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confine projection #305

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merged 6 commits into from
Feb 27, 2020
Merged

confine projection #305

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0db7e5e
Limit projection to stack size of 256 * 1024 * 1024
will-moore Feb 17, 2020
5abeecd
Update projection-enabled when channels turn on/off
will-moore Feb 17, 2020
105a242
Revert "Update projection-enabled when channels turn on/off"
will-moore Feb 19, 2020
2c3e68b
Use sizeC instead of active channels for proj disable
will-moore Feb 19, 2020
205c3ea
Add MAX_PROJECTION_BYTES config to iviewer
will-moore Feb 20, 2020
0322a13
Add settings info to README
will-moore Feb 20, 2020
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14 changes: 14 additions & 0 deletions README.rst
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Expand Up @@ -41,6 +41,20 @@ Install
Instructions on how to add the OMERO.iviewer app to your installed OMERO.web apps
can be found in the `OMERO.iviewer README <plugin/omero_iviewer/README.rst>`_.

Settings
========

OMERO.iviewer limits the size of Z-projections to reduce load on the server.
The limit is defined as the number of bytes of raw pixel data in a Z-stack and
is equivalent to 1024 * 1024 * 256 bytes.
For example, an 8-bit image (1 byte per pixel) of size 1024 * 1024 * 256 is
equal to the default threshold. To double the limit, use::

$ omero config set omero.web.iviewer.max_projection_bytes 536870912

NB: Z-projection is not supported for tiled images in OMERO
(Images larger than 2000 * 2000 pixels per plane are tiled in iviewer).

Supported URLs
==============

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7 changes: 7 additions & 0 deletions plugin/omero_iviewer/iviewer_settings.py
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Expand Up @@ -25,6 +25,13 @@
# load settings
IVIEWER_SETTINGS_MAPPING = {

"omero.web.iviewer.max_projection_bytes":
["MAX_PROJECTION_BYTES",
1024 * 1024 * 256,
int,
("Maximum bytes of raw pixel data allowed for Z-projection. "
"Above this threshold, Z-projection is disabled")],
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Maybe indicate that this value will be ignored if the limit is greater that the one set server-side.
Server side is work-in-progress but when it is in-place that will be the rule.

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Seems wrong for the documentation to describe future functionality.
Since I'll need to open a PR to update the functionality, I can change the description at the time to match (depending on what we end up with).

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we can review the wording later on when we implement the size limit from server
My point is that if people start setting a high limit, this will be ignored later on and will default to the server one. This might come at a surprise for that.


"omero.web.iviewer.roi_page_size":
["ROI_PAGE_SIZE",
500,
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2 changes: 2 additions & 0 deletions plugin/omero_iviewer/views.py
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Expand Up @@ -47,6 +47,7 @@

ROI_PAGE_SIZE = getattr(iviewer_settings, 'ROI_PAGE_SIZE')
ROI_PAGE_SIZE = min(MAX_LIMIT, ROI_PAGE_SIZE)
MAX_PROJECTION_BYTES = getattr(iviewer_settings, 'MAX_PROJECTION_BYTES')

PROJECTIONS = {
'normal': -1,
Expand Down Expand Up @@ -84,6 +85,7 @@ def index(request, iid=None, conn=None, **kwargs):
if settings.FORCE_SCRIPT_NAME is not None:
params['URI_PREFIX'] = settings.FORCE_SCRIPT_NAME
params['ROI_PAGE_SIZE'] = ROI_PAGE_SIZE
params['MAX_PROJECTION_BYTES'] = MAX_PROJECTION_BYTES

return render(
request, 'omero_iviewer/index.html',
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2 changes: 2 additions & 0 deletions src/app/context.js
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Expand Up @@ -439,6 +439,8 @@ export default class Context {
this.interpolate = (interpolate === 'true');
this.version = this.getInitialRequestParam(REQUEST_PARAMS.VERSION);
this.roi_page_size = this.initParams[REQUEST_PARAMS.ROI_PAGE_SIZE] || 500;
this.max_projection_bytes = parseInt(this.initParams[REQUEST_PARAMS.MAX_PROJECTION_BYTES], 10)
|| (1024 * 1024 * 256);
}

/**
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8 changes: 7 additions & 1 deletion src/controls/dimension-slider.js
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Expand Up @@ -517,7 +517,13 @@ export default class DimensionSlider {
*/
getZProjectionDisabled(handle, forwards) {
let dims = this.image_config.image_info.dimensions;
return (handle !== null && forwards || (dims.max_x * dims.max_y) > UNTILED_RETRIEVAL_LIMIT);
let tiled = (dims.max_x * dims.max_y) > UNTILED_RETRIEVAL_LIMIT;
let bytes_per_pixel = Math.ceil(Math.log2(this.image_config.image_info.range[1]) / 8.0);
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you may want to add a TODO and create an issue so we can use the omero-model property when available ome/omero-model#47

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@joshmoore joshmoore Feb 21, 2020 •
edited
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Ah interesting, so: see if someone set a value explicitly for iviewer, then check the server default, then use a client fallback?

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Currently we don't have the config available from the server.
When that is available, we could teach iviewer to use that as a default value, but if it is set in iviewer itself then use that. That could allow iviewer to be more restrictive than the server (but not less restrictive since the server would enforce it's own limit).

let size_c = this.image_config.image_info.channels.length;
let stack_size = dims.max_x * dims.max_y * dims.max_z * bytes_per_pixel * size_c;
let proj_limit = this.context.max_projection_bytes;

return (handle !== null && forwards || tiled || stack_size > proj_limit);
}

/**
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5 changes: 3 additions & 2 deletions src/index-dev.html
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Expand Up @@ -33,8 +33,9 @@
window.INITIAL_REQUEST_PARAMS = {
'VERSION': "DEV_SERVER",
'WEB_API_BASE': 'api/v0/',
'ROI_PAGE_SIZE': 500,
'IMAGES': "79833", // "4420" // "73537",
'ROI_PAGE_SIZE': '500',
'MAX_PROJECTION_BYTES': "268435456", // 1024 * 1024 * 256
'IMAGES': "1252", // "4420" // "73537",
// 'DATASET': "1",
//'WELL': "1"
};
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1 change: 1 addition & 0 deletions src/utils/constants.js
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Expand Up @@ -130,6 +130,7 @@ export const REQUEST_PARAMS = {
WELL_ID: 'WELL',
ZOOM: 'ZM',
ROI_PAGE_SIZE: 'ROI_PAGE_SIZE',
MAX_PROJECTION_BYTES: 'MAX_PROJECTION_BYTES',
}

/**
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