Commit aede078e authored by Joel Collins's avatar Joel Collins
Browse files

Moved user configs to hidden directory

parent b6d0aebc

openflexure_microscope/config.py

+16 −11
Original line number Diff line number Diff line
@@ -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

+7 −7
Original line number Diff line number Diff line
@@ -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()
 
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