Describe the bug
When using the measure2D module in recipes it raises an error due to a naming change of some image properties in the regionpropsmethod.
I am aware of #524 but am suggesting to fix this breakage anyway ahead of unifying the various interfaces.
To Reproduce
Steps to reproduce the behavior:
- Open image in
dh5view
- add
Measure2Dmodule in suitable recipe
- Execute recipe
- See error
Traceback (most recent call last):
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/recipes/recipe.py", line 222, in execute
m.execute(self.namespace)
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/recipes/measurement.py", line 753, in execute
m.addFrameMeasures(i, *self._measureFrame(i, labels, intensity))
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/recipes/measurement.py", line 676, in addFrameMeasures
self._keys.remove('convex_image')
ValueError: list.remove(x): x not in list
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/ui/progress.py", line 153, in func
return fcn(*args, **kwargs)
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/DSView/modules/recipes.py", line 102, in RunCurrentRecipe
self.outp = self.activeRecipe.execute(input=self.image)
File "/Users/csoe002/Documents/src/PYMEsrc/pyme38/PYME/recipes/recipe.py", line 263, in execute
raise RecipeExecutionError('Recipe execution failed in module %s' % self._failing_module._module_name, self ) from e
PYME.recipes.recipe.RecipeExecutionError: Recipe execution failed in module measurement.Measure2D
Reason
Latest skimage.measure.regionprops has renamed some of the XXX_image properties to image_XXX. The patch below fixes this in a backwards compatible manner and is a little more robust in doing it, if ok I can submit as PR.
diff --git a/PYME/recipes/measurement.py b/PYME/recipes/measurement.py
index 6ee1170b7..51668bb0b 100644
--- a/PYME/recipes/measurement.py
+++ b/PYME/recipes/measurement.py
@@ -669,14 +669,21 @@ class Measure2D(ModuleBase):
#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!
+ if 'euler_number' in self._keys:
+ 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')
+ # the naming has changed recently, so check for two possible namings
+ for key in ['convex_image',
+ 'filled_image',
+ 'image_convex',
+ 'image_filled',
+ 'image',
+ 'intensity_image',
+ 'image_intensity']:
+ if key in self._keys:
+ self._keys.remove(key)
if not contours is None:
self._keys += ['contour']Platform (please complete the following information - or copy-paste from error dialog if shown):
- python-microscopy=22.10.03.post0.dev[git]85d65a224ec6
- python=3.8.13, platform=darwin
- numpy=1.23.2, wx=4.2.0 osx-cocoa (phoenix) wxWidgets 3.2.0
Describe the bug
When using the
measure2Dmodule in recipes it raises an error due to a naming change of some image properties in theregionpropsmethod.I am aware of #524 but am suggesting to fix this breakage anyway ahead of unifying the various interfaces.
To Reproduce
Steps to reproduce the behavior:
dh5viewMeasure2Dmodule in suitable recipeReason
Latest
skimage.measure.regionpropshas renamed some of theXXX_imageproperties toimage_XXX. The patch below fixes this in a backwards compatible manner and is a little more robust in doing it, if ok I can submit as PR.Platform (please complete the following information - or copy-paste from error dialog if shown):