iolite Python for LA-ICP-MS Course - Week 1 Discussion

Bence

Please post any questions you have about this week's content here

kai2

Hi Bence! I will start the discussion 🙂 You suggest Anaconda as python IDE and Atom as additional text editor. They are both great! My problem in the past with Iolite and python integration was that I have to use Iolite4 as my python IDE when I try to debug code, and Iolite4 is far from beeing perfect at that job (e.g., problems with indentation errors, syntax highlighting, no color schemes available, insufficient documentation about the inbuilt Iolite methods). Programming in Anaconda or PyCharm, or Spyder (I really like the data explorer here) is so much easier for a python noob like me. As we go forward, what method do you suggest is best for Python development in Iolite? is there any way to import Iolite4 into, say, PyCharm and debug code there?? Or do you plan on expanding Iolite's python capabilities to be a full-blown IDE at some point?

Bence

Hi Kai,

That's a great question and thanks for kicking things off! Spyder is a great tool and I actually recorded a clip of the basics that I eventually cut from the intro video (it was something similar to this).

(If you're a python beginner, don't worry if the following doesn't make much sense; this is really more of an intermediate topic).

Unfortunately, you can't run iolite's API in some other program like PyCharm as iolite is really a C++ program with a python interface (rather than a collection of python packages).

Regarding debugging and developing in iolite: we've also been adding features to the Python Workspace regularly (and would probably have added more if we hadn't been busy with 3D Trace Elements etc recently). However, I should be realistic and say that it will never be as developed as something like PyCharm which has a whole specialised team behind it that just makes IDEs.

That said, Joe and I will be showing you how we use iolite v4 to develop all the plugins we've made. It isn't as flash as Spyder or PyCharm, but you can still get things done quickly and easily, once you know how. 😉

-Bence

hourigan

Bence

Bence,

Kudos to you and Joe for a really excellent course, not to mention the functionality of Iolite 4.

It looks like you and Joe both develop code in Virtual Studio and save any resulting *.py files to the appropriate directories in the Iolite 4 preferences. This allows you to leverage a higher-level IDE than Iolite's Python Workspace for indentation and suggestions for variable names and functions.

I understand Iolite cannot be run from a third-party python IDE but I was wondering if you could provide some suggestions on how you set up the virtual environment and base interpreter so that you can develop in something like Virtual Studio.

BTW: I have finished the Element *.dat binary file importer. I think this could be a powerful addition to iolite that would allow quasi real-time data reduction (rather than waiting 8 hours until the sequence is done and processing the FIN2 files.)

Thanks,
Jeremy

Bence

Hi everyone,

Just letting you know I'm online and ready to help! 👋

FreyaS

Hey! I have a question about the define functions exercises for grading exams. I've written a code that will allow a grade to be given back for a given value between 0.0 and 1.0, as well as give an error message for any (numerical) value outside of that range. Where I've hit a problem however is if a 'sting' value is written into the function - for example examscore(one) as opposed to examscore(1). I'd like that to also give back an error message but haven't been able to find a way to do so. When doing the earlier exam score exercise I got this to work with a try and except, but that doesn't seem to be working now that its being used within a defined function. Is there any work around? It seems to be that the defined function will only except interger or float values to begin with. Cheers!

Bence

Hi FreyaS

Could you please post your code? To format it as code, start the code with a blank like with a back-tick ( ` which is different to a single quotation mark) and end it with a back-tick. Like this:
my_code = some_code

-Bence

FreyaS

Bence

This what I've written for the function:

`def examscore(grade):

if grade>=0.9 and grade<=1.0:
    Score='A'
elif grade>=0.8 and grade<0.9:
    Score='B'
elif grade>=0.7 and grade<0.8:
    Score='C'
elif grade>=0.6 and grade<0.7:
    Score='D'
elif grade<0.6 and grade>0.0:
    Score='F'
else:
    Score='Invalid value'
return Score`

Bence

You can still put a try: ... except: ... clause in your function. It would look something like this:

def examscore(grade):
    
    try:
        g = float(grade)
    except:
        return('Invalid value')
        
    if grade >= 0.9 and grade <= 1.0:
        Score='A'
    elif grade >= 0.8 and grade < 0.9:
        Score='B'
    elif grade >= 0.7 and grade < 0.8:
        Score='C'
    elif grade >= 0.6 and grade < 0.7:
        Score='D'
    elif grade < 0.6 and grade > 0.0:
        Score='F'
    else:
        Score='Invalid value'
    
    return Score

print(examscore(0.7))
print(examscore('one'))

The two tests at the end should print a value of 'C' and 'Invalid value'.

Is that what you were after?

BTW, I got it wrong. You should start and end your code block with three back-ticks 😃

Troy

I already had python 3.9.2 installed on my computer. However, I can't get past the part where I want to make sure I know where I am in the directory. When I type dir I get an error and when I type cd I get an error.

Additionally, I have tried to write a spurious code, but I am just unclear how to get it to run. That is, how does a user know what to enter? Most of the materials from py4all are about numbers but I was trying to do something with words.

Troy

If I quit() python, I can use dir to see what is in the directory. It is all there because I have installed some synchrotron software that uses python. Then when I do cd so that I can go to the folder I created on my desktop, it gives me:
C:\Users\troyr\AppData\Roaming\DemeterPerl
I don't see a way to change the path. I watched the introductory video.

Bence

Hi Troy,

From your second message, I think you've already worked a few things out. In particular, you can't use cd and dir once you have python running in your terminal#. These are "shell" commands that you can use when python is not running. Once you have quit python (using exit()), you can then use these shell commands.

To navigate to your Desktop folder (or whatever folder your script is in), you'll need to use the cd command. For example, if your python script was in your Desktop folder, you would type into the shell cd C:\Users\[your user name]\Desktop
Your prompt in the terminal should now show that you're in the Desktop folder.

Once you're in the folder containing your script, to run it in the terminal, type python [your script name] (e.g. python spuriousPredict.py). You may need to change that to python3 [your script name] depending on how python is setup on your computer. This should run your script. If not, please let us know.

And regarding "How does a person know what to enter?" you can add some text as a prompt to the user in your input() command. For example

word = input("Please enter your favourite word: ")

where the words in the brackets are the prompt that the user will see.

I hope that helps. Please let us know if you have any other questions.

#Just as a footnote, and perhaps as an aside here: python has equivalents of cd and dir that you can use within python. When running a script from within a terminal, whatever folder you were in when you started the script will be the "current working directory" when the script runs ("cwd" for short). If you use the os package, you can get the cwd within python using os.getcwd() (e.g. print(os.getcwd()) will print out what folder python is working in). Similarly, you can change directory within a script using the chdir() function which is also part of the os package. Just note that you'll need to import the package in your script using import os before you can use those functions. There is an overview of what I've just written, with an example, here

Joe

hourigan

Hi Jeremy,

Thanks! We're glad you liked it.

I think Bence and I actually both use editors other than Visual Studio Code most of the time, but wanted to try to keep things somewhat consistent between us and use something easily available for people following along.

No matter what editor you use, the objects, classes, etc. that are built-in to iolite won't be known, so you will not get any completion there (besides suggestions for types/functions you've already used perhaps), but you won't see function parameters and any doc strings. What can be useful, however, is setting up a python virtual environment with things like numpy, scipy, pandas, and any other standard python packages you may be using and configuring your editor to use that. That way you'll get proper completion for all of those packages at least.

You can create a virtual environment as python.exe -m venv .venv (without the '.exe' on Mac) and depending on how you've installed your local copy of python, you may also need to call it python3 rather than python and may also need to fully specify the path (e.g. C:\Users\Me\AppData\Local\Programs\Python\Python38\python.exe). More on virtual environments here.

In Visual Studio Code you can tell it which python interpreter to use by activating the command palette (ctrl + shift + p) then activating "Python: Select Interpreter". If you have a venv in your current folder, it'll probably recommend that one. Once that is done, you can activate "Python: Create Terminal" from the command palette which will give you a terminal with your virtual environment already active. Now you can install whichever packages you want as, e.g. pip install numpy and completion for numpy commands should work automatically.

All the best,