Metadata-Version: 2.1
Name: imaxt-registration-tools
Version: 0.2.1
Summary: Image registration tools for IMAXT
Home-page: https://gitlab.developers.cam.ac.uk/astronomy/camcead/imaxt/imaxt-registration-tools
Author: attr: imaxt_registration.__author__
Author-email: "E.GonzalezSolares@ast.cam.ac.uk"
Project-URL: Bug Tracker, https://gitlab.developers.cam.ac.uk/astronomy/camcead/imaxt/imaxt-registration-tools/-/issues
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown

# IMAXT Registration Tools


## Install Instructions

### Create virtual environment

```
python -m venv ~/Python/registration
```

### Activate environment

```
source ~/Python/registration/bin/activate
```

### Install with pip

```
pip install -U imaxt-registration-tools
```


## Usage

```
usage: imaxtreg axio2stpt [-h] --stpt STPT --axio AXIO --output OUTPUT --pdf PDF [--verbose] [--nprocs NPROCS]
                          [--sections SECTIONS]

optional arguments:
  -h, --help           show this help message and exit
  --stpt STPT          Full path to STPT dataset
  --axio AXIO          Full path to AXIO dataset
  --output OUTPUT      Destination of output correspondence table (csv, parquet, npy, pkl)
  --pdf PDF            Destination of outout PDF quality control file
  --verbose            Verbose output
  --nprocs NPROCS      Number of processes to run in parallel (default 6)
  --sections SECTIONS  Comma separated list of AXIO sections to do (default is all)
  --nblobs NBLOBS      Maximum number of blobs for mask detection (default 1)
  --blobsize BLOBSIZE  Relative blob size for mask detection (default 0.01)
```

To run, e.g.

```
imaxtreg axio2stpt --axio /storage/processed/axio/20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um_Axio \
                   --stpt /storage/processed/stpt/20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um \
                   --out 20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um.csv \
                   --pdf 20220208_MPR_NSG_GFP_4T1_TdTOM_inflated_lung_Day21_200x15um.pdf \
                   --verbose
```
