{"push_id":2464536548,"size":27,"distinct_size":2,"ref":"refs/heads/306-Add-support-for-honeycomb-template","head":"0afa1526ccb16eaaf18ce8f9b60883f5f01c97b3","before":"978192c169017d02b156572d5de2a0f32f8eb16e","commits":[{"sha":"17baad39e670a0ce6126d2f52f317b6e4ec42748","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Fix volume and model display\n\nTurn off marker detection label map by default, fixing\nbug where it was being shown even when the flag was off.\nTodo: add to settings file.\n\nWhen showing volumes on load is turned off, the selection node still\nsets them as active. Fixed the workflow functions to only propagate\nthe specific layer setting.\n\nIf the guide holes model is not showing and the target zone is visible,\nshow the target zone in 3d, not just in the 2d slices. Update target\nzone model 3d visibility when toggle the guide holes model visibility,\nwith checks for when that's done outside of the target step.\nDisable the button that toggles the sheet hole tubes visibility until\nthe model has been created. Enable it after model creation.\n\nIssue #308","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/17baad39e670a0ce6126d2f52f317b6e4ec42748"},{"sha":"54958d37e5a6e6193e9dd7428f1d3656ea44d607","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #317 from nicoleaucoin/308-Fix-scan-loading-and-display-squash\n\nENH: Fix volume and model display","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/54958d37e5a6e6193e9dd7428f1d3656ea44d607"},{"sha":"6392942b3e95d93c84edf3ac2599be6b3ce7eacd","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Add ability to reset calibration parameters\n\nAdd a button to the marker detection parameters frame to allow resetting\nthe calibration parameters back to the module defaults.\nAdded testing it in the VerifyRegistration unit test.\n\nIssue #313","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/6392942b3e95d93c84edf3ac2599be6b3ce7eacd"},{"sha":"8666bb9cff14b0810dbee808609ba762425b37d1","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #318 from nicoleaucoin/313-Add-reset-to-calibration-defaults\n\nENH: Add ability to reset calibration parameters","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/8666bb9cff14b0810dbee808609ba762425b37d1"},{"sha":"ee04b50fbe8fce224bd77e2aee8e79a19edf7afa","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Clean up cancel dicom assignment pop up\n\nUse the workflow functions to pop up the question on if the user wishes\nto cancel the current DICOM assignment.\nIn the popup question method remove the window close button to force the\nuser to answer yes or no.\n\nIssue #314","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/ee04b50fbe8fce224bd77e2aee8e79a19edf7afa"},{"sha":"8dff6f58c41e72a5cfd7160b7e5e0c8e838aedcf","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #319 from nicoleaucoin/314-Keep-DICOM-assignment-window-on-top\n\nENH: Clean up cancel dicom assignment pop up","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/8dff6f58c41e72a5cfd7160b7e5e0c8e838aedcf"},{"sha":"21c4b3f6bfb239831568fe17ae621b018491ae2a","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Use auto window level on target and conf scans\n\nWhen assign target and confirmation scans, turn on auto window level in\ntheir display nodes as the DICOM tags for center and width weren't\nworking very well (too dark).\n\nIssue #315","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/21c4b3f6bfb239831568fe17ae621b018491ae2a"},{"sha":"2d83f3f42e1583657ea65931c2a79a5310e7006c","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #320 from nicoleaucoin/315-Set-better-window-level-on-scans\n\nENH: Use auto window level on target and conf scans","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/2d83f3f42e1583657ea65931c2a79a5310e7006c"},{"sha":"36f2a875a4ec866d85a88a4749a1ae58e35bb46c","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Add Alt-A to add target, needle\n\nAdd shortcuts for the buttons to add targets and needle tips, press Alt\nthen the A key to enter fiducial place mode.\nFixed a typo for error when loading Target ui file.\n\nIssue #321","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/36f2a875a4ec866d85a88a4749a1ae58e35bb46c"},{"sha":"67c02d991ecf9d663d914b256c9b9ea80a99e9df","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #322 from nicoleaucoin/321-Support-key-press-to-add-target-or-needle\n\nENH: Add Alt-A to add target, needle","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/67c02d991ecf9d663d914b256c9b9ea80a99e9df"},{"sha":"3b61e7b7b9340b550524a54bdc57192901f7b2a0","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Add test for scans from different machines\n\nAdded a unit test that registers calibration scans from different types\nof scanners:\nSuemans Verio 3T\nSiemans Aera 1.5T\nHitachi Trillium Oval 3T\nToshiba Titan 3T\nSiemans Skyra 3T\nGE Discovery MR750w 3T\nPhilips Achieva dStream 3T\n\nAllow missing patient DOB so can do the test without turning on\nthe TestingFlag that might hide other issues.\nAlso test target and confirmation scans if available.\n\nWorking on onNewPatient, slicer and dicom assignment scene clean up, remove scalar\nvolumes from the slicer scene, but leave and reinit label maps. Fix\nmodel display.\n\nAdd manual targets in the test functions to work with different volumes\n(places in the middle of the working zone instead of at a hard coded RAS location).\n\nPut good scans for unit tests in archive and updated paths to load the good\ncalibration, target, confirmation scans from the unit tests archive.\n\nRun a statistics image filter on the images to get a sense of\nwhat variance values are in a good range to allow calibration\nof images tht may have an intensity gradient on them. Variance\ndivided by the max intensity value seems to give a good\nmetric, this test for all succeeding calibration scans the range\nis 2-109,\n\nTBD: if can clear both slicer.mrmlScene and the dicom assignment scene\nand get the workfow working (calibration xform missing) it may fix the\nmismatch in node ids on copy, missing slice node or widget that causes\nthe assignment widget to break.\n\nObservation step hadn't been updated to current report format (still\nhad patient name in dir). Updated all steps to use new workflow function\nto start reports.\n\nAdded check that rows and columns are equal in calibration scans.\n\nCurrent data archive is UnitTests-20180323.zip\n\nIssue #217","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/3b61e7b7b9340b550524a54bdc57192901f7b2a0"},{"sha":"352a8b126ee48cd11cb60d9c4d41d0d46714ff65","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #327 from nicoleaucoin/217-Add-unit-tests-for-other-scanners-squash\n\nENH: Add test for scans from different machines","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/352a8b126ee48cd11cb60d9c4d41d0d46714ff65"},{"sha":"91925b5899f04c4c0a482de568e22674781233db","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"BUG: fix check for square calibration scans\n\nCheck for empty strings in rows and columns dicom tags, fixing tests.\n\nIssue #328","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/91925b5899f04c4c0a482de568e22674781233db"},{"sha":"83a7a9636cabfdb390e256f3058a27ff5b783c58","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Add burn parameters\n\nAdd the burn algorithm parameters in marker detection to the Calibration step,\nincluding a flag to not use it. Turn the flag off in the calibrator simulation\ntest as the default settings make markers that run together and don't work\nwell with the burn algorithm.\n\nSet the new parameters in runCalibration rather than passing more\nparameters to the function.\n\nAdded another noise test to exercise the burn algorithm. Shot noise works on\naverage image intensity, so first add some gaussian noise to the binary\ncalibrator simultation image.\nTBD: consider adding gaussian noise to calibrator simulation volume before\nplace markers in it.\n\nIssue #328","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/83a7a9636cabfdb390e256f3058a27ff5b783c58"},{"sha":"ecb026f389a90404651d172169be1aae1ea1693b","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #330 from nicoleaucoin/328-Support-marker-detection-burn-algorithm\n\n328 support marker detection burn algorithm","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/ecb026f389a90404651d172169be1aae1ea1693b"},{"sha":"66150c28c929fcc3101a5d01327ecef804153573","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: Add more information to log files\n\nChanged calls that were just appending to status box to log\ninformation as well.\nAdded logging scan assignments, series description on load, fiducial\nname changes and manual position adjustments.\n\nChanged references to tech report files to log files.\nMoved logging into a workflow function, removing preInitReport and startReport\nfunctionality: anything needing to be logged before the parameter node\nis initialized with the reports dir can go to status box or and\nerror popup. Just keep the step's log file name and pass that in\nwriteReport to the workflow function.\nUpdate the time string to format with leading 0, using it in logs rather than\ndirect calls to datetime.\nAdded logging to Report step.\nUpdated the needle tips test to use the updated code.\n\nIssue #329","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/66150c28c929fcc3101a5d01327ecef804153573"},{"sha":"ca2a884d240f724020db7883723eea69a979dd1c","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #331 from nicoleaucoin/329-Report-more-information\n\nENH: Add more information to log files","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/ca2a884d240f724020db7883723eea69a979dd1c"},{"sha":"b7b0d303ba90ec7c98f5fc1eaab2760ef087b91d","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: remove unused ProstateBxLib files\n\nRemoved unused python files from ProstateBx.\n\nIssue #332","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/b7b0d303ba90ec7c98f5fc1eaab2760ef087b91d"},{"sha":"99c1a86d2d7d1f19dddaa91b3b8d46b1af7221bb","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"Merge pull request #333 from nicoleaucoin/332-Remove-extra-python-files\n\nENH: remove unused ProstateBxLib files","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/99c1a86d2d7d1f19dddaa91b3b8d46b1af7221bb"},{"sha":"ca33ecc63c261d7f73563596e360aeb559ebc1fd","author":{"name":"Nicole Aucoin","email":"be98d4d4270ccba5824b87bd6696ea9df77a2191@harmonus.com"},"message":"ENH: add tooltips for volume names\n\nDICOM scan labels have truncated text, added a workflow function to set\nthe label text and tooltip to the given text to allow accessing full\nDICOM series descriptionn if the label can't hold all of it.\n\nIssue #324","distinct":false,"url":"https://api.github.com/repos/nicoleaucoin/HMS_SlicerModule/commits/ca33ecc63c261d7f73563596e360aeb559ebc1fd"}]}
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