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https://github.com/MicronOxford/SIMcheck
05 April 2024, 21:07:19 UTC
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Revision Author Date Message Commit Date
1ae64cb David Pinto 27 January 2021, 13:10:02 UTC SIMcheck_Manual: update submodule to its dev branch 27 January 2021, 13:10:02 UTC
4f5468c David Miguel Susano Pinto 21 January 2021, 16:05:16 UTC maint: set version to 1.4-SNAPSHOT after 1.3 release 21 January 2021, 16:05:16 UTC
b3512e5 David Miguel Susano Pinto 21 January 2021, 15:53:42 UTC maint: bump version to 1.3 release 21 January 2021, 15:53:42 UTC
669c6ba David Miguel Susano Pinto 21 January 2021, 15:49:42 UTC Update SIMCheck_Manual submodule for latest master. 21 January 2021, 15:49:42 UTC
5739fb5 David Miguel Susano Pinto 21 January 2021, 15:49:17 UTC Use MicronOxford remote for SIMCheck_Manual submodule. 21 January 2021, 15:49:17 UTC
afcaff0 David Miguel Susano Pinto 21 January 2021, 12:03:17 UTC Util_MCNRFilter.java: new "Modulation Contrast Filter" utility. 21 January 2021, 12:03:17 UTC
e5c850d David Pinto 06 June 2018, 10:44:19 UTC maint: set version to 1.3-SNAPSHOT after 1.2 release 06 June 2018, 10:44:19 UTC
0901b08 David Pinto 06 June 2018, 10:33:20 UTC maint: bump version for 1.2 release 06 June 2018, 10:33:20 UTC
58e279c David Pinto 06 June 2018, 10:29:04 UTC maint: document changes for upcoming release 06 June 2018, 10:29:04 UTC
9e45955 David Pinto 05 June 2018, 23:16:53 UTC SIMcheck_.java: fix link to simcheck online help 05 June 2018, 23:16:53 UTC
8bd667a David Pinto 22 November 2017, 19:36:12 UTC maint: set version to 1.2-SNAPSHOT after 1.1 release 22 November 2017, 19:36:12 UTC
3541612 David Pinto 22 November 2017, 19:20:18 UTC maint: update instructions for manual installation on README 22 November 2017, 19:20:18 UTC
ce2e3cd David Pinto 22 November 2017, 18:20:35 UTC Enable building javadocs with Java version 1.7 * pom.xml: use the doclint configuration from maven's javadoc plugin instead of 'additionalparams'. Since javadoc 1.7 did not had the doclint command line option, this enables packaging SIMcheck with Java 1.7. 22 November 2017, 18:20:35 UTC
41182e6 Marcel Müller 06 July 2017, 17:17:39 UTC Exchanged parallel_FFTJ with JTransforms3 * Rewrote FFT3D.java to use JTransforms3 instead of parallel_FFTJ * Added functions to convert between ImageJ stacks, processors and raw float [] arrays * Added some basic functionality to check / warn if all dependencies are accessible 06 July 2017, 17:17:39 UTC
54bbf68 David Pinto 10 April 2017, 17:13:22 UTC pom.xml: fix indentation (no 3 space indentation) 10 April 2017, 17:13:22 UTC
e2d774b Graeme Ball 02 April 2017, 23:08:48 UTC Merge pull request #28 from graemeball/dev updates for SIMcheck 1.1 -- can be released as version 1.1 (no more code changes planned) -- will continue to update Manual & README, then merge into master & tag as v1.1 02 April 2017, 23:08:48 UTC
c8d3d2a Graeme Ball 31 March 2017, 23:01:56 UTC resolve conflict in SI to widefield utility 31 March 2017, 23:01:56 UTC
5b5384a Graeme Ball 31 March 2017, 22:41:06 UTC bump version to 1.1 31 March 2017, 22:41:06 UTC
78927eb Graeme Ball 31 March 2017, 22:17:25 UTC update README and CHANGES for 1.1 31 March 2017, 22:17:25 UTC
6d09ae2 Graeme Ball 07 December 2016, 01:37:09 UTC update Raw_ModContrast and I1l.stackFeatMean so mask image only shown standalone 07 December 2016, 01:37:09 UTC
df2c8d3 Graeme Ball 07 December 2016, 01:24:31 UTC rename rec fourier 'More' button to '2D-FFT options' 07 December 2016, 01:24:31 UTC
22ece89 Graeme Ball 26 November 2016, 23:24:24 UTC fix rec fourier option logic to access 2d FFT when 3d available 26 November 2016, 23:24:24 UTC
979e70e Graeme Ball 26 November 2016, 23:19:27 UTC add 'more' option to access rec fourier 2d with parallel fftj 26 November 2016, 23:19:27 UTC
51cc93f Graeme Ball 26 November 2016, 00:39:16 UTC raw MCNR stat, use feats from blurred MCNR instead of pseudo-wf 26 November 2016, 00:39:16 UTC
c8a18c7 Graeme Ball 17 November 2016, 18:51:47 UTC add window function (XY only) to 3D FFT for rec fourier check 17 November 2016, 18:51:47 UTC
a2673f0 Graeme Ball 17 November 2016, 16:27:59 UTC remove FFT3D from Utilities menu 17 November 2016, 16:27:59 UTC
04f5426 Graeme Ball 17 November 2016, 16:16:55 UTC si to pwf utility - implement option to rescale 2x or not 17 November 2016, 16:16:55 UTC
16a5e2f Graeme Ball 17 November 2016, 03:24:07 UTC 2nd attempt to fix rec fourier 3d ortho padding 17 November 2016, 03:24:07 UTC
3a61bf8 Graeme Ball 16 November 2016, 13:01:55 UTC 1st attempt to fix rec fourier ortho padding 16 November 2016, 13:01:55 UTC
7f76cbb Graeme Ball 11 November 2016, 14:43:38 UTC update README TODO list 16 November 2016, 01:18:56 UTC
db4971b Graeme Ball 11 November 2016, 01:26:05 UTC rename snapshot version from 1.0.1 to 1.1 11 November 2016, 01:26:05 UTC
c92281e Graeme Ball 11 November 2016, 00:58:00 UTC Merge branch 'FFT3D_parallel_fftj' into dev 11 November 2016, 00:58:00 UTC
f5bd080 Graeme Ball 09 November 2016, 00:21:53 UTC implement FTO and FTR (N.B. no rescale/pad yet) for 3D FFT 09 November 2016, 00:21:53 UTC
174ccf3 Graeme Ball 08 November 2016, 23:49:16 UTC implement FFT3D.fftImp and use for FTL in Rec_Fourier 08 November 2016, 23:49:16 UTC
bc47fa5 Graeme Ball 06 November 2016, 23:45:04 UTC ignore lib/ 06 November 2016, 23:45:04 UTC
883ed3d Graeme Ball 06 November 2016, 23:44:36 UTC turn off Xdoclint to prevent error on compile 06 November 2016, 23:44:36 UTC
5d84e0c Graeme Ball 04 November 2016, 00:42:14 UTC fudge parallel_fftj dependency in local lib/ repo for build 04 November 2016, 00:42:14 UTC
975eab3 Graeme Ball 03 November 2016, 16:23:45 UTC implement simple 3D FFT using parallel FFTJ, fudging Eclipse jar import 03 November 2016, 16:23:45 UTC
0964248 Graeme Ball 31 October 2016, 17:16:21 UTC strip out imglib2 "3D FFT" and use raw SIM image in main() test 31 October 2016, 17:16:21 UTC
7b542cb Graeme Ball 19 August 2016, 16:39:12 UTC turn off DocLint to prevent build failure due to javadoc checks in java 8 19 August 2016, 16:39:12 UTC
cabc18a Graeme Ball 19 August 2016, 15:48:52 UTC implement 2-arg stackFeatMean using pwf stack for ROI -- still w. debug show 19 August 2016, 15:48:52 UTC
97c8623 Graeme Ball 18 August 2016, 14:54:20 UTC raw MCNR now calls stackFeatMean using second stack (PWF for feats) 18 August 2016, 14:54:20 UTC
4964350 Graeme Ball 18 August 2016, 14:52:18 UTC add option for AVG w/o rescale to SItoWF util 18 August 2016, 14:52:18 UTC
8cfac19 Graeme Ball 15 August 2016, 08:19:57 UTC fix typo 15 August 2016, 08:19:57 UTC
08dc71e Graeme Ball 16 February 2016, 19:55:30 UTC Merge pull request #25 from carandraug/using-op.image.scale java NullPointerException when running Util_SItoPseudoWidefield in headless mode -- replace ImageJ1 Scale... command with ImageJ2 ops implementation 16 February 2016, 19:55:30 UTC
4a37cac David Pinto 12 February 2016, 17:26:51 UTC Util_SItoPseudoWidefield: use imagej ops for scale (issue #25) Use of IJ.run("scale", ...) prevents SIMcheck to be run in headless mode by scripts and imagej macros. Main issue is that imglib does not currently have bicubic interpolation. 12 February 2016, 17:26:51 UTC
69459dc Graeme Ball 21 January 2016, 19:33:47 UTC add quick and dirty FFT3D using ImgLib2 -- needs finishing, integration 21 January 2016, 19:33:47 UTC
71ee32b Graeme Ball 11 December 2015, 20:46:32 UTC fix SAM menu name typo and bump version to 1.0.1-SNAPSHOT 11 December 2015, 20:46:32 UTC
7ac27c5 Graeme Ball 22 September 2015, 15:02:58 UTC Merge pull request #23 from graemeball/dev SIMcheck 1.0.0 22 September 2015, 15:02:58 UTC
1583550 Graeme Ball 22 September 2015, 14:12:28 UTC update version, pom, manual and plugin.config for SIMcheck 1.0.0 22 September 2015, 14:12:28 UTC
76d8fc5 Graeme Ball 22 September 2015, 13:12:04 UTC update README / TODO list for SIMceheck 1.0 22 September 2015, 13:12:04 UTC
8baae31 Graeme Ball 22 September 2015, 11:11:34 UTC update raw and rec Fourier check log text 22 September 2015, 11:11:34 UTC
d3181ce Graeme Ball 18 September 2015, 21:38:09 UTC update CHANGES.txt for 1.0.0 18 September 2015, 21:38:09 UTC
bfb7814 Graeme Ball 14 September 2015, 22:58:38 UTC log Util_ info upon .run() only 14 September 2015, 22:58:38 UTC
1934bb1 Graeme Ball 12 September 2015, 21:42:26 UTC replace underscores with strings in dialogs to allow macro recording 12 September 2015, 21:42:26 UTC
91dbe2f Graeme Ball 12 September 2015, 20:41:00 UTC CIP: remove commented code and unused imports 12 September 2015, 20:41:00 UTC
4567728 Graeme Ball 12 September 2015, 20:37:28 UTC raw fourier: remove dead code and comments 12 September 2015, 20:37:28 UTC
c245c9a Graeme Ball 11 September 2015, 22:15:29 UTC bugfix, correct FPJ mask setting to minimum 11 September 2015, 22:15:29 UTC
c634cea Graeme Ball 11 September 2015, 21:12:40 UTC correct typo in raw FPJ log 11 September 2015, 21:12:40 UTC
9f5c0d0 Graeme Ball 10 September 2015, 23:46:08 UTC result info titles ending exclam not followed by colon, used in mcm saturation warning 10 September 2015, 23:46:08 UTC
f079fa6 Graeme Ball 10 September 2015, 23:28:39 UTC for rec fourier gamma and blur+lut, use central stripe to get mode for axial display scale 10 September 2015, 23:28:39 UTC
d82ef73 Graeme Ball 10 September 2015, 23:07:03 UTC tweak log text 10 September 2015, 23:07:03 UTC
49aa250 Graeme Ball 10 September 2015, 22:59:05 UTC CIP check, change criteria: maybe 50 to 40, no 70 to 60 10 September 2015, 22:59:05 UTC
8fda3e9 Graeme Ball 10 September 2015, 22:21:37 UTC rec fourier, display mode-max for gamma scaling after blur and lut 10 September 2015, 22:21:37 UTC
a71268d Graeme Ball 10 September 2015, 21:54:26 UTC un-capitalize 'Camera Bit Depth' in main dialog 10 September 2015, 21:54:26 UTC
0555ae0 Graeme Ball 10 September 2015, 20:57:04 UTC bugfix: always do display scaling min-max per channel and remove commented dead code 10 September 2015, 20:57:04 UTC
31a988f Graeme Ball 10 September 2015, 20:54:26 UTC bugfix: I1l.getStatsForChannel now returns StackStatistics (not just stats for current ip) 10 September 2015, 20:54:26 UTC
5c5e986 Graeme Ball 10 September 2015, 20:23:30 UTC rejig rec mcm dialog layout 10 September 2015, 20:23:30 UTC
0c7c82a Graeme Ball 10 September 2015, 20:06:56 UTC raw fourier projection, change gamma scaling to 32-bit log 10 September 2015, 20:06:56 UTC
5a16d6b Graeme Ball 10 September 2015, 17:15:52 UTC tweak mod contrast map dialog formatting 10 September 2015, 17:15:52 UTC
797f01b Graeme Ball 10 September 2015, 17:09:06 UTC 'data' lowercase for dataset selection in main dialog 10 September 2015, 17:09:06 UTC
3b74b84 Graeme Ball 10 September 2015, 17:01:42 UTC fix/update rec fourier display scaling for use with blur and LUT 10 September 2015, 17:01:42 UTC
0b0aa4a Graeme Ball 10 September 2015, 16:31:56 UTC tweak rec fourier dialog formatting 10 September 2015, 16:31:56 UTC
61e1c95 Graeme Ball 10 September 2015, 14:09:55 UTC new raw FFT check procedure using gamma scaling and offset mask 10 September 2015, 14:09:55 UTC
660342f Graeme Ball 10 September 2015, 12:32:20 UTC new CIP intensity decay estimation 10 September 2015, 12:32:20 UTC
72e16c9 Graeme Ball 10 September 2015, 10:37:09 UTC tweak rec Fourier log text 10 September 2015, 10:37:09 UTC
9999cac Graeme Ball 10 September 2015, 10:31:41 UTC revert to old LUT and display range in rec MCM check 10 September 2015, 10:31:41 UTC
92b7e8f Graeme Ball 10 September 2015, 10:29:32 UTC revert to old LUT and display range in raw MCN check 10 September 2015, 10:29:32 UTC
3ad2dd6 Graeme Ball 10 September 2015, 10:05:38 UTC new rec Fourier options, including gamma min-max 10 September 2015, 10:05:38 UTC
e4266f1 Graeme Ball 09 September 2015, 22:52:00 UTC FTR radial profile y-axis label: (a.u.) for log scale only 09 September 2015, 22:52:00 UTC
13033fd Graeme Ball 09 September 2015, 16:29:39 UTC rec MCM plugin: show raw mod contrast image and results if calculated 09 September 2015, 16:29:39 UTC
0546097 Graeme Ball 09 September 2015, 16:16:23 UTC remove util FFT log window printing 09 September 2015, 16:16:23 UTC
1160f6e Graeme Ball 09 September 2015, 15:54:22 UTC no blank line between v. short infos in log (see RIH) 09 September 2015, 15:54:22 UTC
73f8258 Graeme Ball 08 September 2015, 15:38:59 UTC raw CIP check: add second, relative intensity plot 08 September 2015, 15:38:59 UTC
72c195c Graeme Ball 08 September 2015, 12:55:15 UTC fix rec Fourier axial FFT rescale and pad for gamma display 08 September 2015, 12:55:15 UTC
5b450ca Graeme Ball 07 September 2015, 17:55:48 UTC Merge remote-tracking branch 'upstream/dev' into dev 07 September 2015, 17:55:48 UTC
bdb3604 Graeme Ball 07 September 2015, 17:52:06 UTC update LUT and range in rec mod contrast map 07 September 2015, 17:52:06 UTC
cf5eefd Graeme Ball 07 September 2015, 17:43:32 UTC new raw mod contrast lut and display range 07 September 2015, 17:43:32 UTC
0b1a25e Graeme Ball 07 September 2015, 17:39:36 UTC update log file text for rec data checks 07 September 2015, 17:39:36 UTC
c3a8904 Graeme Ball 07 September 2015, 17:38:28 UTC python script for dumping binary LUT file as comma-separated text 07 September 2015, 17:38:28 UTC
943061e Graeme Ball 07 September 2015, 14:45:30 UTC update log file text for raw data checks 07 September 2015, 14:45:30 UTC
fb88922 Graeme Ball 07 September 2015, 14:39:10 UTC print "Statistics:" before stats in log, if stats exist 07 September 2015, 14:39:10 UTC
26a5b03 Graeme Ball 07 September 2015, 14:03:19 UTC print "Result:" before stat results in log 07 September 2015, 14:03:19 UTC
9d4e70a Graeme Ball 06 September 2015, 21:43:54 UTC rescale to 16-bit in Stack FFT util, to match rec Fourier check 06 September 2015, 21:43:54 UTC
e272844 Graeme Ball 03 September 2015, 16:29:09 UTC correct FFT utility dialog text and % display 03 September 2015, 16:29:09 UTC
33a1e2f Graeme Ball 03 September 2015, 15:54:04 UTC fft util: change default gamma from 0.3 to 0.2 03 September 2015, 15:54:04 UTC
7af451e Graeme Ball 26 August 2015, 22:23:17 UTC add warning to RIH and SAM checks: stats only valid for unclipped data 26 August 2015, 22:23:17 UTC
58ef18e Graeme Ball 26 August 2015, 22:07:56 UTC change raw MCN stat check criteria from 3,6 to 4,8 26 August 2015, 22:07:56 UTC
e4b873d Graeme Ball 16 August 2015, 20:51:59 UTC rec fourier, fix setLUT code for gamma scaled FFT 16 August 2015, 20:51:59 UTC
3485287 Graeme Ball 15 August 2015, 21:44:22 UTC rec fourier, update auto cut-off option and winfunc bugfix - was incorrectly applying winfunc by default from main dialog 15 August 2015, 21:44:22 UTC
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