Add a function to display all segmented particles in one frame#25
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YichiWang wants to merge 28 commits into
Open
Add a function to display all segmented particles in one frame#25YichiWang wants to merge 28 commits into
YichiWang wants to merge 28 commits into
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This reverts commit 6ec6344.
Set default store_im to ture to store segmented particles after call ps.ParticleAnalysis
eg. particles.show(). The displayed particles were normalize_boxing. Next step should enable option to display all particle images without normalize_boxing
TomSlater
reviewed
Jul 7, 2020
Owner
|
Thanks Yichi, nice addition. The PR should go to ePSIC-DLS/ParticleSpy rather than here. I can add some documentation / tests too, unless you want to give it a go. |
This reverts commit 67ddc5b.
Allow segmented particle images output as a list of 2D numpy arrays (without hyperspy metadata). e.g. particles = ps.ParticleAnalysis(image, params) particles.normalize_boxing() pim_ls = particles.show(output=True)
Author
Hi Tom, perhaps you could add documentation / tests for this one to show me how it looks like so I can follow in the future. Thanks |
This reverts commit ed2a093.
This reverts commit 1924709.
e.g.
particle_list.show('mask')
or particle_list.show('Image')
Allow show segmented particles in a montage with adjustable number of columns. e.g. particle_list.show(cols=1). Default montage try to display all particles into a square arrangement.
Plus correct particle only image 'p_im'
…lculating image intensity default is True, i.e. perform background subtraction
Default is perform background subtraction for intensity calculation and for stored particle image.
With particle.store['pad']=None and particle.store['store_im']=True, the saved particle image is masked from original survey image and have save dimension as survey image and saved mask.
Main: Use np.ma.masked_array to mask particle image, so intensity std do not calculate the background area. Others: 1. all intensity are background subtracted intensity. 2. Background value are saved as property.
Few more functions. This is a standalone script and not merged with ParticleSpy yet. -find boundary pixel in a clock-wise seqeunce -calculate boundary curvature (signed) use least squre circle fit. -average boundary curvature by given angle interval so at same direction boundary curvatures of two particle with different size (i.e. different boundary pixels) are comparable. Normalised boundary curvature by particle's equivalent diameter is not implemented yet.
This reverts commit e19dbd8.
This reverts commit 1436108.
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e.g.
particles = ps.ParticleAnalysis(image, params)
particles.show()