Manual Align

This is a tool for manually aligning two images from 2-5 selected points

---

Installation

Start by cloning this repo, either by just downloading it here or by running (in your shell):

git clone https://github.com/xkstein/ManualAlign/

I recommend installing the required python packages in a python virtual environment (learn more about them here), to set this up go into the downloaded folder and run

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

This makes a virtual environment in this folder (under venv/), sources it (meaning that you're now using the virtual environment), and installs the required python packages to that virtual environment.

Now just run

python align.py

to open the application!

---

Usage

This program aligns an input image to a reference image. To do this,

1. Load both an image and a reference image (commands can be found under File in the toolbar)
2. Select 2-5 mutual points between them
3. Align them by selecting the Align option under Edit in the toolbar.

The resulting image can either be cropped and exported (using the red square) or exported in full by selecting Save Cropped Aligned Image or Save Aligned Image.¹

Controls

Input	Command
DOUBLE CLICK	Select point
#1-5	Select marker index
h	"Home" the selected image
Backspace	Deletes current selected point

NOTE: This list isn't comprehensive, there are other actions and keybinds which can be found in the file and edit menu items

Functions

Found under Edit in the toolbar:

• Autosave Points (Toggle) - If set, csv points are automatically saved when an image is saved.
• Lock ROI (Toggle) - Immobilizes the ROI (the red square which is used for cropping)

---

Configuration

You can set all of the image path things through the gui's toolbar now, which is kinda nice, or you can do it through the code if that's your thing

TRACE_PATH - Path to the traced image

TRACE_PATH_SAVE - Path to the location where you wanna save the aligned traced image

RAW_PATH - Path to the location of the raw image (that you're aligning to the tracing)

RAW_PATH_SAVE - Where you want to save the aligned raw image²

PTS_CSV_READ - Where to read the alignment points from

PTS_CSV_SAVE - Where to save alignment points²

---

To Do:

• Change from qt imsave backend (to suppress FutureWarning) <= the other options where very slow on my machine so this will take some investigating
• Just better cropping code (in ImagePlot, already TODOed)

---

Credit to this stack overflow post for helping in a major way.

Footnotes

1. NOTE: your cropping is relative to the reference image, and it is saved and loaded with the csv points. ↩

2. NOTE: if you change the raw image, you also will need to set where to save points and where to save the aligned image ↩ ↩²