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[NET-117] Network Test Refactor (#11)
* Starting repository for quick-fix network test refactor over since I screwed up the commit history of the last one. * Added new tests for Network Tests * Added result class for new network tests and fixed some of the test classes * add unit tests for new test classes * reorganize methods in TestPool for readability * lots of edits to NetworkTestResult for methods. I don't think its going to work and need a night to think on it * remove a class i made to test a few things * fixed NetworkTestResult to account for different test methods * did a better job with NetworkTestResult and tests. now its ready to interface with testpool and resultrank * start fixing up testpool and result rank. * added unit tests for NetworkTestResult * this seems way too easy. * copied lots of files needed for permutations and test/result running. Will modify later. Tests run all the way through. * lots of work on network test results and the result app front to get them to interact nicely. some work on resultpool, too * first draft of new class for plotting results parameters. * first batch of plotting tools made. not very pleased, but what can you do * bug squash to get no permutations to display figures * got most of the interfaces and even some of the plotting done. switching to 125 * trying to fix input problems with similar names * Revert "trying to fix input problems with similar names" This reverts commit 291327d. * had to fix bringing in input options due to them being used for plotting and not just testing. grrrr * Add cohens d test * within net pair plotting * fix some code to be more concise * fix some code to be more concise * changed display name for results * added chord plotter and trying to integrate it into no permutations * fixing some chord plotting and adding in trimatrix * fixes for all chords * added comments and some rearrange * added edge tests back that were lost * rewrite network tests tests * Added some unit tests and fixed a few errors * moved a lot of the plotting to seperate functions * Moved plotting into separate functions for hopefully more readability * just a few cleanups * added a test for result rank * added convergence plotting functions/methods * rename some variables * formatting and comments * Added MatrixPlot in * fixed plotting bugs * bug fixes * cleaned up some code and bug fixes * remove outdated tests * Tried to clean up and organize better. Still messy * Added error check to ensure both limit values are input and not none or one * network level chords working * remove two unneeded files * Attempting to get edge chord plotting working * chordplot used in all chord plotting instead of old function * Comments and documentation of chordplot * just some comment refining * integrate chordplot class into net refactor * touch up on formatting * Create development branch. Add initial error logging function * added caption to colorbar for trimatrix plots * added caption to colorbar for trimatrix plots * fixed export yml and python app * trying to fix yml * fixed export and action commit added export files remove matlab folder * [NET-148] Statistical Rank of refactored Network Test Results (#7) * Fix bug in merge function of PermBase when taking single result. Now takes either single result or cell array * NET53 ChordPlot Class (#5) * network level chords working * remove two unneeded files * Attempting to get edge chord plotting working * chordplot used in all chord plotting instead of old function * Comments and documentation of chordplot * just some comment refining * remove commented lines * Create export-mlapp-files.yml * NET-149 Save figures as svg (#6) * add svg option to save figure * remove useless file * remove comment marks * added code to rank by stat. need to fix fron * fixed export yml and python app fixed export yml and python app trying to fix yml * fixed many many conflicts between old network system and new remove unneeded sort * fix merge and squash conflicts * still trying to get this export to work * trying to fix export issues * Add Changes * Update export-mlapp-files.yml * Exported mlapp files * removed old network test folder --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * split resultrank to functions and rewrite tests * added script for tests runner. may not need * Update export-mlapp-files.yml added exit 0 on commit to hopefully stop error * trying to create test runner to make up for mathworks rigid workflows and cludges * Create run_matlab_tests.yml * Update run_matlab_tests.yml * fixing some tests * Update run_matlab_tests.yml * change script to function * Update run_matlab_tests.yml * trying to find magnitude error * Update run_matlab_tests.yml * add rounding in for results as largest offage was 10^-13 * coverage report works. damn. * Exported mlapp files * fixed up testpool to work with new networktestresult * remove accidentally save file * fixed NLAResult * remove coverage report from tests local * Exported mlapp files * fixes for testpool and nlaresult * fixed set up of permutation test in unittest * Exported mlapp files * remove unused binary search * fix deleted file * remove ranking test script --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com>
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‎+nla/+edge/+result/Base.m‎

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,10 @@ function output(obj, net_atlas, flags, prob_label)
4040
matrix_plot.displayImage();
4141
w = matrix_plot.image_dimensions("image_width");
4242
h = matrix_plot.image_dimensions("image_height");
43-
%
43+
44+
if ~isfield(flags, 'display_sig')
45+
flags.display_sig = true;
46+
end
4447
if flags.display_sig
4548
if ~exist('prob_label', 'var')
4649
prob_label = [sprintf('Edge-level Significance (P < %g)', obj.prob_max), prob_label_appended];

‎+nla/+edge/unittests/EdgeTestsTest.m‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
classdef EdgeTestsTest < matlab.unittest.TestCase
2+
3+
properties
4+
variables
5+
end
6+
7+
methods (TestClassSetup)
8+
function loadTestData(testCase)
9+
testCase.variables = load("edgeTestInputStruct.mat");
10+
end
11+
end
12+
13+
methods (TestClassTeardown)
14+
function clearTestData(testCase)
15+
clear
16+
end
17+
end
18+
19+
methods (Test)
20+
function kendallBTest(testCase)
21+
import nla.edge.test.KendallB
22+
% Your guess is as good as mine on why I need the full path
23+
% here and not above
24+
load(fullfile("+nla", "+edge", "unittests", "edgeKendallBResult.mat"), "result");
25+
kendallB = KendallB();
26+
expected = kendallB.run(testCase.variables.input_struct);
27+
testCase.verifyEqual(round(result.coeff.v, 6), round(expected.coeff.v, 6));
28+
end
29+
30+
function pearsonTest(testCase)
31+
import nla.edge.test.Pearson
32+
load(fullfile("+nla", "+edge", "unittests", "edgePearsonResult.mat"), "result");
33+
pearson = Pearson();
34+
expected = pearson.run(testCase.variables.input_struct);
35+
testCase.verifyEqual(round(result.coeff.v, 6), round(expected.coeff.v, 6));
36+
end
37+
38+
function spearmanTest(testCase)
39+
import nla.edge.test.Spearman
40+
load(fullfile("+nla", "+edge", "unittests", "edgeSpearmanResult.mat"), "result");
41+
spearman = Spearman();
42+
expected = spearman.run(testCase.variables.input_struct);
43+
testCase.verifyEqual(round(result.coeff.v, 6), round(expected.coeff.v, 6));
44+
end
45+
46+
function spearmanEstimatorTest(testCase)
47+
import nla.edge.test.SpearmanEstimator
48+
load(fullfile("+nla", "+edge", "unittests", "edgeSpearmanEstimatorResult.mat"), "result");
49+
spearman_estimator = SpearmanEstimator();
50+
expected = spearman_estimator.run(testCase.variables.input_struct);
51+
testCase.verifyEqual(round(result.coeff.v, 6), round(expected.coeff.v, 6));
52+
end
53+
end
54+
end

‎+nla/+edge/unittests/edgeKendallBResult.mat‎

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‎+nla/+edge/unittests/edgePearsonResult.mat‎

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‎+nla/+edge/unittests/edgeSpearmanEstimatorResult.mat‎

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‎+nla/+edge/unittests/edgeSpearmanResult.mat‎

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‎+nla/+edge/unittests/edgeTestInputStruct.mat‎

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‎+nla/+gfx/+plots/MatrixPlot.m‎

Lines changed: 97 additions & 32 deletions
Original file line numberDiff line numberDiff line change
@@ -30,6 +30,7 @@
3030
axes % The axes of the plot
3131
image_display % The actual displayed values
3232
color_bar % The colorbar
33+
colorbar_contextmenu % The right click menu for the colorbar
3334
end
3435

3536
properties (Dependent)
@@ -289,9 +290,19 @@ function addCallback(obj, x)
289290
end
290291
end
291292

292-
function obj = embiggenMatrix(obj)
293+
function obj = embiggenMatrix(obj, varargin)
293294
% Enlarges data points of matrix for easier viewing. Also adds the network colorbars to the left axis and bottom axis.
294-
import nla.gfx.colorChunk nla.gfx.MatrixType nla.gfx.valToColor nla.gfx.drawLine
295+
import nla.gfx.colorChunk nla.gfx.MatrixType nla.gfx.drawLine
296+
297+
% If there are no inputs (like initial rendering) then we use defaults
298+
% If there were inputs, that means we're scaling the colorbar.
299+
if isempty(varargin)
300+
upper_value = obj.upper_limit;
301+
lower_value = obj.lower_limit;
302+
else
303+
upper_value = str2double(varargin{2});
304+
lower_value = str2double(varargin{1});
305+
end
295306
number_of_networks = obj.number_networks;
296307
dimensions = obj.image_dimensions;
297308
network_matrix = obj.network_matrix;
@@ -313,12 +324,7 @@ function addCallback(obj, x)
313324
chunk_height = numel(network_indexes) * obj.elementSize();
314325

315326
% Left side of matrix color bars
316-
top = position_y;
317-
bottom = position_y + chunk_height;
318-
left = dimensions("offset_x") + 2;
319-
right = dimensions("offset_x") + dimensions("label_size") + 1;
320-
obj.image_display.CData(top:bottom, left:right+1, :) = colorChunk(obj.networks(network).color, chunk_height + 1, dimensions("label_size") + 1);
321-
obj = obj.drawLeftLinesOnLabels(top, bottom, left, right);
327+
obj.drawLeftLinesOnLabels(position_y, chunk_height, dimensions, network);
322328

323329
position_x = dimensions("label_size") + dimensions("offset_x") + 3;
324330
starting_x = position_x;
@@ -336,34 +342,33 @@ function addCallback(obj, x)
336342

337343
chunk_width = numel(x_index) * obj.elementSize();
338344

339-
% Fill the chunk with a color mapped to its value
345+
% Get color for chunks
340346
chunk_raw = matrix_as_matrix(network_indexes, x_index);
341-
chunk = valToColor(chunk_raw, obj.lower_limit, obj.upper_limit, obj.color_map);
342-
chunk(isnan(chunk_raw)) = NaN; % puts all NaNs back removed with valToColor
347+
chunk_color = obj.getChunkColor(chunk_raw, upper_value, lower_value);
343348

344349
% Apply colors to chunks
345-
obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x:position_x + chunk_width - 1, :) =...
346-
repelem(chunk, obj.elementSize(), obj.elementSize());
347-
obj.image_display.CData(position_y + chunk_height, position_x:position_x + chunk_width - 1, :) =...
348-
repelem(chunk(size(chunk, 1), 1:size(chunk, 2), :), 1, obj.elementSize());
349-
obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
350-
repelem(chunk(1:size(chunk, 1), size(chunk, 2), :), obj.elementSize(), 1);
350+
obj.applyColorToData(position_x, position_y, chunk_height, chunk_width, chunk_color);
351351

352352
% plot signifance marker
353353
if ~isequal(obj.marked_networks, false) && isequal(obj.marked_networks(network, x), true)
354354
obj.plotSignificanceMark(chunk_width, chunk_height, position_x, position_y);
355355
end
356356

357357
if ~isequal(obj.network_clicked_callback, false)
358-
obj.network_dimensions(x, network, :) = [position_x, position_x + chunk_width - 1, position_y, position_y + chunk_height - 1];
358+
obj.network_dimensions(x, network, :) = [position_x, position_x + chunk_width - 1,...
359+
position_y, position_y + chunk_height - 1];
359360
end
360361
% Add callbacks to all the squares
361-
obj.addCallback(drawLine(obj.axes, [position_x - 1, position_x - 1], [position_y, position_y + chunk_height + 1]));
362-
obj.addCallback(drawLine(obj.axes, [position_x - 2, position_x + chunk_width - 1], [position_y + chunk_height, position_y + chunk_height]));
362+
obj.addCallback(drawLine(obj.axes, [position_x - 1, position_x - 1],...
363+
[position_y, position_y + chunk_height + 1]));
364+
obj.addCallback(drawLine(obj.axes, [position_x - 2, position_x + chunk_width - 1],...
365+
[position_y + chunk_height, position_y + chunk_height]));
363366

364367
if x == maximum_x && obj.matrix_type == MatrixType.TRIMATRIX && ~isequal(network_matrix, false)
365-
obj.addCallback(drawLine(obj.axes, [position_x + chunk_width, position_x + chunk_width], [position_y - 1, position_y + chunk_height + 1]));
366-
obj.addCallback(drawLine(obj.axes, [position_x - 2, position_x + chunk_width], [position_y - 1, position_y - 1]));
368+
obj.addCallback(drawLine(obj.axes, [position_x + chunk_width, position_x + chunk_width],...
369+
[position_y - 1, position_y + chunk_height + 1]));
370+
obj.addCallback(drawLine(obj.axes, [position_x - 2, position_x + chunk_width],...
371+
[position_y - 1, position_y - 1]));
367372
end
368373

369374
% Is this the last network of a TriMatrix. Then we're done and need to add the bottom
@@ -381,16 +386,24 @@ function addCallback(obj, x)
381386
end
382387
position_y = position_y + chunk_height + 1;
383388
end
384-
389+
385390
if obj.matrix_type == MatrixType.TRIMATRIX && ~network_matrix
386-
drawLine(obj.axes, [starting_x - 1, position_x - 1], [starting_y - 3 + obj.elementSize(), position_y - 2], 'w');
387-
drawLine(obj.axes, [starting_x - 2, position_x - 1], [starting_y - 3 + obj.elementSize(), position_y - 1]);
391+
drawLine(obj.axes, [starting_x - 1, position_x - 1],...
392+
[starting_y - 3 + obj.elementSize(), position_y - 2], 'w');
393+
drawLine(obj.axes, [starting_x - 2, position_x - 1],...
394+
[starting_y - 3 + obj.elementSize(), position_y - 1]);
388395
end
389396
end
390397

391-
function obj = drawLeftLinesOnLabels(obj, top, bottom, left, right)
398+
function drawLeftLinesOnLabels(obj, position_y, chunk_height, dimensions, network)
392399
% Draws the left side lines on the plot
393-
import nla.gfx.drawLine
400+
import nla.gfx.drawLine nla.gfx.colorChunk
401+
402+
top = position_y;
403+
bottom = position_y + chunk_height;
404+
left = dimensions("offset_x") + 2;
405+
right = dimensions("offset_x") + dimensions("label_size") + 1;
406+
obj.image_display.CData(top:bottom, left:right+1, :) = colorChunk(obj.networks(network).color, chunk_height + 1, dimensions("label_size") + 1);
394407

395408
drawLine(obj.axes, [left - 1, right], [top - 1, top - 1]);
396409
drawLine(obj.axes, [left - 1, right], [bottom, bottom]);
@@ -462,11 +475,23 @@ function createLegend(obj)
462475
display_legend_width, display_legend_height];
463476
end
464477

465-
function createColorbar(obj)
478+
function createColorbar(obj, varargin)
466479
% Creates the colorbar
467480
% Annoyance: obj.color_map is a property, colormap is a command. Same with color_bar and colorbar
481+
482+
% If there are arguments, it means that this came from changing the colorbar. If not, using defaults
483+
if isempty(varargin)
484+
upper_value = obj.upper_limit;
485+
lower_value = obj.lower_limit;
486+
else
487+
obj.color_bar.TickLabels = {};
488+
obj.color_bar.Ticks = [];
489+
upper_value = str2double(varargin{2});
490+
lower_value = str2double(varargin{1});
491+
end
492+
468493
if obj.discrete_colorbar
469-
number_of_ticks = double(obj.upper_limit - obj.lower_limit);
494+
number_of_ticks = double(upper_value - lower_value);
470495
display_colormap = obj.color_map(floor((size(obj.color_map, 1) - 1) * [0:number_of_ticks] ./ number_of_ticks) + 1, :);
471496
display_colormap = repelem(display_colormap, 2, 1);
472497
display_colormap = display_colormap(2:((number_of_ticks + 1) * 2 - 1), :);
@@ -477,16 +502,16 @@ function createColorbar(obj)
477502
end
478503

479504
obj.color_bar = colorbar(obj.axes);
480-
505+
481506
ticks = [0:number_of_ticks];
482507
obj.color_bar.Ticks = double(ticks) ./ number_of_ticks;
483508

484509
labels = {};
485510
for tick = ticks
486-
labels{tick + 1} = sprintf("%.2g", obj.lower_limit + (tick * ((double(obj.upper_limit - obj.lower_limit) / number_of_ticks))));
511+
labels{tick + 1} = sprintf("%.2g", lower_value + (tick * ((double(upper_value - lower_value) / number_of_ticks))));
487512
end
488513
obj.color_bar.TickLabels = labels;
489-
514+
490515
dimensions = obj.image_dimensions;
491516
obj.color_bar.Units = 'pixels';
492517
obj.color_bar.Location = 'east';
@@ -495,8 +520,48 @@ function createColorbar(obj)
495520
obj.color_bar.Position = [obj.color_bar.Position(1) - dimensions("offset_x"),...
496521
obj.color_bar.Position(2) + dimensions("offset_y"), obj.colorbar_width,...
497522
dimensions("image_height") - (dimensions("offset_y") * 2) - 20];
523+
obj.color_bar.Title.Position(2) = 0 - dimensions("offset_y") * 2 / 3;
524+
obj.color_bar.Title.String = sprintf("Click to\nchange scale\n");
525+
obj.color_bar.Title.FontSize = 7;
526+
527+
% Enables callback for clicking on colorbar to scale data
528+
set(obj.color_bar, 'ButtonDownFcn', @changeColorLimits)
498529

499530
caxis(obj.axes, [0, 1]);
531+
532+
533+
% Callback for clicking on the colorbar.
534+
function changeColorLimits(~, ~)
535+
prompt = {"Enter Lower Limit: ", "Enter Upper Limit: "};
536+
upper_limit_inner = obj.color_bar.TickLabels(end);
537+
lower_limit_inner = obj.color_bar.TickLabels(1);
538+
current_limits = {lower_limit_inner{1}, upper_limit_inner{1}};
539+
new_limits = inputdlg(prompt, "Colorbar Limits", 1, current_limits);
540+
% If "cancel" is pressed or both values deleted use defaults
541+
if isempty(new_limits) || isempty(new_limits{1}) || isempty(new_limits{2})
542+
obj.embiggenMatrix();
543+
obj.createColorbar();
544+
else
545+
obj.embiggenMatrix(new_limits{1}, new_limits{2});
546+
obj.createColorbar(new_limits{1}, new_limits{2});
547+
end
548+
end
549+
end
550+
551+
function chunk_color = getChunkColor(obj, chunk_raw, upper_value, lower_value)
552+
% Get color for the chunk (square)
553+
chunk_color = nla.gfx.valToColor(chunk_raw, lower_value, upper_value, obj.color_map);
554+
chunk_color(isnan(chunk_raw)) = NaN; % puts all NaNs back removed with valToColor
555+
end
556+
557+
function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width, chunk_color)
558+
% Fill in the chunks (squares) with color
559+
obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x:position_x + chunk_width - 1, :) =...
560+
repelem(chunk_color, obj.elementSize(), obj.elementSize());
561+
obj.image_display.CData(position_y + chunk_height, position_x:position_x + chunk_width - 1, :) =...
562+
repelem(chunk_color(size(chunk_color, 1), 1:size(chunk_color, 2), :), 1, obj.elementSize());
563+
obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
564+
repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
500565
end
501566
end
502567
end

‎+nla/+gfx/ProbPlotMethod.m‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
classdef ProbPlotMethod
22
enumeration
3-
DEFAULT, LOG, NEG_LOG_10
3+
DEFAULT, LOG, NEG_LOG_10, STATISTIC
44
end
55
end

‎+nla/+logging/saveErrorObjInTimestampedMatfile.m‎

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
function saveErrorObjInTimestampedMatfile(saveFolder, errorObj)
2+
3+
nowTime = datetime;
4+
nowTime.Format = 'yyyyMMdd-hhmmss';
5+
6+
errFilename = sprintf('error_%s.mat',nowTime);
7+
errFullFilename = fullfile(saveFolder, errFilename);
8+
9+
save(errFullFilename, 'errorObj');
10+
11+
end

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