def example(self):
"""
This function ...
:return:
"""
# Read in the three images downloaded from here:
# g: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-g-001737-5-0039.fits.bz2
# r: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-r-001737-5-0039.fits.bz2
# i: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-i-001737-5-0039.fits.bz2
g = fits.open('frame-g-001737-5-0039.fits.bz2')[0]
r = fits.open('frame-r-001737-5-0039.fits.bz2')[0]
i = fits.open('frame-i-001737-5-0039.fits.bz2')[0]
# remap r and i onto g
r_new, r_mask = reproject_interp(r, g.header)
i_new, i_mask = reproject_interp(i, g.header)
# zero out the unmapped values
i_new[np.logical_not(i_mask)] = 0
r_new[np.logical_not(r_mask)] = 0
# red=i, green=r, blue=g
# make a file with the default scaling
rgb_default = make_lupton_rgb(i_new,
r_new,
g.data,
filename="ngc6976-default.jpeg")
# this scaling is very similar to the one used in Lupton et al. (2004)
rgb = make_lupton_rgb(i_new,
r_new,
g.data,
Q=10,
stretch=0.5,
filename="ngc6976.jpeg")
def make_example_rgbs(self):
"""
This function ...
:return:
"""
# Read in the three images downloaded from here:
# g: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-g-001737-5-0039.fits.bz2
# r: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-r-001737-5-0039.fits.bz2
# i: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-i-001737-5-0039.fits.bz2
g = fits.open('frame-g-001737-5-0039.fits.bz2')[0]
r = fits.open('frame-r-001737-5-0039.fits.bz2')[0]
i = fits.open('frame-i-001737-5-0039.fits.bz2')[0]
# remap r and i onto g
r_new, r_mask = reproject_interp(r, g.header)
i_new, i_mask = reproject_interp(i, g.header)
# zero out the unmapped values
i_new[np.logical_not(i_mask)] = 0
r_new[np.logical_not(r_mask)] = 0
# red=i, green=r, blue=g
# make a file with the default scaling
rgb_default = make_lupton_rgb(i_new, r_new, g.data, filename="ngc6976-default.jpeg")
# this scaling is very similar to the one used in Lupton et al. (2004)
rgb = make_lupton_rgb(i_new, r_new, g.data, Q=10, stretch=0.5, filename="ngc6976.jpeg")
def RGB_with_same_stretch():
red = input("Enter name of the red channel : ")
green = input("Enter name of the green channel : ")
blue = input("Ennter name of the blue channel : ")
#function calling to view stretched image and save them
print("~~~~~~~~~~AVAIABLE STRETCH~~~~~~~~~~\n")
print("\t1.LogStretch(default a=1000)")
#input of stretch choice
st_ch = int(
input("\n\nEnter the number whose stretch you want to apply : "))
if st_ch == 1:
#red file
red = stretch.log(red)
#green file
green = stretch.log(green)
#blue file
blue = stretch.log(blue)
#RGB image using make_lupton_RGB
RGB_image = viz.make_lupton_rgb(red, green, blue, Q=10, stretch=0.5)
plt.imshow(RGB_image)
plt.show()
def view_image_rgb(images, Q=2.0, stretch=4.0, **imshow_kwargs):
"""
Merge images into a single RGB image. This function assumes the image array
is ordered [g, r, i].
Args:
images (List[np.array]): a list of at least 3 2-dimensional arrays of pixel values corresponding to different photometric bandpasses
imshow_kwargs (dict): dictionary of keyword arguments and their values to pass to matplotlib.pyplot.imshow
"""
assert len(images) > 2, "3 images are needed to generate an RGB image"
rgb = make_lupton_rgb(images[2],
images[1],
images[0],
Q=Q,
stretch=stretch)
plt.figure()
plt.imshow(rgb, **imshow_kwargs)
plt.xticks([], [])
plt.yticks([], [])
plt.show(block=True)
plt.close()
return
def plot_RGB(img):
import numpy as np
from astropy.io import fits
from astropy.visualization import SqrtStretch, LogStretch
from astropy.visualization import LinearStretch, AsinhStretch
from astropy.visualization import make_lupton_rgb
forCasting = np.float_()
g = img[0]
r = img[1]
i = img[2]
max_size = np.max([g.shape[0], r.shape[0], i.shape[0]])
image_b = fix_size(g, max_size)
image_g = fix_size(r, max_size)
image_r = fix_size(i, max_size)
norm = np.nanpercentile(image_b, 99)
image_r /= norm
image_g /= norm
image_b /= norm
image = make_lupton_rgb(image_r,
image_g,
image_b,
Q=8,
stretch=0.5,
minimum=image_b.min())
# Cut the top rows - contains black pixels
return image
def master_color(R_hdul, G_hdul, B_hdul, dtype=np.float32, saveto=None,
**kwargs):
r"""
Generate an RGB image based on three science frames (preferable R, V, B).
This use `astropy.visualization.make_lupton_rgb`.
Parameters
----------
R_hdul : astropy.io.fits.HDUList
Used for red channel.
G_hdul : astropy.io.fits.HDUList
Used for green channel (normally use V-filter).
B_hdul : astropy.io.fits.HDUList
Used for blue channel.
dtype : data-type, optional
Type to use for computing, defaults to np.float32.
saveto : str, optional
If this is not set (None, default) files won't be saved.
If this is set to a string, save the file with the string as name.
The format is determined by the file extension.
Files are ALWAYS OVERWRITTEN!
For other parameters see astropy.visualization.make_lupton_rgb.
Returns
-------
data : numpy.ndarray
"""
data = np.array(
[R_hdul[0].data.astype(dtype),
G_hdul[0].data.astype(dtype),
B_hdul[0].data.astype(dtype)],
dtype
)
return make_lupton_rgb(*data, filename=saveto, **kwargs)
def process_image(self, x):
"""Process data."""
if self.augment: # flip and transpose
# this is not correct now, labels change too!!!
x = aug_im(x,
self.rng.rand() > 0.5,
self.rng.rand() > 0.5,
self.rng.rand() > 0.5)
if self.luptonize:
rgb_q = 15
rgb_stretch = 0.5
rgb_min = 0
x = make_lupton_rgb(x[:, :, 2],
x[:, :, 1],
x[:, :, 0],
Q=rgb_q,
stretch=rgb_stretch,
minimum=rgb_min)
#x = make_lupton_rgb(x[:,:,2], x[:,:,2], x[:,:,2],
# Q=rgb_q, stretch=rgb_stretch, minimum=rgb_min)
x = np.array(x)
x = np.array([xi / 255. for xi in x])
if self.smooth:
#x = np.array([gaussian_filter(xi, sigma=1) for xi in x])
x = cv2.blur(x, (5, 5))
if self.normalize:
x = np.arcsinh(x)
x = (x - np.min(x)) / np.ptp(x)
#print(x.shape)
x = x.transpose(2, 0, 1)
#print(x.shape)
x = x.reshape(self.x_shape)
return x
def make_rgb_image(self, stretch=0.4, Q=8):
rgb_image = make_lupton_rgb(self.rgb_data.red,
self.rgb_data.green,
self.rgb_data.blue,
stretch=stretch,
Q=Q)
return rgb_image
def make_rgb(self, rgb_bands='irg', stretch=0.4, Q=8):
from astropy.visualization import make_lupton_rgb
rgb = make_lupton_rgb(self[rgb_bands[0]].getImage().getArray(),
self[rgb_bands[1]].getImage().getArray(),
self[rgb_bands[2]].getImage().getArray(),
stretch=stretch, Q=Q)
return rgb
def draw_snapshot_rgb(s, num, ax, minimum=20.0, stretch=15000, Q=15):
ds = s.load_vtk(num)
dd = ds.get_field(['nH2', 'nHI', 'nH', 'j_X', 'nesq'])
dd['NH_neu'] = (2.0 * dd['nH2'].sum(dim='z') +
2.0 * dd['nHI'].sum(dim='z')) * dd.domain['dx'][2]
dd['I_X'] = dd['j_X'].sum(
dim='z') * dd.domain['dx'][2] * s.u.length.cgs.value
dd['EM'] = dd['nesq'].sum(dim='z') * dd.domain['dx'][2]
# Make r and g to have the same maximum
#norm_b = dd['NH_neu'].data.max()/dd['I_X'].data.max()
#norm_g = dd['NH_neu'].data.max()/dd['EM'].data.max()
#norm_b = 1.0
#norm_g = 1.0
norm_b = 1625343998.93
norm_g = 0.04300
r = dd['NH_neu'].data
b = dd['I_X'].data * norm_b
g = dd['EM'].data * norm_g
#print(r.max(),g.max(),b.max(),r.min(),g.min(),b.min())
#print(norm_b,norm_g)
image = make_lupton_rgb(r, g, b, minimum=minimum, stretch=stretch, Q=Q)
ax.imshow(image, interpolation='bicubic', origin='lower')
ax.set_xticks([])
ax.set_yticks([])
ax.set_xticklabels('')
ax.set_yticklabels('')
return ax, dd, image
def get_images(self, **kwargs):
""" main method: get cutout images for the given options
return a list of (dataid, image). If no images found, return an empty list
"""
if 'ra' in kwargs and 'dec' in kwargs:
self.coord = kwargs['ra'], kwargs['dec']
if 'visit_level' in kwargs:
self.visit_level = kwargs['visit_level']
if 'filter' in kwargs:
self.filter = kwargs['filter']
if 'size' in kwargs:
self.size = kwargs['size']
if 'image_size' in kwargs:
self.image_size = kwargs['image_size']
if 'pixel_scale' in kwargs:
self.pixel_scale = kwargs['pixel_scale']
if len(self.filter) == 3:
results = list(self._iter_dataid_raw_images(limit=3))
if len(results) < 3 or all(image is None for _, image in results):
return []
zero = np.zeros((self.side_pixel, self.side_pixel))
images = [zero if image is None else image for _, image in results]
filters = ''.join(('' if image is None else dataid['filter']
for dataid, image in results))
dataid = dict(results[0][0], filter=filters)
return [(dataid,
self.image_to_png_data(make_lupton_rgb(*images[::-1],
stretch=3,
Q=8),
composite=True))]
return [(dataid, self.image_to_png_data(image))
for dataid, image in self._iter_dataid_raw_images(limit=10)
if image is not None]
def make_rgb(self, rgb_bands='irg', stretch=0.4, Q=8):
from astropy.visualization import make_lupton_rgb
rgb = make_lupton_rgb(self[rgb_bands[0]].getImage().getArray(),
self[rgb_bands[1]].getImage().getArray(),
self[rgb_bands[2]].getImage().getArray(),
stretch=stretch,
Q=Q)
return rgb
def make_rgb(self, rgb_bands='irg', stretch=0.8, Q=8):
rgb = make_lupton_rgb(self.image[rgb_bands[0]],
self.image[rgb_bands[1]],
self.image[rgb_bands[2]],
stretch=stretch,
Q=Q)
return rgb
def plot_batch(self, index=0, filename=None):
# FIXME : Currently hardcoded for a batchsize of 128
if self.batch_size != 128:
warnings.warn('This method is hard coded for batchsize of 128 for now')
if not has_astropy():
warnings.warn('Plotting galaxies requires the astropy package')
return
else:
from astropy.visualization import make_lupton_rgb
(images, ebvs), z_truths = self._get_batch_at(index,
is_categorical=True)
cols = 10
rows = math.ceil(self.batch_size / cols)
fig, axes = plt.subplots(rows, cols,
figsize=(rows, cols))
fig.suptitle(f'batch {index} from the dataset')
for row_count in range(rows):
for col_count in range(cols):
axes[row_count][col_count].tick_params(
axis='x',
which='both',
bottom=False,
top=False,
labelbottom=False
)
axes[row_count][col_count].tick_params(
axis='y',
which='both',
left=False,
right=False,
labelleft=False
)
row_count, col_count = 0, 0
plt.subplots_adjust(hspace=0.8, wspace=0.2)
for i, (image, ebv, z_truth) in enumerate(zip(images, ebvs, z_truths)):
im = make_lupton_rgb(image[:, :, 3],
image[:, :, 2],
image[:, :, 1],
Q=10, stretch=0.5)
axes[row_count, col_count].imshow(im)
axes[row_count, col_count].set_xlabel(f'z = {str(round(z_truth, 6))} \n'
f'ebv = {ebv}',
fontsize=6)
col_count += 1
if col_count == cols:
row_count += 1
col_count = 0
for j in range(col_count, cols):
axes[row_count][j].axis('off')
if filename is None:
filename = f'batch_{index}.png'
plt.savefig(filename, bbox_inches='tight')
def draw_velocity_map(city):
image_r = pickle.load(
open('velocity_arrays/image_r_array_{}.p'.format(city), 'rb'))
image_g = pickle.load(
open('velocity_arrays/image_g_array_{}.p'.format(city), 'rb'))
image_b = pickle.load(
open('velocity_arrays/image_b_array_{}.p'.format(city), 'rb'))
image = make_lupton_rgb(image_r, image_g, image_b, stretch=0.5)
plt.imsave('velocity_maps/{}_velocity_map.png'.format(city), image)
def plot_lupton(img):
g = img[:, :, 1:2]
r = img[:, :, 2:3]
i = img[:, :, 3:4]
rgb = make_lupton_rgb(i, r, g, Q=10, stretch=0.5)
plt.axis('off')
plt.imshow(rgb)
def save_images(X, save_path, luptonize=False, unnormalize=False):
# [0, 1] -> [0,255]
if luptonize:
unnormalize = False
print(X.ndim)
print(X.shape)
print(np.max(X.flatten()), np.min(X.flatten()))
#if isinstance(X.flatten()[0], np.floating):
# X = (255.99*X).astype('uint8')
n_samples = X.shape[0]
rows = int(np.sqrt(n_samples))
while n_samples % rows != 0:
rows -= 1
nh, nw = rows, n_samples / rows
if X.ndim == 2:
X = np.reshape(
X,
(X.shape[0], int(np.sqrt(X.shape[1])), int(np.sqrt(X.shape[1]))))
if X.ndim == 4:
# BCHW -> BHWC
#X = X.transpose(0,2,3,1)
#print("transpose")
#print(X.shape)
if unnormalize:
X = (255. * X).astype('uint8')
h, w = X[0].shape[:2]
img = np.zeros((int(h * nh), int(w * nw), 3))
#X = X.transpose(0,2,3,1)
elif X.ndim == 3:
h, w = X[0].shape[:2]
img = np.zeros((int(h * nh), int(w * nw)))
rgb_q = 15
rgb_stretch = 0.5
rgb_min = 0
for n, x in enumerate(X):
j = n // nw
i = n % nw
if luptonize:
x = make_lupton_rgb(x[:, :, 2],
x[:, :, 1],
x[:, :, 0],
Q=rgb_q,
stretch=rgb_stretch,
minimum=rgb_min)
#x = np.roll(x, 1, axis=2)
if n == 0:
print(x.shape)
print(x[40:-40, 40:-40])
#x = np.roll(x, 1, axis=2)
img[int(j * h):int(j * h + h), int(i * w):int(i * w + w)] = x
imwrite(save_path, img)
def RGB():
Data = fits.getdata(input('input fits file:'))
B = Data[0, :, :]
G = Data[1, :, :]
R = Data[2, :, :]
image = make_lupton_rgb(R, G, B, stretch=0.01)
mean = np.mean(image)
std = np.std(image)
plt.imshow(image) #,vmin = mean-std , vmax = mean+3*std)
plt.show()
def plot_field_rgb(filepath):
fits_im = fits.open(filepath.format('R'))
data_r = fits_im[1].data
fits_im = fits.open(filepath.format('G'))
data_g = fits_im[1].data
fits_im = fits.open(filepath.format('U'))
data_u = fits_im[1].data
im = make_lupton_rgb(data_r, data_g, data_u, stretch=1)
plt.imshow(im, interpolation='nearest')
plt.axis('off')
plt.show()
def show_all_thumbnails(label='j022708p4901_00273', filters=['f775w', 'f814w', 'f098m', 'f105w', 'f110w', 'f125w', 'f140w', 'f160w'], scale_ab=21, close=True):
"""
Show individual filter and RGB thumbnails
"""
from astropy.visualization import make_lupton_rgb
import matplotlib.pyplot as plt
#from PIL import Image
ims = {}
for filter in filters:
drz_files = glob.glob('{0}-{1}*_dr*sci.fits'.format(label, filter))
if len(drz_files) > 0:
im = pyfits.open(drz_files[0])
ims[filter] = im
slx, sly, filts, fig = auto_script.field_rgb(root=label, xsize=4, output_dpi=None, HOME_PATH=None, show_ir=False, pl=1, pf=1, scl=1, rgb_scl=[1, 1, 1], ds9=None, force_ir=False, filters=ims.keys(), add_labels=False, output_format='png', rgb_min=-0.01, xyslice=None, pure_sort=False, verbose=True, force_rgb=None, suffix='.rgb', scale_ab=scale_ab)
if close:
plt.close()
#rgb = np.array(Image.open('{0}.rgb.png'.format(label)))
rgb = plt.imread('{0}.rgb.png'.format(label))
NX = (len(filters)+1)
fig = plt.figure(figsize=[1.5*NX, 1.5])
ax = fig.add_subplot(1, NX, NX)
ax.imshow(rgb, origin='upper', interpolation='nearest')
ax.text(0.5, 0.95, label, ha='center', va='top', transform=ax.transAxes, fontsize=7, bbox=dict(facecolor='w', edgecolor='None', alpha=0.5))
for i, filter in enumerate(filters):
if filter in ims:
zp_i = utils.calc_header_zeropoint(ims[filter], ext=0)
scl = 10**(-0.4*(zp_i-5-scale_ab))
img = ims[filter][0].data*scl
image = make_lupton_rgb(img, img, img, stretch=0.1, minimum=-0.01)
ax = fig.add_subplot(1, NX, i+1)
ax.imshow(255-image, origin='lower', interpolation='nearest')
ax.text(0.5, 0.95, filter, ha='center', va='top', transform=ax.transAxes, fontsize=7, bbox=dict(facecolor='w', edgecolor='None', alpha=0.5))
for ax in fig.axes:
ax.set_xticklabels([])
ax.set_yticklabels([])
ax.set_xticks([])
ax.set_yticks([])
fig.tight_layout(pad=0.1)
fig.savefig('{0}.thumb.png'.format(label))
if close:
plt.close()
def df_color_image(img_r,
img_g,
b=1.0,
vmin=0.0,
Q=10,
stretch=25,
filename=None,
quiet=False):
'''
Display tri-color image of Dragonfly based on ``g`` and ``r`` band images.
The red channel uses ``img_r``, blue channel uses ``b * img_g``,
and we make up the green channel to be ``(img_r + b * img_g) * 0.5``.
Parameters:
img_r (numpy 2-D array): image of r-band. Must have subtracted background.
img_g (numpy 2-D array): image of g-band. Must have subtracted background.
b (float): the proportion of ``img_g`` in blue channel, default is 1.0.
vmin (float): the minimum value shown in tri-color image.
Q (float): The asinh softening parameter. Smaller Q means higher contrast.
stretch (float): The linear stretch of the image. Smaller value gives more low-SB details.
save (bool): whether save the RGB image.
filename (str): Write the resulting RGB image to a file (file type determined from extension).
quiet (bool): whether showing the RGB image.
Returns:
None
'''
from astropy.visualization import make_lupton_rgb
import matplotlib.pyplot as plt
import numpy as np
red = img_r.copy()
blue = img_g.copy()
blue *= b
green = (red + blue) * 0.5
rgb = make_lupton_rgb(red,
green,
blue,
Q=Q,
stretch=stretch,
minimum=vmin,
filename=filename)
if not quiet:
fig = plt.figure(figsize=(13, 13))
plt.imshow(rgb, origin='lower')
plt.axis('off')
plt.show()
if filename is not None:
print('# RGB image has been save at {}'.format(filename))
return rgb
def mergeButton(self, evt):
global r_name
global g_name
global b_name
r0 = fits.open(r_name)[0].data - 255
g0 = fits.open(g_name)[0].data - 255
b0 = fits.open(b_name)[0].data - 255
r=r0.astype(float)
g=g0.astype(float)
b=b0.astype(float)
rgb = make_lupton_rgb(r, g, b, Q=10, stretch=0.1, filename=img_name)
def get_img_paths(nameG, nameR, nameI, stretch):
image_fileG = f'{nameG}'
image_dataG = fits.getdata(image_fileG, ext=0)
image_fileR = f'{nameR}'
image_dataR = fits.getdata(image_fileR, ext=0)
image_fileI = f'{nameI}'
image_dataI = fits.getdata(image_fileI, ext=0)
image = make_lupton_rgb(image_dataI,
image_dataR,
image_dataG,
stretch=stretch,
Q=5)
return image
def show_all_thumbnails(label='j022708p4901_00273', filters=['f775w','f814w','f098m','f105w','f110w','f125w','f140w','f160w'], scale_ab=21, close=True):
"""
Show individual filter and RGB thumbnails
"""
from astropy.visualization import make_lupton_rgb
from PIL import Image
ims = {}
for filter in filters:
drz_files = glob.glob('{0}-{1}*_dr*sci.fits'.format(label, filter))
if len(drz_files) > 0:
im = pyfits.open(drz_files[0])
ims[filter] = im
slx, sly, filts, fig = auto_script.field_rgb(root=label, xsize=4, output_dpi=None, HOME_PATH=None, show_ir=False, pl=1, pf=1, scl=1, rgb_scl=[1, 1, 1], ds9=None, force_ir=False, filters=ims.keys(), add_labels=False, output_format='png', rgb_min=-0.01, xyslice=None, pure_sort=False, verbose=True, force_rgb=None, suffix='.rgb', scale_ab=scale_ab)
if close:
plt.close()
rgb = np.array(Image.open('{0}.rgb.png'.format(label)))
NX = (len(filters)+1)
fig = plt.figure(figsize=[1.5*NX,1.5])
ax = fig.add_subplot(1,NX,NX)
ax.imshow(rgb, origin='upper', interpolation='nearest')
ax.text(0.5, 0.95, label, ha='center', va='top', transform=ax.transAxes, fontsize=7, bbox=dict(facecolor='w', edgecolor='None', alpha=0.5))
for i, filter in enumerate(filters):
if filter in ims:
zp_i = utils.calc_header_zeropoint(ims[filter], ext=0)
scl = 10**(-0.4*(zp_i-5-scale_ab))
img = ims[filter][0].data*scl
image = make_lupton_rgb(img, img, img, stretch=0.1, minimum=-0.01)
ax = fig.add_subplot(1,NX,i+1)
ax.imshow(255-image, origin='lower', interpolation='nearest')
ax.text(0.5, 0.95, filter, ha='center', va='top', transform=ax.transAxes, fontsize=7, bbox=dict(facecolor='w', edgecolor='None', alpha=0.5))
for ax in fig.axes:
ax.set_xticklabels([])
ax.set_yticklabels([])
ax.set_xticks([])
ax.set_yticks([])
fig.tight_layout(pad=0.1)
fig.savefig('{0}.thumb.png'.format(label))
if close:
plt.close()
def luptonize(x):
rgb_q = 15
rgb_stretch = 0.5
rgb_min = 0
if x.ndim == 3:
x = make_lupton_rgb(x[:, :, 2],
x[:, :, 1],
x[:, :, 0],
Q=rgb_q,
stretch=rgb_stretch,
minimum=rgb_min)
elif x.ndim == 4:
x = np.array([
make_lupton_rgb(xi[:, :, 2],
xi[:, :, 1],
xi[:, :, 0],
Q=rgb_q,
stretch=rgb_stretch,
minimum=rgb_min) for xi in x
])
else:
raise ValueError(
f"Wrong number of dimensions! Gave {x.ndim}, need 3 or 4")
return x
def mergeButton(self, evt):
global r_name
global g_name
global b_name
r0 = fits.open(r_name)[0].data - 255
g0 = fits.open(g_name)[0].data - 255
b0 = fits.open(b_name)[0].data - 255
r = r0.astype(float)
g = g0.astype(float)
b = b0.astype(float)
rgb = make_lupton_rgb(r, g, b, Q=10, stretch=0.1, filename=img_name)
plt.imshow(rgb, origin='lower')
plt.waitforbuttonpress()
def make_rgb(self, kind, rgb_bands='irg', stretch=0.8, Q=8):
if not hasattr(self, kind):
logger.error(f'image of kind {kind} not found')
rgb = None
elif getattr(self, kind) is None:
logger.error(f'image of kind {kind} not found')
rgb = None
else:
image = getattr(self, kind)
rgb = make_lupton_rgb(image[rgb_bands[0]],
image[rgb_bands[1]],
image[rgb_bands[2]],
stretch=stretch,
Q=Q)
return rgb
def plot_image(self, idx):
image = images[idx]
new_image = np.empty((3, 45, 45))
new_image[0], new_image[1], new_image[2] = self.normalize_image(image)
new_image = new_image.transpose(1, 2, 0)
new_image = Image.fromarray(np.uint8(255 * new_image)).convert("RGB")
#new_image = Image.fromarray(np.uint16(255*new_image)).convert("RGB")
plt.figure(figsize=(12, 4))
plt.subplot(1, 2, 1)
plt.imshow(np.asarray(new_image))
plt.axis('off')
plt.subplot(1, 2, 2)
rgb = make_lupton_rgb(image[2], image[1], image[0], Q=11., stretch=40.)
plt.imshow(rgb, aspect='equal')
plt.axis('off')
plt.show()
def plt_RGB(filename, fieldnames_list, rad_or_ref, plot=True):
'''
INPUT
filename: - string , filepath to file
fieldnames_list: - string list, contains 500m res and 250m reshape
such that bands 1,4,3 for RGB
i.e. 'EV_500_Aggr1km_RefSB'
RETURN
plots RGB picture of MODIS 02 product data
'''
#make channels for RGB photo (index 01234 -> band 34567)
image_blue = prepare_data(filename, fieldnames_list[0],
rad_or_ref)[0, :, :] #band 3 from 500 meter res
image_green = prepare_data(filename, fieldnames_list[0],
rad_or_ref)[1, :, :] #band 4 from 500 meter res
image_red = prepare_data(filename, fieldnames_list[1],
rad_or_ref)[0, :, :] #band 1 from 250 meter res
#force reflectance values to max out at 1.0/ normalize radiance
if not rad_or_ref:
np.place(image_red, image_red > 1.0,
1.0) #2d image array, condition, value
np.place(image_blue, image_blue > 1.0, 1.0)
np.place(image_green, image_green > 1.0, 1.0)
image_RGB = np.dstack([image_red, image_green, image_blue])
else:
#use astropy to normalize radiance values to usable pixel brightness
from astropy.visualization import make_lupton_rgb
image_RGB = make_lupton_rgb(image_red,
image_green,
image_blue,
stretch=0.5)
#plot or return image
if plot:
plt.imshow(image_RGB)
plt.show()
else:
return image_RGB
def get_img(name, stretch):
PATH_G = "/Users/schwarzam/Documents/cutouts"
PATH_R = "/Users/schwarzam/Documents/cutouts"
PATH_I = "/Users/schwarzam/Documents/cutouts"
print(PATH_G)
image_fileG = f'{PATH_G}/{name}_G.fits'
image_dataG = fits.getdata(image_fileG, ext=0)
image_fileR = f'{PATH_R}/{name}_R.fits'
image_dataR = fits.getdata(image_fileR, ext=0)
image_fileI = f'{PATH_I}/{name}_I.fits'
image_dataI = fits.getdata(image_fileI, ext=0)
image = make_lupton_rgb(image_dataI,
image_dataR,
image_dataG,
stretch=stretch,
Q=5)
return image
def make_rgb_image(self,
ra=None,
dec=None,
width=2.0,
height=None,
band='irg',
stretch=5,
Q=8,
images=None):
"""
Make RGB image.
Parameters
----------
ra, dec : float
in degrees
width, height : float
in arcseconds
band : string of characters
HSC band names for in RGB order
stretch : float
Linear stretch of HSC RGB image
Q : float
The asinh softening parameter for HSC RGB image
images : ndarray
If not None, will make rgb image using these images
Returns
-------
rgb : ndarry
The RGB image
"""
if images is None:
images = self.fetch_hsc_cutout(ra, dec, width, height, band)
rgb = make_lupton_rgb(images[:, :, 0],
images[:, :, 1],
images[:, :, 2],
stretch=stretch,
Q=Q)
return rgb
def make_fir_maps(self):
"""
This function ...
:return:
"""
# Inform the user
log.info("Making RGB maps based on FIR images ...")
# Set method name
method_name = "TIR"
# The RGB maps
maps = dict()
origins = dict()
# Loop over the names
for name in self.available_fir_rgb_names:
# Get the filters
fltr_a, fltr_b, fltr_c = get_filters(name, "-")
# Load and uniformize to same resolution and unit of Jansky
a, b, c = self.get_frames_for_filters(fltr_a, fltr_b, fltr_c, uniformize=True, unit="Jy")
# Make the map
rgb = make_lupton_rgb(a, b, c, Q=self.config.fir_softening, stretch=self.config.optical_stretch)
rgb_image = Image.from_3d_array(rgb, name=name, wcs=a.wcs, names=["r", "g", "b"])
# Add the map
maps[name] = rgb_image
origins[name] = [fltr_a, fltr_b, fltr_c]
# Set the maps
self.maps[method_name] = maps
# Set the origins
self.origins[method_name] = origins
def plot_target_color(ra,dec,filepaths,name,image_size=10):
from astropy.visualization import make_lupton_rgb
#image_size = 10 # "
cutout_b = cutout_image(filepaths["g"],ra,dec,image_size)
cutout_g = cutout_image(filepaths["r"],ra,dec,image_size)
cutout_r = cutout_image(filepaths["i"],ra,dec,image_size)
fig = plt.figure()
ax = fig.add_subplot(111)
rgb = make_lupton_rgb(cutout_r.data, cutout_g.data, cutout_b.data,stretch=10)
plt.imshow(rgb, origin='lower')
add_compass(ax,color='white')
add_scale_bar(ax,1,image_size)
ax.set_yticklabels([])
ax.set_xticklabels([])
plt.xticks([])
plt.yticks([])
plt.title(name+" (DES color image)")
plt.savefig("coadd_color.png",bbox_inches='tight',dpi=100)
plt.close()
def plot_rgb(filename):
arr = np.load(filename)
obj_id = filename.split('/')[-1].replace('.npy', '')
field = obj_id.split('.')[1]
print(obj_id)
im = cv2.imread('../raw-data/train_images/{}.trilogy.png'.format(field))
cat = pd.read_csv('sloan_splus_matches.csv')
obj = cat[cat['id'] == obj_id].iloc[0]
x = obj['x'] #1341
y = 11000 - obj['y'] #11000-3955
d = 10
print(x, y)
obj = im[y - d:y + d, x - d:x + d]
ax1 = plt.subplot(121)
ax1.axis('off')
ax1.imshow(obj)
im_lupton = make_lupton_rgb(arr[:, :, 7],
arr[:, :, 5],
arr[:, :, 0],
stretch=1) #rgu
ax2 = plt.subplot(122)
ax2.imshow(im_lupton, interpolation='nearest', cmap=plt.cm.gray_r)
ax2.axis('off')
plt.show()
result = Observations.query_object('M83')
selected_bands = result[(result['obs_collection'] == 'HST') &
(result['instrument_name'] == 'WFC3/UVIS') &
((result['filters'] == 'F657N') |
(result['filters'] == 'F487N') |
(result['filters'] == 'F336W')) &
(result['target_name'] == 'MESSIER-083')]
prodlist = Observations.get_product_list(selected_bands)
filtered_prodlist = Observations.filter_products(prodlist)
downloaded = Observations.download_products(filtered_prodlist)
blue = fits.open(downloaded['Local Path'][2])
red = fits.open(downloaded['Local Path'][5])
green = fits.open(downloaded['Local Path'][8])
target_header = red['SCI'].header
green_repr, _ = reproject.reproject_interp(green['SCI'], target_header)
blue_repr, _ = reproject.reproject_interp(blue['SCI'], target_header)
rgb_img = make_lupton_rgb(ImageNormalize(vmin=0, vmax=1)(red['SCI'].data),
ImageNormalize(vmin=0, vmax=0.3)(green_repr),
ImageNormalize(vmin=0, vmax=1)(blue_repr),
stretch=0.1,
minimum=0,
)
plt.imshow(rgb_img, origin='lower', interpolation='none')