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spacetelescope / cubeviz

Data analysis package for cubes. https://cubeviz.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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crashed on trying to fit linear model #576

Closed hcferguson closed 3 years ago

hcferguson commented 5 years ago

Tried to fit bjames SINFONI data with a linear model (no ROI)

Stack trace

WARNING: AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError. [astropy.units.quantity]
WARNING:astropy:AstropyDeprecationWarning: The truth value of a Quantity is ambiguous. In the future this will raise a ValueError.
/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/pyqtgraph/graphicsItems/PlotCurveItem.py:131: RuntimeWarning: All-NaN slice encountered
  b = (np.nanmin(d), np.nanmax(d))
/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/pyqtgraph/graphicsItems/PlotCurveItem.py:131: RuntimeWarning: All-NaN slice encountered
  b = (np.nanmin(d), np.nanmax(d))
/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/pyqtgraph/graphicsItems/PlotCurveItem.py:131: RuntimeWarning: All-NaN slice encountered
  b = (np.nanmin(d), np.nanmax(d))
/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/pyqtgraph/graphicsItems/PlotCurveItem.py:131: RuntimeWarning: All-NaN slice encountered
  b = (np.nanmin(d), np.nanmax(d))
/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/pyqtgraph/graphicsItems/PlotCurveItem.py:131: RuntimeWarning: All-NaN slice encountered
  b = (np.nanmin(d), np.nanmax(d))
WARNING: Model is linear in parameters; consider using linear fitting methods. [astropy.modeling.fitting]
WARNING:astropy:Model is linear in parameters; consider using linear fitting methods.
RecursionError: maximum recursion depth exceeded
Fatal Python error: Cannot recover from stack overflow.

Thread 0x000070000df40000 (most recent call first):
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/zmq/utils/garbage.py", line 47 in run
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x000070000da3d000 (most recent call first):
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/asyncio/base_events.py", line 438 in run_forever
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/tornado/platform/asyncio.py", line 132 in start
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/ipykernel/iostream.py", line 78 in _thread_main
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 884 in _bootstrap

Thread 0x000070000c4fe000 (most recent call first):
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 295 in wait
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 551 in wait
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/IPython/core/history.py", line 829 in run
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/IPython/core/history.py", line 58 in needs_sqlite
  File "</Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/decorator.py:decorator-gen-24>", line 2 in run
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x00007fffb1b60380 (most recent call first):
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
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  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 347 in _on_model_item_changed
  File "/Users/hcferguson/anaconda3/envs/cubeviz-v0.3b1/lib/python3.6/site-packages/specviz/plugins/model_editor/model_editor.py", line 128 in <lambda>
  ...
[1]    62271 abort      cubeviz
brechmos-stsci commented 5 years ago

@hcferguson It might be good to try it out in a standalone specviz, then if it is a specviz issue open a ticket there and link back to here. I suspect it is a data / specviz issue not specifically cubeviz.

hcferguson commented 5 years ago

Actually more likely the problem is in specutils (the fitting itself). That should be easier to try standalone anyway.

nmearl commented 5 years ago

This dataset seems to be broken. It's full of nans and is effecting other things in specutils/specviz like the statistics calculations. I'm not surprised that the model fitting fails (although, I believe I've fixed the issue of it crashing).

That said, the statistics and model fitting work when selecting regions that have actual data. I'm going to assume this is sufficient?

nmearl commented 5 years ago

@hcferguson please try with the current master in my fork (pip install git+https://github.com/nmearl/specviz --upgrade) and let me know if you experience the same issue.

hcferguson commented 5 years ago

Mixed success.

I've tried it about a dozen times. It mostly worked. but it crashed twice with a segfault and a complaint abut QTextCursor. That was after a fair amount of adjustment of the plot scaling. I think the ROI did not include the NAN's (the stats looked normal).

Stack trace:

(Make sure 'QTextCursor' is registered using qRegisterMetaType().)
WARNING: Model is linear in parameters; consider using linear fitting methods. [astropy.modeling.fitting]
WARNING:astropy:Model is linear in parameters; consider using linear fitting methods.
[1]    79475 segmentation fault  cubeviz
nmearl commented 5 years ago

@hcferguson Can you update with the latest changes in my fork and give it another shot?

hcferguson commented 5 years ago

@nmearl Tried it about a dozen times with no crash.

Ran into a separate (new) issue when I was a bold and tried fit spaxels and then aborted. I'll file that separately.