from flexdata import data
from flexdata import display
import numpy
import astra
#%% Read data:
path = '/ufs/ciacc/flexbox/good/'
binning = 2
dark = data.read_stack(path, 'di00', sample = binning)
flat = data.read_stack(path, 'io00', sample = binning)
proj = data.read_stack(path, 'scan_', skip = binning, sample = binning)
geom = data.read_flexraylog(path, sample = binning)
#%% Prepro:
flat = (flat - dark).mean(1)
proj = (proj - dark) / flat[:, None, :]
proj = -numpy.log(proj).astype('float32')
proj = numpy.ascontiguousarray(proj)
display.slice(proj, dim = 1, title = 'Projection', cmap = 'magma')
#%% Astra reconstruction:
vol = numpy.zeros([2000 // binning, 2000 // binning, 2000 // binning], dtype = 'float32')
# Initialize ASTRA geometries:
#%% Read image stacks:
# Read files with 'scan_' in them (sampling = 4 for speed):
path = '/ufs/ciacc/flexbox/skull/'
proj = data.read_stack(path, 'scan_', skip=4, sample=4)
# Writing stack:
data.write_stack(path + 'binned', 'scan_', proj, dim=1)
# Display:
display.slice(proj, dim=0, title='Sinogram', cmap='magma')
display.slice(proj, dim=1, title='Projection', cmap='magma')
#%% Read / write a geometry file:
# Parcer for a flexray log file:
geom = data.read_flexraylog(path, sample=4)
print('\nParsing "scan settings.txt":')
print(geom)
# Write TOML format to disk:
data.write_toml(path + 'geometry.toml', geom)
print('\nReading raw TOML:')
print(data.read_toml(path + 'geometry.toml'))
print('\nParsing raw TOML:')
print(data.read_geometry(path, sample=4))