Name | Type | Default | Restrictions | Description |
max_intensity | int | -1 | min: -1 | maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). |
auto_max_stdev_factor | float | 3 | min: 0 max: 999 | parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev |
auto_max_percentile | int | 95 | min: 0 max: 100 | parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile |
auto_mode | int | 0 | min: -1 max: 1 | method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method |
win_len | float | 200 | min: 1 | window length in Thomson |
bin_count | int | 30 | min: 3 | number of bins for intensity values |
stdev_mp | float | 3 | min: 0.01 max: 999 | multiplier for stdev |
min_required_elements | int | 10 | min: 1 | minimum number of elements required in a window (otherwise it is considered sparse) |
noise_for_empty_window | float | 1e+20 | | noise value used for sparse windows |