| 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 |
| 2de74f0 | Kai Wohlfahrt | 22 May 2016, 21:22:09 UTC | Split out sampling code Removes randomness from remaining analysis. Also aims are a little different, sampling randomly from multiple different experiments doesn't make much sense. | 22 May 2016, 21:23:22 UTC |
| 0d529bd | Kai Wohlfahrt | 22 May 2016, 19:34:57 UTC | Add analysis of multiple repeats to fret_analysis Analyses multiple repeats and returns std deviation between repeats in summary statistics. | 22 May 2016, 19:34:57 UTC |
| e34c276 | Kai Wohlfahrt | 22 May 2016, 16:59:15 UTC | Add analysis script Finds series of TIF images per dataset & video in specified directories, and extracts ROIs by calling extract.py | 22 May 2016, 16:59:15 UTC |
| a2a2d79 | Kai Wohlfahrt | 22 May 2016, 12:04:41 UTC | Support multi-file series Adds tiffConcat to concatenate multiple TIFF files in a memory-efficient manner. | 22 May 2016, 12:04:41 UTC |
| 04d718b | Kai Wohlfahrt | 20 May 2016, 10:56:49 UTC | Split ROI extraction and plotting Question is where to plot selected peaks. Data is available in extraction. | 20 May 2016, 10:56:49 UTC |
| 091717e | Kai Wohlfahrt | 19 May 2016, 12:10:55 UTC | Reorganize stat collection Fixes photons/frame (previously was photons/blink/on time). Also reorganizes other functions to be clearer, though possibly slower. | 19 May 2016, 14:19:48 UTC |
| bc2db39 | Kai Wohlfahrt | 19 May 2016, 11:00:09 UTC | Process multiple files This adds processing of multiple datasets. Removes plotting of selected samples on projection for convenience. TODO: - Compute standard deviation between datasets, not between all data points. - Restore plotting of collected samples on projection. | 19 May 2016, 11:00:09 UTC |
| b6f188f | Kai Wohlfahrt | 18 May 2016, 14:59:40 UTC | Move output argument Preparation for accepting multiple image series | 18 May 2016, 14:59:40 UTC |
| f4da1d9 | Kai Wohlfahrt | 18 May 2016, 14:59:18 UTC | Clean up numpy imports | 18 May 2016, 14:59:18 UTC |
| 51eb8bb | Kai Wohlfahrt | 18 May 2016, 14:47:29 UTC | Output summary statistics Print summary statistics to csv/stdout | 18 May 2016, 14:47:29 UTC |
| 1368fd3 | Kai Wohlfahrt | 18 May 2016, 11:17:25 UTC | Add .gitignore | 18 May 2016, 11:17:25 UTC |
| 135b888 | Kai Wohlfahrt | 18 May 2016, 11:16:08 UTC | Add photon count / frame | 18 May 2016, 11:16:08 UTC |
| 79b5752 | Kai Wohlfahrt | 17 May 2016, 14:07:37 UTC | Add png output Currently all plots are the same (~A4) size, can adjust. | 17 May 2016, 14:07:37 UTC |
| 2410e15 | Kai Wohlfahrt | 17 May 2016, 13:27:33 UTC | Count truncated last blink Last blink is always included in the photon count, so also include it in the blink count even if it is truncated. | 17 May 2016, 13:28:05 UTC |
| bb1cf60 | Kai Wohlfahrt | 17 May 2016, 13:26:48 UTC | Parallelize rollingMedian Biggest time taken here, so use parallel map. | 17 May 2016, 13:26:48 UTC |
| 072450c | Kai Wohlfahrt | 17 May 2016, 13:25:40 UTC | Limit histogram bins Limit largest bin to 95th percentile, reduces compression of data by outliers. | 17 May 2016, 13:25:40 UTC |
| e0da62f | Kai Wohlfahrt | 17 May 2016, 12:25:02 UTC | Add per-blink photon counts | 17 May 2016, 12:25:02 UTC |
| 2de233b | Kai Wohlfahrt | 17 May 2016, 11:24:46 UTC | Add total photon count | 17 May 2016, 11:24:46 UTC |
| 11122fa | Kai Wohlfahrt | 17 May 2016, 09:34:10 UTC | Add blink counts Note on-state must be signed int for gradient extraction to work. | 17 May 2016, 10:39:27 UTC |
| 96ccd67 | Kai Wohlfahrt | 17 May 2016, 09:33:21 UTC | Use single level threshold for on/off | 17 May 2016, 09:33:21 UTC |
| abcf3c6 | Kai Wohlfahrt | 17 May 2016, 09:25:21 UTC | Pre-calculate traces/rois, index for samples All ROIs and traces will be needed anyway (ROIs for photon count later). This allows marking the sampled regions in the projection. | 17 May 2016, 09:25:21 UTC |
| 9247de8 | Kai Wohlfahrt | 16 May 2016, 15:13:53 UTC | Make seed parameter for sample selection explicit | 16 May 2016, 15:17:44 UTC |
| 0a52e66 | Kai Wohlfahrt | 13 May 2016, 10:17:40 UTC | Use indices.stop to get subplot dims | 13 May 2016, 10:17:40 UTC |
| 6671c96 | Kai Wohlfahrt | 12 May 2016, 17:08:15 UTC | Pre-filter entire image Applies a median blur to the entire image before spot picking. Reduces number of spurious spots. | 12 May 2016, 17:08:15 UTC |
| 71945f7 | Kai Wohlfahrt | 12 May 2016, 16:13:31 UTC | Divide by pre-computed background | 12 May 2016, 16:13:31 UTC |
| e425e61 | Kai Wohlfahrt | 09 May 2016, 14:24:16 UTC | Display histogram of on-times and blink lengths | 09 May 2016, 14:52:15 UTC |
| b94f66d | Kai Wohlfahrt | 09 May 2016, 14:24:07 UTC | Round ROI size to int 'scale' is np.int64, so cast to python int for round to work correctly. | 09 May 2016, 14:51:55 UTC |
| 3df297d | Kai Wohlfahrt | 09 May 2016, 14:20:04 UTC | Color lines by on/off state Slightly complicated with matplotlib, need to use LineCollection. http://matplotlib.org/examples/pylab_examples/multicolored_line.html | 09 May 2016, 14:20:04 UTC |
| 8ef27a8 | Kai Wohlfahrt | 05 May 2016, 10:19:03 UTC | Initial commit blob.py does Laplacian of Gaussian detection of blobs in nD data extract.py extracts spots from well-separated, static point sources, and plots their on/off state. | 05 May 2016, 10:19:03 UTC |
