Superflat_Scripts
Description
A set of Python scripts to standardize metrology data processing among the participant to the Superflat PCP project
Last updates
31/05/2023:
New features added since November 2022:
-
Computation of the PSD when the ROI contains a small number of invalid data points.
After applying the Tukey window, Invalid data points are interpolated by cubic splines. If the number of bad data points in a line exceeds 20% this line is discarded from further computation. The percentage of invalid points in the ROI is printed to the console.
-
Computation of the sagittal slope errors.
-
Detrending by an X and Y polynomial of specified degree.
-
Saving the processing results in a pickle file for later editing.
-
Bug fixes:
- Extraction of pixel size from some MX files.
- Extra blank lines in .xyz files.
15/11/2022:
ROI selection window now displays rectangle coordinates when dragging with the mouse. 2nd degree detrending was fixed to handle 'invalid data'.
Separate class for .datx file handling. Should work for nearly all MetroPro or MX version. Some older datx versions used szip compression. They are readable providing more recenf Hdf5 dlls than the standard ones are installed in the h5py directory.
Installation
Superflat_Scripts package requires the following scripts are installed:
- h5py
- numpy
- scipy
- matplotlib
It also uses the following packages which should be available with a basic Conda installation
- math
- tkinter
- pathlib
Installation commands with Conda
Optionally create a new environment
conda create -n superflat numpy scipy h5py matplotlibor install the required packages in an existing environment
conda activate myenv
conda install numpy scipy h5py matplotlibDownload the Superflat scripts package, either with git command
git clone https://gitlab.synchrotron-soleil.fr/OPTIQUE/leaps/superflat_scriptseither by getting and unpacking the zip file available from the Superflat git repository
https://gitlab.synchrotron-soleil.fr/OPTIQUE/leaps/superflat_scripts/-/archive/main/superflat_scripts-main.zipTo update the package with a newer version, enter the following command from your superflat_scripts directory
git pull https://gitlab.synchrotron-soleil.fr/OPTIQUE/leaps/superflat_scriptsUsage
Typical use is given by Superflat_main.py. Comment included in this file should help to taylor a script matching your needs
After activating your environment and switching to Superflat_scripts directory simply type:
python Superflat_main.pySupport
In case you are missing some functionnality or have suggestions for upgrades, please contact Fançois Polack: Francois.polack@synchrotron-soleil.fr
known issues
We observed some internal variability in .datx file of different origins. The present implementation is working with .datx files where Surface is stored contiguously without compression. Reading will fail if the Surface dataset is stored in a chunked compressed mode. Please report, with the console output, if you face such an issue.
Some .datx files seem to contain more than one surface dataset. HeightMap.read_Zygofile will read the first "Surface" dataset pointed in the /MetaData table
Contributing
This package was started on sample scripts provided by Uwe Flechsig uwe.flechsig@psi.ch. It has been extended by Fançois Polack francois.polack@synchrotron-soleil.fr, namely to include input from main Zygo interferomtric data formats, exclude invalid data from computations and a prescribed percentage of outlier pixels from the statistics
Authors and acknowledgment
- Fançois POLACK francois.polack@synchrotron-soleil.fr
- Uwe FLECHSIG uwe.flechsig@psi.ch
- Raymond BARRETT barrett@esrf.frt
License
This is an open source projects, no idea of the kind of license we should claim for
Project status
Version 1.0 First release for test pupose