Description
When I make an ExpressionMatrix via AssignTargets.Label, the area coordinate has all nan values.
Steps/Code to Reproduce
# Find spots and decode
p = DetectSpots.BlobDetector(
min_sigma=1,
max_sigma=10,
num_sigma=10,
threshold=0.005,
measurement_type='mean',
)
intensities = p.run(low_passed)
decoded = codebook.decode_per_round_max(intensities)
# Get the mask image
label_image = io.imread('perfect_segmentation_image.tif')
# Get the physical ticks
yc = im.xarray.yc.values
xc = im.xarray.xc.values
physical_ticks = {Coordinates.Y: yc, Coordinates.X:xc}
# Make the mask collection
masks = SegmentationMaskCollection.from_label_image(label_image, physical_ticks=physical_ticks)
# Assign the spots to cells
al = AssignTargets.Label()
labeled = al.run(masks, decoded)
cg = labeled.to_expression_matrix()
Expected Results
I think the area coordinate should contain the area of the corresponding mask.
Actual Results
All of the ExpressionMatrix (cg) area values are nan.
Versions
Darwin-16.7.0-x86_64-i386-64bit
Python 3.6.4 (default, Dec 21 2017, 20:33:17)
NumPy 1.16.4
SciPy 1.3.0
scikit-image 0.15.0
sklearn 0.21.2
pandas 0.25.0
xarray 0.12.3
sympy 1.4
starfish 0.1.4
Description
When I make an
ExpressionMatrixviaAssignTargets.Label, theareacoordinate has all nan values.Steps/Code to Reproduce
Expected Results
I think the area coordinate should contain the area of the corresponding mask.
Actual Results
All of the
ExpressionMatrix(cg)areavalues arenan.Versions
Darwin-16.7.0-x86_64-i386-64bit
Python 3.6.4 (default, Dec 21 2017, 20:33:17)
NumPy 1.16.4
SciPy 1.3.0
scikit-image 0.15.0
sklearn 0.21.2
pandas 0.25.0
xarray 0.12.3
sympy 1.4
starfish 0.1.4