retina won't install - Githubissues

I am new to R, running Windows, and can't make this package work for me. I have followed all the tutorials, and downloaded the current package, and followed the steps to make my own retina to analyze successfully, but R won't run the retina package. All the github links in the tutorial return 404s, and the demos won't run. I have retistruct up and working, but when I follow the tutorial code R can't find retina_object() or any of the other functions associated with the retina package. Please help!

Hi! That sounds frustrating—I'll help you get set up. I'm updating the docs so there will be fewer broken links.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this:

let me know how that goes and then I can support you from there

I keep getting the same errors. I can't get a map to show up at all.

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:25 AM Brian Cohn notifications@github.com wrote:

Hi! That sounds frustrated—I'll help you get set up.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this: [image: image] https://user-images.githubusercontent.com/13772726/74059235-7b43fb00-499c-11ea-9a2e-b2d07ff2cdfa.png

let me know how that goes and then I can support you from there

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bc/retina/issues/48?email_source=notifications&email_token=AOPXY2Q5RLAJADOBHMYENTLRBWYSDA5CNFSM4KROZ62KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELEIA6A#issuecomment-583565432, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOPXY2XVWM22KAQWQX4NWFDRBWYSDANCNFSM4KROZ62A .

Please paste the full command history from R so I can investigate the error messages

From: moonh3 notifications@github.com Sent: Friday, February 7, 2020 23:00 To: bc/retina Cc: Brian Cohn; Comment Subject: Re: [bc/retina] retina won't install (#48)

I keep getting the same errors. I can't get a map to show up at all.

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:25 AM Brian Cohn notifications@github.com wrote:

Hi! That sounds frustrated—I'll help you get set up.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this: [image: image] https://user-images.githubusercontent.com/13772726/74059235-7b43fb00-499c-11ea-9a2e-b2d07ff2cdfa.png

let me know how that goes and then I can support you from there

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bc/retina/issues/48?email_source=notifications&email_token=AOPXY2Q5RLAJADOBHMYENTLRBWYSDA5CNFSM4KROZ62KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELEIA6A#issuecomment-583565432, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOPXY2XVWM22KAQWQX4NWFDRBWYSDANCNFSM4KROZ62A .

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I have put "retina" in several locations on my computer (including the desktop since sometimes the only place windows will write to), and this is the consistent result when I run "source("main.r")" When I follow the step by step tutorial on my own retina the code doesn't recognize the functions "retina_object", ""semi_ellipse_perimeter", and "fit_plots"

source("main.r") Tear 1 child of rim Tear 1 child of rim Tear 2 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Non-adjacent points in rim connected by line: 42 26 In triangle: 52, 122 Other points in triangles: 27 82 Non-adjacent points in rim connected by line: 171 78 In triangle: 44, 294 Other points in triangles: 23 49 Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim i = 33 i0 = 34 j = 36 j0 = 34 sf = 67.2011904656458 sf0 = 0 sb = 92.8237577347524 sb0 = 0 Insert point 185 at 66.834708484687 along backward path; projection from 33 in forward path i = 32 i0 = 33 j = 36 j0 = 185 sf = 134.320487243845 sf0 = 67.2011904656458 sb = 92.8237577347524 sb0 = 66.834708484687 Insert point 186 at 93.3327482785274 along forward path; projection from 36 in backward path i = 32 i0 = 186 j = 35 j0 = 36 sf = 134.320487243845 sf0 = 93.3327482785274 sb = 185.647515469505 sb0 = 92.8237577347524 Insert point 187 at 133.587969889504 along backward path; projection from 32 in forward path i = 4 i0 = 5 j = 127 j0 = 5 sf = 91.6624241442479 sf0 = 0 sb = 75.3077021293307 sb0 = 0 Insert point 188 at 45.8312120721239 along forward path; projection from 127 in backward path i = 13 i0 = 14 j = 146 j0 = 14 sf = 114.85643212289 sf0 = 0 sb = 76.3053078101386 sb0 = 0 Insert point 189 at 98.016166530692 along forward path; projection from 146 in backward path i = 13 i0 = 189 j = 15 j0 = 146 sf = 114.85643212289 sf0 = 98.016166530692 sb = 152.610615620277 sb0 = 76.3053078101386 Insert point 190 at 89.415406838698 along backward path; projection from 13 in forward path i = 12 i0 = 13 j = 15 j0 = 190 sf = 208.670077185855 sf0 = 114.85643212289 sb = 152.610615620277 sb0 = 89.415406838698 Insert point 191 at 196.032333061384 along forward path; projection from 15 in backward path i = 12 i0 = 191 j = 165 j0 = 15 sf = 208.670077185855 sf0 = 196.032333061384 sb = 209.619386875234 sb0 = 152.610615620277 Insert point 192 at 162.449063598566 along backward path; projection from 12 in forward path i = 181 i0 = 12 j = 165 j0 = 192 sf = 275.580465019135 sf0 = 208.670077185855 sb = 209.619386875234 sb0 = 162.449063598566 Insert point 193 at 269.2615929569 along forward path; projection from 165 in backward path i = 181 i0 = 193 j = 16 j0 = 165 sf = 275.580465019135 sf0 = 269.2615929569 sb = 266.628158130191 sb0 = 209.619386875234 Insert point 194 at 214.538610864379 along backward path; projection from 181 in forward path i = 24 i0 = 25 j = 26 j0 = 25 sf = 53.9351462406472 sf0 = 0 sb = 76.1183289359403 sb0 = 0 Insert point 195 at 44.6892981142401 along backward path; projection from 24 in forward path i = 78 i0 = 24 j = 26 j0 = 195 sf = 117.755205783083 sf0 = 53.9351462406472 sb = 76.1183289359403 sb0 = 44.6892981142401 Insert point 196 at 91.8665849765368 along forward path; projection from 26 in backward path i = 78 i0 = 196 j = 27 j0 = 26 sf = 117.755205783083 sf0 = 91.8665849765368 sb = 150.448672672533 sb0 = 76.1183289359403 Insert point 197 at 97.5689853933864 along backward path; projection from 78 in forward path Merging points... Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Projecting to sphere... Optimising mapping with no area constraint using BFGS... E = 0.00351 | E_L = 0.00351 | E_A = 0.00000 | 0 flippped triangles E = 0.00339 | E_L = 0.00339 | E_A = 0.00000 | 1 flippped triangles E = 0.00333 | E_L = 0.00333 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles Optimising mapping with area constraint using FIRE... FIRE: 2 stops. 7 hits of maxmove. 0 hits of dtmax. Frms = 2.8238718594397e-06; Ftanrms = 2.68556013550784e-06 E = 0.00340 | E_L = 0.00340 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with strong area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with weak area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Mapping optimised. Deformation energy E: 0.003238039 ; 0 flipped triangles. Inferring coordinates of PointSet Inferring coordinates of LandmarkSet Inferring coordinates of CountSet Mapping optimised. Deformation eL: 0.05690377 ; 0 flipped triangles. OD not marked up. There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: In read.scale(dataset) : Scale file "scale.csv" does not exist. Scale bar will not be set. 2: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 3: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 4: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 5: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 6: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 7: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 8: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 9: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 10: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 11: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 12: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 13: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 14: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 15: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 16: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 17: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 18: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 19: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 20: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 21: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 22: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 23: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 24: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 25: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 26: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 27: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 28: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 29: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 30: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 31: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 32: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 33: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 34: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 35: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 36: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 37: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 38: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 39: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 40: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 41: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 42: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 43: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 44: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 45: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 46: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 47: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 48: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 49: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 50: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:00 PM Hannah Moon hmoon@hawaii.edu wrote:

I keep getting the same errors. I can't get a map to show up at all.

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:25 AM Brian Cohn notifications@github.com wrote:

Hi! That sounds frustrated—I'll help you get set up.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this: [image: image] https://user-images.githubusercontent.com/13772726/74059235-7b43fb00-499c-11ea-9a2e-b2d07ff2cdfa.png

let me know how that goes and then I can support you from there

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bc/retina/issues/48?email_source=notifications&email_token=AOPXY2Q5RLAJADOBHMYENTLRBWYSDA5CNFSM4KROZ62KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELEIA6A#issuecomment-583565432, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOPXY2XVWM22KAQWQX4NWFDRBWYSDANCNFSM4KROZ62A .

Look in the output folder, are there any files there?

Get Outlook for iOShttps://aka.ms/o0ukef

From: moonh3 notifications@github.com Sent: Saturday, February 8, 2020 10:33:02 AM To: bc/retina retina@noreply.github.com Cc: Brian Cohn brianaco@usc.edu; Comment comment@noreply.github.com Subject: Re: [bc/retina] retina won't install (#48)

I have put "retina" in several locations on my computer (including the desktop since sometimes the only place windows will write to), and this is the consistent result when I run "source("main.r")" When I follow the step by step tutorial on my own retina the code doesn't recognize the functions "retina_object", ""semi_ellipse_perimeter", and "fit_plots"

source("main.r") Tear 1 child of rim Tear 1 child of rim Tear 2 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Non-adjacent points in rim connected by line: 42 26 In triangle: 52, 122 Other points in triangles: 27 82 Non-adjacent points in rim connected by line: 171 78 In triangle: 44, 294 Other points in triangles: 23 49 Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim i = 33 i0 = 34 j = 36 j0 = 34 sf = 67.2011904656458 sf0 = 0 sb = 92.8237577347524 sb0 = 0 Insert point 185 at 66.834708484687 along backward path; projection from 33 in forward path i = 32 i0 = 33 j = 36 j0 = 185 sf = 134.320487243845 sf0 = 67.2011904656458 sb = 92.8237577347524 sb0 = 66.834708484687 Insert point 186 at 93.3327482785274 along forward path; projection from 36 in backward path i = 32 i0 = 186 j = 35 j0 = 36 sf = 134.320487243845 sf0 = 93.3327482785274 sb = 185.647515469505 sb0 = 92.8237577347524 Insert point 187 at 133.587969889504 along backward path; projection from 32 in forward path i = 4 i0 = 5 j = 127 j0 = 5 sf = 91.6624241442479 sf0 = 0 sb = 75.3077021293307 sb0 = 0 Insert point 188 at 45.8312120721239 along forward path; projection from 127 in backward path i = 13 i0 = 14 j = 146 j0 = 14 sf = 114.85643212289 sf0 = 0 sb = 76.3053078101386 sb0 = 0 Insert point 189 at 98.016166530692 along forward path; projection from 146 in backward path i = 13 i0 = 189 j = 15 j0 = 146 sf = 114.85643212289 sf0 = 98.016166530692 sb = 152.610615620277 sb0 = 76.3053078101386 Insert point 190 at 89.415406838698 along backward path; projection from 13 in forward path i = 12 i0 = 13 j = 15 j0 = 190 sf = 208.670077185855 sf0 = 114.85643212289 sb = 152.610615620277 sb0 = 89.415406838698 Insert point 191 at 196.032333061384 along forward path; projection from 15 in backward path i = 12 i0 = 191 j = 165 j0 = 15 sf = 208.670077185855 sf0 = 196.032333061384 sb = 209.619386875234 sb0 = 152.610615620277 Insert point 192 at 162.449063598566 along backward path; projection from 12 in forward path i = 181 i0 = 12 j = 165 j0 = 192 sf = 275.580465019135 sf0 = 208.670077185855 sb = 209.619386875234 sb0 = 162.449063598566 Insert point 193 at 269.2615929569 along forward path; projection from 165 in backward path i = 181 i0 = 193 j = 16 j0 = 165 sf = 275.580465019135 sf0 = 269.2615929569 sb = 266.628158130191 sb0 = 209.619386875234 Insert point 194 at 214.538610864379 along backward path; projection from 181 in forward path i = 24 i0 = 25 j = 26 j0 = 25 sf = 53.9351462406472 sf0 = 0 sb = 76.1183289359403 sb0 = 0 Insert point 195 at 44.6892981142401 along backward path; projection from 24 in forward path i = 78 i0 = 24 j = 26 j0 = 195 sf = 117.755205783083 sf0 = 53.9351462406472 sb = 76.1183289359403 sb0 = 44.6892981142401 Insert point 196 at 91.8665849765368 along forward path; projection from 26 in backward path i = 78 i0 = 196 j = 27 j0 = 26 sf = 117.755205783083 sf0 = 91.8665849765368 sb = 150.448672672533 sb0 = 76.1183289359403 Insert point 197 at 97.5689853933864 along backward path; projection from 78 in forward path Merging points... Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Projecting to sphere... Optimising mapping with no area constraint using BFGS... E = 0.00351 | E_L = 0.00351 | E_A = 0.00000 | 0 flippped triangles E = 0.00339 | E_L = 0.00339 | E_A = 0.00000 | 1 flippped triangles E = 0.00333 | E_L = 0.00333 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles Optimising mapping with area constraint using FIRE... FIRE: 2 stops. 7 hits of maxmove. 0 hits of dtmax. Frms = 2.8238718594397e-06; Ftanrms = 2.68556013550784e-06 E = 0.00340 | E_L = 0.00340 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with strong area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with weak area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Mapping optimised. Deformation energy E: 0.003238039 ; 0 flipped triangles. Inferring coordinates of PointSet Inferring coordinates of LandmarkSet Inferring coordinates of CountSet Mapping optimised. Deformation eL: 0.05690377 ; 0 flipped triangles. OD not marked up. There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: In read.scale(dataset) : Scale file "scale.csv" does not exist. Scale bar will not be set. 2: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 3: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 4: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 5: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 6: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 7: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 8: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 9: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 10: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 11: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 12: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 13: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 14: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 15: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 16: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 17: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 18: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 19: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 20: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 21: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 22: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 23: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 24: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 25: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 26: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 27: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 28: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 29: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 30: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 31: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 32: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 33: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 34: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 35: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 36: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 37: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 38: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 39: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 40: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 41: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 42: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 43: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 44: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 45: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 46: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 47: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 48: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 49: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 50: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:00 PM Hannah Moon hmoon@hawaii.edu wrote:

I keep getting the same errors. I can't get a map to show up at all.

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:25 AM Brian Cohn notifications@github.com wrote:

Hi! That sounds frustrated—I'll help you get set up.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this: [image: image] https://user-images.githubusercontent.com/13772726/74059235-7b43fb00-499c-11ea-9a2e-b2d07ff2cdfa.png

let me know how that goes and then I can support you from there

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bc/retina/issues/48?email_source=notifications&email_token=AOPXY2Q5RLAJADOBHMYENTLRBWYSDA5CNFSM4KROZ62KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELEIA6A#issuecomment-583565432, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOPXY2XVWM22KAQWQX4NWFDRBWYSDANCNFSM4KROZ62A .

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I figured it out! The output folder did have the expected files, and the tutorial kind of gets you to create the correct files. It is a bit outdated at the moment though. The tutorial asks for files with the datapoints as an ID number and the density- what it really wants is the xy coordinates of the datapoints in the order they are entered in the xyz file. Thank you for your time and help, I really appreciate it and it made all the difference in a stressful pre-conference weekend!

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Sat, Feb 8, 2020 at 11:45 AM Brian Cohn notifications@github.com wrote:

Look in the output folder, are there any files there?

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From: moonh3 notifications@github.com Sent: Saturday, February 8, 2020 10:33:02 AM To: bc/retina retina@noreply.github.com Cc: Brian Cohn brianaco@usc.edu; Comment comment@noreply.github.com Subject: Re: [bc/retina] retina won't install (#48)

I have put "retina" in several locations on my computer (including the desktop since sometimes the only place windows will write to), and this is the consistent result when I run "source("main.r")" When I follow the step by step tutorial on my own retina the code doesn't recognize the functions "retina_object", ""semi_ellipse_perimeter", and "fit_plots"

source("main.r") Tear 1 child of rim Tear 1 child of rim Tear 2 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Non-adjacent points in rim connected by line: 42 26 In triangle: 52, 122 Other points in triangles: 27 82 Non-adjacent points in rim connected by line: 171 78 In triangle: 44, 294 Other points in triangles: 23 49 Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim i = 33 i0 = 34 j = 36 j0 = 34 sf = 67.2011904656458 sf0 = 0 sb = 92.8237577347524 sb0 = 0 Insert point 185 at 66.834708484687 along backward path; projection from 33 in forward path i = 32 i0 = 33 j = 36 j0 = 185 sf = 134.320487243845 sf0 = 67.2011904656458 sb = 92.8237577347524 sb0 = 66.834708484687 Insert point 186 at 93.3327482785274 along forward path; projection from 36 in backward path i = 32 i0 = 186 j = 35 j0 = 36 sf = 134.320487243845 sf0 = 93.3327482785274 sb = 185.647515469505 sb0 = 92.8237577347524 Insert point 187 at 133.587969889504 along backward path; projection from 32 in forward path i = 4 i0 = 5 j = 127 j0 = 5 sf = 91.6624241442479 sf0 = 0 sb = 75.3077021293307 sb0 = 0 Insert point 188 at 45.8312120721239 along forward path; projection from 127 in backward path i = 13 i0 = 14 j = 146 j0 = 14 sf = 114.85643212289 sf0 = 0 sb = 76.3053078101386 sb0 = 0 Insert point 189 at 98.016166530692 along forward path; projection from 146 in backward path i = 13 i0 = 189 j = 15 j0 = 146 sf = 114.85643212289 sf0 = 98.016166530692 sb = 152.610615620277 sb0 = 76.3053078101386 Insert point 190 at 89.415406838698 along backward path; projection from 13 in forward path i = 12 i0 = 13 j = 15 j0 = 190 sf = 208.670077185855 sf0 = 114.85643212289 sb = 152.610615620277 sb0 = 89.415406838698 Insert point 191 at 196.032333061384 along forward path; projection from 15 in backward path i = 12 i0 = 191 j = 165 j0 = 15 sf = 208.670077185855 sf0 = 196.032333061384 sb = 209.619386875234 sb0 = 152.610615620277 Insert point 192 at 162.449063598566 along backward path; projection from 12 in forward path i = 181 i0 = 12 j = 165 j0 = 192 sf = 275.580465019135 sf0 = 208.670077185855 sb = 209.619386875234 sb0 = 162.449063598566 Insert point 193 at 269.2615929569 along forward path; projection from 165 in backward path i = 181 i0 = 193 j = 16 j0 = 165 sf = 275.580465019135 sf0 = 269.2615929569 sb = 266.628158130191 sb0 = 209.619386875234 Insert point 194 at 214.538610864379 along backward path; projection from 181 in forward path i = 24 i0 = 25 j = 26 j0 = 25 sf = 53.9351462406472 sf0 = 0 sb = 76.1183289359403 sb0 = 0 Insert point 195 at 44.6892981142401 along backward path; projection from 24 in forward path i = 78 i0 = 24 j = 26 j0 = 195 sf = 117.755205783083 sf0 = 53.9351462406472 sb = 76.1183289359403 sb0 = 44.6892981142401 Insert point 196 at 91.8665849765368 along forward path; projection from 26 in backward path i = 78 i0 = 196 j = 27 j0 = 26 sf = 117.755205783083 sf0 = 91.8665849765368 sb = 150.448672672533 sb0 = 76.1183289359403 Insert point 197 at 97.5689853933864 along backward path; projection from 78 in forward path Merging points... Tear 1 child of rim Tear 2 child of rim Tear 3 child of rim Tear 4 child of rim Projecting to sphere... Optimising mapping with no area constraint using BFGS... E = 0.00351 | E_L = 0.00351 | E_A = 0.00000 | 0 flippped triangles E = 0.00339 | E_L = 0.00339 | E_A = 0.00000 | 1 flippped triangles E = 0.00333 | E_L = 0.00333 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles E = 0.00331 | E_L = 0.00331 | E_A = 0.00000 | 1 flippped triangles Optimising mapping with area constraint using FIRE... FIRE: 2 stops. 7 hits of maxmove. 0 hits of dtmax. Frms = 2.8238718594397e-06; Ftanrms = 2.68556013550784e-06 E = 0.00340 | E_L = 0.00340 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with strong area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Optimising mapping with weak area constraint using BFGS... E = 0.00324 | E_L = 0.00324 | E_A = 0.00000 | 0 flippped triangles Mapping optimised. Deformation energy E: 0.003238039 ; 0 flipped triangles. Inferring coordinates of PointSet Inferring coordinates of LandmarkSet Inferring coordinates of CountSet Mapping optimised. Deformation eL: 0.05690377 ; 0 flipped triangles. OD not marked up. There were 50 or more warnings (use warnings() to see the first 50) warnings() Warning messages: 1: In read.scale(dataset) : Scale file "scale.csv" does not exist. Scale bar will not be set. 2: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 3: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 4: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 5: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 6: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 7: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 8: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 9: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 10: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 11: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 12: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 13: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 14: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 15: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 16: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 17: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 18: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 19: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 20: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 21: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 22: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 23: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 24: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 25: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 26: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 27: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 28: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 29: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 30: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 31: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 32: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 33: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 34: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 35: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 36: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 37: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 38: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 39: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 40: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 41: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 42: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 43: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 44: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 45: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 46: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 47: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 48: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 49: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored 50: In r$mapFlatToSpherical(cbind(X = my_row[[1]], Y = my_row[[2]])) : 1 points outwith the outline will be ignored

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:00 PM Hannah Moon hmoon@hawaii.edu wrote:

I keep getting the same errors. I can't get a map to show up at all.

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Fri, Feb 7, 2020 at 11:25 AM Brian Cohn notifications@github.com wrote:

Hi! That sounds frustrated—I'll help you get set up.

download this release: https://github.com/bc/retina/releases/download/0.2/retina.zip

and run R, on main.R via source("main.r")

should produce this: [image: image] < https://user-images.githubusercontent.com/13772726/74059235-7b43fb00-499c-11ea-9a2e-b2d07ff2cdfa.png

let me know how that goes and then I can support you from there

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/bc/retina/issues/48?email_source=notifications&email_token=AOPXY2Q5RLAJADOBHMYENTLRBWYSDA5CNFSM4KROZ62KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOELEIA6A#issuecomment-583565432 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AOPXY2XVWM22KAQWQX4NWFDRBWYSDANCNFSM4KROZ62A

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Thank you for checking in with me! I was able to reconstruct the retina. I am not sure how to double check if the orientation is correct in the final output. The final image represents the retina projected in a 3D eyecup, yes? Just shifting the location of the dorsal/nasal locations a little bit would really affect the final reconstruction, but if we can accurately reconstruct in-situ density gradients it would be really cool!

Hannah Moon University of Hawaii at Manoa Honolulu, HI 96822 hmoon@hawaii.edu c: 360-367-0808

On Thu, Apr 16, 2020 at 12:39 PM Brian Cohn notifications@github.com wrote:

Any luck?

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As for the retina orientation, do you have a marker on your retina wholemount that indicates the exact dorsal/nasal position?

Yes, I do

On Fri, Apr 17, 2020, 18:32 Lars Schmitz notifications@github.com wrote:

As for the retina orientation, do you have a marker on your retina wholemount that indicates the exact dorsal/nasal position?

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I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt ?

I'm gonna disagree fromy experience. Shifting the dorsal and nasal positions changed the position and angle of the visual streak in the retina I was messing with, and that's relevant for my goals

On Wed, Jun 17, 2020, 23:53 Brian Cohn notifications@github.com wrote:

I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt https://github.com/davidcsterratt ?

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The angle/orientation of the visual streak is expected to change when shifting the dorsal landmark, i.e. it is very important to have a reliable landmark for dorsal. What else is changing besides the orientation of the streak?

On Thu, Jun 18, 2020 at 1:34 AM moonh3 notifications@github.com wrote:

I'm gonna disagree fromy experience. Shifting the dorsal and nasal positions changed the position and angle of the visual streak in the retina I was messing with, and that's relevant for my goals

On Wed, Jun 17, 2020, 23:53 Brian Cohn notifications@github.com wrote:

I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt https://github.com/davidcsterratt ?

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-- Lars Schmitz, PhD Associate Professor of Biology W.M. Keck Science Department Claremont McKenna, Pitzer, and Scripps Colleges schmitzlab.info

The way the retina gets stitched together changes with how the positions are marked sometimes. The current version of the code doesn't open retistruct and let you set nodes on your own- I had to poke around and see how the code shifts with manual input in the line designating coordinates. Little changes in the nasal position (like on the top or bottom of the cut placed to mark it) change the orientation of the visual streak, so it's hard to figure out what conclusions I can draw.

On Thu, Jun 18, 2020, 10:59 Lars Schmitz notifications@github.com wrote:

The angle/orientation of the visual streak is expected to change when shifting the dorsal landmark, i.e. it is very important to have a reliable landmark for dorsal. What else is changing besides the orientation of the streak?

On Thu, Jun 18, 2020 at 1:34 AM moonh3 notifications@github.com wrote:

I'm gonna disagree fromy experience. Shifting the dorsal and nasal positions changed the position and angle of the visual streak in the retina I was messing with, and that's relevant for my goals

On Wed, Jun 17, 2020, 23:53 Brian Cohn notifications@github.com wrote:

I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt https://github.com/davidcsterratt ?

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Yes, the shape and depth of tears can affect reconstruction and it is great you are testing reproducibility. From my experience, the major features of the maps do not change unless the tears had odd/deeply curved shapes that made the "triangulation" of the tear difficult. @Brian Cohn bcohn12@gmail.com we should make the tear definition as easy and versatile as possible. Thanks for pointing that out Hannah!

On Thu, Jun 18, 2020 at 11:10 AM moonh3 notifications@github.com wrote:

The way the retina gets stitched together changes with how the positions are marked sometimes. The current version of the code doesn't open retistruct and let you set nodes on your own- I had to poke around and see how the code shifts with manual input in the line designating coordinates. Little changes in the nasal position (like on the top or bottom of the cut placed to mark it) change the orientation of the visual streak, so it's hard to figure out what conclusions I can draw.

On Thu, Jun 18, 2020, 10:59 Lars Schmitz notifications@github.com wrote:

The angle/orientation of the visual streak is expected to change when shifting the dorsal landmark, i.e. it is very important to have a reliable landmark for dorsal. What else is changing besides the orientation of the streak?

On Thu, Jun 18, 2020 at 1:34 AM moonh3 notifications@github.com wrote:

I'm gonna disagree fromy experience. Shifting the dorsal and nasal positions changed the position and angle of the visual streak in the retina I was messing with, and that's relevant for my goals

On Wed, Jun 17, 2020, 23:53 Brian Cohn notifications@github.com wrote:

I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt https://github.com/davidcsterratt ?

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That's good to know where the program has limits. This retina was from a large eye and was very soft- it definitely has large, curved, and weird tears, sounds like I was testing a hard case!

On Fri, Jun 19, 2020, 12:55 Lars Schmitz notifications@github.com wrote:

Yes, the shape and depth of tears can affect reconstruction and it is great you are testing reproducibility. From my experience, the major features of the maps do not change unless the tears had odd/deeply curved shapes that made the "triangulation" of the tear difficult. @Brian Cohn bcohn12@gmail.com we should make the tear definition as easy and versatile as possible. Thanks for pointing that out Hannah!

On Thu, Jun 18, 2020 at 11:10 AM moonh3 notifications@github.com wrote:

The way the retina gets stitched together changes with how the positions are marked sometimes. The current version of the code doesn't open retistruct and let you set nodes on your own- I had to poke around and see how the code shifts with manual input in the line designating coordinates. Little changes in the nasal position (like on the top or bottom of the cut placed to mark it) change the orientation of the visual streak, so it's hard to figure out what conclusions I can draw.

On Thu, Jun 18, 2020, 10:59 Lars Schmitz notifications@github.com wrote:

The angle/orientation of the visual streak is expected to change when shifting the dorsal landmark, i.e. it is very important to have a reliable landmark for dorsal. What else is changing besides the orientation of the streak?

On Thu, Jun 18, 2020 at 1:34 AM moonh3 notifications@github.com wrote:

I'm gonna disagree fromy experience. Shifting the dorsal and nasal positions changed the position and angle of the visual streak in the retina I was messing with, and that's relevant for my goals

On Wed, Jun 17, 2020, 23:53 Brian Cohn notifications@github.com wrote:

I don't think changing the dorsal/nasal marke affects the reconstruction beyond just defining the axes. Is this correct in retistruct @davidcsterratt https://github.com/davidcsterratt ?

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Given the exact same set of marked up tears, whether you mark a dorsal or nasal point shouldn't change the reconstruction, just the orientation. However, if you change the sets of points in each tear, that will change the reconstruction, especially with tissue with an irregular edge. It's important to try to set the rim angle appropriately. There are two approaches: (i) try to infer the rim angle from measurements of an intact eye; (ii) Optimise the rim angle so as to minimise the reconstruction error. If the angle is away from its optimum, there are more likely to be areas of the reconstruction that are compressed or expanded (in the strain plot). Both approaches are in the original retistruct paper, which also has examples of "good" and "bad" reconstructions.

bc / retina

retina won't install #48