Convert-EMD

Convert-EMD exports images and spectrum data from Velox generated EMD files.

This project is based on RosettaSciIO and emd-converter

Install

Environment requirements: Python >= 3.8

With pip:

pip install convert-emd

Usage

cemd [-h] -f FILE [-o TYPE] [-ns] [-sc COLOR] [-s FLOAT FLOAT FLOAT] [-e Str [Str ...]] [-oe ELEMENT [ELEMENT ...]] [-oa ALPHA] [-sa ALPHA] [-c CONTRAST] [-i INT INT]

Basic Usage

cemd -f INPUT_FILE

Run cemd -h for more information.

NOTICE: ".emd" extension should not be included into input filename. For example, if you want to convert "EXEAMPLE.emd", the input should be cemd -f EXAMPLE rather than cemd -f EXAMPLE.emd

Output Type

The -o/--out option allows users to choose the output image type (default: png).

cemd -f INPUT_FILE -o png ## For PNG type
cemd -f INPUT_FILE -o tif ## For TIF type
...

Scale Bar

Remove Scale Bar

The -ns/--no_scale option can be used to remove the scale bar in images.

cemd -f INPUT_FILE -ns ## No scale bar will be shown

Color of Scale Bar

The -sc/--scale_color option can be used to choose the color of the scale bar (default: white).

cemd -f INPUT_FILE -sc black ## Black scale bar
cemd -f INPUT_FILE -sc "#000000" ## Hex code can also be used

Position and Width of Scale Bar

The -s/--scale option can be used to adjust the postion and width of scale bar (default: x: 0.75, y: 0.9167, width-factor: 150)

cemd -f INPUT_FILE -s X Y WIDTH

NOTICE: Three arguments are required to specify the position and width of scale bar.

X and Y should be in float type and between 0 and 1. They decide the position of scale bar at (X, Y).

WIDTH should be a number more than 1. The width of scale bar is given by this factor as h/f (where h is the height of the image, f is the given WIDTH factor).

Elemental Mapping

Color of Elements

Default colors of elemental mapppings are corresponding to the following list in sequnce (Matplotlib default colors):

1f77b4, ff7f0e, 2ca02c, d62728, 9467bd, 8c564b, e377c2, 7f7f7f, bcbd22, 17becf

Convert-EMD provides -e/--eds option for users to customize the color of elemental mappings.

cemd -f INPUT_FILE -e ELEMENT_1 COLOR_1 ELEMENT_2 COLOR_2 ELEMENT_3 COLOR_3 ...

NOTICE: You don't need to specify all elemental colors, those undefined ones will be set according to the default color list.

Overlayed Mapping

The -oe/--overlay option decides which elements are overlyed (default: all).

cemd -f INPUT_FILE -oe ELEMENT_1 ElEMENT_2 ...

Moreover, -oa/--overlay_alpha and -sa/--substrate_alpha options are provided to adjust the transparency of elemental layers (default: 1.0) and the HAADF layer (default: 0.5) respectively. The argument should be a float number between 0 and 1, 0 means totally transparent.

Contrast (Histogram Equalization)

To improve the contrast (especially for HR-TEM), the -c/--contrast option is provided to introduce the scikit-image histogram equalization method with contrast stretching.

With this method, the image is rescaled to include all intensities that fall within the given percentiles (default: min = 1, max = 99).

cemd -f INPUT_FILE -c MIN MAX