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jengrieshjengriesh
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Stdev_row_extraction eye alignment and added hard coded scale for Adhan data
1 parent 1d61249 commit d006bb6

2 files changed

Lines changed: 98 additions & 20 deletions

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‎.gitignore‎

Lines changed: 71 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1 +1,72 @@
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*.asv
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test_data/1 MAP input/72824906.tif
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test_data/1 MAP input/72824906_coords.csv
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test_data/1 MAP input/74787803.tif
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test_data/1 MAP input/74787803_coords.csv
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test_data/1 MAP input/7657484.tif
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test_data/1 MAP input/7657484_coords.csv
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test_data/1 MAP input/LUT (1) for PCD TIFs.csv
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test_data/1 MAP output/72824906_bounddensity_matrix_13-Nov-2023.csv
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test_data/1 MAP output/72824906_coords_bound_map_13-Nov-2023_Bound_Density_fig.png
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test_data/1 MAP output/72824906_coords_bound_map_13-Nov-2023_Bound_Density_marked.tif
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test_data/1 MAP output/72824906_coords_bound_map_13-Nov-2023_Bound_Density_raw5.tif
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test_data/1 MAP output/74787803_bounddensity_matrix_13-Nov-2023.csv
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test_data/1 MAP output/74787803_coords_bound_map_13-Nov-2023_Bound_Density_fig.png
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test_data/1 MAP output/74787803_coords_bound_map_13-Nov-2023_Bound_Density_marked.tif
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test_data/1 MAP output/74787803_coords_bound_map_13-Nov-2023_Bound_Density_raw5.tif
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test_data/1 MAP output/7657484_bounddensity_matrix_13-Nov-2023.csv
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test_data/1 MAP output/7657484_coords_bound_map_13-Nov-2023_Bound_Density_fig.png
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test_data/1 MAP output/7657484_coords_bound_map_13-Nov-2023_Bound_Density_marked.tif
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test_data/1 MAP output/7657484_coords_bound_map_13-Nov-2023_Bound_Density_raw5.tif
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test_data/2 PCD_CDC input/72824906_bounddensity_matrix_13-Nov-2023.csv
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test_data/2 PCD_CDC input/74787803_bounddensity_matrix_13-Nov-2023.csv
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test_data/2 PCD_CDC input/7657484_bounddensity_matrix_13-Nov-2023.csv
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test_data/2 PCD_CDC input/LUT (1) for PCD TIFs.csv
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test_data/2 PCD_CDC output/72824906_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80.tif
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test_data/2 PCD_CDC output/72824906_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80_only.tif
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test_data/2 PCD_CDC output/72824906_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_contour_80.csv
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test_data/2 PCD_CDC output/72824906_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_marked.tif
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test_data/2 PCD_CDC output/74787803_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80.tif
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test_data/2 PCD_CDC output/74787803_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80_only.tif
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test_data/2 PCD_CDC output/74787803_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_contour_80.csv
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test_data/2 PCD_CDC output/74787803_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_marked.tif
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test_data/2 PCD_CDC output/7657484_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80.tif
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test_data/2 PCD_CDC output/7657484_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_80_only.tif
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test_data/2 PCD_CDC output/7657484_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_contour_80.csv
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test_data/2 PCD_CDC output/7657484_bounddensity_matrix_13-Nov-2023.csv_bestFitEllipse_marked.tif
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test_data/2 PCD_CDC output/Analysis Summary/All_max_coords_80_percentile_13-Nov-2023.csv
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test_data/2 PCD_CDC output/Analysis Summary/PCD_CDC_Analysis_Summary_13-Nov-2023.csv
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test_data/3 Ellipse_contour input/325042804_bounddensity_matrix_13-Nov-2023.csv
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test_data/3 Ellipse_contour input/712805202_bounddensity_matrix_13-Nov-2023.csv
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test_data/3 Ellipse_contour input/LUT (1) for PCD TIFs.csv
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test_data/3 Ellipse_contour output/325042804_bounddensity_matrix_13-Nov-2023.csv
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test_data/3 Ellipse_contour output/325042804_combined_contours.csv
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test_data/3 Ellipse_contour output/325042804_combined_contours.tif
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test_data/3 Ellipse_contour output/712805202_combined_contours.csv
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test_data/3 Ellipse_contour output/712805202_combined_contours.tif
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test_data/3 Ellipse_contour output/EllipseCenterCoords_13-Nov-2023.csv
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test_data/3 Ellipse_contour output/EllipseCenterCoords_28-Nov-2023.csv
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test_data/4 Compare_windows input/CDC_Table.csv
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test_data/4 Compare_windows input/CDC_Table.xlsx
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test_data/4 Compare_windows input/Compare_Observers_Ellipse_Input_Instructions.docx
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test_data/4 Compare_windows input/Compare_Script_Instructions.docx
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test_data/4 Compare_windows input/PCD_Table.csv
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test_data/4 Compare_windows input/PCD_Table.xlsx
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test_data/4 Compare_windows output/72824906.fig
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test_data/4 Compare_windows output/72824906.tif
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test_data/4 Compare_windows output/72824906_95CI_CDC.fig
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test_data/4 Compare_windows output/72824906_95CI_CDC.tif
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test_data/4 Compare_windows output/72824906_95CI_PCD.fig
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test_data/4 Compare_windows output/72824906_95CI_PCD.tif
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test_data/4 Compare_windows output/74787803.fig
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test_data/4 Compare_windows output/74787803.tif
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test_data/4 Compare_windows output/74787803_95CI_CDC.fig
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test_data/4 Compare_windows output/74787803_95CI_CDC.tif
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test_data/4 Compare_windows output/74787803_95CI_PCD.fig
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test_data/4 Compare_windows output/74787803_95CI_PCD.tif
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test_data/4 Compare_windows output/7657484.fig
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test_data/4 Compare_windows output/7657484.tif
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test_data/4 Compare_windows output/7657484_95CI_CDC.fig
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test_data/4 Compare_windows output/7657484_95CI_CDC.tif
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test_data/4 Compare_windows output/7657484_95CI_PCD.fig
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test_data/4 Compare_windows output/7657484_95CI_PCD.tif

‎MAP_Analysis/Stdev_Row_Extraction.m‎

Lines changed: 27 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212
root_path_raw = uigetdir('.','Select directory containing raw stdev csv analyses');
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1414
% get all the file paths that we are interested in in each of the folders
15-
[file_paths_raw] = read_folder_contents_rec(root_path_raw, 'csv', 'raw'); % used for stdev map
15+
[file_paths_raw] = read_folder_contents_rec(root_path_raw, 'csv', 'MINUS'); % used for stdev map
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% [file_paths_raw] = read_folder_contents_rec(root_path_raw, 'csv','coeffvar'); % used for CoV
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% select master cdc file
@@ -63,7 +63,8 @@
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for i=1:size(file_paths_raw,1)
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% get the scale factor
66-
scale = LUT_data{i,10}; % umpp
66+
scale = 0.242;%LUT_data{i,10}; % umpp % hard coded for Iniya's data that is all scaled to a common scale
67+
eye = LUT_data{i,2};
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6869
% load in the stdev data and master cdc coords
6970
stdev_data = load(file_paths_raw{i});
@@ -105,7 +106,13 @@
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xy_h_converted = zeros(length(data.x_h), 2);
106107
xy_v_converted = zeros(length(data.x_v), 2);
107108
for j=1:length(data.x_h)
108-
xy_h_converted(j,1) = (data.x_h(j) - master_cdc_y) * scale; % now in um
109+
% check what eye - if left flip sign so that temporal is negative -
110+
% need eye from the lut file to do this
111+
if strcmp(eye,'OD')
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xy_h_converted(j,1) = (data.x_h(j) - master_cdc_y) * scale; % now in um
113+
else
114+
xy_h_converted(j,1) = -(data.x_h(j) - master_cdc_y) * scale; % now in um
115+
end
109116
xy_v_converted(j,1) = (data.x_v(j) - master_cdc_x) * scale; % now in um
110117
xy_h_converted(j,2) = data.y_h(j);
111118
xy_v_converted(j,2) = data.y_v(j);
@@ -180,24 +187,24 @@
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count_v = 0; % reset value
181188
end
182189

183-
% %% graph individual plots
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% % basic plot of the individual results
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% figure(1)
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% plot(xy_h_converted(:,1), xy_h_converted(:,2));
187-
% title("Horizontal Stdev Through CDC Point");
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% xlabel("Microns");
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% ylabel("Standard Deviation");
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% hold on
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%
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% figure(2)
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% plot(xy_v_converted(:,1), xy_v_converted(:,2));
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% title("Vertical Stdev Through CDC Point");
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% xlabel("Microns");
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% ylabel("Standard Deviation");
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% hold on
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%% graph individual plots
191+
% basic plot of the individual results
192+
figure(1)
193+
plot(xy_h_converted(:,1), xy_h_converted(:,2));
194+
title("Horizontal Stdev Through CDC Point");
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xlabel("Microns");
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ylabel("Standard Deviation");
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hold on
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199+
figure(2)
200+
plot(xy_v_converted(:,1), xy_v_converted(:,2));
201+
title("Vertical Stdev Through CDC Point");
202+
xlabel("Microns");
203+
ylabel("Standard Deviation");
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hold on
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%% format output and save to file
200-
output_fname_h = strcat(num2str(master_cdc{i,1}), '_Horizontal_Bin_Analysis_', string(datetime('now','TimeZone','local','Format','yyyyMMdd')), '.csv');
207+
output_fname_h = strcat(master_cdc{i,1}, '_Horizontal_Bin_Analysis_', string(datetime('now','TimeZone','local','Format','yyyyMMdd')), '.csv');
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% setting up for table creation
203210
BinCenter_h = num2cell(bin_centers_h');
@@ -214,7 +221,7 @@
214221
all_h_data{i} = {bin_centers_h', averages_h};
215222

216223

217-
output_fname_v = strcat(num2str(master_cdc{i,1}), '_Vertical_Bin_Analysis_', string(datetime('now','TimeZone','local','Format','yyyyMMdd')), '.csv');
224+
output_fname_v = strcat(master_cdc{i,1}, '_Vertical_Bin_Analysis_', string(datetime('now','TimeZone','local','Format','yyyyMMdd')), '.csv');
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% setting up for table creation
220227
BinCenter_v = num2cell(bin_centers_v');

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