def clean_up(self):
"""
Closes all open fits files so they don't remain in memory.
"""
print("Closing Fits files...")
for hdul in self.hdul_list:
hdul.close()
logging_tools.log("Fits files closed successfully.")
print("Files closed.")
def convert_catalogue_to_metadata(self):
if 'original_image' not in self.catalogue.columns:
if len(self.images) > 1:
logging_tools.log("""If multiple fits images are used the
original_image column must be provided in
the catalogue to identify which image the
source belongs to.""",
level='ERROR')
raise ValueError("Incorrect input supplied")
else:
self.catalogue['original_image'] = \
[list(self.images.keys())[0]] * len(self.catalogue)
if 'objid' not in self.catalogue.columns:
self.catalogue['objid'] = np.arange(len(self.catalogue))
if 'peak_flux' not in self.catalogue.columns:
self.catalogue['peak_flux'] = [np.NaN] * len(self.catalogue)
cols = ['original_image', 'x', 'y']
for c in cols[1:]:
if c not in self.catalogue.columns:
logging_tools.log("""If a catalogue is provided the x and y
columns (corresponding to pixel values) must be present""",
level='ERROR')
raise ValueError("Incorrect input supplied")
if 'ra' in self.catalogue.columns:
cols.append('ra')
if 'dec' in self.catalogue.columns:
cols.append('dec')
if 'peak_flux' in self.catalogue.columns:
cols.append('peak_flux')
met = {}
for c in cols:
met[c] = self.catalogue[c].values
the_index = np.array(self.catalogue['objid'].values, dtype='str')
self.metadata = pd.DataFrame(met, index=the_index)
self.metadata['x'] = self.metadata['x'].astype('int')
self.metadata['y'] = self.metadata['y'].astype('int')
def _execute_function(self, df):
"""
Does the work in actually running the scaler.
Parameters
----------
df : pd.DataFrame or similar
The input anomaly scores to rescale.
Returns
-------
pd.DataFrame
Contains the same original index and columns of the features input
with the anomaly score scaled according to the input arguments in
__init__.
"""
print('Running anomaly score rescaler...')
if self.column_name == 'all':
cols = df.columns
else:
cols = [self.column_name]
try:
scores = df[cols]
except KeyError:
msg = 'Requested column ' + self.column_name + ' not available in \
input dataframe. No rescaling has been performed'
logging_tools.log(msg, 'WARNING')
return df
if self.lower_is_weirder:
scores = -scores
scores = (self.new_max - self.new_min) * (scores - scores.min()) / \
(scores.max() - scores.min()) + self.new_min
if self.convert_integer:
scores = round(scores)
return scores
def run(self, data):
"""
This is the external-facing function that should always be called
(rather than _execute_function). This function will automatically check
if this stage has already been run with the same arguments and on the
same data. This can allow a much faster user experience avoiding
rerunning functions unnecessarily.
Parameters
----------
data : pd.DataFrame
Input data on which to run this pipeline stage on.
Returns
-------
pd.DataFrame
Output
"""
new_checksum = self.hash_data(data)
if self.args_same and new_checksum == self.checksum:
# This means we've already run this function for all instances in
# the input and with the same arguments
msg = "Pipeline stage %s previously called " \
"with same arguments and same data. Loading from file. " \
"Use 'force_rerun=True' in init args to override this " \
"behavior." % self.class_name
logging_tools.log(msg, level='WARNING')
return self.previous_output
else:
msg_string = self.function_call_signature + ' - checksum: ' + \
(str)(new_checksum)
# print(msg_string)
logging_tools.log(msg_string)
print('Running', self.class_name, '...')
t1 = time.time()
if self.drop_nans:
output = self._execute_function(data.dropna())
else:
output = self._execute_function(data)
self.save(output, self.output_file)
print('Done! Time taken:', (time.time() - t1), 's')
return output
def fit_ellipse(contour, image, return_params=False, filled=True):
"""
Fits an ellipse to a contour and returns a binary image representation of
the ellipse.
Parameters
----------
contour : np.ndarray
Array of x,y values describing the contours (as returned by opencv's
findCountours function)
image : np.ndarray
The original image the contour was fit to.
return_params : bool
If true also returns the parameters of the fitted ellipse
Returns
-------
np.ndarray
2d binary image with representation of the ellipse
"""
if filled:
thickness = -1
y_npix = image.shape[0]
x_npix = image.shape[1]
ellipse_arr = np.zeros([y_npix, x_npix], dtype=np.float)
else:
thickness = 1
ellipse_arr = image.copy()
# Sets some defaults for when the fitting fails
default_return_params = [np.nan] * 5
raised_error = False
try:
((x0, y0), (maj_axis, min_axis), theta) = cv2.fitEllipse(contour)
ellipse_params = x0, y0, maj_axis, min_axis, theta
if np.any(np.isnan(ellipse_params)):
raised_error = True
logging_tools.log('fit_ellipse failed with unknown error:')
except cv2.error as e:
logging_tools.log('fit_ellipse failed with cv2 error:' + e.msg)
raised_error = True
if raised_error:
if return_params:
return ellipse_arr, default_return_params
else:
return ellipse_arr
x0 = int(np.round(x0))
y0 = int(np.round(y0))
maj_axis = int(np.round(maj_axis))
min_axis = int(np.round(min_axis))
theta = int(np.round(theta))
cv2.ellipse(ellipse_arr, (x0, y0), (maj_axis // 2, min_axis // 2), theta,
0, 360, (1, 1, 1), thickness)
if return_params:
return ellipse_arr, ellipse_params
else:
return ellipse_arr
def _execute_function(self, image):
"""
Does the work in actually extracting the ellipse fitted features
Parameters
----------
image : np.ndarray
Input image
Returns
-------
array
Contains the extracted ellipse fitted features
"""
# First check the array is normalised since opencv will cry otherwise
if len(image.shape) > 2:
if self.channel is None:
raise ValueError('Contours cannot be determined for \
multi-channel images, please set the \
channel kwarg.')
else:
this_image = image[:, :, self.channel]
else:
this_image = image
# Get rid of possible NaNs
# this_image = np.nan_to_num(this_image)
x0 = y0 = -1
x_cent = this_image.shape[0] // 2
y_cent = this_image.shape[1] // 2
feats = []
# Start with the closest in contour (highest percentile)
percentiles = np.sort(self.percentiles)[::-1]
if np.all(this_image == 0):
failed = True
failure_message = "Invalid cutout for feature extraction"
else:
failed = False
failure_message = ""
for p in percentiles:
if failed:
contours = []
else:
thresh = np.percentile(this_image[this_image > 0], p)
contours, hierarchy = find_contours(this_image, thresh)
x_contours = np.zeros(len(contours))
y_contours = np.zeros(len(contours))
# First attempt to find the central point of the inner most contour
if len(contours) != 0:
for k in range(len(contours)):
M = cv2.moments(contours[k])
try:
x_contours[k] = int(M["m10"] / M["m00"])
y_contours[k] = int(M["m01"] / M["m00"])
except ZeroDivisionError:
pass
if x0 == -1:
x_diff = x_contours - x_cent
y_diff = y_contours - y_cent
else:
x_diff = x_contours - x0
y_diff = y_contours - y0
# Will try to find the CLOSEST contour to the central one
r_diff = np.sqrt(x_diff**2 + y_diff**2)
ind = np.argmin(r_diff)
if x0 == -1:
x0 = x_contours[ind]
y0 = y_contours[ind]
c = contours[ind]
params = get_ellipse_leastsq(c, this_image)
# Params return in this order:
# residual, x0, y0, maj_axis, min_axis, theta
if np.any(np.isnan(params)):
failed = True
else:
if params[3] == 0 or params[4] == 0:
aspect = 1
else:
aspect = params[4] / params[3]
if aspect < 1:
aspect = 1 / aspect
if aspect > 100:
aspect = 1
new_params = params[:3] + [aspect] + [params[-1]]
feats.append(new_params)
else:
failed = True
failure_message = "No contour found"
if failed:
feats.append([np.nan] * 5)
logging_tools.log(failure_message)
# Now we have the leastsq value, x0, y0, aspect_ratio, theta for each
# sigma
# Normalise things relative to the highest threshold value
# If there were problems with any sigma levels, set all values to NaNs
if np.any(np.isnan(feats)):
return [np.nan] * 4 * len(self.percentiles)
else:
max_ind = np.argmax(self.percentiles)
residuals = []
dist_to_centre = []
aspect = []
theta = []
x0_max_sigma = feats[max_ind][1]
y0_max_sigma = feats[max_ind][2]
aspect_max_sigma = feats[max_ind][3]
theta_max_sigma = feats[max_ind][4]
for n in range(len(feats)):
prms = feats[n]
residuals.append(prms[0])
if prms[1] == 0 or prms[2] == 0:
r = 0
else:
x_diff = prms[1] - x0_max_sigma
y_diff = prms[2] - y0_max_sigma
r = np.sqrt((x_diff)**2 + (y_diff)**2)
dist_to_centre.append(r)
aspect.append(prms[3] / aspect_max_sigma)
theta_diff = np.abs(prms[4] - theta_max_sigma) % 360
# Because there's redundancy about which way an ellipse
# is aligned, we always take the acute angle
if theta_diff > 90:
theta_diff -= 90
theta.append(theta_diff)
return np.hstack((residuals, dist_to_centre, aspect, theta))
def run_on_dataset(self, dataset=None):
"""
This function should be called for pipeline stages that perform feature
extraction so require taking a Dataset object as input.
This is an external-facing function that should always be called
(rather than _execute_function). This function will automatically check
if this stage has already been run with the same arguments and on the
same data. This can allow a much faster user experience avoiding
rerunning functions unnecessarily.
Parameters
----------
dataset : Dataset
The Dataset object on which to run this feature extraction
function, by default None
Returns
-------
pd.Dataframe
Output
"""
# *** WARNING: this has not been tested against adding new data and
# *** ensuring the function is called for new data only
dat = dataset.get_sample(dataset.index[0])
# Have to do a slight hack if the data is too high dimensional
if len(dat.shape) > 2:
dat = dat.ravel()
new_checksum = self.hash_data(dat)
if not self.args_same or new_checksum != self.checksum:
# If the arguments have changed we rerun everything
msg_string = self.function_call_signature + ' - checksum: ' + \
(str)(new_checksum)
logging_tools.log(msg_string)
else:
# Otherwise we only run instances not already in the output
msg = "Pipeline stage %s previously called " \
"with same arguments. Loading from file. Will only run " \
"for new samples. Use 'force_rerun=True' in init args " \
"to override this behavior." % self.class_name
logging_tools.log(msg, level='WARNING')
print('Extracting features using', self.class_name, '...')
t1 = time.time()
logged_nan_msg = False
nan_msg = "NaNs detected in some input images." \
"NaNs will be set to zero. You can change " \
"behaviour by setting drop_nan=False"
new_index = []
output = []
n = 0
for i in dataset.index:
if i not in self.previous_output.index or not self.args_same:
if n % 100 == 0:
print(n, 'instances completed')
input_instance = dataset.get_sample(i)
if self.drop_nans and np.any(np.isnan(input_instance)):
input_instance = np.nan_to_num(input_instance)
if not logged_nan_msg:
print(nan_msg)
logging_tools.log(nan_msg, level='WARNING')
logged_nan_msg = True
out = self._execute_function(input_instance)
if np.any(np.isnan(out)):
logging_tools.log("Feature extraction failed for id " + i)
output.append(out)
new_index.append(i)
n += 1
new_output = pd.DataFrame(data=output,
index=new_index,
columns=self.labels)
index_same = new_output.index.equals(self.previous_output.index)
if self.args_same and not index_same:
output = pd.concat((self.previous_output, new_output))
else:
output = new_output
if self.save_output:
self.save(output, self.output_file)
print('Done! Time taken: ', (time.time() - t1), 's')
return output
def __init__(self, *args, **kwargs):
"""
Base Dataset object that all other dataset objects should inherit from.
Whenever a child of this class is implemented, super().__init__()
should be called and explicitly passed all kwargs of the child class,
to ensure correct logging and saving of files.
Parameters
----------
filename : str
If a single file (of any time) is to be read from, the path can be
given using this kwarg.
directory : str
A directory can be given instead of an explicit list of files. The
child class will load all appropriate files in this directory.
list_of_files : list
Instead of the above, a list of files to be loaded can be
explicitly given.
output_dir : str
The directory to save the log file and all outputs to. Defaults to
'./'
"""
self.data_type = None
if 'filename' in kwargs:
filename = kwargs['filename']
else:
filename = ''
if 'directory' in kwargs:
directory = kwargs['directory']
else:
directory = ''
if 'list_of_files' in kwargs:
list_of_files = kwargs['list_of_files']
else:
list_of_files = []
if len(filename) != 0:
self.files = [filename]
elif len(list_of_files) != 0 and len(directory) == 0:
# Assume the list of files are absolute paths
self.files = list_of_files
elif len(list_of_files) != 0 and len(directory) != 0:
# Assume the list of files are relative paths to directory
fls = list_of_files
self.files = [os.path.join(directory, f) for f in fls]
elif len(directory) != 0:
# Assume directory contains all the files we need
fls = os.listdir(directory)
fls.sort()
self.files = [os.path.join(directory, f) for f in fls]
else:
self.files = []
# Handles automatic file reading and writing
if 'output_dir' in kwargs:
self.output_dir = kwargs['output_dir']
else:
self.output_dir = './'
# This allows the automatic logging every time this class is
# instantiated (i.e. every time this pipeline stage
# is run). That means any class that inherits from this base class
# will have automated logging.
logging_tools.setup_logger(log_directory=self.output_dir,
log_filename='astronomaly.log')
class_name = type(locals()['self']).__name__
function_call_signature = logging_tools.format_function_call(
class_name, *args, **kwargs)
logging_tools.log(function_call_signature)
def __init__(self,
fits_index=None,
window_size=128,
window_shift=None,
display_image_size=128,
band_prefixes=[],
bands_rgb={},
transform_function=None,
display_transform_function=None,
plot_square=False,
catalogue=None,
plot_cmap='hot',
**kwargs):
"""
Read in a set of images either from a directory or from a list of file
paths (absolute). Inherits from Dataset class.
Parameters
----------
filename : str
If a single file (of any time) is to be read from, the path can be
given using this kwarg.
directory : str
A directory can be given instead of an explicit list of files. The
child class will load all appropriate files in this directory.
list_of_files : list
Instead of the above, a list of files to be loaded can be
explicitly given.
output_dir : str
The directory to save the log file and all outputs to. Defaults to
'./'
fits_index : integer, optional
If these are fits files, specifies which HDU object in the list to
work with
window_size : int, tuple or list, optional
The size of the cutout in pixels. If an integer is provided, the
cutouts will be square. Otherwise a list of
[window_size_x, window_size_y] is expected.
window_shift : int, tuple or list, optional
The size of the window shift in pixels. If the shift is less than
the window size, a sliding window is used to create cutouts. This
can be particularly useful for (for example) creating a training
set for an autoencoder. If an integer is provided, the shift will
be the same in both directions. Otherwise a list of
[window_shift_x, window_shift_y] is expected.
display_image_size : The size of the image to be displayed on the
web page. If the image is smaller than this, it will be
interpolated up to the higher number of pixels. If larger, it will
be downsampled.
band_prefixes : list
Allows you to specify a prefix for an image which corresponds to a
band identifier. This has to be a prefix and the rest of the image
name must be identical in order for Astronomaly to detect these
images should be stacked together.
bands_rgb : Dictionary
Maps the input bands (in separate folders) to rgb values to allow
false colour image plotting. Note that here you can only select
three bands to plot although you can use as many bands as you like
in band_prefixes. The dictionary should have 'r', 'g' and 'b' as
keys with the band prefixes as values.
transform_function : function or list, optional
The transformation function or list of functions that will be
applied to each cutout. The function should take an input 2d array
(the cutout) and return an output 2d array. If a list is provided,
each function is applied in the order of the list.
catalogue : pandas.DataFrame or similar
A catalogue of the positions of sources around which cutouts will
be extracted. Note that a cutout of size "window_size" will be
extracted around these positions and must be the same for all
sources.
plot_square : bool, optional
If True this will add a white border indicating the boundaries of
the original cutout when the image is displayed in the webapp.
plot_cmap : str, optional
The colormap with which to plot the image
"""
super().__init__(fits_index=fits_index,
window_size=window_size,
window_shift=window_shift,
display_image_size=display_image_size,
band_prefixes=band_prefixes,
bands_rgb=bands_rgb,
transform_function=transform_function,
display_transform_function=display_transform_function,
plot_square=plot_square,
catalogue=catalogue,
plot_cmap=plot_cmap,
**kwargs)
self.known_file_types = [
'fits', 'fits.fz', 'fits.gz', 'FITS', 'FITS.fz', 'FITS.gz'
]
self.data_type = 'image'
images = {}
tracemalloc.start()
if len(band_prefixes) != 0:
# Get the matching images in different bands
bands_files = {}
for p in band_prefixes:
for f in self.files:
if p in f:
start_ind = f.find(p)
end_ind = start_ind + len(p)
flname = f[end_ind:]
if flname not in bands_files.keys():
bands_files[flname] = [f]
else:
bands_files[flname] += [f]
for k in bands_files.keys():
extension = k.split('.')[-1]
# print(k, extension)
if extension == 'fz' or extension == 'gz':
extension = '.'.join(k.split('.')[-2:])
if extension in self.known_file_types:
try:
astro_img = AstroImage(bands_files[k],
file_type=extension,
fits_index=fits_index,
name=k)
images[k] = astro_img
except Exception as e:
msg = "Cannot read image " + k + "\n \
Exception is: " + (str)(e)
logging_tools.log(msg, level="ERROR")
# Also convert the rgb dictionary into an index dictionary
# corresponding
if len(bands_rgb) == 0:
self.bands_rgb = {'r': 0, 'g': 1, 'b': 2}
else:
self.bands_rgb = {}
for k in bands_rgb.keys():
band = bands_rgb[k]
ind = band_prefixes.index(band)
self.bands_rgb[k] = ind
else:
for f in self.files:
extension = f.split('.')[-1]
if extension == 'fz' or extension == 'gz':
extension = '.'.join(f.split('.')[-2:])
if extension in self.known_file_types:
try:
astro_img = AstroImage([f],
file_type=extension,
fits_index=fits_index)
images[astro_img.name] = astro_img
except Exception as e:
msg = "Cannot read image " + f + "\n \
Exception is: " + (str)(e)
logging_tools.log(msg, level="ERROR")
if len(list(images.keys())) == 0:
msg = "No images found, Astronomaly cannot proceed."
logging_tools.log(msg, level="ERROR")
raise IOError(msg)
try:
self.window_size_x = window_size[0]
self.window_size_y = window_size[1]
except TypeError:
self.window_size_x = window_size
self.window_size_y = window_size
# Allows sliding windows
if window_shift is not None:
try:
self.window_shift_x = window_shift[0]
self.window_shift_y = window_shift[1]
except TypeError:
self.window_shift_x = window_shift
self.window_shift_y = window_shift
else:
self.window_shift_x = self.window_size_x
self.window_shift_y = self.window_size_y
self.images = images
self.transform_function = transform_function
if display_transform_function is None:
self.display_transform_function = transform_function
else:
self.display_transform_function = display_transform_function
self.plot_square = plot_square
self.plot_cmap = plot_cmap
self.catalogue = catalogue
self.display_image_size = display_image_size
self.band_prefixes = band_prefixes
self.metadata = pd.DataFrame(data=[])
if self.catalogue is None:
self.create_catalogue()
else:
self.convert_catalogue_to_metadata()
print('A catalogue of ', len(self.metadata),
'sources has been provided.')
if 'original_image' in self.metadata.columns:
for img in np.unique(self.metadata.original_image):
if img not in images.keys():
logging_tools.log('Image ' + img + """ found in catalogue
but not in provided image data. Removing from
catalogue.""",
level='WARNING')
msk = self.metadata.original_image == img
self.metadata.drop(self.metadata.index[msk], inplace=True)
print('Catalogue reduced to ', len(self.metadata),
'sources')
self.index = self.metadata.index.values
