Public Member Functions
	AutoSAM (int points_per_side=4, int points_per_batch=64, float pred_iou_thresh=0.5f, float stability_score_thresh=0.5f, float stability_score_offset=1.0f, float box_nms_thresh=0.7f, int crop_n_layers=0, float crop_nms_thresh=0.7f, float crop_overlap_ratio=(float) 512/1500, int crop_n_points_downscale_factor=1, List< double[,]> point_grids=null, int min_mask_region_area=0, string output_mode="binary_mask")

MaskData	Generate (BioImage im, int buffer)

Public Attributes
int	points_per_side = 4

float	pred_iou_thresh = 0.88f

float	stability_score_thresh = 0.95f

SAM	mSAM

MicroSAM	microSAM

float[]	mImgEmbedding

bool	isMicro = false

Detailed Description

Definition at line 17 of file AutoSAM.cs.

Constructor & Destructor Documentation

◆ AutoSAM()

BioGTK.AutoSAM.AutoSAM	(	int	points_per_side = 4,
		int	points_per_batch = 64,
		float	pred_iou_thresh = 0::5f,
		float	stability_score_thresh = 0::5f,
		float	stability_score_offset = 1::0f,
		float	box_nms_thresh = 0::7f,
		int	crop_n_layers = 0,
		float	crop_nms_thresh = 0::7f,
		float	crop_overlap_ratio = (float)512 / 1500,
		int	crop_n_points_downscale_factor = 1,
		List< double[,]>	point_grids = null,
		int	min_mask_region_area = 0,
		string	output_mode = "binary_mask" )

Definition at line 38 of file AutoSAM.cs.

        {
            this.points_per_side = points_per_side;
            this.points_per_batch = points_per_batch;
            this.pred_iou_thresh = pred_iou_thresh;
            this.stability_score_thresh = stability_score_thresh;
            this.stability_score_offset = stability_score_offset;
            this.box_nms_thresh = box_nms_thresh;
            this.crop_n_layers = crop_n_layers;
            this.crop_nms_thresh = crop_nms_thresh;
            this.crop_overlap_ratio = crop_overlap_ratio;
            this.crop_n_points_downscale_factor = crop_n_points_downscale_factor;
            this.point_grids = point_grids;
            this.min_mask_region_area = min_mask_region_area;
            this.output_mode = output_mode;
 
            if (SAM.theSingleton == null)
            {
                mSAM = MicroSAM.Instance();
                this.isMicro = true;
            }
            else
                mSAM = SAM.Instance();
            if (points_per_side != 0)
            {
                this.point_grids = build_all_layer_point_grids(
                points_per_side,
                crop_n_layers,
                crop_n_points_downscale_factor);
            }
        }

Member Function Documentation

◆ Generate()

MaskData BioGTK.AutoSAM.Generate	(	BioImage	im,
		int	buffer )

Definition at line 200 of file AutoSAM.cs.

        {
            this.mImage = im;
            mImgEmbedding = ((List<float[]>)im.Tag)[buffer];
            if (points_per_side != 0)
            {
                this.point_grids = build_all_layer_point_grids(
                points_per_side,
                crop_n_layers,
                crop_n_points_downscale_factor);
            }
            MaskData masks = this._generate_masks(this.mImage);
            return masks;
        }

Member Data Documentation

◆ isMicro

bool BioGTK.AutoSAM.isMicro = false

Definition at line 36 of file AutoSAM.cs.

◆ microSAM

MicroSAM BioGTK.AutoSAM.microSAM

Definition at line 34 of file AutoSAM.cs.

◆ mImgEmbedding

float [] BioGTK.AutoSAM.mImgEmbedding

Definition at line 35 of file AutoSAM.cs.

◆ mSAM

SAM BioGTK.AutoSAM.mSAM

Definition at line 33 of file AutoSAM.cs.

◆ points_per_side

int BioGTK.AutoSAM.points_per_side = 4

Definition at line 19 of file AutoSAM.cs.

◆ pred_iou_thresh

float BioGTK.AutoSAM.pred_iou_thresh = 0.88f

Definition at line 21 of file AutoSAM.cs.

◆ stability_score_thresh

float BioGTK.AutoSAM.stability_score_thresh = 0.95f

Definition at line 22 of file AutoSAM.cs.

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

BioGTK/SAM/AutoSAM.cs

Public Member Functions

Public Attributes