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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""TomoPy script to reconstruct a built-in phantom."""
import sys
import os
import argparse
import traceback
import tomopy
import dxchange
import tornado
import matplotlib
import timemory
import timemory.options as options
import signal
import numpy as np
import time as t
import pylab
from tomopy.misc.benchmark import *
def get_basepath(args, algorithm, phantom):
basepath = os.path.join(os.getcwd(), args.output_dir, phantom, algorithm)
if not os.path.exists(basepath):
os.makedirs(basepath)
return basepath
@timemory.util.auto_timer()
def generate(phantom, args):
"""Return the simulated data for the given phantom."""
with timemory.util.auto_timer("[tomopy.misc.phantom.{}]".format(phantom)):
obj = getattr(tomopy.misc.phantom, phantom)(size=args.size)
obj = tomopy.misc.morph.pad(obj, axis=1, mode='constant')
obj = tomopy.misc.morph.pad(obj, axis=2, mode='constant')
if args.partial:
data_size = obj.shape[0]
subset = list(args.subset)
subset.sort()
nbeg, nend = subset[0], subset[1]
if nbeg == nend:
nend += 1
if not args.no_center:
ndiv = (nend - nbeg) // 2
offset = data_size // 2
nbeg = (offset - ndiv)
nend = (offset + ndiv)
print("[partial]> slices = {} ({}, {}) of {}".format(
nend - nbeg, nbeg, nend, data_size))
obj = obj[nbeg:nend,:,:]
with timemory.util.auto_timer("[tomopy.angles]"):
ang = tomopy.angles(args.angles)
with timemory.util.auto_timer("[tomopy.project]"):
prj = tomopy.project(obj, ang)
print("[dims]> projection = {}, angles = {}, object = {}".format(
prj.shape, ang.shape, obj.shape))
return [prj, ang, obj]
@timemory.util.auto_timer()
def run(phantom, algorithm, args, get_recon=False):
"""Run reconstruction benchmarks for phantoms.
Parameters
----------
phantom : string
The name of the phantom to use.
algorithm : string
The name of the algorithm to test.
args : argparser args
Returns
-------
Either rec or imgs
rec : np.ndarray
The reconstructed image.
imgs : list
A list of the original, reconstructed, and difference image
"""
global image_quality
imgs = []
bname = get_basepath(args, algorithm, phantom)
pname = os.path.join(bname, "proj_{}_".format(algorithm))
oname = os.path.join(bname, "orig_{}_".format(algorithm))
fname = os.path.join(bname, "stack_{}_".format(algorithm))
dname = os.path.join(bname, "diff_{}_".format(algorithm))
prj, ang, obj = generate(phantom, args)
proj = np.zeros(shape=[prj.shape[1], prj.shape[0], prj.shape[2]], dtype=np.float)
for i in range(0, prj.shape[1]):
proj[i,:,:] = prj[:,i,:]
# always add algorithm
_kwargs = {"algorithm": algorithm}
# assign number of cores
_kwargs["ncore"] = args.ncores
# don't assign "num_iter" if gridrec or fbp
if algorithm not in ["fbp", "gridrec"]:
_kwargs["num_iter"] = args.num_iter
# use the accelerated version
if algorithm in ["mlem", "sirt"]:
_kwargs["accelerated"] = True
print("kwargs: {}".format(_kwargs))
with timemory.util.auto_timer("[tomopy.recon(algorithm='{}')]".format(
algorithm)):
rec = tomopy.recon(prj, ang, **_kwargs)
print("completed reconstruction...")
obj_min = np.amin(obj)
rec_min = np.amin(rec)
obj_max = np.amax(obj)
rec_max = np.amax(rec)
print("obj bounds = [{:8.3f}, {:8.3f}], rec bounds = [{:8.3f}, {:8.3f}]".format(obj_min, obj_max,
rec_min, rec_max))
obj = normalize(obj)
rec = normalize(rec)
obj_max = np.amax(obj)
rec_max = np.amax(rec)
print("Max obj = {}, rec = {}".format(obj_max, rec_max))
rec = trim_border(rec, rec.shape[0],
rec[0].shape[0] - obj[0].shape[0],
rec[0].shape[1] - obj[0].shape[1])
label = "{} @ {}".format(algorithm.upper(), phantom.upper())
quantify_difference(label + " (self)", rec, np.zeros(rec.shape, dtype=rec.dtype))
quantify_difference(label, obj, rec)
if "orig" not in image_quality:
image_quality["orig"] = obj
dif = obj - rec
image_quality[algorithm] = dif
if get_recon is True:
return rec
print("pname = {}, oname = {}, fname = {}, dname = {}".format(pname, oname, fname, dname))
imgs.extend(output_images(proj, pname, args.format, args.scale, args.ncol))
imgs.extend(output_images(obj, oname, args.format, args.scale, args.ncol))
imgs.extend(output_images(rec, fname, args.format, args.scale, args.ncol))
imgs.extend(output_images(dif, dname, args.format, args.scale, args.ncol))
return imgs
def main(args):
print("using tomopy: {}".format(tomopy.__file__))
global image_quality
manager = timemory.manager()
algorithm = args.algorithm
if len(args.compare) > 0:
algorithm = "comparison"
print(("\nArguments:\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n"
"{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n").format(
"\tPhantom", args.phantom,
"\tAlgorithm", algorithm,
"\tSize", args.size,
"\tAngles", args.angles,
"\tFormat", args.format,
"\tScale", args.scale,
"\tcomparison", args.compare,
"\tnumber of cores", args.ncores,
"\tnumber of columns", args.ncol,
"\tnumber iterations", args.num_iter))
if len(args.compare) > 0:
args.ncol = 1
args.scale = 1
nitr = 1
comparison = None
for alg in args.compare:
print("Reconstructing {} with {}...".format(args.phantom, alg))
tmp = run(args.phantom, alg, args, get_recon=True)
tmp = rescale_image(tmp, args.size, args.scale, transform=False)
if comparison is None:
comparison = image_comparison(
len(args.compare), tmp.shape[0], tmp[0].shape[0],
tmp[0].shape[1], image_quality["orig"]
)
comparison.assign(alg, nitr, tmp)
nitr += 1
bname = get_basepath(args, algorithm, args.phantom)
fname = os.path.join(bname, "stack_{}_".format(comparison.tagname()))
dname = os.path.join(bname, "diff_{}_".format(comparison.tagname()))
imgs = []
imgs.extend(
output_images(comparison.array, fname,
args.format, args.scale, args.ncol))
imgs.extend(
output_images(comparison.delta, dname,
args.format, args.scale, args.ncol))
else:
print("Reconstructing with {}...".format(args.algorithm))
imgs = run(args.phantom, args.algorithm, args)
# timing report to stdout
print('{}\n'.format(manager))
_dir = os.path.abspath(args.output_dir)
timemory.options.output_dir = "{}/{}/{}".format(
_dir, args.phantom, algorithm)
timemory.options.set_report("run_tomopy.out")
timemory.options.set_serial("run_tomopy.json")
manager.report()
# provide ASCII results
try:
notes = manager.write_ctest_notes(
directory="{}/{}/{}".format(args.output_dir, args.phantom,
algorithm))
print('"{}" wrote CTest notes file : {}'.format(__file__, notes))
except Exception as e:
print("Exception - {}".format(e))
if __name__ == "__main__":
parser = argparse.ArgumentParser()
# phantom choices
phantom_choices = ["baboon", "cameraman", "barbara", "checkerboard",
"lena", "peppers", "shepp2d", "shepp3d"]
import multiprocessing as mp
ncores = mp.cpu_count()
parser.add_argument("-p", "--phantom", help="Phantom to use",
default="shepp2d", choices=phantom_choices, type=str)
parser.add_argument("-a", "--algorithm", help="Select the algorithm",
default="sirt", choices=algorithms, type=str)
parser.add_argument("-A", "--angles", help="number of angles",
default=1501, type=int)
parser.add_argument("-s", "--size", help="size of image",
default=512, type=int)
parser.add_argument("-n", "--ncores", help="number of cores",
default=ncores, type=int)
parser.add_argument("-f", "--format", help="output image format",
default="png", type=str)
parser.add_argument("-S", "--scale",
help="scale image by a positive factor",
default=1, type=int)
parser.add_argument("-c", "--ncol", help="Number of images per row",
default=1, type=int)
parser.add_argument("--compare", help="Generate comparison",
nargs='*', default=["none"], type=str)
parser.add_argument("-i", "--num-iter", help="Number of iterations",
default=50, type=int)
parser.add_argument("-P", "--preserve-output-dir", help="Do not clean up output directory",
action='store_true')
parser.add_argument("--partial", help="Enable partial reconstruction of 3D data",
action='store_true')
parser.add_argument("-r", "--subset",
help="Select subset (range) of slices (center enabled by default)",
default=(0, 48), type=int, nargs=2)
parser.add_argument("--no-center",
help="When used with '--subset', do no center subset",
action='store_true')
args = timemory.options.add_args_and_parse_known(parser)
print("\nargs: {}\n".format(args))
if args.output_dir is None:
args.output_dir = "."
if len(args.compare) == 1 and args.compare[0].lower() == "all":
args.compare = list(algorithms)
elif len(args.compare) == 1:
args.compare = []
# unique output directory w.r.t. phantom
adir = os.path.join(os.getcwd(), args.output_dir, args.phantom)
# unique output directory w.r.t. phantom and extension
if len(args.compare) > 0:
adir = os.path.join(adir, "comparison")
else:
adir = os.path.join(adir, args.algorithm)
if not args.preserve_output_dir:
try:
print("removing output from '{}' (if not '{}')...".format(adir, os.getcwd()))
import shutil
if os.path.exists(adir) and adir != os.getcwd():
shutil.rmtree(adir)
os.makedirs(adir)
except:
pass
else:
os.makedirs(adir)
args.output_dir = os.path.abspath(args.output_dir)
ret = 0
try:
with timemory.util.timer('\nTotal time for "{}"'.format(__file__)):
main(args)
except Exception as e:
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type, exc_value, exc_traceback, limit=5)
print('Exception - {}'.format(e))
ret = 1
sys.exit(ret)
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