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Fix Measure2D for recent skimage #1303

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Merged
David-Baddeley merged 1 commit into from
Oct 13, 2022
Merged

Fix Measure2D for recent skimage #1303

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24 changes: 14 additions & 10 deletions PYME/recipes/measurement.py
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Original file line number Diff line number Diff line change
Expand Up @@ -629,6 +629,18 @@ def execute(self, namespace):
namespace[self.outputName] = res


# there are some measurements we don't want / are not particlarly useful (i.e. the ones which just return the image)
# some of these changed in recent versions of skimage (2022), so try both new and old versions
_MEASURE2D_KEYS_TO_IGNORE = ['convex_image',
'filled_image',
'image_convex',
'image_filled',
'image',
'intensity_image',
'image_intensity']

# euler_number calculation can be buggy and cause crashes
_MEASURE2D_KEYS_TO_IGNORE.append('euler_number')

@register_module('Measure2D')
class Measure2D(ModuleBase):
Expand Down Expand Up @@ -665,18 +677,10 @@ def __init__(self):
def addFrameMeasures(self, frameNo, measurements, contours = None):
if len(measurements) == 0:
return

if len(self.measures) == 0:
#first time we've called this - determine our data type
self._keys = ['t', 'x', 'y'] + [r for r in dir(measurements[0]) if not r.startswith('_')]

self._keys.remove('euler_number') #buggy!

# remove all the image measurements - as these will potentially generate export errors
# and are not super-useful
self._keys.remove('convex_image')
self._keys.remove('filled_image')
self._keys.remove('image')
self._keys.remove('intensity_image')
self._keys = ['t', 'x', 'y'] + [r for r in dir(measurements[0]) if not (r.startswith('_') or r in _MEASURE2D_KEYS_TO_IGNORE)]

if not contours is None:
self._keys += ['contour']
Expand Down