Writing localisation tables with added Z column

[Miguel Boland]

• Picasso version: latest
• Python version: 3.10.12
• Operating System: Ubuntu 22.04

Description

I am using an external application to assign Z positions to localisations, and would like to write a h5py file that can be read into Picasso Render to illustrate the results.

What I Did

I can read the hdf5 file from picasso localize as follows

df = pd.read_hdf(dirname+'storm_1_MMStack_Default.ome_locs_undrifted.hdf5', key='locs')

But writing a file as follow:

df.to_hdf('locs.hdf5', key='locs')

causes picasso render to fail silently. Editing the source code to throw the error yields:

[13:30, 01/11/2023] Miguel d'Arcangues Boland: Traceback (most recent call last):
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 11826, in open_file_dialog
    self.view.add_multiple(paths)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5730, in add_multiple
    raise e
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5728, in add_multiple
    self.add(path, render=False)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5613, in add
    locs, info = io.load_locs(path, qt_parent=self)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/io.py", line 1244, in load_locs
    print(locs_file['locs'][...])
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", lin…
[13:30, 01/11/2023] Miguel d'Arcangues Boland: Traceback (most recent call last):
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 11826, in open_file_dialog
    self.view.add_multiple(paths)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5730, in add_multiple
    raise e
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5728, in add_multiple
    self.add(path, render=False)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/gui/render.py", line 5613, in add
    locs, info = io.load_locs(path, qt_parent=self)
  File "/home/miguel/Projects/smlm_z/picasso/picasso/io.py", line 1244, in load_locs
    print(locs_file['locs'][...])
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/miguel/anaconda3/envs/picasso/lib/python3.10/site-packages/h5py/hl/group.py", line 359, in __getitem_
    raise TypeError("Accessing a group is done with bytes or str, "
TypeError: Accessing a group is done with bytes or str, not <class 'ellipsis'>

How can I write a file including the Z position which picasso can read correctly?

[Miguel Boland]

I found the solution

import h5py
with h5py.File('./locs_w_z.hdf5', "w") as locs_file:
    locs_file.create_dataset("locs", data=locs.to_records())