Skip to content

Adding average to zonal_statistics output #467

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
megannissel merged 3 commits into from
Mar 4, 2026
Merged

Adding average to zonal_statistics output #467

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e05b656
Adding average calculations to zonal_statistics.
phargogh Feb 27, 2026
743aec5
Forgot to remove self.maxDiff=None. RE:#370
phargogh Feb 27, 2026
38fae16
Merge branch 'main' into feature/370-average-metric-in-zonal-stats
phargogh Mar 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions HISTORY.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,9 @@ Unreleased Changes
References to the old name and website domain have been updated to reflect
this change.
https://github.com/natcap/pygeoprocessing/issues/458
* The average value of valid pixels is now computed in
``pygeoprocessing.zonal_statistics`` for each feature.
https://github.com/natcap/pygeoprocessing/issues/370
* Handling the case where a floating-point raster passed to
``pygeoprocessing.reclassify_raster`` may have a NaN nodata value.
https://github.com/natcap/pygeoprocessing/issues/454
Expand Down
18 changes: 16 additions & 2 deletions src/pygeoprocessing/geoprocessing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1591,6 +1591,7 @@ def zonal_statistics(
- 'max': maximum valid pixel value
- 'sum': sum of valid pixel values
- 'count': number of valid pixels
- 'average': the mean value of valid pixels
- 'nodata_count': number of nodata pixels
- 'value_counts': number of pixels having each unique value

Expand Down Expand Up @@ -1638,14 +1639,15 @@ def zonal_statistics(
If `base_raster_path_band` is a tuple, the return value is a nested
dictionary of stats for that raster band. Top-level keys are the
aggregate feature FIDs. Each nested FID dictionary then contains
statistics about that feature: 'min', 'max', 'sum', 'count',
statistics about that feature: 'min', 'max', 'sum', 'count', 'average',
'nodata_count', and optionally 'value_counts'. Example::
{
0: {
'min': 0,
'max': 14,
'sum': 42,
'count': 8,
'average': 5.25,
'nodata_count': 1,
'value_counts': {
2: 5,
Expand Down Expand Up @@ -1720,7 +1722,8 @@ def zonal_statistics(
# don't overlap any valid pixels.
def default_aggregate_dict():
default_aggregate_dict = {
'min': None, 'max': None, 'count': 0, 'nodata_count': 0, 'sum': 0}
'min': None, 'max': None, 'count': 0, 'nodata_count': 0, 'sum': 0,
'average': None}
if include_value_counts:
default_aggregate_dict['value_counts'] = collections.Counter()
return default_aggregate_dict
Expand Down Expand Up @@ -1907,6 +1910,10 @@ def default_aggregate_dict():
feature_data.max(), aggregate_stats_list[i][fid]['max'])
aggregate_stats_list[i][fid]['sum'] += feature_data.sum()
aggregate_stats_list[i][fid]['count'] += feature_data.size
aggregate_stats_list[i][fid]['average'] = (
aggregate_stats_list[i][fid]['sum'] /
aggregate_stats_list[i][fid]['count']
)
if include_value_counts:
# .update() here is operating on a Counter, so values are
# ADDED, not replaced.
Expand Down Expand Up @@ -1977,6 +1984,7 @@ def default_aggregate_dict():
aggregate_stats_list[i][unset_fid]['min'] = 0
aggregate_stats_list[i][unset_fid]['max'] = 0
aggregate_stats_list[i][unset_fid]['sum'] = 0
aggregate_stats_list[i][unset_fid]['average'] = 0
else:
aggregate_stats_list[i][unset_fid]['min'] = numpy.min(
unset_fid_block)
Expand All @@ -1987,6 +1995,12 @@ def default_aggregate_dict():
aggregate_stats_list[i][unset_fid]['count'] = unset_fid_block.size
aggregate_stats_list[i][unset_fid]['nodata_count'] = numpy.sum(
unset_fid_nodata_mask)
if aggregate_stats_list[i][unset_fid]['count'] == 0:
aggregate_stats_list[i][unset_fid]['average'] = None
else:
aggregate_stats_list[i][unset_fid]['average'] = (
aggregate_stats_list[i][unset_fid]['sum'] /
aggregate_stats_list[i][unset_fid]['count'])
if include_value_counts:
# .update() here is operating on a Counter, so values are ADDED,
# not replaced.
Expand Down
18 changes: 18 additions & 0 deletions tests/test_geoprocessing.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1183,24 +1183,28 @@ def test_zonal_stats_multiple_rasters(self):
'max': 1,
'min': 1,
'nodata_count': 0,
'average': 1,
'sum': 81},
1: {
'count': 1,
'max': 1,
'min': 1,
'average': 1,
'nodata_count': 0,
'sum': 1}
}, {
0: {
'count': 81,
'max': 2,
'min': 2,
'average': 2,
'nodata_count': 0,
'sum': 162},
1: {
'count': 1,
'max': 2,
'min': 2,
'average': 2,
'nodata_count': 0,
'sum': 2}
}]
Expand Down Expand Up @@ -1345,16 +1349,19 @@ def test_zonal_statistics(self):
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1,
'sum': 81.0},
1: {
'count': 1,
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1,
'sum': 1.0},
2: {
'min': None,
'max': None,
'average': None,
'count': 0,
'nodata_count': 0,
'sum': 0.0}}
Expand Down Expand Up @@ -1435,17 +1442,20 @@ def test_zonal_statistics_3d_polygon(self):
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1.0,
'sum': 81.0},
1: {
'count': 1,
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1.0,
'sum': 1.0},
2: {
'min': None,
'max': None,
'count': 0,
'average': None,
'nodata_count': 0,
'sum': 0.0}}
self.assertEqual(result, expected_result)
Expand Down Expand Up @@ -1489,6 +1499,7 @@ def test_zonal_statistics_multipolygon(self):
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1.0,
'sum': 2
}})

Expand Down Expand Up @@ -1563,6 +1574,7 @@ def test_zonal_statistics_3d_multipolygon(self):
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1,
'sum': 2
}})

Expand Down Expand Up @@ -1623,20 +1635,23 @@ def test_zonal_statistics_value_counts(self):
'min': 1.0,
'nodata_count': 0,
'sum': 81.0,
'average': 1,
'value_counts': {1.0: 81}},
1: {
'count': 1,
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'sum': 1.0,
'average': 1,
'value_counts': {1.0: 1}},
2: {
'min': None,
'max': None,
'count': 0,
'nodata_count': 0,
'sum': 0.0,
'average': None,
'value_counts': {}}
}
self.assertEqual(result, expected_result)
Expand Down Expand Up @@ -1678,6 +1693,7 @@ def test_zonal_statistics_nodata(self):
'max': None,
'min': None,
'nodata_count': 81,
'average': None,
'sum': 0.0}}
self.assertEqual(result, expected_result)

Expand Down Expand Up @@ -1715,6 +1731,7 @@ def test_zonal_statistics_nodata_is_zero(self):
'max': 1,
'min': 1,
'nodata_count': 2,
'average': 1.0,
'sum': 2.0}}
self.assertEqual(result, expected_result)

Expand Down Expand Up @@ -1752,6 +1769,7 @@ def test_zonal_statistics_named_layer(self):
'max': 1.0,
'min': 1.0,
'nodata_count': 0,
'average': 1.0,
'sum': 81.0}}
self.assertEqual(result, expected_result)

Expand Down