id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
869	keyError PhysicalSizeX opening sample OME-TIFF data	Elaine Meng	Tom Goddard	" I tried opening some sample data downloaded from the OME-TIFF website but got tracebacks. I downloaded the Tubhiswt-3D and Tubhiswt-4D data sets from here:
https://docs.openmicroscopy.org/ome-model/5.5.7/ome-tiff/data.html

In each of the resulting folders I started ChimeraX and then tried to open all the *tif files in that folder, but both gave me a traceback (the same one, as far as I could tell):

open tub*tif
Traceback (most recent call last):
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 188, in execute
cmd.run(cmd_text)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2499, in run
result = ci.function(session, **kw_args)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 104, in open
models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/open.py"", line 57, in handle_unknown_kw
return f(*args, **kw)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/models.py"", line 439, in open
session, filenames, format=format, name=name, **kw)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/io.py"", line 435, in open_multiple_data
models, status = open_func(session, paths, name, **kw)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/volume.py"", line 3286, in open_map_format
return open_map(session, stream, name=name, format=format, **kw)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/volume.py"", line 2983, in open_map
grids = data.open_file(map_path, file_type = format)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/data/fileformats.py"", line 132, in open_file
data = module.open(apath)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/data/imagestack/__init__.py"", line 33, in open
grids.extend(ome_tiff.ome_image_grids(p))
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/data/imagestack/ome_tiff.py"", line 14, in ome_image_grids
images = parse_ome_tiff_header(path)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/map/data/imagestack/ome_tiff.py"", line 119, in parse_ome_tiff_header
sx, sy, sz = [float(s) for s in (pa['PhysicalSizeX'], pa['PhysicalSizeY'], pa['PhysicalSizeZ'])]
KeyError: 'PhysicalSizeX'"	defect	closed	major		Input/Output		fixed						all	ChimeraX