Spaces:
Sleeping
Sleeping
Update lab_analyzer.py
Browse files- lab_analyzer.py +177 -177
lab_analyzer.py
CHANGED
|
@@ -1,178 +1,178 @@
|
|
| 1 |
-
import base64
|
| 2 |
-
import os
|
| 3 |
-
from huggingface_hub import InferenceClient
|
| 4 |
-
import asyncio
|
| 5 |
-
from typing import Dict, Any
|
| 6 |
-
import logging
|
| 7 |
-
from dotenv import load_dotenv
|
| 8 |
-
|
| 9 |
-
# Load environment variables from .env file
|
| 10 |
-
load_dotenv()
|
| 11 |
-
|
| 12 |
-
logger = logging.getLogger(__name__)
|
| 13 |
-
|
| 14 |
-
class LabReportAnalyzer:
|
| 15 |
-
"""Lab Report Analysis service using Hugging Face Inference Client"""
|
| 16 |
-
|
| 17 |
-
def __init__(self):
|
| 18 |
-
"""Initialize the analyzer with Hugging Face client"""
|
| 19 |
-
self.client = InferenceClient(
|
| 20 |
-
|
| 21 |
-
|
| 22 |
-
)
|
| 23 |
-
self.model = "google/gemma-3-27b-it"
|
| 24 |
-
|
| 25 |
-
async def analyze_report(self, image_b64: str) -> Dict[str, Any]:
|
| 26 |
-
"""
|
| 27 |
-
Analyze a lab report image and return structured results
|
| 28 |
-
|
| 29 |
-
Args:
|
| 30 |
-
image_b64: Base64 encoded image string
|
| 31 |
-
|
| 32 |
-
Returns:
|
| 33 |
-
Dictionary containing structured analysis results
|
| 34 |
-
"""
|
| 35 |
-
try:
|
| 36 |
-
prompt = self._get_analysis_prompt()
|
| 37 |
-
|
| 38 |
-
# Run the inference in a thread pool to avoid blocking
|
| 39 |
-
loop = asyncio.get_event_loop()
|
| 40 |
-
completion = await loop.run_in_executor(
|
| 41 |
-
None,
|
| 42 |
-
self._run_inference,
|
| 43 |
-
image_b64,
|
| 44 |
-
prompt
|
| 45 |
-
)
|
| 46 |
-
|
| 47 |
-
# Extract and parse the response
|
| 48 |
-
analysis_text = completion.choices[0].message.content.strip()
|
| 49 |
-
|
| 50 |
-
# Parse the structured response
|
| 51 |
-
parsed_result = self._parse_analysis_result(analysis_text)
|
| 52 |
-
|
| 53 |
-
return parsed_result
|
| 54 |
-
|
| 55 |
-
except Exception as e:
|
| 56 |
-
logger.error(f"Error in analyze_report: {str(e)}")
|
| 57 |
-
return {
|
| 58 |
-
"error": True,
|
| 59 |
-
"message": f"Analysis failed: {str(e)}",
|
| 60 |
-
"raw_response": ""
|
| 61 |
-
}
|
| 62 |
-
|
| 63 |
-
def _run_inference(self, image_b64: str, prompt: str):
|
| 64 |
-
"""Run the Hugging Face inference synchronously"""
|
| 65 |
-
return self.client.chat.completions.create(
|
| 66 |
-
model=self.model,
|
| 67 |
-
messages=[
|
| 68 |
-
{
|
| 69 |
-
"role": "user",
|
| 70 |
-
"content": [
|
| 71 |
-
{"type": "text", "text": prompt},
|
| 72 |
-
{
|
| 73 |
-
"type": "image_url",
|
| 74 |
-
"image_url": {
|
| 75 |
-
"url": f"data:image/jpeg;base64,{image_b64}"
|
| 76 |
-
}
|
| 77 |
-
}
|
| 78 |
-
]
|
| 79 |
-
}
|
| 80 |
-
],
|
| 81 |
-
)
|
| 82 |
-
|
| 83 |
-
def _get_analysis_prompt(self) -> str:
|
| 84 |
-
"""Get the structured analysis prompt"""
|
| 85 |
-
return """
|
| 86 |
-
You are a medical analysis assistant.
|
| 87 |
-
|
| 88 |
-
Analyze the following lab report image and give a structured, professional summary
|
| 89 |
-
following these steps:
|
| 90 |
-
|
| 91 |
-
1. Extract the results (with normal ranges if available).
|
| 92 |
-
2. Highlight abnormal values clearly.
|
| 93 |
-
3. Explain what the results suggest in simple terms.
|
| 94 |
-
4. Provide an overall summary of health findings.
|
| 95 |
-
5. End with the disclaimer:
|
| 96 |
-
"This analysis is for educational purposes only and should not replace professional medical advice."
|
| 97 |
-
|
| 98 |
-
If the image is unreadable, respond: "The image text is unclear."
|
| 99 |
-
|
| 100 |
-
Format your response as follows:
|
| 101 |
-
|
| 102 |
-
Summary: (2–3 sentences explaining what the report shows)
|
| 103 |
-
Key Findings: (3–5 bullet points with main abnormal or notable values)
|
| 104 |
-
Interpretation: (1–2 sentences explaining what the findings suggest)
|
| 105 |
-
Note: (One line disclaimer that it's not medical advice)
|
| 106 |
-
|
| 107 |
-
Keep it short, clear, and professional — like a medical summary written for quick review.
|
| 108 |
-
"""
|
| 109 |
-
|
| 110 |
-
def _parse_analysis_result(self, analysis_text: str) -> Dict[str, Any]:
|
| 111 |
-
"""
|
| 112 |
-
Parse the structured analysis result into a dictionary
|
| 113 |
-
|
| 114 |
-
Args:
|
| 115 |
-
analysis_text: Raw analysis text from the model
|
| 116 |
-
|
| 117 |
-
Returns:
|
| 118 |
-
Structured dictionary with parsed components
|
| 119 |
-
"""
|
| 120 |
-
try:
|
| 121 |
-
result = {
|
| 122 |
-
"error": False,
|
| 123 |
-
"summary": "",
|
| 124 |
-
"key_findings": [],
|
| 125 |
-
"interpretation": "",
|
| 126 |
-
"note": "",
|
| 127 |
-
"raw_response": analysis_text
|
| 128 |
-
}
|
| 129 |
-
|
| 130 |
-
# Check if image is unreadable
|
| 131 |
-
if "The image text is unclear" in analysis_text:
|
| 132 |
-
result["error"] = True
|
| 133 |
-
result["message"] = "The image text is unclear or unreadable"
|
| 134 |
-
return result
|
| 135 |
-
|
| 136 |
-
lines = analysis_text.split('\n')
|
| 137 |
-
current_section = None
|
| 138 |
-
|
| 139 |
-
for line in lines:
|
| 140 |
-
line = line.strip()
|
| 141 |
-
if not line:
|
| 142 |
-
continue
|
| 143 |
-
|
| 144 |
-
# Identify sections (handle both plain text and markdown formats)
|
| 145 |
-
if line.startswith('Summary:') or line.startswith('**Summary:**'):
|
| 146 |
-
current_section = 'summary'
|
| 147 |
-
result['summary'] = line.replace('**Summary:**', '').replace('Summary:', '').strip()
|
| 148 |
-
elif line.startswith('Key Findings:') or line.startswith('**Key Findings:**'):
|
| 149 |
-
current_section = 'key_findings'
|
| 150 |
-
elif line.startswith('Interpretation:') or line.startswith('**Interpretation:**'):
|
| 151 |
-
current_section = 'interpretation'
|
| 152 |
-
result['interpretation'] = line.replace('**Interpretation:**', '').replace('Interpretation:', '').strip()
|
| 153 |
-
elif line.startswith('Note:') or line.startswith('**Note:**'):
|
| 154 |
-
current_section = 'note'
|
| 155 |
-
result['note'] = line.replace('**Note:**', '').replace('Note:', '').strip()
|
| 156 |
-
else:
|
| 157 |
-
# Continue previous section
|
| 158 |
-
if current_section == 'summary' and not result['summary']:
|
| 159 |
-
result['summary'] = line
|
| 160 |
-
elif current_section == 'key_findings' and (line.startswith(('•', '-', '*')) or line.strip().startswith('*')):
|
| 161 |
-
# Handle both regular bullets and markdown-style bullets
|
| 162 |
-
clean_line = line.lstrip('•-* ').strip()
|
| 163 |
-
if clean_line:
|
| 164 |
-
result['key_findings'].append(clean_line)
|
| 165 |
-
elif current_section == 'interpretation' and not result['interpretation']:
|
| 166 |
-
result['interpretation'] = line
|
| 167 |
-
elif current_section == 'note' and not result['note']:
|
| 168 |
-
result['note'] = line
|
| 169 |
-
|
| 170 |
-
return result
|
| 171 |
-
|
| 172 |
-
except Exception as e:
|
| 173 |
-
logger.error(f"Error parsing analysis result: {str(e)}")
|
| 174 |
-
return {
|
| 175 |
-
"error": True,
|
| 176 |
-
"message": f"Failed to parse analysis: {str(e)}",
|
| 177 |
-
"raw_response": analysis_text
|
| 178 |
}
|
|
|
|
| 1 |
+
import base64
|
| 2 |
+
import os
|
| 3 |
+
from huggingface_hub import InferenceClient
|
| 4 |
+
import asyncio
|
| 5 |
+
from typing import Dict, Any
|
| 6 |
+
import logging
|
| 7 |
+
from dotenv import load_dotenv
|
| 8 |
+
|
| 9 |
+
# Load environment variables from .env file
|
| 10 |
+
load_dotenv()
|
| 11 |
+
|
| 12 |
+
logger = logging.getLogger(__name__)
|
| 13 |
+
|
| 14 |
+
class LabReportAnalyzer:
|
| 15 |
+
"""Lab Report Analysis service using Hugging Face Inference Client"""
|
| 16 |
+
|
| 17 |
+
def __init__(self):
|
| 18 |
+
"""Initialize the analyzer with Hugging Face client"""
|
| 19 |
+
self.client = InferenceClient(
|
| 20 |
+
token=os.getenv("HUGGINGFACE_API_KEY", "your-api-key-here"),
|
| 21 |
+
|
| 22 |
+
)
|
| 23 |
+
self.model = "google/gemma-3-27b-it"
|
| 24 |
+
|
| 25 |
+
async def analyze_report(self, image_b64: str) -> Dict[str, Any]:
|
| 26 |
+
"""
|
| 27 |
+
Analyze a lab report image and return structured results
|
| 28 |
+
|
| 29 |
+
Args:
|
| 30 |
+
image_b64: Base64 encoded image string
|
| 31 |
+
|
| 32 |
+
Returns:
|
| 33 |
+
Dictionary containing structured analysis results
|
| 34 |
+
"""
|
| 35 |
+
try:
|
| 36 |
+
prompt = self._get_analysis_prompt()
|
| 37 |
+
|
| 38 |
+
# Run the inference in a thread pool to avoid blocking
|
| 39 |
+
loop = asyncio.get_event_loop()
|
| 40 |
+
completion = await loop.run_in_executor(
|
| 41 |
+
None,
|
| 42 |
+
self._run_inference,
|
| 43 |
+
image_b64,
|
| 44 |
+
prompt
|
| 45 |
+
)
|
| 46 |
+
|
| 47 |
+
# Extract and parse the response
|
| 48 |
+
analysis_text = completion.choices[0].message.content.strip()
|
| 49 |
+
|
| 50 |
+
# Parse the structured response
|
| 51 |
+
parsed_result = self._parse_analysis_result(analysis_text)
|
| 52 |
+
|
| 53 |
+
return parsed_result
|
| 54 |
+
|
| 55 |
+
except Exception as e:
|
| 56 |
+
logger.error(f"Error in analyze_report: {str(e)}")
|
| 57 |
+
return {
|
| 58 |
+
"error": True,
|
| 59 |
+
"message": f"Analysis failed: {str(e)}",
|
| 60 |
+
"raw_response": ""
|
| 61 |
+
}
|
| 62 |
+
|
| 63 |
+
def _run_inference(self, image_b64: str, prompt: str):
|
| 64 |
+
"""Run the Hugging Face inference synchronously"""
|
| 65 |
+
return self.client.chat.completions.create(
|
| 66 |
+
model=self.model,
|
| 67 |
+
messages=[
|
| 68 |
+
{
|
| 69 |
+
"role": "user",
|
| 70 |
+
"content": [
|
| 71 |
+
{"type": "text", "text": prompt},
|
| 72 |
+
{
|
| 73 |
+
"type": "image_url",
|
| 74 |
+
"image_url": {
|
| 75 |
+
"url": f"data:image/jpeg;base64,{image_b64}"
|
| 76 |
+
}
|
| 77 |
+
}
|
| 78 |
+
]
|
| 79 |
+
}
|
| 80 |
+
],
|
| 81 |
+
)
|
| 82 |
+
|
| 83 |
+
def _get_analysis_prompt(self) -> str:
|
| 84 |
+
"""Get the structured analysis prompt"""
|
| 85 |
+
return """
|
| 86 |
+
You are a medical analysis assistant.
|
| 87 |
+
|
| 88 |
+
Analyze the following lab report image and give a structured, professional summary
|
| 89 |
+
following these steps:
|
| 90 |
+
|
| 91 |
+
1. Extract the results (with normal ranges if available).
|
| 92 |
+
2. Highlight abnormal values clearly.
|
| 93 |
+
3. Explain what the results suggest in simple terms.
|
| 94 |
+
4. Provide an overall summary of health findings.
|
| 95 |
+
5. End with the disclaimer:
|
| 96 |
+
"This analysis is for educational purposes only and should not replace professional medical advice."
|
| 97 |
+
|
| 98 |
+
If the image is unreadable, respond: "The image text is unclear."
|
| 99 |
+
|
| 100 |
+
Format your response as follows:
|
| 101 |
+
|
| 102 |
+
Summary: (2–3 sentences explaining what the report shows)
|
| 103 |
+
Key Findings: (3–5 bullet points with main abnormal or notable values)
|
| 104 |
+
Interpretation: (1–2 sentences explaining what the findings suggest)
|
| 105 |
+
Note: (One line disclaimer that it's not medical advice)
|
| 106 |
+
|
| 107 |
+
Keep it short, clear, and professional — like a medical summary written for quick review.
|
| 108 |
+
"""
|
| 109 |
+
|
| 110 |
+
def _parse_analysis_result(self, analysis_text: str) -> Dict[str, Any]:
|
| 111 |
+
"""
|
| 112 |
+
Parse the structured analysis result into a dictionary
|
| 113 |
+
|
| 114 |
+
Args:
|
| 115 |
+
analysis_text: Raw analysis text from the model
|
| 116 |
+
|
| 117 |
+
Returns:
|
| 118 |
+
Structured dictionary with parsed components
|
| 119 |
+
"""
|
| 120 |
+
try:
|
| 121 |
+
result = {
|
| 122 |
+
"error": False,
|
| 123 |
+
"summary": "",
|
| 124 |
+
"key_findings": [],
|
| 125 |
+
"interpretation": "",
|
| 126 |
+
"note": "",
|
| 127 |
+
"raw_response": analysis_text
|
| 128 |
+
}
|
| 129 |
+
|
| 130 |
+
# Check if image is unreadable
|
| 131 |
+
if "The image text is unclear" in analysis_text:
|
| 132 |
+
result["error"] = True
|
| 133 |
+
result["message"] = "The image text is unclear or unreadable"
|
| 134 |
+
return result
|
| 135 |
+
|
| 136 |
+
lines = analysis_text.split('\n')
|
| 137 |
+
current_section = None
|
| 138 |
+
|
| 139 |
+
for line in lines:
|
| 140 |
+
line = line.strip()
|
| 141 |
+
if not line:
|
| 142 |
+
continue
|
| 143 |
+
|
| 144 |
+
# Identify sections (handle both plain text and markdown formats)
|
| 145 |
+
if line.startswith('Summary:') or line.startswith('**Summary:**'):
|
| 146 |
+
current_section = 'summary'
|
| 147 |
+
result['summary'] = line.replace('**Summary:**', '').replace('Summary:', '').strip()
|
| 148 |
+
elif line.startswith('Key Findings:') or line.startswith('**Key Findings:**'):
|
| 149 |
+
current_section = 'key_findings'
|
| 150 |
+
elif line.startswith('Interpretation:') or line.startswith('**Interpretation:**'):
|
| 151 |
+
current_section = 'interpretation'
|
| 152 |
+
result['interpretation'] = line.replace('**Interpretation:**', '').replace('Interpretation:', '').strip()
|
| 153 |
+
elif line.startswith('Note:') or line.startswith('**Note:**'):
|
| 154 |
+
current_section = 'note'
|
| 155 |
+
result['note'] = line.replace('**Note:**', '').replace('Note:', '').strip()
|
| 156 |
+
else:
|
| 157 |
+
# Continue previous section
|
| 158 |
+
if current_section == 'summary' and not result['summary']:
|
| 159 |
+
result['summary'] = line
|
| 160 |
+
elif current_section == 'key_findings' and (line.startswith(('•', '-', '*')) or line.strip().startswith('*')):
|
| 161 |
+
# Handle both regular bullets and markdown-style bullets
|
| 162 |
+
clean_line = line.lstrip('•-* ').strip()
|
| 163 |
+
if clean_line:
|
| 164 |
+
result['key_findings'].append(clean_line)
|
| 165 |
+
elif current_section == 'interpretation' and not result['interpretation']:
|
| 166 |
+
result['interpretation'] = line
|
| 167 |
+
elif current_section == 'note' and not result['note']:
|
| 168 |
+
result['note'] = line
|
| 169 |
+
|
| 170 |
+
return result
|
| 171 |
+
|
| 172 |
+
except Exception as e:
|
| 173 |
+
logger.error(f"Error parsing analysis result: {str(e)}")
|
| 174 |
+
return {
|
| 175 |
+
"error": True,
|
| 176 |
+
"message": f"Failed to parse analysis: {str(e)}",
|
| 177 |
+
"raw_response": analysis_text
|
| 178 |
}
|