BoxEditTool source not updated when drawing rects

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.

Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

``

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!

Thanks and all the best,

Zvi

Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

···

On Aug 5, 2018, at 01:09, Zvi Baratz <[email protected]> wrote:

Hi all,

I'm trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

# Create plot
plot = bp.figure(

# Plot image
plot.image(
    image='image',
    x=0,
    y=0,
    dw=image.shape[1],
    dh=image.shape[0],
    source=source,
    palette='Spectral11',
    name='image_plot',
)

# Add tools
hover = HoverTool(tooltips=[('x', '$x'), ('y', '$y'), ('value', '@image')])

roi_source = ColumnDataSource(data=dict(
    x=,
    y=,
    width=,
    height=,
))

r1 = plot.rect(
    x='x',
    y='y',
    width='width',
    height='height',
    source=sources_dict['roi'],
    fill_alpha=0.5,
    fill_color='#DAF7A6',
    dilate=True,
    name='rois',
)

plot.add_tools(
    hover,
    BoxSelectTool(),
    BoxEditTool(renderers=[r1]),
    LassoSelectTool(),
    PolySelectTool(),
)

When I create ROIs and print out the roi_source's data dictionary it returns empty as it was instantiated. I suspect I'm missing something and perhaps defining the source wrong, but I can't seem to find any way to make it return the coordinates and I've started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi

--
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Hi Bryan,

Thank you for your reply!

I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!

Zvi

···

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:

Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(

image='image',
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette='Spectral11',
name='image_plot',

)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(

x=[],
y=[],
width=[],
height=[],

))

r1 = plot.rect(

x='x',
y='y',
width='width',
height='height',
source=sources_dict['roi'],
fill_alpha=0.5,
fill_color='#DAF7A6',
dilate=True,
name='rois',

)

plot.add_tools(

hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),

)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,

Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.

To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].

To post to this group, send email to [email protected].

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For more options, visit https://groups.google.com/a/continuum.io/d/optout.

Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

···

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:

Hi Bryan,

Thank you for your reply!

I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!

Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:

Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(

image='image',
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette='Spectral11',
name='image_plot',

)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(

x=[],
y=[],
width=[],
height=[],

))

r1 = plot.rect(

x='x',
y='y',
width='width',
height='height',
source=sources_dict['roi'],
fill_alpha=0.5,
fill_color='#DAF7A6',
dilate=True,
name='rois',

)

plot.add_tools(

hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),

)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,

Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.

To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].

To post to this group, send email to [email protected].

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/bokeh/71216d5a-f8f3-4dd2-84e1-0e8da9eff185%40continuum.io.

For more options, visit https://groups.google.com/a/continuum.io/d/optout.

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

···

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:

Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:

Hi Bryan,

Thank you for your reply!

I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!

Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:

Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(

image='image',
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette='Spectral11',
name='image_plot',

)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(

x=[],
y=[],
width=[],
height=[],

))

r1 = plot.rect(

x='x',
y='y',
width='width',
height='height',
source=sources_dict['roi'],
fill_alpha=0.5,
fill_color='#DAF7A6',
dilate=True,
name='rois',

)

plot.add_tools(

hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),

)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,

Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.

To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].

To post to this group, send email to [email protected].

To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/bokeh/71216d5a-f8f3-4dd2-84e1-0e8da9eff185%40continuum.io.

For more options, visit https://groups.google.com/a/continuum.io/d/optout.

Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don't want to wait until the next release to try things out, we also publish periodic "dev builds" that can be installed via conda or pip:

  https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are *NOT* guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or "for production". They are for testing/evaluation purposes only.

Thanks,

Bryan

···

On Aug 8, 2018, at 01:40, Zvi Baratz <[email protected]> wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path..? I'm sorry if it's a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I've opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I'll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I've uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I'm relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

> On Aug 5, 2018, at 01:09, Zvi Baratz <[email protected]> wrote:
>
> Hi all,
>
> I'm trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
> Code sample:
>
> source = ColumnDataSource(data=dict(image=[image]))
>
> # Create plot
> plot = bp.figure(
>
> # Plot image
> plot.image(
> image='image',
> x=0,
> y=0,
> dw=image.shape[1],
> dh=image.shape[0],
> source=source,
> palette='Spectral11',
> name='image_plot',
> )
>
> # Add tools
> hover = HoverTool(tooltips=[('x', '$x'), ('y', '$y'), ('value', '@image')])
>
> roi_source = ColumnDataSource(data=dict(
> x=,
> y=,
> width=,
> height=,
> ))
>
> r1 = plot.rect(
> x='x',
> y='y',
> width='width',
> height='height',
> source=sources_dict['roi'],
> fill_alpha=0.5,
> fill_color='#DAF7A6',
> dilate=True,
> name='rois',
> )
>
> plot.add_tools(
> hover,
> BoxSelectTool(),
> BoxEditTool(renderers=[r1]),
> LassoSelectTool(),
> PolySelectTool(),
> )
>
> When I create ROIs and print out the roi_source's data dictionary it returns empty as it was instantiated. I suspect I'm missing something and perhaps defining the source wrong, but I can't seem to find any way to make it return the coordinates and I've started giving up on trying to find an example online.
>
> Any thoughts would be appreciated!
> Thanks and all the best,
> Zvi
>
> --
> You received this message because you are subscribed to the Google Groups "Bokeh Discussion - Public" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
> To post to this group, send email to [email protected].
> To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/bokeh/71216d5a-f8f3-4dd2-84e1-0e8da9eff185%40continuum.io.
> For more options, visit https://groups.google.com/a/continuum.io/d/optout.

--
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For more options, visit https://groups.google.com/a/continuum.io/d/optout.

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,

Zvi

···

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:

Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

    [https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds](https://www.google.com/url?q=https%3A%2F%2Fbokeh.pydata.org%2Fen%2Flatest%2Fdocs%2Finstallation.html%23developer-builds&sa=D&sntz=1&usg=AFQjCNHDn8IQs8yNDjaq9BiirqFRiKEqhA)

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:

Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:

Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!

Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:

Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected]om wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.
To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
To post to this group, send email to [email protected].
To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/bokeh/71216d5a-f8f3-4dd2-84e1-0e8da9eff185%40continuum.io.
For more options, visit https://groups.google.com/a/continuum.io/d/optout.


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.

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For more options, visit https://groups.google.com/a/continuum.io/d/optout.

Hi,

I'm not sure why you would be seeing anything like that locally, it's not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

···

On Aug 9, 2018, at 03:29, Zvi Baratz <[email protected]> wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it's better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,
Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:
Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don't want to wait until the next release to try things out, we also publish periodic "dev builds" that can be installed via conda or pip:

        https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are *NOT* guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or "for production". They are for testing/evaluation purposes only.

Thanks,

Bryan

> On Aug 8, 2018, at 01:40, Zvi Baratz <[email protected]> wrote:
>
> Hi Philipp,
>
> Awesome! Thank you very much.
> Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path..? I'm sorry if it's a silly question, still just getting my bearings :slight_smile:
>
> On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
> Hi Zvi,
>
> This is, I believe a bug, in the way the data is synced on bokeh server. I've opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I'll be working on a number of integration tests and hoping to have it be ready to merge later today.
>
> Philipp
>
> On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
> Hi Bryan,
>
> Thank you for your reply!
> I am running it as a Bokeh server application. I've uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I'm relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.
>
> Thanks again! Bokeh is awesome!
> Zvi
>
>
> On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
> Hi,
>
> Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.
>
> Bryan
>
> > On Aug 5, 2018, at 01:09, Zvi Baratz <[email protected]> wrote:
> >
> > Hi all,
> >
> > I'm trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
> > Code sample:
> >
> > source = ColumnDataSource(data=dict(image=[image]))
> >
> > # Create plot
> > plot = bp.figure(
> >
> > # Plot image
> > plot.image(
> > image='image',
> > x=0,
> > y=0,
> > dw=image.shape[1],
> > dh=image.shape[0],
> > source=source,
> > palette='Spectral11',
> > name='image_plot',
> > )
> >
> > # Add tools
> > hover = HoverTool(tooltips=[('x', '$x'), ('y', '$y'), ('value', '@image')])
> >
> > roi_source = ColumnDataSource(data=dict(
> > x=,
> > y=,
> > width=,
> > height=,
> > ))
> >
> > r1 = plot.rect(
> > x='x',
> > y='y',
> > width='width',
> > height='height',
> > source=sources_dict['roi'],
> > fill_alpha=0.5,
> > fill_color='#DAF7A6',
> > dilate=True,
> > name='rois',
> > )
> >
> > plot.add_tools(
> > hover,
> > BoxSelectTool(),
> > BoxEditTool(renderers=[r1]),
> > LassoSelectTool(),
> > PolySelectTool(),
> > )
> >
> > When I create ROIs and print out the roi_source's data dictionary it returns empty as it was instantiated. I suspect I'm missing something and perhaps defining the source wrong, but I can't seem to find any way to make it return the coordinates and I've started giving up on trying to find an example online.
> >
> > Any thoughts would be appreciated!
> > Thanks and all the best,
> > Zvi
> >
> > --
> > You received this message because you are subscribed to the Google Groups "Bokeh Discussion - Public" group.
> > To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
> > To post to this group, send email to [email protected].
> > To view this discussion on the web visit https://groups.google.com/a/continuum.io/d/msgid/bokeh/71216d5a-f8f3-4dd2-84e1-0e8da9eff185%40continuum.io.
> > For more options, visit https://groups.google.com/a/continuum.io/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups "Bokeh Discussion - Public" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to [email protected].
> To post to this group, send email to [email protected].
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> For more options, visit https://groups.google.com/a/continuum.io/d/optout.

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1.0.0dev5 is building now and should be available shortly

Bryan

···

On Aug 9, 2018, at 13:20, Bryan Van de ven <[email protected]> wrote:

Hi,

I'm not sure why you would be seeing anything like that locally, it's not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz <[email protected]> wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it's better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,
Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:
Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don't want to wait until the next release to try things out, we also publish periodic "dev builds" that can be installed via conda or pip:

       https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are *NOT* guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or "for production". They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz <[email protected]> wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path..? I'm sorry if it's a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I've opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I'll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I've uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I'm relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz <[email protected]> wrote:

Hi all,

I'm trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

# Create plot
plot = bp.figure(

# Plot image
plot.image(
   image='image',
   x=0,
   y=0,
   dw=image.shape[1],
   dh=image.shape[0],
   source=source,
   palette='Spectral11',
   name='image_plot',
)

# Add tools
hover = HoverTool(tooltips=[('x', '$x'), ('y', '$y'), ('value', '@image')])

roi_source = ColumnDataSource(data=dict(
   x=,
   y=,
   width=,
   height=,
))

r1 = plot.rect(
   x='x',
   y='y',
   width='width',
   height='height',
   source=sources_dict['roi'],
   fill_alpha=0.5,
   fill_color='#DAF7A6',
   dilate=True,
   name='rois',
)

plot.add_tools(
   hover,
   BoxSelectTool(),
   BoxEditTool(renderers=[r1]),
   LassoSelectTool(),
   PolySelectTool(),
)

When I create ROIs and print out the roi_source's data dictionary it returns empty as it was instantiated. I suspect I'm missing something and perhaps defining the source wrong, but I can't seem to find any way to make it return the coordinates and I've started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi

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Hi Bryan,

Sorry for the delayed response - I installed the dev release and tried to serve the app, but now I’m not getting anything printed out when connecting a function to the BoxEditTool’s renderer source. In 0.13.0 that printed out the empty data source as configured (example in the original question and the repo), meaning using:

box_edit_source.on_change(‘selected’, create_roi)

with:

def create_roi:
print(box_edit_source.data)

printed out:

{x=, y=, width=, height=}

However, now I’m not getting anything :frowning:

Is it possible I should listen to a different attribute than ‘selected’? or possibly connect differently altogether?

Thank you again for the support,

Zvi

···

On Friday, August 10, 2018 at 7:36:23 PM UTC+3, Bryan Van de ven wrote:

1.0.0dev5 is building now and should be available shortly

Bryan

On Aug 9, 2018, at 13:20, Bryan Van de ven [email protected] wrote:

Hi,

I’m not sure why you would be seeing anything like that locally, it’s not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz [email protected] wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,

Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:

Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

   [https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds](https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds)

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.
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You will have to listen to changes on the data property, so try changing your code to:

box_edit_source.on_change(‘data’, create_roi)

``

Philipp

···

On Sunday, August 12, 2018 at 9:15:30 PM UTC+1, Zvi Baratz wrote:

Hi Bryan,

Sorry for the delayed response - I installed the dev release and tried to serve the app, but now I’m not getting anything printed out when connecting a function to the BoxEditTool’s renderer source. In 0.13.0 that printed out the empty data source as configured (example in the original question and the repo), meaning using:

box_edit_source.on_change(‘selected’, create_roi)

with:

def create_roi:
print(box_edit_source.data)

printed out:

{x=, y=, width=, height=}

However, now I’m not getting anything :frowning:

Is it possible I should listen to a different attribute than ‘selected’? or possibly connect differently altogether?

Thank you again for the support,

Zvi

On Friday, August 10, 2018 at 7:36:23 PM UTC+3, Bryan Van de ven wrote:

1.0.0dev5 is building now and should be available shortly

Bryan

On Aug 9, 2018, at 13:20, Bryan Van de ven [email protected] wrote:

Hi,

I’m not sure why you would be seeing anything like that locally, it’s not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz [email protected] wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,

Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:

Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

   [https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds](https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds)

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.
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Yes! Thank you, It’s working perfectly.

Just to make sure:

  1. Each index in each returned list corresponds to one ROI, where x and y signify the centre of it.

  2. I created the Rect glyph instance (r1) with dilate=True, and I’m getting back fractions. Is this not supported or am I just doing something wrong again?

  3. There isn’t yet a built-in method for extracting the selected data directly, right?

Thanks again for all the help!

Zvi

···

On Monday, August 13, 2018 at 1:45:23 AM UTC+3, Philipp Rudiger wrote:

You will have to listen to changes on the data property, so try changing your code to:

box_edit_source.on_change(‘data’, create_roi)

``

Philipp

On Sunday, August 12, 2018 at 9:15:30 PM UTC+1, Zvi Baratz wrote:

Hi Bryan,

Sorry for the delayed response - I installed the dev release and tried to serve the app, but now I’m not getting anything printed out when connecting a function to the BoxEditTool’s renderer source. In 0.13.0 that printed out the empty data source as configured (example in the original question and the repo), meaning using:

box_edit_source.on_change(‘selected’, create_roi)

with:

def create_roi:
print(box_edit_source.data)

printed out:

{x=, y=, width=, height=}

However, now I’m not getting anything :frowning:

Is it possible I should listen to a different attribute than ‘selected’? or possibly connect differently altogether?

Thank you again for the support,

Zvi

On Friday, August 10, 2018 at 7:36:23 PM UTC+3, Bryan Van de ven wrote:

1.0.0dev5 is building now and should be available shortly

Bryan

On Aug 9, 2018, at 13:20, Bryan Van de ven [email protected] wrote:

Hi,

I’m not sure why you would be seeing anything like that locally, it’s not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz [email protected] wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,

Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:

Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

   [https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds](https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds)

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


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Hi,

I am trying to something similar with the PoinDrawTool. I can not figure out how to assign callback.

Any idea?

Thank you

Hi,

In order for anyone to be able to help you, you need to provide actual code for what you have tried.

Bryan

···

On Aug 17, 2018, at 06:01, Dobrin Botev [email protected] wrote:

Hi,

I am trying to something similar with the PoinDrawTool. I can not figure out how to assign callback.

Any idea?

Thank you

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Hi again,

I’m reposting here because I suspect this has to do with the relevant PR (I’m using Bokeh version 1.0.0dev5). I’ve been playing with the BoxEditTool and came across some issues when sharing a data source with a DataTable. I tried both using the same ColumnDataSource instance and separate ones with callbacks for selection changes and I get the same behaviour. It seems that making a selection in the DataTable synchronizes perfectly with the BoxEditTool, but once a selection is made in the plot itself (using the BoxEditTool) it only updates the DataTable for the first time, and then any further selections no longer trigger the BoxEditTool index change callback. Making selections in the DataTable also no longer has an effect on the plot. I’ve pushed the updated code to GitHub.
An image of the app at its current state might help clarify:

As you can see, here the selection state is after previously making a selection (on box index 2) through the BoxEditTool and then deselecting, leaving the DataTable row selected and rendering any further selection in either obsolete.

The relevant piece of code is:

image_source = ColumnDataSource(

data=dict(

image=[data],

x=[0],

y=[0],

dw=[data.shape[1]],

dh=[data.shape[0]],

))

roi_source = ColumnDataSource(data={})

roi_source.data = dao.get_roi_source(selected_image)

def create_image_figure(image: np.ndarray):

image = image_source.data[‘image’][0]

width = image.shape[1]

height = image.shape[0]

Create figure

plot = bp.figure(= bp.figure(

plot_width=min(width, 800),

plot_height=min(height, 800),

x_range=[[0, width],

y_range=[[0, height],

title=‘Selected Image’,

name=‘image_figure’,

)

Plot image

plot.image(

image=‘image’,

x=0,

y=0,

dw=‘dw’,

dh=‘dh’,

source=image_source,

palette=‘Spectral11’,

name=‘image_plot’,

)

Create hover tool

hover = HoverTool(tooltips=[([(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

Create ROI selection renderer

r1 = plot.rect(

x=‘x’,

y=‘y’,

width=‘width’,

height=‘height’,

source=roi_source,

fill_alpha=0.5,

fill_color=’#DAF7A6’,

dilate=True,

name=‘rois’,

)

Add tools

plot.tools = [

hover,

BoxEditTool(renderers=[r1]),[r1]),

]

return plot

def create_roi_table():

int_formatter = NumberFormatter(format=‘0’)

columns = [

TableColumn(

field=‘x’,

title=‘x’,

formatter=int_formatter,

),

TableColumn(

field=‘y’,

title=‘y’,

formatter=int_formatter,

),

TableColumn(

field=‘width’,

title=‘Width’,

formatter=int_formatter,

),

TableColumn(

field=‘height’,

title=‘Height’,

formatter=int_formatter,

),

]

return DataTable(

source=roi_source,

columns=columns,

width=400,

height=150,

editable=True,

)

In the context of the app the image data is loaded beforehand through a helper class. In the repo there’s also a commented out version of trying to attach callbacks with separate sources (results in same behaviour).

Thanks again! All the best,

Zvi

You will have to listen to changes on the data property, so try changing your code to:

box_edit_source.on_change(‘data’, create_roi)

Philipp

Hi Bryan,

Sorry for the delayed response - I installed the dev release and tried to serve the app, but now I’m not getting anything printed out when connecting a function to the BoxEditTool’s renderer source. In 0.13.0 that printed out the empty data source as configured (example in the original question and the repo), meaning using:

box_edit_source.on_change(‘selected’, create_roi)

with:

def create_roi:
print(box_edit_source.data)

printed out:

{x=, y=, width=, height=}

However, now I’m not getting anything :frowning:

Is it possible I should listen to a different attribute than ‘selected’? or possibly connect differently altogether?

Thank you again for the support,
Zvi

1.0.0dev5 is building now and should be available shortly

Bryan

···

On Monday, August 13, 2018 at 1:45:23 AM UTC+3, Philipp Rudiger wrote:
On Sunday, August 12, 2018 at 9:15:30 PM UTC+1, Zvi Baratz wrote:
On Friday, August 10, 2018 at 7:36:23 PM UTC+3, Bryan Van de ven wrote:

On Aug 9, 2018, at 13:20, Bryan Van de ven [email protected] wrote:

Hi,

I’m not sure why you would be seeing anything like that locally, it’s not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz [email protected] wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,
Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:
Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


You received this message because you are subscribed to the Google Groups “Bokeh Discussion - Public” group.
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Sorry for the bad tabs. Another shot at uploading the image:
Untitled.png

···

On Wednesday, August 22, 2018 at 8:49:37 PM UTC+3, Zvi Baratz wrote:

Hi again,

I’m reposting here because I suspect this has to do with the relevant PR (I’m using Bokeh version 1.0.0dev5). I’ve been playing with the BoxEditTool and came across some issues when sharing a data source with a DataTable. I tried both using the same ColumnDataSource instance and separate ones with callbacks for selection changes and I get the same behaviour. It seems that making a selection in the DataTable synchronizes perfectly with the BoxEditTool, but once a selection is made in the plot itself (using the BoxEditTool) it only updates the DataTable for the first time, and then any further selections no longer trigger the BoxEditTool index change callback. Making selections in the DataTable also no longer has an effect on the plot. I’ve pushed the updated code to GitHub.
An image of the app at its current state might help clarify:

As you can see, here the selection state is after previously making a selection (on box index 2) through the BoxEditTool and then deselecting, leaving the DataTable row selected and rendering any further selection in either obsolete.

The relevant piece of code is:

image_source = ColumnDataSource(

data=dict(

image=[data],

x=[0],

y=[0],

dw=[data.shape[1]],

dh=[data.shape[0]],

))

roi_source = ColumnDataSource(data={})

roi_source.data = dao.get_roi_source(selected_image)

def create_image_figure(image: np.ndarray):

image = image_source.data[‘image’][0]

width = image.shape[1]

height = image.shape[0]

Create figure

plot = bp.figure(= bp.figure(

plot_width=min(width, 800),

plot_height=min(height, 800),

x_range=[[0, width],

y_range=[[0, height],

title=‘Selected Image’,

name=‘image_figure’,

)

Plot image

plot.image(

image=‘image’,

x=0,

y=0,

dw=‘dw’,

dh=‘dh’,

source=image_source,

palette=‘Spectral11’,

name=‘image_plot’,

)

Create hover tool

hover = HoverTool(tooltips=[([(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

Create ROI selection renderer

r1 = plot.rect(

x=‘x’,

y=‘y’,

width=‘width’,

height=‘height’,

source=roi_source,

fill_alpha=0.5,

fill_color=’#DAF7A6’,

dilate=True,

name=‘rois’,

)

Add tools

plot.tools = [

hover,

BoxEditTool(renderers=[r1]),[r1]),

]

return plot

def create_roi_table():

int_formatter = NumberFormatter(format=‘0’)

columns = [

TableColumn(

field=‘x’,

title=‘x’,

formatter=int_formatter,

),

TableColumn(

field=‘y’,

title=‘y’,

formatter=int_formatter,

),

TableColumn(

field=‘width’,

title=‘Width’,

formatter=int_formatter,

),

TableColumn(

field=‘height’,

title=‘Height’,

formatter=int_formatter,

),

]

return DataTable(

source=roi_source,

columns=columns,

width=400,

height=150,

editable=True,

)

In the context of the app the image data is loaded beforehand through a helper class. In the repo there’s also a commented out version of trying to attach callbacks with separate sources (results in same behaviour).

Thanks again! All the best,

Zvi

On Monday, August 13, 2018 at 1:45:23 AM UTC+3, Philipp Rudiger wrote:
You will have to listen to changes on the data property, so try changing your code to:

box_edit_source.on_change(‘data’, create_roi)

Philipp

On Sunday, August 12, 2018 at 9:15:30 PM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Sorry for the delayed response - I installed the dev release and tried to serve the app, but now I’m not getting anything printed out when connecting a function to the BoxEditTool’s renderer source. In 0.13.0 that printed out the empty data source as configured (example in the original question and the repo), meaning using:

box_edit_source.on_change(‘selected’, create_roi)

with:

def create_roi:
print(box_edit_source.data)

printed out:

{x=, y=, width=, height=}

However, now I’m not getting anything :frowning:

Is it possible I should listen to a different attribute than ‘selected’? or possibly connect differently altogether?

Thank you again for the support,
Zvi

On Friday, August 10, 2018 at 7:36:23 PM UTC+3, Bryan Van de ven wrote:
1.0.0dev5 is building now and should be available shortly

Bryan

On Aug 9, 2018, at 13:20, Bryan Van de ven [email protected] wrote:

Hi,

I’m not sure why you would be seeing anything like that locally, it’s not something I have ever encountered. I expect there will be a dev build out today. The next full release will most likely be around mid-September.

Thanks,

Bryan

On Aug 9, 2018, at 03:29, Zvi Baratz [email protected] wrote:

Alright, I built BokehJS locally according to the instructions here and I have a conda env with all the requirements, however when I try to serve the app from that env and use any tools over the image I immediately get the terminal message:

2018-08-09 13:22:14,070 WebSocket connection closed: code=None, reason=None

Maybe it’s better I wait for the next published dev-build. Also, do you have a rough estimation of when these fixes might be merged to the official distribution?

Thank you very much,
Zvi

On Wednesday, August 8, 2018 at 10:17:28 PM UTC+3, Bryan Van de ven wrote:
Hi,

You would also have to build BokehJS locally to make use of this from a source checkout, which is a bit of a chore. However, if you don’t want to wait until the next release to try things out, we also publish periodic “dev builds” that can be installed via conda or pip:

https://bokeh.pydata.org/en/latest/docs/installation.html#developer-builds

we will try to make a new on in the next few days that includes this recent work. Just be advised that the BokehJS resources for dev builds are NOT guaranteed to be available forever. i.e. you should not use dev builds for anything published permanently or “for production”. They are for testing/evaluation purposes only.

Thanks,

Bryan

On Aug 8, 2018, at 01:40, Zvi Baratz [email protected] wrote:

Hi Philipp,

Awesome! Thank you very much.
Does that mean I should wait for the next release? Or do I clone the bokeh repo locally and add it to my path…? I’m sorry if it’s a silly question, still just getting my bearings :slight_smile:

On Tuesday, August 7, 2018 at 3:47:44 PM UTC+3, Philipp Rudiger wrote:
Hi Zvi,

This is, I believe a bug, in the way the data is synced on bokeh server. I’ve opened a PR completely overhauling how the syncing of data is handled for the drawing tools (see https://github.com/bokeh/bokeh/pull/8137), which should fix your issue. I’ll be working on a number of integration tests and hoping to have it be ready to merge later today.

Philipp

On Tuesday, August 7, 2018 at 10:54:04 AM UTC+1, Zvi Baratz wrote:
Hi Bryan,

Thank you for your reply!
I am running it as a Bokeh server application. I’ve uploaded the code to GitHub, it is meant to be used as a GUI application for a flow image correlation spectroscopy (FLICS) analysis which uses two-photon excitation microscopy to learn about blood flow in the brain. The application is meant to be used locally in any lab that has appropriate data (images) and would like to mark regions of interest and run the analysis (in the future perhaps also display a summary of the results). For that, I need to be able to extract the data within a chosen ROI and pass it as input for the analysis, and therefore I’m relying heavily on BoxEditTool. The relevant file is, of course, app/main.py, but please feel free to share any thoughts you may have on the layout of the project so far.

Thanks again! Bokeh is awesome!
Zvi

On Monday, August 6, 2018 at 7:20:14 PM UTC+3, Bryan Van de ven wrote:
Hi,

Are you running this as a Boeh server application? Getting the coordinates back to python code will only work in the context of a Bokeh server application.

Bryan

On Aug 5, 2018, at 01:09, Zvi Baratz [email protected] wrote:

Hi all,

I’m trying to work with the BoxEditTool to draw regions of interest (ROIs) on an image. For some reason, it seems the source I set for the Rect glyph instance is not updated after I make the drawings.
Code sample:

source = ColumnDataSource(data=dict(image=[image]))

Create plot

plot = bp.figure(

Plot image

plot.image(
image=‘image’,
x=0,
y=0,
dw=image.shape[1],
dh=image.shape[0],
source=source,
palette=‘Spectral11’,
name=‘image_plot’,
)

Add tools

hover = HoverTool(tooltips=[(‘x’, ‘$x’), (‘y’, ‘$y’), (‘value’, ‘@image’)])

roi_source = ColumnDataSource(data=dict(
x=,
y=,
width=,
height=,
))

r1 = plot.rect(
x=‘x’,
y=‘y’,
width=‘width’,
height=‘height’,
source=sources_dict[‘roi’],
fill_alpha=0.5,
fill_color=’#DAF7A6’,
dilate=True,
name=‘rois’,
)

plot.add_tools(
hover,
BoxSelectTool(),
BoxEditTool(renderers=[r1]),
LassoSelectTool(),
PolySelectTool(),
)

When I create ROIs and print out the roi_source’s data dictionary it returns empty as it was instantiated. I suspect I’m missing something and perhaps defining the source wrong, but I can’t seem to find any way to make it return the coordinates and I’ve started giving up on trying to find an example online.

Any thoughts would be appreciated!
Thanks and all the best,
Zvi


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