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Enable static linking, libczi is now a submodule.

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This commit is contained in:
Wim Pomp
2025-08-12 18:52:46 +02:00
parent 37ede463e0
commit 999af74dd6
13 changed files with 368 additions and 148 deletions
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10
src/functions.rs
View File

@@ -137,7 +137,7 @@ impl CziReader {
/// available.
/// - In the returned 'SubBlockStatisticsInteropEx' structure, the 'number_of_per_scenes_bounding_boxes' field will be set to the number of per-scene
/// information that is put into this struct (which may be less than number of scenes that are available).
///
///
/// So, the caller is expected to check the returned 'number_of_per_channel_bounding_boxes' to see how many per-channel bounding boxes are available.
/// If this number is greater than the number of elements (given with the 'number_of_per_scenes_bounding_boxes' value in the 'statistics' structure),
/// then the caller should allocate a larger 'statistics' structure and call this function again (with an increased 'number_of_per_scenes_bounding_boxes').
@@ -640,7 +640,13 @@ impl LockedBitmap {
/// \\param \[out\] ptr Pointer to the memory location where the bitmap is to be copied to.
///
/// \\returns A LibCZIApiErrorCode.
pub fn copy(&self, width: u32, height: u32, pixel_type: PixelType, stride: u32) -> Result<Bitmap> {
pub fn copy(
&self,
width: u32,
height: u32,
pixel_type: PixelType,
stride: u32,
) -> Result<Bitmap> {
let mut data = MaybeUninit::<Self>::uninit();
LibCZIApiError::try_from(unsafe {
libCZI_BitmapCopyTo(

29
src/handle.rs
View File

@@ -3,60 +3,61 @@ use crate::sys::*;
use std::mem::MaybeUninit;
use std::ops::Deref;
/// CZI-reader object.
#[derive(Clone, Debug)]
pub struct CziReader(pub (crate) CziReaderObjectHandle);
pub struct CziReader(pub(crate) CziReaderObjectHandle);
/// sub-block object.
#[derive(Clone, Debug)]
pub struct SubBlock(pub (crate) SubBlockObjectHandle);
pub struct SubBlock(pub(crate) SubBlockObjectHandle);
/// input stream object.
#[derive(Clone, Debug)]
pub struct InputStream(pub (crate) InputStreamObjectHandle);
pub struct InputStream(pub(crate) InputStreamObjectHandle);
/// output stream object.
#[derive(Clone, Debug)]
pub struct OutputStream(pub (crate) OutputStreamObjectHandle);
pub struct OutputStream(pub(crate) OutputStreamObjectHandle);
/// memory allocation object - which is a pointer to a memory block, which must be
/// freed with 'libCZI_Free'.
/// TODO(JBL): this is not really used so far, should be removed I guess.
#[derive(Clone, Debug)]
pub struct MemoryAllocation(pub (crate) MemoryAllocationObjectHandle);
pub struct MemoryAllocation(pub(crate) MemoryAllocationObjectHandle);
/// bitmap object.
#[derive(Clone, Debug)]
pub struct Bitmap(pub (crate) BitmapObjectHandle);
pub struct Bitmap(pub(crate) BitmapObjectHandle);
/// metadata segment object.
#[derive(Clone, Debug)]
pub struct MetadataSegment(pub (crate) MetadataSegmentObjectHandle);
pub struct MetadataSegment(pub(crate) MetadataSegmentObjectHandle);
/// attachment object.
#[derive(Clone, Debug)]
pub struct Attachment(pub (crate) AttachmentObjectHandle);
pub struct Attachment(pub(crate) AttachmentObjectHandle);
/// writer object.
#[derive(Clone, Debug)]
pub struct CziWriter(pub (crate) CziWriterObjectHandle);
pub struct CziWriter(pub(crate) CziWriterObjectHandle);
/// single-channel-scaling-tile-accessor.
#[derive(Clone, Debug)]
pub struct SingleChannelScalingTileAccessor(pub (crate) SingleChannelScalingTileAccessorObjectHandle);
pub struct SingleChannelScalingTileAccessor(
pub(crate) SingleChannelScalingTileAccessorObjectHandle,
);
/// document info object.
#[derive(Clone, Debug)]
pub struct CziDocumentInfo(pub (crate) CziDocumentInfoHandle);
pub struct CziDocumentInfo(pub(crate) CziDocumentInfoHandle);
/// display settings object.
#[derive(Clone, Debug)]
pub struct DisplaySettings(pub (crate) DisplaySettingsHandle);
pub struct DisplaySettings(pub(crate) DisplaySettingsHandle);
/// channel display settings object.
#[derive(Clone, Debug)]
pub struct ChannelDisplaySettings(pub (crate) ChannelDisplaySettingsHandle);
pub struct ChannelDisplaySettings(pub(crate) ChannelDisplaySettingsHandle);
macro_rules! impl_struct {
($($n:ident: $t:ty: $s:ty $(,)?)*) => {

163
src/interop.rs
View File

@@ -8,45 +8,45 @@ use std::mem::{ManuallyDrop, MaybeUninit};
/// This struct contains the version information of the libCZIApi-library. For versioning libCZI, SemVer2 (<https://semver.org/>) is used.
/// Note that the value of the tweak version number does not have a meaning (as far as SemVer2 is concerned).
#[derive(Clone, Debug)]
pub struct LibCZIVersionInfo(pub (crate) LibCZIVersionInfoInterop);
pub struct LibCZIVersionInfo(pub(crate) LibCZIVersionInfoInterop);
/// This struct gives information about the build of the libCZIApi-library.
/// Note that all strings must be freed by the caller (using libCZI_Free).
#[derive(Clone, Debug)]
pub struct LibCZIBuildInformation(pub (crate) LibCZIBuildInformationInterop);
pub struct LibCZIBuildInformation(pub(crate) LibCZIBuildInformationInterop);
#[derive(Clone, Debug)]
pub struct InputStreamClassInfo(pub (crate) InputStreamClassInfoInterop);
pub struct InputStreamClassInfo(pub(crate) InputStreamClassInfoInterop);
/// This structure gives additional information about an error that occurred in the external stream.
#[derive(Clone, Debug)]
pub struct ExternalStreamErrorInfo(pub (crate) ExternalStreamErrorInfoInterop);
pub struct ExternalStreamErrorInfo(pub(crate) ExternalStreamErrorInfoInterop);
/// This structure contains information about externally provided functions for reading data from an input stream,
/// and it is used to construct a stream-object to be used with libCZI.
/// Note on lifetime: The function pointers must remain valid until the function 'close_function' is called. The lifetime
/// may extend beyond calling the 'libCZI_ReleaseInputStream' function for the corresponding stream-object.
#[derive(Clone, Debug)]
pub struct ExternalInputStreamStruct(pub (crate) ExternalInputStreamStructInterop);
pub struct ExternalInputStreamStruct(pub(crate) ExternalInputStreamStructInterop);
/// This structure contains information about externally provided functions for writing data to an output stream,
/// and it is used to construct a stream-object to be used with libCZI.
/// Note on lifetime: The function pointers must remain valid until the function 'close_function' is called. The lifetime
/// may extend beyond calling the 'libCZI_ReleaseOutputStream' function for the corresponding stream-object.
#[derive(Clone, Debug)]
pub struct ExternalOutputStreamStruct(pub (crate) ExternalOutputStreamStructInterop);
pub struct ExternalOutputStreamStruct(pub(crate) ExternalOutputStreamStructInterop);
/// This structure gather the information needed to create a reader object.
#[derive(Clone, Debug)]
pub struct ReaderOpenInfo(pub (crate) ReaderOpenInfoInterop);
pub struct ReaderOpenInfo(pub(crate) ReaderOpenInfoInterop);
/// This structure describes a rectangle, given by its top-left corner and its width and height.
#[derive(Clone, Debug)]
pub struct IntRect(pub (crate) IntRectInterop);
pub struct IntRect(pub(crate) IntRectInterop);
/// This structure describes a size, given by its width and height.
#[derive(Clone, Debug)]
pub struct IntSize(pub (crate) IntSizeInterop);
pub struct IntSize(pub(crate) IntSizeInterop);
/// This structure gives the bounds for a set of dimensions.
/// The bit at position `i` in `dimensions_valid` indicates whether the interval for dimension `i+1` is valid. So, bit 0
@@ -56,7 +56,7 @@ pub struct IntSize(pub (crate) IntSizeInterop);
/// An example would be: `dimensions_valid` = 0b00000011, `start` = { 0, 2 }, `size` = { 5, 6 }. This would mean that the
/// dimension 'Z' is valid, and the interval is [0, 5], and the dimension 'C' is valid, and the interval is [2, 8].
#[derive(Clone, Debug)]
pub struct DimBounds(pub (crate) DimBoundsInterop);
pub struct DimBounds(pub(crate) DimBoundsInterop);
/// This structure gives the coordinates (of a sub-block) for a set of dimension.
/// The bit at position `i` in `dimensions_valid` indicates whether the coordinate for dimension `i+1` is valid. So, bit 0
@@ -66,35 +66,35 @@ pub struct DimBounds(pub (crate) DimBoundsInterop);
/// An example would be: `dimensions_valid` = 0b00000011, `value` = { 0, 2 }. This would mean that the
/// dimension 'Z' is valid, and the coordinate for 'Z' is 0, and the dimension 'C' is valid, and the coordinate for 'C' is 2.
#[derive(Clone, Debug)]
pub struct Coordinate(pub (crate) CoordinateInterop);
pub struct Coordinate(pub(crate) CoordinateInterop);
/// This structure contains the bounding boxes for a scene.
#[derive(Clone, Debug)]
pub struct BoundingBoxes(pub (crate) BoundingBoxesInterop);
pub struct BoundingBoxes(pub(crate) BoundingBoxesInterop);
/// This structure contains basic statistics about an CZI-document.
#[derive(Clone, Debug)]
pub struct SubBlockStatistics(pub (crate) SubBlockStatisticsInterop);
pub struct SubBlockStatistics(pub(crate) SubBlockStatisticsInterop);
/// This structure extends on the basic statistics about an CZI-document, and includes per-scene statistics.
#[derive(Debug)]
pub struct SubBlockStatisticsEx(pub (crate) SubBlockStatisticsInteropEx);
pub struct SubBlockStatisticsEx(pub(crate) SubBlockStatisticsInteropEx);
#[derive(Clone, Debug)]
pub struct MetadataAsXml(pub (crate) MetadataAsXmlInterop);
pub struct MetadataAsXml(pub(crate) MetadataAsXmlInterop);
/// Information about the bitmap represented by a bitmap-object.
#[derive(Clone, Debug)]
pub struct BitmapInfo(pub (crate) BitmapInfoInterop);
pub struct BitmapInfo(pub(crate) BitmapInfoInterop);
/// This structure contains information about a locked bitmap-object, allowing direct
/// access to the pixel data.
#[derive(Clone, Debug)]
pub struct BitmapLockInfo(pub (crate) BitmapLockInfoInterop);
pub struct BitmapLockInfo(pub(crate) BitmapLockInfoInterop);
/// This structure contains the information about a sub-block.
#[derive(Clone, Debug)]
pub struct SubBlockInfo(pub (crate) SubBlockInfoInterop);
pub struct SubBlockInfo(pub(crate) SubBlockInfoInterop);
/// This structure contains the information about an attachment.
/// Note that performance reasons we use a fixed-size array for the name. In the rare case that the name is too long to fit into the
@@ -102,35 +102,35 @@ pub struct SubBlockInfo(pub (crate) SubBlockInfoInterop);
/// In addition, the field 'name_in_case_of_overflow' then contains the full text, allocated with 'libCZI_AllocateString' (and responsibility
/// for releasing the memory is with the caller).
#[derive(Clone, Debug)]
pub struct AttachmentInfo(pub (crate) AttachmentInfoInterop);
pub struct AttachmentInfo(pub(crate) AttachmentInfoInterop);
/// This structure contains the information about file-header.
#[derive(Clone, Debug)]
pub struct FileHeaderInfo(pub (crate) FileHeaderInfoInterop);
pub struct FileHeaderInfo(pub(crate) FileHeaderInfoInterop);
/// This structure is used to pass the subblock information to libCZIAPI, describing a subblock to be added to a CZI-file.
#[derive(Clone, Debug)]
pub struct AddSubBlockInfo(pub (crate) AddSubBlockInfoInterop);
pub struct AddSubBlockInfo(pub(crate) AddSubBlockInfoInterop);
/// This structure is used to pass the attachment information to libCZIAPI, describing an attachment to be added to a CZI-file.
#[derive(Clone, Debug)]
pub struct AddAttachmentInfo(pub (crate) AddAttachmentInfoInterop);
pub struct AddAttachmentInfo(pub(crate) AddAttachmentInfoInterop);
/// This structure is used to pass the metadata information to libCZIAPI.
#[derive(Clone, Debug)]
pub struct WriteMetadataInfo(pub (crate) WriteMetadataInfoInterop);
pub struct WriteMetadataInfo(pub(crate) WriteMetadataInfoInterop);
/// This structure is used to pass the accessor options to libCZIAPI.
#[derive(Clone, Debug)]
pub struct AccessorOptions(pub (crate) AccessorOptionsInterop);
pub struct AccessorOptions(pub(crate) AccessorOptionsInterop);
/// This structure gathers all information about a channel for the purpose of multi-channel-composition.
#[derive(Clone, Debug)]
pub struct CompositionChannelInfo(pub (crate) CompositionChannelInfoInterop);
pub struct CompositionChannelInfo(pub(crate) CompositionChannelInfoInterop);
/// This structure gathers the information about the scaling.
#[derive(Clone, Debug)]
pub struct ScalingInfo(pub (crate) ScalingInfoInterop);
pub struct ScalingInfo(pub(crate) ScalingInfoInterop);
macro_rules! impl_ptr {
($($n:ident: $t:ty: $s:ty $(,)?)*) => {
@@ -488,8 +488,83 @@ impl SubBlockStatistics {
}
}
impl SubBlockStatisticsEx {
// pub fn new(
// sub_block_count: i32,
// min_m_index: i32,
// max_m_index: i32,
// bounding_box: IntRect,
// bounding_box_layer0: IntRect,
// dim_bounds: DimBounds,
// per_scenes_bounding_boxes: Vec<BoundingBoxes>
// ) -> Self {
// Self(SubBlockStatisticsInteropEx {
// sub_block_count,
// min_m_index,
// max_m_index,
// bounding_box: bounding_box.0,
// bounding_box_layer0: bounding_box_layer0.0,
// dim_bounds: dim_bounds.0,
// number_of_per_scenes_bounding_boxes: per_scenes_bounding_boxes.len() as i32,
// per_scenes_bounding_boxes: unsafe { transmute::<Vec<BoundingBoxes>, __IncompleteArrayField<BoundingBoxesInterop>>(per_scenes_bounding_boxes) },
// })
// }
pub fn get_sub_block_count(&self) -> i32 {
self.0.sub_block_count
}
pub fn get_min_m_index(&self) -> i32 {
self.0.min_m_index
}
pub fn get_max_m_index(&self) -> i32 {
self.0.max_m_index
}
pub fn get_bounding_box(&self) -> IntRect {
IntRect(self.0.bounding_box)
}
pub fn get_bounding_box_layer0(&self) -> IntRect {
IntRect(self.0.bounding_box_layer0)
}
pub fn get_dim_bounds(&self) -> DimBounds {
DimBounds(self.0.dim_bounds)
}
pub fn get_number_of_per_scenes_bounding_boxes(&self) -> i32 {
self.0.number_of_per_scenes_bounding_boxes
}
// pub fn get_per_scenes_bounding_boxes(&self) -> Vec<BoundingBoxes> {
// unsafe { transmute(&self.0.per_scenes_bounding_boxes) }.clone()
// }
pub fn set_sub_block_count(&mut self, sub_block_count: i32) {
self.0.sub_block_count = sub_block_count;
}
pub fn set_min_m_index(&mut self, min_m_index: i32) {
self.0.min_m_index = min_m_index;
}
pub fn set_max_m_index(&mut self, max_m_index: i32) {
self.0.max_m_index = max_m_index;
}
pub fn set_bounding_box(&mut self, bounding_box: IntRect) {
self.0.bounding_box = bounding_box.0
}
pub fn set_bounding_box_layer0(&mut self, bounding_box_layer0: IntRect) {
self.0.bounding_box_layer0 = bounding_box_layer0.0
}
pub fn set_dim_bounds(&mut self, dim_bounds: DimBounds) {
self.0.dim_bounds = dim_bounds.0
}
pub fn set_number_of_per_scenes_bounding_boxes(
&mut self,
number_of_per_scenes_bounding_boxes: i32,
) {
self.0.number_of_per_scenes_bounding_boxes = number_of_per_scenes_bounding_boxes;
}
// pub fn set_per_scenes_bounding_boxes(&mut self, per_scenes_bounding_boxes: Vec<BoundingBoxes>) {
// self.0.number_of_per_scenes_bounding_boxes = per_scenes_bounding_boxes.len() as i32;
// self.0.per_scenes_bounding_boxes = unsafe { transmute(per_scenes_bounding_boxes) };
// }
}
impl MetadataAsXml {
fn get_data(&self) -> Result<String> {
pub fn get_data(&self) -> Result<String> {
let xml_data = unsafe {
Vec::from_raw_parts(
self.0.data as *mut u8,
@@ -697,12 +772,8 @@ impl AddSubBlockInfo {
physical_height: i32,
pixel_type: PixelType,
compression_mode_raw: i32,
size_data: u32,
data: &[u8],
stride: u32,
size_metadata: u32,
metadata: &[u8],
size_attachment: u32,
attachment: &[u8],
) -> Self {
let data = ManuallyDrop::new(data.to_vec());
@@ -721,12 +792,12 @@ impl AddSubBlockInfo {
physical_height,
pixel_type: pixel_type.into(),
compression_mode_raw,
size_data,
size_data: data.len() as u32,
data: data.as_ptr() as *const c_void,
stride,
size_metadata,
stride: 1,
size_metadata: metadata.len() as u32,
metadata: metadata.as_ptr() as *const c_void,
size_attachment,
size_attachment: attachment.len() as u32,
attachment: attachment.as_ptr() as *const c_void,
})
}
@@ -832,25 +903,16 @@ impl AddSubBlockInfo {
pub fn set_compression_mode_raw(&mut self, compression_mode_raw: i32) {
self.0.compression_mode_raw = compression_mode_raw
}
pub fn set_size_data(&mut self, size_data: u32) {
self.0.size_data = size_data
}
pub fn set_data(&mut self, data: &[u8]) {
let data = ManuallyDrop::new(data.to_vec());
self.0.data = data.as_ptr() as *const c_void;
self.0.size_data = data.len() as u32;
}
pub fn set_size_metadata(&mut self, size_metadata: u32) {
self.0.size_metadata = size_metadata
}
pub fn set_metadata(&mut self, metadata: &[u8]) {
let metadata = ManuallyDrop::new(metadata.to_vec());
self.0.metadata = metadata.as_ptr() as *const c_void;
self.0.size_metadata = metadata.len() as u32;
}
pub fn set_size_attachment(&mut self, size_attachment: u32) {
self.0.size_attachment = size_attachment
}
pub fn set_attachment(&mut self, attachment: &[u8]) {
let attachment = ManuallyDrop::new(attachment.to_vec());
self.0.attachment = attachment.as_ptr() as *const c_void;
@@ -863,7 +925,6 @@ impl AddAttachmentInfo {
guid: [u8; 16],
content_file_type: [u8; 8],
name: [u8; 80],
size_attachment_data: u32,
attachment_data: &[u8],
) -> Self {
let attachment_data = ManuallyDrop::new(attachment_data.to_vec());
@@ -871,7 +932,7 @@ impl AddAttachmentInfo {
guid,
contentFileType: content_file_type,
name,
size_attachment_data,
size_attachment_data: attachment_data.len() as u32,
attachment_data: attachment_data.as_ptr() as *const c_void,
})
}
@@ -905,9 +966,6 @@ impl AddAttachmentInfo {
pub fn set_name(&mut self, name: [u8; 80]) {
self.0.name = name
}
pub fn set_size_attachment_data(&mut self, size_attachment_data: u32) {
self.0.size_attachment_data = size_attachment_data
}
pub fn set_attachment_data(&mut self, attachment_data: &[u8]) {
let attachment_data = ManuallyDrop::new(attachment_data.to_vec());
self.0.attachment_data = attachment_data.as_ptr() as *const c_void;
@@ -916,10 +974,10 @@ impl AddAttachmentInfo {
}
impl WriteMetadataInfo {
pub fn new(size_metadata: u32, metadata: &[u8]) -> Self {
pub fn new(metadata: &[u8]) -> Self {
let metadata = ManuallyDrop::new(metadata.to_vec());
Self(WriteMetadataInfoInterop {
size_metadata,
size_metadata: metadata.len() as u32,
metadata: metadata.as_ptr() as *const c_void,
})
}
@@ -935,9 +993,6 @@ impl WriteMetadataInfo {
)
}
}
pub fn set_size_metadata(&mut self, size_metadata: u32) {
self.0.size_metadata = size_metadata
}
pub fn set_metadata(&mut self, metadata: &[u8]) {
let metadata = ManuallyDrop::new(metadata.to_vec());
self.0.metadata = metadata.as_ptr() as *const c_void;

28
src/lib.rs
View File

@@ -1,3 +1,5 @@
extern crate link_cplusplus;
mod functions;
mod handle;
mod interop;
@@ -7,7 +9,7 @@ pub mod sys;
pub use functions::*;
pub use handle::*;
pub use interop::*;
pub use misc::{LibCZIApiError, RawDataType, PixelType};
pub use misc::{LibCZIApiError, PixelType, RawDataType};
#[cfg(test)]
mod tests {
@@ -15,6 +17,7 @@ mod tests {
use crate::interop::{LibCZIBuildInformation, ReaderOpenInfo};
use anyhow::{Error, Result};
use std::env;
use std::path::PathBuf;
#[test]
fn test_libczi_xml() -> Result<()> {
@@ -37,9 +40,7 @@ mod tests {
#[test]
fn test_libczi_pyramid_statistics() -> Result<()> {
let path = env::home_dir()
.unwrap()
.join("code/rust/ndbioimage/tests/files/Experiment-2029.czi");
let path = PathBuf::from("test-files/Experiment-2029.czi");
assert!(path.exists());
let czi = CziReader::create()?;
let stream = InputStream::create_from_file_utf8(
@@ -54,9 +55,7 @@ mod tests {
#[test]
fn test_libczi_document_info() -> Result<()> {
let path = env::home_dir()
.unwrap()
.join("code/rust/ndbioimage/tests/files/Experiment-2029.czi");
let path = PathBuf::from("test-files/Experiment-2029.czi");
assert!(path.exists());
let czi = CziReader::create()?;
let stream = InputStream::create_from_file_utf8(
@@ -67,16 +66,25 @@ mod tests {
let metadata_segment = czi.get_metadata_segment()?;
let document_info = metadata_segment.get_czi_document_info()?;
let general_document_info = document_info.get_general_document_info()?;
println!("xml: {}", &general_document_info[..general_document_info.len().min(100)]);
println!(
"xml: {}",
&general_document_info[..general_document_info.len().min(100)]
);
Ok(())
}
#[test]
fn test_lib_czi_build_information() -> Result<()> {
let build_info = LibCZIBuildInformation::get()?;
println!("compiler information: {:?}", build_info.get_compiler_information());
println!(
"compiler information: {:?}",
build_info.get_compiler_information()
);
println!("repository url: {:?}", build_info.get_repository_url());
println!("repository branch: {:?}", build_info.get_repository_branch());
println!(
"repository branch: {:?}",
build_info.get_repository_branch()
);
println!("repository tag: {:?}", build_info.get_repository_tag());
Ok(())
}

2
src/misc.rs
View File

@@ -1,4 +1,4 @@
use anyhow::{anyhow, Error, Result};
use anyhow::{Error, Result, anyhow};
use std::fmt;
use std::mem::MaybeUninit;
use std::os::raw::c_int;

4
src/sys.rs
View File

@@ -7,4 +7,8 @@
#![allow(rustdoc::invalid_html_tags)]
#![allow(clippy::missing_safety_doc)]
#[cfg(docsrs)]
include!("lib_czi_api.rs");
#[cfg(not(docsrs))]
include!(concat!(env!("OUT_DIR"), "/lib_czi_api.rs"));