def makeFlat(dir_path, config):
""" Makes a flat field from the files in the given folder. CALSTARS file is needed to estimate the
quality of every image by counting the number of detected stars.
Arguments:
dir_path: [str] Path to the directory which contains the FF files and a CALSTARS file.
config: [config object]
Return:
[2d ndarray] Flat field image as a numpy array. If the flat generation failed, None will be returned.
"""
# Find the CALSTARS file in the given folder
calstars_file = None
for calstars_file in os.listdir(dir_path):
if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file):
break
if calstars_file is None:
print('CALSTARS file could not be found in the given directory!')
return None
# Load the calstars file
calstars_list = CALSTARS.readCALSTARS(dir_path, calstars_file)
# Convert the list to a dictionary
calstars = {ff_file: star_data for ff_file, star_data in calstars_list}
print('CALSTARS file: ' + calstars_file + ' loaded!')
# A list of FF files which have any stars on them
calstars_ff_files = [line[0] for line in calstars_list]
ff_list = []
# Get a list of FF files in the folder
for file_name in os.listdir(dir_path):
if validFFName(file_name) and (file_name in calstars_ff_files):
ff_list.append(file_name)
# Check that there are any FF files in the folder
if not ff_list:
print('No FF files in the selected folder!')
return None
ff_list_good = []
ff_times = []
# Take only those FF files with enough stars on them
for ff_name in ff_list:
if not validFFName(ff_name):
continue
if ff_name in calstars:
# Get the number of stars detected on the FF image
ff_nstars = len(calstars[ff_name])
# Check if the number of stars on the image is over the detection threshold
if ff_nstars > config.ff_min_stars:
# Add the FF file to the list of FF files to be used to make a flat
ff_list_good.append(ff_name)
# Calculate the time of the FF files
ff_time = date2JD(*getMiddleTimeFF(
ff_name, config.fps, ret_milliseconds=True))
ff_times.append(ff_time)
# Check that there are enough good FF files in the folder
if len(ff_times) < config.flat_min_imgs:
print('Not enough FF files have enough stars on them!')
return None
# Make sure the files cover at least 2 hours
if not (max(ff_times) - min(ff_times)) * 24 > 2:
print('Good FF files cover less than 2 hours!')
return None
# Sample FF files if there are more than 200
max_ff_flat = 200
if len(ff_list_good) > max_ff_flat:
ff_list_good = sorted(random.sample(ff_list_good, max_ff_flat))
print('Using {:d} files for flat...'.format(len(ff_list_good)))
c = 0
ff_avg_list = []
median_list = []
# Median combine all good FF files
for i in range(len(ff_list_good)):
# Load 10 files at the time and median combine them, which conserves memory
if c < 10:
ff = readFF(dir_path, ff_list_good[i])
ff_avg_list.append(ff.avepixel)
c += 1
else:
ff_avg_list = np.array(ff_avg_list)
# Median combine the loaded 10 (or less) images
ff_median = np.median(ff_avg_list, axis=0)
median_list.append(ff_median)
ff_avg_list = []
c = 0
# If there are more than 1 calculated median image, combine them
if len(median_list) > 1:
# Median combine all median images
median_list = np.array(median_list)
ff_median = np.median(median_list, axis=0)
else:
ff_median = median_list[0]
# Stretch flat to 0-255
ff_median = ff_median / np.max(ff_median) * 255
# Convert the flat to 8 bits
ff_median = ff_median.astype(np.uint8)
return ff_median
def generateCalibrationReport(config,
night_dir_path,
match_radius=2.0,
platepar=None,
show_graphs=False):
""" Given the folder of the night, find the Calstars file, check the star fit and generate a report
with the quality of the calibration. The report contains information about both the astrometry and
the photometry calibration. Graphs will be saved in the given directory of the night.
Arguments:
config: [Config instance]
night_dir_path: [str] Full path to the directory of the night.
Keyword arguments:
match_radius: [float] Match radius for star matching between image and catalog stars (px).
platepar: [Platepar instance] Use this platepar instead of finding one in the folder.
show_graphs: [bool] Show the graphs on the screen. False by default.
Return:
None
"""
# Find the CALSTARS file in the given folder
calstars_file = None
for calstars_file in os.listdir(night_dir_path):
if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file):
break
if calstars_file is None:
print('CALSTARS file could not be found in the given directory!')
return None
# Load the calstars file
star_list = readCALSTARS(night_dir_path, calstars_file)
### Load recalibrated platepars, if they exist ###
# Find recalibrated platepars file per FF file
platepars_recalibrated_file = None
for file_name in os.listdir(night_dir_path):
if file_name == config.platepars_recalibrated_name:
platepars_recalibrated_file = file_name
break
# Load all recalibrated platepars if the file is available
recalibrated_platepars = None
if platepars_recalibrated_file:
with open(os.path.join(night_dir_path,
platepars_recalibrated_file)) as f:
recalibrated_platepars = json.load(f)
print(
'Loaded recalibrated platepars JSON file for the calibration report...'
)
### ###
### Load the platepar file ###
# Find the platepar file in the given directory if it was not given
if platepar is None:
# Find the platepar file
platepar_file = None
for file_name in os.listdir(night_dir_path):
if file_name == config.platepar_name:
platepar_file = file_name
break
if platepar_file is None:
print('The platepar cannot be found in the night directory!')
return None
# Load the platepar file
platepar = Platepar()
platepar.read(os.path.join(night_dir_path, platepar_file),
use_flat=config.use_flat)
### ###
night_name = os.path.split(night_dir_path.strip(os.sep))[1]
# Go one mag deeper than in the config
lim_mag = config.catalog_mag_limit + 1
# Load catalog stars (load one magnitude deeper)
catalog_stars, mag_band_str, config.star_catalog_band_ratios = StarCatalog.readStarCatalog(\
config.star_catalog_path, config.star_catalog_file, lim_mag=lim_mag, \
mag_band_ratios=config.star_catalog_band_ratios)
### Take only those CALSTARS entires for which FF files exist in the folder ###
# Get a list of FF files in the folder
ff_list = []
for file_name in os.listdir(night_dir_path):
if validFFName(file_name):
ff_list.append(file_name)
# Filter out calstars entries, generate a star dictionary where the keys are JDs of FFs
star_dict = {}
ff_dict = {}
for entry in star_list:
ff_name, star_data = entry
# Check if the FF from CALSTARS exists in the folder
if ff_name not in ff_list:
continue
dt = getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True)
jd = date2JD(*dt)
# Add the time and the stars to the dict
star_dict[jd] = star_data
ff_dict[jd] = ff_name
### ###
# If there are no FF files in the directory, don't generate a report
if len(star_dict) == 0:
print('No FF files from the CALSTARS file in the directory!')
return None
# If the recalibrated platepars file exists, take the one with the most stars
max_jd = 0
using_recalib_platepars = False
if recalibrated_platepars is not None:
max_stars = 0
for ff_name_temp in recalibrated_platepars:
# Compute the Julian date of the FF middle
dt = getMiddleTimeFF(ff_name_temp,
config.fps,
ret_milliseconds=True)
jd = date2JD(*dt)
# Check that this file exists in CALSTARS and the list of FF files
if (jd not in star_dict) or (jd not in ff_dict):
continue
# Check if the number of stars on this FF file is larger than the before
if len(star_dict[jd]) > max_stars:
max_jd = jd
max_stars = len(star_dict[jd])
# Set a flag to indicate if using recalibrated platepars has failed
if max_jd == 0:
using_recalib_platepars = False
else:
print('Using recalibrated platepars, file:', ff_dict[max_jd])
using_recalib_platepars = True
# Select the platepar where the FF file has the most stars
platepar_dict = recalibrated_platepars[ff_dict[max_jd]]
platepar = Platepar()
platepar.loadFromDict(platepar_dict, use_flat=config.use_flat)
filtered_star_dict = {max_jd: star_dict[max_jd]}
# Match stars on the image with the stars in the catalog
n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \
filtered_star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag)
max_matched_stars = n_matched
# Otherwise take the optimal FF file for evaluation
if (recalibrated_platepars is None) or (not using_recalib_platepars):
# If there are more than a set number of FF files to evaluate, choose only the ones with most stars on
# the image
if len(star_dict) > config.calstars_files_N:
# Find JDs of FF files with most stars on them
top_nstars_indices = np.argsort([len(x) for x in star_dict.values()])[::-1][:config.calstars_files_N \
- 1]
filtered_star_dict = {}
for i in top_nstars_indices:
filtered_star_dict[list(star_dict.keys())[i]] = list(
star_dict.values())[i]
star_dict = filtered_star_dict
# Match stars on the image with the stars in the catalog
n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \
star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag)
# If no recalibrated platepars where found, find the image with the largest number of matched stars
if (not using_recalib_platepars) or (max_jd == 0):
max_jd = 0
max_matched_stars = 0
for jd in matched_stars:
_, _, distances = matched_stars[jd]
if len(distances) > max_matched_stars:
max_jd = jd
max_matched_stars = len(distances)
# If there are no matched stars, use the image with the largest number of detected stars
if max_matched_stars <= 2:
max_jd = max(star_dict, key=lambda x: len(star_dict[x]))
distances = [np.inf]
# Take the FF file with the largest number of matched stars
ff_name = ff_dict[max_jd]
# Load the FF file
ff = readFF(night_dir_path, ff_name)
img_h, img_w = ff.avepixel.shape
dpi = 200
plt.figure(figsize=(ff.avepixel.shape[1] / dpi,
ff.avepixel.shape[0] / dpi),
dpi=dpi)
# Take the average pixel
img = ff.avepixel
# Slightly adjust the levels
img = Image.adjustLevels(img, np.percentile(img, 1.0), 1.3,
np.percentile(img, 99.99))
plt.imshow(img, cmap='gray', interpolation='nearest')
legend_handles = []
# Plot detected stars
for img_star in star_dict[max_jd]:
y, x, _, _ = img_star
rect_side = 5 * match_radius
square_patch = plt.Rectangle((x - rect_side/2, y - rect_side/2), rect_side, rect_side, color='g', \
fill=False, label='Image stars')
plt.gca().add_artist(square_patch)
legend_handles.append(square_patch)
# If there are matched stars, plot them
if max_matched_stars > 2:
# Take the solution with the largest number of matched stars
image_stars, matched_catalog_stars, distances = matched_stars[max_jd]
# Plot matched stars
for img_star in image_stars:
x, y, _, _ = img_star
circle_patch = plt.Circle((y, x), radius=3*match_radius, color='y', fill=False, \
label='Matched stars')
plt.gca().add_artist(circle_patch)
legend_handles.append(circle_patch)
### Plot match residuals ###
# Compute preducted positions of matched image stars from the catalog
x_predicted, y_predicted = raDecToXYPP(matched_catalog_stars[:, 0], \
matched_catalog_stars[:, 1], max_jd, platepar)
img_y, img_x, _, _ = image_stars.T
delta_x = x_predicted - img_x
delta_y = y_predicted - img_y
# Compute image residual and angle of the error
res_angle = np.arctan2(delta_y, delta_x)
res_distance = np.sqrt(delta_x**2 + delta_y**2)
# Calculate coordinates of the beginning of the residual line
res_x_beg = img_x + 3 * match_radius * np.cos(res_angle)
res_y_beg = img_y + 3 * match_radius * np.sin(res_angle)
# Calculate coordinates of the end of the residual line
res_x_end = img_x + 100 * np.cos(res_angle) * res_distance
res_y_end = img_y + 100 * np.sin(res_angle) * res_distance
# Plot the 100x residuals
for i in range(len(x_predicted)):
res_plot = plt.plot([res_x_beg[i], res_x_end[i]], [res_y_beg[i], res_y_end[i]], color='orange', \
lw=0.5, label='100x residuals')
legend_handles.append(res_plot[0])
### ###
else:
distances = [np.inf]
# If there are no matched stars, plot large text in the middle of the screen
plt.text(img_w / 2,
img_h / 2,
"NO MATCHED STARS!",
color='r',
alpha=0.5,
fontsize=20,
ha='center',
va='center')
### Plot positions of catalog stars to the limiting magnitude of the faintest matched star + 1 mag ###
# Find the faintest magnitude among matched stars
if max_matched_stars > 2:
faintest_mag = np.max(matched_catalog_stars[:, 2]) + 1
else:
# If there are no matched stars, use the limiting magnitude from config
faintest_mag = config.catalog_mag_limit + 1
# Estimate RA,dec of the centre of the FOV
_, RA_c, dec_c, _ = xyToRaDecPP([jd2Date(max_jd)], [platepar.X_res / 2],
[platepar.Y_res / 2], [1], platepar)
RA_c = RA_c[0]
dec_c = dec_c[0]
fov_radius = np.hypot(*computeFOVSize(platepar))
# Get stars from the catalog around the defined center in a given radius
_, extracted_catalog = subsetCatalog(catalog_stars, RA_c, dec_c,
fov_radius, faintest_mag)
ra_catalog, dec_catalog, mag_catalog = extracted_catalog.T
# Compute image positions of all catalog stars that should be on the image
x_catalog, y_catalog = raDecToXYPP(ra_catalog, dec_catalog, max_jd,
platepar)
# Filter all catalog stars outside the image
temp_arr = np.c_[x_catalog, y_catalog, mag_catalog]
temp_arr = temp_arr[temp_arr[:, 0] >= 0]
temp_arr = temp_arr[temp_arr[:, 0] <= ff.avepixel.shape[1]]
temp_arr = temp_arr[temp_arr[:, 1] >= 0]
temp_arr = temp_arr[temp_arr[:, 1] <= ff.avepixel.shape[0]]
x_catalog, y_catalog, mag_catalog = temp_arr.T
# Plot catalog stars on the image
cat_stars_handle = plt.scatter(x_catalog, y_catalog, c='none', marker='D', lw=1.0, alpha=0.4, \
s=((4.0 + (faintest_mag - mag_catalog))/3.0)**(2*2.512), edgecolor='r', label='Catalog stars')
legend_handles.append(cat_stars_handle)
### ###
# Add info text in the corner
info_text = ff_dict[max_jd] + '\n' \
+ "Matched stars within {:.1f} px radius: {:d}/{:d} \n".format(match_radius, max_matched_stars, \
len(star_dict[max_jd])) \
+ "Median distance = {:.2f} px\n".format(np.median(distances)) \
+ "Catalog lim mag = {:.1f}".format(lim_mag)
plt.text(10, 10, info_text, bbox=dict(facecolor='black', alpha=0.5), va='top', ha='left', fontsize=4, \
color='w', family='monospace')
legend = plt.legend(handles=legend_handles,
prop={'size': 4},
loc='upper right')
legend.get_frame().set_facecolor('k')
legend.get_frame().set_edgecolor('k')
for txt in legend.get_texts():
txt.set_color('w')
### Add FOV info (centre, size) ###
# Mark FOV centre
plt.scatter(platepar.X_res / 2,
platepar.Y_res / 2,
marker='+',
s=20,
c='r',
zorder=4)
# Compute FOV centre alt/az
azim_centre, alt_centre = raDec2AltAz(max_jd, platepar.lon, platepar.lat,
RA_c, dec_c)
# Compute FOV size
fov_h, fov_v = computeFOVSize(platepar)
# Compute the rotation wrt. horizon
rot_horizon = rotationWrtHorizon(platepar)
fov_centre_text = "Azim = {:6.2f}$\\degree$\n".format(azim_centre) \
+ "Alt = {:6.2f}$\\degree$\n".format(alt_centre) \
+ "Rot h = {:6.2f}$\\degree$\n".format(rot_horizon) \
+ "FOV h = {:6.2f}$\\degree$\n".format(fov_h) \
+ "FOV v = {:6.2f}$\\degree$".format(fov_v) \
plt.text(10, platepar.Y_res - 10, fov_centre_text, bbox=dict(facecolor='black', alpha=0.5), \
va='bottom', ha='left', fontsize=4, color='w', family='monospace')
### ###
# Plot RA/Dec gridlines #
addEquatorialGrid(plt, platepar, max_jd)
plt.axis('off')
plt.gca().get_xaxis().set_visible(False)
plt.gca().get_yaxis().set_visible(False)
plt.xlim([0, ff.avepixel.shape[1]])
plt.ylim([ff.avepixel.shape[0], 0])
# Remove the margins
plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_astrometry.jpg'), \
bbox_inches='tight', pad_inches=0, dpi=dpi)
if show_graphs:
plt.show()
else:
plt.clf()
plt.close()
if max_matched_stars > 2:
### PHOTOMETRY FIT ###
# If a flat is used, set the vignetting coeff to 0
if config.use_flat:
platepar.vignetting_coeff = 0.0
# Extact intensities and mangitudes
star_intensities = image_stars[:, 2]
catalog_mags = matched_catalog_stars[:, 2]
# Compute radius of every star from image centre
radius_arr = np.hypot(image_stars[:, 0] - img_h / 2,
image_stars[:, 1] - img_w / 2)
# Fit the photometry on automated star intensities (use the fixed vignetting coeff, use robust fit)
photom_params, fit_stddev, fit_resid, star_intensities, radius_arr, catalog_mags = \
photometryFitRobust(star_intensities, radius_arr, catalog_mags, \
fixed_vignetting=platepar.vignetting_coeff)
photom_offset, _ = photom_params
### ###
### PLOT PHOTOMETRY ###
# Note: An almost identical code exists in RMS.Astrometry.SkyFit in the PlateTool.photometry function
dpi = 130
fig_p, (ax_p, ax_r) = plt.subplots(nrows=2, facecolor=None, figsize=(6.0, 7.0), dpi=dpi, \
gridspec_kw={'height_ratios':[2, 1]})
# Plot raw star intensities
ax_p.scatter(-2.5 * np.log10(star_intensities),
catalog_mags,
s=5,
c='r',
alpha=0.5,
label="Raw")
# If a flat is used, disregard the vignetting
if not config.use_flat:
# Plot intensities of image stars corrected for vignetting
lsp_corr_arr = np.log10(correctVignetting(star_intensities, radius_arr, \
platepar.vignetting_coeff))
ax_p.scatter(-2.5*lsp_corr_arr, catalog_mags, s=5, c='b', alpha=0.5, \
label="Corrected for vignetting")
# Plot photometric offset from the platepar
x_min, x_max = ax_p.get_xlim()
y_min, y_max = ax_p.get_ylim()
x_min_w = x_min - 3
x_max_w = x_max + 3
y_min_w = y_min - 3
y_max_w = y_max + 3
photometry_info = "Platepar: {:+.1f}*LSP + {:.2f} +/- {:.2f}".format(platepar.mag_0, \
platepar.mag_lev, platepar.mag_lev_stddev) \
+ "\nVignetting coeff = {:.5f}".format(platepar.vignetting_coeff) \
+ "\nGamma = {:.2f}".format(platepar.gamma)
# Plot the photometry calibration from the platepar
logsum_arr = np.linspace(x_min_w, x_max_w, 10)
ax_p.plot(logsum_arr, logsum_arr + platepar.mag_lev, label=photometry_info, linestyle='--', \
color='k', alpha=0.5)
# Plot the fitted photometry calibration
fit_info = "Fit: {:+.1f}*LSP + {:.2f} +/- {:.2f}".format(
-2.5, photom_offset, fit_stddev)
ax_p.plot(logsum_arr,
logsum_arr + photom_offset,
label=fit_info,
linestyle='--',
color='b',
alpha=0.75)
ax_p.legend()
ax_p.set_ylabel("Catalog magnitude ({:s})".format(mag_band_str))
ax_p.set_xlabel("Uncalibrated magnitude")
# Set wider axis limits
ax_p.set_xlim(x_min_w, x_max_w)
ax_p.set_ylim(y_min_w, y_max_w)
ax_p.invert_yaxis()
ax_p.invert_xaxis()
ax_p.grid()
### Plot photometry vs radius ###
img_diagonal = np.hypot(img_h / 2, img_w / 2)
# Plot photometry residuals (including vignetting)
ax_r.scatter(radius_arr, fit_resid, c='b', alpha=0.75, s=5, zorder=3)
# Plot a zero line
ax_r.plot(np.linspace(0, img_diagonal, 10), np.zeros(10), linestyle='dashed', alpha=0.5, \
color='k')
# Plot only when no flat is used
if not config.use_flat:
# Plot radius from centre vs. fit residual
fit_resids_novignetting = catalog_mags - photomLine((np.array(star_intensities), \
np.array(radius_arr)), photom_offset, 0.0)
ax_r.scatter(radius_arr,
fit_resids_novignetting,
s=5,
c='r',
alpha=0.5,
zorder=3)
px_sum_tmp = 1000
radius_arr_tmp = np.linspace(0, img_diagonal, 50)
# Plot vignetting loss curve
vignetting_loss = 2.5*np.log10(px_sum_tmp) \
- 2.5*np.log10(correctVignetting(px_sum_tmp, radius_arr_tmp, \
platepar.vignetting_coeff))
ax_r.plot(radius_arr_tmp,
vignetting_loss,
linestyle='dotted',
alpha=0.5,
color='k')
ax_r.grid()
ax_r.set_ylabel("Fit residuals (mag)")
ax_r.set_xlabel("Radius from centre (px)")
ax_r.set_xlim(0, img_diagonal)
### ###
plt.tight_layout()
plt.savefig(os.path.join(night_dir_path,
night_name + '_calib_report_photometry.png'),
dpi=150)
if show_graphs:
plt.show()
else:
plt.clf()
plt.close()
def makeFlat(dir_path, config, nostars=False, use_images=False):
""" Makes a flat field from the files in the given folder. CALSTARS file is needed to estimate the
quality of every image by counting the number of detected stars.
Arguments:
dir_path: [str] Path to the directory which contains the FF files and a CALSTARS file.
config: [config object]
Keyword arguments:
nostars: [bool] If True, all files will be taken regardless of if they have stars on them or not.
use_images: [bool] Use image files instead of FF files. False by default.
Return:
[2d ndarray] Flat field image as a numpy array. If the flat generation failed, None will be returned.
"""
# If only images are used, then don't look for a CALSTARS file
if use_images:
nostars = True
# Load the calstars file if it should be used
if not nostars:
# Find the CALSTARS file in the given folder
calstars_file = None
for calstars_file in os.listdir(dir_path):
if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file):
break
if calstars_file is None:
print('CALSTARS file could not be found in the given directory!')
return None
# Load the calstars file
calstars_list = CALSTARS.readCALSTARS(dir_path, calstars_file)
# Convert the list to a dictionary
calstars = {ff_file: star_data for ff_file, star_data in calstars_list}
print('CALSTARS file: ' + calstars_file + ' loaded!')
# A list of FF files which have any stars on them
calstars_ff_files = [line[0] for line in calstars_list]
else:
calstars = {}
# Use image files
if use_images:
# Find the file type with the highest file frequency in the given folder
file_extensions = []
for file_name in os.listdir(dir_path):
file_ext = file_name.split('.')[-1]
if file_ext.lower() in ['jpg', 'png', 'bmp']:
file_extensions.append(file_ext)
# Get only the most frequent file type
file_freqs = np.unique(file_extensions, return_counts=True)
most_freq_type = file_freqs[0][0]
print('Using image type:', most_freq_type)
# Take only files of that file type
ff_list = [file_name for file_name in sorted(os.listdir(dir_path)) \
if file_name.lower().endswith(most_freq_type)]
# Use FF files
else:
ff_list = []
# Get a list of FF files in the folder
for file_name in os.listdir(dir_path):
if validFFName(file_name) and ((file_name in calstars_ff_files) or nostars):
ff_list.append(file_name)
# Check that there are any FF files in the folder
if not ff_list:
print('No valid FF files in the selected folder!')
return None
ff_list_good = []
ff_times = []
# Take only those FF files with enough stars on them
for ff_name in ff_list:
if (ff_name in calstars) or nostars:
# Disable requiring minimum number of stars if specified
if not nostars:
# Get the number of stars detected on the FF image
ff_nstars = len(calstars[ff_name])
else:
ff_nstars = 0
# Check if the number of stars on the image is over the detection threshold
if (ff_nstars > config.ff_min_stars) or nostars:
# Add the FF file to the list of FF files to be used to make a flat
ff_list_good.append(ff_name)
# If images are used, don't compute the time
if use_images:
ff_time = 0
else:
# Calculate the time of the FF files
ff_time = date2JD(*getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True))
ff_times.append(ff_time)
# Check that there are enough good FF files in the folder
if (len(ff_times) < config.flat_min_imgs) and (not nostars):
print('Not enough FF files have enough stars on them!')
return None
# Make sure the files cover at least 2 hours
if (not (max(ff_times) - min(ff_times))*24 > 2) and (not nostars):
print('Good FF files cover less than 2 hours!')
return None
# Sample FF files if there are more than 200
max_ff_flat = 200
if len(ff_list_good) > max_ff_flat:
ff_list_good = sorted(random.sample(ff_list_good, max_ff_flat))
print('Using {:d} files for flat...'.format(len(ff_list_good)))
c = 0
img_list = []
median_list = []
# Median combine all good FF files
for i in range(len(ff_list_good)):
# Load 10 files at the time and median combine them, which conserves memory
if c < 10:
# Use images
if use_images:
img = scipy.ndimage.imread(os.path.join(dir_path, ff_list_good[i]), -1)
# Use FF files
else:
ff = readFF(dir_path, ff_list_good[i])
# Skip the file if it is corruped
if ff is None:
continue
img = ff.avepixel
img_list.append(img)
c += 1
else:
img_list = np.array(img_list)
# Median combine the loaded 10 (or less) images
ff_median = np.median(img_list, axis=0)
median_list.append(ff_median)
img_list = []
c = 0
# If there are more than 1 calculated median image, combine them
if len(median_list) > 1:
# Median combine all median images
median_list = np.array(median_list)
ff_median = np.median(median_list, axis=0)
else:
if len(median_list) > 0:
ff_median = median_list[0]
else:
ff_median = np.median(np.array(img_list), axis=0)
# Stretch flat to 0-255
ff_median = ff_median/np.max(ff_median)*255
# Convert the flat to 8 bits
ff_median = ff_median.astype(np.uint8)
return ff_median
# Load the calstars file
calstars_list = CALSTARS.readCALSTARS(dir_path, calstars_file)
calstars_dict = {ff_file: star_data for ff_file, star_data in calstars_list}
print('CALSTARS file: ' + calstars_file + ' loaded!')
# Extract star list from CALSTARS file from FF file with most stars
max_len_ff = max(calstars_dict, key=lambda k: len(calstars_dict[k]))
# Take only X, Y (change order so X is first)
calstars_coords = np.array(calstars_dict[max_len_ff])[:, :2]
calstars_coords[:, [0, 1]] = calstars_coords[:, [1, 0]]
# Get the time of the FF file
calstars_time = getMiddleTimeFF(max_len_ff, config.fps, ret_milliseconds=True)
# Align the platepar with stars in CALSTARS
platepar_aligned = alignPlatepar(config, platepar, calstars_time, calstars_coords, show_plot=False)
# Backup the old platepar
shutil.copy(platepar_path, platepar_path + '.bak')
# Save the updated platepar
platepar_aligned.write(platepar_path)
### Testing
sys.exit()
ff_file: star_data
for ff_file, star_data in calstars_list
}
print('CALSTARS file: ' + calstars_file + ' loaded!')
# Extract star list from CALSTARS file from FF file with most stars
max_len_ff = max(calstars_dict, key=lambda k: len(calstars_dict[k]))
# Take only X, Y (change order so X is first)
calstars_coords = np.array(calstars_dict[max_len_ff])[:, :2]
calstars_coords[:, [0, 1]] = calstars_coords[:, [1, 0]]
# Get the time of the FF file
calstars_time = getMiddleTimeFF(max_len_ff,
config.fps,
ret_milliseconds=True)
# Align the platepar with stars in CALSTARS
platepar_aligned = alignPlatepar(config,
platepar,
calstars_time,
calstars_coords,
show_plot=False)
# Backup the old platepar
shutil.copy(platepar_path, platepar_path + '.bak')
# Save the updated platepar
platepar_aligned.write(platepar_path)
def makeFlat(dir_path, config, nostars=False, use_images=False):
""" Makes a flat field from the files in the given folder. CALSTARS file is needed to estimate the
quality of every image by counting the number of detected stars.
Arguments:
dir_path: [str] Path to the directory which contains the FF files and a CALSTARS file.
config: [config object]
Keyword arguments:
nostars: [bool] If True, all files will be taken regardless of if they have stars on them or not.
use_images: [bool] Use image files instead of FF files. False by default.
Return:
[2d ndarray] Flat field image as a numpy array. If the flat generation failed, None will be returned.
"""
# If only images are used, then don't look for a CALSTARS file
if use_images:
nostars = True
# Load the calstars file if it should be used
if not nostars:
# Find the CALSTARS file in the given folder
calstars_file = None
for calstars_file in os.listdir(dir_path):
if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file):
break
if calstars_file is None:
print('CALSTARS file could not be found in the given directory!')
return None
# Load the calstars file
calstars_list = CALSTARS.readCALSTARS(dir_path, calstars_file)
# Convert the list to a dictionary
calstars = {ff_file: star_data for ff_file, star_data in calstars_list}
print('CALSTARS file: ' + calstars_file + ' loaded!')
# A list of FF files which have any stars on them
calstars_ff_files = [line[0] for line in calstars_list]
else:
calstars = {}
calstars_ff_files = []
# Use image files
if use_images:
# Find the file type with the highest file frequency in the given folder
file_extensions = []
for file_name in os.listdir(dir_path):
file_ext = file_name.split('.')[-1]
if file_ext.lower() in ['jpg', 'png', 'bmp']:
file_extensions.append(file_ext)
# Get only the most frequent file type
file_freqs = np.unique(file_extensions, return_counts=True)
most_freq_type = file_freqs[0][0]
print('Using image type:', most_freq_type)
# Take only files of that file type
ff_list = [file_name for file_name in sorted(os.listdir(dir_path)) \
if file_name.lower().endswith(most_freq_type)]
# Use FF files
else:
ff_list = []
# Get a list of FF files in the folder
for file_name in os.listdir(dir_path):
if validFFName(file_name) and ((file_name in calstars_ff_files)
or nostars):
ff_list.append(file_name)
# Check that there are any FF files in the folder
if not ff_list:
print('No valid FF files in the selected folder!')
return None
ff_list_good = []
ff_times = []
# Take only those FF files with enough stars on them
for ff_name in ff_list:
if (ff_name in calstars) or nostars:
# Disable requiring minimum number of stars if specified
if not nostars:
# Get the number of stars detected on the FF image
ff_nstars = len(calstars[ff_name])
else:
ff_nstars = 0
# Check if the number of stars on the image is over the detection threshold
if (ff_nstars > config.ff_min_stars) or nostars:
# Add the FF file to the list of FF files to be used to make a flat
ff_list_good.append(ff_name)
# If images are used, don't compute the time
if use_images:
ff_time = 0
else:
# Calculate the time of the FF files
ff_time = date2JD(*getMiddleTimeFF(
ff_name, config.fps, ret_milliseconds=True))
ff_times.append(ff_time)
# Check that there are enough good FF files in the folder
if (len(ff_times) < config.flat_min_imgs) and (not nostars):
print('Not enough FF files have enough stars on them!')
return None
# Make sure the files cover at least 2 hours
if (not (max(ff_times) - min(ff_times)) * 24 > 2) and (not nostars):
print('Good FF files cover less than 2 hours!')
return None
# Sample FF files if there are more than 200
max_ff_flat = 200
if len(ff_list_good) > max_ff_flat:
ff_list_good = sorted(random.sample(ff_list_good, max_ff_flat))
print('Using {:d} files for flat...'.format(len(ff_list_good)))
c = 0
img_list = []
median_list = []
# Median combine all good FF files
for i in range(len(ff_list_good)):
# Load 10 files at the time and median combine them, which conserves memory
if c < 10:
# Use images
if use_images:
img = loadImage(os.path.join(dir_path, ff_list_good[i]), -1)
# Use FF files
else:
ff = readFF(dir_path, ff_list_good[i])
# Skip the file if it is corruped
if ff is None:
continue
img = ff.avepixel
img_list.append(img)
c += 1
else:
img_list = np.array(img_list)
# Median combine the loaded 10 (or less) images
ff_median = np.median(img_list, axis=0)
median_list.append(ff_median)
img_list = []
c = 0
# If there are more than 1 calculated median image, combine them
if len(median_list) > 1:
# Median combine all median images
median_list = np.array(median_list)
ff_median = np.median(median_list, axis=0)
else:
if len(median_list) > 0:
ff_median = median_list[0]
else:
ff_median = np.median(np.array(img_list), axis=0)
# Stretch flat to 0-255
ff_median = ff_median / np.max(ff_median) * 255
# Convert the flat to 8 bits
ff_median = ff_median.astype(np.uint8)
return ff_median
def generateCalibrationReport(config, night_dir_path, match_radius=2.0, platepar=None, show_graphs=False):
""" Given the folder of the night, find the Calstars file, check the star fit and generate a report
with the quality of the calibration. The report contains information about both the astrometry and
the photometry calibration. Graphs will be saved in the given directory of the night.
Arguments:
config: [Config instance]
night_dir_path: [str] Full path to the directory of the night.
Keyword arguments:
match_radius: [float] Match radius for star matching between image and catalog stars (px).
platepar: [Platepar instance] Use this platepar instead of finding one in the folder.
show_graphs: [bool] Show the graphs on the screen. False by default.
Return:
None
"""
# Find the CALSTARS file in the given folder
calstars_file = None
for calstars_file in os.listdir(night_dir_path):
if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file):
break
if calstars_file is None:
print('CALSTARS file could not be found in the given directory!')
return None
# Load the calstars file
star_list = readCALSTARS(night_dir_path, calstars_file)
### Load recalibrated platepars, if they exist ###
# Find recalibrated platepars file per FF file
platepars_recalibrated_file = None
for file_name in os.listdir(night_dir_path):
if file_name == config.platepars_recalibrated_name:
platepars_recalibrated_file = file_name
break
# Load all recalibrated platepars if the file is available
recalibrated_platepars = None
if platepars_recalibrated_file:
with open(os.path.join(night_dir_path, platepars_recalibrated_file)) as f:
recalibrated_platepars = json.load(f)
print('Loaded recalibrated platepars JSON file for the calibration report...')
### ###
### Load the platepar file ###
# Find the platepar file in the given directory if it was not given
if platepar is None:
# Find the platepar file
platepar_file = None
for file_name in os.listdir(night_dir_path):
if file_name == config.platepar_name:
platepar_file = file_name
break
if platepar_file is None:
print('The platepar cannot be found in the night directory!')
return None
# Load the platepar file
platepar = Platepar()
platepar.read(os.path.join(night_dir_path, platepar_file))
### ###
night_name = os.path.split(night_dir_path.strip(os.sep))[1]
# Go one mag deeper than in the config
lim_mag = config.catalog_mag_limit + 1
# Load catalog stars (load one magnitude deeper)
catalog_stars, mag_band_str, config.star_catalog_band_ratios = StarCatalog.readStarCatalog(\
config.star_catalog_path, config.star_catalog_file, lim_mag=lim_mag, \
mag_band_ratios=config.star_catalog_band_ratios)
### Take only those CALSTARS entires for which FF files exist in the folder ###
# Get a list of FF files in the folder\
ff_list = []
for file_name in os.listdir(night_dir_path):
if validFFName(file_name):
ff_list.append(file_name)
# Filter out calstars entries, generate a star dictionary where the keys are JDs of FFs
star_dict = {}
ff_dict = {}
for entry in star_list:
ff_name, star_data = entry
# Check if the FF from CALSTARS exists in the folder
if ff_name not in ff_list:
continue
dt = getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True)
jd = date2JD(*dt)
# Add the time and the stars to the dict
star_dict[jd] = star_data
ff_dict[jd] = ff_name
### ###
# If there are no FF files in the directory, don't generate a report
if len(star_dict) == 0:
print('No FF files from the CALSTARS file in the directory!')
return None
# If the recalibrated platepars file exists, take the one with the most stars
max_jd = 0
if recalibrated_platepars is not None:
max_stars = 0
for ff_name_temp in recalibrated_platepars:
# Compute the Julian date of the FF middle
dt = getMiddleTimeFF(ff_name_temp, config.fps, ret_milliseconds=True)
jd = date2JD(*dt)
# Check that this file exists in CALSTARS and the list of FF files
if (jd not in star_dict) or (jd not in ff_dict):
continue
# Check if the number of stars on this FF file is larger than the before
if len(star_dict[jd]) > max_stars:
max_jd = jd
max_stars = len(star_dict[jd])
# Set a flag to indicate if using recalibrated platepars has failed
if max_jd == 0:
using_recalib_platepars = False
else:
print('Using recalibrated platepars, file:', ff_dict[max_jd])
using_recalib_platepars = True
# Select the platepar where the FF file has the most stars
platepar_dict = recalibrated_platepars[ff_dict[max_jd]]
platepar = Platepar()
platepar.loadFromDict(platepar_dict)
filtered_star_dict = {max_jd: star_dict[max_jd]}
# Match stars on the image with the stars in the catalog
n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \
filtered_star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag)
max_matched_stars = n_matched
# Otherwise take the optimal FF file for evaluation
if (recalibrated_platepars is None) or (not using_recalib_platepars):
# If there are more than a set number of FF files to evaluate, choose only the ones with most stars on
# the image
if len(star_dict) > config.calstars_files_N:
# Find JDs of FF files with most stars on them
top_nstars_indices = np.argsort([len(x) for x in star_dict.values()])[::-1][:config.calstars_files_N \
- 1]
filtered_star_dict = {}
for i in top_nstars_indices:
filtered_star_dict[list(star_dict.keys())[i]] = list(star_dict.values())[i]
star_dict = filtered_star_dict
# Match stars on the image with the stars in the catalog
n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \
star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag)
# If no recalibrated platepars where found, find the image with the largest number of matched stars
if (not using_recalib_platepars) or (max_jd == 0):
max_jd = 0
max_matched_stars = 0
for jd in matched_stars:
_, _, distances = matched_stars[jd]
if len(distances) > max_matched_stars:
max_jd = jd
max_matched_stars = len(distances)
# If there are no matched stars, use the image with the largest number of detected stars
if max_matched_stars <= 2:
max_jd = max(star_dict, key=lambda x: len(star_dict[x]))
distances = [np.inf]
# Take the FF file with the largest number of matched stars
ff_name = ff_dict[max_jd]
# Load the FF file
ff = readFF(night_dir_path, ff_name)
img_h, img_w = ff.avepixel.shape
dpi = 200
plt.figure(figsize=(ff.avepixel.shape[1]/dpi, ff.avepixel.shape[0]/dpi), dpi=dpi)
# Take the average pixel
img = ff.avepixel
# Slightly adjust the levels
img = Image.adjustLevels(img, np.percentile(img, 1.0), 1.2, np.percentile(img, 99.99))
plt.imshow(img, cmap='gray', interpolation='nearest')
legend_handles = []
# Plot detected stars
for img_star in star_dict[max_jd]:
y, x, _, _ = img_star
rect_side = 5*match_radius
square_patch = plt.Rectangle((x - rect_side/2, y - rect_side/2), rect_side, rect_side, color='g', \
fill=False, label='Image stars')
plt.gca().add_artist(square_patch)
legend_handles.append(square_patch)
# If there are matched stars, plot them
if max_matched_stars > 2:
# Take the solution with the largest number of matched stars
image_stars, matched_catalog_stars, distances = matched_stars[max_jd]
# Plot matched stars
for img_star in image_stars:
x, y, _, _ = img_star
circle_patch = plt.Circle((y, x), radius=3*match_radius, color='y', fill=False, \
label='Matched stars')
plt.gca().add_artist(circle_patch)
legend_handles.append(circle_patch)
### Plot match residuals ###
# Compute preducted positions of matched image stars from the catalog
x_predicted, y_predicted = raDecToXYPP(matched_catalog_stars[:, 0], \
matched_catalog_stars[:, 1], max_jd, platepar)
img_y, img_x, _, _ = image_stars.T
delta_x = x_predicted - img_x
delta_y = y_predicted - img_y
# Compute image residual and angle of the error
res_angle = np.arctan2(delta_y, delta_x)
res_distance = np.sqrt(delta_x**2 + delta_y**2)
# Calculate coordinates of the beginning of the residual line
res_x_beg = img_x + 3*match_radius*np.cos(res_angle)
res_y_beg = img_y + 3*match_radius*np.sin(res_angle)
# Calculate coordinates of the end of the residual line
res_x_end = img_x + 100*np.cos(res_angle)*res_distance
res_y_end = img_y + 100*np.sin(res_angle)*res_distance
# Plot the 100x residuals
for i in range(len(x_predicted)):
res_plot = plt.plot([res_x_beg[i], res_x_end[i]], [res_y_beg[i], res_y_end[i]], color='orange', \
lw=0.5, label='100x residuals')
legend_handles.append(res_plot[0])
### ###
else:
distances = [np.inf]
# If there are no matched stars, plot large text in the middle of the screen
plt.text(img_w/2, img_h/2, "NO MATCHED STARS!", color='r', alpha=0.5, fontsize=20, ha='center',
va='center')
### Plot positions of catalog stars to the limiting magnitude of the faintest matched star + 1 mag ###
# Find the faintest magnitude among matched stars
if max_matched_stars > 2:
faintest_mag = np.max(matched_catalog_stars[:, 2]) + 1
else:
# If there are no matched stars, use the limiting magnitude from config
faintest_mag = config.catalog_mag_limit + 1
# Estimate RA,dec of the centre of the FOV
_, RA_c, dec_c, _ = xyToRaDecPP([jd2Date(max_jd)], [platepar.X_res/2], [platepar.Y_res/2], [1],
platepar)
RA_c = RA_c[0]
dec_c = dec_c[0]
fov_radius = np.hypot(*computeFOVSize(platepar))
# Get stars from the catalog around the defined center in a given radius
_, extracted_catalog = subsetCatalog(catalog_stars, RA_c, dec_c, fov_radius, faintest_mag)
ra_catalog, dec_catalog, mag_catalog = extracted_catalog.T
# Compute image positions of all catalog stars that should be on the image
x_catalog, y_catalog = raDecToXYPP(ra_catalog, dec_catalog, max_jd, platepar)
# Filter all catalog stars outside the image
temp_arr = np.c_[x_catalog, y_catalog, mag_catalog]
temp_arr = temp_arr[temp_arr[:, 0] >= 0]
temp_arr = temp_arr[temp_arr[:, 0] <= ff.avepixel.shape[1]]
temp_arr = temp_arr[temp_arr[:, 1] >= 0]
temp_arr = temp_arr[temp_arr[:, 1] <= ff.avepixel.shape[0]]
x_catalog, y_catalog, mag_catalog = temp_arr.T
# Plot catalog stars on the image
cat_stars_handle = plt.scatter(x_catalog, y_catalog, c='none', marker='D', lw=1.0, alpha=0.4, \
s=((4.0 + (faintest_mag - mag_catalog))/3.0)**(2*2.512), edgecolor='r', label='Catalog stars')
legend_handles.append(cat_stars_handle)
### ###
# Add info text
info_text = ff_dict[max_jd] + '\n' \
+ "Matched stars: {:d}/{:d}\n".format(max_matched_stars, len(star_dict[max_jd])) \
+ "Median distance: {:.2f} px\n".format(np.median(distances)) \
+ "Catalog limiting magnitude: {:.1f}".format(lim_mag)
plt.text(10, 10, info_text, bbox=dict(facecolor='black', alpha=0.5), va='top', ha='left', fontsize=4, \
color='w')
legend = plt.legend(handles=legend_handles, prop={'size': 4}, loc='upper right')
legend.get_frame().set_facecolor('k')
legend.get_frame().set_edgecolor('k')
for txt in legend.get_texts():
txt.set_color('w')
plt.axis('off')
plt.gca().get_xaxis().set_visible(False)
plt.gca().get_yaxis().set_visible(False)
plt.xlim([0, ff.avepixel.shape[1]])
plt.ylim([ff.avepixel.shape[0], 0])
# Remove the margins
plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0)
plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_astrometry.jpg'), \
bbox_inches='tight', pad_inches=0, dpi=dpi)
if show_graphs:
plt.show()
else:
plt.clf()
plt.close()
if max_matched_stars > 2:
### Plot the photometry ###
plt.figure(dpi=dpi)
# Take only those stars which are inside the 3/4 of the shorter image axis from the center
photom_selection_radius = np.min([img_h, img_w])/3
filter_indices = ((image_stars[:, 0] - img_h/2)**2 + (image_stars[:, 1] \
- img_w/2)**2) <= photom_selection_radius**2
star_intensities = image_stars[filter_indices, 2]
catalog_mags = matched_catalog_stars[filter_indices, 2]
# Plot intensities of image stars
#star_intensities = image_stars[:, 2]
plt.scatter(-2.5*np.log10(star_intensities), catalog_mags, s=5, c='r')
# Fit the photometry on automated star intensities
photom_offset, fit_stddev, _ = photometryFit(np.log10(star_intensities), catalog_mags)
# Plot photometric offset from the platepar
x_min, x_max = plt.gca().get_xlim()
y_min, y_max = plt.gca().get_ylim()
x_min_w = x_min - 3
x_max_w = x_max + 3
y_min_w = y_min - 3
y_max_w = y_max + 3
photometry_info = 'Platepar: {:+.2f}LSP {:+.2f} +/- {:.2f} \nGamma = {:.2f}'.format(platepar.mag_0, \
platepar.mag_lev, platepar.mag_lev_stddev, platepar.gamma)
# Plot the photometry calibration from the platepar
logsum_arr = np.linspace(x_min_w, x_max_w, 10)
plt.plot(logsum_arr, logsum_arr + platepar.mag_lev, label=photometry_info, linestyle='--', \
color='k', alpha=0.5)
# Plot the fitted photometry calibration
fit_info = "Fit: {:+.2f}LSP {:+.2f} +/- {:.2f}".format(-2.5, photom_offset, fit_stddev)
plt.plot(logsum_arr, logsum_arr + photom_offset, label=fit_info, linestyle='--', color='red',
alpha=0.5)
plt.legend()
plt.ylabel("Catalog magnitude ({:s})".format(mag_band_str))
plt.xlabel("Uncalibrated magnitude")
# Set wider axis limits
plt.xlim(x_min_w, x_max_w)
plt.ylim(y_min_w, y_max_w)
plt.gca().invert_yaxis()
plt.gca().invert_xaxis()
plt.grid()
plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_photometry.png'), dpi=150)
if show_graphs:
plt.show()
else:
plt.clf()
plt.close()
def trackStack(dir_path,
config,
border=5,
background_compensation=True,
hide_plot=False):
""" Generate a stack with aligned stars, so the sky appears static. The folder should have a
platepars_all_recalibrated.json file.
Arguments:
dir_path: [str] Path to the directory with image files.
config: [Config instance]
Keyword arguments:
border: [int] Border around the image to exclude (px).
background_compensation: [bool] Normalize the background by applying a median filter to avepixel and
use it as a flat field. Slows down the procedure and may sometimes introduce artifacts. True
by default.
"""
# Load recalibrated platepars, if they exist ###
# Find recalibrated platepars file per FF file
platepars_recalibrated_file = None
for file_name in os.listdir(dir_path):
if file_name == config.platepars_recalibrated_name:
platepars_recalibrated_file = file_name
break
# Load all recalibrated platepars if the file is available
recalibrated_platepars = None
if platepars_recalibrated_file is not None:
with open(os.path.join(dir_path, platepars_recalibrated_file)) as f:
recalibrated_platepars = json.load(f)
print(
'Loaded recalibrated platepars JSON file for the calibration report...'
)
# ###
# If the recalib platepars is not found, stop
if recalibrated_platepars is None:
print("The {:s} file was not found!".format(
config.platepars_recalibrated_name))
return False
# Get a list of FF files in the folder
ff_list = []
for file_name in os.listdir(dir_path):
if validFFName(file_name):
ff_list.append(file_name)
# Take the platepar with the middle time as the reference one
ff_found_list = []
jd_list = []
for ff_name_temp in recalibrated_platepars:
if ff_name_temp in ff_list:
# Compute the Julian date of the FF middle
dt = getMiddleTimeFF(ff_name_temp,
config.fps,
ret_milliseconds=True)
jd = date2JD(*dt)
jd_list.append(jd)
ff_found_list.append(ff_name_temp)
if len(jd_list) < 2:
print("Not more than 1 FF image!")
return False
# Take the FF file with the middle JD
jd_list = np.array(jd_list)
jd_middle = np.mean(jd_list)
jd_mean_index = np.argmin(np.abs(jd_list - jd_middle))
ff_mid = ff_found_list[jd_mean_index]
# Load the middle platepar as the reference one
pp_ref = Platepar()
pp_ref.loadFromDict(recalibrated_platepars[ff_mid],
use_flat=config.use_flat)
# Try loading the mask
mask_path = None
if os.path.exists(os.path.join(dir_path, config.mask_file)):
mask_path = os.path.join(dir_path, config.mask_file)
# Try loading the default mask
elif os.path.exists(config.mask_file):
mask_path = os.path.abspath(config.mask_file)
# Load the mask if given
mask = None
if mask_path is not None:
mask = loadMask(mask_path)
print("Loaded mask:", mask_path)
# If the shape of the mask doesn't fit, init an empty mask
if mask is not None:
if (mask.img.shape[0] != pp_ref.Y_res) or (mask.img.shape[1] !=
pp_ref.X_res):
print("Mask is of wrong shape!")
mask = None
if mask is None:
mask = MaskStructure(255 + np.zeros(
(pp_ref.Y_res, pp_ref.X_res), dtype=np.uint8))
# Compute the middle RA/Dec of the reference platepar
_, ra_temp, dec_temp, _ = xyToRaDecPP([jd2Date(jd_middle)],
[pp_ref.X_res / 2],
[pp_ref.Y_res / 2], [1],
pp_ref,
extinction_correction=False)
ra_mid, dec_mid = ra_temp[0], dec_temp[0]
# Go through all FF files and find RA/Dec of image corners to find the size of the stack image ###
# List of corners
x_corns = [0, pp_ref.X_res, 0, pp_ref.X_res]
y_corns = [0, 0, pp_ref.Y_res, pp_ref.Y_res]
ra_list = []
dec_list = []
for ff_temp in ff_found_list:
# Load the recalibrated platepar
pp_temp = Platepar()
pp_temp.loadFromDict(recalibrated_platepars[ff_temp],
use_flat=config.use_flat)
for x_c, y_c in zip(x_corns, y_corns):
_, ra_temp, dec_temp, _ = xyToRaDecPP(
[getMiddleTimeFF(ff_temp, config.fps, ret_milliseconds=True)],
[x_c], [y_c], [1],
pp_ref,
extinction_correction=False)
ra_c, dec_c = ra_temp[0], dec_temp[0]
ra_list.append(ra_c)
dec_list.append(dec_c)
# Compute the angular separation from the middle equatorial coordinates of the reference image to all
# RA/Dec corner coordinates
ang_sep_list = []
for ra_c, dec_c in zip(ra_list, dec_list):
ang_sep = np.degrees(
angularSeparation(np.radians(ra_mid), np.radians(dec_mid),
np.radians(ra_c), np.radians(dec_c)))
ang_sep_list.append(ang_sep)
# Find the maximum angular separation and compute the image size using the plate scale
# The image size will be resampled to 1/2 of the original size to avoid interpolation
scale = 0.5
ang_sep_max = np.max(ang_sep_list)
img_size = int(scale * 2 * ang_sep_max * pp_ref.F_scale)
#
# Create the stack platepar with no distortion and a large image size
pp_stack = copy.deepcopy(pp_ref)
pp_stack.resetDistortionParameters()
pp_stack.X_res = img_size
pp_stack.Y_res = img_size
pp_stack.F_scale *= scale
pp_stack.refraction = False
# Init the image
avg_stack_sum = np.zeros((img_size, img_size), dtype=float)
avg_stack_count = np.zeros((img_size, img_size), dtype=int)
max_deaveraged = np.zeros((img_size, img_size), dtype=np.uint8)
# Load individual FFs and map them to the stack
for i, ff_name in enumerate(ff_found_list):
print("Stacking {:s}, {:.1f}% done".format(
ff_name, 100 * i / len(ff_found_list)))
# Read the FF file
ff = readFF(dir_path, ff_name)
# Load the recalibrated platepar
pp_temp = Platepar()
pp_temp.loadFromDict(recalibrated_platepars[ff_name],
use_flat=config.use_flat)
# Make a list of X and Y image coordinates
x_coords, y_coords = np.meshgrid(
np.arange(border, pp_ref.X_res - border),
np.arange(border, pp_ref.Y_res - border))
x_coords = x_coords.ravel()
y_coords = y_coords.ravel()
# Map image pixels to sky
jd_arr, ra_coords, dec_coords, _ = xyToRaDecPP(
len(x_coords) *
[getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True)],
x_coords,
y_coords,
len(x_coords) * [1],
pp_temp,
extinction_correction=False)
# Map sky coordinates to stack image coordinates
stack_x, stack_y = raDecToXYPP(ra_coords, dec_coords, jd_middle,
pp_stack)
# Round pixel coordinates
stack_x = np.round(stack_x, decimals=0).astype(int)
stack_y = np.round(stack_y, decimals=0).astype(int)
# Cut the image to limits
filter_arr = (stack_x > 0) & (stack_x < img_size) & (stack_y > 0) & (
stack_y < img_size)
x_coords = x_coords[filter_arr].astype(int)
y_coords = y_coords[filter_arr].astype(int)
stack_x = stack_x[filter_arr]
stack_y = stack_y[filter_arr]
# Apply the mask to maxpixel and avepixel
maxpixel = copy.deepcopy(ff.maxpixel)
maxpixel[mask.img == 0] = 0
avepixel = copy.deepcopy(ff.avepixel)
avepixel[mask.img == 0] = 0
# Compute deaveraged maxpixel
max_deavg = maxpixel - avepixel
# Normalize the backgroud brightness by applying a large-kernel median filter to avepixel
if background_compensation:
# # Apply a median filter to the avepixel to get an estimate of the background brightness
# avepixel_median = scipy.ndimage.median_filter(ff.avepixel, size=101)
avepixel_median = cv2.medianBlur(ff.avepixel, 301)
# Make sure to avoid zero division
avepixel_median[avepixel_median < 1] = 1
# Normalize the avepixel by subtracting out the background brightness
avepixel = avepixel.astype(float)
avepixel /= avepixel_median
avepixel *= 50 # Normalize to a good background value, which is usually 50
avepixel = np.clip(avepixel, 0, 255)
avepixel = avepixel.astype(np.uint8)
# plt.imshow(avepixel, cmap='gray', vmin=0, vmax=255)
# plt.show()
# Add the average pixel to the sum
avg_stack_sum[stack_y, stack_x] += avepixel[y_coords, x_coords]
# Increment the counter image where the avepixel is not zero
ones_img = np.ones_like(avepixel)
ones_img[avepixel == 0] = 0
avg_stack_count[stack_y, stack_x] += ones_img[y_coords, x_coords]
# Set pixel values to the stack, only take the max values
max_deaveraged[stack_y, stack_x] = np.max(np.dstack(
[max_deaveraged[stack_y, stack_x], max_deavg[y_coords, x_coords]]),
axis=2)
# Compute the blended avepixel background
stack_img = avg_stack_sum
stack_img[avg_stack_count > 0] /= avg_stack_count[avg_stack_count > 0]
stack_img += max_deaveraged
stack_img = np.clip(stack_img, 0, 255)
stack_img = stack_img.astype(np.uint8)
# Crop image
non_empty_columns = np.where(stack_img.max(axis=0) > 0)[0]
non_empty_rows = np.where(stack_img.max(axis=1) > 0)[0]
crop_box = (np.min(non_empty_rows), np.max(non_empty_rows),
np.min(non_empty_columns), np.max(non_empty_columns))
stack_img = stack_img[crop_box[0]:crop_box[1] + 1,
crop_box[2]:crop_box[3] + 1]
# Plot and save the stack ###
dpi = 200
plt.figure(figsize=(stack_img.shape[1] / dpi, stack_img.shape[0] / dpi),
dpi=dpi)
plt.imshow(stack_img,
cmap='gray',
vmin=0,
vmax=256,
interpolation='nearest')
plt.axis('off')
plt.gca().get_xaxis().set_visible(False)
plt.gca().get_yaxis().set_visible(False)
plt.xlim([0, stack_img.shape[1]])
plt.ylim([stack_img.shape[0], 0])
# Remove the margins (top and right are set to 0.9999, as setting them to 1.0 makes the image blank in
# some matplotlib versions)
plt.subplots_adjust(left=0,
bottom=0,
right=0.9999,
top=0.9999,
wspace=0,
hspace=0)
filenam = os.path.join(dir_path,
os.path.basename(dir_path) + "_track_stack.jpg")
plt.savefig(filenam, bbox_inches='tight', pad_inches=0, dpi=dpi)
#
if hide_plot is False:
plt.show()
def add_fffits_metadata(ff_filename, config, platepars_recalibrated,
fallback_platepar):
"""
Add FITS metadata and WCS to FF files generated by RMS
Args:
ff_filename (str): full or relative path to FF file
config (RMS.Config): config instance
platepars_recalibrated (dict): dictionary with recalibrated platepars
fallback_platepar (RMS.Platepar): platepar with fitted stars
Returns:
None
"""
ff_basename = os.path.basename(ff_filename)
platepar_recalibrated = Platepar()
try:
platepar_data = platepars_recalibrated[ff_basename]
with open("platepar_tmp.cal", "w") as f:
json.dump(platepar_data, f)
platepar_recalibrated.read("platepar_tmp.cal")
except (FileNotFoundError, KeyError):
platepar_recalibrated = fallback_platepar
logger.warning(f"Using non-recalibrated platepar for {ff_basename}")
fftime = getMiddleTimeFF(ff_basename, config.fps)
fit_xy = np.array(fallback_platepar.star_list)[:, 1:3]
_, fit_ra, fit_dec, _ = xyToRaDecPP([fftime] * len(fit_xy),
fit_xy[:, 0],
fit_xy[:, 1], [1] * len(fit_xy),
platepar_recalibrated,
extinction_correction=False)
x0 = platepar_recalibrated.X_res / 2
y0 = platepar_recalibrated.Y_res / 2
_, ra0, dec0, _ = xyToRaDecPP([fftime], [x0], [y0], [1],
platepar_recalibrated,
extinction_correction=False)
w = fit_wcs(fit_xy[:, 0],
fit_xy[:, 1],
fit_ra,
fit_dec,
x0,
y0,
ra0[0],
dec0[0],
5,
projection="ZEA")
hdu_list = fits.open(ff_filename, scale_back=True)
obstime = Time(filenameToDatetime(ff_basename))
header_meta = {}
header_meta["OBSERVER"] = config.stationID.strip()
header_meta["INSTRUME"] = "Global Meteor Network"
header_meta["MJD-OBS"] = obstime.mjd
header_meta["DATE-OBS"] = obstime.fits
header_meta["NFRAMES"] = 256
header_meta["EXPTIME"] = 256 / config.fps
header_meta["SITELONG"] = round(config.longitude, 2)
header_meta["SITELAT"] = round(config.latitude, 2)
for hdu in hdu_list:
if hdu.header[
"NAXIS"] == 0: # First header is not an image so should not get WCS
new_header = Header()
else:
new_header = w.to_fits(relax=True)[0].header
for key, value in header_meta.items():
new_header.append((key, value))
for key, value in new_header.items():
if key in hdu.header:
continue
hdu.header[key] = value
hdu_list.writeto(ff_filename, overwrite=True)
