data_analyzer.md

Data Analyzer

In Auto3DSeg, the data analyzer automatically analyzes given medical image dataset and reports the statistics of image intensity, shape, spacing, etc.

Usage

The ussage of data analyzer is can be found here

Customization

Auto3DSeg also provides the API for users to use their own customized data analyzing function as shown in this notebook.

Output

"datastats.yaml" is a summary of the dataset from the data analyzer. The summary report includes information such as data size, spacing, intensity distribution, etc., for a better understanding of the dataset. An example "datastats.yaml" is shown as follows.

...
stats_summary:
  image_foreground_stats:
    intensity: {max: 1326.0, mean: 353.68545989990236, median: 339.03333333333336,
      min: 0.0, percentile_00_5: 94.70366643269857, percentile_10_0: 210.9, percentile_90_0: 518.3333333333334,
      percentile_99_5: 734.7439453125, stdev: 122.72876790364583}
  image_stats:
    channels:
      max: 2
      mean: 2.0
      median: 2.0
      min: 2
      percentile: [2, 2, 2, 2]
      percentile_00_5: 2
      percentile_10_0: 2
      percentile_90_0: 2
      percentile_99_5: 2
      stdev: 0.0
    intensity: {max: 2965.0, mean: 307.1866872151693, median: 239.9, min: 0.0, percentile_00_5: 1.5333333333333334,
      percentile_10_0: 54.53333333333333, percentile_90_0: 649.3333333333334, percentile_99_5: 1044.0333333333333,
      stdev: 238.39599100748697}
    shape:
      max: [384, 384, 24]
      mean: [317.8666666666667, 317.8666666666667, 18.8]
...