Is there a way to control how the interface is displayed? about papaya

[rii-mango]

You can turn off the top toolbar and bottom coordinate/atlas display by removing them from the HTML. For example:

        <div id="papayaContainer">
            <!-- <div id="papayaToolbar"></div> -->
            <div id="papayaViewer" class="checkForJS" data-params="params"></div>
            <!-- <div id="papayaDisplay"></div> -->
        </div>

Currently there isn't a way to turn off the orthogonal slice views. But I will add this to the requested features list.

[chrisgorgo]

Awesome - thanks!

[chrisgorgo]

Let me put it into the context. At NeuroVault.org we started off using the neurosynth viewer (showcased here: http://neurosynth.org/explore source code here: https://github.com/neurosynth/neurosynth) but we switched to Papaya because the neurosynth viewer can only handle images of particular size, dimension and affine matrix. Papaya has the advantage of reading the header and interpolating the data. We do miss the modularity of neurosynth though. Plus it's so fast! Ability to display panels separately, control, thresholds and opacity through external sliders etc...

[rii-mango]

What changes do you think would most improve Papaya and serve your project? More configurable UI? Faster?

Here are some recently added features: http://ric.uthscsa.edu/mango/versionhistorypapaya.html#v063

The GitHub project also has a new feature, a button, to expand/collapse the button to/from full page. An example here: http://ric.uthscsa.edu/mango/papayabeta/lorem.html

P.S. Neurovault.org looks really cool.

[rii-mango]

Adding sliders for display range and opacity is something we can do for sure. Below is eventually what we want (screenshot from Mango) and should happen soon...

Regarding the need to display the slice panels separately -- you can always toggle which is the main (bigger) slice with the space bar. I can understand wanting to display a single slice panel of a chosen slice orientation -- this is a feature Mango supports. Is this what you are wanting or do you also want to be able to display all three of equal size, side-by-side?

Regarding loading speed, the inflating of the compressed images is the biggest bottleneck. Uncompressed images load almost instantaneously, but of course take longer to transfer. There is room for improvement here...

[chrisgorgo]

On Thu, Feb 13, 2014 at 12:39 AM, RII-Mango [email protected]:

Adding sliders for display range and opacity is something we can do for
sure. Below is eventually what we want (screenshot from Mango) and should
happen soon...
[image: screen shot 2014-02-12 at 5 17 00 pm]https://f.cloud.github.com/assets/1859709/2154870/d00268ec-943b-11e3-8b8d-b8445f0dbe97.png

This looks fantastic! On this note - don't you think that splitting
positive and negative ranges into two "images is a bit confusing? Wouldn't
it be easier to have one image with a two colour map?

https://f.cloud.github.com/assets/1859709/2154870/d00268ec-943b-11e3-8b8d-b8445f0dbe97.png

Regarding the need to display the slice panels separately -- you can
always toggle which is the main (bigger) slice with the space bar. I can
understand wanting to display a single slice panel of a chosen slice
orientation -- this is a feature Mango supports. Is this what you are
wanting or do you also want to be able to display all three of equal size,
side-by-side?

I was looking to display single slice panel of chosen orientation. How can
I do this?

Regarding loading speed, the inflating of the compressed images is the
biggest bottleneck. Uncompressed images load almost instantaneously, but of
course take longer to transfer. There is room for improvement here...

The speed is pretty good. No complaints there! Especially scrolling through
slices is very smooth. Excellent work!

[rii-mango]

I was looking to display single slice panel of chosen orientation. How can
I do this?

I just added this, so after you pull the latest code, try this (also see tests/singleview.html):

   var params = [];
    params["images"] = ["sample_image"];
    params["orthogonal"] = false;
    params["mainView"] = "sagittal";

orthogonal defaults to true if it isn't specified. Use mainView to select which slice direction to use in the main slice panel. The options are 'axial' (default), 'coronal', and 'sagittal'. Also note, that this feature is only supported using the new Papaya HTML declaration (see example on ReadMe.md or tests/).

This should give you something that looks like this. Note the slider at the bottom to change the slice. (Keyboard controls also work.)

don't you think that splitting
positive and negative ranges into two "images is a bit confusing? Wouldn't
it be easier to have one image with a two colour map?

I see it as mainly as a UI issue -- all overlay maps are represented by a color table (e.g. the image icon) and there are widget controls for a single min and max. If there were two color tables associated with an overlay, it would be harder to represent. If you can't assume the positive and negatives ranges are symmetrical, then you'd have to deal with two sets of min/max. So the simple approach we've used so far is each overlay gets one color table, one min, one max.

That said, I get your point. The positive and negative ranges don't overlap and these two overlays derive from the same image volume. So it seems like there should be something tying them together. Currently, the positive range and negative range are treated as differently as two separate image files. I'll give this some thought...

[rii-mango]

We've added a display range and transparency slider. Here's an example:

Eventually, I'd like to add an option to "flatten" the controls from being menu-based to being in a static external controls section. But that feature is not ready yet...

[chrisgorgo]

That's fantastic! I'll try to update Papaya in neurovault next week. Thank
you for your hard work!

On Tue, Feb 25, 2014 at 11:18 PM, RII-Mango [email protected]:

We've added a display range and transparency slider. Here's an example:

[image: screen shot 2014-02-25 at 4 08 10 pm]https://f.cloud.github.com/assets/1859709/2263819/5637291a-9e6a-11e3-85fb-1816c9cd7fa2.png

Eventually, I'd like to add an option to "flatten" the controls from being
menu-based to being in a static external controls section. But that feature
is not ready yet...

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-36065669
.

[rii-mango]

Wouldn't it be easier to have one image with a two colour map?

You can now set combineParametric (global parameter) to true to collapse the button/menu into one, when loading parametric overlays (see screenshot below).

Also, there are a few new UI options:

showControls (this is true by default) -- this will display overlaid increment/decrement, swap main slice and goto origin and center buttons (some buttons will be hidden if the viewer is not big enough)

showControlBar -- if true (and also showControls is true) the control buttons will be displayed as a bar beneath the viewer. If you combine this with kioskMode, the image button/menus will appear there in the control bar as well.

This issue is pretty old, so i'm not sure if you are still actively using Papaya -- but if so, let me know if this addresses the issues you had or if there are still some things you'd like to see.