rustdf/data/
dataset.rs

1use crate::data::acquisition::AcquisitionMode;
2use crate::data::handle::{IndexConverter, TimsData, TimsDataLoader};
3use crate::data::meta::{read_global_meta_sql, read_meta_data_sql};
4use mscore::timstof::frame::{RawTimsFrame, TimsFrame};
5use mscore::timstof::slice::TimsSlice;
6
7pub struct TimsDataset {
8    pub loader: TimsDataLoader,
9}
10
11impl TimsDataset {
12    pub fn new(
13        bruker_lib_path: &str,
14        data_path: &str,
15        in_memory: bool,
16        use_bruker_sdk: bool,
17    ) -> Self {
18        // TODO: error handling
19        let global_meta_data = read_global_meta_sql(data_path).unwrap();
20        let meta_data = read_meta_data_sql(data_path).unwrap();
21
22        let scan_max_index = meta_data.iter().map(|x| x.num_scans).max().unwrap() as u32;
23        let im_lower = global_meta_data.one_over_k0_range_lower;
24        let im_upper = global_meta_data.one_over_k0_range_upper;
25
26        let tof_max_index = global_meta_data.tof_max_index;
27        let mz_lower = global_meta_data.mz_acquisition_range_lower;
28        let mz_upper = global_meta_data.mz_acquisition_range_upper;
29
30        let loader = match in_memory {
31            true => TimsDataLoader::new_in_memory(
32                bruker_lib_path,
33                data_path,
34                use_bruker_sdk,
35                scan_max_index,
36                im_lower,
37                im_upper,
38                tof_max_index,
39                mz_lower,
40                mz_upper,
41            ),
42            false => TimsDataLoader::new_lazy(
43                bruker_lib_path,
44                data_path,
45                use_bruker_sdk,
46                scan_max_index,
47                im_lower,
48                im_upper,
49                tof_max_index,
50                mz_lower,
51                mz_upper,
52            ),
53        };
54
55        TimsDataset { loader }
56    }
57}
58
59impl TimsData for TimsDataset {
60    // Get a frame by its id
61    fn get_frame(&self, frame_id: u32) -> TimsFrame {
62        self.loader.get_frame(frame_id)
63    }
64    // Get a raw frame by its id
65    fn get_raw_frame(&self, frame_id: u32) -> RawTimsFrame {
66        self.loader.get_raw_frame(frame_id)
67    }
68    // Get a collection of frames by their ids
69    fn get_slice(&self, frame_ids: Vec<u32>, num_threads: usize) -> TimsSlice {
70        self.loader.get_slice(frame_ids, num_threads)
71    }
72    // Get the acquisition mode, DDA or DIA
73    fn get_acquisition_mode(&self) -> AcquisitionMode {
74        self.loader.get_acquisition_mode().clone()
75    }
76    // Get total number of frames in the dataset
77    fn get_frame_count(&self) -> i32 {
78        self.loader.get_frame_count()
79    }
80    // Get the path to the data
81    fn get_data_path(&self) -> &str {
82        &self.loader.get_data_path()
83    }
84}
85
86impl IndexConverter for TimsDataset {
87    fn tof_to_mz(&self, frame_id: u32, tof_values: &Vec<u32>) -> Vec<f64> {
88        self.loader
89            .get_index_converter()
90            .tof_to_mz(frame_id, tof_values)
91    }
92    // convert m/z values to TOF values given a valid data handle and frame id
93    fn mz_to_tof(&self, frame_id: u32, mz_values: &Vec<f64>) -> Vec<u32> {
94        self.loader
95            .get_index_converter()
96            .mz_to_tof(frame_id, mz_values)
97    }
98    // convert inverse mobility values to scan values given a valid data handle and frame id
99    fn scan_to_inverse_mobility(&self, frame_id: u32, scan_values: &Vec<u32>) -> Vec<f64> {
100        self.loader
101            .get_index_converter()
102            .scan_to_inverse_mobility(frame_id, scan_values)
103    }
104    // convert scan values to inverse mobility values given a valid data handle and frame id
105    fn inverse_mobility_to_scan(
106        &self,
107        frame_id: u32,
108        inverse_mobility_values: &Vec<f64>,
109    ) -> Vec<u32> {
110        self.loader
111            .get_index_converter()
112            .inverse_mobility_to_scan(frame_id, inverse_mobility_values)
113    }
114}
rustdf/data/dataset.rs

rustdf/data/
dataset.rs
