Struct Acquisition 

pub struct Acquisition<R> { /* private fields */ }

Acquisition represents a single region analysed by IMC.

Implementations

impl<R> Acquisition<R>

pub fn id(&self) -> u16

Returns the ID associated with the acquisition

pub fn description(&self) -> &str

Returns a description of the acquisition

pub fn order_number(&self) -> i16

Returns a number representing the order in which the acquisition was acquired (0 being first).

pub fn width(&self) -> i32

Returns the width of the acquired region (in pixels)

pub fn height(&self) -> i32

Returns the height of the acquired region (in pixels)

pub fn ablation_frequency(&self) -> f64

Returns the ablation frequency

pub fn acquisition_roi_id(&self) -> i16

Returns the region ID for the acquisition

pub fn profiling_type(&self) -> Option<&ProfilingType>

Returns the profiling type for the acquisition, if one is present. This is not present in version 1 of the schema

pub fn before_ablation_image(&self) -> OpticalImage<R>

Returns the optical image of the acquisition region prior to ablation

pub fn after_ablation_image(&self) -> OpticalImage<R>

Returns the optical image of the acquisition region after ablation

pub fn channels(&self) -> &[AcquisitionChannel]

Returns a list of all channels acquired within this acquisition

pub fn is_complete(&self) -> bool

Returns whether the acquisition has run to completion (checks the size of the recorded data compared to the expected data size)

pub fn pixels_in(&self, region: &BoundingBox<f64>) -> Option<Region>

Returns a Region describing the pixel region contained within the specified bounding box

pub fn in_region(&self, region: &BoundingBox<f64>) -> bool

Tests whether the acquisition is (at least partially) contained within the specified bounding box (slide coordinates).

pub fn spectrum_size(&self) -> usize

Returns the size of a single spectrum in bytes

pub fn num_spectra(&self) -> usize

Returns the number of spectra acquired as part of the acquisition

impl<R: Read + Seek> Acquisition<R>

pub fn channel_image<C: Into<ChannelIdentifier>>( &self, identifier: C, region: Option<Region>, ) -> Result<ChannelImage>

Returns the ChannelImage for the channel matching the ChannelIdentifier. This contains the intensities of the channel for each detected pixel, the number of valid pixels and the width and height of the image.

pub fn channel_images<C: AsRef<ChannelIdentifier>>( &self, identifiers: &[C], region: Option<Region>, ) -> Result<Vec<ChannelImage>>

Returns array of ChannelImages for the channels matching the ChannelIdentifiers. This contains the intensities of the channel for each detected pixel, the number of valid pixels and the width and height of the image.

pub fn channel<C: AsRef<ChannelIdentifier>>( &self, identifier: C, ) -> Option<&AcquisitionChannel>

Returns the channel which matches the given identifier, or None if no match found

impl<R: Read + Seek> Acquisition<R>

pub fn spectra(&self) -> SpectrumIterator<'_, R>

Provides an iterator over all spectra (each pixel) within the acquisition

pub fn spectrum(&self, x: u32, y: u32) -> Result<Vec<f32>>

Returns a spectrum at the specified (x, y) coordinate

Trait Implementations

impl<R> Clone for Acquisition<R>

fn clone(&self) -> Self

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<R: Debug> Debug for Acquisition<R>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<R> Display for Acquisition<R>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<R> OnSlide for Acquisition<R>

fn to_slide_transform(&self) -> AffineTransform<f64>

Returns the affine transformation from pixel coordinates within the acquisition to to the slide coordinates (μm)

fn slide_bounding_box(&self) -> BoundingBox<f64>

Returns the bounding box encompasing the acquisition area on the slide (in μm)

impl<R> Print for Acquisition<R>

fn print<W: Write + ?Sized>(&self, writer: &mut W, indent: usize) -> Result

Formats and prints to writer