Class: SectionImage

Inherits:
SubImage
  • Object
show all
Includes:
CoreBase
Defined in:
app/models/section_image.rb

Overview

SectionImages belong to a [SectionDataSet], which is an experiment comprised of sectioned tissue.

Associations:

Direct Known Subclasses

AtlasImage, MicroarrayPostImage, MicroarrayPreImage

Instance Method Summary (collapse)

Instance Method Details

- (Object) image_to_reference(sx, sy)

Find the closest specified 3D location to user specified 2D position



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# File 'app/models/section_image.rb', line 24

def image_to_reference(sx, sy)

  ds = self.section_data_set

  return nil if not ds

  # ---- transform sub_image sx,sy to volume vx,vy,vz
  vz = self.section_number * ds.section_thickness

  xvs = self.alignment2d

  if xvs
    vx = xvs.tsv_00 * sx + xvs.tsv_01 * sy + xvs.tsv_04
    vy = xvs.tsv_02 * sx + xvs.tsv_03 * sy + xvs.tsv_05
  else
    return nil
  end

  # ---- transform volume vx,vy,vx to reference rx,ry,rz
  xrv = ds.alignment3d

  if xrv
    rx = xrv.tvr_00 * vx + xrv.tvr_01 * vy + xrv.tvr_02 * vz + xrv.tvr_09
    ry = xrv.tvr_03 * vx + xrv.tvr_04 * vy + xrv.tvr_05 * vz + xrv.tvr_10
    rz = xrv.tvr_06 * vx + xrv.tvr_07 * vy + xrv.tvr_08 * vz + xrv.tvr_11
  else
    return nil
  end

  return rx, ry, rz

end

- (Object) reference_to_location(rx, ry, rz)

Find the closest (x,y) location in this image to user specified 3D location



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# File 'app/models/section_image.rb', line 58

def reference_to_location(rx, ry, rz)

  ds = self.section_data_set
  return nil if not ds

  # ------ transform reference rx,ry,rz to volume vx,vy,vz
  xrv = ds.alignment3d

  if xrv
    vx = xrv.trv_00 * rx + xrv.trv_01 * ry + xrv.trv_02 * rz + xrv.trv_09
    vy = xrv.trv_03 * rx + xrv.trv_04 * ry + xrv.trv_05 * rz + xrv.trv_10
    # vz = xrv.trv_06 * rx + xrv.trv_07 * ry + xrv.trv_08 * rz + xrv.trv_11
  else
    vx = rx
    vy = ry
    # vz = rz
  end

  # ------ transform vx,vy to sub_image sx,sy
  xvs = self.alignment2d

  if xvs
    sx = xvs.tvs_00 * vx + xvs.tvs_01 * vy + xvs.tvs_04
    sy = xvs.tvs_02 * vx + xvs.tvs_03 * vy + xvs.tvs_05
  else
    return nil
  end

  return sx, sy

end