Improvements to image stacking #1302

graeme-winter · 2020-06-12T15:04:15Z

Means the images are on a sensible scale when stacked so look OK

graeme-winter · 2020-06-12T15:06:51Z

Before:

adding 10 images =>

After:

adding 10 images gives:

which I think is much more what you would want?

dagewa · 2020-06-12T15:07:56Z

The function name sum_images is not really appropriate if the result is actually to calculate a mean

graeme-winter · 2020-06-12T15:09:28Z

@dagewa valid - but don't want to rename it to compute_mean_over_N_images or something? 🤔

graeme-winter · 2020-06-12T15:16:52Z

Set max brightness to 1000 to reproduce feel of stacking 10 images as before

graeme-winter · 2020-06-12T15:20:41Z

While I am thinking about this, wonder if we should have a show-max mode as well? 🤔 so maximum pixel over the range rather than mean value?

dagewa · 2020-06-12T15:27:59Z

Could definitely be useful - has been used for virtual powder patterns I think

rjgildea · 2020-06-12T15:28:24Z

util/image_viewer/spotfinder_frame.py

@@ -811,7 +811,7 @@ def draw_resolution_rings(self, unit_cell=None, space_group=None):
                update=False,
            )

-    def sum_images(self):
+    def stack_images(self):
        if self.params.sum_images > 1:


Would it make sense to also change the command line parameter to stack_images (possibly keeping around sum_images with a deprecation warning for the time being)?

... maybe, provided the people's national bikeshed committee are satisfied with the nomenclature of stacking the images?

I don't know how to make one phil parameter alias another, and deprecate one or the other, otherwise I would have done this...

I could replace the name and just break the cl api

R.e. marking phil parameters as deprecated:
cctbx/cctbx_project#452 (comment)

I would either:

Rename sum_images to stack_images and re-add sum_images with .deprecated attribute, and ignore. That way it doesn't fail, but users get a warning.

Just rename and accept that very few people likely use the CLI to the image viewer.

Pushed change to this effect, if you use old command line option you get

Grey-Area 0 :) $ dials.image_viewer imported.expt strong.refl sum_images=10 DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235 Sorry: Unknown command line parameter definition: sum_images = 10

which I think is OK

ndevenish · 2020-06-12T15:34:26Z

I worry that if summing over a range to try to find weak signal, or signal only present on a few, that this might hide it? A "max pixel" mode might be appropriate. Maybe this does deserve a setting, but maybe that's just avoiding making a decision...

graeme-winter · 2020-06-15T05:08:16Z

I worry that if summing over a range to try to find weak signal, or signal only present on a few, that this might hide it? A "max pixel" mode might be appropriate. Maybe this does deserve a setting, but maybe that's just avoiding making a decision...

My thinking was about simulating a wider image in the first instance, but the max is useful as you say for getting the pattern out. I think the universe has space for both...

Also add a selector pull-down to select preferred stack type. Set max mode as default since that could well be more useful to the average user

graeme-winter · 2020-06-15T08:13:37Z

@ndevenish added a mean / max pulldown - illustrated difference:

Max:

Mean:

rjgildea · 2020-06-15T21:46:43Z

As far as I can tell, you can only change the number of images to stack via the command line but not via the GUI, and conversely, you can only change the stack "type" in the GUI but not via the command line. This means that if you load the image viewer with default options, then there is a "stack type" dropdown that doesn't do anything.

The stack_type setting should probably be exposed via the command line, and it only makes really makes sense to have the "stack type" dropdown in the GUI settings panel if you can also control the number of images there too.

rjgildea · 2020-06-15T22:01:41Z

This seems incompatible with setting the "image type" to be "raw":

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10

Select "raw" in the "image type" dropdown:

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2140, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1175, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 836, in stack_images
    sel = data > rd
TypeError: '>' not supported between instances of 'double' and 'int'

rjgildea · 2020-06-15T22:04:55Z

Another oddity, this behaviour was probably at least in part already present before this PR - if you're in stack/sum images mode, then press the "image" button, then the displayed image goes back to the individual, rather than stacked, image, until you re-select an item from the "stack type" dropdown menu. I'm not entirely sure what the expected should be for the various thresholding maps - should we be running the threshold algorithms on the stacked image?

graeme-winter · 2020-06-16T04:38:38Z

As far as I can tell, you can only change the number of images to stack via the command line but not via the GUI, and conversely, you can only change the stack "type" in the GUI but not via the command line. This means that if you load the image viewer with default options, then there is a "stack type" dropdown that doesn't do anything.

The stack_type setting should probably be exposed via the command line, and it only makes really makes sense to have the "stack type" dropdown in the GUI settings panel if you can also control the number of images there too.

There is a "Stack" box at the top of the image window? I've been using this extensively so know that works 😉

I had wondered whether the stack_type should be exposed via command line, but not followed up on.

graeme-winter · 2020-06-16T04:40:13Z

This seems incompatible with setting the "image type" to be "raw":

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10

Select "raw" in the "image type" dropdown:

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2140, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1175, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 836, in stack_images
    sel = data > rd
TypeError: '>' not supported between instances of 'double' and 'int'

Reproduced this, will look

graeme-winter · 2020-06-16T04:52:16Z

Another oddity, this behaviour was probably at least in part already present before this PR - if you're in stack/sum images mode, then press the "image" button, then the displayed image goes back to the individual, rather than stacked, image, until you re-select an item from the "stack type" dropdown menu. I'm not entirely sure what the expected should be for the various thresholding maps - should we be running the threshold algorithms on the stacked image?

Thresholding should be fine against summed, mean requires some discussion re: "gain" equivalent, max just plain wrong. Not sure if this should be imposed.

Re: the oddity - the internals of the image viewer are something of a tangled mess. Should fixing this be a necessary precondition of the PR features being made available?

graeme-winter · 2020-06-16T05:00:35Z

This seems incompatible with setting the "image type" to be "raw":

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10

Select "raw" in the "image type" dropdown:

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2140, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1175, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 836, in stack_images
    sel = data > rd
TypeError: '>' not supported between instances of 'double' and 'int'

Reproduced this, will look

Fixed / worked around in c3d54cc

graeme-winter · 2020-06-16T05:42:49Z

As far as I can tell, you can only change the number of images to stack via the command line but not via the GUI, and conversely, you can only change the stack "type" in the GUI but not via the command line. This means that if you load the image viewer with default options, then there is a "stack type" dropdown that doesn't do anything.
The stack_type setting should probably be exposed via the command line, and it only makes really makes sense to have the "stack type" dropdown in the GUI settings panel if you can also control the number of images there too.

There is a "Stack" box at the top of the image window? I've been using this extensively so know that works 😉

I had wondered whether the stack_type should be exposed via command line, but not followed up on.

Done, in a2910e0

graeme-winter · 2020-06-16T06:15:20Z

Another oddity, this behaviour was probably at least in part already present before this PR - if you're in stack/sum images mode, then press the "image" button, then the displayed image goes back to the individual, rather than stacked, image, until you re-select an item from the "stack type" dropdown menu. I'm not entirely sure what the expected should be for the various thresholding maps - should we be running the threshold algorithms on the stacked image?

Thresholding should be fine against summed, mean requires some discussion re: "gain" equivalent, max just plain wrong. Not sure if this should be imposed.

Re: the oddity - the internals of the image viewer are something of a tangled mess. Should fixing this be a necessary precondition of the PR features being made available?

I have looked at the code for a while and can't see where the change should go to make this oddity go away - however since it is not a new oddity I am not too worried about this. I have made sum the default, so if someone stacks images and then looks through the filters the results should be by default meaningful.

rjgildea · 2020-06-16T07:16:18Z

There is a "Stack" box at the top of the image window? I've been using this extensively so know that works 😉

Ah ok - I had missed that because I was naively expecting related controls to be in the same window at the very least. Does it really make sense for the control for number of images to stack and the control for stack type to be in different windows?

rjgildea · 2020-06-16T07:18:49Z

I have looked at the code for a while and can't see where the change should go to make this oddity go away - however since it is not a new oddity I am not too worried about this. I have made sum the default, so if someone stacks images and then looks through the filters the results should be by default meaningful.

I'm not convinced the thresholding maps are acting on the sum/mean/max images in any case - I suspect they are effectively switching to stack_images=1 without updating any of the controls to reflect this.

graeme-winter · 2020-06-16T07:23:47Z

There is a "Stack" box at the top of the image window? I've been using this extensively so know that works 😉

Ah ok - I had missed that because I was naively expecting related controls to be in the same window at the very least. Does it really make sense for the control for number of images to stack and the control for stack type to be in different windows?

Respectfully acknowledged. However also mention that stacking images is related to loading images, which is all controlled above the image... and selecting the view kinda lives with the other settings, so maybe (just maybe) the viewer is poorly designed 🤷‍♂️

rjgildea · 2020-06-16T07:24:48Z

util/image_viewer/spotfinder_frame.py

-                    rd += image_data_i[j]
+                    data = image_data_i[j]
+                    if mode == "max":
+                        if type(rd) != type(data):


I think you can call .as_double() even on an array that is already flex.double(), so you could avoid having to explicitly check the type and always both sides to double.

a = flex.random_double(10).as_double()

graeme-winter · 2020-06-16T07:25:23Z

I have looked at the code for a while and can't see where the change should go to make this oddity go away - however since it is not a new oddity I am not too worried about this. I have made sum the default, so if someone stacks images and then looks through the filters the results should be by default meaningful.

I'm not convinced the thresholding maps are acting on the sum/mean/max images in any case - I suspect they are effectively switching to stack_images=1 without updating any of the controls to reflect this.

Quite possibly: perhaps this is also in the realm of 🤷‍♂️ - since stack images existed before this I am not sure it's a new bug...

rjgildea · 2020-06-16T07:26:43Z

This seems incompatible with setting the "image type" to be "raw":

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10

Select "raw" in the "image type" dropdown:

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2140, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1175, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 836, in stack_images
    sel = data > rd
TypeError: '>' not supported between instances of 'double' and 'int'

Reproduced this, will look

Fixed / worked around in c3d54cc

This still breaks for me:

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10
DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
The following parameters have been modified:

stack_images = 10
input {
  experiments = <image files>
}

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2141, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1177, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 839, in stack_images
    rd += data
Boost.Python.ArgumentError: Python argument types in
    int.__iadd__(int, double)
did not match C++ signature:
    __iadd__(scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, int)
    __iadd__(scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >)```

rjgildea · 2020-06-16T07:29:34Z

Also "max" stack mode + "raw" image type looks very much like it is displaying the single image, and not a stacked image.

graeme-winter · 2020-06-16T07:30:29Z

<- is wondering about abandoning this project as to fix all the problems here will probably require rewriting the image viewer.

graeme-winter · 2020-06-16T07:32:16Z

Also "max" stack mode + "raw" image type looks very much like it is displaying the single image, and not a stacked image.

Sometimes the raw image is ints, sometimes doubles, sometimes the image you are adding is ints, sometimes doubles, and they need to be added in-place so will need to cast images-for-adding to the same type as image-already-there - cannot stick with one "standard" type - so this will be some horrible hodge-podge 😞

Having many random data types for images is plain annoying && unhelpful - just have doubles to make life simple

graeme-winter · 2020-06-16T07:46:48Z

This seems incompatible with setting the "image type" to be "raw":

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10

Select "raw" in the "image type" dropdown:

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2140, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1175, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 836, in stack_images
    sel = data > rd
TypeError: '>' not supported between instances of 'double' and 'int'

Reproduced this, will look

Fixed / worked around in c3d54cc

This still breaks for me:

$ dials.image_viewer $(dials.data get -q x4wide)/*.cbf stack_images=10
DIALS (2018) Acta Cryst. D74, 85-97. https://doi.org/10.1107/S2059798317017235
The following parameters have been modified:

stack_images = 10
input {
  experiments = <image files>
}

Traceback (most recent call last):
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 2141, in OnUpdateImage
    self.GetParent().GetParent().reload_image()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 513, in reload_image
    self.load_image(self.images.selected, refresh=True)
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 558, in load_image
    show_untrusted=show_untrusted,
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/slip_viewer/frame.py", line 499, in load_image
    self.update_settings()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 1177, in update_settings
    self.stack_images()
  File "/Users/rjgildea/software/cctbx/modules/dials/util/image_viewer/spotfinder_frame.py", line 839, in stack_images
    rd += data
Boost.Python.ArgumentError: Python argument types in
    int.__iadd__(int, double)
did not match C++ signature:
    __iadd__(scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, int)
    __iadd__(scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > {lvalue}, scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >)```

... try with 372120f

graeme-winter · 2020-06-16T07:55:29Z

I have looked at the code for a while and can't see where the change should go to make this oddity go away - however since it is not a new oddity I am not too worried about this. I have made sum the default, so if someone stacks images and then looks through the filters the results should be by default meaningful.

I'm not convinced the thresholding maps are acting on the sum/mean/max images in any case - I suspect they are effectively switching to stack_images=1 without updating any of the controls to reflect this.

I'm pretty sure this is properly broken. Could disable these buttons if stack != 1? Alternative will be rewriting the way that it works.

graeme-winter · 2020-06-16T08:23:03Z

@rjgildea disabled the buttons if stack now - so behaviour is consistent at least!

graeme-winter · 2020-06-16T08:40:11Z

Summary:

using double for all image data (raw; corrected) so internally consistent
if stack: disable image filter buttons
command-line control of stack number, stack mode
tests with raw and corrected images work

Otherwise clicking on the "image" button will take you back to the single image, even though stack_images is still set to > 1 Also reset the settings.display parameter to "image" in case we were in another view when entering stack_images mode.

image_data has already been cast to double by get_image_data(). Casting it again to double at this point means that we are modifying a copy of the image data instead of the actual data that is displayed.

rjgildea

I've also disabled the "image" button, as clicking on it when in stack mode would reset to displaying a single image, and fixed the "max" stack mode option so that now it actually works.

It now appears to work as expected, and I haven't managed to break it yet 🙂

If stacking images, divide through

7d0b071

Means the images are on a sensible scale when stacked so look OK

News

8fcbe56

graeme-winter added 2 commits June 12, 2020 16:13

sum_images -> stack_images

6d783a9

Max brightness -> 1000

b5f21c0

graeme-winter marked this pull request as ready for review June 12, 2020 15:17

rjgildea reviewed Jun 12, 2020

View reviewed changes

Implement max mode as well as mean

f236ea9

Also add a selector pull-down to select preferred stack type. Set max mode as default since that could well be more useful to the average user

graeme-winter changed the title ~~If stacking images, divide through~~ Improvements to image stacking Jun 15, 2020

sum_images -> stack_images; news update

3245074

Handle raw mode

c3d54cc

stack_type from command line

a2910e0

graeme-winter added 2 commits June 16, 2020 06:46

Reinstate sum mode, almost free

91062d1

Rewrite news, reset stack default to sum

6116e7a

stack_type -> stack_mode

00efe19

rjgildea reviewed Jun 16, 2020

View reviewed changes

graeme-winter added 2 commits June 16, 2020 08:33

double.as_double() is fine - suggestion from @rjgildea

4e9469f

Settle on double for images

372120f

Having many random data types for images is plain annoying && unhelpful - just have doubles to make life simple

If (stack) disable view buttons

0ef01b1

rjgildea added 2 commits June 18, 2020 23:01

Fix max stack_mode

8f9b597

image_data has already been cast to double by get_image_data(). Casting it again to double at this point means that we are modifying a copy of the image data instead of the actual data that is displayed.

rjgildea approved these changes Jun 18, 2020

View reviewed changes

graeme-winter merged commit f123a66 into master Jun 24, 2020

Anthchirp deleted the scale-when-stacking branch October 2, 2020 15:25

Improvements to image stacking #1302

Improvements to image stacking #1302

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graeme-winter commented Jun 16, 2020

rjgildea commented Jun 16, 2020

rjgildea commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

graeme-winter commented Jun 16, 2020

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