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silx.gui.colors: Add "percentile" mode for autoscaling #4154

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merged 6 commits into from
Oct 7, 2024
Merged

silx.gui.colors: Add "percentile" mode for autoscaling #4154

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8c0ff5d
Add "percentile" mode for autoscaling
clemisch Aug 5, 2024
a278a74
Tweak percentile mode variable names
clemisch Aug 13, 2024
a153088
Compute 1st and 99th percentiles simultaneously
clemisch Aug 15, 2024
1c95a86
Add tests for percentile 1-99 autoscale
t20100 Oct 7, 2024
e9edc4f
sanitize data before calling np.percentile
t20100 Oct 7, 2024
c88921e
Merge pull request #1 from t20100/pr4154
clemisch Oct 7, 2024
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5 changes: 4 additions & 1 deletion src/silx/gui/colors.py
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Expand Up @@ -331,7 +331,10 @@ class Colormap(qt.QObject):
"""constant for autoscale using mean +/- 3*std(data)
with a clamp on min/max of the data"""

AUTOSCALE_MODES = (MINMAX, STDDEV3)
PERCENTILE_1_99 = "percentile_1_99"
"""constant for autoscale using 1st and 99th percentile of data"""

AUTOSCALE_MODES = (MINMAX, STDDEV3, PERCENTILE_1_99)
"""Tuple of managed auto scale algorithms"""

sigChanged = qt.Signal()
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1 change: 1 addition & 0 deletions src/silx/gui/dialog/ColormapDialog.py
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Expand Up @@ -234,6 +234,7 @@ class _AutoscaleModeComboBox(qt.QComboBox):
DATA = {
Colormap.MINMAX: ("Min/max", "Use the data min/max"),
Colormap.STDDEV3: ("Mean±3std", "Use the data mean ± 3 × standard deviation"),
Colormap.PERCENTILE_1_99: ("Percentile 1-99", "Use 1st to 99th percentile of data"),
}

def __init__(self, parent: qt.QWidget):
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3 changes: 3 additions & 0 deletions src/silx/math/colormap.py
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Expand Up @@ -265,6 +265,9 @@ def autoscale(self, data, mode):
vmax = dmax
else:
vmax = min(dmax, stdmax)
elif mode == "percentile_1_99":
vmin = numpy.nanpercentile(data, 1)
vmax = numpy.nanpercentile(data, 99)

else:
raise ValueError("Unsupported mode: %s" % mode)
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