Moved user configs to hidden directory

openflexure_microscope/config.py

@@ -4,8 +4,10 @@ import logging
 import shutil
 
 HERE = os.path.abspath(os.path.dirname(__file__))
-DEFAULT_CONFIG_PATH = os.path.join(HERE, 'openflexurerc.default.yaml')
-USER_CONFIG_PATH = os.path.join(os.path.expanduser("~"), "openflexurerc.yaml")
+DEFAULT_CONFIG_PATH = os.path.join(HERE, 'microscoperc.default.yaml')
+
+USER_CONFIG_DIR = os.path.join(os.path.expanduser("~"), ".openflexure")
+USER_CONFIG_FILE = os.path.join(USER_CONFIG_DIR, "microscoperc.yaml")
 
 TYPES = {
     'stream_resolution': tuple,
@@ -36,17 +38,20 @@ def load_config(config_path: str=None) -> dict:
     Args:
         config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
     """
-    global DEFAULT_CONFIG_PATH, USER_CONFIG_PATH
+    global DEFAULT_CONFIG_PATH, USER_CONFIG_FILE
 
     if not config_path:
-        if os.path.exists(USER_CONFIG_PATH):  # If user config file already exists
-            config_path = USER_CONFIG_PATH  # Load it
+        if os.path.exists(USER_CONFIG_FILE):  # If user config file already exists
+            config_path = USER_CONFIG_FILE  # Load it
         else:  # If user config file doesn't yet exist
             logging.warning("No user config found. Loading system defaults...")
+            if not os.path.exists(USER_CONFIG_DIR):
+                logging.info("Making user config directory...")
+                os.makedirs(USER_CONFIG_DIR)
             logging.info("Copying default config to user config...")
-            shutil.copyfile(DEFAULT_CONFIG_PATH, USER_CONFIG_PATH)
+            shutil.copyfile(DEFAULT_CONFIG_PATH, USER_CONFIG_FILE)
             logging.info("Loading user config...")
-            config_path = USER_CONFIG_PATH  # Load defaults in
+            config_path = USER_CONFIG_FILE  # Load defaults in
 
     with open(config_path) as config_file:
         config_data = yaml.load(config_file)
@@ -63,9 +68,9 @@ def save_config(config_dict: dict, config_path: str=None, safe: bool=False):
         config_dict (dict): Dictionary of config data to save.
         config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
     """
-    global USER_CONFIG_PATH
+    global USER_CONFIG_FILE
     if not config_path:
-        config_path = USER_CONFIG_PATH
+        config_path = USER_CONFIG_FILE
 
     with open(config_path, 'w') as outfile:
         if not safe:
@@ -82,9 +87,9 @@ def merge_config(config_dict: dict, config_path: str=None, safe: bool=False, bac
         config_dict (dict): Dictionary of config data to save.
         config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
     """
-    global USER_CONFIG_PATH
+    global USER_CONFIG_FILE
     if not config_path:
-        config_path = USER_CONFIG_PATH
+        config_path = USER_CONFIG_FILE
 
     config_data = load_config(config_path=config_path)
 

utilities/recalibrate.py

@@ -12,6 +12,7 @@ import os
 import logging, sys
 logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
 
+
 def lens_shading_correction_from_rgb(rgb_array, binsize=64):
     """Calculate a correction to a lens shading table from an RGB image.
 
@@ -66,13 +67,15 @@ def lens_shading_correction_from_rgb(rgb_array, binsize=64):
     gains = 1.0/lens_shading  # 32 is unity gain
     return gains
 
+
 def gains_to_lst(gains):
     """Given a lens shading gains table (where no gain=1.0), convert to 8-bit."""
     lst = gains / np.min(gains)*32 # minimum gain is 32 (= unity gain)
     lst[lst > 255] = 255 # clip at 255
     return lst.astype(np.uint8)
 
-def generate_lens_shading_table_closed_loop(output_fname="shadingtable.npy", 
+
+def generate_lens_shading_table_closed_loop(output_fname="microscopelst.npy",
                                             n_iterations=5,
                                             images_to_average=5):
     """Reset the camera's parameters, and recalibrate the lens shading to get unifrom images.
@@ -103,7 +106,6 @@ def generate_lens_shading_table_closed_loop(output_fname="shadingtable.npy",
 
     # Open the microscope and start with flat (i.e. no) lens shading correction.
         cam.start_preview()
-        logging.info("Stopping worker thread during calibration, to avoid GPU memory issues")
 
         def get_rgb_image():  # shorthand for taking an RGB image
             return cam.array(use_video_port=True, resize=(max_res[0]//2, max_res[1]//2))
@@ -146,7 +148,7 @@ def generate_lens_shading_table_closed_loop(output_fname="shadingtable.npy",
         lens_shading_table = cam.camera.lens_shading_table
 
         # Saving shading table to disk
-        output_path = os.path.join(os.path.expanduser("~"), output_fname)
+        output_path = os.path.join(config.USER_CONFIG_DIR, output_fname)
         np.save(output_path, lens_shading_table)
         print("Lens shading table written to {}".format(output_path))
 
@@ -160,8 +162,6 @@ def generate_lens_shading_table_closed_loop(output_fname="shadingtable.npy",
         logging.debug("Merging config...")
         config.merge_config(settings, safe=True, backup=True)
 
-        #cam.resume_stream_for_capture()
-
 
 if __name__ == '__main__':
     generate_lens_shading_table_closed_loop()