def main():
print('\n')
print('###############################################')
print('###############################################')
print('#### ####')
print('#### RUN ANALYSIS OF THE RECONSTRUCTIONS ####')
print('#### ####')
print('###############################################')
print('###############################################')
print('\n')
## Get input arguments
args = getArgs()
## Get input path
pathin = args.pathin
if pathin.find(':') == -1:
sys.exit('\nERROR: path to input reconstructions with odd indeces' +
' must be separated with a ":" from the reconstructions with' +
' even indeces')
else:
pathin = pathin.split(':')
if pathin[0][len(pathin[0])-1] != '/':
pathin[0] += '/'
if pathin[1][len(pathin[1])-1] != '/':
pathin[1] += '/'
print('\nInput paths:\n', pathin[0],'\n', pathin[1])
## Get reconstruction files
label = args.label
curr_dir = os.getcwd()
os.chdir( pathin[0] )
rec_list1 = sorted( glob.glob( '*' + label + '*' ) )
num_files1 = len( rec_list1 )
os.chdir( curr_dir )
os.chdir( pathin[1] )
rec_list2 = sorted( glob.glob( '*' + label + '*' ) )
num_files2 = len( rec_list2 )
os.chdir( curr_dir )
if num_files1 != num_files2:
sys.exit('\nERROR: number of files in path1 = ' + str( num_files1 )
+ ' differ from number of files in path2 = ' + str( num_files2 ) )
else:
num_files = num_files1
print('\nNumber of input files in both paths: ', num_files)
## Organize input files
plot_axes = args.plot_axes
axes = []
file_label = []
if plot_axes.find(',') == -1:
flag_plot3d = 0
plot_axes_aux = plot_axes_aux.split(':')
file_label.append( plot_axes_aux[0] )
for j in range( 1 , len( plot_axes_aux ) ):
axes.append( plot_axes_aux[j] )
print('\nPlot 2D selected using file label: ', file_label)
print('Axis x values: ', axes )
else:
plot_axes = plot_axes.split(',')
flag_plt3d = 1
for i in range( len( plot_axes ) ):
plot_axes_aux = plot_axes[i]
plot_axes_aux = plot_axes_aux.split(':')
file_label.append( plot_axes_aux[0] )
axes_values = []
for j in range( 1 , len( plot_axes_aux ) ):
axes_values.append( plot_axes_aux[j] )
axes.append( axes_values )
print('\nPlot 3D selected using file labels: ', file_label)
print('Axis x values: ', axes[0])
print('Axis y values: ', axes[1])
xlen = len( axes[0] )
ylen = len( axes[1] )
x = np.array( axes[0] ).astype( myFloat )
y = np.array( axes[1] ).astype( myFloat )
result = np.zeros( ( xlen , ylen ) , dtype=myFloat )
axes_label = args.axes_label
if axes_label.find(':') == -1:
flag_plot3d = 0
print('\nPlot 2D selected using file label: ', axes_label)
else:
flag_plot3d = 1
axes_label = axes_label.split(':')
print('\nPlot 3D selected using file labels: ', axes_label)
## Perform analisys
if args.resol_square is True:
print('Enabled analisys inside resolution square')
print('\n\n')
f = 0
for i in range( xlen ):
for j in range( ylen ):
filein = rec_list1[f]
image1 = io.readImage( pathin[0] + filein )
print('\n\nInput image 1:\n', filein)
filein = rec_list2[f]
image2 = io.readImage( pathin[1] + filein )
print('\nInput image 2:\n', filein)
print('\n')
## Preprocess input image and oracle
if args.resol_square is True:
image1 = an.select_resolution_square( image1 )
image2 = an.select_resolution_square( image2 )
## Perform analysis
frc , resol = an.fourier_ring_corr( image1 , image2 )
result[i,j] = resol
#x = np.arange( len( frc ) )
#plt.plot( x , frc )
#plt.show()
f += 1
## Write data for bar plot 3D to text file
if result.shape[0] * result.shape[1] != len( x ) * len( y ):
sys.exit('\nERROR: number of results = ' + str( len( result ) ) +
' does not match the product between number of x values = '
+ str( len( x ) ) + ' and the number of the y values = '
+ str( len( y ) ) + '\n')
fileout = args.fileout
if os.path.isfile( fileout ) is True:
sys.exit('\nERROR: output file:\n' + fileout + '\nalready exists!')
print('\nWriting data for bar plot 3D to file:\n', fileout)
fout = open( args.fileout , 'w' )
fout.write('x:' + axes_label[0].upper() + ':' + str( len( x ) ) )
for i in range( len( x ) ):
fout.write('\n%4f' % x[i])
fout.write('\ny:' + axes_label[1].upper() + ':' + str( len( y ) ) )
for i in range( len( y ) ):
fout.write('\n%4f' % y[i])
fout.write('\nz:FRC:' + str( len( result.flatten() ) ) )
for j in range( result.shape[1] ):
for i in range( result.shape[0] ):
fout.write('\n%4f' % result[i,j])
fout.close()
#print( x )
#print( y )
#print( result )
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = Axes3D(fig)
lx= len(result[0]) # Work out matrix dimensions
ly= len(result[:,0])
xpos = np.arange(0,lx,1) # Set up a mesh of positions
ypos = np.arange(0,ly,1)
xpos, ypos = np.meshgrid(xpos+0.25, ypos+0.25)
xpos = xpos.flatten() # Convert positions to 1D array
ypos = ypos.flatten()
zpos = np.zeros(lx*ly)
dx = 0.5 * np.ones_like(zpos)
dy = dx.copy()
dz = result.flatten()
ax.bar3d(xpos,ypos,zpos, dx, dy, dz, color='b', alpha=0.8)
column_names = axes[1]
row_names = axes[0]
ax.w_xaxis.set_ticklabels(column_names)
ax.w_yaxis.set_ticklabels(row_names)
ax.set_xlabel( axes_label[1].upper() )
ax.set_ylabel( axes_label[0].upper() )
ax.set_zlabel( 'FRC' )
plt.show()
print('\n')
def main():
print('\n')
print('###############################################')
print('###############################################')
print('#### ####')
print('#### RUN ANALYSIS OF THE RECONSTRUCTIONS ####')
print('#### ####')
print('###############################################')
print('###############################################')
print('\n')
## Get input arguments
args = getArgs()
## Get input path
pathin = args.pathin
if pathin[len(pathin)-1] != '/':
pathin += '/'
print('\nInput path:\n', pathin)
## Get reconstruction files
if args.imagein is not None:
imagein = args.imagein
image_file1 = imagein.split(':')[0]
image_file2 = imagein.split(':')[1]
num_pair = 1
elif args.allin:
curr_dir = os.getcwd()
os.chdir( pathin )
image_file1 = sorted( glob.glob( '*odd*' ) )
image_file2 = sorted( glob.glob( '*even*' ) )
if len( image_file1 ) != len( image_file2 ):
sys.exit('\nERROR: number of labelled "odd" = ' + str( len( image_file1 ) )
+ ' dies not correspond to the number of labelled "even" = '
+ str( len( image_file1 ) ) )
num_pair = len( image_file1 )
## Create output names
if num_pair == 1:
fileout = args.fileout
else:
aux_out = args.fileout
aux_out = aux_out.split(':')
pathout = aux_out[0]
if pathout[len(pathout)-1] != '/':
pathout += '/'
alg = aux_out[1]
nproj = aux_out[2:]
base_name = 'data_plot2d_frc_' + alg + '_proj_'
if len( nproj ) != num_pair:
sys.exit('\nERROR: number of image pair = ' + str( num_pair )
+ ' does not match with number of labels = ' +
+ str( nproj ) )
## Perform analisys
if args.resol_square is True:
print('Enabled analisys inside resolution square')
print('\n\n')
for i in range( num_pair ):
## Read images
if num_pair == 1:
image1 = io.readImage( pathin + image_file1 )
print('\n\nInput image 1:\n', image_file1 )
image2 = io.readImage( pathin + image_file2 )
print('\nInput image 2:\n', image_file2 )
else:
image1 = io.readImage( pathin + image_file1[i] )
print('\n\nInput image 1:\n', image_file1[i] )
image2 = io.readImage( pathin + image_file2[i] )
print('\nInput image 2:\n', image_file2[i] )
print('\n')
## Preprocess input image and oracle
if args.resol_square is True:
image1 = an.select_resolution_square( image1 )
image2 = an.select_resolution_square( image2 )
## Perform analysis
frc , resol , x = an.fourier_ring_corr( image1 , image2 )
## Write output file
if num_pair > 1:
fileout = pathout + base_name + nproj[i] + '.txt'
if os.path.isfile( fileout ) is True:
sys.exit('\nERROR: output file:\n' + fileout + '\nalready exists!')
print('\nWriting data for bar plot 3D to file:\n', fileout)
fout = open( fileout , 'w' )
fout.write('x:' + ':' + str( len( x ) ) )
for i in range( len( x ) ):
fout.write('\n%4f' % x[i])
fout.write('\ny:FRC:' + str( len( frc ) ) )
for i in range( len( frc ) ):
fout.write('\n%4f' % frc[i])
fout.close()
#print( x )
#print( resol )
#print( frc )
## Plot FRC curve
if num_pair == 1:
fig = plt.figure()
plt.plot( x , frc , 'o' , color='b' , markersize=12 )
plt.xlabel( 'Spatial frequencies' , fontsize=20 , position=(0.5,-0.2) )
plt.ylabel( 'FRC' , fontsize=20 , position=(0.5,0.5) )
plt.show()
print('\n')