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use crate::frame::{Array, Frame, Header, HeaderEntry}; use byteorder::{LittleEndian, ReadBytesExt}; use std::collections::HashMap; use std::fs::File; use std::io::Read; use std::num::ParseFloatError; use std::path::Path; use std::{io, mem}; pub struct BrukerFrame { header: Header, array: Array, data_start: usize, overflow_start: usize, dim1: usize, dim2: usize, } impl BrukerFrame { pub fn new() -> BrukerFrame { BrukerFrame { header: HashMap::new(), array: Array::new(), data_start: 0, overflow_start: 0, dim1: 0, dim2: 0, } } pub fn read_file<P: AsRef<Path>>(path: P) -> io::Result<BrukerFrame> { let mut file = File::open(path)?; let size = file.metadata()?.len() as usize; let mut data = Vec::with_capacity(size); unsafe { data.set_len(size) }; file.read_exact(&mut data)?; let mut frame = BrukerFrame::new(); frame.read(&data)?; Ok(frame) } fn read(&mut self, data: &[u8]) -> io::Result<()> { self.read_header(data)?; self.read_array(data)?; self.read_overflow(data)?; self.check_linearity(); Ok(()) } fn read_header_chunks(&mut self, start: usize, end: usize, data: &[u8]) -> io::Result<()> { for i in (start..end).step_by(HEADER_CHUNK_SIZE) { let j = i + HEADER_CHUNK_SIZE; if j >= data.len() { return Err(io::Error::new( io::ErrorKind::UnexpectedEof, "not enough data in buffer", )); } self.fill_header(&data[i..j]) } Ok(()) } fn read_header(&mut self, data: &[u8]) -> io::Result<()> { self.read_header_chunks(0, N_BLOCKS, data)?; if let Ok(v) = self.get_header_str_as_i64(KEY_HEADER_BLOCKS) { self.data_start = v as usize; } else { self.data_start = N_HEADER_BLOCKS }; self.data_start *= BLOCK_SIZE; self.read_header_chunks(N_BLOCKS, self.data_start, data)?; if let Ok(dim1) = self.get_header_str_as_i64(KEY_N_ROWS) { if let Ok(dim2) = self.get_header_str_as_i64(KEY_N_COLS) { if dim1 == 0 || dim2 == 0 { return Err(io::Error::new( io::ErrorKind::InvalidData, "zero dimensions in the header", )); } self.dim1 = dim1 as usize; self.dim2 = dim2 as usize; } else { return Err(io::Error::new( io::ErrorKind::InvalidData, "could not find dim2 in the header", )); } } else { return Err(io::Error::new( io::ErrorKind::InvalidData, "could not find dim1 in the header", )); }; if let Ok(v) = self.get_header_str_as_i64(KEY_VERSION) { if v != VERSION { return Err(io::Error::new( io::ErrorKind::InvalidData, format!("version {} is not yet supported", v), )); } } Ok(()) } fn fill_header(&mut self, chunk: &[u8]) { if chunk.is_empty() { return; } let chunk = unsafe { std::str::from_utf8_unchecked(chunk) }; let parts: Vec<&str> = chunk.split(':').map(|x| x.trim()).collect(); if parts.len() < 2 { return; } self.header .entry(parts[0].to_string()) .or_insert(HeaderEntry::String(parts[1].to_string())); } fn read_array(&mut self, data: &[u8]) -> io::Result<()> { let npixelb; if let Ok(v) = self.get_header_str_as_i64(KEY_N_PIXELB) { npixelb = v as usize; } else { return Err(io::Error::new( io::ErrorKind::InvalidData, format!("could not find {} in the header", KEY_N_PIXELB), )); } if self.data_start >= data.len() { return Err(io::Error::new( io::ErrorKind::UnexpectedEof, "not enough binary data", )); } let array = &data[self.data_start..]; self.array = match npixelb { SIZE_U8 => Array::from_slice_u8(self.dim1, self.dim2, array)?, SIZE_U16 => Array::from_slice_u16::<LittleEndian>(self.dim1, self.dim2, array)?, SIZE_U32 => Array::from_slice_u32::<LittleEndian>(self.dim1, self.dim2, array)?, _ => { return Err(io::Error::new( io::ErrorKind::InvalidData, format!("bad value for {} = {} in the header", KEY_N_PIXELB, npixelb), )) } }; self.overflow_start = self.array.len() * npixelb + self.data_start; Ok(()) } fn check_linearity(&mut self) { if let Ok(s) = self.get_header_str(KEY_LINEAR) { let parts: Vec<Result<f64, ParseFloatError>> = s .split_ascii_whitespace() .map(|x| x.trim().parse::<f64>()) .collect(); if parts.len() < 2 { return; } if let Ok(slope) = parts[0] { if let Ok(offset) = parts[1] { if slope != 1.0 || offset != 0.0 { for value in self.array.data_mut() { *value = *value * slope + offset; } } } } } } fn read_overflow(&mut self, data: &[u8]) -> io::Result<()> { let mut n; if let Ok(v) = self.get_header_str_as_i64(KEY_N_OVERFLOW) { n = v as usize; } else { return Err(io::Error::new( io::ErrorKind::InvalidData, format!("bad value for {} in the header", KEY_N_OVERFLOW), )); } let mut reader = io::Cursor::new(&data[self.overflow_start..]); while n > 0 { let intensity = reader.read_u64::<LittleEndian>()? as f64; reader.read_u8()?; let position = reader.read_u32::<LittleEndian>()? as usize; if position >= self.array.len() { return Err(io::Error::new( io::ErrorKind::InvalidData, format!("bad overflow position: {}", position), )); } reader.read_u24::<LittleEndian>()?; self.array[position] = intensity; n -= 1; } Ok(()) } } impl Frame for BrukerFrame { fn array(&self) -> &Array { &self.array } fn header(&self) -> &Header { &self.header } fn header_mut(&mut self) -> &mut Header { &mut self.header } fn array_mut(&mut self) -> &mut Array { &mut self.array } fn set_array(&mut self, array: Array) { self.array = array; } } const BLOCK_SIZE: usize = 512; const N_HEADER_BLOCKS: usize = 5; const VERSION: i64 = 8; const HEADER_CHUNK_SIZE: usize = 80; const N_BLOCKS: usize = BLOCK_SIZE * N_HEADER_BLOCKS; const KEY_HEADER_BLOCKS: &'static str = "HDRBLKS"; const KEY_N_ROWS: &'static str = "NROWS"; const KEY_N_COLS: &'static str = "NCOLS"; const KEY_N_PIXELB: &'static str = "NPIXELB"; const KEY_N_OVERFLOW: &'static str = "NOVERFL"; const KEY_LINEAR: &'static str = "LINEAR"; const KEY_VERSION: &'static str = "VERSION"; const SIZE_U8: usize = mem::size_of::<u8>(); const SIZE_U16: usize = mem::size_of::<u16>(); const SIZE_U32: usize = mem::size_of::<u32>(); #[cfg(test)] mod tests { use crate::bruker::BrukerFrame; use crate::frame::Frame; use std::path::Path; fn read_test_file<P: AsRef<Path>>(path: P) { let frame = BrukerFrame::read_file(path).unwrap(); if frame.dim1() != 1024 || frame.dim2() != 1024 { panic!( "Bad frame dimensions: expected 1024x1024, found {}x{}", frame.dim1(), frame.dim2(), ); } let sum = frame.sum(); if sum != 21268323. { panic!("Expected sum is 21268323 but found {}", sum); } let min = frame.min(); if min != 0. { panic!("Expected min is 0 but found {}", min); } let max = frame.max(); if max != 6886. { panic!("Expected max is 6886. but found {}", max); } } #[test] fn test_bruker_read() { read_test_file("testdata/test.gfrm"); } }