JIRA [IMG-713] SaveImages (save module display window)

[thouis]

SaveImages should support saving the ENTIRE cpfigure window (rather than just an axis) associated with a given module.

Here's the help text:
"Module display window: The window associated with a module can be saved, which will include all the panels and text within that window."

Original reporter: afraser
Jira link: https://jira.broadinstitute.org/browse/IMG-713
Assignee: afraser

Comment from mbray on Fri, 18 Jun 2010 12:12:31 -0400:
Remember to update help. Currently it says it's not implemented.

[braymp]

I've now had a couple of users request this feature, so I'm giving it a bump.

If this is not doable, either now or in the immediate future, it should be removed as an option.

[LeeKamentsky]

It's not something that can be done in a couple of minutes and the
implementation of it has some facets that suggest it would be best done
when we revisited CP outputs.

In Matlab, figures were always produced and were always on the screen to be
picked up by SaveImages. Now, that's not the case and for headless
operation, figures would have to be created outside of their WX canvas
context. Also, there's the issue of the Matplotlib backend which can't be
WX. It's not impossible, but a naive attempt to implement this won't work.

On Wed, May 1, 2013 at 1:53 PM, Mark Bray notifications@github.com wrote:

I've now had a couple of users request this feature, so I'm giving it a
bump.

If this is not doable, either now or in the immediate future, it should be
removed as an option.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/193#issuecomment-17295328
.

[AnneCarpenter]

I agree it's not urgent enough for the current FileUI release. Maybe not
even for the "Next" release.

On Wed, May 1, 2013 at 2:21 PM, LeeKamentsky notifications@github.comwrote:

It's not something that can be done in a couple of minutes and the
implementation of it has some facets that suggest it would be best done
when we revisited CP outputs.

In Matlab, figures were always produced and were always on the screen to
be
picked up by SaveImages. Now, that's not the case and for headless
operation, figures would have to be created outside of their WX canvas
context. Also, there's the issue of the Matplotlib backend which can't be
WX. It's not impossible, but a naive attempt to implement this won't work.

On Wed, May 1, 2013 at 1:53 PM, Mark Bray notifications@github.com
wrote:

I've now had a couple of users request this feature, so I'm giving it a
bump.

If this is not doable, either now or in the immediate future, it should
be
removed as an option.

—
Reply to this email directly or view it on GitHub<
https://github.com/CellProfiler/CellProfiler/issues/193#issuecomment-17295328>

.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/193#issuecomment-17297177
.

[braymp]

In that case, the option should be removed and help updated. A warning should be put in place for the folks upgrading from MATLAB that this option does not exist upon loading the module. The default value should be substituted in save_image_or_figure in SaveImages for this case.

[LeeKamentsky]

Did it work in the last release?

On Wed, May 1, 2013 at 4:08 PM, Mark Bray notifications@github.com wrote:

In that case, the option should be removed and help updated. A warning
should be put in place for the folks upgrading from MATLAB that this option
does not exist upon loading the module. The default value should be
substituted in save_image_or_figure in SaveImages for this case.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/193#issuecomment-17303368
.

[braymp]

No. The error msg and the documentation saying as much has been around since porting CP to Python, AFAIK.

[dlogan]

Choosing Module Window still explodes in the CP 2.1 release:

Traceback (most recent call last):
  File "wx\_misc.pyc", line 1357, in Notify
  File "wx\_core.pyc", line 14742, in Notify
  File "cellprofiler\gui\moduleview.pyc", line 2088, in do_reset
  File "cellprofiler\gui\moduleview.pyc", line 486, in set_selection
  File "cellprofiler\gui\moduleview.pyc", line 697, in make_choice_control
AssertionError

I agree that we should remove the option, but leave the Help text as "This option is not yet available"

[LeeKamentsky]

Oops - I removed the help... sry.

Regarding the feasibility of implementing this - it's very difficult to do this in the context of headlessness and multiprocessing. Not impossible, just very difficult. The display gets drawn in the user interface and is shared among all of the workers. To make things work, you'd probably have to touch the code of every module. The logic of the whole thing is also rather unfortunate - you have to do a lot of special-case plumbing to let SaveImages communicate with the displays which will inject some unfortunate spaghetti-code and dependencies into CellProfiler. At this point, I'd rather make saving figures more central instead of being one module's responsibility - something that you could check-off on the module itself and specify how to save the figure at that point.

[dlogan]

Closing now, for future consideration.