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Update to latest version of imc
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@AlanRace
AlanRace committed Nov 15, 2022
1 parent 433c1cf commit b993972
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Showing 3 changed files with 83 additions and 83 deletions.
17 changes: 9 additions & 8 deletions Cargo.lock
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145 changes: 73 additions & 72 deletions src/imc.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -103,11 +103,7 @@ fn handle_imc_event(
IMCEvent::Load(location) => {
let path = location.clone();

let load_task = thread_pool.spawn(async move {
let file = BufReader::new(File::open(&path)?);

MCD::parse_with_dcm(file, path.to_str().unwrap())
});
let load_task = thread_pool.spawn(async move { MCD::from_path(path)?.with_dcm() });

commands.spawn(LoadIMC(load_task));

Expand Down Expand Up @@ -416,7 +412,7 @@ fn apply_classifier(
for (entity, imc) in q_imc.iter() {
for acquisition in imc.acquisitions_in(region) {
let acq_entity = imc
.acquisition_entity(&AcquisitionIdentifier::Id(acquisition.id()))
.acquisition_entity(AcquisitionIdentifier::Id(acquisition.id()))
.unwrap();

let region = acquisition.pixels_in(region).unwrap();
Expand Down Expand Up @@ -710,65 +706,67 @@ fn process_classifier_results(
.add_child(pixel_annotation);
}
ClassifierOutput::File { location } => {
let mut mcd_location = PathBuf::from(acquisition.mcd().location());
mcd_location.set_extension("");
println!("Filename: {:?}", mcd_location.file_name());

let mut filename: String = mcd_location
.file_name()
.and_then(|s| s.to_str())
.map(|s| s.to_string())
.unwrap();

write!(filename, "_{}", mcd_acquisition.description()).unwrap();
//let output = location.join("path")

if region.x != 0
|| region.y != 0
|| region.width != acquisition.width() as u32
|| region.height != acquisition.height() as u32
{
// A sub region of the acquitision was classified, so include this in the name
write!(
filename,
"_Region_x_{}_{}_y_{}_{}",
region.x,
region.x + region.width,
region.y,
region.y + region.height
)
.unwrap();
}
if let Some(location) = acquisition.mcd().location() {
let mut mcd_location = PathBuf::from(location);
mcd_location.set_extension("");
println!("Filename: {:?}", mcd_location.file_name());

let mut filename: String = mcd_location
.file_name()
.and_then(|s| s.to_str())
.map(|s| s.to_string())
.unwrap();

let mut data = vec![
vec![0_u8; (region.width * region.height) as usize];
result.labels.len()
];
write!(filename, "_{}", mcd_acquisition.description()).unwrap();
//let output = location.join("path")

if region.x != 0
|| region.y != 0
|| region.width != acquisition.width() as u32
|| region.height != acquisition.height() as u32
{
// A sub region of the acquitision was classified, so include this in the name
write!(
filename,
"_Region_x_{}_{}_y_{}_{}",
region.x,
region.x + region.width,
region.y,
region.y + region.height
)
.unwrap();
}

for (index, label) in result.predicted_labels.iter().enumerate() {
let label = *label as usize;
let mut data = vec![
vec![0_u8; (region.width * region.height) as usize];
result.labels.len()
];

data[label][index] = 255;
}
for (index, label) in result.predicted_labels.iter().enumerate() {
let label = *label as usize;

data[label][index] = 255;
}

for (index, label) in result.labels.iter().enumerate() {
let mut filename = filename.clone();
write!(filename, "_{}", label.description).unwrap();
for (index, label) in result.labels.iter().enumerate() {
let mut filename = filename.clone();
write!(filename, "_{}", label.description).unwrap();

let mut location = location.join(filename);
location.set_extension("tiff");
let mut location = location.join(filename);
location.set_extension("tiff");

let img_file = File::create(location).expect("Cannot find test image!");
let mut writer = BufWriter::new(img_file);
let img_file = File::create(location).expect("Cannot find test image!");
let mut writer = BufWriter::new(img_file);

let mut tiff = TiffEncoder::new(&mut writer).unwrap();
let mut tiff = TiffEncoder::new(&mut writer).unwrap();

tiff.write_image::<colortype::Gray8>(
region.width,
region.height,
&data[index],
)
.unwrap();
tiff.write_image::<colortype::Gray8>(
region.width,
region.height,
&data[index],
)
.unwrap();
}
}
}
}
Expand All @@ -777,7 +775,7 @@ fn process_classifier_results(
}

#[derive(Component)]
pub(crate) struct LoadIMC(pub Task<Result<MCD<BufReader<File>>, MCDError>>);
pub(crate) struct LoadIMC(pub Task<Result<MCD<File>, MCDError>>);

#[derive(Component)]
pub struct Slide {
Expand All @@ -789,20 +787,20 @@ pub struct Panorama {}

#[derive(Component, Clone)]
pub struct Acquisition {
mcd: Arc<MCD<BufReader<File>>>,
mcd: Arc<MCD<File>>,
imc_dataset: Entity,

id: u16,
}

impl Acquisition {
fn mcd(&self) -> &MCD<BufReader<File>> {
fn mcd(&self) -> &MCD<File> {
&self.mcd
}

fn mcd_acquisition(&self) -> &imc_rs::Acquisition<BufReader<File>> {
fn mcd_acquisition(&self) -> &imc_rs::Acquisition<File> {
self.mcd
.acquisition(&AcquisitionIdentifier::Id(self.id))
.acquisition(AcquisitionIdentifier::Id(self.id))
.unwrap()
}

Expand Down Expand Up @@ -1121,14 +1119,14 @@ fn load_imc(
});
})
.insert(PrimaryUiEntry {
description: format!("IMC: {}", mcd.location()),
description: format!("IMC: {:?}", mcd.location()),
})
.insert(IMCDataset {
mcd,
panoramas,
acquisitions: acquisition_entities.into_iter().collect(),
})
.insert_bundle(SpatialBundle::default());
.insert(SpatialBundle::default());
}
}
}
Expand Down Expand Up @@ -1159,31 +1157,34 @@ impl ChannelImage {

#[derive(Component, Clone)]
pub struct IMCDataset {
mcd: Arc<MCD<BufReader<File>>>,
mcd: Arc<MCD<File>>,

pub panoramas: Vec<Entity>,
pub acquisitions: HashMap<u16, Entity>,
}

impl IMCDataset {
pub fn name(&self) -> &str {
self.mcd.location()
self.mcd
.location()
.map(|path| path.to_str().unwrap_or("Unknown name"))
.unwrap_or("Unknown name")
}

pub fn acquisition(
&self,
identifier: &AcquisitionIdentifier,
) -> Option<&imc_rs::Acquisition<BufReader<File>>> {
identifier: AcquisitionIdentifier,
) -> Option<&imc_rs::Acquisition<File>> {
self.mcd.acquisition(identifier)
}

pub fn acquisition_entity(&self, identifier: &AcquisitionIdentifier) -> Option<Entity> {
pub fn acquisition_entity(&self, identifier: AcquisitionIdentifier) -> Option<Entity> {
let acquisition = self.mcd.acquisition(identifier)?;

self.acquisitions.get(&acquisition.id()).copied()
}

pub fn acquisitions(&self) -> Vec<&imc_rs::Acquisition<BufReader<File>>> {
pub fn acquisitions(&self) -> Vec<&imc_rs::Acquisition<File>> {
self.mcd.acquisitions()
}

Expand All @@ -1199,7 +1200,7 @@ impl IMCDataset {
Ok(data) => {
image_map.insert(acquisition.id(), ChannelImage(data));
}
Err(MCDError::NoSuchChannel { acquisition: _ }) => {
Err(MCDError::InvalidChannel { channel }) => {
// No such channel, so we don't add data
}
_ => todo!(),
Expand All @@ -1212,7 +1213,7 @@ impl IMCDataset {
pub fn acquisitions_in(
&self,
region: &imc_rs::BoundingBox<f64>,
) -> Vec<&imc_rs::Acquisition<BufReader<File>>> {
) -> Vec<&imc_rs::Acquisition<File>> {
self.mcd.acquisitions_in(region)
}
}
Expand Down
4 changes: 1 addition & 3 deletions src/main.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -164,9 +164,7 @@ fn load_test_data(mut commands: Commands) {
};

let load_task = thread_pool.spawn(async move {
let reader = BufReader::new(file);

let mcd = MCD::parse_with_dcm(reader, path.to_str().unwrap())?;
let mcd = MCD::from_path(path)?.with_dcm()?;

// let xml = mcd.xml()?;
// std::fs::write("mcd.xml", xml);
Expand Down

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