _resolve_band_rect(
350
+ desired: XYXYBox,
351
+ box_xyxy: XYXYBox,
352
+ image_height: int,
353
+ placed_bands: Sequence[XYXYBox],
354
+ ) -> XYXYBox:
355
+ """Return the label-band rectangle to draw, nudged vertically clear of placed bands.
356
+
357
+ A desired rectangle that overlaps no already-placed band is returned
358
+ unchanged, so a lone label renders exactly at its anchored position. On
359
+ collision the band keeps its horizontal extent (it stays anchored to its
360
+ box) and tries vertical positions in order: just below the box's bottom
361
+ edge, then band-height steps downward from there, then band-height steps
362
+ upward from the desired position, up to ``_LABEL_NUDGE_ATTEMPTS`` steps per
363
+ direction. Every candidate is clamped fully on-image; when no candidate
364
+ clears all placed bands the last clamped candidate is returned, so the
365
+ result is always an on-image rectangle and rendering never fails.
366
+
367
+ Args:
368
+ desired: The preferred band rectangle ``(left, top, right, bottom)``,
369
+ already clamped on-image by the caller.
370
+ box_xyxy: The owning box in absolute pixels ``(x_min, y_min, x_max,
371
+ y_max)``, anchoring the below-box candidate.
372
+ image_height: The canvas height in pixels, for vertical clamping.
373
+ placed_bands: Band rectangles already drawn on this canvas.
374
+
375
+ Returns:
376
+ The chosen band rectangle ``(left, top, right, bottom)``.
377
+ """
378
+ left, desired_top, right, desired_bottom = desired
379
+ band_height = desired_bottom - desired_top
380
+ lowest_top = max(0.0, image_height - band_height)
381
+ below_box_top = min(box_xyxy[3], lowest_top)
382
+
383
+ candidate_tops = [desired_top, below_box_top]
384
+ candidate_tops.extend(min(below_box_top + step * band_height, lowest_top) for step in range(1, _LABEL_NUDGE_ATTEMPTS + 1))
385
+ candidate_tops.extend(max(0.0, desired_top - step * band_height) for step in range(1, _LABEL_NUDGE_ATTEMPTS + 1))
386
+
387
+ band = desired
388
+ for top in candidate_tops:
389
+ band = (left, top, right, top + band_height)
390
+ if not any(_rects_overlap(band, placed) for placed in placed_bands):
391
+ return band
392
+ return band
393
+
394
+
395
  def _draw_label(
396
  draw: ImageDraw.ImageDraw,
397
  box_xyxy: XYXYBox,
 
400
  color: tuple[int, int, int],
401
  font: LoadedFont,
402
  image_size: tuple[int, int],
403
+ placed_bands: Sequence[XYXYBox],
404
+ ) -> XYXYBox:
405
  """Draw a filled, high-contrast label band anchored to a box, clamped on-image.
406
 
407
  The label sits just above the box top by default, but flips to just below the
408
  box top when there is no room above (the box touches the top edge), and its
409
  left edge is clamped so the band never runs off the right side of the image.
410
+ When the resulting band would overlap a band already drawn on this canvas it
411
+ is nudged vertically clear (see ``_resolve_band_rect``) so neighboring labels
412
+ never clip each other. The band is filled with ``color`` and the text is
413
+ drawn in a contrasting ink so it is legible over a grayscale X-ray.
414
 
415
  Args:
416
  draw: The active drawing context.
 
419
  color: The band fill color (the cluster's status color).
420
  font: The scaled font to measure and render with.
421
  image_size: ``(width, height)`` of the canvas, for on-image clamping.
422
+ placed_bands: Band rectangles already drawn on this canvas, used to
423
+ resolve collisions; the caller records the returned rectangle.
424
+
425
+ Returns:
426
+ The band rectangle ``(left, top, right, bottom)`` actually drawn.
427
  """
428
  image_width, image_height = image_size
429
  x_min, y_min, _x_max, _y_max = box_xyxy
 
444
  band_left = max(0, image_width - band_width)
445
  band_top = max(0, min(band_top, image_height - band_height))
446
 
447
+ desired = (band_left, band_top, band_left + band_width, band_top + band_height)
448
+ band = _resolve_band_rect(desired, box_xyxy, image_height, placed_bands)
449
+
450
+ draw.rectangle(band, fill=color)
451
+ draw.text((band[0] + pad, band[1] + pad), text, fill=_contrast_ink(color), font=font)
452
+ return band
453
 
454
 
455
  def _contrast_ink(color: tuple[int, int, int]) -> tuple[int, int, int]:
 
474
  (see ``cluster_overlay_boxes``) so each region is drawn exactly once, colored by
475
  audit status (see the module color legend). Urgent regions are drawn in red with
476
  a doubled, thicker border and an "(URGENT)" tag so they stand out. Every label
477
+ uses the human-readable display name, and label bands that would overlap an
478
+ earlier band are nudged vertically clear of it (see ``_resolve_band_rect``) so
479
+ neighboring labels stay readable. Findings without a localizable box
480
  contribute no drawing (they still appear in the table and panel).
481
 
482
  Args:
 
500
  # stay proportionate on both tiny test fixtures and canvas-capped X-rays.
501
  base_width = max(2, round(max(width, height) / 320))
502
 
503
+ # Bands already drawn on this canvas; each new label is nudged clear of them.
504
+ placed_bands: list[XYXYBox] = []
505
  for cluster in cluster_overlay_boxes(categorize_image_findings(outcome)):
506
  box_xyxy = normalized_to_xyxy_abs(cluster.box, width, height)
507
  x_min, y_min, x_max, y_max = box_xyxy
 
516
  outline=color,
517
  width=max(1, base_width),
518
  )
519
+ placed_bands.append(
520
+ _draw_label(
521
+ draw,
522
+ box_xyxy,
523
+ _combined_label(cluster),
524
+ color=color,
525
+ font=font,
526
+ image_size=(width, height),
527
+ placed_bands=placed_bands,
528
+ )
529
+ )
530
 
531
  return canvas
532
 
 
593
  def audit_panel_markdown(outcome: AuditOutcome) -> str:
594
  """Render the audit verdict as a plain-English Markdown panel.
595
 
596
+ When the outcome carries a draft-degradation note (the draft could not be
597
+ parsed and the audit proceeded image-only), that note leads the panel so the
598
+ user re-checks the draft manually. Then comes a short "How to read this"
599
+ orientation line, urgent flags first (most important), missing findings,
600
+ and unsupported claims, with per-item detail (draft spans for unsupported
601
+ claims). Every finding is shown by its human-readable display name. When
602
+ nothing is flagged, reports agreement.
603
 
604
  Args:
605
  outcome: The audit outcome.
 
608
  A Markdown string.
609
  """
610
  audit = outcome.result.audit
611
+ lines: list[str] = []
612
+ if outcome.draft_parse_note is not None:
613
+ lines.extend(
614
+ [
615
+ f"**Draft not analyzed:** {outcome.draft_parse_note} "
616
+ "This audit reflects the image only - re-check the draft text manually.",
617
+ "",
618
+ ]
619
+ )
620
+ lines.extend(
621
+ [
622
+ "**How to read this:** this panel compares what the AI sees in the image against the draft text. "
623
+ "It is a research aid, not a diagnosis - always confirm with a qualified radiologist.",
624
+ "",
625
+ ]
626
+ )
627
 
628
  if audit.urgent_review_flags:
629
  lines.append("### URGENT - needs radiologist review")
cxr_auditor/schema.py CHANGED
@@ -202,33 +202,39 @@ class SchemaParseError(ValueError):
202
  super().__init__(message)
203
  self.raw_text = raw_text
204
 
 
 
205
 
206
- def extract_first_json_object(text: str) -> dict[str, Any]:
207
- """Extract the first balanced top-level JSON object from raw model text.
 
208
 
209
- Vision-language models frequently wrap their JSON in prose, markdown code
210
- fences, or trailing commentary. This scans for the first ``{`` and walks the
211
- string tracking brace depth (while respecting JSON string literals and escape
212
- sequences) to find the matching close brace, then parses that slice.
 
 
 
 
 
 
 
 
213
 
214
  Args:
215
- text: Raw model output that contains a JSON object somewhere inside it.
 
 
 
216
 
217
  Returns:
218
- The parsed object as a dict.
219
-
220
- Raises:
221
- SchemaParseError: If no balanced JSON object is found, or the candidate
222
- slice is not valid JSON, or the top-level value is not an object.
223
  """
224
- start = text.find("{")
225
- if start == -1:
226
- raise SchemaParseError("no JSON object found in model text", text)
227
-
228
  depth = 0
229
  in_string = False
230
  escaped = False
231
- end = -1
232
  for index in range(start, len(text)):
233
  char = text[index]
234
  if in_string:
@@ -241,14 +247,38 @@ def extract_first_json_object(text: str) -> dict[str, Any]:
241
  continue
242
  if char == '"':
243
  in_string = True
244
- elif char == "{":
245
  depth += 1
246
- elif char == "}":
247
  depth -= 1
248
  if depth == 0:
249
- end = index
250
- break
 
 
 
 
 
 
 
 
 
251
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
252
  if end == -1:
253
  raise SchemaParseError("no balanced JSON object found in model text", text)
254
 
@@ -295,13 +325,70 @@ def _strip_code_fences(text: str) -> str:
295
  return text
296
 
297
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
298
  def extract_finding_list(text: str) -> list[dict[str, Any]]:
299
  """Extract a JSON array of finding dicts from raw model text.
300
 
301
  MedGemma's native grounding output is a JSON *list* of ``{label, box_2d}``
302
  objects rather than a wrapping object. This finds the first balanced
303
  top-level JSON array and parses it. A bare object is tolerated and wrapped in
304
- a single-element list.
 
 
305
 
306
  Args:
307
  text: Raw model output containing a JSON array (or a single object).
@@ -310,8 +397,9 @@ def extract_finding_list(text: str) -> list[dict[str, Any]]:
310
  A list of dicts (one per finding). Non-dict array elements are rejected.
311
 
312
  Raises:
313
- SchemaParseError: If no balanced JSON array/object is found, the slice is
314
- invalid JSON, or an array element is not an object.
 
315
  """
316
  stripped = _strip_code_fences(text)
317
 
@@ -322,37 +410,20 @@ def extract_finding_list(text: str) -> list[dict[str, Any]]:
322
  if array_start == -1 or (object_start != -1 and object_start < array_start):
323
  return [extract_first_json_object(stripped)]
324
 
325
- depth = 0
326
- in_string = False
327
- escaped = False
328
- end = -1
329
- for index in range(array_start, len(stripped)):
330
- char = stripped[index]
331
- if in_string:
332
- if escaped:
333
- escaped = False
334
- elif char == "\\":
335
- escaped = True
336
- elif char == '"':
337
- in_string = False
338
- continue
339
- if char == '"':
340
- in_string = True
341
- elif char == "[":
342
- depth += 1
343
- elif char == "]":
344
- depth -= 1
345
- if depth == 0:
346
- end = index
347
- break
348
-
349
  if end == -1:
 
 
 
350
  raise SchemaParseError("no balanced JSON array found in model text", text)
351
 
352
  candidate = stripped[array_start : end + 1]
353
  try:
354
  parsed = json.loads(candidate)
355
  except json.JSONDecodeError as exc:
 
 
 
356
  raise SchemaParseError(f"candidate JSON array is invalid: {exc}", text) from exc
357
 
358
  if not isinstance(parsed, list):
 
202
  super().__init__(message)
203
  self.raw_text = raw_text
204
 
205
+ def __reduce__(self) -> tuple[type[SchemaParseError], tuple[str, str]]:
206
+ """Support pickling across process boundaries (for example a GPU worker).
207
 
208
+ The default exception reduction re-invokes the class with ``self.args``
209
+ only, which omits the required ``raw_text`` argument; returning both
210
+ constructor arguments keeps the error fully reconstructable.
211
 
212
+ Returns:
213
+ The ``(callable, args)`` pair pickle uses to rebuild the error.
214
+ """
215
+ return (type(self), (str(self.args[0]) if self.args else "", self.raw_text))
216
+
217
+
218
+ def _find_balanced_end(text: str, start: int, open_char: str, close_char: str) -> int:
219
+ """Find the index of the close delimiter balancing ``text[start]``.
220
+
221
+ Walks the string from ``start`` (which must point at ``open_char``) tracking
222
+ nesting depth while respecting JSON string literals and escape sequences, so
223
+ a delimiter inside a quoted string never affects the depth count.
224
 
225
  Args:
226
+ text: The text to scan.
227
+ start: Index of the opening delimiter to balance.
228
+ open_char: The opening delimiter (for example ``"{"`` or ``"["``).
229
+ close_char: The matching closing delimiter (``"}"`` or ``"]"``).
230
 
231
  Returns:
232
+ The index of the balancing close delimiter, or ``-1`` when the text ends
233
+ before the delimiter closes.
 
 
 
234
  """
 
 
 
 
235
  depth = 0
236
  in_string = False
237
  escaped = False
 
238
  for index in range(start, len(text)):
239
  char = text[index]
240
  if in_string:
 
247
  continue
248
  if char == '"':
249
  in_string = True
250
+ elif char == open_char:
251
  depth += 1
252
+ elif char == close_char:
253
  depth -= 1
254
  if depth == 0:
255
+ return index
256
+ return -1
257
+
258
+
259
+ def extract_first_json_object(text: str) -> dict[str, Any]:
260
+ """Extract the first balanced top-level JSON object from raw model text.
261
+
262
+ Vision-language models frequently wrap their JSON in prose, markdown code
263
+ fences, or trailing commentary. This scans for the first ``{`` and walks the
264
+ string tracking brace depth (while respecting JSON string literals and escape
265
+ sequences) to find the matching close brace, then parses that slice.
266
 
267
+ Args:
268
+ text: Raw model output that contains a JSON object somewhere inside it.
269
+
270
+ Returns:
271
+ The parsed object as a dict.
272
+
273
+ Raises:
274
+ SchemaParseError: If no balanced JSON object is found, or the candidate
275
+ slice is not valid JSON, or the top-level value is not an object.
276
+ """
277
+ start = text.find("{")
278
+ if start == -1:
279
+ raise SchemaParseError("no JSON object found in model text", text)
280
+
281
+ end = _find_balanced_end(text, start, "{", "}")
282
  if end == -1:
283
  raise SchemaParseError("no balanced JSON object found in model text", text)
284
 
 
325
  return text
326
 
327
 
328
+ # Upper bound on elements recovered by ``salvage_finding_list``. A degenerate
329
+ # repetition loop can emit the same element until the token budget is exhausted;
330
+ # the cap bounds the salvage work while comfortably exceeding any realistic
331
+ # finding count for one image.
332
+ _SALVAGE_MAX_ELEMENTS: int = 64
333
+
334
+
335
+ def salvage_finding_list(text: str) -> list[dict[str, Any]]:
336
+ """Recover the complete leading elements of a truncated or malformed array.
337
+
338
+ A generation that exhausts its token budget mid-array leaves the JSON array
339
+ unclosed (or its tail malformed), which would otherwise discard every element
340
+ the model emitted. This walks the array's elements from the first ``[``,
341
+ extracting each balanced ``{...}`` slice and parsing it independently, and
342
+ stops at the first incomplete or invalid element, at the array's closing
343
+ bracket, or after ``_SALVAGE_MAX_ELEMENTS`` elements - so the complete
344
+ leading elements survive a broken tail. Markdown code fences are stripped
345
+ before scanning.
346
+
347
+ Args:
348
+ text: Raw model output containing at least the head of a JSON array.
349
+
350
+ Returns:
351
+ The successfully recovered element dicts, possibly empty.
352
+ """
353
+ stripped = _strip_code_fences(text)
354
+ array_start = stripped.find("[")
355
+ if array_start == -1:
356
+ return []
357
+
358
+ elements: list[dict[str, Any]] = []
359
+ cursor = array_start + 1
360
+ while len(elements) < _SALVAGE_MAX_ELEMENTS:
361
+ element_start = stripped.find("{", cursor)
362
+ if element_start == -1:
363
+ break
364
+ # A closing bracket between elements means the array ended; anything
365
+ # after it lies outside the array and must not be salvaged into it.
366
+ if "]" in stripped[cursor:element_start]:
367
+ break
368
+ element_end = _find_balanced_end(stripped, element_start, "{", "}")
369
+ if element_end == -1:
370
+ break
371
+ candidate = stripped[element_start : element_end + 1]
372
+ try:
373
+ parsed = json.loads(candidate)
374
+ except json.JSONDecodeError:
375
+ break
376
+ if not isinstance(parsed, dict):
377
+ break
378
+ elements.append(parsed)
379
+ cursor = element_end + 1
380
+ return elements
381
+
382
+
383
  def extract_finding_list(text: str) -> list[dict[str, Any]]:
384
  """Extract a JSON array of finding dicts from raw model text.
385
 
386
  MedGemma's native grounding output is a JSON *list* of ``{label, box_2d}``
387
  objects rather than a wrapping object. This finds the first balanced
388
  top-level JSON array and parses it. A bare object is tolerated and wrapped in
389
+ a single-element list. When the array never closes or its slice is invalid
390
+ JSON (a truncated or degenerate generation), the complete leading elements
391
+ are recovered via ``salvage_finding_list`` before declaring failure.
392
 
393
  Args:
394
  text: Raw model output containing a JSON array (or a single object).
 
397
  A list of dicts (one per finding). Non-dict array elements are rejected.
398
 
399
  Raises:
400
+ SchemaParseError: If no balanced JSON array/object is found and nothing
401
+ can be salvaged, the slice is invalid JSON and nothing can be
402
+ salvaged, or a well-formed array contains a non-object element.
403
  """
404
  stripped = _strip_code_fences(text)
405
 
 
410
  if array_start == -1 or (object_start != -1 and object_start < array_start):
411
  return [extract_first_json_object(stripped)]
412
 
413
+ end = _find_balanced_end(stripped, array_start, "[", "]")
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
414
  if end == -1:
415
+ salvaged = salvage_finding_list(text)
416
+ if salvaged:
417
+ return salvaged
418
  raise SchemaParseError("no balanced JSON array found in model text", text)
419
 
420
  candidate = stripped[array_start : end + 1]
421
  try:
422
  parsed = json.loads(candidate)
423
  except json.JSONDecodeError as exc:
424
+ salvaged = salvage_finding_list(text)
425
+ if salvaged:
426
+ return salvaged
427
  raise SchemaParseError(f"candidate JSON array is invalid: {exc}", text) from exc
428
 
429
  if not isinstance(parsed, list):