issues with fabian on windows

[clairezurkowski]

Hello! I am getting my mXRD tools setup on my PC and was able to install Fabian and open the gui, however, I noticed this warning message when I installed it initially:
DEPRECATION: Loading egg at c:\users\zurkowski1\appdata\local\anaconda3\lib\site-packages\fabian-0.7.0-py3.11.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..

Then, I had to go in and adjust the median.py file and am now trying to build and install fabian again. I am receiving this error:
error: [WinError 32] The process cannot access the file because it is being used by another process: 'c:\users\zurkowski1\appdata\local\anaconda3\lib\site-packages\fabian-0.7.0-py3.11.egg'

I installed fabian form the fabian-master folder downloaded from github. Is there by chance a pip install option that already has the updated median.py file?

This egg file issue probably highlights my naivety with python, but as I am trying to google and figure it out, I figured I would post the discussion here in case anyone has experience with this. Thank you, Claire

[jonwright]

You can normally install latest versions from git using pip like this:

pip install git+https://github.com/FABLE-3DXRD/fabian.git

I will create an issue over in the fabian repository to remind us to upload something to pypi - I think the problem is coming up with a name because fabian is already taken...

[smerkel]

To add to John's comment, we did update the median.py (and other calls to deprecated time functions) since your last visit in Lille. The fabian version on github should be up-to-date.

We should document the pip installation procedure in the README. Could you let people know if the code suggested by John is actually working?

[clairezurkowski]

Hi all, thank you for these responses. I was able to install git for windows and run the pip install code that Jon provided. However, I am still getting this error when I run:

median.py -i C189_BL1_P1_q1_s2_241.edf -o C189_BL1_P1_q1_s2_median -f 1

-l 120 C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py:4: *DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html <https://setuptools.pypa.io/en/latest/pkg_resources.html>* * __import__('pkg_resources').run_script('fabian==0.7.0', 'median.py')* No file name supplied [-i filename] The number of the first image is missing [-f filenumber] The length of the file seris is missing [-l filelength] Usage: median.py [options] Options: -h, --help show this help message and exit -i FILENAME, --filename=FILENAME Name of an image file -o MEDIAN_FILESTEM, --output=MEDIAN_FILESTEM Stem of median file -f FIRST, --first=FIRST first file in file series -l FILTERLENGTH, --length=FILTERLENGTH length of file series -s DELTA, --step=DELTA step in between number of files to be used -S SLIDE, --slide=SLIDE no of median images -d, --debug Run in debug mode Again, I apologize if I am missing something here. I appreciate your help.

…

On Wed, Dec 20, 2023 at 3:10 AM Sébastien Merkel ***@***.***> wrote: To add to John's comment, we did update the median.py (and other calls to deprecated time functions) since your last visit in Lille. The fabian version on github should be up-to-date. We should document the pip installation procedure in the README. Could you let people know if the code suggested by John is actually working? — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVKVG5MSGSUX7YSJAESOJADYKLBTTAVCNFSM6AAAAABA3TOO7GVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSMBXGEYDE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- ~Claire Zurkowski~ https://clairezurkowski.github.io/go/

[jonwright]

(This is a guess). If the first filename in your sequence is: C189_BL1_P1_q1_s2_241.edf then it is expecting -f 241 in order to start from frame number 241 and the -l 120 means it will look for:
C189_BL1_P1_q1_s2_241.edf
C189_BL1_P1_q1_s2_242.edf
C189_BL1_P1_q1_s2_243.edf
...
C189_BL1_P1_q1_s2_361.edf

I don't see the error about pkg_resources - if that is eating sys.argv then you can also try:

python C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py -i C189_BL1_P1_q1_s2_241.edf -f 241 -l 10 -o median -d

Note that you have the same functionality in pyFAI-average, that is somewhat better maintained these days (min, median): https://pyfai.readthedocs.io/en/master/man/pyFAI-average.html

[clairezurkowski]

Thanks so much! I did try this yesterday and got the same error, but let me try again now and let you know. ~Claire Zurkowski~ https://clairezurkowski.github.io/go/

…

On Wed, Dec 20, 2023 at 9:04 AM Jon Wright ***@***.***> wrote: (This is a guess). If the first filename in your sequence is: C189_BL1_P1_q1_s2_241.edf then it is expecting -f 241 in order to start from frame number 241 and the -l 120 means it will look for: C189_BL1_P1_q1_s2_241.edf C189_BL1_P1_q1_s2_242.edf C189_BL1_P1_q1_s2_243.edf ... C189_BL1_P1_q1_s2_361.edf I don't see the error about pkg_resources - if that is eating sys.argv then you can also try: python C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py -i C189_BL1_P1_q1_s2_241.edf -f 241 -l 10 -o median -d Note that you have the same functionality in pyFAI-average, that is somewhat better maintained these days (min, median): https://pyfai.readthedocs.io/en/master/man/pyFAI-average.html — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVKVG5OJYLYTNKHMOWAIQ63YKMLCVAVCNFSM6AAAAABA3TOO7GVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSMJQGUZDQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[clairezurkowski]

okay, so I tried this one: python C:\Users\zurkowski1\AppData\ Local\anaconda3\Scripts\median.py -i C189_BL1_P1_q1_s2_241.edf -f 241 -l 10 -o median -d and got a bit further this time. I received the error code: C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('fabian==0.7.0', 'median.py') Traceback (most recent call last): File "C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py", line 4, in <module> __import__('pkg_resources').run_script('fabian==0.7.0', 'median.py') File "C:\Users\zurkowski1\AppData\Local\anaconda3\Lib\site-packages\pkg_resources\__init__.py", line 722, in run_script self.require(requires)[0].run_script(script_name, ns) File "C:\Users\zurkowski1\AppData\Local\anaconda3\Lib\site-packages\pkg_resources\__init__.py", line 1572, in run_script exec(script_code, namespace, namespace) File "C:\Users\zurkowski1\AppData\Local\anaconda3\Lib\site-packages\fabian-0.7.0-py3.11.egg\EGG-INFO\scripts\median.py", line 88, in <module> File "C:\Users\zurkowski1\AppData\Local\anaconda3\Lib\site-packages\fabian-0.7.0-py3.11.egg\EGG-INFO\scripts\median.py", line 62, in start AttributeError: module 'time' has no attribute 'clock' when I was visiting Lille, Sébastien helped me to go into these folders and modify median.py /fabian-master/scripts - Open median.py and replace *time.clock* with *time.process_time* in all places /fabian-master/Fabian - Replace *self.median=N.zeros((d2,d1)).astype(n.float) *with* self.median=N.zeros((d2,d1)).astype(float)* Is this something I need to do again? This time I installed fabian with the pip, but I can go into the \Scripts\median.py and adjust the script if needed. Thank you! On Wed, Dec 20, 2023 at 9:05 AM Claire Zurkowski ***@***.***> wrote:

…

Thanks so much! I did try this yesterday and got the same error, but let me try again now and let you know. ~Claire Zurkowski~ https://clairezurkowski.github.io/go/ On Wed, Dec 20, 2023 at 9:04 AM Jon Wright ***@***.***> wrote: > (This is a guess). If the first filename in your sequence is: > C189_BL1_P1_q1_s2_241.edf then it is expecting -f 241 in order to start > from frame number 241 and the -l 120 means it will look for: > C189_BL1_P1_q1_s2_241.edf > C189_BL1_P1_q1_s2_242.edf > C189_BL1_P1_q1_s2_243.edf > ... > C189_BL1_P1_q1_s2_361.edf > > I don't see the error about pkg_resources - if that is eating sys.argv > then you can also try: > > python C:\Users\zurkowski1\AppData\Local\anaconda3\Scripts\median.py -i > C189_BL1_P1_q1_s2_241.edf -f 241 -l 10 -o median -d > > Note that you have the same functionality in pyFAI-average, that is > somewhat better maintained these days (min, median): > https://pyfai.readthedocs.io/en/master/man/pyFAI-average.html > > — > Reply to this email directly, view it on GitHub > <#37 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AVKVG5OJYLYTNKHMOWAIQ63YKMLCVAVCNFSM6AAAAABA3TOO7GVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSMJQGUZDQ> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

-- ~Claire Zurkowski~ https://clairezurkowski.github.io/go/

[jonwright]

Where it says:
AttributeError: module 'time' has no attribute 'clock'
... then it seems you lost your changes? If you can change the clock to a time then it might run.

To understand what went wrong: when you did the pip install, maybe there is another pip installing for another python somewhere on your computer (where pip and where python to check on that). You can also use python -m pip to call on the pip matching your python.

[clairezurkowski]

Okay, I got things working. I went into \anaconda3\lib\site-packages then deleted the fabian-0.7.0-py3.11.egg file. Then, reinstalled fabian by going into my fabian-master folder and doing the build and install commands. I had already had the median.py files updated in this folder. After rerunning the median.py [options] command, I now have a median file for my data. Thank you for your help!

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On Wed, Dec 20, 2023 at 9:40 AM Jon Wright ***@***.***> wrote: Where it says: AttributeError: module 'time' has no attribute 'clock' ... then it seems you lost your changes? If you can change the clock to a time then it might run. To understand what went wrong: when you did the pip install, maybe there is another pip installing for another python somewhere on your computer (where pip and where python to check on that). You can also use python -m pip to call on the pip matching your python. — Reply to this email directly, view it on GitHub <#37 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AVKVG5OUZE4BCAN6MSIGGTDYKMPJNAVCNFSM6AAAAABA3TOO7GVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TSMJQHAYDS> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- ~Claire Zurkowski~ https://clairezurkowski.github.io/go/