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Added ability to set background opacity for IMC data
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@AlanRace
AlanRace committed Nov 17, 2022
1 parent 0d01913 commit 40a7c71
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Showing 2 changed files with 114 additions and 84 deletions.
182 changes: 103 additions & 79 deletions src/imc.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ use bevy::{
sprite::Anchor,
tasks::{AsyncComputeTaskPool, Task},
};
use egui::Color32;
use futures_lite::future;

use nalgebra::Matrix4;
Expand Down Expand Up @@ -85,9 +86,9 @@ pub enum IMCEvent {
output: ClassifierOutput,
},

SetBackgroundColour {
SetBackgroundOpacity {
entity: Entity,
colour: Colour,
opacity: f32,
},

SetHistogramScale {
Expand Down Expand Up @@ -117,9 +118,9 @@ fn handle_imc_event(

//load_imc(mcd, &mut commands, &mut textures, &thread_pool);
}
IMCEvent::SetBackgroundColour { entity, colour } => {
IMCEvent::SetBackgroundOpacity { entity, opacity } => {
if let Ok(mut imc) = q_imc.get_mut(*entity) {
imc.background_colour = colour.clone();
imc.background_alpha = *opacity;
}
}
IMCEvent::SetHistogramScale { entity, scale } => {
Expand Down Expand Up @@ -1139,7 +1140,7 @@ fn load_imc(
.insert(IMCDataset {
mcd,
histogram_scale: HistogramScale::None,
background_colour: Colour::Bevy(Color::BLACK),
background_alpha: 1.0,
panoramas,
acquisitions: acquisition_entities.into_iter().collect(),
})
Expand Down Expand Up @@ -1185,7 +1186,7 @@ pub struct IMCDataset {

// Settings
histogram_scale: HistogramScale,
background_colour: Colour,
background_alpha: f32,

pub panoramas: Vec<Entity>,
pub acquisitions: HashMap<u16, Entity>,
Expand All @@ -1199,8 +1200,8 @@ impl IMCDataset {
.unwrap_or("Unknown name")
}

pub fn background_colour(&self) -> &Colour {
&self.background_colour
pub fn background_alpha(&self) -> f32 {
self.background_alpha
}
pub fn histogram_scale(&self) -> &HistogramScale {
&self.histogram_scale
Expand Down Expand Up @@ -1357,87 +1358,110 @@ fn generate_histogram(
}
}

// This needs rethinking. Ideally want to generate the mixture between the various
fn image_control_changed(
q_control: Query<(&ImageControl, &Children), Changed<ImageControl>>,
q_imc: Query<(&IMCDataset, &Children, ChangeTrackers<IMCDataset>)>,
q_control: Query<(&ImageControl, &Children, ChangeTrackers<ImageControl>)>,
q_acquisition: Query<&Handle<Image>, With<Acquisition>>,
q_acquisition_images: Query<&AcquisitionChannelImage>,
channel_data: Res<Assets<ChannelImage>>,
mut textures: ResMut<Assets<Image>>,
) {
for (control, children) in q_control.iter() {
// Check each AcquisitionChannelImage (child of ImageControl)
for child in children.iter() {
if let Ok(acq_channel_image) = q_acquisition_images.get(*child) {
if let Ok(image) = q_acquisition.get(acq_channel_image.acquisition_entity) {
if let Some(image) = textures.get_mut(image) {
match &acq_channel_image.data {
Some(data) => {
if let Some(channel_image) = channel_data.get(data) {
for (index, intensity) in
channel_image.intensities().iter().enumerate()
{
let intensity = ((intensity - control.colour_domain.0)
/ (control.colour_domain.1 - control.colour_domain.0)
* 255.0)
as u8;

match control.image_update_type {
ImageUpdateType::Red => {
image.data[index * 4] = intensity;
}
ImageUpdateType::Green => {
image.data[index * 4 + 1] = intensity;
}
ImageUpdateType::Blue => {
image.data[index * 4 + 2] = intensity;
}
ImageUpdateType::All => {
image.data[index * 4] = intensity;
image.data[index * 4 + 1] = intensity;
image.data[index * 4 + 2] = intensity;
}
}
for (imc, children, imc_tracker) in q_imc.iter() {
let requires_update = imc_tracker.is_changed();

// let intensity = image.data[index * 4 + 2]
// .max(image.data[index * 4 + 1])
// .max(image.data[index * 4]);
// let alpha = match intensity {
// 0..=25 => intensity * 10,
// _ => 255,
// };
for (control_index, (control, children, control_tracker)) in q_control.iter().enumerate() {
// Check each AcquisitionChannelImage (child of ImageControl)

// image.data[index * 4 + 3] = alpha;
image.data[index * 4 + 3] = 255;
}
}
}
None => {
// There is no data associated with this acquisition, so remove the previous data
for chunk in image.data.chunks_mut(4) {
match control.image_update_type {
ImageUpdateType::Red => {
chunk[0] = 0;
}
ImageUpdateType::Green => {
chunk[1] = 0;
}
ImageUpdateType::Blue => {
chunk[2] = 0;
}
ImageUpdateType::All => {
chunk[0] = 0;
chunk[1] = 0;
chunk[2] = 0;
}
}
if control_tracker.is_changed() || requires_update {
info!(
"Channel image updated => recalculating | {:?}",
imc.background_alpha()
);

let intensity = chunk[2].max(chunk[1].max(chunk[0]));
let alpha = match intensity {
0..=25 => intensity * 10,
_ => 255,
};
for child in children.iter() {
if let Ok(acq_channel_image) = q_acquisition_images.get(*child) {
if let Ok(image) = q_acquisition.get(acq_channel_image.acquisition_entity) {
if let Some(image) = textures.get_mut(image) {
match &acq_channel_image.data {
Some(data) => {
if let Some(channel_image) = channel_data.get(data) {
for (index, intensity) in
channel_image.intensities().iter().enumerate()
{
if control_index == 0 {
image.data[index * 4 + 3] =
(imc.background_alpha() * 255.0) as u8;
}

let intensity = ((intensity
- control.colour_domain.0)
/ (control.colour_domain.1
- control.colour_domain.0)
* 255.0)
as u8;

if intensity > 0 {
match control.image_update_type {
ImageUpdateType::Red => {
image.data[index * 4] = intensity;
}
ImageUpdateType::Green => {
image.data[index * 4 + 1] = intensity;
}
ImageUpdateType::Blue => {
image.data[index * 4 + 2] = intensity;
}
ImageUpdateType::All => {
image.data[index * 4] = intensity;
image.data[index * 4 + 1] = intensity;
image.data[index * 4 + 2] = intensity;
}
}

chunk[3] = alpha;
// let intensity = image.data[index * 4 + 2]
// .max(image.data[index * 4 + 1])
// .max(image.data[index * 4]);
// let alpha = match intensity {
// 0..=25 => intensity * 10,
// _ => 255,
// };

// image.data[index * 4 + 3] = alpha;
image.data[index * 4 + 3] = 255;
}
}
}
}
None => {
// // There is no data associated with this acquisition, so remove the previous data
// for chunk in image.data.chunks_mut(4) {
// match control.image_update_type {
// ImageUpdateType::Red => {
// chunk[0] = 0;
// }
// ImageUpdateType::Green => {
// chunk[1] = 0;
// }
// ImageUpdateType::Blue => {
// chunk[2] = 0;
// }
// ImageUpdateType::All => {
// chunk[0] = 0;
// chunk[1] = 0;
// chunk[2] = 0;
// }
// }

// let intensity = chunk[2].max(chunk[1].max(chunk[0]));
// let alpha = match intensity {
// 0..=25 => intensity * 10,
// _ => 255,
// };

// chunk[3] = alpha;
// }
}
}
}
}
Expand Down
16 changes: 11 additions & 5 deletions src/ui/mod.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -524,14 +524,20 @@ fn ui_imc_panel(world: &mut World, ui: &mut Ui) {
.num_columns(2)
.spacing([40.0, 4.0])
.show(ui, |ui| {
ui.label("Background colour");
let mut colour = imc.background_colour().egui();
ui.label("Background opacity");
let mut alpha = imc.background_alpha();

if ui.color_edit_button_srgba(&mut colour).changed() {
let opacity = ui.add(
Slider::new(&mut alpha, 0.0..=1.0)
.step_by(0.01)
.clamp_to_range(true)
.orientation(egui::SliderOrientation::Horizontal),
);
if opacity.changed() {
ui_events.push(UiEvent::Data(DataEvent::IMCEvent(
IMCEvent::SetBackgroundColour {
IMCEvent::SetBackgroundOpacity {
entity,
colour: colour.into(),
opacity: alpha,
},
)));
}
Expand Down

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