histograms #4703

will-moore · 2016-06-09T22:26:45Z

This adds histograms to Preview panel of web (will also add to image viewer - not ready yet).
Based on designs at ome/design#37
Also https://trello.com/c/6gKn8FT2/40-histogram

To test (NB: start with refresh of browser to avoid cached js files)

Open image in Preview Tab
Click "Show Histogram"
Need full test of editing rendering settings (few code changes in this)
Histogram should show channel being edited (slider/colour-picker/toggle)
Lines on histogram showing start/end of channel sliders should be shown on histogram and updated when adjusting sliders.
Also test histogram updates to 'current channel' and start/end lines in sync with slider values during Save, Save To All, Undo / Redo, Copy / Paste, 'Imported' settings, greyscale etc.
Test similar in full image viewer.

NB: I have removed the 'rangewidget' which gives channel start/end inputs their up/down buttons. I think this wasn't useful functionality and looks better with it gone. See before (above) and after (below)

joshmoore · 2016-06-10T07:05:53Z

Think a file is missing:

https://cowfish.openmicroscopy.org/webmerge/static/webgateway/js/ome.histogram.js Failed to load resource: the server responded with a status of 404 (Not Found)

We try to only trigger channel changes when a channel changes and if several channels change E.g. setModel(greyscale) then the active channel is triggered last. Also have tried not to use rgb colours anywhere since the coversion between rgb and hex colours is unecessary and we don't want to have to handle both when channel change is triggered

atarkowska · 2016-06-11T09:12:15Z

components/tools/OmeroWeb/omeroweb/webclient/templates/webclient/base/base_container.html

@@ -113,6 +115,7 @@
    <script type="text/javascript" src="{% static "3rdparty/aop-1.3.js" %}"></script>
    <script type="text/javascript" src="{% static "webgateway/js/ome.postit.js"|add:url_suffix %}"></script>
    <script type="text/javascript" src="{% static "3rdparty/farbtastic-1.2/farbtastic.js" %}"></script>
+    <script type="text/javascript" src="{% static "webgateway/js/ome.histogram.js" %}"></script>


you are missing url_suffix

Not much use to be able to click up and down a single value. Also made the UI more cluttered.

pwalczysko · 2016-06-14T08:56:53Z

Behaviour:

turn one channel off
then observe that the turned off channel is still displayed on histogram
there is a discrepancy now between the preview image and the histogram shown
suggest: do get in sync when channel are being turned off with the Preview, if a channel is turned off, show the next channel which is ON in the histogram
when the user starts adjusting the bars of a channel which is OFF, put the histogram of that channel on display (this is a discrepancy with the preview image, but directly user-caused one)

Edit:

just realized: when a channel is turned on, the histogram should show that channel (this is atm actually the only way how to switch between channels in histogram without moving the bars !)

pwalczysko · 2016-06-14T09:15:46Z

RFE:

the bar in the histogram on the right-hand side tends to completely disappear as I drag the right slider to the right, this happens quite readily even when I am at Min/Max settings
I understand that the Histogram is meant to show just the "relevant" part of the range, but what is it actually showing then when not Min and Max ?

pwalczysko · 2016-06-14T09:55:12Z

RFE:

be on second channel (second channel is selected in Histogram)
click "Imported"
observe that the "Imported" Rnd settings have been indeed applied, but
there is a third channel now displayed in Histogram (the last one on the image)
I think the channel selection should not change if I apply "Imported" (or anything else indeed), as there is a clear "deal" that the Histogram channel changes only when I drag the bars or switch the channel on

pwalczysko · 2016-06-14T10:00:43Z

Bug: Unsolicited switching of channels in histogram after first open.

In Preview panel, navigate to image https://cowfish.openmicroscopy.org/webmerge/webclient/?show=image-21920
this image has two channels, green and yellow
start dragging the green right bar to the left, let it go
observe that the Histogram became yellow -> not expected, the yelow channel was not touched nor was it switched on or off (both channels are still on as they were when you opened the image)

pwalczysko · 2016-06-14T10:13:05Z

Couple of RFEs and one bug. Stopping testing for today.

gusferguson · 2016-06-14T10:30:11Z

Issues with default channel shown by histogram:

Opens - shows top channel by default - leave unchanged or change any channel - click Imported - histogram changes to bottom channel. Ditto for the Min/Max and Full Range buttons.
As user-3 went to image belonging to user-5 which had been changed by owner - adjusted top channel using slider - on release of slider histogram jumped to bottom channel.
Saved settings as user-3 - clicked on user-5 settings - histogram showed bottom channel by default. Ditto when clicking back onto user-3 settings.

Selecting slider on another channel or clicking into text box does not change histogram - have to change value to trigger - no way to just look at the histogram of a channel as it is without having to change something and then change it back.

If I decrease the minimum value in a channel or increase the maximum value then there is no change to range displayed in the histogram

The font size of the values displayed on the histogram needs to be reduced - too intrusive.

Find it very confusing only having the max value text on the histogram only appearing as the line moves to the left. Only having the min value displayed by default just triggers “what is that number?”. Should have the max value to the left of the max line, not to the right. I think it may also be better to have the text colour the same as the channel and line as this will make context more obvious.

If I increase the max value beyond the default using the text box, then use the slider to reduce it and - without releasing slider - go back to max - the value decreases. Releasing the slider and then repeating this - the max value continues to decrease progressively until the default maximum is reached and then it seems to stablise on that. I think this may have something to do with the slider still taking in values after the cursor on the slider has gone beyond the max point of the slider. In Insight the moment you click on the max slider button the max value returns to the default value. Min slider button/values behaves the same as max in both. This does occur in 5.2.3 but is intermittent.

gusferguson · 2016-06-15T08:37:13Z

@will-moore @pwalczysko
Another thought - I would prefer the Show histogram and Greyscale checkboxes to be swapped - makes Histogram more visible - will be used more than the Greyscale checkbox - and puts Greyscale over colour pickers - which is a bit better logic/association.

Don't set histogram to different channel on 'channelChange' since this is triggered multiple times when settings are pasted/reset etc. Instead, trigger specific 'channelToggle' when channels are toggled on/off

will-moore · 2016-06-16T15:02:25Z

Should be mostly fixed now.

Histogram channel changes when you Toggle a channel (if toggle off, histogram switches to different channel)
Also changes channel when you click on the text start/stop inputs or drag slider.
Doesn't change channel when you Paste/Reset/Undo/MinMax etc.
Changes to the enabled channel when greyscale enabled and when channels toggled.
I removed the numbers on histogram markers as they were redundant and confusing.
Fixed the disappearance of histogram markers going off the right of the chart.

Other things I forgot to mention before:

Test that histogram updates when you change Z/T sliders.
Also check that histogram can't be turned on for Big images.

gusferguson · 2016-06-17T09:19:00Z

Better without the numbers in the histogram.

Toggling channel works as expected.
Not defaulting to bottom channel when resetting to imported/min/max etc. - fixed.
Greyscale selection works as expected.
Changes with Z and T change works as expected.
Disabled with big images works as expected.

Histogram not changing colour when selecting a slider on another channel - only when moving - is this because selecting a slider without moving it does nor trigger an event?
Does change when clicking into range text box.

Like @pwalczysko - finding the behaviour between full range/min/max confusing. Histogram only shows between min and max and lines only appear on histogram when min/max is reached.
It is logical but the behaviour is not transparent.
Not sure if possible/worth trying to make it easier to grasp.

Would still like histogram and greyscale boxes swapped sides.

will-moore · 2016-12-01T11:16:44Z

TODO: remove rendering-engine code for histograms of projected images.
Either disable in the UI when projection enabled or temporarily use non-projected histogram.

This prevents unnecessary triggering of events when channels are not turned on/off. See ome#4703 (comment)

will-moore · 2016-12-01T16:18:32Z

Removed rendering-engine based code for histograms of Z-projection images.
Fixed 'problem' with greyscale flipping of histogram channel reported above histograms #4703 (comment)
Added ?bins=100 parameter to the json histogram. Test with E.g. webgateway/histogram_json/IMAGEID/channel/0/?bins=10 or remove bins parameter to get 256 bins.
Added histogram test to test this. Should be green.

gusferguson · 2016-12-02T11:24:38Z

@will-moore

Tested using http://web-dev-merge.openmicroscopy.org/webclient/ user-3

Behaves as expected.
Works with Z-projected images.
Greyscale issue appears to be fixed.
Did not repeat the comparison with Fiji - @pwalczysko to do that if required.

Good to merge from my POV.

jburel · 2016-12-02T12:49:42Z

components/tools/OmeroWeb/omeroweb/webclient/views.py

@@ -1570,7 +1570,11 @@ def load_metadata_preview(request, c_type, c_id, conn=None, share_id=None,
            'c': ",".join(chs),
            'm': r['model'] == 'greyscale' and 'g' or 'c'
            })
+    maxW, maxH = conn.getMaxPlaneSize()


could you for the new variables use max_w etc.?

jburel · 2016-12-02T13:17:48Z

components/tools/OmeroWeb/test/integration/test_histogram.py

+    @pytest.mark.parametrize("bins", [None, 10])
+    def test_histogram_bin_count(self, bins):
+        """
+        Test that the we get histogram json of the expected size.


jburel · 2016-12-02T13:18:15Z

components/tools/OmeroWeb/test/integration/test_histogram.py

+        size_x = 125
+        size_y = 125
+        img_id = self.create_test_image(size_x=size_x, size_y=size_y,
+                                        session=self.sf).id.val


getId().getValue() is preferrable

Hmmm - why is .getValue() preferable?
We use .val a lot everywhere. E.g.

OmeroWeb wmoore$ grep ".val" -r test/integration/ | wc 727 3229 64263

In the Python stack we almost universally prefer the id.val style rather than using the accessor methods.

understood so will need to go over the inconsistency I have noticed in various locations
The style probably evolves through time

jburel · 2016-12-02T13:22:54Z

components/tools/OmeroWeb/omeroweb/webgateway/urls.py

+"""
+Gets a histogram of 256 columns (grey levels) for the chosen
+channel of an image. A single plane is specified by ?theT=1&theZ=2
+or use ?p=intmax for a projection.


this is no longer the case
no pintmax

waxenegger · 2016-12-05T18:34:49Z

Looks all good, tested on eel as well as locally.

Histogram working in Preview panel

38b1584

will-moore added 6 commits June 10, 2016 10:00

histogram.js missing from previous commit

e70d92a

Adding d3.js and upading licenses README

12e1e09

Handle which channel with black histogram

43595a8

Move histogram-viewport code to histogram.js. Handle z/t change

c892113

Add histogram into image viewer

c151e37

atarkowska reviewed Jun 11, 2016
View reviewed changes

will-moore added 2 commits June 12, 2016 23:26

Add url_suffix to histogram.js

80814b5

Don't use rangewidget for channel start/end inputs

176490a

Not much use to be able to click up and down a single value. Also made the UI more cluttered.

sbesson added the develop label Jun 13, 2016

will-moore closed this Jun 13, 2016

will-moore reopened this Jun 13, 2016

Disable histogram for 'big' images

219d63e

will-moore added 4 commits June 16, 2016 13:13

Remove start/end labels from lines in histogram

ec2bb26

Fix end marker disappearing off chart

102ebe8

Don't change histogram channel except on channelToggle

317d9eb

Don't set histogram to different channel on 'channelChange' since this is triggered multiple times when settings are pasted/reset etc. Instead, trigger specific 'channelToggle' when channels are toggled on/off

Switch histogram channel when focus on start/end inputs

aa0cf2e

Trigger histogram channel switch when greyscale enabled

32ce068

will-moore added 4 commits December 1, 2016 14:48

Only setChannelActive() if active state has changed

db56463

This prevents unnecessary triggering of events when channels are not turned on/off. See ome#4703 (comment)

Remove support for Z-projected histograms via renderingEngine

bc3a394

Merge remote-tracking branch 'origin/develop' into histograms

3d35da4

Add ?bins=10 parameter to histogram_json

6926595

will-moore mentioned this pull request Dec 1, 2016

Histogram (Server) #4931

Merged

will-moore added 2 commits December 1, 2016 16:11

Add integration/test_histogram.py

35d67f6

flake8 fix

bec7b6b

will-moore closed this Dec 1, 2016

will-moore reopened this Dec 1, 2016

will-moore closed this Dec 1, 2016

will-moore reopened this Dec 1, 2016

will-moore closed this Dec 1, 2016

will-moore reopened this Dec 1, 2016

will-moore added 2 commits December 2, 2016 10:30

Merge remote-tracking branch 'origin/develop' into histograms

7826330

Renaming self.create_test_image() for updated testlib

ecb2c1b

jburel reviewed Dec 2, 2016

View reviewed changes

Fix typos and docs

eb1de20

This was referenced Dec 13, 2016

Disable lineplot for tiled images #4996

Closed

Disable lineplot for tiled images #4997

Merged

jburel merged commit 359263e into ome:develop Dec 14, 2016

jburel added this to the 5.3.0 milestone Mar 29, 2017

will-moore deleted the histograms branch February 18, 2019 04:09

sbesson mentioned this pull request Oct 25, 2023

Allow Tiled Image Histograms ome/omero-web#456

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histograms #4703

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histograms #4703

histograms #4703

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