BioImager.MicroManager Class Reference

Classes
struct	Conf
class	Objectives
class	Shutters

Static Public Member Functions
static Conf[]	GetConfigs (string Class, string Type)
static bool	Initialize (string config)
static BioImage	TakeImage (string name)
static void	SetExposure (float f)
static void	SetPosition (Point3D p)
static void	SetPosition (PointD p)
static void	GetPosition3D (out Point3D p, bool update)
static void	GetPosition (out PointD p, bool update)

Static Public Attributes
static mmcorej.CMMCore	core
static MMStudio	studio
static PointD	location
static double	focus
static Dictionary< string, List< Conf > >	Config = new Dictionary<string, List<Conf>>()
static bool	initialized = false
static string	TurretName = ""

Detailed Description

Definition at line 18 of file MicroManager.cs.

Member Function Documentation

GetConfigs()

static Conf[] BioImager.MicroManager.GetConfigs ( string Class, string Type )

static

Definition at line 46 of file MicroManager.cs.

        {
            List<Conf> configs = new List<Conf>();
            foreach (var conf in Config[Class]) 
            {
                if(conf.Type == Type) configs.Add(conf);
            }
            return configs.ToArray();
        }

GetPosition()

static void BioImager.MicroManager.GetPosition ( out PointD p, bool update )

static

Definition at line 168 of file MicroManager.cs.

        {
            var pos = core.getXYStagePosition();
            p = new PointD(pos.x, pos.y);
        }

GetPosition3D()

static void BioImager.MicroManager.GetPosition3D ( out Point3D p, bool update )

static

Definition at line 162 of file MicroManager.cs.

        {
            var pos = core.getXYStagePosition();
            var f = core.getPosition();
            p = new Point3D(pos.x, pos.y, f);
        }

Initialize()

static bool BioImager.MicroManager.Initialize ( string config )

static

Definition at line 57 of file MicroManager.cs.

        {
            try
            {
                Directory.SetCurrentDirectory("C:/Program Files/Micro-Manager-2.0/");
                java.lang.System.setProperty("force.annotation.index", "true");
                // Set the library path (adjust the path as needed)
                java.lang.System.setProperty("org.micromanager.corej.path", "C:/Program Files/Micro-Manager-2.0");
                java.lang.System.setProperty("user.dir", "C:/Program Files/Micro-Manager-2.0/");
                MMStudio.main(new string[] { });
                studio = MMStudio.getInstance();
                core = (CMMCore)studio.core();
                Objectives.Initialize();
                Directory.SetCurrentDirectory(Path.GetDirectoryName(Environment.ProcessPath));
                return true;
            }
            catch (Exception e)
            {
                // Log the exception message
                Console.WriteLine("Error during Micro-Manager initialization: " + e.Message);
                return false; // Return false on failure
            }
        }

SetExposure()

static void BioImager.MicroManager.SetExposure ( float f )

static

Definition at line 149 of file MicroManager.cs.

        {
            core.setExposure(f);
        }

SetPosition() [1/2]

static void BioImager.MicroManager.SetPosition ( Point3D p )

static

Definition at line 153 of file MicroManager.cs.

        {
            core.setXYPosition(p.X, p.Y);
            core.setPosition(p.Z);
        }

SetPosition() [2/2]

static void BioImager.MicroManager.SetPosition ( PointD p )

static

Definition at line 158 of file MicroManager.cs.

        {
            core.setXYPosition(p.X, p.Y);
        }

TakeImage()

static BioImage BioImager.MicroManager.TakeImage ( string name )

static

Definition at line 81 of file MicroManager.cs.

        {
            int width, height, depth, bits, channels = 0;
            AForge.Bitmap[] bm;
            TakeImage(name,out width,out height,out depth,out bits,out channels, out bm);
            BioImage im = new BioImage(name);
            foreach (AForge.Bitmap item in bm)
            {
                item.Stats = Statistics.FromBytes(item);
            }
            im.Buffers.AddRange(bm);
            //Set the physical size based on objective view
            RectangleD rec = Microscope.GetViewRectangle(false);
            Point3D p = Microscope.GetPosition();
            Resolution res = new Resolution(width, height, im.Buffers[0].PixelFormat, rec.W / im.Buffers[0].SizeX, rec.H / im.Buffers[0].SizeY, 1, p.X, p.Y, p.Z);
            im.Volume.Location = p;
            im.Volume.Width = rec.W;
            im.Volume.Height = rec.H;
            im.UpdateCoords(1, 1, 1);
            im.Resolutions.Add(res);
            for (int c = 0; c < bm.Length; c++)
            {
                im.Channels.Add(new Channel(c, bm[c].BitsPerPixel, bm[c].RGBChannelsCount));
            }
            BioImage.AutoThreshold(im, false);
            return im;
        }

Member Data Documentation

Config

Dictionary<string, List<Conf> > BioImager.MicroManager.Config = new Dictionary<string, List<Conf>>()

static

Definition at line 24 of file MicroManager.cs.

core

mmcorej.CMMCore BioImager.MicroManager.core

static

Definition at line 20 of file MicroManager.cs.

focus

double BioImager.MicroManager.focus

static

Definition at line 23 of file MicroManager.cs.

initialized

bool BioImager.MicroManager.initialized = false

static

Definition at line 55 of file MicroManager.cs.

location

PointD BioImager.MicroManager.location

static

Definition at line 22 of file MicroManager.cs.

studio

MMStudio BioImager.MicroManager.studio

static

Definition at line 21 of file MicroManager.cs.

TurretName

string BioImager.MicroManager.TurretName = ""

static

Definition at line 56 of file MicroManager.cs.

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

• BioImager/MicroManager/MicroManager.cs