From a727206fe9fa2c338c9332a558d70de62dbd3e4e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Cl=C3=A9ment=20POIRET?= <poiret.clement@outlook.fr>
Date: Mon, 12 Jul 2021 10:12:10 +0200
Subject: [PATCH] 0.1.0 release * Added support for poetry scripts

---
 README.rst                    |  5 +++--
 pyproject.toml                |  8 +++++++-
 roiloc.py => roiloc/roiloc.py | 11 ++++++-----
 roiloc/template.py            | 15 ++++++++++-----
 4 files changed, 26 insertions(+), 13 deletions(-)
 rename roiloc.py => roiloc/roiloc.py (95%)

diff --git a/README.rst b/README.rst
index bbe3a96..4e47823 100644
--- a/README.rst
+++ b/README.rst
@@ -15,11 +15,12 @@ It requires the following packages:
 
 - ANTs (Can be a system installation or anaconda installation),
 - ANTsPyX,
+- importlib_resources,
 - NiBabel,
 - Pandas,
 - Rich.
 
-usage: roiloc.py [-h] -p PATH -i INPUTPATTERN [-r ROI] -c CONTRAST [-b BET] [-t TRANSFORM] [-m MARGIN [MARGIN ...]] [--mask MASK]
+usage: roiloc [-h] -p PATH -i INPUTPATTERN [-r ROI] -c CONTRAST [-b BET] [-t TRANSFORM] [-m MARGIN [MARGIN ...]] [--mask MASK]
 
 arguments::
 
@@ -57,7 +58,7 @@ Let's say I have a main database folder, containing one subfolder for each subje
 
 Therefore, to extract both left and right hippocampi (``Hippocampus``), I can run: 
 
-``python roiloc.py -p "~/Datasets/MemoDev/ManualSegmentation/" -i "**/tse.nii.gz" -r "hippocampus" -c "t2" -b True -t "AffineFast" -m 8 8 2 --mask "*brain_mask.nii``
+``roiloc -p "~/Datasets/MemoDev/ManualSegmentation/" -i "**/tse.nii.gz" -r "hippocampus" -c "t2" -b True -t "AffineFast" -m 8 8 2 --mask "*brain_mask.nii``
 
 
 Supported Registrations
diff --git a/pyproject.toml b/pyproject.toml
index 183f00c..91de368 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,14 +2,20 @@
 name = "ROILoc"
 version = "0.1.0"
 description = ""
+license = "MIT"
+readme = "README.rst"
 authors = ["Clément POIRET <poiret.clement@outlook.fr>"]
 
 [tool.poetry.dependencies]
-python = "^3.9"
+python = "^3.7"
 antspyx = "^0.2.7"
 nibabel = "^3.2.1"
 pandas = "^1.3.0"
 rich = "^10.5.0"
+importlib-resources = "^5.2.0"
+
+[tool.poetry.scripts]
+roiloc = 'roiloc.roiloc:start'
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"
diff --git a/roiloc.py b/roiloc/roiloc.py
similarity index 95%
rename from roiloc.py
rename to roiloc/roiloc.py
index 02f0101..cfefccc 100644
--- a/roiloc.py
+++ b/roiloc/roiloc.py
@@ -7,7 +7,7 @@
 from pathlib import Path
 
 import ants
-import pandas as pd
+import importlib_resources
 from rich import print
 from rich.console import Console
 from rich.progress import track
@@ -39,9 +39,10 @@ def main(args):
         )
 
     mni = get_mni(args.contrast, args.bet)
-    atlas = ants.image_read(
-        "./roiloc/MNI/cerebra/mni_icbm152_CerebrA_tal_nlin_sym_09c.nii",
-        pixeltype="unsigned int")
+    res = importlib_resources.files("roiloc")
+    data = str(res / "MNI" / "cerebra" /
+               "mni_icbm152_CerebrA_tal_nlin_sym_09c.nii")
+    atlas = ants.image_read(data, pixeltype="unsigned int")
 
     for image_path in track(images):
         stem = image_path.stem.split(".")[0]
@@ -83,7 +84,7 @@ def main(args):
     print("[bold green]Done! :)")
 
 
-if __name__ == "__main__":
+def start():
     parser = argparse.ArgumentParser(
         description=
         "Locate the Hippocampus or any other CerebrA ROI by using MNI152 Template and CerebrA Atlas"
diff --git a/roiloc/template.py b/roiloc/template.py
index 2bc286c..dfcdb64 100644
--- a/roiloc/template.py
+++ b/roiloc/template.py
@@ -1,4 +1,5 @@
 import ants
+import importlib_resources
 import pandas as pd
 from ants.core.ants_image import ANTsImage
 
@@ -20,13 +21,17 @@ def get_mni(contrast: str, bet: bool) -> ANTsImage:
 
     betstr = "bet" if bet else ""
 
-    return ants.image_read(
-        f"roiloc/MNI/icbm152/mni_icbm152_{contrast}{betstr}_tal_nlin_sym_09c.nii",
-        pixeltype="float")
+    template = f"mni_icbm152_{contrast}{betstr}_tal_nlin_sym_09c.nii"
+    res = importlib_resources.files("roiloc")
+    data = str(res / "MNI" / "icbm152" / template)
+    return ants.image_read(str(data), pixeltype="float")
 
 
 def get_roi_indices(roi: str) -> list:
     roi = roi.title()
-    cerebra = pd.read_csv("roiloc/MNI/cerebra/CerebrA_LabelDetails.csv",
-                          index_col="Label Name")
+
+    res = importlib_resources.files("roiloc")
+    data = str(res / "MNI" / "cerebra" / "CerebrA_LabelDetails.csv")
+    cerebra = pd.read_csv(data, index_col="Label Name")
+
     return [cerebra.loc[roi, "RH Label"], cerebra.loc[roi, "LH Labels"]]