Struct MCD

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

Represents a imaging mass cytometry (*.mcd) file.

Implementations

impl MCD<File>

pub fn from_path<P: AsRef<Path>>(path: P) -> Result<MCD<File>>

Open an .mcd file from the specified path.

pub fn location(&self) -> Option<&Path>

Returns the location (path) of the .mcd file

pub fn set_location<P: AsRef<Path>>(&mut self, location: P)

Returns the location (path) of the .mcd file

pub fn with_dcm(self) -> Result<Self>

Use a temporary file for faster access to channel images.

If this file does not already exist, then it is created.

Data is stored in the .mcd file spectrum-wise which means to load a single image, the entire acquired acquisition must be loaded first. This method creates a temporary file (.dcm) in the same location as the *.mcd file (if it doesn’t already exist) which has the channel data stored image-wise. If this file is present and loaded, then Mcd will choose the fastest method to use to return the requested data.

Errors

If the location is not set either automatically via MCD::from_path or manually via MCD::set_location then a MCDError::LocationNotSpecified will occur.

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

pub fn parse(reader: R) -> Result<Self>

Parse *.mcd format

pub fn xml(&self) -> Result<String>

Returns the raw XML metadata stored in the .mcd file

impl<R> MCD<R>

pub fn slide_ids(&self) -> Vec<u16>

Returns a copy of the slide IDs, sorted by ID number

pub fn slide(&self, id: u16) -> Option<&Slide<R>>

Returns slide with a given ID number, or None if no such slide exists

pub fn slides(&self) -> Vec<&Slide<R>>

Returns a vector of references to slides sorted by ID number. This allocates a new vector on each call.

pub fn acquisitions(&self) -> Vec<&Acquisition<R>>

Return a vector of references to all acquisitions in the .mcd file (iterates over all slides and all panoramas).

pub fn acquisition<A: Into<AcquisitionIdentifier>>( &self, identifier: A, ) -> Option<&Acquisition<R>>

Return an acquisition which matches the supplied AcquisitionIdentifier or None if no match found

pub fn acquisitions_in(&self, region: &BoundingBox<f64>) -> Vec<&Acquisition<R>>

Returns a list of acquisitions which are at least partially contained within the specified bounding box.

pub fn channels(&self) -> Vec<&AcquisitionChannel>

Returns a vector of all channels present within any acquisition performed on the slide, sorted by channel order number.

pub fn channels_excluding( &self, exclusion_list: Vec<&str>, ) -> Vec<&AcquisitionChannel>

Returns a vector of all channels, excluding those from the acquisitions with names matching those specified

pub fn calibration_final(&self, id: u16) -> Option<&CalibrationFinal>

Returns an instance of CalibrationFinal with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

pub fn calibration_params(&self, id: u16) -> Option<&CalibrationParams>

Returns an instance of CalibrationParams with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

pub fn calibration_channels(&self, id: u16) -> Option<&CalibrationChannel>

Returns an instance of CalibrationChannel with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

pub fn calibration(&self, id: u16) -> Option<&Calibration>

Returns an instance of Calibration with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

pub fn slide_fiducal_marks(&self, id: u16) -> Option<&SlideFiducialMarks>

Returns an instance of SlideFiducialMarks with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

pub fn slide_profile(&self, id: u16) -> Option<&SlideProfile>

Returns an instance of SlideProfile with the specified ID, or None if none exists (this is always the case in version 1 of the Schema)

Trait Implementations

impl<R: Debug> Debug for MCD<R>

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

Formats the value using the given formatter.

impl<R> Display for MCD<R>

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

Formats the value using the given formatter.

impl<R> Print for MCD<R>

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

Formats and prints to writer