def gen_thumbs(dirname, key='/*/*decon.tif', where='host', level=2, figsize=6,
redo=True, gamma=1.0, **kwargs):
'''
Main function to generate and save thumbnail pngs
'''
# load data
data = load_data(dirname, key)
if data:
# can clean the dirnames here
foldername = os.path.abspath(dirname).split(os.path.sep)[-level]
if where == 'host':
save_name = 'Thumbs ' + foldername + '.png'
elif where == 'in folder':
save_name = os.path.abspath(
os.path.join(dirname, 'Thumbs ' + foldername + '.png'))
else:
save_name = os.path.abspath(
os.path.join(where, 'Thumbs ' + foldername + '.png'))
if not redo and os.path.exists(save_name):
print(save_name, "already exists, skipping")
return dirname + os.path.sep + key
data = {clean_dirname(k, figsize): adjust_gamma(abs(v), gamma)
for k, v in data.items()}
fig, ax = display_grid(data, figsize=figsize, **kwargs)
# make the layout 'tight'
fig.tight_layout()
# save the figure
print('Saving', save_name, 'on', os.getpid(), '...')
fig.savefig(save_name, bbox_inches='tight')
print('finished saving', save_name)
# mark data for gc
del data
return dirname + os.path.sep + key
def plot_blob_grid(self, window=11, **kwargs):
"""Display a grid of blobs"""
return display_grid(
{
i: self.data[slice_maker((y, x), window)]
for i, (y, x, s, r) in enumerate(self.blobs)
}, **kwargs)
def plot_peaks(self):
'''
A utility function to plot the found peaks.
'''
peaks = self.peaks
FoM = self.FoM
g_mean_data = self.g_mean_data
nz, ny, nx = g_mean_data.shape
# plot the found peaks in the SNR trace
self._plot_peaks_lines()
data_dict = {'{}, Max SNR {:.3f}'.format(peak, FoM[peak]):
g_mean_data[0, peak, :]
for peak in peaks}
return display_grid(data_dict)
def plot_peaks(self):
'''
A utility function to plot the found peaks.
'''
peaks = self.peaks
FoM = self.FoM
g_mean_data = self.g_mean_data
nz, ny, nx = g_mean_data.shape
# plot the found peaks in the SNR trace
self._plot_peaks_lines()
data_dict = {
'{}, Max SNR {:.3f}'.format(peak, FoM[peak]): g_mean_data[0,
peak, :]
for peak in peaks
}
return display_grid(data_dict)
# test if filename has mrc in it
filename = arg['<myfile>']
name = os.path.basename(os.path.split(os.path.abspath(filename))[0])
data = Mrc.Mrc(filename).data
nphases = int(arg['<numphases>'])
ft_data_diff, ft_data_avg_abs, ft_data_avg = simcheck(data, nphases)
norients = data.shape[0]//nphases
orients = ['Orientation {}'.format(i) for i in range(norients)]
# Plot everything and save
fig1, ax1 = display_grid({k: v/v.max()
for k, v in zip(orients, ft_data_avg_abs)},
figsize=6, cmap='gnuplot2', norm=LogNorm())
filename1 = name + ' Average of Powers'
fig1.suptitle(filename1, fontsize=16)
fig2, ax2 = display_grid({k: abs(v/v.max())
for k, v in zip(orients, ft_data_avg)},
figsize=6, cmap='gnuplot2', norm=LogNorm())
filename2 = name + ' Power of Average'
fig2.suptitle(filename2, fontsize=16)
# fig3, ax3 = display_grid({k : v for k, v in zip(orients, ft_data_diff)}, figsize=6,
# cmap ='bwr', vmin = ft_data_diff.min(), vmax = ft_data_diff.max())
# filename3 = name + ' Difference of Averages'
# fig3.suptitle(filename3, fontsize=16)
