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The core package of the SIMEX platform providing the calculator interfaces. https://simex-lite.readthedocs.io/

License: Other

Makefile 0.37% Python 70.89% Shell 0.71% GLSL 21.45% HTML 6.58%

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catchears godot11 junceee pinkdiamond1 mrakitin

simex-lite's Issues

Missed dependencies or redundant import

[esobolev@max-display009]~/proj/simex1/diffraction_noise_geom% python diffr_2nip.py
Traceback (most recent call last):
  File "/home/esobolev/proj/simex1/diffraction_noise_geom/diffr_2nip.py", line 1, in <module>
    from SimExLite.DiffractionCalculators import SingFELPDBDiffractionCalculator
  File "/home/esobolev/envs/dev-202301/lib/python3.9/site-packages/SimExLite/DiffractionCalculators/__init__.py", line 3, in <module>
    from .CrystfelDiffractionCalculator import CrystfelDiffractionCalculator
  File "/home/esobolev/envs/dev-202301/lib/python3.9/site-packages/SimExLite/DiffractionCalculators/CrystfelDiffractionCalculator.py", line 6, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

Add a Iterator to the data API

This will benefit the converting function of data wrappers in SimEx to save time.

In some files, this error about XMDYN exist

File /gpfs/exfel/data/user/juncheng/SimExLite/SimExLite/PMIData/XMDYNFormat.py:52, in XMDYNFormat.read(cls, filename, format)
     50 time_step = data_dict[step]
     51 # Time of each step in second
---> 52 time_step["time"] = h5["misc/time"][snp][()]
     53 time_step["atomic_numbers"] = step_in["Z"][()]
     54 # Velocity of each atom. The unit is m/s

Enhancement: Process beamlines downloaded from SiRepo's SRW tool

SiRepo makes it very intuitive and simple to configure a beamline and to propagate a Gaussian beam through it. Downloading
a beamline configuration is supported. A py script is generated that contains the beamline definition using srwpy's syntax.

Make a utility in simex(-lite) that reads (imports) the downloaded srwpy script and constructs a valid WPG beamline out of it that can be digested by the WPGPropagator.

DiffractionData

Detector data + Geometry data =|Assemble|> DiffractionData

Improve documentation

I found the following issues with the documentation;

Quickstart expectations: I would expect an example simulation as part of a quickstart, not just instructions for installation.

Redundant sections: Introduction/Quickstart and Users/Installation are more or less identical, remove one of them

installation uses python setup.py which is kind of old fashioned. `pip install -e .` is the way to go.

Calculators: Really just one Calculator? Can we have more?

PhenomSourceCalculator:

should describe that this is a XFEL pulse and how it is modeled
being picky: Why do we need all this wpg stuff, can't we put all that in some common namespace or (better) provide wrappers for common plotting tasks?
While at it, should also show how to use the sampling check in wpg.
also, since backengine installation only comes next, wpg might not be available, yet

Backengine installation

install from git without cloning:

pip install git+https://github.com/...@simex

mention that mpi is a requirement

WPG:

why install from juncheng repo, not central WPG?

Usage

Add introductory explanation of what is being done, what are the steps

add comments to code
turn doi into html
explain the img_gaussian parameters
What does "Larger slop and intercept gets larger noise" mean?

DiffractionCalculator in SimExLite

Tutorial page for the singfel calculator

SimEx-Lite GaussianSourceCalculator test

@godot11 Could you please help test the GaussianSourceCalculator in the libpyvinyl branch of SimEx-Lite?

Quickstart

git clone https://github.com/PaNOSC-ViNYL/SimEx-Lite.git
git checkout libpyvinyl

And then have a look at tests/test_GaussianSourceCalculator.py. The WPG package needs to be installed for that.

After testing, could you please let me know:

What do you think blocked you from using the program?
What do you think is needed to let you start easier?

diffr_ori = dd.get_data(pattern_shape=(81, 81))

WPG calculator in SimEx-Lite

Calculator test
WavefrontData test
Modify data_to_return in BaseData to accept extra data.

I'd write somewhere in the documentation:
SimEx-Lite depends on WPG (github.com/Samoyl/WPG). Please download and build WPG as per their documentation. Then, you have to make the WPG library "visible" to SimEx-Lite. To this end, do one of the following:

$PYTHONPATH: If you have the environment variable $PYTHONPATH set, copy the WPG/ directory into any directory listed in $PYTHONPATH.
conda: If you installed SimEx-Lite in a conda environment, activate that environment and copy the WPG/ directory to $CONDA_PREFIX/lib/python3.x/site-packages/ (x is your python minor version).
pip: If you installed SimEx-Lite with pip install, copy the WPG directory into $HOME/.local/lib/python3.x/site-packages
Test that WPG can be imported by running:

$> python -c 'import WPG.Beamline'