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neurodata / ndstore

code for storing neurodata images and image annotations
http://neurodata.io
Apache License 2.0
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unable to view control239 #341

Open alexbaden opened 8 years ago

alexbaden commented 8 years ago

http://dsp063.pha.jhu.edu/ocp/ca/Control239/Grayscale/xy/5/0,500/0,500/5/

It is theoretically properly windowed (at least, it is similar to all the rest of the CLARITY brains). I tried multiple window values, no dice.

I also tried a bunch of different z-indices, and all came up black. There is data in the DB though:

mysql> select count(*) from res5;
+----------+
| count(*) |
+----------+
|     2640 |
+----------+
1 row in set (0.42 sec)

Any ideas?

( @kkutten1 @jovo )

kkutten1 commented 8 years ago

Resolution 0 is still available...

http://dsp063.pha.jhu.edu/ocp/ca/Control239/Grayscale/xy/0/10000,11000/10000,11000/5/

...but the lower resolutions (1-5) are missing. I think @kunallillaney needs to repropagate the Grayscale channel.

jovo commented 8 years ago

@kkutten1 I think you can propagate it ?

On Wednesday, August 17, 2016, kkutten1 notifications@github.com wrote:

Resolution 0 is still available...

http://dsp063.pha.jhu.edu/ocp/ca/Control239/Grayscale/xy/0/ 10000,11000/10000,11000/5/

...but the lower resolutions 1-5 are missing. I think @kunallillaney https://github.com/kunallillaney just needs to repropagate the Grayscale channel.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurodata/ndstore/issues/341#issuecomment-240541404, or mute the thread https://github.com/notifications/unsubscribe-auth/AACjckLcSb7R1nVQjSFQvpyQYlT2Stazks5qg3JFgaJpZM4Jm1EE .

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kunallillaney commented 8 years ago

@jovo @kkutten1 the docs to propagate are pretty clear. Send an email to @Aeusman and me if you have any questions.

kkutten1 commented 8 years ago

@kunallillaney @Aeusman It won't let me propagate. Probably because the channel is readonly. 

>>> import ndio.remote.neurodata as neurodata
>>> nd = neurodata()
>>> # Returns 0 indicating that token isn't propagated
>>> nd.get_propagate_status("Control239", "Grayscale")
u'0'
>>> nd.propagate("Control239", "Grayscale")
>>> # Should be 1 if propagation service started but returns 0
>>> nd.get_propagate_status("Control239", "Grayscale") 
u'0'

Can you change readonly to 0. I don't think I have permissions to do it myself.

wrgr commented 8 years ago

This functionality is available in the console if you have permissions there!

kkutten1 commented 8 years ago

I don't have permissions there either :( I can only see projects that I created.

kunallillaney commented 8 years ago

@kkutten1 Now it is not read-only.

kkutten1 commented 8 years ago

I still can't propagate the Grayscale channel even though @kunallillaney has turned off readonly.

kunallillaney commented 8 years ago

@kkutten1 Can you please be more specific on this? What request are you making and if there is an error what is it?

kkutten1 commented 8 years ago

OK it appears to be working now as the following url returns 1 

http://openconnecto.me/ocp/ca/Control239/Grayscale/getPropagate/

I initiated propagation using

http://openconnecto.me/ocp/ca/Control239/Grayscale/setPropagate/1/

Strangely this did not work when I used ndio.remote.neurodata.propagate() which may warrent further investigation. I'll close the issue once propagation is done

kunallillaney commented 8 years ago

"Strangely"? I guess ndio version of propagate does not work. You can open an issue there to confirm. :)

kkutten1 commented 8 years ago

So how long does propagate take? It's been over a week and the url

http://openconnecto.me/ocp/ca/Control239/Grayscale/getPropagate/

still returns '1'

kunallillaney commented 8 years ago

@kkutten1 This is done now. the propagate was not the issue. This is an old channel format and someone changed the channel-id underneath(I can explain but does not concern this discussion).

Here is a sample cutout http://openconnecto.me/ocp/ca/Control239/xy/1/5000,6500/4500,5500/100/window/0,500/

kkutten1 commented 8 years ago

@kunallillaney The resolutions 0 and 1 look fine

But the data for resolutions 2-5 is still missing

Can you change the channel-id for these resolutions as well?

kunallillaney commented 8 years ago

Okay. I will check what is going on.

kunallillaney commented 8 years ago

@alexbaden Can you migrate this to new schema from old channel? How hard is it?

alexbaden commented 8 years ago

It should be pretty easy, especially since we only have to migrate the base resolution. The catch is that I can't do the migration in place -- meaning, we'll need to do something like make a Control239new DB. But, we can either alias the old token, or rename the DB once the migration is done. I'll start the process this afternoon, based on past experience it should take about a day.

On Thu, Sep 1, 2016 at 11:33 AM Kunal Lillaney notifications@github.com wrote:

@alexbaden https://github.com/alexbaden Can you migrate this to new schema from old channel? How hard is it?

— You are receiving this because you were mentioned.

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alexbaden commented 8 years ago

FYI, checked in on the job again this morning. The migration is still running on res0.