rahix/openflexure-microscope-server
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Moved user configs to hidden directory

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This commit is contained in:
Joel Collins 2018-12-05 12:03:22 +00:00
parent b6d0aebc1b
commit aede078eb9
3 changed files with 23 additions and 18 deletions
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14
utilities/recalibrate.py
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@ -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.
@ -103,9 +106,8 @@ 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
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))
# Adjust the shutter speed until the brightest pixels are giving a set value (say 220)
@ -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()