BioGTK.SAMTool Class Reference

Inheritance diagram for BioGTK.SAMTool:

Public Member Functions
void	Init (bool wait=false)

Static Public Member Functions
static SAMTool	Create (bool micro_SAM)

Public Attributes
List< Promotion >	Promotions = new List<Promotion>()
bool	init = false
MenuBar	MainMenu

Static Public Attributes
static SAM	sam
static MicroSAM	microsam

Protected Member Functions
	SAMTool (Builder builder, IntPtr handle)
void	SetupHandlers ()
	This function sets up the event handlers for the menu items.
void	saveSelectedTiffClick (object sender, EventArgs a)

Properties
static bool	microSAM [get]

Detailed Description

Definition at line 16 of file SAMTool.cs.

Constructor & Destructor Documentation

SAMTool()

BioGTK.SAMTool.SAMTool ( Builder builder, IntPtr handle )

protected

Definition at line 123 of file SAMTool.cs.

                                                          : base(handle)
        {
            //First lets make sure the model files are installed.
            string app = System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().Location);
            if (microSAM)
            {
                if (!File.Exists(app + "/micro-sam-decoder.onnx") || !File.Exists(app + "/micro-sam-encoder.onnx"))
                {
                    MessageDialog dialog = new MessageDialog(
                 this,
                 DialogFlags.Modal,
                 MessageType.Info,
                 ButtonsType.Ok,
                 "Place Model files \"micro-sam-decoder.onnx\" and \"micro-sam-encoder.onnx\" in the application folder to use SAM Tool.");
                    dialog.Run();
                    return;
                }
            }
            else
            {
                if (!File.Exists(app + "/decoder-quant.onnx") || !File.Exists(app + "/encoder-quant.onnx"))
                {
                    MessageDialog dialog = new MessageDialog(
                 this,
                 DialogFlags.Modal,
                 MessageType.Info,
                 ButtonsType.Ok,
                 "Place Model files \"decoder-quant.onnx\" and \"encoder-quant.onnx\" in the application folder to use SAM Tool.");
                    dialog.Run();
                    return;
                }
            }
            view = App.viewer;
            _builder = builder;
            builder.Autoconnect(this);
            thresholdBar.Adjustment.Lower = 0;
            if (ImageView.SelectedImage.SelectedBuffer.BitsPerPixel > 8)
                thresholdBar.Adjustment.Upper = ushort.MaxValue;
            else
                thresholdBar.Adjustment.Upper = 255;
            stabilityBar.Adjustment.Lower = 0;
            stabilityBar.Adjustment.Upper = 1;
            stabilityBar.Adjustment.StepIncrement = 0.05;
            stabilityBar.Value = 0.5;
            predictionBar.Adjustment.Lower = 0;
            predictionBar.Adjustment.Upper = 1;
            predictionBar.Adjustment.StepIncrement = 0.05;
            predictionBar.Value = 0.5;
            pointsBar.Adjustment.Lower = 0;
            pointsBar.Adjustment.Upper = 100;
            pointsBar.Adjustment.StepIncrement = 1;
            pointsBar.Value = 4;
            layersBar.Adjustment.Lower = 0;
            layersBar.Adjustment.Upper = 4;
            layersBar.Value = 0;
            minAreaBar.Value = 0;
            minAreaBar.Adjustment.Upper = ImageView.SelectedImage.Volume.Width * ImageView.SelectedImage.Volume.Height;
            minAreaBar.Adjustment.Lower = 0;
            
            maxAreaBar.Adjustment.Upper = ImageView.SelectedImage.Volume.Width * ImageView.SelectedImage.Volume.Height;
            maxAreaBar.Adjustment.Lower = 0;
            maxAreaBar.Value = ImageView.SelectedImage.Volume.Width * ImageView.SelectedImage.Volume.Height;
            foregroundBut.Active = true;
            Directory.CreateDirectory("Masks");
            filechooser =
            new Gtk.FileChooserDialog("Choose file to open",
            this,
            FileChooserAction.Open,
            "Cancel", ResponseType.Cancel,
            "OK", ResponseType.Accept);
            SetupHandlers();
            Init();
            App.ApplyStyles(this);
            init = true;
        }

Member Function Documentation

Create()

static SAMTool BioGTK.SAMTool.Create ( bool micro_SAM )

static

It creates a new instance of the SAMTool class, which is a class that inherits from Gtk.Window

Returns

A new instance of the SAMTool class.

Definition at line 109 of file SAMTool.cs.

        {
            Builder builder = new Builder(new FileStream(System.IO.Path.GetDirectoryName(Environment.ProcessPath) + "/" + "Glade/SAM.glade", FileMode.Open));
            if (micro_SAM)
            {
                sam = MicroSAM.Instance();
                microsam = MicroSAM.Instance();
            }
            else
                sam = SAM.Instance();
            return new SAMTool(builder, builder.GetObject("SAMTool").Handle);
        }

Init()

void BioGTK.SAMTool.Init

(

bool

wait = false

)

The Init function loads an ONNX model, calculates image embedding, and updates the status accordingly.

Returns

If the condition ImageView.SelectedImage == null is true, then nothing is being returned and the method will exit. If the condition is false, then the method will continue executing the remaining code without returning anything.

Definition at line 376 of file SAMTool.cs.

        {
            if (ImageView.SelectedImage == null)
                return;
            if (MicroSAM.theSingleton == null)
            {
                sam.LoadONNXModel();
                Thread th2 = new Thread(sam.Encode);
                th2.Start();
            }
            else
            {
                microsam.LoadONNXModel();
                Thread th2 = new Thread(microsam.Encode);
                th2.Start();
            }
            do
            {
                Thread.Sleep(250);
                if (microsam.Initialized)
                    break;
            } while (wait);
            BioLib.Recorder.AddLine("App.samTool.Init(true);",false);
        }

saveSelectedTiffClick()

void BioGTK.SAMTool.saveSelectedTiffClick ( object sender, EventArgs a )

protected

It creates a file chooser dialog, and if the user selects a file, it saves the selected image to that file

Parameters

sender	The object that triggered the event.
EventArgs	This is the event that is being passed to the method.

Returns

The response type of the dialog.

Definition at line 488 of file SAMTool.cs.

        {
            filechooser.Action = FileChooserAction.Save;
            //Saving Tiff can cause a crash on Windows so we check the platform.
            if (Environment.OSVersion.Platform == PlatformID.Win32NT)
            {
                filechooser.Title = "Save File PNG";
            }
            else
            {
                filechooser.Title = "Save File Tiff";
            }
            if (filechooser.Run() != (int)ResponseType.Accept)
                return;
            if (Environment.OSVersion.Platform == PlatformID.Win32NT)
            {
                SelectedROI.roiMask.Pixbuf.Save(filechooser.Filename, "png");
            }
            else
            {
                SelectedROI.roiMask.Pixbuf.Save(filechooser.Filename, "tiff");
            }
            filechooser.Hide();
        }

SetupHandlers()

void BioGTK.SAMTool.SetupHandlers ( )

protected

This function sets up the event handlers for the menu items.

Definition at line 204 of file SAMTool.cs.

        {
            saveSelected.ButtonPressEvent += saveSelectedTiffClick;
            view.ButtonReleaseEvent += PictureBox_ButtonReleaseEvent;
            setAutoSave.ButtonPressEvent += SetAutoSave_ButtonPressEvent;
            this.DeleteEvent += SAMTool_DeleteEvent;
            textBox.Changed += TextBox_Changed;
            toROIMenu.ButtonPressEvent += ToROIMenu_ButtonPressEvent;
            runButton.ButtonPressEvent += AutoSAMMenu_ButtonPressEvent;
            clearButton.ButtonPressEvent += ClearButton_ButtonPressEvent;
            deleteDuplicatesBut.ButtonPressEvent += DeleteDuplicatesBut_ButtonPressEvent;
            SAMEncodeBut.ButtonPressEvent += SAMEncodeBut_ButtonPressEvent;
            clearSliceBut.ButtonPressEvent += ClearSliceBut_ButtonPressEvent;
        }

Member Data Documentation

init

bool BioGTK.SAMTool.init = false

Definition at line 24 of file SAMTool.cs.

MainMenu

MenuBar BioGTK.SAMTool.MainMenu

Definition at line 62 of file SAMTool.cs.

microsam

MicroSAM BioGTK.SAMTool.microsam

static

Definition at line 22 of file SAMTool.cs.

Promotions

List<Promotion> BioGTK.SAMTool.Promotions = new List<Promotion>()

Definition at line 23 of file SAMTool.cs.

sam

SAM BioGTK.SAMTool.sam

static

Definition at line 21 of file SAMTool.cs.

Property Documentation

microSAM

bool BioGTK.SAMTool.microSAM

staticget

Definition at line 25 of file SAMTool.cs.

        {
            get
            {
                if (microsam == null)
                    return false;
                else
                    return true;
            }
        }

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The documentation for this class was generated from the following file:

• BioGTK/SAM/SAMTool.cs