savu.data.stats.statistics module¶
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class
Statistics
[source] -
calc_rmsd
(array1, array2)[source]
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static
calc_rss
(array1, array2)[source]
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calc_slice_stats
(my_slice, base_slice=None, pad=True)[source] Calculates and returns slice stats for the current slice.
- Parameters
my_slice – The slice whose stats are being calculated.
base_slice – Provide a base slice to calculate residuals from, to calculate RMSD.
pad – Specify whether slice is padded or not (usually can leave as True even if slice is not padded).
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calc_stats_residuals
(stats_before, stats_after)[source]
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calc_volume_stats
(slice_stats)[source] Calculates and returns volume-wide stats from slice-wide stats.
- Parameters
slice_stats – The slice-wide stats that the volume-wide stats are calculated from.
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static
calc_zeros
(my_slice)[source]
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get_stats
(p_num=None, stat=None, instance=- 1)[source] Returns stats associated with a certain plugin, given the plugin number (its place in the process list).
- Parameters
p_num – Plugin number of the plugin whose associated stats are being fetched. If p_num <= 0, it is relative to the plugin number of the current plugin being run. E.g current plugin number = 5, p_num = -2 –> will return stats of the third plugin. By default will gather stats for the current plugin.
stat – Specify the stat parameter you want to fetch, i.e ‘max’, ‘mean’, ‘median_std_dev’. If left blank will return the whole dictionary of stats: {‘max’: , ‘min’: , ‘mean’: , ‘mean_std_dev’: , ‘median_std_dev’: , ‘NRMSD’: }
instance – In cases where there are multiple set of stats associated with a plugin due to iterative loops or multi-parameters, specify which set you want to retrieve, i.e 3 to retrieve the stats associated with the third run of a plugin. Pass ‘all’ to get a list of all sets. By default will retrieve the most recent set.
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get_stats_from_dataset
(dataset, stat=None, instance=- 1)[source] Returns stats associated with a dataset.
- Parameters
dataset – The dataset whose associated stats are being fetched.
stat – Specify the stat parameter you want to fetch, i.e ‘max’, ‘mean’, ‘median_std_dev’. If left blank will return the whole dictionary of stats: {‘max’: , ‘min’: , ‘mean’: , ‘mean_std_dev’: , ‘median_std_dev’: , ‘NRMSD’: }
instance – In cases where there are multiple set of stats associated with a dataset due to iterative loops or multi-parameters, specify which set you want to retrieve, i.e 3 to retrieve the stats associated with the third run of a plugin. Pass ‘all’ to get a list of all sets. By default will retrieve the most recent set.
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get_stats_from_name
(plugin_name, n=None, stat=None, instance=- 1)[source] Returns stats associated with a certain plugin.
- Parameters
plugin_name – name of the plugin whose associated stats are being fetched.
n – In a case where there are multiple instances of plugin_name in the process list, specify the nth instance. Not specifying will select the first (or only) instance.
stat – Specify the stat parameter you want to fetch, i.e ‘max’, ‘mean’, ‘median_std_dev’. If left blank will return the whole dictionary of stats: {‘max’: , ‘min’: , ‘mean’: , ‘mean_std_dev’: , ‘median_std_dev’: , ‘NRMSD’: }
instance – In cases where there are multiple set of stats associated with a plugin due to iterative loops or multi-parameters, specify which set you want to retrieve, i.e 3 to retrieve the stats associated with the third run of a plugin. Pass ‘all’ to get a list of all sets. By default will retrieve the most recent set.
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static
rmsd_from_rss
(rss, n)[source]
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set_slice_stats
(my_slice, base_slice=None, pad=True)[source] Sets slice stats for the current slice.
- Parameters
my_slice – The slice whose stats are being set.
base_slice – Provide a base slice to calculate residuals from, to calculate RMSD.
pad – Specify whether slice is padded or not (usually can leave as True even if slice is not padded).
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set_stats_key
(stats_key)[source] Changes which stats are to be calculated for the current plugin.
- Parameters
stats_key – List of stats to be calculated.
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set_stats_residuals
(residuals)[source]
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set_time
(seconds)[source] Sets time taken for plugin to complete.
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set_volume_stats
()[source] Calculates volume-wide statistics from slice stats, and updates class-wide arrays with these values. Links volume stats with the output dataset and writes slice stats to file.
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setup
(plugin_self, pattern=None)[source]
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start_time
()[source] Called at the start of a plugin.
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stop_time
()[source] Called at the ebd of a plugin.
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write_slice_stats_to_file
(slice_stats=None, p_num=None, comm=<Mock name='mock.MPI.COMM_WORLD' id='140070287344848'>)[source] Writes slice statistics to a h5 file. Placed in the stats folder in the output directory. Currently unused.
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