Starfish-develop / Starfish-develop/Starfish

Issues running the example WASP14: pca problem

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bug
Dominant language
Python
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Description

Hi! I installed Starfish in my laptop computer (Ubuntu 16.04). I followed the instructions and had no issues until trying to follow the example for WASP14.

The error appear when trying to run:
$ pca.py --create

$ File "pca.py", line 33, in
$ myHDF5 = HDF5Interface()
$ File "/home/angelica/Documentos/Starfish-master/Starfish/grid_tools.py", line 835, in init
$ self.grid_points = hdf5["pars"][:]
$ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2840)
$ File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2798)
$ File "/home/angelica/.local/lib/python3.5/site-packages/h5py/_hl/group.py", line 169, in getitem
$ oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
$ File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2840)
$ File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-huypgcah-build/h5py/_objects.c:2798)
$ File "h5py/h5o.pyx", line 190, in h5py.h5o.open (/tmp/pip-huypgcah-build/h5py/h5o.c:3734)
$ KeyError: "Unable to open object (Object 'pars' doesn't exist)"

Apparently the parameter 'pars' is not defined. I looked in the code 'grid_tools.py' and everything seems to be in order. I have not modified anything in the 'grid_tools.py' code.

I do not know what's wrong, I'd appreciate checking my problem.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by running pca.py --create for the WASP14 example and trace the HDF5Interface initialization in Starfish/grid_tools.py, especially the access to hdf5["pars"]. Inspect the generated HDF5 contents and determine why the pars object is absent; done means the example runs without the reported KeyError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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