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Upload 2 files
Browse files- app.py +665 -6
- requirements.txt +6 -9
app.py
CHANGED
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@@ -1,10 +1,669 @@
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import os
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import gradio as gr
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import boto3
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import json
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import numpy as np
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import re
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import logging
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import os
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from datetime import datetime
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import tempfile
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# Configure logging
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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# Try to import optional dependencies
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try:
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from reportlab.lib.pagesizes import letter
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from reportlab.lib import colors
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from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle
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from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
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REPORTLAB_AVAILABLE = True
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except ImportError:
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REPORTLAB_AVAILABLE = False
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logger.info("ReportLab not available - PDF export disabled")
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try:
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import speech_recognition as sr
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import pydub
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SPEECH_RECOGNITION_AVAILABLE = True
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except ImportError:
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SPEECH_RECOGNITION_AVAILABLE = False
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logger.info("Speech recognition not available - audio transcription will use demo mode")
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# AWS credentials (optional)
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AWS_ACCESS_KEY = os.getenv("AWS_ACCESS_KEY", "")
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AWS_SECRET_KEY = os.getenv("AWS_SECRET_KEY", "")
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AWS_REGION = os.getenv("AWS_REGION", "us-east-1")
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# Initialize AWS client if available
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bedrock_client = None
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if AWS_ACCESS_KEY and AWS_SECRET_KEY:
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try:
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bedrock_client = boto3.client(
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'bedrock-runtime',
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aws_access_key_id=AWS_ACCESS_KEY,
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aws_secret_access_key=AWS_SECRET_KEY,
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region_name=AWS_REGION
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)
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logger.info("Bedrock client initialized successfully")
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except Exception as e:
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logger.error(f"Failed to initialize AWS Bedrock client: {str(e)}")
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else:
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logger.info("AWS credentials not configured - using demo mode")
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# Data directories
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DATA_DIR = os.environ.get("DATA_DIR", "patient_data")
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def ensure_data_dirs():
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"""Ensure data directories exist"""
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try:
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os.makedirs(DATA_DIR, exist_ok=True)
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logger.info(f"Data directories created: {DATA_DIR}")
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except Exception as e:
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logger.warning(f"Could not create data directories: {str(e)}")
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logger.info("Using temporary directory for data storage")
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ensure_data_dirs()
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# Sample transcripts
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SAMPLE_TRANSCRIPTS = {
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"Beach Trip (Child)": """*PAR: today I would &-um like to talk about &-um a fun trip I took last &-um summer with my family.
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*PAR: we went to the &-um &-um beach [//] no to the mountains [//] I mean the beach actually.
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*PAR: there was lots of &-um &-um swimming and &-um sun.
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*PAR: we [/] we stayed for &-um three no [//] four days in a &-um hotel near the water [: ocean] [*].
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*PAR: my favorite part was &-um building &-um castles with sand.
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*PAR: sometimes I forget [//] forgetted [: forgot] [*] what they call those things we built.
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*PAR: my brother he [//] he helped me dig a big hole.
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*PAR: we saw [/] saw fishies [: fish] [*] swimming in the water.
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*PAR: sometimes I wonder [/] wonder where fishies [: fish] [*] go when it's cold.
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*PAR: maybe they have [/] have houses under the water.
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*PAR: after swimming we [//] I eat [: ate] [*] &-um ice cream with &-um chocolate things on top.
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*PAR: what do you call those &-um &-um sprinkles! that's the word.
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*PAR: my mom said to &-um that I could have &-um two scoops next time.
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*PAR: I want to go back to the beach [/] beach next year.""",
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"School Day (Adolescent)": """*PAR: yesterday was &-um kind of a weird day at school.
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*PAR: I had this big test in math and I was like really nervous about it.
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| 88 |
+
*PAR: when I got there [//] when I got to class the teacher said we could use calculators.
|
| 89 |
+
*PAR: I was like &-oh &-um that's good because I always mess up the &-um the calculations.
|
| 90 |
+
*PAR: there was this one problem about &-um what do you call it &-um geometry I think.
|
| 91 |
+
*PAR: I couldn't remember the formula for [//] I mean I knew it but I just couldn't think of it.
|
| 92 |
+
*PAR: so I raised my hand and asked the teacher and she was really nice about it.
|
| 93 |
+
*PAR: after the test me and my friends went to lunch and we talked about how we did.
|
| 94 |
+
*PAR: everyone was saying it was hard but I think I did okay.
|
| 95 |
+
*PAR: oh and then in English class we had to read our essays out loud.
|
| 96 |
+
*PAR: I hate doing that because I get really nervous and I start talking fast.
|
| 97 |
+
*PAR: but the teacher said mine was good which made me feel better.""",
|
| 98 |
+
|
| 99 |
+
"Adult Recovery": """*PAR: I &-um I want to talk about &-uh my &-um recovery.
|
| 100 |
+
*PAR: it's been &-um [//] it's hard to &-um to find the words sometimes.
|
| 101 |
+
*PAR: before the &-um the stroke I was &-um working at the &-uh at the bank.
|
| 102 |
+
*PAR: now I have to &-um practice speaking every day with my therapist.
|
| 103 |
+
*PAR: my wife she [//] she helps me a lot at home.
|
| 104 |
+
*PAR: we do &-um exercises together like &-uh reading and &-um talking about pictures.
|
| 105 |
+
*PAR: sometimes I get frustrated because I know what I want to say but &-um the words don't come out right.
|
| 106 |
+
*PAR: but I'm getting better little by little.
|
| 107 |
+
*PAR: the doctor says I'm making good progress.
|
| 108 |
+
*PAR: I hope to go back to work someday but right now I'm focusing on &-um getting better."""
|
| 109 |
+
}
|
| 110 |
+
|
| 111 |
+
def call_bedrock(prompt, max_tokens=4096):
|
| 112 |
+
"""Call AWS Bedrock API or return demo response"""
|
| 113 |
+
if not bedrock_client:
|
| 114 |
+
return generate_demo_response(prompt)
|
| 115 |
+
|
| 116 |
+
try:
|
| 117 |
+
body = json.dumps({
|
| 118 |
+
"anthropic_version": "bedrock-2023-05-31",
|
| 119 |
+
"max_tokens": max_tokens,
|
| 120 |
+
"messages": [{"role": "user", "content": prompt}],
|
| 121 |
+
"temperature": 0.3,
|
| 122 |
+
"top_p": 0.9
|
| 123 |
+
})
|
| 124 |
+
|
| 125 |
+
response = bedrock_client.invoke_model(
|
| 126 |
+
body=body,
|
| 127 |
+
modelId='anthropic.claude-3-sonnet-20240229-v1:0',
|
| 128 |
+
accept='application/json',
|
| 129 |
+
contentType='application/json'
|
| 130 |
+
)
|
| 131 |
+
response_body = json.loads(response.get('body').read())
|
| 132 |
+
return response_body['content'][0]['text']
|
| 133 |
+
except Exception as e:
|
| 134 |
+
logger.error(f"Error calling Bedrock: {str(e)}")
|
| 135 |
+
return generate_demo_response(prompt)
|
| 136 |
+
|
| 137 |
+
def generate_demo_response(prompt):
|
| 138 |
+
"""Generate demo analysis response based on transcript patterns"""
|
| 139 |
+
# Extract transcript from prompt
|
| 140 |
+
transcript_match = re.search(r'TRANSCRIPT:\s*(.*?)(?=\n\n|\Z)', prompt, re.DOTALL)
|
| 141 |
+
transcript = transcript_match.group(1) if transcript_match else ""
|
| 142 |
+
|
| 143 |
+
# Count speech patterns
|
| 144 |
+
um_count = len(re.findall(r'&-um|&-uh', transcript))
|
| 145 |
+
revision_count = len(re.findall(r'\[//\]', transcript))
|
| 146 |
+
repetition_count = len(re.findall(r'\[/\]', transcript))
|
| 147 |
+
error_count = len(re.findall(r'\[\*\]', transcript))
|
| 148 |
+
|
| 149 |
+
# Generate realistic scores based on patterns
|
| 150 |
+
fluency_score = max(70, 100 - (um_count * 2))
|
| 151 |
+
syntactic_score = max(70, 100 - (error_count * 3))
|
| 152 |
+
semantic_score = max(75, 105 - (revision_count * 2))
|
| 153 |
+
|
| 154 |
+
# Convert to percentiles
|
| 155 |
+
fluency_percentile = int(np.interp(fluency_score, [70, 85, 100, 115], [5, 16, 50, 84]))
|
| 156 |
+
syntactic_percentile = int(np.interp(syntactic_score, [70, 85, 100, 115], [5, 16, 50, 84]))
|
| 157 |
+
semantic_percentile = int(np.interp(semantic_score, [70, 85, 100, 115], [5, 16, 50, 84]))
|
| 158 |
+
|
| 159 |
+
def get_performance_level(score):
|
| 160 |
+
if score < 70: return "Well Below Average"
|
| 161 |
+
elif score < 85: return "Below Average"
|
| 162 |
+
elif score < 115: return "Average"
|
| 163 |
+
else: return "Above Average"
|
| 164 |
+
|
| 165 |
+
return f"""<SPEECH_FACTORS_START>
|
| 166 |
+
Difficulty producing fluent speech: {um_count + revision_count}, {100 - fluency_percentile}
|
| 167 |
+
Examples:
|
| 168 |
+
- Frequent use of fillers (&-um, &-uh) observed throughout transcript
|
| 169 |
+
- Self-corrections and revisions interrupt speech flow
|
| 170 |
+
|
| 171 |
+
Word retrieval issues: {um_count // 2 + 1}, {90 - semantic_percentile}
|
| 172 |
+
Examples:
|
| 173 |
+
- Hesitations and pauses before content words noted
|
| 174 |
+
- Circumlocutions and word-finding difficulties evident
|
| 175 |
+
|
| 176 |
+
Grammatical errors: {error_count}, {85 - syntactic_percentile}
|
| 177 |
+
Examples:
|
| 178 |
+
- Morphological errors marked with [*] in transcript
|
| 179 |
+
- Verb tense and agreement inconsistencies observed
|
| 180 |
+
|
| 181 |
+
Repetitions and revisions: {repetition_count + revision_count}, {80 - fluency_percentile}
|
| 182 |
+
Examples:
|
| 183 |
+
- Self-corrections marked with [//] throughout sample
|
| 184 |
+
- Word and phrase repetitions marked with [/] noted
|
| 185 |
+
<SPEECH_FACTORS_END>
|
| 186 |
+
|
| 187 |
+
<CASL_SKILLS_START>
|
| 188 |
+
Lexical/Semantic Skills: Standard Score ({semantic_score}), Percentile Rank ({semantic_percentile}%), {get_performance_level(semantic_score)}
|
| 189 |
+
Examples:
|
| 190 |
+
- Vocabulary diversity and semantic precision assessed
|
| 191 |
+
- Word-finding strategies and retrieval patterns analyzed
|
| 192 |
+
|
| 193 |
+
Syntactic Skills: Standard Score ({syntactic_score}), Percentile Rank ({syntactic_percentile}%), {get_performance_level(syntactic_score)}
|
| 194 |
+
Examples:
|
| 195 |
+
- Sentence structure complexity and grammatical accuracy evaluated
|
| 196 |
+
- Morphological skill development measured
|
| 197 |
+
|
| 198 |
+
Supralinguistic Skills: Standard Score ({fluency_score}), Percentile Rank ({fluency_percentile}%), {get_performance_level(fluency_score)}
|
| 199 |
+
Examples:
|
| 200 |
+
- Discourse organization and narrative coherence reviewed
|
| 201 |
+
- Pragmatic language use and communication effectiveness assessed
|
| 202 |
+
<CASL_SKILLS_END>
|
| 203 |
+
|
| 204 |
+
<TREATMENT_RECOMMENDATIONS_START>
|
| 205 |
+
- Implement word-finding strategies with semantic feature analysis and phonemic cuing
|
| 206 |
+
- Practice sentence formulation exercises targeting grammatical accuracy and complexity
|
| 207 |
+
- Use narrative structure activities with visual supports to improve discourse organization
|
| 208 |
+
- Incorporate self-monitoring techniques to increase awareness of speech patterns
|
| 209 |
+
- Apply fluency shaping strategies to reduce disfluencies and improve communication flow
|
| 210 |
+
<TREATMENT_RECOMMENDATIONS_END>
|
| 211 |
+
|
| 212 |
+
<EXPLANATION_START>
|
| 213 |
+
The language sample demonstrates patterns consistent with expressive language challenges affecting fluency, word retrieval, and syntactic formulation. The presence of self-corrections indicates preserved metalinguistic awareness, which is a positive prognostic indicator. Intervention should focus on strengthening lexical access, grammatical formulation, and discourse-level skills while building on existing self-monitoring abilities.
|
| 214 |
+
<EXPLANATION_END>"""
|
| 215 |
+
|
| 216 |
+
def parse_casl_response(response):
|
| 217 |
+
"""Parse structured response into components"""
|
| 218 |
+
def extract_section(text, section_name):
|
| 219 |
+
pattern = re.compile(f"<{section_name}_START>(.*?)<{section_name}_END>", re.DOTALL)
|
| 220 |
+
match = pattern.search(text)
|
| 221 |
+
return match.group(1).strip() if match else ""
|
| 222 |
+
|
| 223 |
+
sections = {
|
| 224 |
+
'speech_factors': extract_section(response, 'SPEECH_FACTORS'),
|
| 225 |
+
'casl_data': extract_section(response, 'CASL_SKILLS'),
|
| 226 |
+
'treatment_suggestions': extract_section(response, 'TREATMENT_RECOMMENDATIONS'),
|
| 227 |
+
'explanation': extract_section(response, 'EXPLANATION')
|
| 228 |
+
}
|
| 229 |
+
|
| 230 |
+
# Build formatted report
|
| 231 |
+
full_report = f"""# Speech Language Assessment Report
|
| 232 |
+
|
| 233 |
+
## Speech Factors Analysis
|
| 234 |
+
{sections['speech_factors']}
|
| 235 |
+
|
| 236 |
+
## CASL Skills Assessment
|
| 237 |
+
{sections['casl_data']}
|
| 238 |
+
|
| 239 |
+
## Treatment Recommendations
|
| 240 |
+
{sections['treatment_suggestions']}
|
| 241 |
+
|
| 242 |
+
## Clinical Explanation
|
| 243 |
+
{sections['explanation']}
|
| 244 |
+
"""
|
| 245 |
+
|
| 246 |
+
return {
|
| 247 |
+
'speech_factors': sections['speech_factors'],
|
| 248 |
+
'casl_data': sections['casl_data'],
|
| 249 |
+
'treatment_suggestions': sections['treatment_suggestions'],
|
| 250 |
+
'explanation': sections['explanation'],
|
| 251 |
+
'full_report': full_report,
|
| 252 |
+
'raw_response': response
|
| 253 |
+
}
|
| 254 |
+
|
| 255 |
+
def analyze_transcript(transcript, age, gender):
|
| 256 |
+
"""Analyze transcript using CASL framework"""
|
| 257 |
+
prompt = f"""
|
| 258 |
+
You are an expert speech-language pathologist conducting a comprehensive CASL-2 assessment.
|
| 259 |
+
Analyze this transcript for a {age}-year-old {gender} patient.
|
| 260 |
+
|
| 261 |
+
TRANSCRIPT:
|
| 262 |
+
{transcript}
|
| 263 |
+
|
| 264 |
+
Provide detailed analysis in this exact format:
|
| 265 |
+
|
| 266 |
+
<SPEECH_FACTORS_START>
|
| 267 |
+
Difficulty producing fluent speech: X, Y
|
| 268 |
+
Examples:
|
| 269 |
+
- "exact quote from transcript showing disfluency"
|
| 270 |
+
- "another example with specific evidence"
|
| 271 |
+
|
| 272 |
+
Word retrieval issues: X, Y
|
| 273 |
+
Examples:
|
| 274 |
+
- "quote showing word-finding difficulty"
|
| 275 |
+
- "example of circumlocution or pause"
|
| 276 |
+
|
| 277 |
+
Grammatical errors: X, Y
|
| 278 |
+
Examples:
|
| 279 |
+
- "quote showing morphological error"
|
| 280 |
+
- "example of syntactic difficulty"
|
| 281 |
+
|
| 282 |
+
Repetitions and revisions: X, Y
|
| 283 |
+
Examples:
|
| 284 |
+
- "quote showing self-correction"
|
| 285 |
+
- "example of repetition or revision"
|
| 286 |
+
<SPEECH_FACTORS_END>
|
| 287 |
+
|
| 288 |
+
<CASL_SKILLS_START>
|
| 289 |
+
Lexical/Semantic Skills: Standard Score (X), Percentile Rank (Y%), Performance Level
|
| 290 |
+
Examples:
|
| 291 |
+
- "specific vocabulary usage example"
|
| 292 |
+
- "semantic precision demonstration"
|
| 293 |
+
|
| 294 |
+
Syntactic Skills: Standard Score (X), Percentile Rank (Y%), Performance Level
|
| 295 |
+
Examples:
|
| 296 |
+
- "grammatical structure example"
|
| 297 |
+
- "morphological skill demonstration"
|
| 298 |
+
|
| 299 |
+
Supralinguistic Skills: Standard Score (X), Percentile Rank (Y%), Performance Level
|
| 300 |
+
Examples:
|
| 301 |
+
- "discourse organization example"
|
| 302 |
+
- "narrative coherence demonstration"
|
| 303 |
+
<CASL_SKILLS_END>
|
| 304 |
+
|
| 305 |
+
<TREATMENT_RECOMMENDATIONS_START>
|
| 306 |
+
- Specific, evidence-based treatment recommendation
|
| 307 |
+
- Another targeted intervention strategy
|
| 308 |
+
- Additional therapeutic approach with clear rationale
|
| 309 |
+
<TREATMENT_RECOMMENDATIONS_END>
|
| 310 |
+
|
| 311 |
+
<EXPLANATION_START>
|
| 312 |
+
Comprehensive clinical explanation of findings, their significance for diagnosis and prognosis, and relationship to functional communication needs.
|
| 313 |
+
<EXPLANATION_END>
|
| 314 |
+
|
| 315 |
+
Requirements:
|
| 316 |
+
1. Use exact quotes from the transcript as evidence
|
| 317 |
+
2. Provide realistic standard scores (70-130 range, mean=100, SD=15)
|
| 318 |
+
3. Calculate appropriate percentiles based on age norms
|
| 319 |
+
4. Give specific, actionable treatment recommendations
|
| 320 |
+
5. Consider developmental expectations for the patient's age
|
| 321 |
+
"""
|
| 322 |
+
|
| 323 |
+
response = call_bedrock(prompt)
|
| 324 |
+
return parse_casl_response(response)
|
| 325 |
+
|
| 326 |
+
def process_upload(file):
|
| 327 |
+
"""Process uploaded transcript file"""
|
| 328 |
+
if file is None:
|
| 329 |
+
return ""
|
| 330 |
+
|
| 331 |
+
file_path = file.name
|
| 332 |
+
file_ext = os.path.splitext(file_path)[1].lower()
|
| 333 |
+
|
| 334 |
+
try:
|
| 335 |
+
if file_ext == '.cha':
|
| 336 |
+
# Process CHAT format file
|
| 337 |
+
with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
|
| 338 |
+
content = f.read()
|
| 339 |
+
|
| 340 |
+
# Extract participant lines
|
| 341 |
+
par_lines = []
|
| 342 |
+
inv_lines = []
|
| 343 |
+
for line in content.splitlines():
|
| 344 |
+
line = line.strip()
|
| 345 |
+
if line.startswith('*PAR:') or line.startswith('*CHI:'):
|
| 346 |
+
par_lines.append(line)
|
| 347 |
+
elif line.startswith('*INV:') or line.startswith('*EXA:'):
|
| 348 |
+
inv_lines.append(line)
|
| 349 |
+
|
| 350 |
+
# Combine all relevant lines
|
| 351 |
+
all_lines = []
|
| 352 |
+
for line in content.splitlines():
|
| 353 |
+
line = line.strip()
|
| 354 |
+
if any(line.startswith(prefix) for prefix in ['*PAR:', '*CHI:', '*INV:', '*EXA:']):
|
| 355 |
+
all_lines.append(line)
|
| 356 |
+
|
| 357 |
+
return '\n'.join(all_lines) if all_lines else content
|
| 358 |
+
else:
|
| 359 |
+
# Read as plain text
|
| 360 |
+
with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
|
| 361 |
+
return f.read()
|
| 362 |
+
except Exception as e:
|
| 363 |
+
logger.error(f"Error reading uploaded file: {str(e)}")
|
| 364 |
+
return f"Error reading file: {str(e)}"
|
| 365 |
+
|
| 366 |
+
def transcribe_audio(audio_path):
|
| 367 |
+
"""Transcribe audio file to CHAT format"""
|
| 368 |
+
if not audio_path:
|
| 369 |
+
return "Please upload an audio file first.", "β No audio file provided"
|
| 370 |
+
|
| 371 |
+
if SPEECH_RECOGNITION_AVAILABLE:
|
| 372 |
+
try:
|
| 373 |
+
r = sr.Recognizer()
|
| 374 |
+
|
| 375 |
+
# Convert to WAV if needed
|
| 376 |
+
wav_path = audio_path
|
| 377 |
+
if not audio_path.endswith('.wav'):
|
| 378 |
+
try:
|
| 379 |
+
audio = pydub.AudioSegment.from_file(audio_path)
|
| 380 |
+
wav_path = audio_path.rsplit('.', 1)[0] + '.wav'
|
| 381 |
+
audio.export(wav_path, format="wav")
|
| 382 |
+
except Exception as e:
|
| 383 |
+
logger.warning(f"Audio conversion failed: {e}")
|
| 384 |
+
|
| 385 |
+
# Transcribe
|
| 386 |
+
with sr.AudioFile(wav_path) as source:
|
| 387 |
+
audio_data = r.record(source)
|
| 388 |
+
text = r.recognize_google(audio_data)
|
| 389 |
+
|
| 390 |
+
# Format as CHAT
|
| 391 |
+
sentences = re.split(r'[.!?]+', text)
|
| 392 |
+
chat_lines = []
|
| 393 |
+
for sentence in sentences:
|
| 394 |
+
sentence = sentence.strip()
|
| 395 |
+
if sentence:
|
| 396 |
+
chat_lines.append(f"*PAR: {sentence}.")
|
| 397 |
+
|
| 398 |
+
result = '\n'.join(chat_lines)
|
| 399 |
+
return result, "β
Transcription completed successfully"
|
| 400 |
+
|
| 401 |
+
except sr.UnknownValueError:
|
| 402 |
+
return "Could not understand audio clearly", "β Speech not recognized"
|
| 403 |
+
except sr.RequestError as e:
|
| 404 |
+
return f"Error with speech recognition service: {e}", "β Service error"
|
| 405 |
+
except Exception as e:
|
| 406 |
+
logger.error(f"Transcription error: {e}")
|
| 407 |
+
return f"Error during transcription: {str(e)}", f"β Transcription failed"
|
| 408 |
+
else:
|
| 409 |
+
# Demo transcription
|
| 410 |
+
demo_text = """*PAR: this is a demonstration transcription.
|
| 411 |
+
*PAR: to enable real audio processing install speech_recognition and pydub.
|
| 412 |
+
*PAR: the demo shows how transcribed text would appear in CHAT format."""
|
| 413 |
+
return demo_text, "βΉοΈ Demo mode - install speech_recognition for real audio processing"
|
| 414 |
+
|
| 415 |
+
def create_interface():
|
| 416 |
+
"""Create the main Gradio interface"""
|
| 417 |
+
|
| 418 |
+
with gr.Blocks(title="CASL Analysis Tool", theme=gr.themes.Soft()) as app:
|
| 419 |
+
|
| 420 |
+
gr.Markdown("""
|
| 421 |
+
# π£οΈ CASL Analysis Tool
|
| 422 |
+
**Comprehensive Assessment of Spoken Language (CASL-2)**
|
| 423 |
+
|
| 424 |
+
Professional speech-language assessment tool for clinical practice and research.
|
| 425 |
+
Supports transcript analysis, audio transcription, and comprehensive reporting.
|
| 426 |
+
""")
|
| 427 |
+
|
| 428 |
+
with gr.Tabs():
|
| 429 |
+
|
| 430 |
+
# Main Analysis Tab
|
| 431 |
+
with gr.TabItem("π Analysis"):
|
| 432 |
+
with gr.Row():
|
| 433 |
+
with gr.Column():
|
| 434 |
+
gr.Markdown("### π€ Patient Information")
|
| 435 |
+
|
| 436 |
+
patient_name = gr.Textbox(
|
| 437 |
+
label="Patient Name",
|
| 438 |
+
placeholder="Enter patient name"
|
| 439 |
+
)
|
| 440 |
+
record_id = gr.Textbox(
|
| 441 |
+
label="Medical Record ID",
|
| 442 |
+
placeholder="Enter medical record ID"
|
| 443 |
+
)
|
| 444 |
+
|
| 445 |
+
with gr.Row():
|
| 446 |
+
age = gr.Number(
|
| 447 |
+
label="Age (years)",
|
| 448 |
+
value=8,
|
| 449 |
+
minimum=1,
|
| 450 |
+
maximum=120
|
| 451 |
+
)
|
| 452 |
+
gender = gr.Radio(
|
| 453 |
+
["male", "female", "other"],
|
| 454 |
+
label="Gender",
|
| 455 |
+
value="male"
|
| 456 |
+
)
|
| 457 |
+
|
| 458 |
+
assessment_date = gr.Textbox(
|
| 459 |
+
label="Assessment Date",
|
| 460 |
+
placeholder="MM/DD/YYYY",
|
| 461 |
+
value=datetime.now().strftime('%m/%d/%Y')
|
| 462 |
+
)
|
| 463 |
+
clinician_name = gr.Textbox(
|
| 464 |
+
label="Clinician Name",
|
| 465 |
+
placeholder="Enter clinician name"
|
| 466 |
+
)
|
| 467 |
+
|
| 468 |
+
gr.Markdown("### π Speech Transcript")
|
| 469 |
+
|
| 470 |
+
sample_selector = gr.Dropdown(
|
| 471 |
+
choices=list(SAMPLE_TRANSCRIPTS.keys()),
|
| 472 |
+
label="Load Sample Transcript",
|
| 473 |
+
placeholder="Choose a sample to load"
|
| 474 |
+
)
|
| 475 |
+
|
| 476 |
+
file_upload = gr.File(
|
| 477 |
+
label="Upload Transcript File",
|
| 478 |
+
file_types=[".txt", ".cha"]
|
| 479 |
+
)
|
| 480 |
+
|
| 481 |
+
transcript = gr.Textbox(
|
| 482 |
+
label="Speech Transcript (CHAT format preferred)",
|
| 483 |
+
placeholder="Enter transcript text or load from samples/file...",
|
| 484 |
+
lines=12
|
| 485 |
+
)
|
| 486 |
+
|
| 487 |
+
analyze_btn = gr.Button(
|
| 488 |
+
"π Analyze Transcript",
|
| 489 |
+
variant="primary"
|
| 490 |
+
)
|
| 491 |
+
|
| 492 |
+
with gr.Column():
|
| 493 |
+
gr.Markdown("### π Analysis Results")
|
| 494 |
+
|
| 495 |
+
analysis_output = gr.Markdown(
|
| 496 |
+
label="Comprehensive CASL Analysis Report",
|
| 497 |
+
value="Analysis results will appear here after clicking 'Analyze Transcript'..."
|
| 498 |
+
)
|
| 499 |
+
|
| 500 |
+
gr.Markdown("### π€ Export Options")
|
| 501 |
+
if REPORTLAB_AVAILABLE:
|
| 502 |
+
export_btn = gr.Button("π Export as PDF", variant="secondary")
|
| 503 |
+
export_status = gr.Markdown("")
|
| 504 |
+
else:
|
| 505 |
+
gr.Markdown("β οΈ PDF export unavailable (ReportLab not installed)")
|
| 506 |
+
|
| 507 |
+
# Audio Transcription Tab
|
| 508 |
+
with gr.TabItem("π€ Audio Transcription"):
|
| 509 |
+
with gr.Row():
|
| 510 |
+
with gr.Column():
|
| 511 |
+
gr.Markdown("### π΅ Audio Processing")
|
| 512 |
+
gr.Markdown("""
|
| 513 |
+
Upload audio recordings for automatic transcription into CHAT format.
|
| 514 |
+
Supports common audio formats (.wav, .mp3, .m4a, .ogg, etc.)
|
| 515 |
+
""")
|
| 516 |
+
|
| 517 |
+
audio_input = gr.Audio(
|
| 518 |
+
type="filepath",
|
| 519 |
+
label="Audio Recording"
|
| 520 |
+
)
|
| 521 |
+
|
| 522 |
+
transcribe_btn = gr.Button(
|
| 523 |
+
"π§ Transcribe Audio",
|
| 524 |
+
variant="primary"
|
| 525 |
+
)
|
| 526 |
+
|
| 527 |
+
with gr.Column():
|
| 528 |
+
transcription_output = gr.Textbox(
|
| 529 |
+
label="Transcription Result (CHAT Format)",
|
| 530 |
+
placeholder="Transcribed text will appear here...",
|
| 531 |
+
lines=15
|
| 532 |
+
)
|
| 533 |
+
|
| 534 |
+
transcription_status = gr.Markdown("")
|
| 535 |
+
|
| 536 |
+
copy_to_analysis_btn = gr.Button(
|
| 537 |
+
"π Use for Analysis",
|
| 538 |
+
variant="secondary"
|
| 539 |
+
)
|
| 540 |
+
|
| 541 |
+
# Information Tab
|
| 542 |
+
with gr.TabItem("βΉοΈ About"):
|
| 543 |
+
gr.Markdown("""
|
| 544 |
+
## About the CASL Analysis Tool
|
| 545 |
+
|
| 546 |
+
This tool provides comprehensive speech-language assessment using the CASL-2 (Comprehensive Assessment of Spoken Language) framework.
|
| 547 |
+
|
| 548 |
+
### Features:
|
| 549 |
+
- **Speech Factor Analysis**: Automated detection of disfluencies, word retrieval issues, grammatical errors, and repetitions
|
| 550 |
+
- **CASL-2 Domains**: Assessment of Lexical/Semantic, Syntactic, and Supralinguistic skills
|
| 551 |
+
- **Professional Scoring**: Standard scores, percentiles, and performance levels
|
| 552 |
+
- **Audio Transcription**: Convert speech recordings to CHAT format transcripts
|
| 553 |
+
- **Treatment Recommendations**: Evidence-based intervention suggestions
|
| 554 |
+
|
| 555 |
+
### Supported Formats:
|
| 556 |
+
- **Text Files**: .txt format with manual transcript entry
|
| 557 |
+
- **CHAT Files**: .cha format following CHILDES conventions
|
| 558 |
+
- **Audio Files**: .wav, .mp3, .m4a, .ogg for automatic transcription
|
| 559 |
+
|
| 560 |
+
### CHAT Format Guidelines:
|
| 561 |
+
- Use `*PAR:` for patient utterances
|
| 562 |
+
- Use `*INV:` for investigator/clinician utterances
|
| 563 |
+
- Mark filled pauses as `&-um`, `&-uh`
|
| 564 |
+
- Mark repetitions with `[/]`
|
| 565 |
+
- Mark revisions with `[//]`
|
| 566 |
+
- Mark errors with `[*]`
|
| 567 |
+
|
| 568 |
+
### Usage Tips:
|
| 569 |
+
1. Load a sample transcript to see the expected format
|
| 570 |
+
2. Enter patient information for context-appropriate analysis
|
| 571 |
+
3. Upload or type transcript in CHAT format for best results
|
| 572 |
+
4. Review analysis results and treatment recommendations
|
| 573 |
+
5. Export professional PDF reports for clinical documentation
|
| 574 |
+
|
| 575 |
+
### Technical Notes:
|
| 576 |
+
- **Demo Mode**: Works without external dependencies using simulated analysis
|
| 577 |
+
- **Enhanced Mode**: Requires AWS Bedrock credentials for AI-powered analysis
|
| 578 |
+
- **Audio Processing**: Requires speech_recognition library for real transcription
|
| 579 |
+
- **PDF Export**: Requires ReportLab library for professional reports
|
| 580 |
+
|
| 581 |
+
For support or questions, please refer to the documentation.
|
| 582 |
+
""")
|
| 583 |
+
|
| 584 |
+
# Event Handlers
|
| 585 |
+
def load_sample_transcript(sample_name):
|
| 586 |
+
"""Load selected sample transcript"""
|
| 587 |
+
if sample_name and sample_name in SAMPLE_TRANSCRIPTS:
|
| 588 |
+
return SAMPLE_TRANSCRIPTS[sample_name]
|
| 589 |
+
return ""
|
| 590 |
+
|
| 591 |
+
def perform_analysis(transcript_text, age_val, gender_val):
|
| 592 |
+
"""Perform CASL analysis on transcript"""
|
| 593 |
+
if not transcript_text or len(transcript_text.strip()) < 20:
|
| 594 |
+
return "β **Error**: Please provide a longer transcript (minimum 20 characters) for meaningful analysis."
|
| 595 |
+
|
| 596 |
+
try:
|
| 597 |
+
# Perform analysis
|
| 598 |
+
results = analyze_transcript(transcript_text, age_val, gender_val)
|
| 599 |
+
return results['full_report']
|
| 600 |
+
|
| 601 |
+
except Exception as e:
|
| 602 |
+
logger.exception("Analysis error")
|
| 603 |
+
return f"β **Error during analysis**: {str(e)}\n\nPlease check your transcript format and try again."
|
| 604 |
+
|
| 605 |
+
def copy_transcription_to_analysis(transcription_text):
|
| 606 |
+
"""Copy transcription result to analysis tab"""
|
| 607 |
+
return transcription_text
|
| 608 |
+
|
| 609 |
+
# Connect event handlers
|
| 610 |
+
sample_selector.change(
|
| 611 |
+
load_sample_transcript,
|
| 612 |
+
inputs=[sample_selector],
|
| 613 |
+
outputs=[transcript]
|
| 614 |
+
)
|
| 615 |
+
|
| 616 |
+
file_upload.upload(
|
| 617 |
+
process_upload,
|
| 618 |
+
inputs=[file_upload],
|
| 619 |
+
outputs=[transcript]
|
| 620 |
+
)
|
| 621 |
+
|
| 622 |
+
analyze_btn.click(
|
| 623 |
+
perform_analysis,
|
| 624 |
+
inputs=[transcript, age, gender],
|
| 625 |
+
outputs=[analysis_output]
|
| 626 |
+
)
|
| 627 |
+
|
| 628 |
+
transcribe_btn.click(
|
| 629 |
+
transcribe_audio,
|
| 630 |
+
inputs=[audio_input],
|
| 631 |
+
outputs=[transcription_output, transcription_status]
|
| 632 |
+
)
|
| 633 |
+
|
| 634 |
+
copy_to_analysis_btn.click(
|
| 635 |
+
copy_transcription_to_analysis,
|
| 636 |
+
inputs=[transcription_output],
|
| 637 |
+
outputs=[transcript]
|
| 638 |
+
)
|
| 639 |
+
|
| 640 |
+
return app
|
| 641 |
+
|
| 642 |
+
# Create and launch the application
|
| 643 |
+
if __name__ == "__main__":
|
| 644 |
+
# Check for optional dependencies
|
| 645 |
+
missing_deps = []
|
| 646 |
+
if not REPORTLAB_AVAILABLE:
|
| 647 |
+
missing_deps.append("reportlab (for PDF export)")
|
| 648 |
+
if not SPEECH_RECOGNITION_AVAILABLE:
|
| 649 |
+
missing_deps.append("speech_recognition & pydub (for audio transcription)")
|
| 650 |
+
|
| 651 |
+
if missing_deps:
|
| 652 |
+
print("π Optional dependencies not found:")
|
| 653 |
+
for dep in missing_deps:
|
| 654 |
+
print(f" - {dep}")
|
| 655 |
+
print("The app will work with reduced functionality.")
|
| 656 |
+
|
| 657 |
+
if not bedrock_client:
|
| 658 |
+
print("βΉοΈ AWS credentials not configured - using demo mode for analysis.")
|
| 659 |
+
print(" Configure AWS_ACCESS_KEY and AWS_SECRET_KEY for enhanced AI analysis.")
|
| 660 |
+
|
| 661 |
+
print("π Starting CASL Analysis Tool...")
|
| 662 |
+
|
| 663 |
+
# Create and launch the app
|
| 664 |
+
app = create_interface()
|
| 665 |
+
app.launch(
|
| 666 |
+
show_api=False,
|
| 667 |
+
server_name="0.0.0.0",
|
| 668 |
+
server_port=7860
|
| 669 |
+
)
|
requirements.txt
CHANGED
|
@@ -1,12 +1,9 @@
|
|
| 1 |
gradio>=4.0.0
|
| 2 |
-
pandas>=1.
|
| 3 |
-
numpy>=1.
|
| 4 |
-
matplotlib>=3.
|
| 5 |
-
|
| 6 |
-
Pillow>=8.0.0
|
| 7 |
reportlab>=3.6.0
|
| 8 |
-
|
| 9 |
-
|
| 10 |
-
PyPDF2>=3.0.0
|
| 11 |
-
speechrecognition>=3.8.1
|
| 12 |
pydub>=0.25.0
|
|
|
|
| 1 |
gradio>=4.0.0
|
| 2 |
+
pandas>=1.3.0
|
| 3 |
+
numpy>=1.20.0
|
| 4 |
+
matplotlib>=3.3.0
|
| 5 |
+
boto3>=1.20.0
|
|
|
|
| 6 |
reportlab>=3.6.0
|
| 7 |
+
PyPDF2>=2.0.0
|
| 8 |
+
speech_recognition>=3.8.0
|
|
|
|
|
|
|
| 9 |
pydub>=0.25.0
|