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BioGTK
6.0.0
A .NET library & program for annotating, editing various microscopy imaging formats using Bioformats supported images. Including whole slide, pyramidal, and series.
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Public Types | |
enum | ViewMode { Raw , Filtered , RGBImage , Emission } |
Public Member Functions | |
void | SetCoordinate (int z, int c, int t) |
ZCT | GetCoordinate () |
void | AddImage (BioImage im) |
void | SetTitle (string s) |
void | UpdateImages (bool updatePyramidal=false) |
It updates the images. | |
void | UpdateImage (bool updatePyramidal=false) |
It updates the image. | |
void | UpdateGUI () |
It updates the GUI to reflect the current state of the image. | |
void | CopySelection () |
It takes the selected ROIs and copies them to the clipboard. | |
void | PasteSelection () |
void | UpdateStatus () |
It updates the status of the user. | |
void | UpdateView (bool update=false, bool updateImages=false) |
It updates the view. | |
double | GetScale () |
List< ROI > | GetSelectedROIs () |
PointD | ImageToViewSpace (double x, double y) |
PointF | ToViewSpace (PointF p) |
PointD | ToViewSpace (PointD p) |
PointD | ToViewSpace (double x, double y) |
double | ToViewSizeH (double d) |
double | ToViewW (double d) |
double | ToViewH (double d) |
PointD | ToScreenSpace (double x, double y) |
PointD | ToScreenSpace (PointD p) |
PointF | ToScreenSpace (PointF p) |
PointF[] | ToScreenSpace (PointF[] p) |
PointF | ToScreenSpace (Point3D p) |
float | ToScreenScaleW (double x) |
float | ToScreenScaleH (double y) |
PointF | ToScreenScale (PointD p) |
RectangleD | ToScreenRect (double x, double y, double w, double h) |
RectangleD | ToScreenSpace (RectangleD p) |
RectangleD | ToScreenSpace (RectangleF p) |
RectangleD[] | ToScreenSpace (RectangleD[] p) |
PointD[] | ToScreenSpace (PointD[] p) |
double | ToScreenW (double x) |
float | ToScreenH (double y) |
void | GoToImage () |
This function is used to go to the image at the specified index. | |
void | GoToImage (int i) |
Static Public Member Functions | |
static ImageView | Create (BioImage bm) |
static SKImage | Convert16bppBitmapToSKImage (Bitmap sourceBitmap) |
static SKImage | BitmapToSKImage (AForge.Bitmap bitm) |
static Cairo.Color | FromColor (Color color) |
Public Attributes | |
List< BioImage > | Images = new List<BioImage>() |
List< SKImage > | SKImages = new List<SKImage>() |
List< Bitmap > | Bitmaps = new List<Bitmap>() |
Gtk.Box | mainBox |
Menu | contextMenu |
bool | showRROIs = true |
bool | showGROIs = true |
bool | showBROIs = true |
Static Public Attributes | |
static List< ROI > | selectedAnnotations = new List<ROI>() |
static int | waitz = 1000 |
static int | waitc = 1000 |
static int | waitt = 1000 |
static int | startz = 0 |
static int | startc = 0 |
static int | startt = 0 |
static int | endz = 0 |
static int | endc = 0 |
static int | endt = 0 |
static Gdk.Key | keyDown = Gdk.Key.Key_3270_Test |
static bool | x1State |
static bool | x2State |
static bool | mouseLeftState |
static ModifierType | Modifiers |
Protected Member Functions | |
ImageView (Builder builder, IntPtr handle, BioImage im) | |
void | SetupHandlers () |
Sets up the handlers. | |
Properties | |
double | PxWmicron [get, set] |
double | PxHmicron [get, set] |
bool | AllowNavigation [get, set] |
bool | ShowMasks [get, set] |
static AForge.Bitmap | SelectedBuffer [get] |
int | SelectedIndex [get, set] |
bool | ShowOverview [get, set] |
int? | MacroResolution [get] |
int? | LabelResolution [get] |
bool | OpenSlide [get, set] |
static BioImage | SelectedImage [get, set] |
ViewMode | Mode [get, set] |
Channel | RChannel [get] |
Channel | GChannel [get] |
Channel | BChannel [get] |
PointD | Origin [get, set] |
PointD | TopRightOrigin [get] |
PointD | PyramidalOriginTransformed [get, set] |
PointD | PyramidalOrigin [get, set] |
double | Resolution [get, set] |
int | Level [get, set] |
SizeF | Scale [get, set] |
PointD | MouseDownInt [get, set] |
PointD | MouseMoveInt [get, set] |
PointD | MouseUpInt [get, set] |
PointD | MouseDown [get, set] |
PointD | MouseUp [get, set] |
PointD | MouseMove [get, set] |
Definition at line 24 of file ImageView.cs.
enum BioGTK.ImageView.ViewMode |
Definition at line 1803 of file ImageView.cs.
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Definition at line 247 of file ImageView.cs.
void BioGTK.ImageView.AddImage | ( | BioImage | im | ) |
It adds an image to the list of images, and then updates the GUI and the images
BioImage | a class that contains the image data and metadata |
Definition at line 65 of file ImageView.cs.
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Definition at line 713 of file ImageView.cs.
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Definition at line 679 of file ImageView.cs.
void BioGTK.ImageView.CopySelection | ( | ) |
It takes the selected ROIs and copies them to the clipboard.
Definition at line 1763 of file ImageView.cs.
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The function creates an ImageView object using a BioImage object and returns it.
BioImage | The BioImage parameter is an object that represents an image in a biological context. It likely contains information about the image file, such as the filename, and possibly additional metadata related to the image. |
Definition at line 236 of file ImageView.cs.
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It takes a System.Drawing.Color and returns a Cairo.Color
Color | The color to convert |
Definition at line 1450 of file ImageView.cs.
ZCT BioGTK.ImageView.GetCoordinate | ( | ) |
It returns the coordinate of the selected image
Definition at line 58 of file ImageView.cs.
double BioGTK.ImageView.GetScale | ( | ) |
Definition at line 2054 of file ImageView.cs.
List< ROI > BioGTK.ImageView.GetSelectedROIs | ( | ) |
Definition at line 2064 of file ImageView.cs.
void BioGTK.ImageView.GoToImage | ( | ) |
This function is used to go to the image at the specified index.
Definition at line 2827 of file ImageView.cs.
void BioGTK.ImageView.GoToImage | ( | int | i | ) |
It takes an image index and centers the image in the viewport
i | the index of the image to go to |
Definition at line 2836 of file ImageView.cs.
PointD BioGTK.ImageView.ImageToViewSpace | ( | double | x, |
double | y ) |
It takes a point in the image space and returns the point in the view space
x | the x coordinate of the point in the image |
y | the y coordinate of the point in the image |
Definition at line 2525 of file ImageView.cs.
void BioGTK.ImageView.PasteSelection | ( | ) |
The function takes the text from the clipboard and splits it into lines. Each line is then converted into an ROI object and added to the list of annotations
Definition at line 1784 of file ImageView.cs.
void BioGTK.ImageView.SetCoordinate | ( | int | z, |
int | c, | ||
int | t ) |
Definition at line 33 of file ImageView.cs.
void BioGTK.ImageView.SetTitle | ( | string | s | ) |
Definition at line 731 of file ImageView.cs.
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Sets up the handlers.
Definition at line 863 of file ImageView.cs.
float BioGTK.ImageView.ToScreenH | ( | double | y | ) |
Convert a value in microns to a value in pixels
y | the y coordinate of the point to be converted |
Definition at line 2822 of file ImageView.cs.
RectangleD BioGTK.ImageView.ToScreenRect | ( | double | x, |
double | y, | ||
double | w, | ||
double | h ) |
It converts a rectangle in microns to a rectangle in pixels
x | The x coordinate of the rectangle |
y | -0.0015 |
w | width of the image in microns |
h | height of the rectangle |
Definition at line 2735 of file ImageView.cs.
PointF BioGTK.ImageView.ToScreenScale | ( | PointD | p | ) |
Convert a point in the world coordinate system to a point in the screen coordinate system
PointD |
Definition at line 2721 of file ImageView.cs.
float BioGTK.ImageView.ToScreenScaleH | ( | double | y | ) |
Convert a value in microns to a value in pixels
y | the y coordinate of the point to be converted |
Definition at line 2712 of file ImageView.cs.
float BioGTK.ImageView.ToScreenScaleW | ( | double | x | ) |
ToScreenScaleW() returns the number of pixels that correspond to the given number of microns
x | the x coordinate of the point to be converted |
Definition at line 2703 of file ImageView.cs.
PointD BioGTK.ImageView.ToScreenSpace | ( | double | x, |
double | y ) |
It converts a point in world space to a point in screen space
x | The x coordinate of the point to convert. |
y | The y coordinate of the point to transform. |
Definition at line 2650 of file ImageView.cs.
PointF BioGTK.ImageView.ToScreenSpace | ( | Point3D | p | ) |
It converts a 3D point to a 2D point
Point3D |
Definition at line 2693 of file ImageView.cs.
PointD BioGTK.ImageView.ToScreenSpace | ( | PointD | p | ) |
Converts a point from world space to screen space
PointD | A class that contains an X and Y value. |
Definition at line 2660 of file ImageView.cs.
PointD[] BioGTK.ImageView.ToScreenSpace | ( | PointD[] | p | ) |
Convert a list of points from world space to screen space
p | The point to convert |
Definition at line 2798 of file ImageView.cs.
PointF BioGTK.ImageView.ToScreenSpace | ( | PointF | p | ) |
Convert a point in the world coordinate system to the screen coordinate system
PointF | The point you want to convert to screen space. |
Definition at line 2669 of file ImageView.cs.
PointF[] BioGTK.ImageView.ToScreenSpace | ( | PointF[] | p | ) |
It takes an array of points and returns an array of points
p | The point to convert |
Definition at line 2679 of file ImageView.cs.
RectangleD BioGTK.ImageView.ToScreenSpace | ( | RectangleD | p | ) |
It converts a rectangle from world space to screen space
RectangleD | The rectangle to convert. |
Definition at line 2765 of file ImageView.cs.
RectangleD[] BioGTK.ImageView.ToScreenSpace | ( | RectangleD[] | p | ) |
It takes an array of RectangleD objects and returns an array of RectangleF objects
p | The rectangle to convert |
Definition at line 2783 of file ImageView.cs.
RectangleD BioGTK.ImageView.ToScreenSpace | ( | RectangleF | p | ) |
It converts a rectangle from world space to screen space
RectangleF | The rectangle to convert. |
Definition at line 2774 of file ImageView.cs.
double BioGTK.ImageView.ToScreenW | ( | double | x | ) |
ToScreenW(x) = x * PxWmicron
x | the x coordinate of the point to be converted |
Definition at line 2813 of file ImageView.cs.
double BioGTK.ImageView.ToViewH | ( | double | d | ) |
Convert a distance in microns to a distance in pixels
d | the distance in microns |
Definition at line 2634 of file ImageView.cs.
double BioGTK.ImageView.ToViewSizeH | ( | double | d | ) |
Convert a value in microns to a value in pixels
d | the size in microns |
Definition at line 2604 of file ImageView.cs.
PointD BioGTK.ImageView.ToViewSpace | ( | double | x, |
double | y ) |
ToViewSpace(x, y) = (ToViewSizeW(x - (ViewWidth / 2)) / Scale.Width) - Origin.X;
x | The x coordinate of the point to convert |
y | The y coordinate of the point to convert. |
Definition at line 2561 of file ImageView.cs.
PointD BioGTK.ImageView.ToViewSpace | ( | PointD | p | ) |
Converts a point from world space to view space
PointD | A class that contains an X and Y value. |
Definition at line 2551 of file ImageView.cs.
PointF BioGTK.ImageView.ToViewSpace | ( | PointF | p | ) |
Convert a point from world space to view space
PointF | The point to convert |
Definition at line 2541 of file ImageView.cs.
double BioGTK.ImageView.ToViewW | ( | double | d | ) |
Convert a distance in microns to a distance in pixels on the screen
d | the distance in microns |
Definition at line 2619 of file ImageView.cs.
void BioGTK.ImageView.UpdateGUI | ( | ) |
It updates the GUI to reflect the current state of the image.
Definition at line 1693 of file ImageView.cs.
void BioGTK.ImageView.UpdateImage | ( | bool | updatePyramidal = false | ) |
void BioGTK.ImageView.UpdateImages | ( | bool | updatePyramidal = false | ) |
It updates the images.
Definition at line 737 of file ImageView.cs.
void BioGTK.ImageView.UpdateStatus | ( | ) |
It updates the status of the user.
Definition at line 2023 of file ImageView.cs.
void BioGTK.ImageView.UpdateView | ( | bool | update = false, |
bool | updateImages = false ) |
It updates the view.
Definition at line 2039 of file ImageView.cs.
List<Bitmap> BioGTK.ImageView.Bitmaps = new List<Bitmap>() |
Definition at line 32 of file ImageView.cs.
Menu BioGTK.ImageView.contextMenu |
Definition at line 190 of file ImageView.cs.
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List<BioImage> BioGTK.ImageView.Images = new List<BioImage>() |
Definition at line 30 of file ImageView.cs.
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Gtk.Box BioGTK.ImageView.mainBox |
Definition at line 180 of file ImageView.cs.
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bool BioGTK.ImageView.showBROIs = true |
Definition at line 2052 of file ImageView.cs.
bool BioGTK.ImageView.showGROIs = true |
Definition at line 2051 of file ImageView.cs.
bool BioGTK.ImageView.showRROIs = true |
Definition at line 2050 of file ImageView.cs.
List<SKImage> BioGTK.ImageView.SKImages = new List<SKImage>() |
Definition at line 31 of file ImageView.cs.
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