| 5975d88 | Kai Wohlfahrt | 24 April 2017, 16:04:39 UTC | Update README for paper Just some rephrasing of documentation. Notably mention of `--size` in blob find removed due to confusion with ROI size | 24 April 2017, 16:32:11 UTC |
| a154211 | Kai Wohlfahrt | 24 April 2017, 15:59:26 UTC | Update docs re smooth.py This has been moved to tiffutil. | 24 April 2017, 15:59:26 UTC |
| 19b8d02 | Kai Wohlfahrt | 20 March 2017, 15:42:17 UTC | Don't return empty ROI for empty peaks | 20 March 2017, 15:42:17 UTC |
| 8f31b9e | Kai Wohlfahrt | 16 March 2017, 17:05:38 UTC | Remove smooth.py, moved to tiffutil | 16 March 2017, 17:05:38 UTC |
| e8b6e7b | Kai Wohlfahrt | 10 March 2017, 16:23:12 UTC | Make off/on smoothing independent Note order of parameter is same order corrections are applied in: - fill gaps of less than N_0 frames - remove peaks of less than N_1 frames | 10 March 2017, 16:23:12 UTC |
| e29e62f | Kai Wohlfahrt | 07 March 2017, 15:18:26 UTC | Also smooth single on-frames Currently using same radius as off-frame smoothing | 07 March 2017, 15:18:26 UTC |
| 85db256 | Kai Wohlfahrt | 28 February 2017, 15:16:43 UTC | Sort CSV columns Makes order reproducible | 28 February 2017, 15:16:43 UTC |
| f2169c2 | Kai Wohlfahrt | 27 February 2017, 15:05:37 UTC | Reverse index order Extraction script was not updated in converting to human-readable format (xyz order instead of zyx order). | 27 February 2017, 15:05:37 UTC |
| 95e8c55 | Kai Wohlfahrt | 27 February 2017, 14:47:58 UTC | Add plot of categorization Currently border is 255 if on, could use dynamic value instead. | 27 February 2017, 14:57:24 UTC |
| e0989d4 | Kai Wohlfahrt | 23 February 2017, 14:14:01 UTC | Clean up imports | 23 February 2017, 14:14:01 UTC |
| 9f334bc | Kai Wohlfahrt | 23 February 2017, 13:17:35 UTC | Update README Minor spelling and usage errors | 23 February 2017, 13:56:39 UTC |
| 098471b | Kai Wohlfahrt | 23 February 2017, 12:51:17 UTC | Use .csv for peaks and stats Makes things human-readable throughout the process. | 23 February 2017, 13:56:38 UTC |
| 86c9713 | Kai Wohlfahrt | 22 February 2017, 16:00:50 UTC | Make categorizing masks variable size | 22 February 2017, 16:12:29 UTC |
| 24ca319 | Kai Wohlfahrt | 22 February 2017, 15:40:49 UTC | Make analysis tools installable Use same dynamic loading technique as image_utils. | 22 February 2017, 15:40:49 UTC |
| fd1b90d | Kai Wohlfahrt | 22 February 2017, 11:57:38 UTC | Remove project.py Now done by tiffutils script. | 22 February 2017, 11:57:38 UTC |
| 992d464 | Kai Wohlfahrt | 26 January 2017, 15:13:27 UTC | Fix README instruction for project.py | 26 January 2017, 15:14:00 UTC |
| 2ad7abf | Kai Wohlfahrt | 07 October 2016, 12:29:19 UTC | Use independent fg/bg masks Suggested by Steve, for now same mask but just split for further editing later. | 26 January 2017, 15:13:58 UTC |
| 1ea23e4 | Kai Wohlfahrt | 07 October 2016, 10:44:31 UTC | Add link to blob-detection | 07 October 2016, 10:44:31 UTC |
| 31c7da4 | Kai Wohlfahrt | 07 October 2016, 10:43:03 UTC | Add README | 07 October 2016, 10:43:03 UTC |
| 6160457 | Kai Wohlfahrt | 07 October 2016, 10:19:23 UTC | Update smoothing tests Found that binary_closing removes a single "True" if it is at the beginning of data. Check that this is not the case for lone values in the middle. | 07 October 2016, 10:21:33 UTC |
| c6f1c83 | Kai Wohlfahrt | 06 October 2016, 13:16:37 UTC | Add slicing in extraction Does not read more files than necessary (as opposed to previous uncommited version, which sliced ROIs after reading). | 06 October 2016, 13:18:08 UTC |
| 41b791f | Kai Wohlfahrt | 06 October 2016, 12:56:56 UTC | Add smoothing to categorize Requires a minimum number of consecutive off-frames to count as an off-blink. | 06 October 2016, 12:56:56 UTC |
| e558099 | Kai Wohlfahrt | 05 October 2016, 16:43:08 UTC | Update tests - rollingMedian moved to project - peakEnclosed moved to blob repo - extraction no longer takes individual sizes | 06 October 2016, 12:56:27 UTC |
| f4ea35d | Kai Wohlfahrt | 05 October 2016, 13:45:35 UTC | Remove HMM analysis Split out to different folder as not used (or ready) for publication. | 05 October 2016, 13:45:54 UTC |
| 1d8a66c | Kai Wohlfahrt | 23 September 2016, 16:05:17 UTC | Make csv header order consistent | 23 September 2016, 16:05:17 UTC |
| e744e6b | Kai Wohlfahrt | 23 September 2016, 16:04:39 UTC | Add binning metadata Don't just multiply exposure, because isn't strictly the same. | 23 September 2016, 16:04:39 UTC |
| 41e9840 | Kai Wohlfahrt | 26 August 2016, 17:27:23 UTC | Add CSVify Converts stats.pickle to CSV for interop with other software. | 26 August 2016, 17:27:23 UTC |
| 40d1202 | Kai Wohlfahrt | 26 August 2016, 11:46:00 UTC | Keep empty tracks Ensures each stat item corresponds to matching peak | 26 August 2016, 11:46:00 UTC |
| 7d78a0b | Kai Wohlfahrt | 26 August 2016, 11:45:43 UTC | Ensure stat names all present Simplifies plotting code | 26 August 2016, 11:45:43 UTC |
| f4e720b | Kai Wohlfahrt | 26 August 2016, 11:45:00 UTC | Always take mean Per-frame/track stats never used. Would bias analysis towards long-lasting tracks. | 26 August 2016, 11:45:00 UTC |
| 20ec8c5 | Kai Wohlfahrt | 26 August 2016, 10:29:16 UTC | Test only if center greater than | 26 August 2016, 10:33:00 UTC |
| e6bfe93 | Kai Wohlfahrt | 25 August 2016, 15:02:44 UTC | Ignore py.test cache | 26 August 2016, 10:32:59 UTC |
| d708c61 | Kai Wohlfahrt | 25 August 2016, 14:37:45 UTC | Split out categorization Makes plotting on/off frames possible. Cost is more HDD reads, and need to import mask for analysis (to separate signal/background) | 26 August 2016, 10:32:57 UTC |
| 2265164 | Kai Wohlfahrt | 25 August 2016, 14:01:09 UTC | Clean up fret_analysis | 26 August 2016, 10:30:50 UTC |
| 4de0dd1 | Kai Wohlfahrt | 25 August 2016, 13:33:35 UTC | Remove plotting from fret_analysis | 26 August 2016, 10:30:44 UTC |
| d0862cc | Kai Wohlfahrt | 23 August 2016, 14:05:33 UTC | Fix initialization of projection Previous bug was due to initializer element being used once, which in case of numpy arrays was always an iterable, so it silently used a row multiple times. Fix by explicitly tee-ing the iterable. Should be OK memory-use wise, but keep an eye on it. | 23 August 2016, 14:05:54 UTC |
| a7f8fab | Kai Wohlfahrt | 23 August 2016, 12:07:50 UTC | Disable multifile .ome.tif saves other images in the series and would so load duplicates. Also causes issues if files are renamed. | 23 August 2016, 12:07:50 UTC |
| bc71a86 | Kai Wohlfahrt | 23 August 2016, 12:01:26 UTC | Add start/end to project.py | 23 August 2016, 12:01:26 UTC |
| 3012e80 | Kai Wohlfahrt | 22 August 2016, 14:53:38 UTC | Generalize smooth ball to ellipses Note the ellipsis also takes a z-height parameter, which for a ball is one additional repeat of the radius. | 22 August 2016, 14:53:38 UTC |
| e647719 | Kai Wohlfahrt | 22 August 2016, 13:21:31 UTC | Add binning script | 22 August 2016, 13:21:31 UTC |
| 5de39fb | Kai Wohlfahrt | 22 August 2016, 13:19:54 UTC | Remove peakEnclosed Now part of blob detection | 22 August 2016, 13:19:54 UTC |
| f868507 | Kai Wohlfahrt | 17 August 2016, 10:36:35 UTC | Fix smooth.py Use opening/closing instead of erosion/dilation. Gives correct result for >1D cases. | 17 August 2016, 10:45:25 UTC |
| f43b6cb | Kai Wohlfahrt | 11 August 2016, 16:48:25 UTC | Fix memory leak in projection Not consuming the map entirely (i.e. until it ran out, not just every element) kept every frame around in memory. | 11 August 2016, 16:48:25 UTC |
| aecaa8f | Kai Wohlfahrt | 11 August 2016, 15:31:09 UTC | Add rolling-ball smoothing script Grey dilation/erosion is equivalent to a rolling-ball above or below the data. | 11 August 2016, 15:41:22 UTC |
| e9bb69f | Kai Wohlfahrt | 11 August 2016, 14:01:31 UTC | Add multiple projection methods This is useful to produce multiple projections while only reading/smoothing the video once (the time intensive part). | 11 August 2016, 14:01:31 UTC |
| 9e6c673 | Kai Wohlfahrt | 09 August 2016, 15:05:47 UTC | Multiple changes to output Produce output for one dataset only. Simplifies generating figures. Keep stats in lists per-trace. Makes it possible to plot mean of a stat against e.g. total on time. | 09 August 2016, 15:05:47 UTC |
| f158783 | Kai Wohlfahrt | 09 August 2016, 15:05:04 UTC | Fix extract.py Previously extracted only the first image, due to map running out (and start/end being wrong). | 09 August 2016, 15:05:04 UTC |
| ff9a428 | Kai Wohlfahrt | 09 August 2016, 15:04:30 UTC | Remove sample.py Random sampling is included in plotting scripts, not general analysis. Moved to thesis directory. | 09 August 2016, 15:04:30 UTC |
| 4249898 | Kai Wohlfahrt | 09 August 2016, 15:02:29 UTC | Remove blob detection Factored out to standalone script/repository for Nature Hi-C paper. | 09 August 2016, 15:02:29 UTC |
| a383505 | Kai Wohlfahrt | 09 August 2016, 15:01:11 UTC | Add executable permission to project | 09 August 2016, 15:01:11 UTC |
| eee39c4 | Kai Wohlfahrt | 04 August 2016, 16:27:29 UTC | Re-work pipeline for Makefile-type operation Store more expensive calculations as intermediate files (notably projection). This does require reading in .tif files multiple times (for projection, then for ROI extraction), but overall fits the figure-generation workflow better. | 04 August 2016, 16:27:29 UTC |
| a456029 | Kai Wohlfahrt | 03 August 2016, 10:26:21 UTC | Factor out threshold calculation So changes only need to be made in one file, not in both analysis and sample. | 03 August 2016, 10:26:42 UTC |
| affc815 | Kai Wohlfahrt | 02 August 2016, 15:35:01 UTC | Factor out pre-extract projection Will be needed for making figures | 03 August 2016, 10:24:39 UTC |
| 8e5c005 | Kai Wohlfahrt | 02 August 2016, 15:13:46 UTC | Remove unused arrangeSubplots | 03 August 2016, 10:24:37 UTC |
| d0cee97 | Kai Wohlfahrt | 02 August 2016, 10:45:20 UTC | Separate out plotting/analysis functions This allows adding metadata per-ROI at the analysis stage, and should make it simpler to use the script with a Makefile like setup for generating figures. | 03 August 2016, 10:24:37 UTC |
| d66c4c3 | Kai Wohlfahrt | 02 August 2016, 15:00:35 UTC | Cap maximum intensity on projection Useful for non-binned frames, as these can have cosmic ray streaks. | 02 August 2016, 15:09:08 UTC |
| 99ca2bb | Kai Wohlfahrt | 02 August 2016, 14:58:15 UTC | Remove pre-extraction normalization No longer used | 02 August 2016, 15:09:07 UTC |
| dc8df56 | Kai Wohlfahrt | 01 August 2016, 14:28:44 UTC | Factor out grand-mean/variation | 01 August 2016, 14:28:44 UTC |
| 692a2a0 | Kai Wohlfahrt | 01 August 2016, 14:28:04 UTC | Fix bin an stats Previously used references to non-local variables. | 01 August 2016, 14:28:04 UTC |
| 7a4608a | Kai Wohlfahrt | 01 August 2016, 10:46:51 UTC | Factor out stat calculation | 01 August 2016, 10:46:51 UTC |
| 83a0b5f | Kai Wohlfahrt | 01 August 2016, 10:35:57 UTC | Factor out binning | 01 August 2016, 10:35:57 UTC |
| 3e7c3e5 | Kai Wohlfahrt | 31 July 2016, 18:40:11 UTC | Plot survival time of molecules Plots a decay curve of molecules with lifetime > than a given number. | 31 July 2016, 18:40:11 UTC |
| b2c1379 | Kai Wohlfahrt | 27 July 2016, 15:57:52 UTC | Make median-filter length variable | 27 July 2016, 15:57:52 UTC |
| d204b61 | Kai Wohlfahrt | 27 July 2016, 15:31:07 UTC | Use subplots instead of add_subplot | 27 July 2016, 15:31:07 UTC |
| 14f6254 | Kai Wohlfahrt | 27 July 2016, 15:30:35 UTC | Show total number of traces analyzed | 27 July 2016, 15:30:35 UTC |
| be43081 | Kai Wohlfahrt | 26 July 2016, 13:04:43 UTC | Use nearest interpolation for extract plot | 26 July 2016, 13:25:34 UTC |
| dd5a755 | Kai Wohlfahrt | 26 July 2016, 13:02:46 UTC | Add another dataset | 26 July 2016, 13:25:29 UTC |
| 216123f | Kai Wohlfahrt | 25 July 2016, 15:22:51 UTC | Add another dataset | 25 July 2016, 15:23:24 UTC |
| 3dc46da | Kai Wohlfahrt | 25 July 2016, 15:06:53 UTC | Handle 1-sample case roundMean failed because no variance available (i.e. log10 failed). | 25 July 2016, 15:06:53 UTC |
| 7026e9d | Kai Wohlfahrt | 07 July 2016, 12:58:52 UTC | Add power dependency samples to extract.fish | 07 July 2016, 13:04:27 UTC |
| ec13e3b | Kai Wohlfahrt | 07 July 2016, 12:58:24 UTC | Add binning to fret analysis | 07 July 2016, 13:04:27 UTC |
| a398dd7 | Kai Wohlfahrt | 06 July 2016, 11:53:00 UTC | Add poisson HMM Adds an initial poisson-based HMM. Test for a further expansion to simulate CCD (poisson photon count + multiplier + gaussian noise). Also includes some simple code to demonstrate hmmlearn. | 06 July 2016, 15:36:26 UTC |
| 9032521 | Kai Wohlfahrt | 04 July 2016, 09:47:52 UTC | Round mean/variation to correct significant figs | 04 July 2016, 09:47:52 UTC |
| 8cab0d6 | Kai Wohlfahrt | 04 July 2016, 09:47:35 UTC | Plot mean/variation lines | 04 July 2016, 09:47:35 UTC |
| 0012cfb | Kai Wohlfahrt | 04 July 2016, 09:46:36 UTC | Add padding to sample plot Matplotlib was cutting off first few pixels, which caused a few things to apparently have no spots. | 04 July 2016, 09:46:36 UTC |
| 40fbb01 | Kai Wohlfahrt | 04 July 2016, 09:46:01 UTC | Exclude dataset from extraction Has y-axis drift | 04 July 2016, 09:46:01 UTC |
| 218b5cc | Kai Wohlfahrt | 04 July 2016, 09:45:34 UTC | Explicitly specify params in extraction script Don't rely on defaults, might change accidentally. | 04 July 2016, 09:45:34 UTC |
| e7ad0cf | Kai Wohlfahrt | 04 July 2016, 09:41:25 UTC | Use halfway point as threshold Same as done by Steve's program. | 04 July 2016, 09:41:25 UTC |
| 7c7af27 | Kai Wohlfahrt | 01 July 2016, 15:41:42 UTC | Test array path for excludeFrames | 01 July 2016, 15:41:42 UTC |
| 7df0c15 | Kai Wohlfahrt | 01 July 2016, 12:59:50 UTC | Add plotting to extract.py | 01 July 2016, 15:39:27 UTC |
| 043d12a | Kai Wohlfahrt | 01 July 2016, 11:24:26 UTC | Add peakEnclosed test for arrays | 01 July 2016, 15:39:27 UTC |
| dd83628 | Kai Wohlfahrt | 30 June 2016, 20:10:33 UTC | Add extract for iterables | 01 July 2016, 15:39:26 UTC |
| cda7683 | Kai Wohlfahrt | 30 June 2016, 16:49:17 UTC | Remove unused argument | 01 July 2016, 15:39:25 UTC |
| 3ded372 | Kai Wohlfahrt | 30 June 2016, 16:48:42 UTC | Add excludeFrames for iterable sequence | 01 July 2016, 15:39:24 UTC |
| b6a4da4 | Kai Wohlfahrt | 30 June 2016, 15:45:44 UTC | Add 561 dataset to extract.fish | 30 June 2016, 16:30:20 UTC |
| 52d8ceb | Kai Wohlfahrt | 30 June 2016, 15:45:02 UTC | Make extract normalization optional Later data-sets have no background variance. | 30 June 2016, 16:30:20 UTC |
| b327694 | Kai Wohlfahrt | 30 June 2016, 14:38:04 UTC | Crop samples symmetrically | 30 June 2016, 14:38:04 UTC |
| 9f810a3 | Kai Wohlfahrt | 29 June 2016, 16:21:10 UTC | Use fwd + backward derivative for laplacian This makes the picked points better centered on the source points. | 29 June 2016, 16:21:10 UTC |
| bad571d | Kai Wohlfahrt | 29 June 2016, 16:20:41 UTC | Improve blob.py plotting | 29 June 2016, 16:20:41 UTC |
| 0af46a4 | Kai Wohlfahrt | 21 June 2016, 09:15:20 UTC | Use mean instead of max per frame Should give better signal/noise. Also reduce the sampling area. | 21 June 2016, 09:15:20 UTC |
| 61f05c8 | Kai Wohlfahrt | 21 June 2016, 09:12:55 UTC | Add pickle format for blob.py output | 21 June 2016, 09:12:55 UTC |
| 0444c79 | Kai Wohlfahrt | 20 June 2016, 10:20:35 UTC | Move analyze.fish -> extract.fish | 20 June 2016, 10:20:35 UTC |
| 48c389b | Kai Wohlfahrt | 13 June 2016, 13:10:04 UTC | Extract raw frames Extracts raw frames (instead of median-filtered), and allows for excluding frame ranges at the extraction level. This makes further processing a bit more flexible. | 13 June 2016, 13:10:04 UTC |
| 8d99b66 | Kai Wohlfahrt | 09 June 2016, 11:23:02 UTC | Improve blob.py command line Adds plotting and CSV writing (as opposed to print). | 09 June 2016, 11:23:02 UTC |
| 3779e95 | Kai Wohlfahrt | 03 June 2016, 14:20:38 UTC | Update blob.py as executable Prints coordinates from an image passed on the command line, instead of a fixed demo. | 03 June 2016, 14:20:38 UTC |
| ace0531 | Kai Wohlfahrt | 02 June 2016, 14:54:48 UTC | Fix sphere intersection Intersection only valid if volumes actually intersect and d != 0, so check for this. Clamp all other values to 0 (not strictly correct for d == 0). | 02 June 2016, 14:54:48 UTC |
| 12130f1 | Kai Wohlfahrt | 27 May 2016, 10:02:15 UTC | Load traces on demand, keep only stats | 27 May 2016, 10:02:15 UTC |
| 55c08bf | Kai Wohlfahrt | 27 May 2016, 10:00:41 UTC | Pad sample if rows cannot be factorized | 27 May 2016, 10:00:41 UTC |
| e9cff56 | Kai Wohlfahrt | 22 May 2016, 22:34:03 UTC | Compare multiple datasets in analysis Nested dicts are a little awkward to work with. Maybe time to consider SQL? | 22 May 2016, 22:34:03 UTC |
| 1d451cd | Kai Wohlfahrt | 22 May 2016, 21:36:36 UTC | Rework stat organization Organize into dict to keep title and stat together. | 22 May 2016, 21:36:36 UTC |
