error while installing quantiphyse-cvr widget

[JSIERO]

dear quantiphyse team,
great work btw
I am trying to install the cvr widget for quantiphyse (pip install quantiphyse-cvr), but unfortunately I get a error message on the numpy/tensorflow dependencies (think related to the needed vaby package)
NB Quantiphyse did run properly before installing the CVR module

I noticed that for the CVR widget the numpy package got downgraded to 1.19.5

this is what I see when running quantiphyse after the install op the CVR widget:

Installing collected packages: numpy, quantiphyse-cvr
Attempting uninstall: numpy
Found existing installation: numpy 1.20.3
Uninstalling numpy-1.20.3:
Successfully uninstalled numpy-1.20.3
Successfully installed numpy-1.19.5 quantiphyse-cvr-0.0.2.post4
jeroen@stein(18):~$ quantiphyse
===== 2021.06.15 13:06:34 =====
Traceback (most recent call last):
File "/home/jeroen/.local/bin/quantiphyse", line 8, in
sys.exit(main())
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse/qpmain.py", line 146, in main
win = MainWindow(load_data=args.data, widgets=not args.qv)
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse/gui/main_window.py", line 175, in init
widgets = get_plugins("widgets")
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse/utils/plugins.py", line 104, in get_plugins
_load_plugins_from_entry_points(PLUGIN_MANIFEST)
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse/utils/plugins.py", line 84, in _load_plugins_from_entry_points
for key, val in ep.load().items():
File "/usr/local/fsl/6.0.4/fslpython/lib/python3.8/site-packages/pkg_resources/init.py", line 2447, in load
return self.resolve()
File "/usr/local/fsl/6.0.4/fslpython/lib/python3.8/site-packages/pkg_resources/init.py", line 2453, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse_sv/init.py", line 7, in
from .widgets import PerfSlicWidget
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse_sv/widgets.py", line 14, in
from .process import SupervoxelsProcess
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "/home/jeroen/.local/lib/python3.8/site-packages/quantiphyse_sv/process.py", line 9, in
import maskslic
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "/home/jeroen/.local/lib/python3.8/site-packages/maskslic/init.py", line 6, in
from .slic_superpixels import slic
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "/home/jeroen/.local/lib/python3.8/site-packages/maskslic/slic_superpixels.py", line 25, in
from ._slic import _slic_cython, _enforce_label_connectivity_cython
File "/home/jeroen/.local/lib/python3.8/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 142, in _import
return original_import(name, *args, **kwargs)
File "maskslic/_slic.pyx", line 1, in init maskslic._slic
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

If I upgrade numpy back to 1.20.3 and uninstall the quantiphyse-cvr package, the quantiphyse runs again.

If you have any tips, much appreciated

Best Jeroen

[mcraig-ibme]

Hi, sorry for not replying sooner. I would initially try uninstalling quantiphyse-sv and maskslic as these are the packages that use Cython and have built against a particular binary API for Numpy. If that enables quantiphyse to run you could then try reinstalling quantiphyse-sv which would then potentially rebuild against the installed version of Numpy, however you don't need quantiphyse-sv for the CVR plugin.

[JSIERO]

Hi Martin,

Thanks for this - uninstalling quantiphyse-sv and then install quantiphyse-cvr did the trick to get the quantiphyse with CVR widget to run!
uninstalling maskslic resulted in an error for oxasl unfortunately, also reinstalling quantiphyse-sv resulted in a numpy incompatibility.

best J