'Run optimize' button blocked

1

Hi,

We are running Shapeworks 6.6.0-dev and at the moment it is not possible to run the optimization step in Studio. The ‘Run optimize’ button is blocked for all users and we don’t know why. Are you familiar with this?

run_optimize_blocked
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Thanks in advance

Derek

2

Hi, I have some additional information.

  • Shapeworks is installed for all users on a windows computer.
  • The python environment is installed via Miniconda and is accessible for all users.
  • Of the three users of the computer, 1 user can optimize in Shapeworks Studio, while 2 (including the user with administration rights who installed everything) cannot.
  • Optimize via python prompt does work for all users.
3

Have you run the groom step first? Either run Groom or click the box “Skip Grooming” in the Groom module. Sorry this is not more clear.

4

Thanks for the reply. Unfortunately, this not solves the problem: we have tried this in several ways, but no success. We will try the normal 6.5 release this week to see if this problem only persists in the dev version.

We do have another question though. If we use the python optimizer, sometimes we get the error ‘Inconsistency in parameters… m_domains_per_shape != m_number_of_particles.size()’. If we use one of the examples we do not get this error, but once we change the data input, sometimes this error raises. Do you know what prevents this error? Because there is no parameter to set for ‘domains_per_shape’.

5

If you are finding differences between users, this suggests a permission problem and Studio is not able to save the changes to the project.

For the m_domains_per_shape != m_number_of_particles.size() message, this indicates that the number of particles is not set for each domain. E.g. if you have two domains, then two numbers of particles need to be specified. E.g. in Studio:

image
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Are you running this in Studio and still having this problem, or are you setting the parameters in another way?

6

Thanks for the answer. (and excuse me for the silence).

I am using Python, not the studio version. In studio, there are indeed the same number of field as there are domains. In the python script however, it is not possible to set the value for ‘m_domains_per_shape’, which is weird, because the error does say that is is not equal to the amount of domains, which I have set for each subject and it is 1. The length of the particle list in Python is also 1.

7

For python, have a look at a multiple domain example:

https://raw.githubusercontent.com/SCIInstitute/ShapeWorks/refs/heads/master/Examples/Python/ellipsoid_multiple_domain.py

    num_particles = [128,128]
...
    parameters.set("number_of_particles" ,sw.Variant(num_particles))
8

Hello,

I was wondering what solved the issue of not being able to click on ‘‘Run Optimize’’?

I have the same problem.

Kind regards.

9

Hi Iris,

No, we have never solved this issue, unfortunately. We have run ShapeWorks from an Anaconda prompt instead, which is not ideal. We run ShapeWorks on Windows 10 and 11 and have encountered this problem since version 6.3. New versions have not solved it.

10

Thanks for your reply.

I have solved the issue by doing the following! :slight_smile:

^ so the crucial thing was to change the decimal point to ‘.’ instead of ‘,’'.

Hope this helps!

11

This should be fixed now in the nightly/development version and in future versions of ShapeWorks:

12

Good to hear that this is fixed! Unfortunately, when I install the the python environment, I get the following error:

ERROR: Ignored the following versions that require a different python version
ERROR: Could not find a version that satisfies the requirement bokeh==3.0.8
ERROR: No matching distribution found for bokeh==3.8.0.

It looks like the bokeh package only works with python 3.10. Could there be something wrong with the version of the bokeh package in combination with python 3.9, which is needed for shapeworks?

13

You may need to start your shapeworks conda environment over from scratch. It should be Python 3.12 now with the development version of ShapeWorks.

14

Are you sure? I just downloaded the most recent development version of ShapeWorks (released 3 days ago, for windows) and reinstalled miniconda. I still receive this error. It looks like Python version 3.9.13 is installed, not 3.12.

Screenshot 2025-12-01 135335
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15

Hi, it looks like the install_shapeworks.bat file, for windows, didn’t get updated. I’ll fix this and respond back here.

16

This has been updated in the latest development version. Windows now uses Python 3.12 as well.

17

Thanks you so much Alan! I will try it this Thursday