[NET-193] Fix denominator calc by pollaro · Pull Request #41 · WheelockLab/NetworkLevelAnalysis

pollaro · 2024-06-26T18:38:38Z

No description provided.

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * fix cohensd --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * [NET-196] Fix Cohen's D test not running (#43) fix cohensd * fixed winkler error and westfall_young storage --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

[NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix [NET-193] Fix denominator calc (#41) fix error in denominator calculation [NET-196] Fix Cohen's D test not running (#43) fix cohensd [NET-197] Fix Winkler math (#45) fixed winkler error and westfall_young storage

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * fix cohensd --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * [NET-196] Fix Cohen's D test not running (#43) fix cohensd * fixed winkler error and westfall_young storage --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * fix cohensd --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

* 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 * Switched to python and it works first try! Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added license variable from mathworks specified version cache install for speed Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap Update export-mlapp-files.yml more really getting sick of this Update export-mlapp-files.yml Update export-mlapp-files.yml added exported file hoping it fixes the github action Update export-mlapp-files.yml added build matrix fixed version number error Update export-mlapp-files.yml added toolboxes Update export-mlapp-files.yml fixed spaces to underscores in toolboxes Update export-mlapp-files.yml bug fix Update export-mlapp-files.yml changing commands to run from command line Update export-mlapp-files.yml trying a script Update export-mlapp-files.yml i hate matlab add script still trying to export crap really getting sick of this Update export-mlapp-files.yml change export script to use unzip. deal with the xml header and footer later stupid typo hoping this actually works. created blank files first add python script Update export-mlapp-files.yml Switch to real language remove intermediate files remove intermediate files * Add Myers Dec2023 50 Pct Thresh Network Atlas * Hotfix - Run edge/net perms together, don't save all edgePerm coeffs/p vals for all permutations * Update export-mlapp-files.yml * Exported mlapp files * [NET-161] Remove "Import nla.*" from functions (#14) * removed as many import nla.* as I could find and attempted to wrap lines longer than 120 * Exported mlapp files * found a few places for nla.helpers * fixed some missed imports --------- Co-authored-by: Github Action <action@github.com> * [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> * [NET-59] Better scaling options for TriMatrix plots (#12) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * [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> * Exported mlapp files * remove unneeded file * remove unneeded file * fixed merge errors --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * [NET-157] Enable colormap choice for TriMatrix (#13) * 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 * 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 * 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 * first commit * remove some unneeded function and variable names * formatting and comments * seems to be working correctly * some formatting * added negative log10 ability * fix mistake * merge fixes * renamed forlder and added tests for colormaps * [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> * [NET-59] Better scaling options for TriMatrix plots (#9) * first commit * remove some unneeded function and variable names * formatting and comments * added negative log10 ability * fix mistake * fixed lots of merge errors * lots of merge errors causing repeated code * remove unneeded file * more stupid merge errors * uneeded file * fixed a merge error where color map got reset to default --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> * NET168 - Fix error in naming a variable in NetworkTestResult (#17) stupid error * NET-168 Welch's T (#18) going back to this * fix typo * NET-173 - Glass Brain Images error (#19) renamed variable to be consistent * NET174-Edge Chord Plots won't work (#20) fix stupid error * NET-167 Brain Visualization quick fix to show coeff (#21) * fix some missing imports * short term fix for NET167 * [NET-176] Convergence Map Fix (#22) convergence map fixes * Code monkey forgot to use parfor * BugFix for selecting Precalculated in GUI: Add missing prefixes * NET-181 Fix permutation results in ResultPool (#23) added copy for permutation results * remove unneded folder * NET179 - Cohen's D threshold fix and move (#24) * moved cohens d threshold. and actually made it work! * moved cohens d threshold. and actually made it work! * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * NET182 - Fix matrixplot scaling (#25) add read-only property * remove duplicate unittest folder * [NET-183] Flipped Colorbar choices around (#26) * remove duplicate unittest folder * flipped colors around * NET-188 Consolidate Plotters (#27) consolidated plotters into one * fix stupid nla import * NET190 - Hotfix for data handling (#28) * some better result/test handling * variable name fix * NET184 - Save functionality fix (#29) * Fixed save issues * Changed function name * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * Update Chi^2 calculation Old calculation used ./ New calculation uses legacy code style with .* to the -1 power. * correct chi squared test to account for multiply instead of divide * [NET-192] Diagnostic Plot for permutation histogram fix (#31) changed no_permutations in histogram to actual no_permutations * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * [NET-196] Fix Cohen's D test not running (#43) fix cohensd * fixed winkler error and westfall_young storage --------- Co-authored-by: Andy <me@something.com> Co-authored-by: Github Action <action@github.com> Co-authored-by: arisegel00 <81254996+arisegel00@users.noreply.github.com>

* moved diagnostic plots to there own class * fixed up gui * [NET-193] - Integrate Winkler Method and Westfall-Young method into NLA (#38) * fixed network test result and NLA_GUI and NLAResult for new rankings * Exported mlapp files * fixing up result rank and network test result to add new rankings * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com> * [NET-193] Fix for ResultRank tests (#40) * fix for result rank tests * finally found all errors * another test fix * [NET-193] Fix denominator calc (#41) fix error in denominator calculation * [NET-196] Fix Cohen's D test not running (#43) fix cohensd * [NET-197] Fix Winkler math (#45) fixed winkler error and westfall_young storage * removed diagnostic plots * changed size of some figures * start of large plot wrapper * trying to figure out where to go * add button object to input fields * doing better on drawing options * finally got buttons in correct spots * adding in the trimatrix options * trying to add colorbar choice * trying to get the colormap choice. this is a rough, but there's improvements still * able to get changes and sort them into the correct function to use * semicolon * fixing some errors found * getting matrix plot attached * data showing up in trimatrix * scaling and colorbar work correctly * fixed checkbox error * fix cohend test * fix winkler math * chord plotting seems to be working. no guarantees * starting to add convergence * convergence plot * finally figured out cohen's d issues * changes to background colors * adding title to single plot * starting to integrate single plot. * adding chord plotting and cohens d filter to networktestplot * trying to streamline chords * edge chord plotting with selector appears to function * Things are starting to work well, except that the options panel is too short * fixed options panel size and p-max threshold * [NET-214] Error plotting Chi-squared and Hypergeometric within network pair (#58) added check for tests without single sample * added in one plot and wired it up * changes to networktestresult to eliminate lots of code, result rank to fix issues * Exported mlapp files * fixes to diagnostic plots * Exported mlapp files * Exported mlapp files --------- Co-authored-by: Github Action <action@github.com>

fix error in denominator calculation

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pollaro merged commit 1a3757f into master Jun 26, 2024

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[NET-193] Fix denominator calc#41

[NET-193] Fix denominator calc#41
pollaro merged 1 commit intomasterfrom
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pollaro commented Jun 26, 2024

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pollaro commented Jun 26, 2024

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