fix(data): bypass load_dataset() to fix HF Spaces streaming hang and OOM (#16)
Browse files* fix(data): bypass load_dataset() to fix HF Spaces streaming hang and OOM
Two bugs blocked HF Spaces deployment:
1. PyArrow streaming bug (apache/arrow#45214) hangs on parquet iteration
2. load_dataset() full download OOMs on 99GB dataset
Solution:
- Pre-compute 149 case IDs in constants.py (static challenge dataset)
- Use HfFileSystem + pyarrow to download individual cases (~50MB, ~2s)
- Remove all load_dataset() calls from HF path
Fixes dropdown hang and prevents OOM crash on case selection.
* chore: remove dead code and add defensive assertion
- Remove unused create_mock_parquet_data helper function
- Remove unused Any import
- Add assertion to verify ISLES24_CASE_IDS matches ISLES24_NUM_FILES
- docs/specs/08-bug-hf-spaces-dataset-loop.md +199 -126
- src/stroke_deepisles_demo/data/adapter.py +130 -61
- src/stroke_deepisles_demo/data/constants.py +181 -0
- tests/data/test_hf_adapter.py +205 -97
- tests/data/test_loader.py +16 -6
docs/specs/08-bug-hf-spaces-dataset-loop.md
CHANGED
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@@ -1,166 +1,239 @@
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# Bug Spec: HuggingFace Spaces Dataset Loading
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**Status:**
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**Priority:** P0 (Blocks deployment)
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**Branch:** `
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**Date:** 2025-12-08
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##
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1. Application starts successfully (`Running on local URL: http://0.0.0.0:7860`)
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2. Dataset download completes (`Downloading data: 100%|ββββββββββ| 149/149`)
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3. "Generating train split" begins processing
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4. **Container restarts** (new `Application Startup` timestamp)
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5. Cycle repeats indefinitely
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```
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- Processing 149 NIfTI files into HF Dataset format
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- Each file loaded into memory for processing
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- T4-small may have limited RAM
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- **Evidence:** Restart happens during "Generating train split" phase
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- `demo.load()` has internal timeout?
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- 7+ minutes for dataset loading exceeds limit?
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- **Evidence:** UI shows "Preparing Space" during load
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- Even though port 7860 is bound, health check may require response
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- Long-running `demo.load()` blocks event loop?
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- **Evidence:** Container restarts after ~13 min total
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###
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- Our try/except returns `gr.Dropdown(info=f"Error: {e}")`
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- But Gradio shows generic "Error" not our message
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- Something crashes before our handler
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### `src/stroke_deepisles_demo/ui/app.py:34-56`
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```python
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logger.info("Initializing dataset for case selector...")
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case_ids = list_case_ids() # <-- This triggers full dataset load
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if not case_ids:
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return gr.Dropdown(choices=[], info="No cases found in dataset.")
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return gr.Dropdown(
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choices=case_ids,
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value=case_ids[0],
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info="Choose a case from isles24-stroke dataset",
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interactive=True,
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)
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except Exception as e:
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logger.exception("Failed to initialize dataset")
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return gr.Dropdown(choices=[], info=f"Error loading data: {e!s}")
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```
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### Fix 1: Streaming Mode (Recommended)
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```python
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```
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- **Pros:** Zero disk usage, immediate start
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- **Cons:** Can't random access, must iterate
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###
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- Enable HF Spaces Persistent Storage add-on
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- Cache survives restarts
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- **Cons:** Costs money, doesn't fix root cause
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- Run dataset load in background thread
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- Show "Loading..." in dropdown immediately
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- Update dropdown when ready (if ever)
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- Check for OOM killer, SIGKILL, etc.
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3.
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- Does `streaming=True` work with our dataset?
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- Can we still get case IDs?
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- Is there a timeout?
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- Does long-running load block health checks?
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-
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2. Open Logs tab
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3. Watch download complete (5 min)
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4. Watch "Generating train split" start
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5. Observe container restart (~7-13 min mark)
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6. See download start over from 0%
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- This suggests disk space IS a factor
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- Personal space may have same limit but hits it slower
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##
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+
# Bug Spec: HuggingFace Spaces Dataset Loading Issues
|
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+
**Status:** Root Causes Identified β Comprehensive Fix Ready
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**Priority:** P0 (Blocks deployment)
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+
**Branch:** `fix/pipeline-resource-leak`
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**Date:** 2025-12-08
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+
**Updated:** 2025-12-08
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+
## Executive Summary
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+
Two distinct bugs prevent the HuggingFace Spaces deployment from working:
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| Bug | Symptom | Root Cause | Impact | Fix |
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|-----|---------|------------|--------|-----|
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| **#1** | Dropdown never populates | PyArrow streaming bug | App hangs at startup | Pre-computed case IDs |
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+
| **#2** | OOM on case selection | `load_dataset()` downloads 99GB | App crashes on first use | HfFileSystem + pyarrow |
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+
Both bugs stem from fundamental incompatibilities between the `datasets` library and our 99GB parquet dataset on resource-constrained HF Spaces hardware.
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---
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+
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## Bug #1: Streaming Iteration Hang
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### Summary
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+
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The dropdown never populates because `load_dataset(..., streaming=True)` hangs indefinitely on parquet datasets. This is a **known PyArrow bug**, not a HuggingFace datasets bug.
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+
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### The Bug Chain
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+
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1. **Our code** calls `load_dataset("hugging-science/isles24-stroke", streaming=True)`
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2. **HF datasets** internally uses `ParquetFileFragment.to_batches()` for streaming
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3. **PyArrow** hangs when iterating batches from parquet with partial consumption
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+
4. **Result:** Script hangs forever, never returns case IDs
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+
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### Upstream Issues
|
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+
|
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+
- **PyArrow Issue:** [apache/arrow#45214](https://github.com/apache/arrow/issues/45214) - Root cause
|
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+
- **HF Datasets Issue:** [huggingface/datasets#7467](https://github.com/huggingface/datasets/issues/7467) - HF tracking
|
| 39 |
+
- **Status:** Open, no fix ETA
|
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+
- **Maintainer:** @lhoestq (HF datasets core dev) correctly escalated to PyArrow team
|
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+
|
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+
### Minimal Reproduction (Pure PyArrow, no HF)
|
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+
|
| 44 |
+
```python
|
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import pyarrow.dataset as ds
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+
|
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file = "test-00000-of-00003.parquet"
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with open(file, "rb") as f:
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parquet_fragment = ds.ParquetFileFormat().make_fragment(f)
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for record_batch in parquet_fragment.to_batches():
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print(len(record_batch))
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+
break # β Partial consumption causes hang
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# Script hangs here forever
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```
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+
This proves the bug is in **PyArrow's C++ layer**, not HuggingFace datasets.
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+
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### Fix: Pre-computed Case ID List
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+
**Why this is professional, not hacky:**
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|
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+
1. **ISLES24 is a static challenge dataset** - case IDs will never change
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+
2. **Industry standard** - many production ML systems pre-define dataset indices
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+
3. **Zero startup latency** - dropdown populates instantly
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+
4. **No network dependency** - works offline for dropdown population
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+
5. **Bypasses upstream bug** - doesn't depend on PyArrow fix timeline
|
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|
| 68 |
+
---
|
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|
| 70 |
+
## Bug #2: Full Dataset OOM on Case Access
|
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| 72 |
+
### Summary
|
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| 73 |
|
| 74 |
+
Even after fixing Bug #1, the application would crash immediately upon selecting a case. The current `get_case()` implementation calls:
|
| 75 |
|
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| 76 |
```python
|
| 77 |
+
# adapter.py:213
|
| 78 |
+
self._hf_dataset = load_dataset(self.dataset_id, split="train")
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```
|
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|
| 81 |
+
This attempts to download the **entire 99GB dataset** into memory, which OOMs on HF Spaces.
|
| 82 |
+
|
| 83 |
+
### Why This Wasn't Caught
|
| 84 |
+
|
| 85 |
+
The bug document initially focused on the dropdown hang (Bug #1). Bug #2 would only manifest after Bug #1 was fixed and a user actually selected a case.
|
| 86 |
+
|
| 87 |
+
### Investigation Results
|
| 88 |
+
|
| 89 |
+
| Approach | Result | Time | Memory |
|
| 90 |
+
|----------|--------|------|--------|
|
| 91 |
+
| `load_dataset(..., streaming=True)` | **HANGS** | β | N/A |
|
| 92 |
+
| `load_dataset(...)` (full download) | **OOMs** | ~10 min | 99GB+ |
|
| 93 |
+
| `HfFileSystem` + `pyarrow` (single file) | **WORKS** | 1.7s | ~50MB |
|
| 94 |
|
| 95 |
+
### Dataset Structure Discovery
|
| 96 |
+
|
| 97 |
+
Critical finding: Each case is stored in a **separate parquet file**:
|
| 98 |
+
|
| 99 |
+
- **149 parquet files** named `train-00000-of-00149.parquet` through `train-00148-of-00149.parquet`
|
| 100 |
+
- **Each file = one case** (~600-700MB raw data per case)
|
| 101 |
+
- **Schema:** `subject_id`, `dwi`, `adc`, `lesion_mask` (NIfTI bytes stored as binary)
|
| 102 |
+
|
| 103 |
+
This means we can **directly access individual cases** without loading the full dataset!
|
| 104 |
+
|
| 105 |
+
### Fix: Direct Parquet Access via HfFileSystem
|
| 106 |
|
|
|
|
| 107 |
```python
|
| 108 |
+
from huggingface_hub import HfFileSystem
|
| 109 |
+
import pyarrow.parquet as pq
|
| 110 |
|
| 111 |
+
fs = HfFileSystem()
|
| 112 |
+
fpath = f"datasets/{dataset_id}/data/train-{idx:05d}-of-00149.parquet"
|
| 113 |
+
|
| 114 |
+
with fs.open(fpath, 'rb') as f:
|
| 115 |
+
pf = pq.ParquetFile(f)
|
| 116 |
+
table = pf.read(columns=['subject_id', 'dwi', 'adc', 'lesion_mask'])
|
| 117 |
+
# Extract ~50MB for one case in ~2 seconds
|
| 118 |
```
|
|
|
|
|
|
|
| 119 |
|
| 120 |
+
**Benefits:**
|
| 121 |
+
- Downloads only the single case needed (~50MB vs 99GB)
|
| 122 |
+
- Completes in 1.7 seconds (vs hanging or OOM)
|
| 123 |
+
- No dependency on `datasets` library for data access
|
| 124 |
+
- Bypasses both PyArrow streaming bug and memory constraints
|
| 125 |
+
|
| 126 |
+
---
|
| 127 |
+
|
| 128 |
+
## Comprehensive Fix Implementation
|
| 129 |
+
|
| 130 |
+
### 1. Create `constants.py` with case ID β file index mapping
|
| 131 |
|
| 132 |
+
```python
|
| 133 |
+
# src/stroke_deepisles_demo/data/constants.py
|
| 134 |
+
|
| 135 |
+
# Pre-computed case IDs for ISLES24 dataset (static challenge dataset)
|
| 136 |
+
# Extracted via HfFileSystem enumeration on 2025-12-08
|
| 137 |
+
ISLES24_CASE_IDS: tuple[str, ...] = (
|
| 138 |
+
"sub-stroke0001", "sub-stroke0002", ..., "sub-stroke0189"
|
| 139 |
+
)
|
| 140 |
+
|
| 141 |
+
# Mapping from case ID to parquet file index (0-indexed)
|
| 142 |
+
ISLES24_CASE_INDEX: dict[str, int] = {
|
| 143 |
+
case_id: idx for idx, case_id in enumerate(ISLES24_CASE_IDS)
|
| 144 |
+
}
|
| 145 |
+
```
|
| 146 |
|
| 147 |
+
### 2. Rewrite `HuggingFaceDataset.get_case()` to use HfFileSystem
|
|
|
|
|
|
|
|
|
|
| 148 |
|
| 149 |
+
Replace `load_dataset()` call with direct parquet access:
|
|
|
|
|
|
|
|
|
|
| 150 |
|
| 151 |
+
```python
|
| 152 |
+
def get_case(self, case_id: str | int) -> CaseFiles:
|
| 153 |
+
from huggingface_hub import HfFileSystem
|
| 154 |
+
import pyarrow.parquet as pq
|
| 155 |
|
| 156 |
+
idx = self._case_index[case_id]
|
| 157 |
+
fpath = f"datasets/{self.dataset_id}/data/train-{idx:05d}-of-00149.parquet"
|
|
|
|
| 158 |
|
| 159 |
+
fs = HfFileSystem()
|
| 160 |
+
with fs.open(fpath, 'rb') as f:
|
| 161 |
+
table = pq.ParquetFile(f).read(columns=['dwi', 'adc', 'lesion_mask'])
|
| 162 |
+
# Extract bytes and write to temp files...
|
| 163 |
+
```
|
| 164 |
|
| 165 |
+
### 3. Remove all `load_dataset()` calls from HuggingFace path
|
|
|
|
|
|
|
| 166 |
|
| 167 |
+
The `datasets` library is completely bypassed for the HuggingFace workflow.
|
|
|
|
|
|
|
| 168 |
|
| 169 |
+
---
|
| 170 |
|
| 171 |
+
## All 149 Case IDs (Extracted via HfFileSystem)
|
|
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|
|
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|
|
| 172 |
|
| 173 |
+
```
|
| 174 |
+
sub-stroke0001, sub-stroke0002, sub-stroke0003, sub-stroke0004, sub-stroke0005,
|
| 175 |
+
sub-stroke0006, sub-stroke0007, sub-stroke0008, sub-stroke0009, sub-stroke0010,
|
| 176 |
+
sub-stroke0011, sub-stroke0012, sub-stroke0013, sub-stroke0014, sub-stroke0015,
|
| 177 |
+
sub-stroke0016, sub-stroke0017, sub-stroke0019, sub-stroke0020, sub-stroke0021,
|
| 178 |
+
sub-stroke0022, sub-stroke0025, sub-stroke0026, sub-stroke0027, sub-stroke0028,
|
| 179 |
+
sub-stroke0030, sub-stroke0033, sub-stroke0036, sub-stroke0037, sub-stroke0038,
|
| 180 |
+
sub-stroke0040, sub-stroke0043, sub-stroke0045, sub-stroke0047, sub-stroke0048,
|
| 181 |
+
sub-stroke0049, sub-stroke0052, sub-stroke0053, sub-stroke0054, sub-stroke0055,
|
| 182 |
+
sub-stroke0057, sub-stroke0062, sub-stroke0066, sub-stroke0068, sub-stroke0070,
|
| 183 |
+
sub-stroke0071, sub-stroke0073, sub-stroke0074, sub-stroke0075, sub-stroke0076,
|
| 184 |
+
sub-stroke0077, sub-stroke0078, sub-stroke0079, sub-stroke0080, sub-stroke0081,
|
| 185 |
+
sub-stroke0082, sub-stroke0083, sub-stroke0084, sub-stroke0085, sub-stroke0086,
|
| 186 |
+
sub-stroke0087, sub-stroke0088, sub-stroke0089, sub-stroke0090, sub-stroke0091,
|
| 187 |
+
sub-stroke0092, sub-stroke0093, sub-stroke0094, sub-stroke0095, sub-stroke0096,
|
| 188 |
+
sub-stroke0097, sub-stroke0098, sub-stroke0099, sub-stroke0100, sub-stroke0101,
|
| 189 |
+
sub-stroke0102, sub-stroke0103, sub-stroke0104, sub-stroke0105, sub-stroke0106,
|
| 190 |
+
sub-stroke0107, sub-stroke0108, sub-stroke0109, sub-stroke0110, sub-stroke0111,
|
| 191 |
+
sub-stroke0112, sub-stroke0113, sub-stroke0114, sub-stroke0115, sub-stroke0116,
|
| 192 |
+
sub-stroke0117, sub-stroke0118, sub-stroke0119, sub-stroke0133, sub-stroke0134,
|
| 193 |
+
sub-stroke0135, sub-stroke0136, sub-stroke0137, sub-stroke0138, sub-stroke0139,
|
| 194 |
+
sub-stroke0140, sub-stroke0141, sub-stroke0142, sub-stroke0143, sub-stroke0144,
|
| 195 |
+
sub-stroke0145, sub-stroke0146, sub-stroke0147, sub-stroke0148, sub-stroke0149,
|
| 196 |
+
sub-stroke0150, sub-stroke0151, sub-stroke0152, sub-stroke0153, sub-stroke0154,
|
| 197 |
+
sub-stroke0155, sub-stroke0156, sub-stroke0157, sub-stroke0158, sub-stroke0159,
|
| 198 |
+
sub-stroke0161, sub-stroke0162, sub-stroke0163, sub-stroke0164, sub-stroke0165,
|
| 199 |
+
sub-stroke0166, sub-stroke0167, sub-stroke0168, sub-stroke0169, sub-stroke0170,
|
| 200 |
+
sub-stroke0171, sub-stroke0172, sub-stroke0173, sub-stroke0174, sub-stroke0175,
|
| 201 |
+
sub-stroke0176, sub-stroke0177, sub-stroke0178, sub-stroke0179, sub-stroke0180,
|
| 202 |
+
sub-stroke0181, sub-stroke0182, sub-stroke0183, sub-stroke0184, sub-stroke0185,
|
| 203 |
+
sub-stroke0186, sub-stroke0187, sub-stroke0188, sub-stroke0189
|
| 204 |
+
```
|
| 205 |
|
| 206 |
+
---
|
|
|
|
|
|
|
| 207 |
|
| 208 |
+
## Environment
|
| 209 |
|
| 210 |
+
- **Space:** `VibecoderMcSwaggins/stroke-deepisles-demo`
|
| 211 |
+
- **Hardware:** T4-small GPU (limited memory)
|
| 212 |
+
- **Dataset:** `hugging-science/isles24-stroke` (149 parquet files, ~99GB total)
|
| 213 |
+
- **Dependencies:**
|
| 214 |
+
- `datasets @ git+https://github.com/CloseChoice/datasets.git@c1c15aa...` (fork with Nifti support)
|
| 215 |
+
- `pyarrow` (inherited, contains Bug #1)
|
| 216 |
+
- `huggingface_hub` (used for Bug #2 fix)
|
| 217 |
+
|
| 218 |
+
---
|
| 219 |
+
|
| 220 |
+
## References
|
| 221 |
+
|
| 222 |
+
- [PyArrow Issue #45214](https://github.com/apache/arrow/issues/45214) - Bug #1 root cause
|
| 223 |
+
- [PyArrow Issue #43604](https://github.com/apache/arrow/issues/43604) - Related hang issue
|
| 224 |
+
- [HF Datasets Issue #7467](https://github.com/huggingface/datasets/issues/7467) - HF tracking issue
|
| 225 |
+
- [HF Datasets Issue #7357](https://github.com/huggingface/datasets/issues/7357) - Original report
|
| 226 |
+
|
| 227 |
+
---
|
| 228 |
+
|
| 229 |
+
## Checklist
|
| 230 |
+
|
| 231 |
+
1. [x] Identify Bug #1 root cause (PyArrow streaming hang)
|
| 232 |
+
2. [x] Identify Bug #2 root cause (OOM on full download)
|
| 233 |
+
3. [x] Extract all 149 case IDs via HfFileSystem
|
| 234 |
+
4. [x] Validate direct parquet access works (1.7s per case)
|
| 235 |
+
5. [x] Implement pre-computed case ID list (`constants.py`)
|
| 236 |
+
6. [x] Rewrite `get_case()` to use HfFileSystem + pyarrow
|
| 237 |
+
7. [x] Update tests
|
| 238 |
+
8. [ ] Test on HF Spaces
|
| 239 |
+
9. [ ] Monitor PyArrow issue for upstream fix
|
src/stroke_deepisles_demo/data/adapter.py
CHANGED
|
@@ -7,7 +7,7 @@ import shutil
|
|
| 7 |
import tempfile
|
| 8 |
from dataclasses import dataclass, field
|
| 9 |
from pathlib import Path
|
| 10 |
-
from typing import TYPE_CHECKING,
|
| 11 |
|
| 12 |
from stroke_deepisles_demo.core.exceptions import DataLoadError
|
| 13 |
from stroke_deepisles_demo.core.logging import get_logger
|
|
@@ -145,11 +145,16 @@ class HuggingFaceDataset:
|
|
| 145 |
"""Dataset adapter for HuggingFace ISLES24 dataset.
|
| 146 |
|
| 147 |
Wraps the HuggingFace dataset and provides the same interface as LocalDataset.
|
| 148 |
-
When get_case() is called,
|
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|
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|
|
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|
|
| 149 |
|
| 150 |
IMPORTANT: Use as a context manager to ensure temp files are cleaned up:
|
| 151 |
|
| 152 |
-
with
|
| 153 |
case = ds.get_case(0)
|
| 154 |
# ... process case ...
|
| 155 |
# temp files automatically cleaned up
|
|
@@ -158,8 +163,8 @@ class HuggingFaceDataset:
|
|
| 158 |
"""
|
| 159 |
|
| 160 |
dataset_id: str
|
| 161 |
-
_hf_dataset: Any = field(repr=False)
|
| 162 |
_case_ids: list[str] = field(default_factory=list)
|
|
|
|
| 163 |
_temp_dir: Path | None = field(default=None, repr=False)
|
| 164 |
_cached_cases: dict[str, CaseFiles] = field(default_factory=dict, repr=False)
|
| 165 |
|
|
@@ -182,18 +187,27 @@ class HuggingFaceDataset:
|
|
| 182 |
def get_case(self, case_id: str | int) -> CaseFiles:
|
| 183 |
"""Get files for a case by ID or index.
|
| 184 |
|
| 185 |
-
|
| 186 |
-
|
|
|
|
|
|
|
|
|
|
| 187 |
|
| 188 |
Raises:
|
| 189 |
-
|
|
|
|
| 190 |
"""
|
|
|
|
| 191 |
if isinstance(case_id, int):
|
| 192 |
-
|
| 193 |
-
|
|
|
|
|
|
|
| 194 |
else:
|
| 195 |
subject_id = case_id
|
| 196 |
-
|
|
|
|
|
|
|
| 197 |
|
| 198 |
# Return cached case if already materialized
|
| 199 |
if subject_id in self._cached_cases:
|
|
@@ -204,17 +218,9 @@ class HuggingFaceDataset:
|
|
| 204 |
self._temp_dir = Path(tempfile.mkdtemp(prefix="isles24_hf_"))
|
| 205 |
logger.debug("Created temp directory: %s", self._temp_dir)
|
| 206 |
|
| 207 |
-
#
|
| 208 |
-
|
| 209 |
-
|
| 210 |
-
from datasets import load_dataset
|
| 211 |
-
|
| 212 |
-
logger.info("Loading full dataset for case access (lazy load)...")
|
| 213 |
-
self._hf_dataset = load_dataset(self.dataset_id, split="train")
|
| 214 |
-
logger.info("Full dataset loaded: %d examples", len(self._hf_dataset))
|
| 215 |
-
|
| 216 |
-
# Get the HuggingFace example
|
| 217 |
-
example = self._hf_dataset[idx]
|
| 218 |
|
| 219 |
# Create case subdirectory
|
| 220 |
case_dir = self._temp_dir / subject_id
|
|
@@ -225,19 +231,9 @@ class HuggingFaceDataset:
|
|
| 225 |
adc_path = case_dir / f"{subject_id}_ses-02_adc.nii.gz"
|
| 226 |
mask_path = case_dir / f"{subject_id}_ses-02_lesion-msk.nii.gz"
|
| 227 |
|
| 228 |
-
# Extract bytes with defensive error handling
|
| 229 |
-
try:
|
| 230 |
-
dwi_bytes = example["dwi"]["bytes"]
|
| 231 |
-
adc_bytes = example["adc"]["bytes"]
|
| 232 |
-
except (KeyError, TypeError) as e:
|
| 233 |
-
raise DataLoadError(
|
| 234 |
-
f"Malformed HuggingFace data for {subject_id}: missing 'dwi' or 'adc' bytes. "
|
| 235 |
-
f"The dataset schema may have changed. Error: {e}"
|
| 236 |
-
) from e
|
| 237 |
-
|
| 238 |
# Write the gzipped NIfTI bytes
|
| 239 |
-
dwi_path.write_bytes(dwi_bytes)
|
| 240 |
-
adc_path.write_bytes(adc_bytes)
|
| 241 |
|
| 242 |
case_files: CaseFiles = {
|
| 243 |
"dwi": dwi_path,
|
|
@@ -245,20 +241,89 @@ class HuggingFaceDataset:
|
|
| 245 |
}
|
| 246 |
|
| 247 |
# Write lesion mask if available
|
| 248 |
-
|
| 249 |
-
|
| 250 |
-
|
| 251 |
-
mask_path.write_bytes(mask_data["bytes"])
|
| 252 |
-
case_files["ground_truth"] = mask_path
|
| 253 |
-
except (KeyError, TypeError):
|
| 254 |
-
# Mask is optional, log and continue
|
| 255 |
-
logger.debug("No lesion mask available for %s", subject_id)
|
| 256 |
|
| 257 |
# Cache for subsequent calls
|
| 258 |
self._cached_cases[subject_id] = case_files
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 259 |
|
| 260 |
return case_files
|
| 261 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 262 |
def cleanup(self) -> None:
|
| 263 |
"""Remove temp directory and clear cache."""
|
| 264 |
if self._temp_dir and self._temp_dir.exists():
|
|
@@ -270,10 +335,11 @@ class HuggingFaceDataset:
|
|
| 270 |
|
| 271 |
def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
|
| 272 |
"""
|
| 273 |
-
|
| 274 |
|
| 275 |
-
Uses
|
| 276 |
-
|
|
|
|
| 277 |
|
| 278 |
Args:
|
| 279 |
dataset_id: HuggingFace dataset identifier (e.g., "hugging-science/isles24-stroke")
|
|
@@ -281,26 +347,29 @@ def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
|
|
| 281 |
Returns:
|
| 282 |
HuggingFaceDataset providing case access
|
| 283 |
"""
|
| 284 |
-
from
|
| 285 |
-
|
| 286 |
-
|
| 287 |
-
|
| 288 |
-
|
| 289 |
-
# This avoids the "Generating train split" phase that hangs on HF Spaces
|
| 290 |
-
logger.info("Streaming dataset to enumerate case IDs...")
|
| 291 |
-
streaming_ds = load_dataset(dataset_id, split="train", streaming=True)
|
| 292 |
|
| 293 |
-
#
|
| 294 |
-
|
| 295 |
-
|
| 296 |
-
|
| 297 |
-
|
|
|
|
|
|
|
|
|
|
| 298 |
|
| 299 |
-
logger.info(
|
|
|
|
|
|
|
|
|
|
|
|
|
| 300 |
|
| 301 |
-
# Return dataset with lazy loading - full data downloaded only when get_case() called
|
| 302 |
return HuggingFaceDataset(
|
| 303 |
dataset_id=dataset_id,
|
| 304 |
-
|
| 305 |
-
|
| 306 |
)
|
|
|
|
| 7 |
import tempfile
|
| 8 |
from dataclasses import dataclass, field
|
| 9 |
from pathlib import Path
|
| 10 |
+
from typing import TYPE_CHECKING, Self
|
| 11 |
|
| 12 |
from stroke_deepisles_demo.core.exceptions import DataLoadError
|
| 13 |
from stroke_deepisles_demo.core.logging import get_logger
|
|
|
|
| 145 |
"""Dataset adapter for HuggingFace ISLES24 dataset.
|
| 146 |
|
| 147 |
Wraps the HuggingFace dataset and provides the same interface as LocalDataset.
|
| 148 |
+
When get_case() is called, downloads NIfTI bytes from individual parquet files
|
| 149 |
+
and writes them to temp files.
|
| 150 |
+
|
| 151 |
+
This implementation bypasses `load_dataset()` entirely to avoid:
|
| 152 |
+
1. PyArrow streaming bug (apache/arrow#45214) that hangs on parquet iteration
|
| 153 |
+
2. Memory issues from downloading the full 99GB dataset
|
| 154 |
|
| 155 |
IMPORTANT: Use as a context manager to ensure temp files are cleaned up:
|
| 156 |
|
| 157 |
+
with build_huggingface_dataset(dataset_id) as ds:
|
| 158 |
case = ds.get_case(0)
|
| 159 |
# ... process case ...
|
| 160 |
# temp files automatically cleaned up
|
|
|
|
| 163 |
"""
|
| 164 |
|
| 165 |
dataset_id: str
|
|
|
|
| 166 |
_case_ids: list[str] = field(default_factory=list)
|
| 167 |
+
_case_index: dict[str, int] = field(default_factory=dict)
|
| 168 |
_temp_dir: Path | None = field(default=None, repr=False)
|
| 169 |
_cached_cases: dict[str, CaseFiles] = field(default_factory=dict, repr=False)
|
| 170 |
|
|
|
|
| 187 |
def get_case(self, case_id: str | int) -> CaseFiles:
|
| 188 |
"""Get files for a case by ID or index.
|
| 189 |
|
| 190 |
+
Downloads NIfTI bytes from the individual parquet file for this case
|
| 191 |
+
and writes to temp files. Returns cached paths on subsequent calls.
|
| 192 |
+
|
| 193 |
+
This uses HfFileSystem + pyarrow to download only the single case (~50MB)
|
| 194 |
+
instead of the full dataset (99GB), completing in ~2 seconds.
|
| 195 |
|
| 196 |
Raises:
|
| 197 |
+
DataLoadError: If HuggingFace data is malformed or missing required fields.
|
| 198 |
+
KeyError: If case_id is not found in the dataset.
|
| 199 |
"""
|
| 200 |
+
# Resolve case_id to subject_id and file index
|
| 201 |
if isinstance(case_id, int):
|
| 202 |
+
if case_id < 0 or case_id >= len(self._case_ids):
|
| 203 |
+
raise IndexError(f"Case index {case_id} out of range [0, {len(self._case_ids)})")
|
| 204 |
+
subject_id = self._case_ids[case_id]
|
| 205 |
+
file_idx = case_id
|
| 206 |
else:
|
| 207 |
subject_id = case_id
|
| 208 |
+
if subject_id not in self._case_index:
|
| 209 |
+
raise KeyError(f"Case ID '{subject_id}' not found in dataset")
|
| 210 |
+
file_idx = self._case_index[subject_id]
|
| 211 |
|
| 212 |
# Return cached case if already materialized
|
| 213 |
if subject_id in self._cached_cases:
|
|
|
|
| 218 |
self._temp_dir = Path(tempfile.mkdtemp(prefix="isles24_hf_"))
|
| 219 |
logger.debug("Created temp directory: %s", self._temp_dir)
|
| 220 |
|
| 221 |
+
# Download case data from individual parquet file
|
| 222 |
+
logger.info("Downloading case %s from HuggingFace...", subject_id)
|
| 223 |
+
case_data = self._download_case_from_parquet(file_idx, subject_id)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 224 |
|
| 225 |
# Create case subdirectory
|
| 226 |
case_dir = self._temp_dir / subject_id
|
|
|
|
| 231 |
adc_path = case_dir / f"{subject_id}_ses-02_adc.nii.gz"
|
| 232 |
mask_path = case_dir / f"{subject_id}_ses-02_lesion-msk.nii.gz"
|
| 233 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 234 |
# Write the gzipped NIfTI bytes
|
| 235 |
+
dwi_path.write_bytes(case_data["dwi_bytes"])
|
| 236 |
+
adc_path.write_bytes(case_data["adc_bytes"])
|
| 237 |
|
| 238 |
case_files: CaseFiles = {
|
| 239 |
"dwi": dwi_path,
|
|
|
|
| 241 |
}
|
| 242 |
|
| 243 |
# Write lesion mask if available
|
| 244 |
+
if case_data.get("mask_bytes"):
|
| 245 |
+
mask_path.write_bytes(case_data["mask_bytes"])
|
| 246 |
+
case_files["ground_truth"] = mask_path
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 247 |
|
| 248 |
# Cache for subsequent calls
|
| 249 |
self._cached_cases[subject_id] = case_files
|
| 250 |
+
logger.info(
|
| 251 |
+
"Case %s ready: DWI=%.1fMB, ADC=%.1fMB",
|
| 252 |
+
subject_id,
|
| 253 |
+
len(case_data["dwi_bytes"]) / 1024 / 1024,
|
| 254 |
+
len(case_data["adc_bytes"]) / 1024 / 1024,
|
| 255 |
+
)
|
| 256 |
|
| 257 |
return case_files
|
| 258 |
|
| 259 |
+
def _download_case_from_parquet(self, file_idx: int, subject_id: str) -> dict[str, bytes]:
|
| 260 |
+
"""Download case data directly from individual parquet file.
|
| 261 |
+
|
| 262 |
+
Uses HfFileSystem + pyarrow to read only the columns we need from
|
| 263 |
+
a single parquet file, avoiding the need to download the full dataset.
|
| 264 |
+
|
| 265 |
+
Args:
|
| 266 |
+
file_idx: Index of the parquet file (0-148)
|
| 267 |
+
subject_id: Expected subject ID (for validation)
|
| 268 |
+
|
| 269 |
+
Returns:
|
| 270 |
+
Dict with dwi_bytes, adc_bytes, and optionally mask_bytes
|
| 271 |
+
"""
|
| 272 |
+
import pyarrow.parquet as pq # type: ignore[import-untyped]
|
| 273 |
+
from huggingface_hub import HfFileSystem
|
| 274 |
+
|
| 275 |
+
from stroke_deepisles_demo.data.constants import ISLES24_NUM_FILES
|
| 276 |
+
|
| 277 |
+
# Construct path to the specific parquet file
|
| 278 |
+
fpath = f"datasets/{self.dataset_id}/data/train-{file_idx:05d}-of-{ISLES24_NUM_FILES:05d}.parquet"
|
| 279 |
+
|
| 280 |
+
try:
|
| 281 |
+
fs = HfFileSystem()
|
| 282 |
+
with fs.open(fpath, "rb") as f:
|
| 283 |
+
pf = pq.ParquetFile(f)
|
| 284 |
+
# Read only the columns we need
|
| 285 |
+
table = pf.read(columns=["subject_id", "dwi", "adc", "lesion_mask"])
|
| 286 |
+
df = table.to_pandas()
|
| 287 |
+
|
| 288 |
+
if len(df) != 1:
|
| 289 |
+
raise DataLoadError(f"Expected 1 row in parquet file, got {len(df)}: {fpath}")
|
| 290 |
+
|
| 291 |
+
row = df.iloc[0]
|
| 292 |
+
|
| 293 |
+
# Validate subject_id matches
|
| 294 |
+
actual_subject_id = row["subject_id"]
|
| 295 |
+
if actual_subject_id != subject_id:
|
| 296 |
+
raise DataLoadError(
|
| 297 |
+
f"Subject ID mismatch: expected {subject_id}, got {actual_subject_id} in {fpath}"
|
| 298 |
+
)
|
| 299 |
+
|
| 300 |
+
# Extract bytes with defensive error handling
|
| 301 |
+
try:
|
| 302 |
+
dwi_bytes = row["dwi"]["bytes"]
|
| 303 |
+
adc_bytes = row["adc"]["bytes"]
|
| 304 |
+
except (KeyError, TypeError) as e:
|
| 305 |
+
raise DataLoadError(
|
| 306 |
+
f"Malformed HuggingFace data for {subject_id}: missing 'dwi' or 'adc' bytes. "
|
| 307 |
+
f"The dataset schema may have changed. Error: {e}"
|
| 308 |
+
) from e
|
| 309 |
+
|
| 310 |
+
result: dict[str, bytes] = {
|
| 311 |
+
"dwi_bytes": dwi_bytes,
|
| 312 |
+
"adc_bytes": adc_bytes,
|
| 313 |
+
}
|
| 314 |
+
|
| 315 |
+
# Extract mask if available
|
| 316 |
+
mask_data = row.get("lesion_mask")
|
| 317 |
+
if mask_data is not None and isinstance(mask_data, dict) and mask_data.get("bytes"):
|
| 318 |
+
result["mask_bytes"] = mask_data["bytes"]
|
| 319 |
+
|
| 320 |
+
return result
|
| 321 |
+
|
| 322 |
+
except Exception as e:
|
| 323 |
+
if isinstance(e, DataLoadError):
|
| 324 |
+
raise
|
| 325 |
+
raise DataLoadError(f"Failed to download case {subject_id} from {fpath}: {e}") from e
|
| 326 |
+
|
| 327 |
def cleanup(self) -> None:
|
| 328 |
"""Remove temp directory and clear cache."""
|
| 329 |
if self._temp_dir and self._temp_dir.exists():
|
|
|
|
| 335 |
|
| 336 |
def build_huggingface_dataset(dataset_id: str) -> HuggingFaceDataset:
|
| 337 |
"""
|
| 338 |
+
Build ISLES24 dataset adapter for HuggingFace Hub.
|
| 339 |
|
| 340 |
+
Uses pre-computed case IDs to avoid streaming enumeration (which hangs
|
| 341 |
+
due to PyArrow bug apache/arrow#45214). Actual data is downloaded lazily
|
| 342 |
+
from individual parquet files when get_case() is called.
|
| 343 |
|
| 344 |
Args:
|
| 345 |
dataset_id: HuggingFace dataset identifier (e.g., "hugging-science/isles24-stroke")
|
|
|
|
| 347 |
Returns:
|
| 348 |
HuggingFaceDataset providing case access
|
| 349 |
"""
|
| 350 |
+
from stroke_deepisles_demo.data.constants import (
|
| 351 |
+
ISLES24_CASE_IDS,
|
| 352 |
+
ISLES24_CASE_INDEX,
|
| 353 |
+
ISLES24_DATASET_ID,
|
| 354 |
+
)
|
|
|
|
|
|
|
|
|
|
| 355 |
|
| 356 |
+
# Validate dataset_id matches our pre-computed constants
|
| 357 |
+
if dataset_id != ISLES24_DATASET_ID:
|
| 358 |
+
logger.warning(
|
| 359 |
+
"Dataset ID '%s' does not match pre-computed constants for '%s'. "
|
| 360 |
+
"Case IDs may be incorrect.",
|
| 361 |
+
dataset_id,
|
| 362 |
+
ISLES24_DATASET_ID,
|
| 363 |
+
)
|
| 364 |
|
| 365 |
+
logger.info(
|
| 366 |
+
"Building HuggingFace dataset adapter: %s (%d cases, pre-computed)",
|
| 367 |
+
dataset_id,
|
| 368 |
+
len(ISLES24_CASE_IDS),
|
| 369 |
+
)
|
| 370 |
|
|
|
|
| 371 |
return HuggingFaceDataset(
|
| 372 |
dataset_id=dataset_id,
|
| 373 |
+
_case_ids=list(ISLES24_CASE_IDS),
|
| 374 |
+
_case_index=dict(ISLES24_CASE_INDEX),
|
| 375 |
)
|
src/stroke_deepisles_demo/data/constants.py
ADDED
|
@@ -0,0 +1,181 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""Pre-computed constants for ISLES24 dataset.
|
| 2 |
+
|
| 3 |
+
The ISLES24 challenge dataset is static (case IDs will never change).
|
| 4 |
+
Pre-computing these values avoids:
|
| 5 |
+
1. PyArrow streaming bug (apache/arrow#45214) that hangs on parquet iteration
|
| 6 |
+
2. Memory issues from downloading the full 99GB dataset
|
| 7 |
+
|
| 8 |
+
See docs/specs/08-bug-hf-spaces-dataset-loop.md for full investigation.
|
| 9 |
+
"""
|
| 10 |
+
|
| 11 |
+
# Pre-computed case IDs for ISLES24 dataset
|
| 12 |
+
# Extracted via HfFileSystem enumeration on 2025-12-08
|
| 13 |
+
# Order matches parquet file indices (train-00000-of-00149.parquet = index 0)
|
| 14 |
+
ISLES24_CASE_IDS: tuple[str, ...] = (
|
| 15 |
+
"sub-stroke0001",
|
| 16 |
+
"sub-stroke0002",
|
| 17 |
+
"sub-stroke0003",
|
| 18 |
+
"sub-stroke0004",
|
| 19 |
+
"sub-stroke0005",
|
| 20 |
+
"sub-stroke0006",
|
| 21 |
+
"sub-stroke0007",
|
| 22 |
+
"sub-stroke0008",
|
| 23 |
+
"sub-stroke0009",
|
| 24 |
+
"sub-stroke0010",
|
| 25 |
+
"sub-stroke0011",
|
| 26 |
+
"sub-stroke0012",
|
| 27 |
+
"sub-stroke0013",
|
| 28 |
+
"sub-stroke0014",
|
| 29 |
+
"sub-stroke0015",
|
| 30 |
+
"sub-stroke0016",
|
| 31 |
+
"sub-stroke0017",
|
| 32 |
+
"sub-stroke0019",
|
| 33 |
+
"sub-stroke0020",
|
| 34 |
+
"sub-stroke0021",
|
| 35 |
+
"sub-stroke0022",
|
| 36 |
+
"sub-stroke0025",
|
| 37 |
+
"sub-stroke0026",
|
| 38 |
+
"sub-stroke0027",
|
| 39 |
+
"sub-stroke0028",
|
| 40 |
+
"sub-stroke0030",
|
| 41 |
+
"sub-stroke0033",
|
| 42 |
+
"sub-stroke0036",
|
| 43 |
+
"sub-stroke0037",
|
| 44 |
+
"sub-stroke0038",
|
| 45 |
+
"sub-stroke0040",
|
| 46 |
+
"sub-stroke0043",
|
| 47 |
+
"sub-stroke0045",
|
| 48 |
+
"sub-stroke0047",
|
| 49 |
+
"sub-stroke0048",
|
| 50 |
+
"sub-stroke0049",
|
| 51 |
+
"sub-stroke0052",
|
| 52 |
+
"sub-stroke0053",
|
| 53 |
+
"sub-stroke0054",
|
| 54 |
+
"sub-stroke0055",
|
| 55 |
+
"sub-stroke0057",
|
| 56 |
+
"sub-stroke0062",
|
| 57 |
+
"sub-stroke0066",
|
| 58 |
+
"sub-stroke0068",
|
| 59 |
+
"sub-stroke0070",
|
| 60 |
+
"sub-stroke0071",
|
| 61 |
+
"sub-stroke0073",
|
| 62 |
+
"sub-stroke0074",
|
| 63 |
+
"sub-stroke0075",
|
| 64 |
+
"sub-stroke0076",
|
| 65 |
+
"sub-stroke0077",
|
| 66 |
+
"sub-stroke0078",
|
| 67 |
+
"sub-stroke0079",
|
| 68 |
+
"sub-stroke0080",
|
| 69 |
+
"sub-stroke0081",
|
| 70 |
+
"sub-stroke0082",
|
| 71 |
+
"sub-stroke0083",
|
| 72 |
+
"sub-stroke0084",
|
| 73 |
+
"sub-stroke0085",
|
| 74 |
+
"sub-stroke0086",
|
| 75 |
+
"sub-stroke0087",
|
| 76 |
+
"sub-stroke0088",
|
| 77 |
+
"sub-stroke0089",
|
| 78 |
+
"sub-stroke0090",
|
| 79 |
+
"sub-stroke0091",
|
| 80 |
+
"sub-stroke0092",
|
| 81 |
+
"sub-stroke0093",
|
| 82 |
+
"sub-stroke0094",
|
| 83 |
+
"sub-stroke0095",
|
| 84 |
+
"sub-stroke0096",
|
| 85 |
+
"sub-stroke0097",
|
| 86 |
+
"sub-stroke0098",
|
| 87 |
+
"sub-stroke0099",
|
| 88 |
+
"sub-stroke0100",
|
| 89 |
+
"sub-stroke0101",
|
| 90 |
+
"sub-stroke0102",
|
| 91 |
+
"sub-stroke0103",
|
| 92 |
+
"sub-stroke0104",
|
| 93 |
+
"sub-stroke0105",
|
| 94 |
+
"sub-stroke0106",
|
| 95 |
+
"sub-stroke0107",
|
| 96 |
+
"sub-stroke0108",
|
| 97 |
+
"sub-stroke0109",
|
| 98 |
+
"sub-stroke0110",
|
| 99 |
+
"sub-stroke0111",
|
| 100 |
+
"sub-stroke0112",
|
| 101 |
+
"sub-stroke0113",
|
| 102 |
+
"sub-stroke0114",
|
| 103 |
+
"sub-stroke0115",
|
| 104 |
+
"sub-stroke0116",
|
| 105 |
+
"sub-stroke0117",
|
| 106 |
+
"sub-stroke0118",
|
| 107 |
+
"sub-stroke0119",
|
| 108 |
+
"sub-stroke0133",
|
| 109 |
+
"sub-stroke0134",
|
| 110 |
+
"sub-stroke0135",
|
| 111 |
+
"sub-stroke0136",
|
| 112 |
+
"sub-stroke0137",
|
| 113 |
+
"sub-stroke0138",
|
| 114 |
+
"sub-stroke0139",
|
| 115 |
+
"sub-stroke0140",
|
| 116 |
+
"sub-stroke0141",
|
| 117 |
+
"sub-stroke0142",
|
| 118 |
+
"sub-stroke0143",
|
| 119 |
+
"sub-stroke0144",
|
| 120 |
+
"sub-stroke0145",
|
| 121 |
+
"sub-stroke0146",
|
| 122 |
+
"sub-stroke0147",
|
| 123 |
+
"sub-stroke0148",
|
| 124 |
+
"sub-stroke0149",
|
| 125 |
+
"sub-stroke0150",
|
| 126 |
+
"sub-stroke0151",
|
| 127 |
+
"sub-stroke0152",
|
| 128 |
+
"sub-stroke0153",
|
| 129 |
+
"sub-stroke0154",
|
| 130 |
+
"sub-stroke0155",
|
| 131 |
+
"sub-stroke0156",
|
| 132 |
+
"sub-stroke0157",
|
| 133 |
+
"sub-stroke0158",
|
| 134 |
+
"sub-stroke0159",
|
| 135 |
+
"sub-stroke0161",
|
| 136 |
+
"sub-stroke0162",
|
| 137 |
+
"sub-stroke0163",
|
| 138 |
+
"sub-stroke0164",
|
| 139 |
+
"sub-stroke0165",
|
| 140 |
+
"sub-stroke0166",
|
| 141 |
+
"sub-stroke0167",
|
| 142 |
+
"sub-stroke0168",
|
| 143 |
+
"sub-stroke0169",
|
| 144 |
+
"sub-stroke0170",
|
| 145 |
+
"sub-stroke0171",
|
| 146 |
+
"sub-stroke0172",
|
| 147 |
+
"sub-stroke0173",
|
| 148 |
+
"sub-stroke0174",
|
| 149 |
+
"sub-stroke0175",
|
| 150 |
+
"sub-stroke0176",
|
| 151 |
+
"sub-stroke0177",
|
| 152 |
+
"sub-stroke0178",
|
| 153 |
+
"sub-stroke0179",
|
| 154 |
+
"sub-stroke0180",
|
| 155 |
+
"sub-stroke0181",
|
| 156 |
+
"sub-stroke0182",
|
| 157 |
+
"sub-stroke0183",
|
| 158 |
+
"sub-stroke0184",
|
| 159 |
+
"sub-stroke0185",
|
| 160 |
+
"sub-stroke0186",
|
| 161 |
+
"sub-stroke0187",
|
| 162 |
+
"sub-stroke0188",
|
| 163 |
+
"sub-stroke0189",
|
| 164 |
+
)
|
| 165 |
+
|
| 166 |
+
# Mapping from case ID to parquet file index (0-indexed)
|
| 167 |
+
# train-00000-of-00149.parquet contains sub-stroke0001
|
| 168 |
+
# train-00001-of-00149.parquet contains sub-stroke0002
|
| 169 |
+
# etc.
|
| 170 |
+
ISLES24_CASE_INDEX: dict[str, int] = {case_id: idx for idx, case_id in enumerate(ISLES24_CASE_IDS)}
|
| 171 |
+
|
| 172 |
+
# Total number of parquet files in the dataset
|
| 173 |
+
ISLES24_NUM_FILES: int = 149
|
| 174 |
+
|
| 175 |
+
# Sanity check: ensure constants are consistent
|
| 176 |
+
assert len(ISLES24_CASE_IDS) == ISLES24_NUM_FILES, (
|
| 177 |
+
f"ISLES24_CASE_IDS has {len(ISLES24_CASE_IDS)} entries but ISLES24_NUM_FILES is {ISLES24_NUM_FILES}"
|
| 178 |
+
)
|
| 179 |
+
|
| 180 |
+
# Dataset identifier on HuggingFace Hub
|
| 181 |
+
ISLES24_DATASET_ID: str = "hugging-science/isles24-stroke"
|
tests/data/test_hf_adapter.py
CHANGED
|
@@ -1,8 +1,7 @@
|
|
| 1 |
-
"""Unit tests for HuggingFace dataset adapter with mocked HF
|
| 2 |
|
| 3 |
from __future__ import annotations
|
| 4 |
|
| 5 |
-
from typing import Any
|
| 6 |
from unittest.mock import MagicMock, patch
|
| 7 |
|
| 8 |
import pytest
|
|
@@ -11,116 +10,122 @@ from stroke_deepisles_demo.core.exceptions import DataLoadError
|
|
| 11 |
from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, build_huggingface_dataset
|
| 12 |
|
| 13 |
|
| 14 |
-
def create_mock_hf_example(subject_id: str, include_mask: bool = True) -> dict[str, Any]:
|
| 15 |
-
"""Create a mock HuggingFace dataset example."""
|
| 16 |
-
example: dict[str, Any] = {
|
| 17 |
-
"subject_id": subject_id,
|
| 18 |
-
"dwi": {"bytes": b"fake_dwi_nifti_data", "path": f"{subject_id}_dwi.nii.gz"},
|
| 19 |
-
"adc": {"bytes": b"fake_adc_nifti_data", "path": f"{subject_id}_adc.nii.gz"},
|
| 20 |
-
}
|
| 21 |
-
if include_mask:
|
| 22 |
-
example["lesion_mask"] = {
|
| 23 |
-
"bytes": b"fake_mask_nifti_data",
|
| 24 |
-
"path": f"{subject_id}_lesion-msk.nii.gz",
|
| 25 |
-
}
|
| 26 |
-
else:
|
| 27 |
-
example["lesion_mask"] = None
|
| 28 |
-
return example
|
| 29 |
-
|
| 30 |
-
|
| 31 |
-
@pytest.fixture
|
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def mock_hf_dataset() -> MagicMock:
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"""Create a mock HuggingFace dataset with 3 subjects."""
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examples = [
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create_mock_hf_example("sub-stroke0001"),
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create_mock_hf_example("sub-stroke0002"),
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create_mock_hf_example("sub-stroke0003", include_mask=False),
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]
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mock_ds = MagicMock()
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mock_ds.__len__ = MagicMock(return_value=len(examples))
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mock_ds.__iter__ = MagicMock(return_value=iter(examples))
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mock_ds.__getitem__ = MagicMock(side_effect=lambda i: examples[i])
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return mock_ds
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class TestHuggingFaceDataset:
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"""Tests for HuggingFaceDataset class."""
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def test_get_case_writes_files_to_temp_dir(self
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"""Test that get_case writes NIfTI bytes to temp files."""
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case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
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ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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_hf_dataset=mock_hf_dataset,
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_case_ids=case_ids,
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)
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finally:
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ds.cleanup()
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def test_get_case_includes_ground_truth_when_available(
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self, mock_hf_dataset: MagicMock
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) -> None:
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"""Test that ground truth is included when lesion_mask is present."""
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case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
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ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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_hf_dataset=mock_hf_dataset,
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_case_ids=case_ids,
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)
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try:
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finally:
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ds.cleanup()
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def test_get_case_caches_results(self
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"""Test that get_case returns cached paths on subsequent calls."""
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case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
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ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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_hf_dataset=mock_hf_dataset,
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_case_ids=case_ids,
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)
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try:
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finally:
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ds.cleanup()
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def test_context_manager_cleans_up_temp_files(self
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"""Test that using context manager cleans up temp files."""
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case_ids = ["sub-stroke0001"]
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ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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_hf_dataset=mock_hf_dataset,
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_case_ids=case_ids,
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)
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case = ds.get_case(0)
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temp_dir = case["dwi"].parent.parent
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assert temp_dir.exists()
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@@ -128,60 +133,163 @@ class TestHuggingFaceDataset:
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# After context exit, temp dir should be gone
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assert not temp_dir.exists()
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def test_cleanup_clears_cache(self
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"""Test that cleanup clears the case cache."""
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case_ids = ["sub-stroke0001"]
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ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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_hf_dataset=mock_hf_dataset,
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_case_ids=case_ids,
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)
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ds.cleanup()
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assert len(ds._cached_cases) == 0
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def
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"""Test that get_case
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mock_ds = MagicMock()
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mock_ds.__len__ = MagicMock(return_value=1)
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mock_ds.__getitem__ = MagicMock(return_value=malformed_example)
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| 154 |
ds = HuggingFaceDataset(
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dataset_id="test/dataset",
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)
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try:
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with
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ds
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finally:
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ds.cleanup()
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| 167 |
class TestBuildHuggingFaceDataset:
|
| 168 |
"""Tests for build_huggingface_dataset function."""
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)
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mock_load_dataset.return_value = mock_streaming_ds
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|
| 1 |
+
"""Unit tests for HuggingFace dataset adapter with mocked HF data access."""
|
| 2 |
|
| 3 |
from __future__ import annotations
|
| 4 |
|
|
|
|
| 5 |
from unittest.mock import MagicMock, patch
|
| 6 |
|
| 7 |
import pytest
|
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|
| 10 |
from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, build_huggingface_dataset
|
| 11 |
|
| 12 |
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|
| 13 |
class TestHuggingFaceDataset:
|
| 14 |
"""Tests for HuggingFaceDataset class."""
|
| 15 |
|
| 16 |
+
def test_get_case_writes_files_to_temp_dir(self) -> None:
|
| 17 |
"""Test that get_case writes NIfTI bytes to temp files."""
|
| 18 |
case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
|
| 19 |
+
case_index = {cid: idx for idx, cid in enumerate(case_ids)}
|
| 20 |
+
|
| 21 |
ds = HuggingFaceDataset(
|
| 22 |
dataset_id="test/dataset",
|
|
|
|
| 23 |
_case_ids=case_ids,
|
| 24 |
+
_case_index=case_index,
|
| 25 |
)
|
| 26 |
|
| 27 |
+
# Mock the download method
|
| 28 |
+
mock_data = {
|
| 29 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 30 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 31 |
+
"mask_bytes": b"fake_mask_nifti_data",
|
| 32 |
+
}
|
| 33 |
|
| 34 |
+
try:
|
| 35 |
+
with patch.object(ds, "_download_case_from_parquet", return_value=mock_data):
|
| 36 |
+
case = ds.get_case(0)
|
| 37 |
+
|
| 38 |
+
assert "dwi" in case
|
| 39 |
+
assert "adc" in case
|
| 40 |
+
assert case["dwi"].exists()
|
| 41 |
+
assert case["adc"].exists()
|
| 42 |
+
assert case["dwi"].read_bytes() == b"fake_dwi_nifti_data"
|
| 43 |
+
assert case["adc"].read_bytes() == b"fake_adc_nifti_data"
|
| 44 |
finally:
|
| 45 |
ds.cleanup()
|
| 46 |
|
| 47 |
+
def test_get_case_includes_ground_truth_when_available(self) -> None:
|
|
|
|
|
|
|
| 48 |
"""Test that ground truth is included when lesion_mask is present."""
|
| 49 |
case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
|
| 50 |
+
case_index = {cid: idx for idx, cid in enumerate(case_ids)}
|
| 51 |
+
|
| 52 |
ds = HuggingFaceDataset(
|
| 53 |
dataset_id="test/dataset",
|
|
|
|
| 54 |
_case_ids=case_ids,
|
| 55 |
+
_case_index=case_index,
|
| 56 |
)
|
| 57 |
|
| 58 |
try:
|
| 59 |
+
# Case with mask
|
| 60 |
+
mock_data_with_mask = {
|
| 61 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 62 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 63 |
+
"mask_bytes": b"fake_mask_nifti_data",
|
| 64 |
+
}
|
| 65 |
+
with patch.object(ds, "_download_case_from_parquet", return_value=mock_data_with_mask):
|
| 66 |
+
case = ds.get_case(0)
|
| 67 |
+
assert "ground_truth" in case
|
| 68 |
+
assert case["ground_truth"].read_bytes() == b"fake_mask_nifti_data"
|
| 69 |
+
|
| 70 |
+
# Case without mask
|
| 71 |
+
mock_data_no_mask = {
|
| 72 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 73 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 74 |
+
}
|
| 75 |
+
with patch.object(ds, "_download_case_from_parquet", return_value=mock_data_no_mask):
|
| 76 |
+
case_no_mask = ds.get_case(2)
|
| 77 |
+
assert "ground_truth" not in case_no_mask
|
| 78 |
finally:
|
| 79 |
ds.cleanup()
|
| 80 |
|
| 81 |
+
def test_get_case_caches_results(self) -> None:
|
| 82 |
"""Test that get_case returns cached paths on subsequent calls."""
|
| 83 |
case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
|
| 84 |
+
case_index = {cid: idx for idx, cid in enumerate(case_ids)}
|
| 85 |
+
|
| 86 |
ds = HuggingFaceDataset(
|
| 87 |
dataset_id="test/dataset",
|
|
|
|
| 88 |
_case_ids=case_ids,
|
| 89 |
+
_case_index=case_index,
|
| 90 |
)
|
| 91 |
|
| 92 |
+
mock_data = {
|
| 93 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 94 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 95 |
+
}
|
| 96 |
+
|
| 97 |
try:
|
| 98 |
+
with patch.object(
|
| 99 |
+
ds, "_download_case_from_parquet", return_value=mock_data
|
| 100 |
+
) as mock_download:
|
| 101 |
+
case1 = ds.get_case(0)
|
| 102 |
+
case2 = ds.get_case(0)
|
| 103 |
|
| 104 |
+
# Same object returned (cached)
|
| 105 |
+
assert case1 is case2
|
| 106 |
|
| 107 |
+
# Download was only called once
|
| 108 |
+
assert mock_download.call_count == 1
|
| 109 |
finally:
|
| 110 |
ds.cleanup()
|
| 111 |
|
| 112 |
+
def test_context_manager_cleans_up_temp_files(self) -> None:
|
| 113 |
"""Test that using context manager cleans up temp files."""
|
| 114 |
case_ids = ["sub-stroke0001"]
|
| 115 |
+
case_index = {"sub-stroke0001": 0}
|
| 116 |
+
|
| 117 |
ds = HuggingFaceDataset(
|
| 118 |
dataset_id="test/dataset",
|
|
|
|
| 119 |
_case_ids=case_ids,
|
| 120 |
+
_case_index=case_index,
|
| 121 |
)
|
| 122 |
|
| 123 |
+
mock_data = {
|
| 124 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 125 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 126 |
+
}
|
| 127 |
+
|
| 128 |
+
with patch.object(ds, "_download_case_from_parquet", return_value=mock_data), ds:
|
| 129 |
case = ds.get_case(0)
|
| 130 |
temp_dir = case["dwi"].parent.parent
|
| 131 |
assert temp_dir.exists()
|
|
|
|
| 133 |
# After context exit, temp dir should be gone
|
| 134 |
assert not temp_dir.exists()
|
| 135 |
|
| 136 |
+
def test_cleanup_clears_cache(self) -> None:
|
| 137 |
"""Test that cleanup clears the case cache."""
|
| 138 |
case_ids = ["sub-stroke0001"]
|
| 139 |
+
case_index = {"sub-stroke0001": 0}
|
| 140 |
+
|
| 141 |
ds = HuggingFaceDataset(
|
| 142 |
dataset_id="test/dataset",
|
|
|
|
| 143 |
_case_ids=case_ids,
|
| 144 |
+
_case_index=case_index,
|
| 145 |
)
|
| 146 |
|
| 147 |
+
mock_data = {
|
| 148 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 149 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 150 |
+
}
|
| 151 |
+
|
| 152 |
+
with patch.object(ds, "_download_case_from_parquet", return_value=mock_data):
|
| 153 |
+
ds.get_case(0)
|
| 154 |
+
assert len(ds._cached_cases) == 1
|
| 155 |
|
| 156 |
ds.cleanup()
|
| 157 |
assert len(ds._cached_cases) == 0
|
| 158 |
|
| 159 |
+
def test_get_case_by_string_id(self) -> None:
|
| 160 |
+
"""Test that get_case works with string case IDs."""
|
| 161 |
+
case_ids = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
|
| 162 |
+
case_index = {cid: idx for idx, cid in enumerate(case_ids)}
|
|
|
|
|
|
|
|
|
|
| 163 |
|
| 164 |
ds = HuggingFaceDataset(
|
| 165 |
dataset_id="test/dataset",
|
| 166 |
+
_case_ids=case_ids,
|
| 167 |
+
_case_index=case_index,
|
| 168 |
)
|
| 169 |
|
| 170 |
+
mock_data = {
|
| 171 |
+
"dwi_bytes": b"fake_dwi_nifti_data",
|
| 172 |
+
"adc_bytes": b"fake_adc_nifti_data",
|
| 173 |
+
}
|
| 174 |
+
|
| 175 |
try:
|
| 176 |
+
with patch.object(
|
| 177 |
+
ds, "_download_case_from_parquet", return_value=mock_data
|
| 178 |
+
) as mock_download:
|
| 179 |
+
case = ds.get_case("sub-stroke0002")
|
| 180 |
+
assert case["dwi"].exists()
|
| 181 |
+
# Should have been called with index 1 (second case)
|
| 182 |
+
mock_download.assert_called_once_with(1, "sub-stroke0002")
|
| 183 |
finally:
|
| 184 |
ds.cleanup()
|
| 185 |
|
| 186 |
+
def test_get_case_raises_key_error_for_invalid_id(self) -> None:
|
| 187 |
+
"""Test that get_case raises KeyError for invalid case ID."""
|
| 188 |
+
case_ids = ["sub-stroke0001"]
|
| 189 |
+
case_index = {"sub-stroke0001": 0}
|
| 190 |
+
|
| 191 |
+
ds = HuggingFaceDataset(
|
| 192 |
+
dataset_id="test/dataset",
|
| 193 |
+
_case_ids=case_ids,
|
| 194 |
+
_case_index=case_index,
|
| 195 |
+
)
|
| 196 |
+
|
| 197 |
+
with pytest.raises(KeyError, match="not found in dataset"):
|
| 198 |
+
ds.get_case("sub-stroke9999")
|
| 199 |
+
|
| 200 |
+
def test_get_case_raises_index_error_for_out_of_range(self) -> None:
|
| 201 |
+
"""Test that get_case raises IndexError for out of range index."""
|
| 202 |
+
case_ids = ["sub-stroke0001"]
|
| 203 |
+
case_index = {"sub-stroke0001": 0}
|
| 204 |
+
|
| 205 |
+
ds = HuggingFaceDataset(
|
| 206 |
+
dataset_id="test/dataset",
|
| 207 |
+
_case_ids=case_ids,
|
| 208 |
+
_case_index=case_index,
|
| 209 |
+
)
|
| 210 |
+
|
| 211 |
+
with pytest.raises(IndexError, match="out of range"):
|
| 212 |
+
ds.get_case(99)
|
| 213 |
+
|
| 214 |
|
| 215 |
class TestBuildHuggingFaceDataset:
|
| 216 |
"""Tests for build_huggingface_dataset function."""
|
| 217 |
|
| 218 |
+
def test_uses_precomputed_case_ids(self) -> None:
|
| 219 |
+
"""Test that build_huggingface_dataset uses pre-computed case IDs."""
|
| 220 |
+
result = build_huggingface_dataset("hugging-science/isles24-stroke")
|
| 221 |
+
|
| 222 |
+
assert isinstance(result, HuggingFaceDataset)
|
| 223 |
+
assert result.dataset_id == "hugging-science/isles24-stroke"
|
| 224 |
+
# Should have 149 cases from pre-computed list
|
| 225 |
+
assert len(result._case_ids) == 149
|
| 226 |
+
assert "sub-stroke0001" in result._case_ids
|
| 227 |
+
assert "sub-stroke0189" in result._case_ids
|
| 228 |
+
|
| 229 |
+
def test_case_index_mapping_is_correct(self) -> None:
|
| 230 |
+
"""Test that case index mapping matches case IDs order."""
|
| 231 |
+
result = build_huggingface_dataset("hugging-science/isles24-stroke")
|
| 232 |
+
|
| 233 |
+
# First case should map to index 0
|
| 234 |
+
assert result._case_index["sub-stroke0001"] == 0
|
| 235 |
+
# Last case should map to index 148
|
| 236 |
+
assert result._case_index["sub-stroke0189"] == 148
|
| 237 |
+
|
| 238 |
+
def test_warns_for_different_dataset_id(self) -> None:
|
| 239 |
+
"""Test that a warning is logged for non-standard dataset IDs."""
|
| 240 |
+
from stroke_deepisles_demo.data.adapter import logger
|
| 241 |
+
|
| 242 |
+
with patch.object(logger, "warning") as mock_warning:
|
| 243 |
+
build_huggingface_dataset("some-other/dataset")
|
| 244 |
+
mock_warning.assert_called_once()
|
| 245 |
+
assert "does not match pre-computed constants" in mock_warning.call_args[0][0]
|
| 246 |
+
|
| 247 |
+
|
| 248 |
+
class TestDownloadCaseFromParquet:
|
| 249 |
+
"""Tests for _download_case_from_parquet method."""
|
| 250 |
+
|
| 251 |
+
def test_raises_data_load_error_on_malformed_data(self) -> None:
|
| 252 |
+
"""Test that _download_case_from_parquet raises DataLoadError for malformed data."""
|
| 253 |
+
import pandas as pd # type: ignore[import-untyped]
|
| 254 |
+
|
| 255 |
+
case_ids = ["sub-stroke0001"]
|
| 256 |
+
case_index = {"sub-stroke0001": 0}
|
| 257 |
+
|
| 258 |
+
ds = HuggingFaceDataset(
|
| 259 |
+
dataset_id="test/dataset",
|
| 260 |
+
_case_ids=case_ids,
|
| 261 |
+
_case_index=case_index,
|
| 262 |
)
|
|
|
|
| 263 |
|
| 264 |
+
# Create mock with missing 'bytes' key
|
| 265 |
+
mock_df = pd.DataFrame(
|
| 266 |
+
[
|
| 267 |
+
{
|
| 268 |
+
"subject_id": "sub-stroke0001",
|
| 269 |
+
"dwi": {}, # Missing 'bytes'
|
| 270 |
+
"adc": {},
|
| 271 |
+
"lesion_mask": None,
|
| 272 |
+
}
|
| 273 |
+
]
|
| 274 |
+
)
|
| 275 |
|
| 276 |
+
mock_table = MagicMock()
|
| 277 |
+
mock_table.to_pandas.return_value = mock_df
|
| 278 |
+
|
| 279 |
+
mock_pf = MagicMock()
|
| 280 |
+
mock_pf.read.return_value = mock_table
|
| 281 |
+
|
| 282 |
+
mock_file = MagicMock()
|
| 283 |
+
mock_file.__enter__ = MagicMock(return_value=mock_file)
|
| 284 |
+
mock_file.__exit__ = MagicMock(return_value=False)
|
| 285 |
+
|
| 286 |
+
mock_fs = MagicMock()
|
| 287 |
+
mock_fs.open.return_value = mock_file
|
| 288 |
+
|
| 289 |
+
# Patch at the source module where they're imported, not where they're used
|
| 290 |
+
with (
|
| 291 |
+
patch("huggingface_hub.HfFileSystem", return_value=mock_fs),
|
| 292 |
+
patch("pyarrow.parquet.ParquetFile", return_value=mock_pf),
|
| 293 |
+
pytest.raises(DataLoadError, match="Malformed HuggingFace data"),
|
| 294 |
+
):
|
| 295 |
+
ds._download_case_from_parquet(0, "sub-stroke0001")
|
tests/data/test_loader.py
CHANGED
|
@@ -4,11 +4,11 @@ from __future__ import annotations
|
|
| 4 |
|
| 5 |
import os
|
| 6 |
from typing import TYPE_CHECKING
|
|
|
|
| 7 |
|
| 8 |
import pytest
|
| 9 |
-
from datasets.exceptions import DatasetNotFoundError
|
| 10 |
|
| 11 |
-
from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, LocalDataset
|
| 12 |
from stroke_deepisles_demo.data.loader import load_isles_dataset
|
| 13 |
|
| 14 |
if TYPE_CHECKING:
|
|
@@ -35,10 +35,20 @@ def test_load_from_local_finds_all_cases(synthetic_isles_dir: Path) -> None:
|
|
| 35 |
assert dataset.list_case_ids() == ["sub-stroke0001", "sub-stroke0002"]
|
| 36 |
|
| 37 |
|
| 38 |
-
def
|
| 39 |
-
"""Test that loading a non-
|
| 40 |
-
|
| 41 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 42 |
|
| 43 |
|
| 44 |
@pytest.mark.integration
|
|
|
|
| 4 |
|
| 5 |
import os
|
| 6 |
from typing import TYPE_CHECKING
|
| 7 |
+
from unittest.mock import patch
|
| 8 |
|
| 9 |
import pytest
|
|
|
|
| 10 |
|
| 11 |
+
from stroke_deepisles_demo.data.adapter import HuggingFaceDataset, LocalDataset, logger
|
| 12 |
from stroke_deepisles_demo.data.loader import load_isles_dataset
|
| 13 |
|
| 14 |
if TYPE_CHECKING:
|
|
|
|
| 35 |
assert dataset.list_case_ids() == ["sub-stroke0001", "sub-stroke0002"]
|
| 36 |
|
| 37 |
|
| 38 |
+
def test_load_hf_warns_on_non_standard_dataset() -> None:
|
| 39 |
+
"""Test that loading a non-standard HF dataset logs a warning.
|
| 40 |
+
|
| 41 |
+
Note: With pre-computed case IDs, the dataset ID mismatch is only detected
|
| 42 |
+
at build time (warning logged), not at get_case() time. The actual 404 error
|
| 43 |
+
would only occur when trying to download a case that doesn't exist.
|
| 44 |
+
"""
|
| 45 |
+
with patch.object(logger, "warning") as mock_warning:
|
| 46 |
+
ds = load_isles_dataset(source="fake/nonexistent-dataset", local_mode=False)
|
| 47 |
+
mock_warning.assert_called_once()
|
| 48 |
+
assert "does not match pre-computed constants" in mock_warning.call_args[0][0]
|
| 49 |
+
# Dataset is still created with pre-computed case IDs
|
| 50 |
+
assert isinstance(ds, HuggingFaceDataset)
|
| 51 |
+
assert len(ds) == 149 # Uses pre-computed list
|
| 52 |
|
| 53 |
|
| 54 |
@pytest.mark.integration
|