From 761682d249dae7342a74dcfd733662da4429f0af Mon Sep 17 00:00:00 2001
From: Robert Stein <rdstein@caltech.edu>
Date: Tue, 20 Aug 2024 13:11:06 -0700
Subject: [PATCH] Fix #957

---
 mirar/paths.py                                |  3 ++
 .../processors/astromatic/config/__init__.py  |  4 +-
 .../astromatic/sextractor/__init__.py         |  3 ++
 .../astromatic/sextractor/settings.py         | 40 +++++++++++++------
 4 files changed, 36 insertions(+), 14 deletions(-)

diff --git a/mirar/paths.py b/mirar/paths.py
index daa5bd135..c6fbb86ae 100644
--- a/mirar/paths.py
+++ b/mirar/paths.py
@@ -73,6 +73,9 @@
 ml_models_dir = base_output_dir.joinpath("ml_models")
 ml_models_dir.mkdir(exist_ok=True)
 
+config_dir = base_output_dir.joinpath("configs")
+config_dir.mkdir(exist_ok=True)
+
 
 def raw_img_dir(
     sub_dir: str = "", raw_dir: Path = base_raw_dir, img_sub_dir: str = RAW_IMG_SUB_DIR
diff --git a/mirar/processors/astromatic/config/__init__.py b/mirar/processors/astromatic/config/__init__.py
index 4740011aa..c036f0201 100644
--- a/mirar/processors/astromatic/config/__init__.py
+++ b/mirar/processors/astromatic/config/__init__.py
@@ -2,6 +2,6 @@
 Module for configs of astrometry
 """
 
-import os
+from pathlib import Path
 
-astromatic_config_dir = os.path.dirname(__file__)
+astromatic_config_dir = Path(__file__).parent
diff --git a/mirar/processors/astromatic/sextractor/__init__.py b/mirar/processors/astromatic/sextractor/__init__.py
index e69de29bb..bf2807ef8 100644
--- a/mirar/processors/astromatic/sextractor/__init__.py
+++ b/mirar/processors/astromatic/sextractor/__init__.py
@@ -0,0 +1,3 @@
+"""
+Module for interfacing with SExtractor.
+"""
diff --git a/mirar/processors/astromatic/sextractor/settings.py b/mirar/processors/astromatic/sextractor/settings.py
index 864a6cb67..0f8b57b0b 100644
--- a/mirar/processors/astromatic/sextractor/settings.py
+++ b/mirar/processors/astromatic/sextractor/settings.py
@@ -2,15 +2,31 @@
 Module with sextractor utilities
 """
 
-import os
+import shutil
 from pathlib import Path
 
+from mirar.paths import config_dir
 from mirar.processors.astromatic.config import astromatic_config_dir
 
-default_param_path = os.path.join(astromatic_config_dir, "temp.param")
-default_conv_path = os.path.join(astromatic_config_dir, "sex.conv")
-default_config_path = os.path.join(astromatic_config_dir, "sex.config")
-default_starnnw_path = os.path.join(astromatic_config_dir, "default.nnw")
+readonly_param_path = astromatic_config_dir / "temp.param"
+default_param_path = config_dir / "default.param"
+if not default_param_path.exists():
+    shutil.copy(readonly_param_path, default_param_path)
+
+readonly_conv_path = astromatic_config_dir / "sex.conv"
+default_conv_path = config_dir / "default.conv"
+if not default_conv_path.exists():
+    shutil.copy(readonly_conv_path, default_conv_path)
+
+readonly_config_path = astromatic_config_dir / "sex.conv"
+default_config_path = config_dir / "default.config"
+if not default_config_path.exists():
+    shutil.copy(readonly_config_path, default_config_path)
+
+readonly_starnnw_path = astromatic_config_dir / "default.nnw"
+default_starnnw_path = config_dir / "default.nnw"
+if not default_starnnw_path.exists():
+    shutil.copy(readonly_starnnw_path, default_starnnw_path)
 
 
 def parse_sextractor_config(config_file: str | Path):
@@ -18,7 +34,7 @@ def parse_sextractor_config(config_file: str | Path):
     Parse a sextractor config file into a dictionary
     param config_file: path to sextractor config file
     """
-    with open(config_file, "r") as f:
+    with open(config_file, "r", encoding="utf8") as f:
         data = f.readlines()
 
     keys, values = [], []
@@ -48,12 +64,12 @@ def write_sextractor_config_to_file(config_dict: dict, config_filename: str | Pa
     param config_dict: dictionary of sextractor config parameters
     param config_filename: path to write config file
     """
-    with open(config_filename, "w") as f:
+    with open(config_filename, "w", encoding="utf8") as f:
         for key in config_dict:
             f.write(f"{key.ljust(20, ' ')}   {config_dict[key]} \n")
 
 
-def write_param_file(param_path: str = default_param_path, params: list = None):
+def write_param_file(param_path: str | Path = default_param_path, params: list = None):
     """
     Write a default parameter file for sextractor
     param param_path: path to write parameter file
@@ -76,7 +92,7 @@ def write_param_file(param_path: str = default_param_path, params: list = None):
             param_f.write(f"{param}\n")
 
 
-def write_conv_file(conv_path: str = default_conv_path):
+def write_conv_file(conv_path: str | Path = default_conv_path):
     """
     Write a default convolution file for sextractor
     """
@@ -91,9 +107,9 @@ def write_conv_file(conv_path: str = default_conv_path):
 
 
 def write_config_file(
-    param_path: str = default_param_path,
-    conv_path: str = default_conv_path,
-    config_path: str = default_config_path,
+    param_path: str | Path = default_param_path,
+    conv_path: str | Path = default_conv_path,
+    config_path: str | Path = default_config_path,
     saturation_key: str = "SATURATE",
 ):
     """