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Linked Data Visualizations Across Multiple Files
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Extract slice does not work #2418

Closed astrohector closed 1 year ago

astrohector commented 1 year ago

Describe the bug I am trying to extract a slice from an astronomical data cube using the slice tool to create a position-velocity diagram. I am able to draw the path on the image. However, when I press return it does not extract the slice and it does not display it in a new widow (as it is shown in the demo).

To Reproduce

  1. Import data cube
  2. Click and Drag cube to Tab and display as 2D image
  3. Click on slice tool on upper right corner of 2D image window
  4. Create path
  5. press Return when done
  6. notice that nothing comes up

Expected behavior As shown in demo: http://docs.glueviz.org/en/latest/gui_guide/slice.html

Details: I see this behavior in two different versions of glue I have: Version 1:

Version 2:

jfoster17 commented 1 year ago

Hey Héctor -- thanks for the bug report. In the very top-right of the glue window there is an "Error Console" button (depending on your screen size, it might be tucked away in a fold-down menu). Is there any error message shown when you click that?

Alternatively, in the version where you launch glue from the command line (version 2?) if you launch glue with the -v flag (glue -v) can you copy the full output of that after you try to extract a PV slice?

astrohector commented 1 year ago

Hi Jonathan, Thanks for getting back to me on this! It was great to receive an email from someone I know! I had not noticed the error log. Thanks for pointing it out to me. Please see below for the error that comes up when I press return to get the slice (i.e., p-v diagram) Would you like me to report the error using the "Send Bug Report" ? Thanks! Héctor

Traceback (most recent call last):

File "matplotlib/cbook/init.py", line 307, in process

File "glue/viewers/matplotlib/toolbar_mode.py", line 207, in key

self._finish_roi(self._last_event)

File "glue/viewers/matplotlib/toolbar_mode.py", line 101, in _finish_roi

self._roi_callback(self)

File "/Applications/glue 2023.02.0.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 41, in _extract_callback

self._build_from_vertices(vx, vy)

File "/Applications/glue 2023.02.0.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 44, in _build_from_vertices

pv_slice, x, y, wcs = _slice_from_path(vx, vy, self.viewer.state.reference_data,

File "/Applications/glue 2023.02.0.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 202, in _slice_from_path

from pvextractor import Path, extract_pv_slice

ModuleNotFoundError: No module named 'pvextractor'

On Mon, Jun 12, 2023 at 6:40 PM Jonathan Foster @.***> wrote:

Hey Héctor -- thanks for the bug report. In the very top-right of the glue window there is an "Error Console" button (depending on your screen size, it might be tucked away in a fold-down menu). Is there any error message shown when you click that?

Alternatively, in the version where you launch glue from the command line (version 2?) if you launch glue with the -v flag (glue -v) can you copy the full output of that after you try to extract a PV slice?

— Reply to this email directly, view it on GitHub https://github.com/glue-viz/glue/issues/2418#issuecomment-1588202242, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUMUR75YW53HDIG6JFAC4LXK6LFVANCNFSM6AAAAAAZDUW6LA . You are receiving this because you authored the thread.Message ID: @.***>

jfoster17 commented 1 year ago

(No need to e-mail the bug report, this is fine.)

It happens that both your versions of glue are missing the pvextractor module. For the stand-alone application you would need to download the latest Nightly Build (http://docs.glueviz.org/en/stable/installation/standalone.html#nightly-builds).

I'm not too familiar with the Anaconda navigator but you should be able to do something like

conda update glueviz

which hopefully will upgrade you to at least v1.2, still an old version but one that should fix your specific problem.

astrohector commented 1 year ago

Hi Jonathan, Thanks for your quick reply. I downloaded the nightly build and it still gives me the same error (see below). I have yet to try it on my other computer (with the different set-up). Thanks, Héctor

Traceback (most recent call last):

File "matplotlib/cbook/init.py", line 304, in process

File "glue/viewers/matplotlib/toolbar_mode.py", line 207, in key

self._finish_roi(self._last_event)

File "glue/viewers/matplotlib/toolbar_mode.py", line 101, in _finish_roi

self._roi_callback(self)

File "/Volumes/Glue/glue nightly.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 41, in _extract_callback

self._build_from_vertices(vx, vy)

File "/Volumes/Glue/glue nightly.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 44, in _build_from_vertices

pv_slice, x, y, wcs = _slice_from_path(vx, vy, self.viewer.state.reference_data,

File "/Volumes/Glue/glue nightly.app/Contents/MacOS/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 202, in _slice_from_path

from pvextractor import Path, extract_pv_slice

ModuleNotFoundError: No module named 'pvextractor'

On Tue, Jun 13, 2023 at 10:26 AM Jonathan Foster @.***> wrote:

(No need to e-mail the bug report, this is fine.)

It happens that both your versions of glue are missing the pvextractor module. For the stand-alone application you would need to download the latest Nightly Build ( http://docs.glueviz.org/en/stable/installation/standalone.html#nightly-builds ).

I'm not too familiar with the Anaconda navigator but you should be able to do something like

conda update glueviz

which hopefully will upgrade you to at least v1.2, still an old version but one that should fix your specific problem.

— Reply to this email directly, view it on GitHub https://github.com/glue-viz/glue/issues/2418#issuecomment-1589425531, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUMUR3OSOF5OVFWI3SA4ELXLB2BLANCNFSM6AAAAAAZDUW6LA . You are receiving this because you authored the thread.Message ID: @.***>

jfoster17 commented 1 year ago

Yes, I see. Okay, we need to fix this in the standalones. For now, trying to upgrade your version through conda is probably quickest.

astrohector commented 1 year ago

Hi Jonathan, I updated glue to v1.2 in my other computer using the anaconda navigator, and I still get the same error message:

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/matplotlib/cbook/init.py", line 287, in process

func(*args, **kwargs)

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/glue/viewers/matplotlib/toolbar_mode.py", line 207, in key

self._finish_roi(self._last_event)

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/glue/viewers/matplotlib/toolbar_mode.py", line 101, in _finish_roi

self._roi_callback(self)

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 41, in _extract_callback

self._build_from_vertices(vx, vy)

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 44, in _build_from_vertices

pv_slice, x, y, wcs = _slice_from_path(vx, vy, self.viewer.state.reference_data,

File "/Users/hga7/opt/anaconda3/lib/python3.9/site-packages/glue/plugins/tools/pv_slicer/qt/pv_slicer.py", line 202, in _slice_from_path

from pvextractor import Path, extract_pv_slice

ModuleNotFoundError: No module named 'pvextractor'

Thanks,

Héctor

On Tue, Jun 13, 2023 at 1:51 PM Jonathan Foster @.***> wrote:

Yes, I see. Okay, we need to fix this in the standalones. For now, trying to upgrade your version through conda is probably quickest.

— Reply to this email directly, view it on GitHub https://github.com/glue-viz/glue/issues/2418#issuecomment-1589773457, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUMURY24A2WKS5BN3UQQHTXLCSCBANCNFSM6AAAAAAZDUW6LA . You are receiving this because you authored the thread.Message ID: @.***>

jfoster17 commented 1 year ago

Sorry this took a while. Can you try the new standalone version here:

http://glueviz.s3.amazonaws.com/installers/2023.06.3/glue%202023.06.3.dmg

This should fix the problem for real.

astrohector commented 1 year ago

Hi Jonathan, I was away for a few days. I was able to download the new standalone version, and it worked! Thanks! Héctor

On Thu, Jun 22, 2023 at 5:36 PM Jonathan Foster @.***> wrote:

Sorry this took a while. Can you try the new standalone version here:

http://glueviz.s3.amazonaws.com/installers/2023.06.3/glue%202023.06.3.dmg

This should fix the problem for real.

— Reply to this email directly, view it on GitHub https://github.com/glue-viz/glue/issues/2418#issuecomment-1603347106, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUMUR2DLU4AQZUCTSLZZRLXMS3FFANCNFSM6AAAAAAZDUW6LA . You are receiving this because you authored the thread.Message ID: @.***>

jfoster17 commented 1 year ago

Great to hear that it works at last, and thanks for uncovering this bug for us.