full refactor without retistruct GUI

[bc]

• [x] run @lschmitz 's new retina through the gambit
• [x] verify that @ades12345 's retina works

[bc]

full_retina.zip source files:

• datapoints.csv
• outline.roi
• xyz.csv
• T.csv
• P.csv
• markup.csv
• falc.txt
• mapping_scriptAutosavedR.r

[bc]

got flatmoutn plot to represent the same orientation as in ImageJ.

[bc]

good overlap with datapoints.csv and outline.roi. should be no data outwith the outline

[bc]

flipped Y and the axes match perfectly. updated tear_markup_plot to match with some refactoring

[bc]

now the sampling points work

[bc]

outline and grid do not align

[bc]

points on red are being excluded. somehow the units of those points need to be converted to match the coordinate frame of the outline.roi, as it is entered in retistruct

[bc]

grid point align correctly with output dtt dataframe

[bc]

raw coordinates from outline.ROI

[bc]

roi	retistruct

        x   y
 [1,] 866 480
 [2,] 867 461
 [3,] 830 324
 [4,] 711 218
 [5,] 620 229
 [6,] 657  83
 [7,] 562  29
 [8,] 484   7
 [9,] 402   0
[10,] 233  27
[11,] 150  69
[12,] 172 201
[13,] 221 281
[14,] 287 375
[15,] 138 408
[16,]  28 438
[17,]  19 529
[18,]  20 601
[19,]  41 663
[20,]  91 734
[21,] 140 787
[22,] 179 838
[23,] 249 925
[24,] 353 851
[25,] 406 841
[26,] 419 916
[27,] 426 990
[28,] 560 940
[29,] 667 875
[30,] 767 772
[31,] 831 701
[32,] 793 665
[33,] 737 628
[34,] 697 574
[35,] 865 495
```   |    

r$> load_roi(roi_path)$coords x y [1,] 866 516 [2,] 867 535 [3,] 830 672 [4,] 711 778 [5,] 620 767 [6,] 657 913 [7,] 562 967 [8,] 484 989 [9,] 402 996 [10,] 233 969 [11,] 150 927 [12,] 172 795 [13,] 221 715 [14,] 287 621 [15,] 138 588 [16,] 28 558 [17,] 19 467 [18,] 20 395 [19,] 41 333 [20,] 91 262 [21,] 140 209 [22,] 179 158 [23,] 249 71 [24,] 353 145 [25,] 406 155 [26,] 419 80 [27,] 426 6 [28,] 560 56 [29,] 667 121 [30,] 767 224 [31,] 831 295 [32,] 793 331 [33,] 737 368 [34,] 697 422 [35,] 865 501

[bc]

when using the retistruct-style outline approach, no items land outside the outline!

[bc]

      x   y        phi     lambda   phi_deg lambda_deg
 1: 866 480  0.0000000  1.6927944   0.00000   96.98998
 2: 867 461  0.0000000  1.6286314   0.00000   93.31371
 3: 830 324  0.0000000  1.1685015   0.00000   66.95021
 4: 711 218  0.0000000  0.6643378   0.00000   38.06375
 5: 620 229 -0.4002356  0.6113949 -22.93181   35.03035
 6: 657  83  0.0000000  0.6643378   0.00000   38.06375
 7: 562  29  0.0000000  0.2725197   0.00000   15.61423
 8: 484   7  0.0000000  0.0000000   0.00000    0.00000
 9: 402   0  0.0000000 -0.2740023   0.00000  -15.69918
10: 233  27  0.0000000 -0.8313582   0.00000  -47.63331
11: 150  69  0.0000000 -1.1627718   0.00000  -66.62192
12: 172 201 -0.4266316 -1.1430187 -24.44419  -65.49015
13: 221 281 -0.6982187 -1.0705789 -40.00499  -61.33965
14: 287 375 -1.0169022 -0.9527973 -58.26421  -54.59126
15: 138 408 -0.4623417 -1.1268234 -26.49023  -64.56222
16:  28 438  0.0000000 -1.1627718   0.00000  -66.62192
17:  19 529  0.0000000 -1.4589114   0.00000  -83.58947
18:  20 601  0.0000000 -1.6741254   0.00000  -95.92032
19:  41 663  0.0000000 -1.8640987   0.00000 -106.80499
20:  91 734  0.0000000 -2.1198834   0.00000 -121.46037
21: 140 787  0.0000000 -2.3413462   0.00000 -134.14926
22: 179 838  0.0000000 -2.5415106   0.00000 -145.61783
23: 249 925  0.0000000 -2.8942786   0.00000 -165.82995
24: 353 851 -0.3497687 -2.9756204 -20.04027 -170.49049
25: 406 841 -0.4705284 -3.0322503 -26.95929 -173.73515
26: 419 916 -0.2477825 -2.9523932 -14.19689 -169.15967
27: 426 990  0.0000000 -2.8942786   0.00000 -165.82995
28: 560 940  0.0000000  2.9224854   0.00000  167.44608
29: 667 875  0.0000000  2.5295023   0.00000  144.92981
30: 767 772  0.0000000  2.0670298   0.00000  118.43209
31: 831 701  0.0000000  1.7436827   0.00000   99.90566
32: 793 665 -0.1915390  1.7586750 -10.97437  100.76465
33: 737 628 -0.4175587  1.7924179 -23.92435  102.69798
34: 697 574 -0.6189636  1.7930998 -35.46400  102.73705
35: 865 495  0.0000000  1.7436827   0.00000   99.90566```

[bc]

      x   y        phi     lambda   phi_deg lambda_deg successful_mapping
 1: 866 480  0.0000000  1.6927944   0.00000   96.98998               TRUE
 2: 867 461  0.0000000  1.6286314   0.00000   93.31371               TRUE
 3: 830 324  0.0000000  1.1685015   0.00000   66.95021               TRUE
 4: 711 218  0.0000000  0.6643378   0.00000   38.06375               TRUE
 5: 620 229 -0.4002356  0.6113949 -22.93181   35.03035               TRUE
 6: 657  83  0.0000000  0.6643378   0.00000   38.06375               TRUE
 7: 562  29  0.0000000  0.2725197   0.00000   15.61423               TRUE
 8: 484   7  0.0000000  0.0000000   0.00000    0.00000               TRUE
 9: 402   0  0.0000000 -0.2740023   0.00000  -15.69918               TRUE
10: 233  27  0.0000000 -0.8313582   0.00000  -47.63331               TRUE
11: 150  69  0.0000000 -1.1627718   0.00000  -66.62192               TRUE
12: 172 201 -0.4266316 -1.1430187 -24.44419  -65.49015               TRUE
13: 221 281 -0.6982187 -1.0705789 -40.00499  -61.33965               TRUE
14: 287 375 -1.0169022 -0.9527973 -58.26421  -54.59126               TRUE
15: 138 408 -0.4623417 -1.1268234 -26.49023  -64.56222               TRUE
16:  28 438  0.0000000 -1.1627718   0.00000  -66.62192               TRUE
17:  19 529  0.0000000 -1.4589114   0.00000  -83.58947               TRUE
18:  20 601  0.0000000 -1.6741254   0.00000  -95.92032               TRUE
19:  41 663  0.0000000 -1.8640987   0.00000 -106.80499               TRUE
20:  91 734  0.0000000 -2.1198834   0.00000 -121.46037               TRUE
21: 140 787  0.0000000 -2.3413462   0.00000 -134.14926               TRUE
22: 179 838  0.0000000 -2.5415106   0.00000 -145.61783               TRUE
23: 249 925  0.0000000 -2.8942786   0.00000 -165.82995               TRUE
24: 353 851 -0.3497687 -2.9756204 -20.04027 -170.49049               TRUE
25: 406 841 -0.4705284 -3.0322503 -26.95929 -173.73515               TRUE
26: 419 916 -0.2477825 -2.9523932 -14.19689 -169.15967               TRUE
27: 426 990  0.0000000 -2.8942786   0.00000 -165.82995               TRUE
28: 560 940  0.0000000  2.9224854   0.00000  167.44608               TRUE
29: 667 875  0.0000000  2.5295023   0.00000  144.92981               TRUE
30: 767 772  0.0000000  2.0670298   0.00000  118.43209               TRUE
31: 831 701  0.0000000  1.7436827   0.00000   99.90566               TRUE
32: 793 665 -0.1915390  1.7586750 -10.97437  100.76465               TRUE
33: 737 628 -0.4175587  1.7924179 -23.92435  102.69798               TRUE
34: 697 574 -0.6189636  1.7930998 -35.46400  102.73705               TRUE
35: 865 495  0.0000000  1.7436827   0.00000   99.90566               TRUE```
with successful mapping plotting true for all outline points

[bc]

a perfect glorious match between expected and observed outline location and success parameters:

[bc]

misalignment of measured datapoints.csv, appears as though it's only a vertical bias offset

[bc]

target

[bc]

issue identified: both the points and the outline, when run through retistruct's imageJ transformation have 0 as the minimum point. But we know from the raw data that the minY val for the outline was 6:

and the min Y val for the datapoints was 24

[bc]

aligned ✅

[bc]

aligns well after refactoring

[bc]

added outline path

[bc]

The azimuthal plot is aligned correctly

[bc]

completed flatplot, nonsmoothed/predicted

[bc]

looks like a 180 flip after projection

[bc]

my_retina_figure.pdf reimplemented falciform

[bc]

new tear markup plotter now shows where the datapoints are:

plus if you zoom in on the PDF, it will show the data measurement indices (row indices from the measurements)

outline_coordinates.pdf

[bc]

deformation plots

[bc]

added notes on flatmount for how the retina was reconstructed

[bc]