config = cr.parse(".config")
# Get the list of FR bin files (fireball detections) in the given directory
fr_list = [
fr for fr in os.listdir(dir_path)
if fr[0:2] == "FR" and fr.endswith('bin')
]
fr_list = sorted(fr_list)
if not fr_list:
print("No files found!")
sys.exit()
# Get the list of FF bin files (compressed video frames)
ff_list = [ff for ff in os.listdir(dir_path) if FFfile.validFFName(ff)]
ff_list = sorted(ff_list)
i = 0
while True:
# Break the loop if at the end
if i >= len(fr_list):
break
fr = fr_list[i]
ff_match = None
# Strip extensions
if __name__ == "__main__":
time_start = time.clock()
# Load config file
config = cr.parse(".config")
if not len(sys.argv) == 2:
print("Usage: python -m RMS.ExtractStars /path/to/FF/files/")
sys.exit()
# Get paths to every FF bin file in a directory
ff_dir = os.path.abspath(sys.argv[1])
ff_list = [
ff_name for ff_name in os.listdir(ff_dir)
if FFfile.validFFName(ff_name)
]
# Check if there are any file in the directory
if (len(ff_list) == None):
print("No files found!")
sys.exit()
# Try loading a flat field image
flat_struct = None
if config.use_flat:
# Check if there is flat in the data directory
if os.path.exists(os.path.join(ff_dir, config.flat_file)):
flat_struct = Image.loadFlat(ff_dir, config.flat_file)
def generateThumbnails(dir_path, config, mosaic_type, file_list=None):
""" Generates a mosaic of thumbnails from all FF files in the given folder and saves it as a JPG image.
Arguments:
dir_path: [str] Path of the night directory.
config: [Conf object] Configuration.
mosaic_type: [str] Type of the mosaic (e.g. "Captured" or "Detected")
Keyword arguments:
file_list: [list] A list of file names (without full path) which will be searched for FF files. This
is used when generating separate thumbnails for captured and detected files.
Return:
file_name: [str] Name of the thumbnail file.
"""
if file_list is None:
file_list = sorted(os.listdir(dir_path))
# Make a list of all FF files in the night directory
ff_list = []
for file_name in file_list:
if FFfile.validFFName(file_name):
ff_list.append(file_name)
# Calculate the dimensions of the binned image
bin_w = int(config.width/config.thumb_bin)
bin_h = int(config.height/config.thumb_bin)
### RESIZE AND STACK THUMBNAILS ###
##########################################################################################################
timestamps = []
stacked_imgs = []
for i in range(0, len(ff_list), config.thumb_stack):
img_stack = np.zeros((bin_h, bin_w))
# Stack thumb_stack images using the 'if lighter' method
for j in range(config.thumb_stack):
if (i + j) < len(ff_list):
# Read maxpixel image
img = FFfile.read(dir_path, ff_list[i + j]).maxpixel
# Resize the image
img = cv2.resize(img, (bin_w, bin_h))
# Stack the image
img_stack = stackIfLighter(img_stack, img)
else:
break
# Save the timestamp of the first image in the stack
timestamps.append(FFfile.filenameToDatetime(ff_list[i]))
# Save the stacked image
stacked_imgs.append(img_stack)
# cv2.imshow('test', img_stack)
# cv2.waitKey(0)
# cv2.destroyAllWindows()
##########################################################################################################
### ADD THUMBS TO ONE MOSAIC IMAGE ###
##########################################################################################################
header_height = 20
timestamp_height = 10
# Calculate the number of rows for the thumbnail image
n_rows = int(np.ceil(float(len(ff_list))/config.thumb_stack/config.thumb_n_width))
# Calculate the size of the mosaic
mosaic_w = int(config.thumb_n_width*bin_w)
mosaic_h = int((bin_h + timestamp_height)*n_rows + header_height)
mosaic_img = np.zeros((mosaic_h, mosaic_w), dtype=np.uint8)
# Write header text
header_text = 'Station: ' + str(config.stationID) + ' Night: ' + os.path.basename(dir_path) \
+ ' Type: ' + mosaic_type
cv2.putText(mosaic_img, header_text, (0, header_height//2), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255,255,255), 1)
for row in range(n_rows):
for col in range(config.thumb_n_width):
# Calculate image index
indx = row*config.thumb_n_width + col
if indx < len(stacked_imgs):
# Calculate position of the text
text_x = col*bin_w
text_y = row*bin_h + (row + 1)*timestamp_height - 1 + header_height
# Add timestamp text
cv2.putText(mosaic_img, timestamps[indx].strftime('%H:%M:%S'), (text_x, text_y), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255, 255, 255), 1)
# Add the image to the mosaic
img_pos_x = col*bin_w
img_pos_y = row*bin_h + (row + 1)*timestamp_height + header_height
mosaic_img[img_pos_y : img_pos_y + bin_h, img_pos_x : img_pos_x + bin_w] = stacked_imgs[indx]
else:
break
##########################################################################################################
thumb_name = "{:s}_{:s}_{:s}_thumbs.jpg".format(str(config.stationID), os.path.basename(dir_path), \
mosaic_type)
# Save the mosaic
cv2.imwrite(os.path.join(dir_path, thumb_name), mosaic_img, [int(cv2.IMWRITE_JPEG_QUALITY), 80])
return thumb_name
action="store_true",
help="""Show a histogram of stddevs of PSFs of all detected stars. """)
# Parse the command line arguments
cml_args = arg_parser.parse_args()
#########################
# Load the config file
config = cr.loadConfigFromDirectory(cml_args.config, cml_args.dir_path)
# Get paths to every FF bin file in a directory
ff_dir = os.path.abspath(cml_args.dir_path[0])
ff_list = [
ff_name for ff_name in os.listdir(ff_dir)
if FFfile.validFFName(ff_name)
]
# Check if there are any file in the directory
if (len(ff_list) == None):
print("No files found!")
sys.exit()
# Run extraction and save the resulting CALSTARS file
star_list = extractStarsAndSave(config, ff_dir)
fwhm_list = []
intensity_list = []
x_list = []
y_list = []
def extractStarsAndSave(config, ff_dir):
""" Extract stars in the given folder and save the CALSTARS file.
Arguments:
config: [config object] configuration object (loaded from the .config file)
ff_dir: [str] Path to directory where FF files are.
Return:
star_list: [list] A list of [ff_name, star_data] entries, where star_data contains a list of
(column, row, amplitude, intensity, fwhm) values for every star.
"""
time_start = time.time()
# Load mask, dark, flat
mask, dark, flat_struct = loadImageCalibration(ff_dir, config)
extraction_list = []
# Go through all files in the directory and add them to the detection list
for ff_name in sorted(os.listdir(ff_dir)):
# Check if the given file is a valid FF file
if not FFfile.validFFName(ff_name):
continue
extraction_list.append(ff_name)
# Run the QueuedPool for detection
workpool = QueuedPool(extractStars, cores=-1, backup_dir=ff_dir)
# Add jobs for the pool
for ff_name in extraction_list:
print('Adding for extraction:', ff_name)
workpool.addJob([
ff_dir, ff_name, config, None, None, None, None, flat_struct, dark,
mask
])
print('Starting pool...')
# Start the detection
workpool.startPool()
print('Waiting for the detection to finish...')
# Wait for the detector to finish and close it
workpool.closePool()
# Get extraction results
star_list = []
for result in workpool.getResults():
ff_name, x2, y2, amplitude, intensity, fwhm_data = result
# Skip if no stars were found
if not x2:
continue
# Construct the table of the star parameters
star_data = list(zip(x2, y2, amplitude, intensity, fwhm_data))
# Add star info to the star list
star_list.append([ff_name, star_data])
dir_name = os.path.basename(os.path.abspath(ff_dir))
if dir_name.startswith(config.stationID):
prefix = dir_name
else:
prefix = "{:s}_{:s}".format(config.stationID, dir_name)
# Generate the name for the CALSTARS file
calstars_name = 'CALSTARS_' + prefix + '.txt'
# Write detected stars to the CALSTARS file
CALSTARS.writeCALSTARS(star_list, ff_dir, calstars_name, config.stationID,
config.height, config.width)
# Delete QueudPool backed up files
workpool.deleteBackupFiles()
print('Total time taken: {:.2f} s'.format(time.time() - time_start))
return star_list
def generateThumbnails(dir_path,
config,
mosaic_type,
file_list=None,
no_stack=False):
""" Generates a mosaic of thumbnails from all FF files in the given folder and saves it as a JPG image.
Arguments:
dir_path: [str] Path of the night directory.
config: [Conf object] Configuration.
mosaic_type: [str] Type of the mosaic (e.g. "Captured" or "Detected")
Keyword arguments:
file_list: [list] A list of file names (without full path) which will be searched for FF files. This
is used when generating separate thumbnails for captured and detected files.
Return:
file_name: [str] Name of the thumbnail file.
no_stack: [bool] Don't stack the images using the config.thumb_stack option. A max of 1000 images
are supported with this option. If there are more, stacks will be done according to the
config.thumb_stack option.
"""
if file_list is None:
file_list = sorted(os.listdir(dir_path))
# Make a list of all FF files in the night directory
ff_list = []
for file_name in file_list:
if FFfile.validFFName(file_name):
ff_list.append(file_name)
# Calculate the dimensions of the binned image
bin_w = int(config.width / config.thumb_bin)
bin_h = int(config.height / config.thumb_bin)
### RESIZE AND STACK THUMBNAILS ###
##########################################################################################################
timestamps = []
stacked_imgs = []
thumb_stack = config.thumb_stack
# Check if no stacks should be done (max 1000 images for no stack)
if no_stack and (len(ff_list) < 1000):
thumb_stack = 1
for i in range(0, len(ff_list), thumb_stack):
img_stack = np.zeros((bin_h, bin_w))
# Stack thumb_stack images using the 'if lighter' method
for j in range(thumb_stack):
if (i + j) < len(ff_list):
tmp_file_name = ff_list[i + j]
# Read the FF file
ff = FFfile.read(dir_path, tmp_file_name)
# Skip the FF if it is corruped
if ff is None:
continue
img = ff.maxpixel
# Resize the image
img = cv2.resize(img, (bin_w, bin_h))
# Stack the image
img_stack = stackIfLighter(img_stack, img)
else:
break
# Save the timestamp of the first image in the stack
timestamps.append(FFfile.filenameToDatetime(ff_list[i]))
# Save the stacked image
stacked_imgs.append(img_stack)
# cv2.imshow('test', img_stack)
# cv2.waitKey(0)
# cv2.destroyAllWindows()
##########################################################################################################
### ADD THUMBS TO ONE MOSAIC IMAGE ###
##########################################################################################################
header_height = 20
timestamp_height = 10
# Calculate the number of rows for the thumbnail image
n_rows = int(
np.ceil(float(len(ff_list)) / thumb_stack / config.thumb_n_width))
# Calculate the size of the mosaic
mosaic_w = int(config.thumb_n_width * bin_w)
mosaic_h = int((bin_h + timestamp_height) * n_rows + header_height)
mosaic_img = np.zeros((mosaic_h, mosaic_w), dtype=np.uint8)
# Write header text
header_text = 'Station: ' + str(config.stationID) + ' Night: ' + os.path.basename(dir_path) \
+ ' Type: ' + mosaic_type
cv2.putText(mosaic_img, header_text, (0, header_height//2), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255,255,255), 1)
for row in range(n_rows):
for col in range(config.thumb_n_width):
# Calculate image index
indx = row * config.thumb_n_width + col
if indx < len(stacked_imgs):
# Calculate position of the text
text_x = col * bin_w
text_y = row * bin_h + (
row + 1) * timestamp_height - 1 + header_height
# Add timestamp text
cv2.putText(mosaic_img, timestamps[indx].strftime('%H:%M:%S'), (text_x, text_y), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255, 255, 255), 1)
# Add the image to the mosaic
img_pos_x = col * bin_w
img_pos_y = row * bin_h + (
row + 1) * timestamp_height + header_height
mosaic_img[img_pos_y:img_pos_y + bin_h,
img_pos_x:img_pos_x + bin_w] = stacked_imgs[indx]
else:
break
##########################################################################################################
# Only add the station ID if the dir name already doesn't start with it
dir_name = os.path.basename(os.path.abspath(dir_path))
if dir_name.startswith(config.stationID):
prefix = dir_name
else:
prefix = "{:s}_{:s}".format(config.stationID, dir_name)
thumb_name = "{:s}_{:s}_thumbs.jpg".format(prefix, mosaic_type)
# Save the mosaic
if USING_IMAGEIO:
# Use imageio to write the image
imwrite(os.path.join(dir_path, thumb_name), mosaic_img, quality=80)
else:
# Use OpenCV to save the image
imwrite(os.path.join(dir_path, thumb_name), mosaic_img,
[int(cv2.IMWRITE_JPEG_QUALITY), 80])
return thumb_name
def generateThumbnails(dir_path, config, mosaic_type, file_list=None):
""" Generates a mosaic of thumbnails from all FF files in the given folder and saves it as a JPG image.
Arguments:
dir_path: [str] Path of the night directory.
config: [Conf object] Configuration.
mosaic_type: [str] Type of the mosaic (e.g. "Captured" or "Detected")
Keyword arguments:
file_list: [list] A list of file names (without full path) which will be searched for FF files. This
is used when generating separate thumbnails for captured and detected files.
Return:
file_name: [str] Name of the thumbnail file.
"""
if file_list is None:
file_list = sorted(os.listdir(dir_path))
# Make a list of all FF files in the night directory
ff_list = []
for file_name in file_list:
if FFfile.validFFName(file_name):
ff_list.append(file_name)
# Calculate the dimensions of the binned image
bin_w = int(config.width/config.thumb_bin)
bin_h = int(config.height/config.thumb_bin)
### RESIZE AND STACK THUMBNAILS ###
##########################################################################################################
timestamps = []
stacked_imgs = []
for i in range(0, len(ff_list), config.thumb_stack):
img_stack = np.zeros((bin_h, bin_w))
# Stack thumb_stack images using the 'if lighter' method
for j in range(config.thumb_stack):
if (i + j) < len(ff_list):
tmp_file_name = ff_list[i + j]
# Read the FF file
ff = FFfile.read(dir_path, tmp_file_name)
# Skip the FF if it is corruped
if ff is None:
continue
img = ff.maxpixel
# Resize the image
img = cv2.resize(img, (bin_w, bin_h))
# Stack the image
img_stack = stackIfLighter(img_stack, img)
else:
break
# Save the timestamp of the first image in the stack
timestamps.append(FFfile.filenameToDatetime(ff_list[i]))
# Save the stacked image
stacked_imgs.append(img_stack)
# cv2.imshow('test', img_stack)
# cv2.waitKey(0)
# cv2.destroyAllWindows()
##########################################################################################################
### ADD THUMBS TO ONE MOSAIC IMAGE ###
##########################################################################################################
header_height = 20
timestamp_height = 10
# Calculate the number of rows for the thumbnail image
n_rows = int(np.ceil(float(len(ff_list))/config.thumb_stack/config.thumb_n_width))
# Calculate the size of the mosaic
mosaic_w = int(config.thumb_n_width*bin_w)
mosaic_h = int((bin_h + timestamp_height)*n_rows + header_height)
mosaic_img = np.zeros((mosaic_h, mosaic_w), dtype=np.uint8)
# Write header text
header_text = 'Station: ' + str(config.stationID) + ' Night: ' + os.path.basename(dir_path) \
+ ' Type: ' + mosaic_type
cv2.putText(mosaic_img, header_text, (0, header_height//2), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255,255,255), 1)
for row in range(n_rows):
for col in range(config.thumb_n_width):
# Calculate image index
indx = row*config.thumb_n_width + col
if indx < len(stacked_imgs):
# Calculate position of the text
text_x = col*bin_w
text_y = row*bin_h + (row + 1)*timestamp_height - 1 + header_height
# Add timestamp text
cv2.putText(mosaic_img, timestamps[indx].strftime('%H:%M:%S'), (text_x, text_y), \
cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255, 255, 255), 1)
# Add the image to the mosaic
img_pos_x = col*bin_w
img_pos_y = row*bin_h + (row + 1)*timestamp_height + header_height
mosaic_img[img_pos_y : img_pos_y + bin_h, img_pos_x : img_pos_x + bin_w] = stacked_imgs[indx]
else:
break
##########################################################################################################
thumb_name = "{:s}_{:s}_{:s}_thumbs.jpg".format(str(config.stationID), os.path.basename(dir_path), \
mosaic_type)
# Save the mosaic
cv2.imwrite(os.path.join(dir_path, thumb_name), mosaic_img, [int(cv2.IMWRITE_JPEG_QUALITY), 80])
return thumb_name
# Load the configuration file
config = cr.parse(".config")
# Get the list of FR bin files (fireball detections) in the given directory
fr_list = [fr for fr in os.listdir(dir_path) if fr[0:2]=="FR" and fr.endswith('bin')]
fr_list = sorted(fr_list)
if not fr_list:
print("No files found!")
sys.exit()
# Get the list of FF bin files (compressed video frames)
ff_list = [ff for ff in os.listdir(dir_path) if FFfile.validFFName(ff)]
ff_list = sorted(ff_list)
i = 0
while True:
# Break the loop if at the end
if i >= len(fr_list):
break
fr = fr_list[i]
ff_match = None
if __name__ == "__main__":
time_start = time.clock()
# Load config file
config = cr.parse(".config")
if not len(sys.argv) == 2:
print("Usage: python -m RMS.ExtractStars /path/to/FF/files/")
sys.exit()
# Get paths to every FF bin file in a directory
ff_dir = os.path.abspath(sys.argv[1])
ff_list = [ff_name for ff_name in os.listdir(ff_dir) if FFfile.validFFName(ff_name)]
# Check if there are any file in the directory
if(len(ff_list) == None):
print("No files found!")
sys.exit()
# Try loading a flat field image
flat_struct = None
if config.use_flat:
# Check if there is flat in the data directory
if os.path.exists(os.path.join(ff_dir, config.flat_file)):
help="Path to a config file which will be used instead of the default one.")
arg_parser.add_argument('-s', '--showstd', action="store_true", help="""Show a histogram of stddevs of PSFs of all detected stars. """)
# Parse the command line arguments
cml_args = arg_parser.parse_args()
#########################
# Load the config file
config = cr.loadConfigFromDirectory(cml_args.config, cml_args.dir_path)
# Get paths to every FF bin file in a directory
ff_dir = os.path.abspath(cml_args.dir_path[0])
ff_list = [ff_name for ff_name in os.listdir(ff_dir) if FFfile.validFFName(ff_name)]
# Check if there are any file in the directory
if(len(ff_list) == None):
print("No files found!")
sys.exit()
# Try loading a flat field image
flat_struct = None
if config.use_flat:
# Check if there is flat in the data directory
if os.path.exists(os.path.join(ff_dir, config.flat_file)):