Extract slice does not work #2418
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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 ( |
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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?
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(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
which hopefully will upgrade you to at least v1.2, still an old version but one that should fix your specific problem. |
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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
<#2418 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABUMUR3OSOF5OVFWI3SA4ELXLB2BLANCNFSM6AAAAAAZDUW6LA>
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Yes, I see. Okay, we need to fix this in the standalones. For now, trying to upgrade your version through conda is probably quickest. |
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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
<#2418 (comment)>,
or unsubscribe
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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. |
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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.
—
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Great to hear that it works at last, and thanks for uncovering this bug for us. |
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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
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:
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