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@jurjen93
jurjen93 committed Apr 4, 2021
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4 changes: 3 additions & 1 deletion .gitignore
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Expand Up @@ -21,4 +21,6 @@ __pycache__
#git
.git
#csv files
*.csv
*.csv
#files not for github
make_movie_highres.py
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -12,7 +12,7 @@ You need to clone this repo with:
```git clone https://github.com/jurjen93/advanced_astro_visualiziation.git```

### Catalogue csv file
You need to have a catalogue with sources. We have an example given in the folder 'catalogue'.\
You need to have a catalogue with sources for the poster (for the video it is optional). We have an example given in the folder 'catalogue'.\
Use the following fields:
* ```source_id``` -> id of the source
* ```RA``` -> right ascension of the object
Expand Down Expand Up @@ -41,7 +41,7 @@ Run:\
```python make_video.py```\
where you can use the following flags
* ```-d``` -> Choose to download a specific fits file from the internet. Use ```1``` if you want to, leave empty otherwise.
* ```-csv``` -> Give a specific csv file with sources to include as cutouts in the poster.
* ```-csv``` -> Give a specific csv file with sources to include as cutouts in the poster. If you leave it empty, it goes through the whole field.
* ```-N``` -> Number of sources to use
* ```-fr``` -> Frame rate of the video. Advice is to use ```60``` to make the video smooth.
* ```-fi``` -> Fits file to use. (If you don't download your fits file)
Expand Down
122 changes: 91 additions & 31 deletions make_movie.py
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Expand Up @@ -17,21 +17,23 @@
args = parser.parse_args()

def distance(obj_1, obj_2):
return sqrt((obj_1[0]-obj_2[0])**2+(obj_1[1]-obj_2[1])**2)
return sqrt((obj_1[0]-obj_2[0])**2+4*(obj_1[1]-obj_2[1])**2)

def isNaN(a):
return a!=a

if __name__ == '__main__':
start = timer()

if args.framerate: FRAMERATE = args.framerate
else: FRAMERATE = 64
else: FRAMERATE = 60

if args.sourcenum: N = args.sourcenum
else: N = 2

if args.csvfile: df = pd.read_csv(args.csvfile)[['RA', 'DEC']]
else: df = pd.read_csv('catalogue/'+os.listdir('catalogue')[0])[0:N]

if args.downloading == 1:
download = input('Paste here your url where to find the fits file: ')
fits_download = True
Movie = MovieMaker(fits_download=True,
imsize=0.4,#defaul imsize
framerate=FRAMERATE)
Expand All @@ -43,32 +45,90 @@ def distance(obj_1, obj_2):
file = 'fits/lockman_hole.fits'
Movie = MovieMaker(fits_file=get_pkg_data_filename(file),
imsize=0.4,#defaul imsize
framerate=FRAMERATE)
framerate=FRAMERATE, zoom_effect=False)

start_coord = Movie.wcs.pixel_to_world(Movie.image_data.shape[0]/2, Movie.image_data.shape[0]/2)
start_dec = start_coord.dec.degree
start_ra = start_coord.ra.degree
Movie.zoom_in(N_frames=1000, first_time=True)
for n in range(len(df)):#stack multiple sources
if n > 0:
dist = distance([last_RA, last_DEC], [df['RA'].values[n], df['DEC'].values[n]])
move_to_frames = int(300*dist)
else:
dist = distance([start_ra, start_dec], [df['RA'].values[n], df['DEC'].values[n]])
move_to_frames = int(300*dist)
print(f'Number of frames {move_to_frames}')
Movie.move_to(N_frames=move_to_frames, ra=df['RA'].values[n], dec=df['DEC'].values[n])
Movie.zoom_in(N_frames=300, imsize_out=df['imsize'].values[n])
if n<len(df)-1 and df['imsize'].values[n+1]>df['imsize'].values[n]:
im_out = max(df['imsize'].values[n+1]+0.1, 0.3)
else:
im_out = max(df['imsize'].values[n] + 0.1, 0.3)
Movie.zoom_out(N_frames=300, imsize_out=im_out)
last_RA, last_DEC = df['RA'].values[n], df['DEC'].values[n]
Movie.move_to(N_frames=int(600*distance([start_ra, start_dec], [df['RA'].values[N-1], df['DEC'].values[N-1]])), ra=start_ra, dec=start_dec)
Movie.zoom_out(N_frames=1000, imsize_out=2)
Movie.record()
if args.csvfile:#go through all objects in csv file
df = pd.read_csv(args.csvfile)[['RA', 'DEC']]

start_coord = Movie.wcs.pixel_to_world(Movie.image_data.shape[0]/2, Movie.image_data.shape[0]/2)
start_dec = start_coord.dec.degree
start_ra = start_coord.ra.degree

Movie.zoom_in(N_frames=800, first_time=True)
for n in range(len(df)):#stack multiple sources
if n > 0:
dist = distance([last_RA, last_DEC], [df['RA'].values[n], df['DEC'].values[n]])
move_to_frames = int(250*dist)
else:
dist = distance([start_ra, start_dec], [df['RA'].values[n], df['DEC'].values[n]])
move_to_frames = int(250*dist)
print(f'Number of frames {move_to_frames}')
Movie.move_to(N_frames=move_to_frames, ra=df['RA'].values[n], dec=df['DEC'].values[n])
Movie.zoom_in(N_frames=300, imsize_out=df['imsize'].values[n])
if n<len(df)-1 and df['imsize'].values[n+1]>df['imsize'].values[n]:
im_out = max(df['imsize'].values[n+1]+0.1, 0.3)
else:
im_out = max(df['imsize'].values[n] + 0.1, 0.3)
Movie.zoom_out(N_frames=300, imsize_out=im_out)
last_RA, last_DEC = df['RA'].values[n], df['DEC'].values[n]
print(f"Number of frames {int(400*distance([start_ra, start_dec], [df['RA'].values[N-1], df['DEC'].values[N-1]]))}")
Movie.move_to(N_frames=int(400*distance([start_ra, start_dec], [df['RA'].values[N-1], df['DEC'].values[N-1]])), ra=start_ra, dec=start_dec)
Movie.zoom_out(N_frames=800, imsize_out=2)
Movie.record()

end = timer()
print(f'MovieMaker took {int(end - start)} seconds')

else:#go through whole field
from numpy import sqrt, abs, isnan
fits_header = Movie.wcs.to_header()

number_of_steps = int(fits_header['CRPIX1']*2/3500)
if number_of_steps%2==0:
number_of_steps+=1 # make number of steps uneven to come back in the center

# clean_image = Movie.image_data[~isnan(Movie.image_data).all(axis=1),:]
# clean_image = clean_image[:,~isnan(clean_image).all(axis=0)]
pix_x_size = fits_header['CRPIX1']*2 #pixel x axis size
pix_y_size = fits_header['CRPIX2']*2 #pixel y axis size
# x_cut = pix_x_size-clean_image.shape[0] #how much cut x
# y_cut = pix_y_size-clean_image.shape[1] #how much cut y
step_size_x = int(pix_x_size/number_of_steps)
step_size_y = int(pix_y_size/number_of_steps)
start_pix_x = int((pix_x_size)/(number_of_steps*2))
start_pix_y = int(pix_y_size*((number_of_steps*2-1)/(number_of_steps*2)))

pos_x = start_pix_x
pos_y = start_pix_y
positions = [[start_pix_x, start_pix_y]]
for i in range(number_of_steps-1):
pos_x+=step_size_x
positions.append([pos_x, pos_y])

for i in range(1,number_of_steps)[::-1]:
for j in range(i):
pos_y = pos_y + ((-1)**(i+number_of_steps))*step_size_y
positions.append([pos_x, pos_y])
for j in range(i):
pos_x = pos_x + ((-1)**(i+number_of_steps))*step_size_x
positions.append([pos_x, pos_y])

end = timer()
print(f'MovieMaker took {int(end - start)} seconds')
positions = [(p.ra.degree, p.dec.degree) for p in [Movie.wcs.pixel_to_world(position[0], position[1])
for position in positions
if not isNaN(Movie.image_data[position[0], position[1]])]]

Movie.imsize = 2*abs(fits_header['CDELT1']*fits_header['CRPIX1']/7)
Movie.zoom_in(N_frames=600, first_time=True)
start_coord = Movie.wcs.pixel_to_world(Movie.image_data.shape[0] / 2, Movie.image_data.shape[0] / 2)
start_dec = start_coord.dec.degree
start_ra = start_coord.ra.degree
for n, position in enumerate(positions):
if n==0:
dist = distance([start_ra, start_dec], [position[0], position[1]])
else:
dist = distance([position[0], position[1]], [positions[n-1][0], positions[n-1][1]])
move_to_frames = int(200 * dist)
print(f'Number of frames {move_to_frames}')
Movie.move_to(N_frames=move_to_frames, ra=position[0], dec=position[1])
Movie.zoom_out(N_frames=600, imsize_out=3)
Movie.record()
29 changes: 16 additions & 13 deletions poster/scripts/imaging.py
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Expand Up @@ -15,7 +15,7 @@

class ImagingLofar:
def __init__(self, fits_file=None, fits_download: bool=False, vmin: float = None, vmax: float = None,
image_directory: str='poster/images', verbose=True):
image_directory: str='poster/images', verbose: bool = True, zoom_effect: bool = True):
"""
Make LOFAR images (also applicable on other telescope surveys)
------------------------------------------------------------
Expand All @@ -28,6 +28,7 @@ def __init__(self, fits_file=None, fits_download: bool=False, vmin: float = None
"""
self.fits_file = fits_file
self.verbose = verbose
self.zoom_effect = zoom_effect
if self.verbose:
print(f"Started imaging {fits_file.split('/')[-1].replace('.fits','').replace('_',' ').replace('.',' ').title()}...")
if fits_download:
Expand Down Expand Up @@ -62,8 +63,10 @@ def __init__(self, fits_file=None, fits_download: bool=False, vmin: float = None
if 'cutout' in self.fits_file:
self.image_data = gaussian_filter(self.tonemap(image_data=self.image_data, b=0.25, threshold=self.vmin), sigma=3)
else:
# self.image_data = gaussian_filter(self.tonemap(image_data=self.image_data, b=0.5, threshold=0), sigma=2)
self.image_data = gaussian_filter(self.tonemap(image_data=self.image_data, b=0.25, threshold=self.vmin/100), sigma=1)
if self.zoom_effect:
self.image_data = gaussian_filter(self.tonemap(image_data=self.image_data, b=0.5, threshold=0), sigma=2)
else:
self.image_data = gaussian_filter(self.tonemap(image_data=self.image_data, b=0.25, threshold=self.vmin / 100), sigma=1)

def tonemap(self, image_data=None, b: float = 0.25, threshold: float = None):
"""
Expand Down Expand Up @@ -118,17 +121,17 @@ def imaging(self, image_data=None, wcs=None, image_name: str = 'Nameless', dpi:
if 'cutout' in self.fits_file:
plt.imshow(image_data, origin='lower', cmap=cmap, vmin=self.vmin*2)
else:
plt.imshow(np.clip(image_data, a_min=None, a_max=self.vmax),
norm=LogNorm(vmin=self.vmin/1.4, vmax=self.vmax), origin='lower', cmap=cmap)
#HIGH RES VIDEO:
# vmax = self.vmax
# vmin = min((2/max(imsize,0.2))*(self.vmin/100), self.vmax/20)
# if imsize<1:
# vmax/=max(imsize,0.2)
# plt.imshow(image_data,
# norm=SymLogNorm(linthresh=vmin*20, vmin=self.vmin/1.4, vmax=vmax), origin='lower', cmap=cmap)
#OLD VIDEO:
# plt.imshow(image_data, norm=SymLogNorm(linthresh=self.vmin/20, vmin=self.vmin/50, vmax=self.vmax), origin='lower', cmap=cmap)
if self.zoom_effect:
vmax = self.vmax
vmin = min((2/max(imsize,0.2))*(self.vmin/100), self.vmax/20)
if imsize<1:
vmax/=max(imsize,0.2)
plt.imshow(image_data,
norm=SymLogNorm(linthresh=vmin*20, vmin=self.vmin/1.4, vmax=vmax), origin='lower', cmap=cmap)
else:
plt.imshow(np.clip(image_data, a_min=None, a_max=self.vmax),
norm=LogNorm(vmin=self.vmin / 1.4, vmax=self.vmax), origin='lower', cmap=cmap)
if text:
plt.annotate(
s=text,
Expand Down
18 changes: 11 additions & 7 deletions video/scripts/moviemaker.py
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Expand Up @@ -14,23 +14,27 @@ class MovieMaker(ImagingLofar):
MovieMaker makes it possible to make individual frames and turn them into a video.
"""
def __init__(self, fits_file: str = None, imsize: float = None, framerate: float = None, process: str = None,
fits_download: bool=False, new: bool = True, text: str = None):
fits_download: bool=False, new: bool = True, text: str = None, vmin: float = None, vmax: float = None, zoom_effect: bool = False,
output_file: str = 'video/frames'):
"""
:param fits_file: fits file name
:param imsize: initial image size
:param framerate: frame rate
:param process: process [multiprocess, multithread, None]
:param fits_download: download fits file
"""
super().__init__(fits_file = fits_file, image_directory='video/frames', verbose=False, fits_download = fits_download)
self.output_file = output_file
super().__init__(fits_file = fits_file, image_directory=self.output_file, verbose=False, fits_download=fits_download, vmin=vmin, vmax=vmax, zoom_effect=zoom_effect)
self.process = process
self.imsize = imsize
self.framerate = framerate
self.ra = None
self.dec = None
self.text = text
self.zoom_effect = zoom_effect
if new:
os.system('rm -rf video/frames; mkdir video/frames')
os.system(f'rm -rf {output_file}; mkdir {output_file}')


def __call__(self, imsize: float = None, process: str = None):
"""
Expand Down Expand Up @@ -86,10 +90,10 @@ def make_frames(self):
Record individual frames and save in video/frames/
------------------------------------------------------------
"""
N_max = len(os.listdir('video/frames'))+len(self.ragrid) #max number of videos
N_min = len(os.listdir('video/frames')) #min number of videos
N_max = len(os.listdir(self.output_file))+len(self.ragrid) #max number of videos
N_min = len(os.listdir(self.output_file)) #min number of videos
inputs = zip(range(N_min, N_max), self.ragrid, self.decgrid, self.imsizes,
np.clip(200/np.array(self.imsizes), a_min=250, a_max=600).astype(int))
np.clip(200/np.array(self.imsizes), a_min=450, a_max=700).astype(int))
if self.process == "multithread":
print(f"Multithreading")
print(f"Might get error or bad result because multithreading is difficult with imaging.")
Expand Down Expand Up @@ -177,7 +181,7 @@ def record(self, audio: str = None):
------------------------------------------------------------
:param audio: add audio (True or False).
"""
os.system(f'rm movie.mp4; ffmpeg -f image2 -r {self.framerate} -start_number 0 -i video/frames/image_%05d.png -vf "scale=960:540,setsar=1" movie.mp4')
os.system(f'rm movie.mp4; ffmpeg -f image2 -r {self.framerate} -start_number 0 -i {self.output_file}/image_%05d.png movie.mp4')
if audio:
try:
audio_file = input(audio)
Expand Down

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