pelican-nlp 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

pelican_nlp/configuration_files/config_fluency.yml

@@ -0,0 +1,108 @@
+# Configuration file for fluency task
+# =======================================
+input_file: "text" #or 'audio'
+fluency_task: &fluency_flag true
+#========================================
+
+#general configurations; always adapt
+PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/FluencyTest"
+language: "german"
+multiple_sessions: &session_flag false
+
+corpus_names: #names of fluency tasks (e.g. "animals", "clothes")
+  - "animals"
+  - "clothes"
+  - "food"
+
+#Specify linguistic metrics to extract
+metric_to_extract: 'embeddings' #Possible options: 'embeddings', 'logits'
+output_document_information: true
+#====================================================================
+
+#Optional configurations; Change with preference. However, default settings recommended
+cleaning_options:
+  general_cleaning: true
+  #Options for fluency tasks
+  fluency_task: *fluency_flag
+  word_splitter: ';' #default split with ',' add different word_splitter if necessary
+  remove_hyphens: true
+  remove_duplicates: false
+  lowercase: false
+  #Optional cleaning
+  remove_brackets_and_bracketcontent: false #default 'false'
+  remove_timestamps: false #default 'false'
+  timestamp_pattern_example: null #e.g. "#00:00:23-00#"
+  remove_punctuation: false #Careful!: If set to true word_splitter might be removed
+
+options_embeddings:
+  tokenization_method: "whitespace" #or "model"
+  model_name: "fastText" #e.g. "fastText", "xlm-roberta-base"
+  pytorch_based_model: false
+  method: "model_instance"
+  max_length: null
+  clean_embedding_tokens: true
+
+  semantic-similarity: true
+  distance-from-randomness: false
+
+options_dis_from_randomness:
+  window_size: 8
+  min_len: null
+  bootstrap: 10000
+  shuffle_mode: 'include0_includeN'
+  parallel_computing: false #not yet set up
+
+options_semantic-similarity:
+  window_sizes: #'all' or window size as integer
+    - 2
+    - 8
+#==================================================================
+
+#Extra configurations;
+task_name: "fluency"
+create_aggregation_of_results: true
+
+pipeline_options:
+  quality_check: false
+  clean_text: true
+  tokenize_text: false
+  normalize_text: false
+
+general_cleaning_options:
+  strip_whitespace: true
+  merge_multiple_whitespaces: true
+  remove_whitespace_before_punctuation: true
+  merge_newline_characters: true
+  remove_backslashes: true
+
+has_multiple_sections: false
+has_section_titles: false
+section_identification: null
+number_of_sections: 1
+number_of_speakers: 1
+discourse: false
+
+document_information_output:
+  parameters:
+    - subject_ID
+    - fluency_word_count
+    - fluency_duplicate_count
+
+#================================================================
+
+#Detail configurations; Changes optional, mostly used for quality checking / error handling
+recompute_everything: true
+number_of_subjects: null
+
+# Filename components configuration
+filename_components:
+  subject: true    # mandatory
+  session: *session_flag
+  task: true       # mandatory
+  task_addition: false
+  corpus: true    # typically true for fluency tasks (e.g., "animals", "clothes")
+  metric: true
+  additional_tags: []
+
+
+

pelican_nlp/configuration_files/config_general.yml

@@ -0,0 +1,131 @@
+# Master Configuration File
+# ========================
+
+# Basic Settings
+# -------------
+input_file: "text"  # Options: 'text' or 'audio'
+PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/FluencyTest"
+language: "german"  # Options: 'german', 'english'
+recompute_everything: true  # If false, reuses previously computed results
+
+# Task Configuration
+# -----------------
+task_name: "fluency"  # Options: 'fluency', 'interview'
+fluency_task: &fluency_flag true  # Flag for fluency-specific settings
+discourse: &discourse_flag false  # Flag for discourse-specific settings
+corpus_names:  # List of task corpora
+  - "animals"
+
+# Session and Subject Settings
+# --------------------------
+multiple_sessions: false
+number_of_subjects: null  # If null, auto-detected
+number_of_speakers: 1
+subject_speakertag: null  # Speaker tag for subject (e.g., "B")
+
+# Document Structure
+# ----------------
+has_multiple_sections: false
+has_section_titles: false
+section_identification: null  # e.g., "Section:"
+number_of_sections: 1  # If null, auto-detected
+
+# Processing Pipeline
+# -----------------
+pipeline_options:
+  quality_check: false
+  clean_text: true
+  tokenize_text: false
+  normalize_text: false
+
+# Metric Extraction
+# ---------------
+metric_to_extract: "embeddings"  # Options: 'embeddings', 'logits'
+extract_logits: null
+extract_embeddings: true
+
+# Cleaning Options
+# --------------
+cleaning_options:
+  general_cleaning: true
+  remove_punctuation: false
+  lowercase: true
+  remove_brackets_and_bracketcontent: false
+  remove_timestamps: false
+  timestamp_pattern_example: null  # e.g., "#00:00:23-00#"
+  # Fluency-specific options
+  fluency_task: *fluency_flag
+  word_splitter: ';'
+  remove_hyphens: true
+  remove_duplicates: true
+
+general_cleaning_options:
+  strip_whitespace: true
+  merge_multiple_whitespaces: true
+  remove_whitespace_before_punctuation: true
+  merge_newline_characters: true
+  remove_backslashes: true
+
+# Embedding Options
+# ---------------
+options_embeddings:
+  tokenization_method: "whitespace"  # Options: 'whitespace', 'model'
+  model_name: "fastText"  # Options: 'fastText', 'xlm-roberta-base'
+  pytorch_based_model: false
+  method: "model_instance"
+  max_length: 512
+  clean_embedding_tokens: true
+  remove_punctuation: false
+  lowercase: false
+  keep_speakertags: false
+  semantic-similarity: true
+  window_size: null
+  clean_tokens: true
+  divergence_from_optimality: false
+  output_options:
+    exclude_special_tokens: true
+    remove_'_'_character: true
+    remove_speaker_labels: true
+    remove_punctuation_and_symbols: true
+    remove_brackets_and_content: true
+
+# Logits Options
+# -------------
+options_logits:
+  chunk_size: 128
+  overlap_size: 64
+  tokenization_method: "model"
+  model_name: "DiscoResearch/Llama3-German-8B-32k"
+  remove_punctuation: true
+  lowercase: true
+  keep_speakertags: true
+
+# Analysis Options
+# --------------
+options_semantic-similarity:
+  window_sizes:  # 'all' or window size as integer
+    - 2
+    - 8
+
+options_dis_from_randomness:
+  window_size: 8
+  min_len: null
+  bootstrap: 10000
+  shuffle_mode: 'include0_includeN'
+  parallel_computing: false
+
+# Normalization Options
+# -------------------
+normalization_options:
+  method: "lemmatization"  # Options: 'lemmatization', 'stemming'
+
+# Filename Configuration
+# --------------------
+filename_components:
+  subject: true    # mandatory
+  session: false
+  task: true       # mandatory
+  task_addition: false
+  corpus: true
+  metric: true
+  additional_tags: []

pelican_nlp/configuration_files/config_morteza.yml

@@ -0,0 +1,103 @@
+# Configuration file: variable parameters
+# =======================================
+input_file: "text" #or 'audio'
+discourse: &discourse_flag true
+
+#PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/KetamineStudy/KetamineStudy_ProjectFolder/" # Set default to home directory, e.g., '/home/usr/...'
+PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/Morteza/"
+language: "german" # Possibly add options for German and English
+
+task_name: "interview" # Give name of task used for creation of the input file (e.g., ['fluency', 'interview'])
+corpus_names:
+  - "schizophrenia"
+
+
+number_of_subjects: null # Specify number of subjects; if 'null', number of subjects is automatically detected
+multiple_sessions: false # Set to True if multiple sessions per subject
+
+recompute_everything: true #If set to 'false' pelican-nlp will try to reuse previously computed results stored on your drive
+
+has_multiple_sections: false #evaluated independently
+has_section_titles: false
+section_identification: null #e.g. "Section:", 'null' if file does not have multiple sections, use pattern that is unlikely to appear in rest of transcript
+number_of_sections: null #if 'null' number of sections automatically detected, however, specifying number recommended if known.
+
+number_of_speakers: 3
+subject_speakertag: "B"
+
+metric_to_extract: "embeddings"
+extract_logits: false
+extract_embeddings: true
+
+pipeline_options:
+  quality_check: false
+  clean_text: true
+  tokenize_text: false
+  normalize_text: false
+
+tokenization: "wordLevel" # Options: 'characterLevel', 'subWordLevel'
+
+# Options for extract_logits
+chunk_size: null
+overlap_size: null
+
+# Options for extract_embeddings
+window_sizes: [2]
+metric_function: cosine_similarity
+aggregation_functions: mean_of_means
+
+
+fluency_task: &fluency_flag false
+cleaning_options:
+  general_cleaning: true # General cleaning options used for most text preprocessing, default: True.
+  remove_brackets_and_bracketcontent: true
+  remove_timestamps: true
+  timestamp_pattern_example: "#00:00:19-0#"
+  #Options for fluency tasks
+  fluency_task: *fluency_flag
+  word_splitter: null
+  remove_hyphens: null
+  remove_duplicates: null
+
+general_cleaning_options:
+  strip_whitespace: true
+  merge_multiple_whitespaces: true
+  remove_whitespace_before_punctuation: true
+  merge_newline_characters: true
+  remove_backslashes: true
+
+tokenization_options_logits:
+  method: "model_instance" # Options: model_instance, regex, nltk, etc.
+  model_name: "DiscoResearch/Llama3-German-8B-32k" # Replace with your model instance name
+  remove_punctuation: true
+  lowercase: true
+
+options_embeddings:
+  tokenization_method: "model_roberta" #or "whitespace", "model"
+  max_length: 512 #max sequence length
+  model_name: "xlm-roberta-base" #e.g. "fastText", "xlm-roberta-base"
+  pytorch_based_model: true
+  method: "model_instance"
+  remove_punctuation: false
+  lowercase: false
+  keep_speakertags: true
+  clean_embedding_tokens: true
+  output_options:
+    exclude_special_tokens: true
+    remove_'_'_character: true
+    remove_speaker_labels: true
+    remove_punctuation_and_symbols: true
+    remove_brackets_and_content: true
+
+  window_size: null
+
+  semantic-similarity: false
+  distance-from-randomness: false
+
+normalization_options:
+  method: "lemmatization" #Options: lemmatization or stemming
+
+create_aggregation_of_results: false
+output_document_information: false
+
+

pelican_nlp/praat/__init__.py

@@ -0,0 +1,29 @@
+import os
+
+# Get the directory where the Praat scripts are stored
+PRAAT_SCRIPTS_DIR = os.path.dirname(os.path.abspath(__file__))
+
+# Define paths to individual scripts
+PROSOMAIN_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosomain.praat')
+PROSOGRAM_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosogram.praat')
+PROSOPLOT_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosoplot.praat')
+SEGMENT_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'segment.praat')
+STYLIZE_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'stylize.praat')
+POLYTONIA_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'polytonia.praat')
+UTIL_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'util.praat')
+EPS_CONV_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'eps_conv.praat')
+SETUP_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'setup.praat')
+
+# Export all script paths
+__all__ = [
+    'PRAAT_SCRIPTS_DIR',
+    'PROSOMAIN_SCRIPT',
+    'PROSOGRAM_SCRIPT',
+    'PROSOPLOT_SCRIPT',
+    'SEGMENT_SCRIPT',
+    'STYLIZE_SCRIPT',
+    'POLYTONIA_SCRIPT',
+    'UTIL_SCRIPT',
+    'EPS_CONV_SCRIPT',
+    'SETUP_SCRIPT'
+]

{pelican_nlp-0.1.0.dist-info → pelican_nlp-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pelican_nlp
-Version: 0.1.0
+Version: 0.1.2
 Summary: Preprocessing and Extraction of Linguistic Information for Computational Analysis
 Author-email: Yves Pauli <yves.pauli@gmail.com>
 License-Expression: CC-BY-NC-4.0
@@ -51,7 +51,7 @@ PELICAN_nlp
 PELICAN_nlp stands for "Preprocessing and Extraction of Linguistic Information for Computational Analysis - Natural Language Processing". This package enables the creation of standardized and reproducible language processing pipelines, extracting linguistic features from various tasks like discourse, fluency, and image descriptions.
 
 .. image:: https://img.shields.io/pypi/v/package-name.svg
-    :target: https://pypi.org/project/package-name/
+    :target: https://pypi.org/project/pelican-nlp/
     :alt: PyPI version
 
 .. image:: https://img.shields.io/github/license/username/package-name.svg
@@ -59,7 +59,7 @@ PELICAN_nlp stands for "Preprocessing and Extraction of Linguistic Information f
     :alt: License
 
 .. image:: https://img.shields.io/pypi/pyversions/package-name.svg
-    :target: https://pypi.org/project/package-name/
+    :target: https://pypi.org/project/pelican-nlp/
     :alt: Supported Python Versions
 
 Installation
@@ -75,13 +75,16 @@ For the latest development version:
 
 .. code-block:: bash
 
-    pip install git+https://github.com/ypauli/PELICAN_nlp.git
+    pip install https://github.com/yourusername/yourrepo/releases/tag/v0.1.0-alpha
 
 Usage
 =====
 
 To use the pelican_nlp package:
 
+Adapt your configuration file to your needs.
+ALWAYS change the specified project folder location.
+
 .. code-block:: python
 
     from pelican_nlp.main import Pelican
@@ -94,7 +97,7 @@ For reliable operation, data must be stored in the *Language Processing Data Str
 
 Text and audio files should follow this naming convention:
 
-subjectID_sessionID_task_task-supplement_corpus.extension
+[subjectID]_[sessionID]_[task]_[task-supplement]_[corpus].[extension]
 
 - subjectID: ID of subject (e.g., sub-01), mandatory
 - sessionID: ID of session (e.g., ses-01), if available
@@ -104,7 +107,8 @@ subjectID_sessionID_task_task-supplement_corpus.extension
 - extension: file extension (e.g., txt / pdf / docx / rtf), mandatory
 
 Example filenames:
-- sub-01_ses-01_interview_schizophrenia.rtf
+
+- sub-01_interview_schizophrenia.rtf
 - sub-03_ses-02_fluency_semantic_animals.docx
 
 To optimize performance, close other programs and limit GPU usage during language processing.
@@ -121,26 +125,15 @@ Features
 Examples
 ========
 
-Here's a detailed usage example:
-
-.. code-block:: python
-
-    from package_name import SomeClass
-
-    configuration_file = "config_fluency.yml"
-    pelican.run(configuration_file)
-
-*Link to config_fluency.yml*
-
-Sample folder for data collection of the semantic fluency task:
-*Link to sample_folder*
+You can find example setups in the [`examples/`](https://github.com/ypauli/PELICAN-nlp/examples) folder.
+ALWAYS change the path to the project folder specified in the configuration file to your specific project location.
 
 Contributing
 ============
 
-Contributions are welcome! Please check out the `contributing guide <https://github.com/ypauli/PELICAN/blob/main/CONTRIBUTING.md>`_.
+Contributions are welcome! Please check out the `contributing guide <https://github.com/ypauli/PELICAN-nlp/blob/main/CONTRIBUTING.md>`_.
 
 License
 =======
 
-This project is licensed under Attribution-NonCommercial 4.0 International. See the `LICENSE <https://github.com/ypauli/PELICAN/blob/main/LICENSE>`_ file for details.
+This project is licensed under Attribution-NonCommercial 4.0 International. See the `LICENSE <https://github.com/ypauli/PELICAN-nlp/blob/main/LICENSE>`_ file for details.

pelican_nlp-0.1.2.dist-info/RECORD

@@ -0,0 +1,75 @@
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