pelican-nlp 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

pelican_nlp/Nils_backup/fluency/plotting_utils.py

@@ -0,0 +1,170 @@
+"""
+Shared utilities and constants for plotting functions.
+"""
+
+# Colors for different groups
+COLORS = {
+    "Patients": '#242424',
+    "Psychosis": '#242424',
+    "HS": '#6d6d6d',
+    "LS": '#b6b6b6',
+    "Low Sczt": '#b6b6b6',
+    "High Sczt": '#6d6d6d',
+}
+
+# Colors for different outcomes
+OUTCOME_COLORS = {
+    "Age": '#2b2b2b',
+    "Education": '#cc78bc',
+    "Male Gender": '#949494',
+    "German Native":  'sienna',
+    "Other Native": 'slategrey', 
+    'Working Memory': '#2b2b2b',
+    'Psychomotor Speed': '#cc78bc',
+    'Negative Inhibition': '#949494',
+    'MSS Pos':  'sienna',
+    'MSS Neg': 'slategrey', 
+    'PANSS Gen': '#ca9161',
+    'MSS Dis': '#ca9161',
+    'PANSS Pos':  'sienna',
+    'PANSS Neg': 'slategrey'
+}
+
+# Ordered list of outcomes for consistent plotting
+SORTED_OUTCOMES = [
+    'Age',
+    'Education',
+    'Male Gender',
+    "German Native",  
+    "Other Native",
+    'Working Memory',
+    'Psychomotor Speed',
+    'Negative Inhibition',
+    'MSS Pos',
+    'MSS Neg',
+    'MSS Dis',
+    'PANSS Pos',
+    'PANSS Neg',
+    'PANSS Gen',
+    'Age of Disease Onset',
+    'Duration of Untreated Illness',
+    'Duration of Antipsychotic Treatment',
+    "Risperidone Equivalent",
+]
+
+# Group dictionary for consistent naming
+GROUP_DICT = {
+    "ls": "Low Sczt",
+    "hs": "High Sczt", 
+    "control": "Healthy Controls",
+    "patient": "Psychosis"
+}
+
+# Variable name mapping for plots
+NAMES = {
+    "const": "Constant",
+    "gender_male": "Male Gender",
+    "age": "Age",
+    "education": "Education",
+    "age_onset": "Age of Disease Onset",
+    "antipsy_duration": "Duration of Antipsychotic Treatment",
+    "duration_untreated": "Duration of Untreated Illness",
+    "first_language_German": "German Native",  
+    "first_language_Other": "Other Native",
+    "total_risp_eq": "Risperidone Equivalent",
+    "semantic_coherence_0_mean_of_window_means": "Average Sim",
+    "semantic_coherence_2_mean_of_window_means": "Coherence 2",
+    "semantic_coherence_5_mean_of_window_means": "Coherence 5",
+    "semantic_coherence_8_mean_of_window_means": "Coherence 8",
+    "semantic_coherence_16_mean_of_window_means": "Coherence 16",
+    "semantic_coherence_32_mean_of_window_means": "Coherence 32",
+    "number_tokens": "\# Items",
+    "z_Real_semantic_include0_includeN_5": "Optimality 5",
+    "z_Real_semantic_include0_includeN_8": "Optimality 8",
+    "z_Real_semantic_include0_includeN_16": "Optimality 16",
+    "z_Real_semantic_include0_includeN_32": "Optimality 32",
+    "panss_p_total": "PANSS Pos",
+    "panss_g_total": "PANSS Gen",
+    "panss_n_total": "PANSS Neg",
+    "panss_total": "PANSS Total",
+    "mss_sum": "MSS",
+    "mss_pos_sum": "MSS Pos",
+    "mss_neg_sum": "MSS Neg",
+    "mss_dis_sum": "MSS Dis",
+    "tlc_mean": "TLC Mean",
+    "stroop_psychomotor": "Psychomotor Speed",
+    "stroop_attention": "Selective Attention",
+    "stroop_inhibition": "Negative Inhibition",
+    "working_memory": "Working Memory",
+    'panss_sim_total': "PANSS Similarities",
+    'tangentiality_mean': "Tangentiality Mean", 
+    'derailment_mean': "Derailment Mean",
+    "top_p": "Probability Mass Cutoff",
+    "temperature": "Temperature",
+    "semantic_coherence_": "Semantic Similarity Metric"
+}
+
+# Key metrics for analysis
+METRICS = [
+    "semantic_coherence_2_mean_of_window_means",
+    "semantic_coherence_8_mean_of_window_means",
+    "z_Real_semantic_include0_includeN_8",
+    "number_tokens"
+]
+
+# Cognitive variables
+COG_VAR = [
+    'working_memory',
+    'stroop_inhibition'
+]
+
+def format_p_value(p_value: float) -> str:
+    """
+    Format a p-value according to APA style.
+
+    Args:
+        p_value: The p-value to format.
+
+    Returns:
+        A string representing the formatted p-value.
+    """
+    if p_value < 0.001:
+        return "p < .001"
+    elif p_value < 0.01:
+        return f"p = .{str(round(p_value, 3))[2:]}"
+    else:
+        return f"p = .{str(round(p_value, 2))[2:]}"
+
+def set_size(width: float = 750, fraction: float = 1, subplots: tuple = (1, 1)) -> tuple:
+    """
+    Set figure dimensions to avoid scaling in LaTeX.
+
+    Args:
+        width: Document width in points, or string of predefined document type
+        fraction: Fraction of the width which you wish the figure to occupy
+        subplots: The number of rows and columns of subplots.
+
+    Returns:
+        Dimensions of figure in inches
+    """
+    if width == "thesis":
+        width_pt = 426.79135
+    elif width == "beamer":
+        width_pt = 307.28987
+    else:
+        width_pt = width
+
+    # Width of figure (in pts)
+    fig_width_pt = width_pt * fraction
+    # Convert from pt to inches
+    inches_per_pt = 1 / 72.27
+
+    # Golden ratio to set aesthetic figure height
+    golden_ratio = (5**0.5 - 1) / 2
+
+    # Figure width in inches
+    fig_width_in = fig_width_pt * inches_per_pt
+    # Figure height in inches
+    fig_height_in = fig_width_in * golden_ratio * (subplots[0] / subplots[1])
+
+    return (fig_width_in, fig_height_in) 

pelican_nlp/Nils_backup/fluency/questionnaires_data.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Process VELAS questionnaire data.
+
+This script:
+1. Loads questionnaire data from master file
+2. Selects relevant columns
+3. Outputs selected questionnaire scores
+"""
+import pandas as pd
+from utils import ensure_output_dir
+from config import QUESTIONNAIRES_CONFIG
+
+def load_questionnaire_data(questionnaire_path: str) -> pd.DataFrame:
+    """
+    Load questionnaire data from master file.
+    
+    Args:
+        questionnaire_path: Path to master questionnaire data
+    
+    Returns:
+        DataFrame with questionnaire data
+    """
+    return pd.read_csv(questionnaire_path)
+
+def save_questionnaire_data(df: pd.DataFrame, output_path: str) -> None:
+    """Save processed questionnaire data to CSV."""
+    ensure_output_dir(output_path)
+    df[QUESTIONNAIRES_CONFIG["columns_to_save"]].to_csv(output_path, index=False)
+
+def main():
+    # Get paths from config
+    paths = QUESTIONNAIRES_CONFIG["paths"]
+    
+    # Process data
+    df = load_questionnaire_data(paths["input"])
+    save_questionnaire_data(df, paths["output"])
+    
+    print("Questionnaire data processed successfully!")
+
+if __name__ == "__main__":
+    main()