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use super::{
byteorder::ByteOrder,
datatype::FcsDataType,
header::Header,
keyword::{
ByteKeyword, FloatKeyword, IntegerKeyword, IntegerableKeyword, Keyword,
KeywordCreationResult, MixedKeyword, StringKeyword, match_and_parse_keyword,
},
};
use anyhow::{Result, anyhow};
use memmap3::Mmap;
use regex::bytes::Regex;
use rustc_hash::FxHashMap;
use serde::{Deserialize, Serialize};
use std::sync::Arc;
use uuid::Uuid;
pub type KeywordMap = FxHashMap<String, Keyword>;
/// Contains keyword-value pairs and delimiter from the TEXT segment of an FCS file
///
/// The TEXT segment contains all metadata about the FCS file, including:
/// - File information (GUID, filename, cytometer type)
/// - Data structure information (number of events, parameters, data type, byte order)
/// - Parameter metadata (names, labels, ranges, transforms)
/// - Optional information (compensation matrices, timestamps, etc.)
///
/// Keywords are stored in a hashmap for fast lookup, with type-safe accessors
/// for different keyword types (integer, float, string, byte, mixed).
#[derive(Default, Debug, Clone, Serialize, Deserialize)]
pub struct Metadata {
pub keywords: KeywordMap,
pub delimiter: char,
}
impl Metadata {
#[must_use]
pub fn new() -> Self {
Self {
keywords: FxHashMap::default(),
delimiter: ' ',
}
}
/// Prints all keywords sorted alphabetically by key name
///
/// This is a debugging utility that displays all keyword-value pairs
/// in the metadata, sorted for easy reading.
pub fn print_sorted_by_keyword(&self) {
// Step 1: Get a Vector from existing text HashMap.
let mut sorted: Vec<_> = self.keywords.iter().collect();
// Step 2: sort Vector by key from HashMap.
// ... This sorts by HashMap keys.
// Each tuple is sorted by its first item [.0] (the key).
sorted.sort_by_key(|a| a.0);
// Step 3: loop over sorted vector.
for (key, value) in &sorted {
println!("{key}: {value}");
}
}
/// Reads the text segment of the fcs file and returns an `Metadata` struct
///
/// Uses memchr for fast delimiter finding (5-10x faster than byte-by-byte iteration)
#[must_use]
pub fn from_mmap(mmap: &Mmap, header: &Header) -> Self {
// Read the first byte of the text segment to determine the delimiter:
let delimiter = mmap[*header.text_offset.start()];
// Read the text content
// header.text_offset is RangeInclusive, so we use it directly but SKIP the first byte, which is the delimiter (used above)
let text_slice = &mmap[(*header.text_offset.start() + 1)..=*header.text_offset.end()];
// Extract keyword value pairs using memchr for fast delimiter finding
let mut keywords: KeywordMap = FxHashMap::default();
// Find all delimiter positions using SIMD-accelerated search
// This is 5-10x faster than manual iteration
let delimiter_positions: Vec<usize> = memchr::memchr_iter(delimiter, text_slice).collect();
// Parse keyword-value pairs
// FCS format: |KEY1|VALUE1|KEY2|VALUE2|...
// delimiter_positions gives us the split points
let mut prev_pos = 0;
let mut is_keyword = true;
let mut current_key = String::new();
for &pos in &delimiter_positions {
// Extract the slice between delimiters
let segment = &text_slice[prev_pos..pos];
// SAFETY: FCS spec requires TEXT segment to be ASCII/UTF-8
let text = std::str::from_utf8(segment).unwrap_or_default();
if is_keyword {
// This is a keyword
current_key = text.to_string();
is_keyword = false;
} else {
// This is a value - parse and store the keyword-value pair
if !current_key.is_empty() {
// Normalize key: ensure it has $ prefix (FCS spec requires it)
// Store with $ prefix for consistent lookups
let normalized_key: String = if current_key.starts_with('$') {
current_key.clone()
} else {
format!("${}", current_key)
};
match match_and_parse_keyword(¤t_key, text) {
KeywordCreationResult::Int(int_keyword) => {
keywords.insert(normalized_key.clone(), Keyword::Int(int_keyword));
}
KeywordCreationResult::Float(float_keyword) => {
keywords.insert(normalized_key.clone(), Keyword::Float(float_keyword));
}
KeywordCreationResult::String(string_keyword) => {
keywords
.insert(normalized_key.clone(), Keyword::String(string_keyword));
}
KeywordCreationResult::Byte(byte_keyword) => {
keywords.insert(normalized_key.clone(), Keyword::Byte(byte_keyword));
}
KeywordCreationResult::Mixed(mixed_keyword) => {
keywords.insert(normalized_key.clone(), Keyword::Mixed(mixed_keyword));
}
KeywordCreationResult::UnableToParse => {
eprintln!(
"Unable to parse keyword: {} with value: {}",
current_key, text
);
}
}
}
current_key.clear();
is_keyword = true;
}
prev_pos = pos + 1;
}
// Handle the segment after the last delimiter (if any)
if prev_pos < text_slice.len() {
let segment = &text_slice[prev_pos..];
let text = std::str::from_utf8(segment).unwrap_or_default();
if !text.is_empty() {
if is_keyword {
// This is a keyword without a value - shouldn't happen in valid FCS files
eprintln!(
"Warning: Keyword '{}' at end of text segment has no value \n {:?}",
text, header
);
} else {
// This is a value - store the keyword-value pair
if !current_key.is_empty() {
let normalized_key: String = if current_key.starts_with('$') {
current_key.clone()
} else {
format!("${}", current_key)
};
match match_and_parse_keyword(¤t_key, text) {
KeywordCreationResult::Int(int_keyword) => {
keywords.insert(normalized_key.clone(), Keyword::Int(int_keyword));
}
KeywordCreationResult::Float(float_keyword) => {
keywords
.insert(normalized_key.clone(), Keyword::Float(float_keyword));
}
KeywordCreationResult::String(string_keyword) => {
keywords.insert(
normalized_key.clone(),
Keyword::String(string_keyword),
);
}
KeywordCreationResult::Byte(byte_keyword) => {
keywords
.insert(normalized_key.clone(), Keyword::Byte(byte_keyword));
}
KeywordCreationResult::Mixed(mixed_keyword) => {
keywords
.insert(normalized_key.clone(), Keyword::Mixed(mixed_keyword));
}
KeywordCreationResult::UnableToParse => {
eprintln!(
"Unable to parse keyword: {} with value: {}",
current_key, text
);
}
}
}
}
}
}
Self {
keywords,
delimiter: delimiter as char,
}
}
/// Check that required keys are present in the TEXT segment of the metadata
/// # Errors
/// Will return `Err` if:
/// - any of the required keywords are missing from the keywords hashmap
/// - the number of parameters can't be obtained from the $PAR keyword in the TEXT section
/// - any keyword has a Pn[X] value where n is greater than the number of parameters indicated by the $PAR keyword
pub fn validate_text_segment_keywords(&self, header: &Header) -> Result<()> {
println!("Validating FCS file...{}", header.version);
let required_keywords = header.version.get_required_keywords();
for keyword in required_keywords {
if !self.keywords.contains_key(*keyword) {
return Err(anyhow!(
"Invalid FCS {:?} file: Missing keyword: {}",
header.version,
keyword
));
}
}
Ok(())
}
/// Validates if a GUID is present in the file's metadata, and if not, generates a new one.
pub fn validate_guid(&mut self) {
if self.get_string_keyword("GUID").is_err() {
self.insert_string_keyword("GUID".to_string(), Uuid::new_v4().to_string());
}
}
/// Confirm that no stored keyword has a value greater than the $PAR keyword indicates
#[allow(unused)]
fn validate_number_of_parameters(&self) -> Result<()> {
let n_params = self.get_number_of_parameters()?;
let n_params_string = n_params.to_string();
let n_digits = n_params_string.chars().count().to_string();
let regex_string = r"[PR]\d{1,".to_string() + &n_digits + "}[BENRDFGLOPSTVIW]";
let param_keywords = Regex::new(®ex_string)?;
for keyword in self.keywords.keys() {
if !param_keywords.is_match(keyword.as_bytes()) {
continue; // Skip to the next iteration if the keyword doesn't match
}
// If the keyword starts with a $P, then the value of the next non-terminal characters should be less than or equal to the number of parameters
if keyword.starts_with("$P") {
let param_number = keyword
.chars()
.nth(1)
.ok_or_else(|| anyhow!("Keyword '{}' should have a second character after '$P'", keyword))?
.to_digit(10)
.ok_or_else(|| anyhow!("Keyword '{}' should have a digit as the second character to count parameters", keyword))? as usize;
if param_number > *n_params {
return Err(anyhow!(
"Invalid FCS file: {} keyword value exceeds number of parameters",
keyword
));
}
}
}
Ok(())
}
/// Generic function to get the unwrapped unsigned integer value associated with a numeric keyword (e.g. $PAR, $TOT, etc.)
fn get_keyword_value_as_usize(&self, keyword: &str) -> Result<&usize> {
Ok(self.get_integer_keyword(keyword)?.get_usize())
}
/// Return the number of parameters in the file from the $PAR keyword in the metadata TEXT section
/// # Errors
/// Will return `Err` if the $PAR keyword is not present in the metadata keywords hashmap
pub fn get_number_of_parameters(&self) -> Result<&usize> {
self.get_keyword_value_as_usize("$PAR")
}
/// Return the number of events in the file from the $TOT keyword in the metadata TEXT section
/// # Errors
/// Will return `Err` if the $TOT keyword is not present in the metadata keywords hashmap
pub fn get_number_of_events(&self) -> Result<&usize> {
self.get_keyword_value_as_usize("$TOT")
}
/// Return the data type from the $DATATYPE keyword in the metadata TEXT section, unwraps and returns it if it exists.
/// # Errors
/// Will return `Err` if the $DATATYPE keyword is not present in the metadata keywords hashmap
pub fn get_data_type(&self) -> Result<&FcsDataType> {
let keyword = self.get_byte_keyword("$DATATYPE")?;
if let ByteKeyword::DATATYPE(data_type) = keyword {
Ok(data_type)
} else {
Err(anyhow!("No $DATATYPE value stored."))
}
}
/// Get the data type for a specific channel/parameter (FCS 3.2+)
///
/// First checks for `$PnDATATYPE` keyword to see if this parameter has a specific data type override.
/// If not found, falls back to the default `$DATATYPE` keyword.
///
/// # Arguments
/// * `parameter_number` - 1-based parameter index
///
/// # Errors
/// Will return `Err` if neither `$PnDATATYPE` nor `$DATATYPE` is present
pub fn get_data_type_for_channel(&self, parameter_number: usize) -> Result<FcsDataType> {
// First try to get parameter-specific data type (FCS 3.2+)
if let Ok(pn_datatype_keyword) =
self.get_parameter_byte_metadata(parameter_number, "DATATYPE")
{
if let ByteKeyword::PnDATATYPE(data_type) = pn_datatype_keyword {
Ok(*data_type)
} else {
// Shouldn't happen, but fall back to default
Ok(self.get_data_type()?.clone())
}
} else {
// Fall back to default $DATATYPE
Ok(self.get_data_type()?.clone())
}
}
/// Calculate the total bytes per event by summing bytes per parameter
///
/// Uses `$PnB` (bits per parameter) divided by 8 to get bytes per parameter,
/// then sums across all parameters. This is more accurate than using `$DATATYPE`
/// which only provides a default value.
///
/// # Errors
/// Will return `Err` if the number of parameters cannot be determined or
/// if any required `$PnB` keyword is missing
pub fn calculate_bytes_per_event(&self) -> Result<usize> {
let number_of_parameters = self.get_number_of_parameters()?;
let mut total_bytes = 0;
for param_num in 1..=*number_of_parameters {
// Get $PnB (bits per parameter)
let bits = self.get_parameter_numeric_metadata(param_num, "B")?;
if let IntegerKeyword::PnB(bits_value) = bits {
// Convert bits to bytes (round up if not divisible by 8)
let bytes = (bits_value + 7) / 8;
total_bytes += bytes;
} else {
return Err(anyhow!(
"$P{}B keyword found but is not the expected PnB variant",
param_num
));
}
}
Ok(total_bytes)
}
/// Get bytes per parameter for a specific channel
///
/// Uses `$PnB` (bits per parameter) divided by 8 to get bytes per parameter.
///
/// # Arguments
/// * `parameter_number` - 1-based parameter index
///
/// # Errors
/// Will return `Err` if the `$PnB` keyword is missing for this parameter
pub fn get_bytes_per_parameter(&self, parameter_number: usize) -> Result<usize> {
let bits = self.get_parameter_numeric_metadata(parameter_number, "B")?;
if let IntegerKeyword::PnB(bits_value) = bits {
// Convert bits to bytes (round up if not divisible by 8)
Ok((bits_value + 7) / 8)
} else {
Err(anyhow!(
"$P{}B keyword found but is not the expected PnB variant",
parameter_number
))
}
}
/// Return the byte order from the $BYTEORD keyword in the metadata TEXT section, unwraps and returns it if it exists.
/// # Errors
/// Will return `Err` if the $BYTEORD keyword is not present in the keywords hashmap
pub fn get_byte_order(&self) -> Result<&ByteOrder> {
let keyword = self.get_byte_keyword("$BYTEORD")?;
if let ByteKeyword::BYTEORD(byte_order) = keyword {
Ok(byte_order)
} else {
Err(anyhow!("No $BYTEORD value stored."))
}
}
/// Returns a keyword that holds numeric data from the keywords hashmap, if it exists
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_integer_keyword(&self, keyword: &str) -> Result<&IntegerKeyword> {
if let Some(keyword) = self.keywords.get(keyword) {
match keyword {
Keyword::Int(integer) => Ok(integer),
_ => Err(anyhow!("Keyword is not integer variant")),
}
} else {
Err(anyhow!("No {keyword} keyword stored."))
}
}
/// Returns a keyword that holds numeric data from the keywords hashmap, if it exists
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_float_keyword(&self, keyword: &str) -> Result<&FloatKeyword> {
if let Some(keyword) = self.keywords.get(keyword) {
match keyword {
Keyword::Float(float) => Ok(float),
_ => Err(anyhow!("Keyword is not float variant")),
}
} else {
Err(anyhow!("No {keyword} keyword stored."))
}
}
/// Returns a keyword that holds string data from the keywords hashmap, if it exists
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_string_keyword(&self, keyword: &str) -> Result<&StringKeyword> {
if let Some(keyword) = self.keywords.get(keyword) {
match keyword {
Keyword::String(string) => Ok(string),
_ => Err(anyhow!("Keyword is not a string variant")),
}
} else {
Err(anyhow!("No {keyword} keyword stored."))
}
}
/// Returns a keyword that holds byte-orientation data from the keywords hashmap, if it exists
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_byte_keyword(&self, keyword: &str) -> Result<&ByteKeyword> {
if let Some(keyword) = self.keywords.get(keyword) {
match keyword {
Keyword::Byte(byte) => Ok(byte),
_ => Err(anyhow!("Keyword is not a byte variant")),
}
} else {
Err(anyhow!("No {keyword} keyword stored."))
}
}
/// Returns a keyword that holds mixed data from the keywords hashmap, if it exists
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_mixed_keyword(&self, keyword: &str) -> Result<&MixedKeyword> {
if let Some(keyword) = self.keywords.get(keyword) {
match keyword {
Keyword::Mixed(mixed) => Ok(mixed),
_ => Err(anyhow!("Keyword is not a mixed variant")),
}
} else {
Err(anyhow!("No {keyword} keyword stored."))
}
}
/// General function to get a given parameter's string keyword from the file's metadata (e.g. `$PnN` or `$PnS`)
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_string_metadata(
&self,
parameter_number: usize,
suffix: &str,
) -> Result<&StringKeyword> {
// Interpolate the parameter number into the keyword:
let keyword = format!("$P{parameter_number}{suffix}");
self.get_string_keyword(&keyword)
}
/// Generic function to get a given parameter's integer keyword from the file's metadata (e.g. `$PnN`, `$PnS`)
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_numeric_metadata(
&self,
parameter_number: usize,
suffix: &str,
) -> Result<&IntegerKeyword> {
// Interpolate the parameter number into the keyword:
let keyword = format!("$P{parameter_number}{suffix}");
self.get_integer_keyword(&keyword)
}
/// Generic function to get a given parameter's byte keyword from the file's metadata (e.g. `$PnDATATYPE`)
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_byte_metadata(
&self,
parameter_number: usize,
suffix: &str,
) -> Result<&ByteKeyword> {
// Interpolate the parameter number into the keyword:
let keyword = format!("$P{parameter_number}{suffix}");
self.get_byte_keyword(&keyword)
}
/// Get excitation wavelength(s) for a parameter from `$PnL` keyword
/// Returns the first wavelength if multiple are present (for co-axial lasers)
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_excitation_wavelength(
&self,
parameter_number: usize,
) -> Result<Option<usize>> {
let keyword = format!("$P{parameter_number}L");
// Try as integer keyword first (older FCS format)
if let Ok(int_keyword) = self.get_integer_keyword(&keyword) {
if let IntegerKeyword::PnL(wavelength) = int_keyword {
return Ok(Some(*wavelength));
}
}
// Try as mixed keyword (FCS 3.1+ format, can have multiple wavelengths)
if let Ok(mixed_keyword) = self.get_mixed_keyword(&keyword) {
if let MixedKeyword::PnL(wavelengths) = mixed_keyword {
// Return the first wavelength if multiple are present
return Ok(wavelengths.first().copied());
}
}
Ok(None)
}
/// Return the name of the parameter's channel from the `$PnN` keyword in the metadata TEXT section, where `n` is the provided parameter index (1-based)
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_channel_name(&self, parameter_number: usize) -> Result<&str> {
if let StringKeyword::PnN(name) =
self.get_parameter_string_metadata(parameter_number, "N")?
{
Ok(name.as_ref())
} else {
Err(anyhow!(
"$P{parameter_number}N keyword not found in metadata TEXT section",
))
}
}
/// Return the label name of the parameter from the `$PnS` keyword in the metadata TEXT section, where `n` is the provided parameter number
/// # Errors
/// Will return `Err` if the keyword is not present in the keywords hashmap
pub fn get_parameter_label(&self, parameter_number: usize) -> Result<&str> {
if let StringKeyword::PnS(label) =
self.get_parameter_string_metadata(parameter_number, "S")?
{
Ok(label.as_ref())
} else {
Err(anyhow!(
"$P{parameter_number}S keyword not found in metadata TEXT section",
))
}
}
/// Transform the metadata keywords hashmap into a JSON object via serde
/// # Errors
/// Will return `Err` if the metadata keywords hashmap is empty
pub fn get_metadata_as_json_string(&self) -> Result<String> {
if self.keywords.is_empty() {
Err(anyhow!("No metadata keywords stored."))
} else {
let json = serde_json::to_string(&self.keywords)?;
Ok(json)
}
}
/// Insert or update a string keyword in the metadata
pub fn insert_string_keyword(&mut self, key: String, value: String) {
let normalized_key = if key.starts_with('$') {
key
} else {
format!("${key}")
};
let parsed = match_and_parse_keyword(&normalized_key, value.as_str());
let string_keyword = match parsed {
KeywordCreationResult::String(string_keyword) => string_keyword,
// If parsing fails (or parses to a non-string keyword), fall back to `Other`.
_ => StringKeyword::Other(Arc::from(value)),
};
self.keywords
.insert(normalized_key, Keyword::String(string_keyword));
}
/// Create metadata from a DataFrame and ParameterMap
///
/// This helper function creates all required FCS metadata keywords from scratch,
/// including file structure keywords ($BYTEORD, $DATATYPE, $MODE, $PAR, $TOT, $NEXTDATA)
/// and parameter-specific keywords ($PnN, $PnS, $PnB, $PnE, $PnR) for each parameter.
///
/// # Arguments
/// * `df` - The DataFrame containing event data
/// * `params` - The ParameterMap containing parameter metadata
///
/// # Returns
/// A new Metadata struct with all required keywords populated
pub fn from_dataframe_and_parameters(
df: &polars::prelude::DataFrame,
params: &super::parameter::ParameterMap,
) -> Result<Self> {
let mut metadata = Self::new();
let n_events = df.height();
let n_params = df.width();
// Required file structure keywords
// BYTEORD - use LittleEndian as default (1,2,3,4)
metadata.keywords.insert(
"$BYTEORD".to_string(),
Keyword::Byte(ByteKeyword::BYTEORD(ByteOrder::LittleEndian)),
);
// DATATYPE - use F (float32) as default
metadata.keywords.insert(
"$DATATYPE".to_string(),
Keyword::Byte(ByteKeyword::DATATYPE(FcsDataType::F)),
);
// MODE
metadata.insert_string_keyword("$MODE".to_string(), "L".to_string());
// PAR
metadata.keywords.insert(
"$PAR".to_string(),
Keyword::Int(IntegerKeyword::PAR(n_params)),
);
// TOT
metadata.keywords.insert(
"$TOT".to_string(),
Keyword::Int(IntegerKeyword::TOT(n_events)),
);
// NEXTDATA
metadata.insert_string_keyword("$NEXTDATA".to_string(), "0".to_string());
// Add parameter keywords ($PnN, $PnS, $PnB, $PnE, $PnR)
// Get column names from DataFrame in order
let column_names = df.get_column_names();
for (param_idx, param_name) in column_names.iter().enumerate() {
let param_num = param_idx + 1;
// Get parameter from ParameterMap if available
// Convert PlSmallStr to Arc<str> for ParameterMap lookup
let param_name_arc: Arc<str> = Arc::from(param_name.as_str());
if let Some(param) = params.get(¶m_name_arc) {
// $PnN - Parameter name
metadata.insert_string_keyword(format!("$P{}N", param_num), param_name.to_string());
// $PnS - Parameter label (short name)
metadata.insert_string_keyword(
format!("$P{}S", param_num),
param.label_name.to_string(),
);
// $PnB - Bits per parameter (default: 32 for float32)
metadata.keywords.insert(
format!("$P{}B", param_num),
Keyword::Int(IntegerKeyword::PnB(32)),
);
// $PnE - Amplification (default: 0,0)
metadata.insert_string_keyword(format!("$P{}E", param_num), "0,0".to_string());
// $PnR - Range (default: 262144)
metadata.keywords.insert(
format!("$P{}R", param_num),
Keyword::Int(IntegerKeyword::PnR(262144)),
);
} else {
// Fallback if parameter not in ParameterMap
metadata.insert_string_keyword(format!("$P{}N", param_num), param_name.to_string());
metadata.insert_string_keyword(format!("$P{}S", param_num), param_name.to_string());
metadata.keywords.insert(
format!("$P{}B", param_num),
Keyword::Int(IntegerKeyword::PnB(32)),
);
metadata.insert_string_keyword(format!("$P{}E", param_num), "0,0".to_string());
metadata.keywords.insert(
format!("$P{}R", param_num),
Keyword::Int(IntegerKeyword::PnR(262144)),
);
}
}
// Generate GUID
metadata.validate_guid();
Ok(metadata)
}
}