matlab(tdcs): scenario derivation + derived data export
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Experiments DB Dev
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function [S, meta] = tdcs_scenario_data(scenario)
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%TDCS_SCENARIO_DATA Build one merge/window scenario from the curated tDCS data.
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% [S, META] = TDCS_SCENARIO_DATA(SCENARIO) loads the curated 12-animal
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% table via TDCS_LOAD_DATA, applies the requested group-merge map from
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% TDCS_CONFIG, restricts to day <= maxDay per the scenario's window
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% suffix, adds mean-centered day covariates DAY_C / DAY_C2, and recodes
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% GROUP as a categorical with CFG.REF ('Electrode-Box-B2') as the FIRST
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% (reference) category via REORDERCATS. S is also written to
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% analysis/matlab/derived/<SCENARIO>.csv via WRITETABLE (the derived/
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% folder is created if it does not already exist).
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%
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% SCENARIO must be one of:
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% unmerged_full, unmerged_d0_10, mergeA2_full, mergeA2_d0_10,
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% mergeB2_full, mergeB2_d0_10
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%
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% The scenario name is split into:
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% - a merge key: 'unmerged' | 'mergeA2' | 'mergeB2', selecting which
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% containers.Map from TDCS_CONFIG (if any) to apply to relabel
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% GROUP. 'unmerged' applies no relabeling (identity) -- it is not
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% backed by a config map at all, since only the two "unknown"
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% conditions (Electrode-Box-A, Right-Electrode) are ever merge
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% targets, and the unmerged scenario reports them unmerged/as-is.
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% - a day window: '_full' -> maxDay = 26, '_d0_10' -> maxDay = 10.
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%
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% META is a struct with fields:
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% .mergeKey 'unmerged' | 'mergeA2' | 'mergeB2'
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% .maxDay 26 or 10
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% .isUnmerged true only when mergeKey == 'unmerged'
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[mergeKey, maxDay] = localParseScenario(scenario);
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cfg = tdcs_config();
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T = tdcs_load_data();
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switch mergeKey
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case 'unmerged'
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% Identity: no relabeling. An empty map means isKey(...) is
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% always false below, so every group passes through unchanged.
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mergeMap = containers.Map('KeyType', 'char', 'ValueType', 'char');
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case 'mergeA2'
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mergeMap = cfg.mergeA2;
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case 'mergeB2'
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mergeMap = cfg.mergeB2;
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otherwise
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error('tdcs_scenario_data:badScenario', ...
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'Unrecognized scenario "%s".', scenario);
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end
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% Relabel GROUP per the merge map. Groups that are not a key in the map
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% (e.g. Naive, Electrode-Box-A2, Electrode-Box-B2 under mergeA2/mergeB2,
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% or every group under the empty 'unmerged' map) are left unchanged --
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% only the two "unknown" conditions are ever merge-map keys.
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groupCell = cellstr(T.group);
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for i = 1:numel(groupCell)
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if isKey(mergeMap, groupCell{i})
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groupCell{i} = mergeMap(groupCell{i});
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end
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end
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% Day window (applied after relabeling, before centering, per the plan).
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dayMask = T.day <= maxDay;
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S = T(dayMask, :);
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groupCell = groupCell(dayMask);
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% Recode GROUP as categorical with cfg.ref first (the GLME reference
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% level). Only categories actually present after merge+window survive.
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S.group = categorical(groupCell);
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allCats = categories(S.group);
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otherCats = allCats(~strcmp(allCats, cfg.ref));
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S.group = reordercats(S.group, [{cfg.ref}; otherCats]);
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% Mean-centered day covariates, computed on the post-window data.
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S.day_c = S.day - mean(S.day);
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S.day_c2 = S.day_c .^ 2;
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% Persist the derived scenario table.
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thisDir = fileparts(mfilename('fullpath'));
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derivedDir = fullfile(thisDir, 'derived');
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if ~exist(derivedDir, 'dir')
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mkdir(derivedDir);
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end
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outFile = fullfile(derivedDir, [char(scenario) '.csv']);
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writetable(S, outFile);
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meta = struct();
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meta.mergeKey = mergeKey;
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meta.maxDay = maxDay;
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meta.isUnmerged = strcmp(mergeKey, 'unmerged');
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end
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function [mergeKey, maxDay] = localParseScenario(scenario)
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%LOCALPARSESCENARIO Split "<mergeKey>_full" / "<mergeKey>_d0_10" apart.
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scenario = char(scenario);
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if endsWith(scenario, '_full')
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maxDay = 26;
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mergeKey = scenario(1:end - numel('_full'));
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elseif endsWith(scenario, '_d0_10')
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maxDay = 10;
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mergeKey = scenario(1:end - numel('_d0_10'));
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else
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error('tdcs_scenario_data:badScenario', ...
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'Scenario "%s" does not end in "_full" or "_d0_10".', scenario);
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end
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if ~ismember(mergeKey, {'unmerged', 'mergeA2', 'mergeB2'})
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error('tdcs_scenario_data:badScenario', ...
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'Scenario "%s" has unrecognized merge key "%s".', scenario, mergeKey);
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end
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end
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classdef tScenarioData < matlab.unittest.TestCase
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%TSCENARIODATA Tests for tdcs_scenario_data (Task 2).
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%
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% Authored per TDD: written before tdcs_scenario_data.m existed, so
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% it is expected to fail until the function is implemented. As of
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% this commit MATLAB is not licensed in this environment, so this
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% suite has been authored and reviewed by hand but has NOT been
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% executed. Expected per-scenario subject-per-group counts were
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% hand-derived from the Task 1 curated counts (Naive=4,
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% Electrode-Box-A2=3, Electrode-Box-B2=3, Electrode-Box-A=1,
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% Right-Electrode=1) plus each scenario's merge map, and cross-
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% checked against task-2-brief.md's table (see task-2-report.md).
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properties (TestParameter)
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scenarioCase = struct( ...
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'unmerged_full', struct( ...
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'scenario', 'unmerged_full', ...
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'maxDay', 26, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A', 'Electrode-Box-A2', ...
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'Electrode-Box-B2', 'Naive', 'Right-Electrode'}, ...
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{1, 3, 3, 4, 1})), ...
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'unmerged_d0_10', struct( ...
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'scenario', 'unmerged_d0_10', ...
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'maxDay', 10, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A', 'Electrode-Box-A2', ...
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'Electrode-Box-B2', 'Naive', 'Right-Electrode'}, ...
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{1, 3, 3, 4, 1})), ...
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'mergeA2_full', struct( ...
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'scenario', 'mergeA2_full', ...
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'maxDay', 26, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A2', 'Electrode-Box-B2', 'Naive'}, ...
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{4, 4, 4})), ...
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'mergeA2_d0_10', struct( ...
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'scenario', 'mergeA2_d0_10', ...
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'maxDay', 10, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A2', 'Electrode-Box-B2', 'Naive'}, ...
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{4, 4, 4})), ...
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'mergeB2_full', struct( ...
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'scenario', 'mergeB2_full', ...
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'maxDay', 26, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A2', 'Electrode-Box-B2', 'Naive'}, ...
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{3, 5, 4})), ...
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'mergeB2_d0_10', struct( ...
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'scenario', 'mergeB2_d0_10', ...
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'maxDay', 10, ...
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'counts', containers.Map( ...
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{'Electrode-Box-A2', 'Electrode-Box-B2', 'Naive'}, ...
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{3, 5, 4})) ...
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)
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end
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methods (Test)
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function testGroupCountsWindowAndReference(testCase, scenarioCase)
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[S, meta] = tdcs_scenario_data(scenarioCase.scenario);
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% Day window.
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testCase.verifyEqual(meta.maxDay, scenarioCase.maxDay);
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testCase.verifyLessThanOrEqual(max(S.day), scenarioCase.maxDay);
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% meta fields derived from the scenario name.
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expectedMergeKey = regexprep(scenarioCase.scenario, '_full$|_d0_10$', '');
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testCase.verifyEqual(meta.mergeKey, expectedMergeKey);
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testCase.verifyEqual(meta.isUnmerged, strcmp(expectedMergeKey, 'unmerged'));
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% Reference (first) category of S.group is Electrode-Box-B2.
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allCats = categories(S.group);
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testCase.verifyEqual(allCats{1}, 'Electrode-Box-B2');
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% Per-group subject counts.
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actualCounts = tScenarioData.localSubjectCountsByGroup(S);
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expectedCounts = scenarioCase.counts;
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testCase.verifyEqual(actualCounts.Count, expectedCounts.Count);
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actualNames = keys(actualCounts);
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for i = 1:numel(actualNames)
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name = actualNames{i};
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testCase.verifyTrue(isKey(expectedCounts, name), ...
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sprintf('Unexpected group "%s" in scenario "%s".', ...
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name, scenarioCase.scenario));
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testCase.verifyEqual(actualCounts(name), expectedCounts(name), ...
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sprintf('Subject count mismatch for group "%s" in scenario "%s".', ...
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name, scenarioCase.scenario));
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end
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end
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function testMergeB2FullCsvIsWrittenAndReloads(testCase)
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[S, ~] = tdcs_scenario_data('mergeB2_full');
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thisDir = fileparts(mfilename('fullpath'));
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matlabDir = fileparts(thisDir);
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csvFile = fullfile(matlabDir, 'derived', 'mergeB2_full.csv');
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testCase.verifyTrue(isfile(csvFile), ...
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'derived/mergeB2_full.csv was not written.');
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Sreload = readtable(csvFile);
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Sreload.group = categorical(Sreload.group);
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countsOrig = tScenarioData.localSubjectCountsByGroup(S);
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countsReload = tScenarioData.localSubjectCountsByGroup(Sreload);
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testCase.verifyEqual(countsReload.Count, countsOrig.Count);
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namesOrig = keys(countsOrig);
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for i = 1:numel(namesOrig)
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name = namesOrig{i};
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testCase.verifyTrue(isKey(countsReload, name), ...
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sprintf('Group "%s" missing after CSV reload.', name));
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testCase.verifyEqual(countsReload(name), countsOrig(name), ...
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sprintf('Subject count mismatch for group "%s" after CSV reload.', name));
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end
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end
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end
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methods (Static)
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function m = localSubjectCountsByGroup(T)
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%LOCALSUBJECTCOUNTSBYGROUP containers.Map group name -> #unique subjects.
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subjGroup = unique(T(:, {'subject', 'group'}));
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group = subjGroup.group;
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if ~iscategorical(group)
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group = categorical(group);
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end
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counts = countcats(group);
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catNames = categories(group);
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m = containers.Map('KeyType', 'char', 'ValueType', 'double');
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for i = 1:numel(catNames)
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m(catNames{i}) = counts(i);
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end
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end
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end
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end
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