Class: SectionDataSet

Inherits:
DataSet
  • Object
show all
Includes:
CoreBase
Defined in:
app/models/section_data_set.rb

Overview

SectionDataSet is an experiment conducted on sections of tissue. These sections are ordered respecting their position in the brain. The images are represented by the [SectionImage] model.

Associations:

Direct Known Subclasses

AtlasDataSet

Instance Method Summary (collapse)

Methods inherited from DataSet

#get_product_ids

Instance Method Details

- (Object) label 



27
28
29
 
# File 'app/models/section_data_set.rb', line 27

def label
  "#{treatments[0].label} - #{probes[0].label} - #{specimen.donor.organism.label}"
end

- (Object) reference_images

method to allow override of images used for reference



82
83
84
 
# File 'app/models/section_data_set.rb', line 82

def reference_images
  self.section_images
end

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

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



32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
 
# File 'app/models/section_data_set.rb', line 32

def reference_to_image( rx, ry, rz )

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

  # ---- search for closest sub_image
  #thickness = 25 # thickness hardcode to 25 micron should be a function of image-series
  min_diff = 10**6
  min_sub_image = nil

  self.reference_images.each { |si|
    # no need to check for failed sub-images in warehouse
    if (!si.nil? && !si.section_number.nil? && !self.section_thickness.nil?)
      diff = (si.section_number * self.section_thickness - vz).abs
      if diff < min_diff
        min_diff = diff
        min_sub_image = si
      end
    end
  }

  if min_sub_image == nil
    return nil
  end

  # transfrom vx,vy to sub_image sx,sy
  xvs = min_sub_image.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 min_sub_image.id, min_sub_image.section_number, sx, sy

end