pyme-fsc

A Fourier shell (ring) correlation recipe module written for PYME.

Supports calculation from localization or image data.

System requirements

• Windows, Linux or OS X
• Python 2.7
• PYME (>18.7.18) and dependencies

• Tested on Windows 10 with PYME (18.7.18)

Installation

1. Clone repository.
2. Run the following in the project folder.

   	python setup.py develop
   

3. Start dh5view or VisGUI (PYME).

(Runtime < 5 min)

Demo

For localization data:

1. Open this simulated dataset (wormlike_simulated.h5r) with VisGUI (PYME).
2. Load and run this demo recipe (frc_from_locs.yaml).
3. The results will display in a new window.

(Runtime < 5 min)

For image data:

1. Open this simulated image (wormlike_simulated_img_pair.h5) with dh5view (PYME).
2. Load and run this demo recipe (frc_from_images.yaml).
3. The results will display in a new window.

(Runtime < 5 min)

Instructions

For localization data:

1. Refer to PYME documention for general use of PYME.
2. Open localization file with VisGUI (PYME).
3. Add the module FSCFromLocs. Detailed description the module and its inputs, outputs and parameters are accessible in PYME.
4. The recipe should autorun.
5. The results will display in a new window.

For image data:

1. Refer to PYME documention for general use of PYME.
2. Open image file with dh5view (PYME).
3. Add the module FSCFromImages. Detailed description the module and its inputs, outputs and parameters are accessible in PYME.
4. Need to at least provide the file path of the 2nd image (image_b_path).
5. Run recipe.
6. The results will display in a new window.

To do's

• Find method to calculate resolution per (pair of) dimension.
• Implement support for running multiply times to estimate errors.