spi-processing 0.1.3

Module for processing of diffraction images in CXI format.

Installation

Processing scripts require Python 3.6 or higher.

You can install stable version by:

pip install spi-processing

To install from git, clone the repository and use:

cd spi_processing
pip install .

File format

All scripts work with data in CXI format. The following internal structure is expected:

file.cxi 
   ├─ cxi_version
   └─ entry_1
       ├─ image_1
       │   ├─ data (N, y, x)
       │   ├─ mask (y, x)
       │   └─ image_center (3) [x, y, z]
       │
       ├─ image_2
       │   ├─ data
       │   ├─ mask
       │   └─ image_center
...
       └─ image_M
           ├─ data
           ├─ mask
           └─ image_center

Each image_k group should have data dataset with images and mask dataset indicate bad pixels, image_center is contain coordinates of image center in pixels. Scripts spi_estimate_size.py and spi_refine_center.py require image_center to be set. Other groups and datasets are optional.

Scripts follow presented internal structure. Images are combined in the same image_k group if they have the same mask and image_center values.

Hit processing

This section describe scripts for processing of diffraction images in CXI format.

Compute photons number

Calculate number of photons and number of litpixels for every frame in CXI files. Results are saved in datasets num_photons and num_litpixels.

spi_compute_photons.py [-h] [-o OUTPUT_DIR] FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, data will be added to input files inplace.

Combine data

Combine multiple CXI files into single file. Combine inner CXI structure when possible. Arrays with same path in different files are concateneted along first dimention.

spi_combine.py [-h] -o OUTPUT_FILE FILE [FILE ...]

CXI files should include one or multiple image groups with path /entry_1/image_n . Image groups from input files will be combined into one image group in output file if they include same mask and image_center datasets.

Filter data

Filter data in CXI file by values in some dataset. Other datasets are filtered if they have the same first dimension as filtering dataset.

spi_filter.py [-h] -d DSET [-o OUTPUT_DIR] [--outfile OUTPUT_FILE] [-m MIN_VALUE] [-M MAX_VALUE] [-r REPORT] FILE [FILE ...]

Options:

• -d DSET - path to dataset within /entry_1/image_n/ groups.
• -m MIN_VALUE, -M MAX_VALUE - minimun and maximum allowed values in dataset, ends are included.
• -o OUTPUT_DIR - store results in provided folder with the same filenames. Alternative is --outfile OUTPUT_FILE to combine filtered data into single file.
• -r REPORT - generate PDF report.

Plot histogram

Create PDF histogram of values in dataset in one or many CXI files.

spi_plot_histogram.py [-h] -d DSET [-r START:END] [-s START:END] [-b BINS] [-o OUTPUT_FILE] FILE [FILE ...]

Options:

• -d DSET - path to selected dataset within /entry_1/image_n groups. Data in all image groups in all files will be concatenated.
• -r START:END - set range of histogram values
• -s START:END - add selection box between values
• -b BINS - number of histogram bins
• -o OUTPUT_FILE - name of output PDF file.

Correct background

Correct background scattering in CXI files by analysis of intensity distribution.

spi_correct_background.py [-h] [-o OUTPUT_DIR] [-M MAX] [-O OVERFLOW] [-r REPORT] [--no-correct] FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, input files will be corrected inplace.
• -M MAX - maximum possible background intensity, affects performance.
• -O OVERFLOW - do not correct intensities above OVERFLOW value.
• -r REPORT - generate PDF report.
• --no-correct - do not prosess data, only generate report by comparison of data in input files and existing files in OUTPUT_DIR.

Estimate center

Estimate center of diffraction images from scattering data. Estimation is based on rotational symmetry of averaged image. Results are saved into image_center dataset.

spi_estimate_center.py [-h] [-o OUTPUT_DIR] [-s] [-r REPORT] FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, image_center dataset will be added to input files.
• -s - all input files are considered to have the same beam position.

Refine center

Refine values of image_center by correlation with simulated sphere scattering. For correct result, average frame should have dictinct fringes (frames should have tight range of particle sizes). Input files must include image_center data that is used as starting point.

spi_refine_center.py [-h] [-o OUTPUT_DIR] [-s] [-r REPORT] [--max-shift MAX_SHIFT] [-R RADIUS] -w WAVELENGTH -d DISTANCE --pix PIXEL FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, image_center dataset will be updated in input files.
• -s - all input files are considered to have the same beam position.
• --max-shift MAX_SHIFT - maximum distance between old and new positions in pixels.
• -R RADIUS - maximum considered radius of simulated scattering pattern (pixels). Data outside this radius do not affect result.
• -w WAVELENGTH - radiation wavelenght (Angstrom).
• -d DISTANCE - detector distance (m).
• --pix PIXEL - pixel size (m).

Set center position

Set specific value of image_center in CXI file.

spi_set_center.py [-h] [-o OUTPUT_DIR] [-x CENTER_X] [-y CENTER_Y] [-z CENTER_Z] [-i FILE] FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, image_center dataset will be updated in input files.
• -x CENTER_X, -y CENTER_Y and -z CENTER_Z - image_center values. Alternatively, -i FILE can be provided to copy value of image_center from file.

Estimate size

Estimate size of particles in data by fitting power spectral density (PSD) against spherical form factor. Input files must include image_center data.

Inside each image group, new psd group will be created with datasets:

• data - PSD values for each frame
• size - estimated particle size for each frame
• scale - estimated intensity scale for each frame
• size_score - fidelity score of size estimation.
• size_range - tested range of particle sizes
• fit_diff - difference between PSD and each spherical form factor for each frame.

spi_estimate_size.py [-h] [-o OUTPUT_DIR] [-p PERCENTAGE] [-m S_MIN] [-M S_MAX] [-r R_MIN] [-R R_MAX] -w WAVELENGTH -d DISTANCE --pix PIXEL [-i INTERP] [-n NSIZE] [--icosahedron] FILE [FILE ...]

Options:

• -o OUTPUT_DIR - store results in provided folder with the same filenames. Otherwise, image_center dataset will be updated in input files.
• -p PERCENTAGE - use only brightest fraction of angular data for PSD estimation.
• -m S_MIN and -M S_MAX - range of sphere sizes in Angstrom, -n NSIZE of equally distributed sizes will be tested against each frame.
• -r R_MIN and -R R_MAX - area on frames between R_MIN and R_MAX (pixels) will be considered for size estimation.
• -w WAVELENGTH - radiation wavelenght (Angstrom).
• -d DISTANCE - detector distance (m).
• --pix PIXEL - pixel size (m).
• -i INTERP - number of sphere form factor points per 1 pixel. Allow to reduce errors for fringe size ~3 pixels and lower.
• -n NSIZE - Number of sizes tested within size range.
• --icosahedron - Size of particle will be computed with assumption that it is a regular icosahedron.