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

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Files changed (43) hide show
  1. pelican_nlp/Nils_backup/__init__.py +0 -0
  2. pelican_nlp/Nils_backup/extract_acoustic_features.py +274 -0
  3. pelican_nlp/Nils_backup/fluency/__init__.py +0 -0
  4. pelican_nlp/Nils_backup/fluency/aggregate_fluency_results.py +186 -0
  5. pelican_nlp/Nils_backup/fluency/behavioral_data.py +42 -0
  6. pelican_nlp/Nils_backup/fluency/check_duplicates.py +169 -0
  7. pelican_nlp/Nils_backup/fluency/coherence.py +653 -0
  8. pelican_nlp/Nils_backup/fluency/config.py +231 -0
  9. pelican_nlp/Nils_backup/fluency/main.py +182 -0
  10. pelican_nlp/Nils_backup/fluency/optimality_without_tsa.py +466 -0
  11. pelican_nlp/Nils_backup/fluency/plot_fluency.py +573 -0
  12. pelican_nlp/Nils_backup/fluency/plotting_utils.py +170 -0
  13. pelican_nlp/Nils_backup/fluency/questionnaires_data.py +43 -0
  14. pelican_nlp/Nils_backup/fluency/stats_fluency.py +930 -0
  15. pelican_nlp/Nils_backup/fluency/utils.py +41 -0
  16. pelican_nlp/Nils_backup/speaker_diarization_Nils.py +328 -0
  17. pelican_nlp/Nils_backup/transcription/__init__.py +0 -0
  18. pelican_nlp/Nils_backup/transcription/annotation_tool.py +1001 -0
  19. pelican_nlp/Nils_backup/transcription/annotation_tool_boundaries.py +1122 -0
  20. pelican_nlp/Nils_backup/transcription/annotation_tool_sandbox.py +985 -0
  21. pelican_nlp/Nils_backup/transcription/output/holmes_control_nova_all_outputs.json +7948 -0
  22. pelican_nlp/Nils_backup/transcription/test.json +1 -0
  23. pelican_nlp/Nils_backup/transcription/transcribe_audio.py +314 -0
  24. pelican_nlp/Nils_backup/transcription/transcribe_audio_chunked.py +695 -0
  25. pelican_nlp/Nils_backup/transcription/transcription.py +801 -0
  26. pelican_nlp/Nils_backup/transcription/transcription_gui.py +955 -0
  27. pelican_nlp/Nils_backup/transcription/word_boundaries.py +190 -0
  28. pelican_nlp/Silvia_files/Opensmile/opensmile_feature_extraction.py +66 -0
  29. pelican_nlp/Silvia_files/prosogram/prosogram.py +104 -0
  30. pelican_nlp/__init__.py +1 -1
  31. pelican_nlp/_version.py +1 -0
  32. pelican_nlp/configuration_files/config_audio.yml +150 -0
  33. pelican_nlp/configuration_files/config_discourse.yml +104 -0
  34. pelican_nlp/configuration_files/config_fluency.yml +108 -0
  35. pelican_nlp/configuration_files/config_general.yml +131 -0
  36. pelican_nlp/configuration_files/config_morteza.yml +103 -0
  37. pelican_nlp/praat/__init__.py +29 -0
  38. {pelican_nlp-0.1.1.dist-info → pelican_nlp-0.1.3.dist-info}/METADATA +15 -14
  39. pelican_nlp-0.1.3.dist-info/RECORD +75 -0
  40. pelican_nlp-0.1.1.dist-info/RECORD +0 -39
  41. {pelican_nlp-0.1.1.dist-info → pelican_nlp-0.1.3.dist-info}/WHEEL +0 -0
  42. {pelican_nlp-0.1.1.dist-info → pelican_nlp-0.1.3.dist-info}/licenses/LICENSE +0 -0
  43. {pelican_nlp-0.1.1.dist-info → pelican_nlp-0.1.3.dist-info}/top_level.txt +0 -0
@@ -0,0 +1,108 @@
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+ # Configuration file for fluency task
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+ # =======================================
3
+ input_file: "text" #or 'audio'
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+ fluency_task: &fluency_flag true
5
+ #========================================
6
+
7
+ #general configurations; always adapt
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+ PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/FluencyTest"
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+ language: "german"
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+ multiple_sessions: &session_flag false
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+
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+ corpus_names: #names of fluency tasks (e.g. "animals", "clothes")
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+ - "animals"
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+ - "clothes"
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+ - "food"
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+
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+ #Specify linguistic metrics to extract
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+ metric_to_extract: 'embeddings' #Possible options: 'embeddings', 'logits'
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+ output_document_information: true
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+ #====================================================================
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+
22
+ #Optional configurations; Change with preference. However, default settings recommended
23
+ cleaning_options:
24
+ general_cleaning: true
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+ #Options for fluency tasks
26
+ fluency_task: *fluency_flag
27
+ word_splitter: ';' #default split with ',' add different word_splitter if necessary
28
+ remove_hyphens: true
29
+ remove_duplicates: false
30
+ lowercase: false
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+ #Optional cleaning
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+ remove_brackets_and_bracketcontent: false #default 'false'
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+ remove_timestamps: false #default 'false'
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+ timestamp_pattern_example: null #e.g. "#00:00:23-00#"
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+ remove_punctuation: false #Careful!: If set to true word_splitter might be removed
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+
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+ options_embeddings:
38
+ tokenization_method: "whitespace" #or "model"
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+ model_name: "fastText" #e.g. "fastText", "xlm-roberta-base"
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+ pytorch_based_model: false
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+ method: "model_instance"
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+ max_length: null
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+ clean_embedding_tokens: true
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+
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+ semantic-similarity: true
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+ distance-from-randomness: false
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+
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+ options_dis_from_randomness:
49
+ window_size: 8
50
+ min_len: null
51
+ bootstrap: 10000
52
+ shuffle_mode: 'include0_includeN'
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+ parallel_computing: false #not yet set up
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+
55
+ options_semantic-similarity:
56
+ window_sizes: #'all' or window size as integer
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+ - 2
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+ - 8
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+ #==================================================================
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+
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+ #Extra configurations;
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+ task_name: "fluency"
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+ create_aggregation_of_results: true
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+
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+ pipeline_options:
66
+ quality_check: false
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+ clean_text: true
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+ tokenize_text: false
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+ normalize_text: false
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+
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+ general_cleaning_options:
72
+ strip_whitespace: true
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+ merge_multiple_whitespaces: true
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+ remove_whitespace_before_punctuation: true
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+ merge_newline_characters: true
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+ remove_backslashes: true
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+
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+ has_multiple_sections: false
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+ has_section_titles: false
80
+ section_identification: null
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+ number_of_sections: 1
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+ number_of_speakers: 1
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+ discourse: false
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+
85
+ document_information_output:
86
+ parameters:
87
+ - subject_ID
88
+ - fluency_word_count
89
+ - fluency_duplicate_count
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+
91
+ #================================================================
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+
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+ #Detail configurations; Changes optional, mostly used for quality checking / error handling
94
+ recompute_everything: true
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+ number_of_subjects: null
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+
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+ # Filename components configuration
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+ filename_components:
99
+ subject: true # mandatory
100
+ session: *session_flag
101
+ task: true # mandatory
102
+ task_addition: false
103
+ corpus: true # typically true for fluency tasks (e.g., "animals", "clothes")
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+ metric: true
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+ additional_tags: []
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+
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+
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+
@@ -0,0 +1,131 @@
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+ # Master Configuration File
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+ # ========================
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+
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+ # Basic Settings
5
+ # -------------
6
+ input_file: "text" # Options: 'text' or 'audio'
7
+ PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/FluencyTest"
8
+ language: "german" # Options: 'german', 'english'
9
+ recompute_everything: true # If false, reuses previously computed results
10
+
11
+ # Task Configuration
12
+ # -----------------
13
+ task_name: "fluency" # Options: 'fluency', 'interview'
14
+ fluency_task: &fluency_flag true # Flag for fluency-specific settings
15
+ discourse: &discourse_flag false # Flag for discourse-specific settings
16
+ corpus_names: # List of task corpora
17
+ - "animals"
18
+
19
+ # Session and Subject Settings
20
+ # --------------------------
21
+ multiple_sessions: false
22
+ number_of_subjects: null # If null, auto-detected
23
+ number_of_speakers: 1
24
+ subject_speakertag: null # Speaker tag for subject (e.g., "B")
25
+
26
+ # Document Structure
27
+ # ----------------
28
+ has_multiple_sections: false
29
+ has_section_titles: false
30
+ section_identification: null # e.g., "Section:"
31
+ number_of_sections: 1 # If null, auto-detected
32
+
33
+ # Processing Pipeline
34
+ # -----------------
35
+ pipeline_options:
36
+ quality_check: false
37
+ clean_text: true
38
+ tokenize_text: false
39
+ normalize_text: false
40
+
41
+ # Metric Extraction
42
+ # ---------------
43
+ metric_to_extract: "embeddings" # Options: 'embeddings', 'logits'
44
+ extract_logits: null
45
+ extract_embeddings: true
46
+
47
+ # Cleaning Options
48
+ # --------------
49
+ cleaning_options:
50
+ general_cleaning: true
51
+ remove_punctuation: false
52
+ lowercase: true
53
+ remove_brackets_and_bracketcontent: false
54
+ remove_timestamps: false
55
+ timestamp_pattern_example: null # e.g., "#00:00:23-00#"
56
+ # Fluency-specific options
57
+ fluency_task: *fluency_flag
58
+ word_splitter: ';'
59
+ remove_hyphens: true
60
+ remove_duplicates: true
61
+
62
+ general_cleaning_options:
63
+ strip_whitespace: true
64
+ merge_multiple_whitespaces: true
65
+ remove_whitespace_before_punctuation: true
66
+ merge_newline_characters: true
67
+ remove_backslashes: true
68
+
69
+ # Embedding Options
70
+ # ---------------
71
+ options_embeddings:
72
+ tokenization_method: "whitespace" # Options: 'whitespace', 'model'
73
+ model_name: "fastText" # Options: 'fastText', 'xlm-roberta-base'
74
+ pytorch_based_model: false
75
+ method: "model_instance"
76
+ max_length: 512
77
+ clean_embedding_tokens: true
78
+ remove_punctuation: false
79
+ lowercase: false
80
+ keep_speakertags: false
81
+ semantic-similarity: true
82
+ window_size: null
83
+ clean_tokens: true
84
+ divergence_from_optimality: false
85
+ output_options:
86
+ exclude_special_tokens: true
87
+ remove_'_'_character: true
88
+ remove_speaker_labels: true
89
+ remove_punctuation_and_symbols: true
90
+ remove_brackets_and_content: true
91
+
92
+ # Logits Options
93
+ # -------------
94
+ options_logits:
95
+ chunk_size: 128
96
+ overlap_size: 64
97
+ tokenization_method: "model"
98
+ model_name: "DiscoResearch/Llama3-German-8B-32k"
99
+ remove_punctuation: true
100
+ lowercase: true
101
+ keep_speakertags: true
102
+
103
+ # Analysis Options
104
+ # --------------
105
+ options_semantic-similarity:
106
+ window_sizes: # 'all' or window size as integer
107
+ - 2
108
+ - 8
109
+
110
+ options_dis_from_randomness:
111
+ window_size: 8
112
+ min_len: null
113
+ bootstrap: 10000
114
+ shuffle_mode: 'include0_includeN'
115
+ parallel_computing: false
116
+
117
+ # Normalization Options
118
+ # -------------------
119
+ normalization_options:
120
+ method: "lemmatization" # Options: 'lemmatization', 'stemming'
121
+
122
+ # Filename Configuration
123
+ # --------------------
124
+ filename_components:
125
+ subject: true # mandatory
126
+ session: false
127
+ task: true # mandatory
128
+ task_addition: false
129
+ corpus: true
130
+ metric: true
131
+ additional_tags: []
@@ -0,0 +1,103 @@
1
+ # Configuration file: variable parameters
2
+ # =======================================
3
+ input_file: "text" #or 'audio'
4
+ discourse: &discourse_flag true
5
+
6
+ #PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/KetamineStudy/KetamineStudy_ProjectFolder/" # Set default to home directory, e.g., '/home/usr/...'
7
+ PATH_TO_PROJECT_FOLDER: "/home/yvespauli/PycharmProjects/Morteza/"
8
+ language: "german" # Possibly add options for German and English
9
+
10
+ task_name: "interview" # Give name of task used for creation of the input file (e.g., ['fluency', 'interview'])
11
+ corpus_names:
12
+ - "schizophrenia"
13
+
14
+
15
+ number_of_subjects: null # Specify number of subjects; if 'null', number of subjects is automatically detected
16
+ multiple_sessions: false # Set to True if multiple sessions per subject
17
+
18
+ recompute_everything: true #If set to 'false' pelican-nlp will try to reuse previously computed results stored on your drive
19
+
20
+ has_multiple_sections: false #evaluated independently
21
+ has_section_titles: false
22
+ 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
23
+ number_of_sections: null #if 'null' number of sections automatically detected, however, specifying number recommended if known.
24
+
25
+ number_of_speakers: 3
26
+ subject_speakertag: "B"
27
+
28
+ metric_to_extract: "embeddings"
29
+ extract_logits: false
30
+ extract_embeddings: true
31
+
32
+ pipeline_options:
33
+ quality_check: false
34
+ clean_text: true
35
+ tokenize_text: false
36
+ normalize_text: false
37
+
38
+ tokenization: "wordLevel" # Options: 'characterLevel', 'subWordLevel'
39
+
40
+ # Options for extract_logits
41
+ chunk_size: null
42
+ overlap_size: null
43
+
44
+ # Options for extract_embeddings
45
+ window_sizes: [2]
46
+ metric_function: cosine_similarity
47
+ aggregation_functions: mean_of_means
48
+
49
+
50
+ fluency_task: &fluency_flag false
51
+ cleaning_options:
52
+ general_cleaning: true # General cleaning options used for most text preprocessing, default: True.
53
+ remove_brackets_and_bracketcontent: true
54
+ remove_timestamps: true
55
+ timestamp_pattern_example: "#00:00:19-0#"
56
+ #Options for fluency tasks
57
+ fluency_task: *fluency_flag
58
+ word_splitter: null
59
+ remove_hyphens: null
60
+ remove_duplicates: null
61
+
62
+ general_cleaning_options:
63
+ strip_whitespace: true
64
+ merge_multiple_whitespaces: true
65
+ remove_whitespace_before_punctuation: true
66
+ merge_newline_characters: true
67
+ remove_backslashes: true
68
+
69
+ tokenization_options_logits:
70
+ method: "model_instance" # Options: model_instance, regex, nltk, etc.
71
+ model_name: "DiscoResearch/Llama3-German-8B-32k" # Replace with your model instance name
72
+ remove_punctuation: true
73
+ lowercase: true
74
+
75
+ options_embeddings:
76
+ tokenization_method: "model_roberta" #or "whitespace", "model"
77
+ max_length: 512 #max sequence length
78
+ model_name: "xlm-roberta-base" #e.g. "fastText", "xlm-roberta-base"
79
+ pytorch_based_model: true
80
+ method: "model_instance"
81
+ remove_punctuation: false
82
+ lowercase: false
83
+ keep_speakertags: true
84
+ clean_embedding_tokens: true
85
+ output_options:
86
+ exclude_special_tokens: true
87
+ remove_'_'_character: true
88
+ remove_speaker_labels: true
89
+ remove_punctuation_and_symbols: true
90
+ remove_brackets_and_content: true
91
+
92
+ window_size: null
93
+
94
+ semantic-similarity: false
95
+ distance-from-randomness: false
96
+
97
+ normalization_options:
98
+ method: "lemmatization" #Options: lemmatization or stemming
99
+
100
+ create_aggregation_of_results: false
101
+ output_document_information: false
102
+
103
+
@@ -0,0 +1,29 @@
1
+ import os
2
+
3
+ # Get the directory where the Praat scripts are stored
4
+ PRAAT_SCRIPTS_DIR = os.path.dirname(os.path.abspath(__file__))
5
+
6
+ # Define paths to individual scripts
7
+ PROSOMAIN_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosomain.praat')
8
+ PROSOGRAM_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosogram.praat')
9
+ PROSOPLOT_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'prosoplot.praat')
10
+ SEGMENT_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'segment.praat')
11
+ STYLIZE_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'stylize.praat')
12
+ POLYTONIA_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'polytonia.praat')
13
+ UTIL_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'util.praat')
14
+ EPS_CONV_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'eps_conv.praat')
15
+ SETUP_SCRIPT = os.path.join(PRAAT_SCRIPTS_DIR, 'setup.praat')
16
+
17
+ # Export all script paths
18
+ __all__ = [
19
+ 'PRAAT_SCRIPTS_DIR',
20
+ 'PROSOMAIN_SCRIPT',
21
+ 'PROSOGRAM_SCRIPT',
22
+ 'PROSOPLOT_SCRIPT',
23
+ 'SEGMENT_SCRIPT',
24
+ 'STYLIZE_SCRIPT',
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+ 'POLYTONIA_SCRIPT',
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+ 'UTIL_SCRIPT',
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+ 'EPS_CONV_SCRIPT',
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+ 'SETUP_SCRIPT'
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+ ]
@@ -1,13 +1,13 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pelican_nlp
3
- Version: 0.1.1
3
+ Version: 0.1.3
4
4
  Summary: Preprocessing and Extraction of Linguistic Information for Computational Analysis
5
5
  Author-email: Yves Pauli <yves.pauli@gmail.com>
6
6
  License-Expression: CC-BY-NC-4.0
7
- Project-URL: Homepage, https://github.com/ypauli/PELICAN_nlp
8
- Project-URL: Repository, https://github.com/ypauli/PELICAN_nlp
9
- Project-URL: Documentation, https://github.com/ypauli/PELICAN_nlp#readme
10
- Project-URL: Bug Tracker, https://github.com/ypauli/PELICAN_nlp/issues
7
+ Project-URL: Homepage, https://github.com/ypauli/pelican_nlp
8
+ Project-URL: Repository, https://github.com/ypauli/pelican_nlp
9
+ Project-URL: Documentation, https://github.com/ypauli/pelican_nlp#readme
10
+ Project-URL: Bug Tracker, https://github.com/ypauli/pelican_nlp/issues
11
11
  Keywords: nlp,linguistics,preprocessing,language-processing,text-analysis
12
12
  Classifier: Development Status :: 1 - Planning
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13
  Classifier: Intended Audience :: Science/Research
@@ -48,18 +48,18 @@ Dynamic: license-file
48
48
  PELICAN_nlp
49
49
  ====================================
50
50
 
51
- 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.
51
+ 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.
52
52
 
53
53
  .. image:: https://img.shields.io/pypi/v/package-name.svg
54
- :target: https://pypi.org/project/pelican-nlp/
54
+ :target: https://pypi.org/project/pelican_nlp/
55
55
  :alt: PyPI version
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56
 
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57
  .. image:: https://img.shields.io/github/license/username/package-name.svg
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- :target: https://github.com/ypauli/PELICAN-nlp/blob/main/LICENSE
58
+ :target: https://github.com/ypauli/pelican_nlp/blob/main/LICENSE
59
59
  :alt: License
60
60
 
61
61
  .. image:: https://img.shields.io/pypi/pyversions/package-name.svg
62
- :target: https://pypi.org/project/pelican-nlp/
62
+ :target: https://pypi.org/project/pelican_nlp/
63
63
  :alt: Supported Python Versions
64
64
 
65
65
  Installation
@@ -75,7 +75,7 @@ For the latest development version:
75
75
 
76
76
  .. code-block:: bash
77
77
 
78
- pip install git+https://github.com/ypauli/PELICAN_nlp.git
78
+ pip install https://github.com/ypauli/pelican_nlp/releases/tag/v0.1.2-alpha
79
79
 
80
80
  Usage
81
81
  =====
@@ -107,7 +107,8 @@ Text and audio files should follow this naming convention:
107
107
  - extension: file extension (e.g., txt / pdf / docx / rtf), mandatory
108
108
 
109
109
  Example filenames:
110
- - sub-01_ses-01_interview_schizophrenia.rtf
110
+
111
+ - sub-01_interview_schizophrenia.rtf
111
112
  - sub-03_ses-02_fluency_semantic_animals.docx
112
113
 
113
114
  To optimize performance, close other programs and limit GPU usage during language processing.
@@ -124,15 +125,15 @@ Features
124
125
  Examples
125
126
  ========
126
127
 
127
- You can find example setups in the [`examples/`](https://github.com/ypauli/PELICAN-nlp/examples) folder.
128
+ You can find example setups in the [`examples/`](https://github.com/ypauli/pelican_nlp/examples) folder.
128
129
  ALWAYS change the path to the project folder specified in the configuration file to your specific project location.
129
130
 
130
131
  Contributing
131
132
  ============
132
133
 
133
- Contributions are welcome! Please check out the `contributing guide <https://github.com/ypauli/PELICAN-nlp/blob/main/CONTRIBUTING.md>`_.
134
+ Contributions are welcome! Please check out the `contributing guide <https://github.com/ypauli/pelican_nlp/blob/main/CONTRIBUTING.md>`_.
134
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135
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  License
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  =======
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- 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.
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+ 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.
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