Closed svw26 closed 3 years ago
OK, the correct command to use is
pip install RSSMOSPipeline --upgrade --force-reinstall
which ends with
Successfully installed RSSMOSPipeline-0.1.0 astropy-3.2.3 cycler-0.10.0 kiwisolver-1.1.0 matplotlib-3.0.3 numpy-1.18.5 pyparsing-2.4.7 python-dateutil-2.8.1 scipy-1.4.1 setuptools-50.3.1 six-1.15.0
You are using pip version 9.0.1, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
I ran this after 11:14 this morning, and judging from the timestamps below, the new .pickle file still wasn't picked up:
Sarahs-MacBook-Pro:modelArcSpectra sarahwhite$ ls -ltr
total 1000
-rw-r--r-- 1 sarahwhite staff 13831 Oct 15 23:06 RefModel_PG0900_Xe_2x4.pickle
-rw-r--r-- 1 sarahwhite staff 207 Oct 16 11:17 PG0900_Ar_2x2.txt
-rw-r--r-- 1 sarahwhite staff 180 Oct 16 11:17 PG0900_Ar_2x2_1.txt
-rw-r--r-- 1 sarahwhite staff 539 Oct 16 11:17 PG0900_Ne_1x2.txt
-rw-r--r-- 1 sarahwhite staff 386 Oct 16 11:17 PG0900_Ne_2x2.txt
-rw-r--r-- 1 sarahwhite staff 515 Oct 16 11:17 PG0900_Ne_2x2_1.txt
-rw-r--r-- 1 sarahwhite staff 431 Oct 16 11:17 PG0900_Xe_2x2.txt
-rw-r--r-- 1 sarahwhite staff 359 Oct 16 11:17 PG1300_Ar_1x2.txt
-rw-r--r-- 1 sarahwhite staff 366 Oct 16 11:17 PG1300_Ar_2x2.txt
-rw-r--r-- 1 sarahwhite staff 290 Oct 16 11:17 PG1300_Ar_2x2_1.txt
-rw-r--r-- 1 sarahwhite staff 431 Oct 16 11:17 PG1300_Cu Ar_2x2.txt
-rw-r--r-- 1 sarahwhite staff 440 Oct 16 11:17 PG1300_Ne_1x2.txt
-rw-r--r-- 1 sarahwhite staff 794 Oct 16 11:17 PG1800_Ne_2x2.txt
-rw-r--r-- 1 sarahwhite staff 381 Oct 16 11:17 README
-rw-r--r-- 1 sarahwhite staff 32847 Oct 16 11:17 RefModel_PG0900_Ar_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 33604 Oct 16 11:17 RefModel_PG0900_Ar_2x2_1.pickle
-rw-r--r-- 1 sarahwhite staff 27444 Oct 16 11:17 RefModel_PG0900_Ne_1x2.pickle
-rw-r--r-- 1 sarahwhite staff 34187 Oct 16 11:17 RefModel_PG0900_Ne_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 35018 Oct 16 11:17 RefModel_PG0900_Ne_2x2_1.pickle
-rw-r--r-- 1 sarahwhite staff 33034 Oct 16 11:17 RefModel_PG0900_Xe_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 26987 Oct 16 11:17 RefModel_PG1300_Ar_1x2.pickle
-rw-r--r-- 1 sarahwhite staff 34697 Oct 16 11:17 RefModel_PG1300_Ar_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 33350 Oct 16 11:17 RefModel_PG1300_Ar_2x2_1.pickle
-rw-r--r-- 1 sarahwhite staff 35891 Oct 16 11:17 RefModel_PG1300_Cu Ar_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 27115 Oct 16 11:17 RefModel_PG1300_Ne_1x2.pickle
-rw-r--r-- 1 sarahwhite staff 34415 Oct 16 11:17 RefModel_PG1800_Ne_2x2.pickle
-rw-r--r-- 1 sarahwhite staff 706 Oct 16 11:17 convertPickles.py
-rw-r--r-- 1 sarahwhite staff 540 Oct 16 11:17 fixPickles.py
-rw-r--r-- 1 sarahwhite staff 9048 Oct 16 11:17 fixRefModel.py
drwxr-xr-x 5 sarahwhite staff 160 Oct 16 11:18 __pycache__
-rw-r--r-- 1 sarahwhite staff 155 Oct 16 11:34 PG0900_Xe_2x4.txt
(I removed a newline from PG0900_Xe_2x4.txt, hence the updated timestamp for that new file.) x
If you have copied the .txt and .pickle file to a directory where the code can find it and it's still not picked up, try deleting the product/imageInfo.pkl
file and re-running the pipeline. It's a bit clunky and only checks for matching arc models the first time it scans the FITS headers in the product/ directory (it works like this so you can keep dumping data into product/
as it comes in, without forcing a re-build of imageInfo.pkl
each time - it just scans images that aren't listed in imageInfo.pkl
). The latest version in 'master' prints a warning message about deleting imageInfo.pkl
if you add a new arc model.
Haha, yes, I couldn't find a imageInfo.pkl file in the raw
directory but the product
directory instead. No worries, but maybe I didn't get the warning message because the latest version in 'master' hasn't been released via PyPI yet? (Since I went the pip install
route.)
Anyway, deleting that file and re-running makes lots of things happen, and I get many files and folders appearing in the 'reduced' directory, including 'diagnostics' where 5 'slits' have been detected per exposure. Awesome! :tada: And do I have permissions to commit my RefModel_PG0900_Xe_2x4.pickle and PG0900_Xe_2x4.txt files to a branch of this repository, or would you prefer I emailed them? x
(This was my first pass, so totally cool if you'd prefer me to do more quality-assessment first!) x
Hiya again again :)
Having got the main test to run through fine, I then followed each of the instructions given below:
For me (using a virtual conda environment), this meant moving the .pickle and .txt files to /Users/sarahwhite/anaconda/envs/rsspipeline_conda/lib/python3.5/site-packages/RSSMOSPipeline/data/modelArcSpectra . Because I installed RSSMOSPipeline via
I thought that an equivalent way of re-running the setup.py script would be to do
Unfortunately this gives me the following:
Then, when I re-run
rss_mos_reducer product reduced all
I get:which seems to confirm that it is not picking up the new .pickle and .txt files.
Now that I've written this out(!), I've had the idea to restart the container... so let me try that. Other suggestions also welcome.
Thanks, Sarah x