pelican-nlp 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

pelican_nlp/Nils_backup/fluency/utils.py

@@ -0,0 +1,41 @@
+"""
+Utility functions for the VELAS fluency analysis pipeline.
+"""
+import os
+from pathlib import Path
+from typing import List, Dict
+
+def ensure_output_dir(path: str) -> None:
+    """
+    Create output directory if it doesn't exist.
+    
+    Args:
+        path: Path to create. Can be a directory path or a file path.
+              If it's a file path, the directory containing the file will be created.
+              If it's a directory path, the directory itself will be created.
+    """
+    # If path ends with a file extension, get its directory
+    if '.' in os.path.basename(path):
+        dir_path = os.path.dirname(os.path.abspath(path))
+    else:
+        dir_path = os.path.abspath(path)
+    
+    Path(dir_path).mkdir(parents=True, exist_ok=True)
+
+def validate_input_data(filepaths: Dict[str, str]) -> Dict[str, str]:
+    """
+    Check if input files exist and return any errors.
+    
+    Args:
+        filepaths: Dictionary mapping file descriptions to their paths
+                  e.g., {"behavioral_data": "/path/to/behav.csv"}
+    
+    Returns:
+        Dictionary of error messages for missing files.
+        Empty dict if all files exist.
+    """
+    errors = {}
+    for description, path in filepaths.items():
+        if not os.path.exists(path):
+            errors[description] = f"File not found: {path}"
+    return errors 

pelican_nlp/Nils_backup/speaker_diarization_Nils.py

@@ -0,0 +1,328 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Jul  3 14:21:27 2024
+
+@author: nilsl
+"""
+
+import re
+from collections import defaultdict, OrderedDict
+import os
+import re
+import chardet
+from collections import defaultdict, OrderedDict
+from nltk.tokenize import sent_tokenize, word_tokenize
+from nltk.corpus import stopwords
+from striprtf.striprtf import rtf_to_text
+import numpy as np
+from text_cleaner import TextCleaner
+
+protocol = {
+    "1": [
+        "täglichen Leben",
+        "ein paar Dinge",
+        "ein paar Sachen",
+        "über sich erzählen",
+    ],
+    "2": [
+        "etwas Wichtiges",
+        "Ihrer Kindheit",
+        "letzte Woche",
+        "in Ihrem Leben",
+        "beliebigen Zeit",
+        "zurückdenken",
+    ],
+    "3": [
+        "Ihre Gesundheit",
+        "Gesundheit sprechen",
+        "psychische Krankheit",
+        "seit Beginn",
+        "wie Sie sich gefühlt haben",
+    ],
+    "4": [
+        "erste Bild",
+        "Bild Nummer",
+        "zweite Bild",
+        "dritte Bild",
+        "auf dem Bild",
+        "Bild sehen",
+    ],
+    "5": [
+        "Geschichte zeigen",
+        "der Reihe nach",
+        "Bilder aus einer Geschichte",
+        "Bilder weg",
+        "ein paar Bilder",
+        "Bilderreihe",
+        "Geschichte aus Bilder",
+        "Geschichte aus Bildern",
+        "so viel Zeit",
+    ],
+    "6": [
+        "wiederkehrende Träume",
+        "solche Träume",
+        "Träume",
+        "wiederkehrenden Traum",
+    ],
+    "7": [
+        "einseitige",
+        "geschriebene Geschichte",
+        "Geschichte geschrieben",
+        "Blatt",
+        "eine Minute",
+        "eigenen Worten",
+        "eigene Worte",
+        "laut vorzulesen",
+        "laut vorlesen",
+    ],
+}
+
+def load_rtf_files(directory):
+    """Load and aggregate RTF files by patient and task."""
+    content_by_patient_and_task = defaultdict(lambda: defaultdict(str))
+
+    for filename in os.listdir(directory):
+        if filename.endswith(".rtf") and not filename.startswith("."):
+            file_path = os.path.join(directory, filename)
+            patient_id, task = parse_filename(filename)
+            base_task_name = (
+                "_".join(task.split("_")[:-1]) if "teil" in task else task
+            )
+            try:
+                rtf_content = read_rtf(file_path)
+                content_by_patient_and_task[patient_id][
+                    base_task_name
+                ] += f" {rtf_content}"
+            except:
+                continue
+
+    return content_by_patient_and_task
+
+
+def parse_filename(filename):
+    """Parse filename to extract patient ID and task."""
+    filename = filename[:-4]
+    parts = filename.split("_")
+    patient_id = parts[0]
+    task = parts[2] if len(parts) > 2 else "unknown"
+    part_info = parts[3] if len(parts) > 3 else ""
+    full_task = f"{task}_{part_info}" if part_info else task
+    return patient_id, full_task
+
+
+def read_rtf(file_path):
+    """Read RTF file and convert its content to plain text."""
+    with open(file_path, "rb") as file:
+        raw_data = file.read()
+        result = chardet.detect(raw_data)
+        encoding = result["encoding"]
+
+    with open(file_path, "r", encoding=encoding, errors="ignore") as file:
+        rtf_content = file.read()
+
+    return rtf_to_text(rtf_content)
+
+
+def split_into_lines(text):
+    """Split text into lines, filtering out empty lines and unwanted content."""
+    lines = text.splitlines()
+    return [
+        line
+        for line in lines
+        if line.strip() and ".mp3" not in line and "audio" not in line
+    ]
+
+
+def extract_and_remove_hashtags(text):
+    """Extract and remove hashtags from the text."""
+    pattern = r"#(.*?)#"
+    matches = re.findall(pattern, text)
+    text_without_hashtags = re.sub(pattern, "", text)
+    return text_without_hashtags, matches
+
+
+class Line:
+    """Represents a line of text with associated metadata."""
+
+    def __init__(self, speaker, text, line_number, tokenizer=None):
+        self.speaker = speaker
+        self.text = text
+        self.line_number = line_number
+        self.length_in_words = len(self.text.split())
+
+
+def process_lines(
+        pat_id,
+        task,
+        lines,
+        stopwords_list,
+        remove_numbers=False,
+
+):
+    """Process lines of text to create a Document object."""
+    document = Document(pat_id, task)
+    for i, line_text in enumerate(lines, start=1):
+        speaker = (
+            "Investigator"
+            if line_text.startswith(("I:", "I::", "I1:", "I2:"))
+            else "Subject"
+        )
+        cleaned_line = TextCleaner.clean_text_diarization_all(line_text, stopwords_list, remove_numbers)
+        if cleaned_line != ".":
+            line = Line(speaker, cleaned_line, i)
+            document.add_line(line)
+    return document
+
+
+def main(
+        transcripts_dict,
+        output_path,
+        task_dir,
+        protocol,
+        remove_stopwords,
+        remove_numbers,
+):
+    """Main function to process documents."""
+    if not os.path.exists(output_path):
+        os.makedirs(output_path)
+        print(f"Folder '{output_path}' was created.")
+    else:
+        print(f"Folder '{output_path}' already exists.")
+
+    if remove_stopwords:
+        stop_list = list(stopwords.words("german"))
+    else:
+        stop_list = []
+
+    for patient_id, tasks in transcripts_dict.items():
+        for task, rtf_content in tasks.items():
+
+            no_hashtags, hashtags = extract_and_remove_hashtags(
+                rtf_content
+            )
+
+            lines = split_into_lines(no_hashtags)
+            document = process_lines(
+                patient_id,
+                task,
+                lines,
+                stop_list,
+                remove_numbers=remove_numbers,
+            )
+
+            if task_dir == "discourse":
+                document.segment_task(protocol)
+
+            document.compile_texts_and_tags()
+            s_tok = np.array(document.word_tags) == "s"
+            words = np.array(document.words)
+
+            with open(output_path + f"{patient_id}_{task}.txt", 'w', encoding='utf-8') as file:
+                file.write(" ".join(words[s_tok]))
+
+
+#Document class from original diarization script
+class Document:
+    """Represents a document with multiple lines of text and associated metadata."""
+
+    def __init__(self, pat_id, task, lines=None):
+        self.pat_id = pat_id
+        self.task = task
+        self.lines = lines if lines is not None else []
+        self.has_segments = True if task == "discourse" else False
+        self.sections = {}
+        self.section_metrics = {}
+        self.length_in_lines = len(self.lines)
+        self.length_in_words = sum(line.length_in_words for line in self.lines)
+
+        # Initialize segments to a default value if no sections are applicable
+        self.segments = ['default'] * len(self.lines) if not self.has_segments else []
+
+    def add_line(self, line):
+        self.lines.append(line)
+        self.length_in_lines = len(self.lines)
+        self.length_in_words += line.length_in_words
+
+        if not self.has_segments:
+            self.segments.append('default')
+
+    def compile_texts_and_tags(self):
+        """Compile lists of all words and tokens with corresponding speaker tags."""
+        self.words, self.word_tags, = (
+            [],
+            [],
+        )
+        self.word_segments = []
+
+        for line, segment in zip(self.lines, self.segments):
+            line_words = line.text.split()
+            tag = "i" if line.speaker.lower() == "investigator" else "s"
+
+            self.word_segments.extend([segment] * len(line_words))
+            self.words.extend(line_words)
+            self.word_tags.extend([tag] * len(line_words))
+
+    def segment_task(self, protocol, cutoff=1):
+        """Segment the document based on the given protocol and store sections."""
+        if not self.has_segments:
+            return self.segments  # Return default segments if segmentation not applicable
+
+        patterns = {
+            section: re.compile(
+                "|".join(f"(?:\\b{re.escape(term)}\\b)" for term in terms),
+                re.IGNORECASE,
+            )
+            for section, terms in protocol.items()
+        }
+
+        match_scores = defaultdict(list)
+        for section, pattern in patterns.items():
+            for line_index, line in enumerate(self.lines):
+                if pattern.search(line.text):
+                    match_scores[section].append(line_index)
+
+        section_order = sorted(protocol.keys(), key=lambda x: int(x))
+        section_starts = OrderedDict()
+        last_index_used = -1
+
+        for section in section_order:
+            line_indices = match_scores[section]
+            valid_starts = [idx for idx in line_indices if idx > last_index_used and len(line_indices) >= cutoff]
+            if valid_starts:
+                start_line = min(valid_starts)
+                section_starts[section] = start_line
+                last_index_used = start_line
+
+        segment_names = ["1"] * len(self.lines)
+        current_section = None
+        for i in range(len(self.lines)):
+            if i in section_starts.values():
+                current_section = [sec for sec, start in section_starts.items() if start == i][0]
+            segment_names[i] = current_section if current_section else "default"
+
+        self.segments = segment_names
+        self.sections = self._create_sections(segment_names)
+        return segment_names
+
+    def _create_sections(self, segment_names):
+        sections = defaultdict(list)
+        for line, segment in zip(self.lines, segment_names):
+            sections[segment].append(line)
+        return sections
+
+
+if __name__ == "__main__":
+    for task_dir in ["interview"]:
+        transcripts_directory = os.path.join(
+            "..", "..", "..", "data", "language", task_dir, "transcripts")
+
+        transcripts_dict = load_rtf_files(transcripts_directory)
+        print(transcripts_dict.keys())
+
+        args = {
+            "remove_stopwords": False,
+            "remove_numbers": False,
+        }
+        output_path = f"/Users/nilsl/Documents/PUK/VELAS/data/language/{task_dir}/preprocessed_transcripts/"
+        main(transcripts_dict, output_path, task_dir, protocol, **args)