Bug: Opening Relion 3-style .star file results in type checking error in ChimeraX 1.10.1

[bwmr]

Hi,

With the newest version of ChimeraX, opening a standard Relion-3 style star file fails with a type checking error. The star file looks like this:

data_

loop_
_rlnMicrographName #1
_rlnCoordinateX #2
_rlnCoordinateY #3
_rlnCoordinateZ #4
_rlnAngleRot #5
_rlnAngleTilt #6
_rlnAnglePsi #7
Position_1_ali.tomostar	1185.011000	1830.586000	721.641000	-51.494000	138.327000	149.882000
Position_1_ali.tomostar	1419.641000	1761.641000	712.586000	110.320000	142.700000	-94.925000
Position_1_ali.tomostar	1335.326000	1707.326000	577.956000	65.899000	71.599000	6.616000

The error message in ChimeraX is pasted below. TL,DR this is probably caused by newer numpy / pandas versions. I will implement a fix and submit a PR.

Best,
Benedikt

Traceback (most recent call last):
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
    run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215, in provider_open
    models, status = collated_open(session, None, [data], data_format, _add_models,
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526, in collated_open
    return remember_data_format()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
    models, status = func(*func_args, **func_kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/formats.py", line 25, in open
    return open_particle_list(session, data, file_name, format_name=self.name, from_chimx=True)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
    data = formats[format_name].particle_data(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in __init__
    super().__init__(
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
    self.read_file()
  File "/Users/bwi/Library/Application Support/ChimeraX/1.10/lib/python/site-packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in read_file
    if np.issubdtype(df.dtypes[key], np.number):
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/numerictypes.py", line 417, in issubdtype
    arg1 = dtype(arg1).type
           ^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type

TypeError: Cannot interpret '' as a data type

[sroet]

Some more info to add to this issue

My users ran into the same issue on chimeraX 1.8, however we also did have users that could run it (same version of ChimeraX and ArtiaX.

We figured out that all broken installations had pandas=3.0.x while the working install came with pandas=2.3.3
Specifically the df.dtypes[key] on a column with string values like _rlnMicrographName returns a weird empty string (that does not equate to False but also doesn't print anything even when used in type(df.dtypes[key])) that numpy doesn't like.

I do think the fix in #44 should work as that function exists for both version of pandas