tlambert03
commented
1 year ago also gave the examples a shot:
$ python examples/parallel_psf.py
...
Traceback (most recent call last):
File "/Users/talley/dev/forks/chromatix/examples/parallel_psf.py", line 33, in <module>
widefield_psf = compute_psf(z)
File "/Users/talley/dev/forks/chromatix/examples/parallel_psf.py", line 29, in compute_psf
return optical_model.apply({}, z).intensity
File "/Users/talley/dev/forks/chromatix/src/chromatix/systems/optical_system.py", line 31, in __call__
field = self.elements[0](*args, **kwargs) # allow field to be initialized
File "/Users/talley/dev/forks/chromatix/src/chromatix/elements/sources.py", line 115, in __call__
f = register(self, "f")
File "/Users/talley/dev/forks/chromatix/src/chromatix/elements/utils.py", line 26, in register
return module.variable(
flax.errors.ScopeCollectionNotFound: Tried to access "_f" from collection "state" in "/elements_0" but the collection is empty. (https://flax.readthedocs.io/en/latest/api_reference/flax.errors.html#flax.errors.ScopeCollectionNotFound)and
$ python examples/parallel_psf.py
...
Traceback (most recent call last):
File "/Users/talley/dev/forks/chromatix/examples/parallel_imaging.py", line 54, in <module>
params = init_params(jax.random.PRNGKey(6022), volume, z)
File "/Users/talley/dev/forks/chromatix/examples/parallel_imaging.py", line 43, in init_params
params = microscope.init(key, volume, z)
File "/Users/talley/dev/forks/chromatix/src/chromatix/systems/microscopes.py", line 87, in __call__
system_psf = self.psf(*args, **kwargs)
File "/Users/talley/dev/forks/chromatix/src/chromatix/systems/microscopes.py", line 99, in psf
return self.system_psf(self, *args, **kwargs)
File "/Users/talley/dev/forks/chromatix/src/chromatix/systems/microscopes.py", line 211, in __call__
psf = system(z)
File "/Users/talley/dev/forks/chromatix/src/chromatix/systems/optical_system.py", line 33, in __call__
field = element(field)
File "/Users/talley/dev/forks/chromatix/src/chromatix/elements/phase_masks.py", line 68, in __call__
phase = register(
File "/Users/talley/dev/forks/chromatix/src/chromatix/elements/utils.py", line 24, in register
return module.param(f"_{name}", parse_init(init.val), *args)
File "/Users/talley/dev/forks/chromatix/src/chromatix/functional/phase_masks.py", line 49, in flat_phase
return jnp.full(shape, value)
File "/Users/talley/mambaforge/envs/chromatix/lib/python3.10/site-packages/jax/_src/numpy/lax_numpy.py", line 2058, in full
return lax.full(shape, fill_value, dtype)
jaxlib.xla_extension.XlaRuntimeError: UNKNOWN: <unknown>:0: error: invalid shape type=11, dims=[3235068045,3032181039]:
<unknown>:0: note: see current operation: "func.return"(%0) : (tensor<3235068045x3032181039xf32>) -> ()not complaining! I know how hard it is to develop a very new project and keep the docs/examples working. 😄
anyway, really excited for what's happening here and look forward to digging in some more!
GJBoth
diptodip
just a courtesy note: the "chromatix 101 docs" appear to be out of date.