workflow_dataset_to_rkns

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workflow_dataset_to_rkns [2025/10/20 12:48] – [Conversion Workflow] fabricioworkflow_dataset_to_rkns [2025/10/20 14:03] (current) – [AI-Assisted Mapping Generation] fabricio
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 Uses regex mappings in ''assets/replace_channels.json'' to rename EDF channels to standardized names (e.g., "EEG(sec)" → "EEG-C3-A2"). Uses regex mappings in ''assets/replace_channels.json'' to rename EDF channels to standardized names (e.g., "EEG(sec)" → "EEG-C3-A2").
  
-===== 1.2 Add Annotations =====+==== 1.2 Add Annotations ====
 Converts the TSV file to BIDS-compatible format and adds events: Converts the TSV file to BIDS-compatible format and adds events:
 <code python> <code python>
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 </code> </code>
  
-===== 1.3 Extract and Categorize Metadata =====+==== 1.3 Extract and Categorize Metadata ====
   - Matches participant ID (e.g., "sub-0001") from the EDF filename.   - Matches participant ID (e.g., "sub-0001") from the EDF filename.
   - Looks up the participant in ''participants.tsv''.   - Looks up the participant in ''participants.tsv''.
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   - Groups metadata by category and adds each to the RKNS object.   - Groups metadata by category and adds each to the RKNS object.
  
-===== 1.4 Finalize and Export =====+==== 1.4 Finalize and Export ====
 <code python> <code python>
 rkns_obj.populate()                     # Build internal structure rkns_obj.populate()                     # Build internal structure
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 </code> </code>
  
-===== 1.5 Validate =====+==== 1.5 Validate ====
 <code python> <code python>
 validate_rkns_checksum(output_file)     # Verify checksums on all data validate_rkns_checksum(output_file)     # Verify checksums on all data
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 ---- ----
  
-===== 3. Standardizing Names via Regex Mappings =====+====== 3. Standardizing Names via Regex Mappings ======
  
 Once you have a compliant TSV, normalize channel and event names non-destructively using regex mappings defined in two JSON files. Once you have a compliant TSV, normalize channel and event names non-destructively using regex mappings defined in two JSON files.
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 <code> <code>
-I will provide you a list of EEG channels extracted from the original EDFs.   +I will provide you a list of physiological signal channels (e.g., EEG, EOG, EMG, respiratory, cardiac) extracted from original EDF files.   
-I require an output in JSON format that maps channel names to new standardized names using grep-style regex replacements.  +I require an output in JSON format that maps each raw channel name to a standardized name using **sequential, grep-style regex replacements**.
  
-For example, this is a reference mapping. Note that replacements are applied in sequential order: +Key requirements: 
-```+1. **Include early normalization rules** to handle common delimiters (e.g., `_`, spaces, `.`, `/`, parentheses) by converting them to hyphens (`-`), collapsing multiple hyphens, and trimming leading/trailing hyphens. 
 +2. All patterns must be **case-insensitive** (use `(?i)`). 
 +3. Use **physiologically meaningful, NSRR/AASM-aligned names**, such as: 
 +   - `EEG-C3-M2` (not `EEG-C3_A2` or ambiguous forms) 
 +   - `EMG-LLEG` / `EMG-RLEG` for leg EMG (not `LAT`/`RAT` as position) 
 +   - `RESP-AIRFLOW-THERM` or `RESP-AIRFLOW-PRES` (not generic `RESP-NASAL`) 
 +   - `EOG-LOC` / `EOG-ROC` for eye channels 
 +   - `EMG-CHIN` for chin EMG 
 +   - `PULSE` for heart rate or pulse signals (unless raw ECG → `ECG`) 
 +4. **Do not include a final catch-all rule** (e.g., `^(.+)$ → MISC-\1`) unless explicitly requested—most channels in the input list should be known and mapped specifically. 
 +5. Replacements are applied **in order**, with each rule operating on the result of the previous one. 
 + 
 +Example reference snippet: 
 +```json
 { {
-  "(?i)^ABDO\\sRES\\s*$": "RESP-ABD", +  "(?i)[\\s_\\./\\(\\),]+": "-", 
-  "(?i)^THOR\\sRES\\s*$": "RESP-CHEST", +  "-+": "-", 
-  "(?i)^EEG\\(sec\\)\\s*$": "EEG-C3-A2", +  "^-|-$": "", 
-  "_": "-"+  "(?i)^abdomen$": "RESP-ABD", 
 +  "(?i)^c3_m2$": "EEG-C3-M2", 
 +  "(?i)^lat$": "EMG-LLEG"
 } }
 ``` ```
  
-The keys are regex patterns (case-insensitive), and the values are replacement strings. Groups in the pattern can be referenced in the replacement (e.g., ''\1''). +Now, generate a similar JSON mapping for the following list of channel names:
- +
-Based on the above example, generate a similar JSON mapping for the following list of channel names:+
 ``` ```
 [INSERT YOUR UNIQUE CHANNEL LIST HERE] [INSERT YOUR UNIQUE CHANNEL LIST HERE]
 ``` ```
  
-Provide the output within a JSON code block.+Provide the output **within a JSON code block only**—no explanations.
 </code> </code>
 ===== Event Descriptions → assets/event_description_mapping.json ===== ===== Event Descriptions → assets/event_description_mapping.json =====
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  • Last modified: 2025/10/20 12:48
  • by fabricio