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DOI

tpx3EventViewer

This software converts the sparse event stream (in HDF5) generated by tpx3HitParser from Timepix3 data to frames.

Processing

The green blocks are performed by tpx3HitParser while the blue blocks are done by tpx3EventViewer.

Getting ready

Download

git clone https://github.com/M4I-nanoscopy/tpx3EventViewer.git
cd tpx3EventViewer

Recommended way is to use a Python virtualenv. But this is optional.

virtualenv tpx3
source tpx3/bin/activate

Install Python dependencies

pip install -r requirements.txt

Running

$./tpx3HitParser.py --help
usage: tpx3EventViewer.py [-h] [-t] [--uint32] [--uint8] [-m] [-f FILE] [-o] [-n] [-r ROTATION] [-g GAIN] [--animation] [--power_spectrum] [--flip_x] [--flip_y] [--hits] [--hits_tot] [--hits_toa] [--gauss GAUSS] [--events_sumtot] [--events_nhits] [--timing_stats]
                          [--tot_threshold TOT_THRESHOLD] [--tot_limit TOT_LIMIT] [--chip CHIP] [--normalize] [--exposure EXPOSURE] [--start START] [--end END] [--super_res N] [--cluster_stats] [--cluster_stats_tot CLUSTER_STATS_TOT] [--cluster_stats_size CLUSTER_STATS_SIZE]
                          FILE

positional arguments:
  FILE                  Input .h5 file

options:
  -h, --help            show this help message and exit
  -t                    Store uint16 .tif file
  --uint32              Store uint32 tif (not supported by all readers!)
  --uint8               Store uint8 tif (supported by almost all readers)
  -m                    Store as mrc file
  -f FILE               File name for .tif file (default is .h5 file with .tif extension)
  -o                    Overwrite existing file
  -n                    Don't show interactive viewer
  -r ROTATION, --rotation ROTATION
                        Rotate 90 degrees (1: clockwise, -1 anti-clockwise, 0: none). Default: 0
  -g GAIN, --gain GAIN  MRC file with gain correction.
  --animation           Store as animated mp4 file
  --power_spectrum      Show power spectrum
  --flip_x              Flip image in X
  --flip_y              Flip image in Y
  --hits                Use hits (default in counting mode)
  --hits_tot            Use hits in ToT mode
  --hits_toa            Use hits in ToA mode
  --gauss GAUSS         Use events, but place back as gaussian with a certain lambda. Default: None
  --events_sumtot       Use events in sumToT mode
  --events_nhits        Use events in nHits mode
  --timing_stats        Show timing stats
  --tot_threshold TOT_THRESHOLD
                        In hits show only hits above ToT threshold
  --tot_limit TOT_LIMIT
                        In hits show only hits below ToT limit
  --chip CHIP           Limit display to certain chip
  --normalize           Normalize to the average (useful for showing ToT)
  --exposure EXPOSURE   Max exposure time in seconds (0: infinite)
  --start START         Start time in seconds
  --end END             End time in seconds
  --super_res N         Up scale the amount of pixels by N factor
  --cluster_stats       Show cluster stats
  --cluster_stats_tot CLUSTER_STATS_TOT
                        Override cluster_stats ToT limit
  --cluster_stats_size CLUSTER_STATS_SIZE
                        Override cluster_stats size limit

Citing

DOI

Please consider citing either or both the Zenodo deposit of this code and our two papers:

  • van Schayck, J. Paul. (2020). M4I-nanoscopy/tpx3EventViewer. Zenodo. https://doi.org/10.5281/zenodo.3693990
  • Schayck, J. P. van, Genderen, E. van, Maddox, E., Roussel, L., Boulanger, H., Fröjdh, E., Abrahams, J.-P., Peters, P. J. & Ravelli, R. B. G. (2020). Sub-pixel electron detection using a convolutional neural network. Ultramicroscopy, 218, 113091. https://doi.org/10.1016/j.ultramic.2020.113091
  • J Paul van Schayck, Yue Zhang, Kèvin Knoops, Peter J Peters, Raimond B G Ravelli, Integration of an Event-driven Timepix3 Hybrid Pixel Detector into a Cryo-EM Workflow, Microscopy and Microanalysis, Volume 29, Issue 1, February 2023, Pages 352–363, https://doi.org/10.1093/micmic/ozac009

Copyright

(c) Maastricht University

License

MIT license

Authors