From 580833ed4af8a821f5e50a4a2c7a01351c4ed02f Mon Sep 17 00:00:00 2001
From: layton aho <aho.layton@gmail.com>
Date: Fri, 31 Jan 2025 10:56:04 -0500
Subject: [PATCH] Remove kymo language
---
readme.md | 2 +-
src/MATLAB/phantomKymograph/createPhantom.m | 4 ++--
src/MATLAB/phantomKymograph/createSyntheticDataset.m | 4 ++--
src/MATLAB/phantomKymograph/getPhantomClipLimits.m | 2 +-
src/MATLAB/phantomKymograph/goFigure.m | 6 +++---
src/MATLAB/phantomKymograph/goSyntheticDataset.m | 2 +-
src/MATLAB/phantomKymograph/goSyntheticSSF.m | 6 +++---
7 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/readme.md b/readme.md
index d9790a8..73d3cc9 100644
--- a/readme.md
+++ b/readme.md
@@ -54,7 +54,7 @@ To create a new synethetic dataset:
- phantomVelocity_mu: the different mean velocity values per class i.e., the number of means determines the number of classes.
- phantomVelocity_sigma: the standard deviation for velocity per class.
- numOutput: how many phantom images to generate per class.
-2. Run phantomVelocitySS\goFigure.m, specifying the saved .mat file as the input.
+2. Run phantomVelocitySSF\goFigure.m, specifying the saved .mat file as the input.
## Notes
1. The NCD code uses the [FLIF](https://flif.info/) compression library. The thunker file for the FLIF library was generated on Ubuntu 22.04 and **may not work** on other Unix platforms.
diff --git a/src/MATLAB/phantomKymograph/createPhantom.m b/src/MATLAB/phantomKymograph/createPhantom.m
index b30bde5..7cae33e 100644
--- a/src/MATLAB/phantomKymograph/createPhantom.m
+++ b/src/MATLAB/phantomKymograph/createPhantom.m
@@ -1,4 +1,4 @@
-function phantomKymo = createPhantom(phSize,phTracks,phVel_mu,phVel_sigma)
+function phantomVelcocityOutput = createPhantom(phSize,phTracks,phVel_mu,phVel_sigma)
tmp = zeros(phSize,'uint8');
@@ -39,6 +39,6 @@ for i = 1:length(trackSrcPts)
end
-phantomKymo = tmp;
+phantomVelcocityOutput = tmp;
end
\ No newline at end of file
diff --git a/src/MATLAB/phantomKymograph/createSyntheticDataset.m b/src/MATLAB/phantomKymograph/createSyntheticDataset.m
index 9799c51..c046c80 100644
--- a/src/MATLAB/phantomKymograph/createSyntheticDataset.m
+++ b/src/MATLAB/phantomKymograph/createSyntheticDataset.m
@@ -10,7 +10,7 @@ for i = 1:length(datasetParameters.phantomVelocity_mu)
phVel_mu = datasetParameters.phantomVelocity_mu(i);
phVel_sigma = datasetParameters.phantomVelocity_sigma(i);
- for j = 1:datasetParameters.numKymos
+ for j = 1:datasetParameters.numOutput
tmp = [];
tmp.phantomName = strcat(num2str(i),'_',num2str(j));
@@ -19,7 +19,7 @@ for i = 1:length(datasetParameters.phantomVelocity_mu)
tmp.phantomSize = phSize;
tmp.numTracks = phTracks;
tmp.phantomVelocity = [phVel_mu;phVel_sigma];
- tmp.phantomKymo = createPhantom(phSize,phTracks,phVel_mu,phVel_sigma);
+ tmp.phantomVelocityOutput = createPhantom(phSize,phTracks,phVel_mu,phVel_sigma);
syntheticDataset = [syntheticDataset;tmp];
diff --git a/src/MATLAB/phantomKymograph/getPhantomClipLimits.m b/src/MATLAB/phantomKymograph/getPhantomClipLimits.m
index c8bbfc8..e25d3c2 100644
--- a/src/MATLAB/phantomKymograph/getPhantomClipLimits.m
+++ b/src/MATLAB/phantomKymograph/getPhantomClipLimits.m
@@ -1,7 +1,7 @@
function clipLimits = getPhantomClipLimits(syntheticDataset,targetChannel)
for ff = 1:length(syntheticDataset)
- im_ff = syntheticDataset(ff).phantomKymo(:,:,:,targetChannel);
+ im_ff = syntheticDataset(ff).phantomVelocityOutput(:,:,:,targetChannel);
kp = im_ff(find(im_ff));
diff --git a/src/MATLAB/phantomKymograph/goFigure.m b/src/MATLAB/phantomKymograph/goFigure.m
index b7d3fbd..7d7c972 100644
--- a/src/MATLAB/phantomKymograph/goFigure.m
+++ b/src/MATLAB/phantomKymograph/goFigure.m
@@ -2,9 +2,9 @@ load('sampleDataset_01.mat');
K = 3;
-tmp_xy(:,:,1) = squeeze(max(syntheticDataset(1).phantomKymo(:,:,:,1),[],2));
-tmp_xy(:,:,2) = squeeze(max(syntheticDataset(11).phantomKymo(:,:,:,1),[],2));
-tmp_xy(:,:,3) = squeeze(max(syntheticDataset(21).phantomKymo(:,:,:,1),[],2));
+tmp_xy(:,:,1) = squeeze(max(syntheticDataset(1).phantomVelocityOutput(:,:,:,1),[],2));
+tmp_xy(:,:,2) = squeeze(max(syntheticDataset(11).phantomVelocityOutput(:,:,:,1),[],2));
+tmp_xy(:,:,3) = squeeze(max(syntheticDataset(21).phantomVelocityOutput(:,:,:,1),[],2));
figure('Position',[300,200,900,300]);
layout1 = tiledlayout(1,3,'TileSpacing','compact','Padding','tight');
diff --git a/src/MATLAB/phantomKymograph/goSyntheticDataset.m b/src/MATLAB/phantomKymograph/goSyntheticDataset.m
index 7a241c1..c70cae0 100644
--- a/src/MATLAB/phantomKymograph/goSyntheticDataset.m
+++ b/src/MATLAB/phantomKymograph/goSyntheticDataset.m
@@ -6,7 +6,7 @@ synthDatasetParameters.phantomSize = [200,200,25];
synthDatasetParameters.phantomTracks = 10;
synthDatasetParameters.phantomVelocity_mu = [1,3,5];
synthDatasetParameters.phantomVelocity_sigma = [.5,.5,.5];
-synthDatasetParameters.numKymos = 50;
+synthDatasetParameters.numOutput = 50;
syntheticDataset = createSyntheticDataset(synthDatasetParameters);
diff --git a/src/MATLAB/phantomKymograph/goSyntheticSSF.m b/src/MATLAB/phantomKymograph/goSyntheticSSF.m
index 7278619..44e1132 100644
--- a/src/MATLAB/phantomKymograph/goSyntheticSSF.m
+++ b/src/MATLAB/phantomKymograph/goSyntheticSSF.m
@@ -21,14 +21,14 @@ parfor i=1:H
continue
end
- im_ff = syntheticDataset(ff).phantomKymo(:,:,:,targetChannel);
+ im_ff = syntheticDataset(ff).phantomVelocityOutput(:,:,:,targetChannel);
if ff == gg
d1 = SSF.ncd_ssf_volume(im_ff,im_ff);
dxx(i,j) = d1;
else
- im_ff = syntheticDataset(ff).phantomKymo(:,:,:,targetChannel);
- im_gg = syntheticDataset(gg).phantomKymo(:,:,:,targetChannel);
+ im_ff = syntheticDataset(ff).phantomVelocityOutput(:,:,:,targetChannel);
+ im_gg = syntheticDataset(gg).phantomVelocityOutput(:,:,:,targetChannel);
d1 = SSF.ncd_ssf_volume(im_ff,im_gg);
d2 = SSF.ncd_ssf_volume(im_gg,im_ff);
--
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