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point quiver enginer/layer for single molecule orientation microscopy data#1520

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point quiver enginer/layer for single molecule orientation microscopy data#1520
barentine wants to merge 3 commits into
python-microscopy:masterfrom
barentine:smolmrender

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@barentine barentine commented Jun 7, 2024

Addresses issue #1504 .

Is this a bugfix or an enhancement?
enhancement
Proposed changes:

image

MWE, from a jupyter notebook:

from PYME.LMVis import VisGUI
%gui wx

pymevis = VisGUI.ipython_pymevisualize()
pipeline = pymevis.pipeline


import numpy as np
from PYME.IO import tabular, MetaDataHandler

n_points = 100
ds = tabular.DictSource({'x': np.linspace(0, 100, n_points),
                         'y': np.linspace(0, 100, n_points),
                         'z': np.zeros(n_points),
                         'azimuth': np.linspace(0, 2* np.pi, n_points),
          
                         'zenith': np.linspace(0, np.pi, n_points)})

ds.mdh = MetaDataHandler.DictMDHandler()


pipeline.addDataSource('points', ds)
pipeline.selectDataSource('points')

from PYME.recipes.localisations import LocalizationOrientationAngles
mod = LocalizationOrientationAngles(pipeline.recipe, input_name='points', output_name='oriented_points')

pipeline.recipe.add_modules_and_execute([mod])

pipeline.selectDataSource('oriented_points')

pymevis.add_point_quiver_layer('oriented_points')

remaining:

  • refactor how orientation angles / unit vectors get identified. Hacking them into a potentially large array as an attribute is certainly not the way to do it.
  • make this accessible from the 'add layer' menu (might be able to tie in the orientation/unit vector parameter identification to this part too)

@David-Baddeley , any thoughts on how best to identify what datasource columns correspond to azimuth/zenith or mu_x/mu_y_mu_z?

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barentine commented Jun 10, 2024 •
edited
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Couple outstanding issues:

  • color/alpha variation along vectors [unintentional] that then doesn't match orientation
  • not all points getting drawn, it seems

image

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barentine commented Jun 11, 2024

OK, that's sorted.
I was only drawing half the vertices, and was only providing colors for that half (so each half of the line was taking a different color value rather). Fixed:
image

@David-Baddeley David-Baddeley mentioned this pull request Jul 23, 2024
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