mritopng 2.2

Easily convert MRI filed based on the DICOM format to a PNG image

Convert DICOM Files to PNG
===========================

[](https://circleci.com/gh/danishm/mritopng) [](https://opensource.org/licenses/MIT)

*Important Changes*
- **8/26/2018** - Ability to apply auto-contrast to the converted images

Introduction
------------
A simple python module to make it easy to batch convert a binary DICOM file, which is usually an output from
an MRI scan to a PNG image.

The MRI scanning facilities typically hand you a CD containing your MRI scans. This CD will typically not contain
any image files in traditional formats that can be opened up by your default image viewing program. The CD contains
a list of DICOM files, which can only be viewed by the included viewer, which is mostly only supported on a Windows machine.

This module should help you convert all the DICOM based scans to PNG files. This tool can be used as a command line tools as well as a library in your python code

Installation
------------

To have known to work dependencies use beforehand::

pip install -r requirements.txt

`mritopng` comes with a `setup.py` script to use with distutils. After unpacking the distribution, `cd` into the directory and execute the command::

python setup.py install


This will install two things

* The `mritopng` module will be installed; `import mritopng` will allow you to use it
* A command line utility called `mritopng` which can be used from the console

Quick Start
-----------
`mritopng` will install a command line utility that can be used to convert individual DICOM files or folders

### Getting Help

```
$ mritopng --help
usage: mritopng [-h] [-f] [-c] dicom_path png_path

Convert a dicom MRI file to png. To conver a whole folder recursivly, use the
-f option

positional arguments:
dicom_path Full path to the mri file
png_path Full path to the generated png file

optional arguments:
-h, --help show this help message and exit
-f, --folder Convert a whole folder instead of a single file
-c, --auto-contrast Apply contrast after converting default image
```

### Convert Single File

```sh
# Converts the file /DICOM/SCAN1 to a file called output.png,
# while applying auto contrast
$ mritopng --auto-contrast /DICOM/SCAN1 output.png
```

**Note:** If file `output.png` already exists, it will be overwritten

### Convert Folder Tree

The utility can also be used to convert a whole folder recursively by using the `-f` option::

```sh
# Takes all the files in /DICOM, converts the files to png and
# puts them in the /PNG folder with the same structure as /DICOM.
$ mritopng -f /DICOM /PNG
```

**Note:**
- Existing top level folder will NOT be over-written e.g. the example above will fail of the folder `/PNG` already exists
- The tool will try to convert as many files as it can, skipping the ones that it can't

Using it as a Library
---------------------

It's pretty easy to get up and running with `mritopng` in your own project

```py
import mritopng

# Convert a single file with auto-contrast
mritopng.convert_file('/home/user/DICOM/SCAN1', '/home/user/output.png', auto_contrast=True)

# Convert a whole folder recursively
mritopng.convert_folder('/home/user/DICOM/', '/home/user/PNG/')
```