David@rustdf

IMSJL/src/Data.jl

@@ -1,22 +1,7 @@
-"""
-# module Data
-
-- Julia version: 
-- Author: davidteschner
-- Date: 2023-09-27
-
-# Examples
-
-```jldoctest
-julia>
-```
-"""
 module Data
 
 import Base.show
 
-export TimsFrame
-
 struct TimsFrame
     frame_id::Int32
     ms_type_numeric::Int32
@@ -29,8 +14,10 @@ struct TimsFrame
 end
 
 function show(io::IO, frame::TimsFrame)
-    num_peaks = length(frame.mz)  # or whichever array represents peaks
+    num_peaks = length(frame.mz)
     print(io, "TimsFrame(frame_id=$(frame.frame_id), ms_type=$(frame.ms_type_numeric), num_peaks=$num_peaks)")
 end
 
+export TimsFrame
+
 end

IMSJL/src/JuliaDataHandle.jl → IMSJL/src/DataHandle.jl

@@ -1,22 +1,6 @@
-"""
-# module JuliaDataHandle
+module DataHandle
 
-- Julia version: 
-- Author: davidteschner
-- Date: 2023-09-27
-
-# Examples
-
-```jldoctest
-julia>
-```
-"""
-module JuliaDataHandle
-
-include("RustCAPI.jl")
-include("Data.jl")
-
-export TimsDataHandle, get_tims_frame
+using IMSJL.Data, IMSJL.RustCAPI
 
 struct TimsDataHandle
     data_path::String
@@ -30,7 +14,7 @@ struct TimsDataHandle
         bruker_binary_path = determine_bruker_binary_path()
 
         # Acquire the actual handle from the C-exposed Rust object
-        handle = RustcApi.TimsDataHandle_new(data_path, bruker_binary_path)
+        handle = RustCAPI.TimsDataHandle_new(data_path, bruker_binary_path)
 
         # Construct the instance
         new(data_path, bruker_binary_path, handle)
@@ -46,8 +30,10 @@ function determine_imsjl_connector_path()::String
 end
 
 function get_tims_frame(handle::TimsDataHandle, frame_id::Number)::TimsFrame
-    ctims_frame = RustcApi.TimsDataHandle_get_frame(handle.handle, Int32(frame_id))
-    return RustcApi.ctims_frame_to_julia_tims_frame(ctims_frame)
+    ctims_frame = RustCAPI.TimsDataHandle_get_frame(handle.handle, Int32(frame_id))
+    return RustCAPI.ctims_frame_to_julia_tims_frame(ctims_frame)
 end
 
+export TimsDataHandle, get_tims_frame
+
 end

IMSJL/src/IMSJL.jl

@@ -1,9 +1,9 @@
 module IMSJL
 
-include("RustCAPI.jl")
-include("JuliaDataHandle.jl")
 include("Data.jl")
+include("RustCAPI.jl")
+include("DataHandle.jl")
 
-export JuliaDataHandle.TimsDataHandle, JuliaDataHandle.get_tims_frame, Data.TimsFrame
+export Data, RustCAPI, DataHandle
 
-end # module IMSJL
+end

IMSJL/src/RustCAPI.jl

@@ -1,40 +1,26 @@
-"""
-# module RustCAPI
-
-- Julia version:
-- Author: davidteschner
-- Date: 2023-09-27
-
-# Examples
-
-```jldoctest
-julia>
-```
-"""
-module RustcApi
-
-export TimsDataHandle_new, TimsDataHandle_get_data_path, TimsFrame_get_bruker_binary_path, TimsDataHandle_destroy, TimsDataHandle_get_frame_count, TimsDataHandle_get_frame, ctims_frame_to_julia_tims_frame
+module RustCAPI
 
+using IMSJL.Data
 
 struct CTimsFrame
-frame_id::Int32
-ms_type::Int32
-retention_time::Float64
+    frame_id::Int32
+    ms_type::Int32
+    retention_time::Float64
 
-scan::Ptr{Int32}
-scan_size::UInt64
+    scan::Ptr{Int32}
+    scan_size::UInt64
 
-inv_mobility::Ptr{Float64}
-inv_mobility_size::UInt64
+    inv_mobility::Ptr{Float64}
+    inv_mobility_size::UInt64
 
-tof::Ptr{Int32}
-tof_size::UInt64
+    tof::Ptr{Int32}
+    tof_size::UInt64
 
-mz::Ptr{Float64}
-mz_size::UInt64
+    mz::Ptr{Float64}
+    mz_size::UInt64
 
-intensity::Ptr{Float64}
-intensity_size::UInt64
+    intensity::Ptr{Float64}
+    intensity_size::UInt64
 end
 
 const lib = "/home/administrator/Documents/promotion/rustims/imsjl_connector/target/release/libimsjl_connector.so"
@@ -61,7 +47,7 @@ function ctims_frame_to_julia_tims_frame(ctims_frame::CTimsFrame)::TimsFrame
 
     TimsFrame(
         ctims_frame.frame_id,
-        ctims_frame.ms_type,  # Note that I've changed ms_type_numeric to ms_type
+        ctims_frame.ms_type,
         ctims_frame.retention_time,
         julia_scan,
         julia_inv_mobility,
@@ -71,4 +57,6 @@ function ctims_frame_to_julia_tims_frame(ctims_frame::CTimsFrame)::TimsFrame
     )
 end
 
+export TimsDataHandle_new, TimsDataHandle_get_data_path, TimsDataHandle_get_bruker_binary_path, TimsDataHandle_destroy, TimsDataHandle_get_frame_count, TimsDataHandle_get_frame, ctims_frame_to_julia_tims_frame
+
 end

imsjl_connector/src/handle.rs

@@ -20,10 +20,9 @@ pub extern "C" fn tims_data_handle_new(data_path: *const c_char, bruker_lib_path
     let data_path = unsafe { std::ffi::CStr::from_ptr(data_path) }.to_str().unwrap();
     let bruker_lib_path = unsafe { std::ffi::CStr::from_ptr(bruker_lib_path) }.to_str().unwrap();
 
-    // Create your structure
     let handle = TimsDataHandle::new(bruker_lib_path, data_path).unwrap();
 
-    // Box the structure to keep it on the heap and return a pointer
+    // Box structure to keep it on heap and return pointer
     Box::into_raw(Box::new(CTimsDataHandle { inner: handle }))
 }
 
@@ -55,6 +54,6 @@ pub extern "C" fn tims_data_handle_destroy(handle: *mut CTimsDataHandle) {
 
 #[no_mangle]
 pub extern "C" fn tims_data_handle_get_frame(handle: &TimsDataHandle, frame_id: i32) -> CTimsFrame {
-    let frame = handle.get_frame(frame_id as u32).unwrap(); // Ensure proper error handling if get_frame can fail
+    let frame = handle.get_frame(frame_id as u32).unwrap();
     convert_to_ctims_frame(frame)
 }