Fix reactivate channels

[will-moore]

Previously, img.set_active_channels(reactivatechannels) was turning OFF the channels
that were active and edited in the previous set_active_channels() call.

To test, find an Image with 3 Channels, all Active.
Run:

$ omero render set Image:1 settings.yml

with less than 3 Channels specified, e.g.

settings.yml

---
channels:
    1:
        active: true
        start: 0
        end: 255
greyscale: false
version: 2

This should only edit the first Channel. All 3 channels should stay Active.

[joshmoore]

Also note the now merged update to the readme:

https://github.com/ome/omero-cli-render/pull/41/files#diff-7c3731557868b1b97ef87421dd10cf92R119

# Omitted channels will not be disabled unless --disable is used.

[sbesson]

Tested using a fake image with four channels test&sizeC=4.fake as the input file with original.yml containing the original rendering settings:

---
channels:
    1:
        active: true
        color: FF0000
        end: 255.0
        label: '0'
        max: 255.0
        min: 0.0
        start: 0.0
    2:
        active: true
        color: 00FF00
        end: 255.0
        label: '1'
        max: 255.0
        min: 0.0
        start: 0.0
    3:
        active: true
        color: 0000FF
        end: 255.0
        label: '2'
        max: 255.0
        min: 0.0
        start: 0.0
    4:
        active: false
        color: FF0000
        end: 255.0
        label: '3'
        max: 255.0
        min: 0.0
        start: 0.0
greyscale: false
t: 1
version: 2
z: 1

and test.yml as suggested from the PR description

---
channels:
    1:
        active: true
        start: 0
        end: 100
greyscale: false
version: 2

Running bin/omero render set Image:123223 test.yaml && bin/omero render info Image:123223 updates the rendering window of channel 1 as expected

rdefv2: model=color, z=0, t=0
tiles: False
ch0: active=True,color=FF0000,label=0,min=0.0,start=0.0,end=100.0,max=255.0
ch1: active=True,color=00FF00,label=1,min=0.0,start=0.0,end=255.0,max=255.0
ch2: active=True,color=0000FF,label=2,min=0.0,start=0.0,end=255.0,max=255.0
ch3: active=False,color=FF0000,label=3,min=0.0,start=0.0,end=255.0,max=255.0

Running bin/omero render set Image:123223 test.yaml --disable && bin/omero render info Image:123223 disables channels 2 and 3 as expected

rdefv2: model=color, z=0, t=0
tiles: False
ch0: active=True,color=FF0000,label=0,min=0.0,start=0.0,end=100.0,max=255.0
ch1: active=False,color=00FF00,label=1,min=0.0,start=0.0,end=255.0,max=255.0
ch2: active=False,color=0000FF,label=2,min=0.0,start=0.0,end=255.0,max=255.0
ch3: active=False,color=FF0000,label=3,min=0.0,start=0.0,end=255.0,max=255.0

However, trying to restore the original YAML file with bin/omero render set Image:123223 original.yml && bin/omero render info Image:123223 still gives channels 2 and 3 as disabled

rdefv2: model=color, z=0, t=0
tiles: False
ch0: active=True,color=FF0000,label=0,min=0.0,start=0.0,end=255.0,max=255.0
ch1: active=False,color=00FF00,label=1,min=0.0,start=0.0,end=255.0,max=255.0
ch2: active=False,color=0000FF,label=2,min=0.0,start=0.0,end=255.0,max=255.0
ch3: active=False,color=FF0000,label=3,min=0.0,start=0.0,end=255.0,max=255.0

Passing bin/omero render set Image:123223 original.yml --disable && bin/omero render info Image:123223 gives the expected outcome

rdefv2: model=color, z=0, t=0
tiles: False
ch0: active=True,color=FF0000,label=0,min=0.0,start=0.0,end=255.0,max=255.0
ch1: active=True,color=00FF00,label=1,min=0.0,start=0.0,end=255.0,max=255.0
ch2: active=True,color=0000FF,label=2,min=0.0,start=0.0,end=255.0,max=255.0
ch3: active=False,color=FF0000,label=3,min=0.0,start=0.0,end=255.0,max=255.0

So it looks like there is still an issue when switching the channel state from disactive to active and --disable is not passed.

[will-moore]

@sbesson Thanks for catching that. Should be fixed now

[sbesson]

Thanks @will-moore. Quickly looking at the code, the latest logic makes sense to me i.e. activate a channel:

• either if active: true is passed
• or if the channel is already active and active: false is not set

Note this particular functionality has already been the object of previous work in #15. In addition to manual testing, could we look into adding an integration test covering the expected channel activation behavior with/without --disable for the scenario described in this PR?

[dominikl]

I think the whole issue is actually one level higher, that one has to call set_active_channels in order change the rendering settings. De/Activating channels and modifying the various channel settings should be two separate things.

[will-moore]

I guess that set_active_channels() behaves as if we're using a --disable flag, and you'd like an option to "ignore unlisted channels"?
I guess that could be a useful update to the BlitzGateway.
Anyway, I'll look at adding more integration tests...

[dominikl]

Looks good to me 👍

[will-moore]

"Good to merge"
Merge needed to avoid conflict with #42 - thanks

[sbesson]

Released as https://pypi.org/project/omero-cli-render/0.5.1/