Wrappers for generating CTest files
Project description
Results from running the TomoPy example can be found at the TomoPy CDash Testing Dashboard @ NERSC
CTestTestfile.cmake generation
Generates test_output/CTestTestfile.cmake but does not submit to dashboard
#!/usr/bin/env python
import os
import pyctest
#------------------------------------------------------------------------------#
def modify(test):
pyctest.remove_test(test)
pyctest.add_test(test)
test.SetProperty("RUN_SERIAL", "ON")
#------------------------------------------------------------------------------#
def info(name):
test = pyctest.find_test(name)
print('Found test "{}" with RUN_SERIAL property = {}'.format(
test.GetName(), test.GetProperty("RUN_SERIAL")))
#------------------------------------------------------------------------------#
def generate(name):
test = pyctest.test()
test.SetName(name)
test.SetCommand(["ls", "-a", os.getcwd()])
test.SetProperty("WORKING_DIRECTORY", os.getcwd())
test.SetProperty("RUN_SERIAL", "0")
test.SetProperty("ENVIRONMENT", "DIR1={};DIR2={}".format(os.getcwd(),
os.path.join(os.getcwd(), "test_output")))
info(name)
modify(test)
info(name)
#------------------------------------------------------------------------------#
if __name__ == "__main__":
generate("dummy_a")
generate("dummy_b")
generate("dummy_c")
pyctest.generate("test_output")Python Output
Command : python test.py && echo -e "\n\t### test_output/CTestTestfile.cmake ###\n" && cat test_output/CTestTestfile.cmake
Created test "0x7fc03f51d140"...
Found test "dummy_a" with RUN_SERIAL property = 0
Found test "dummy_a" with RUN_SERIAL property = ON
Created test "0x7fc03f51d880"...
Found test "dummy_b" with RUN_SERIAL property = 0
Found test "dummy_b" with RUN_SERIAL property = ON
Created test "0x7fc03f51dbc0"...
Found test "dummy_c" with RUN_SERIAL property = 0
Found test "dummy_c" with RUN_SERIAL property = ON
Writing CTest test file: "test_output/CTestTestfile.cmake"...
Generating test "dummy_a"...
Generating test "dummy_b"...
Generating test "dummy_c"...
### test_output/CTestTestfile.cmake ###
add_test(dummy_a "ls" "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
set_tests_properties(dummy_a PROPERTIES ENVIRONMENT "DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug;DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output" RUN_SERIAL "ON" WORKING_DIRECTORY "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
add_test(dummy_b "ls" "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
set_tests_properties(dummy_b PROPERTIES ENVIRONMENT "DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug;DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output" RUN_SERIAL "ON" WORKING_DIRECTORY "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
add_test(dummy_c "ls" "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
set_tests_properties(dummy_c PROPERTIES ENVIRONMENT "DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug;DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output" RUN_SERIAL "ON" WORKING_DIRECTORY "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug")
CTest Output
Command : ctest -V
UpdateCTestConfiguration from :/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output/DartConfiguration.tcl
UpdateCTestConfiguration from :/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output/DartConfiguration.tcl
Test project /Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: dummy_a
1: Test command: /bin/ls "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug"
1: Environment variables:
1: DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug
1: DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output
1: Test timeout computed to be: 10000000
1: .
1: ..
1: .ninja_deps
1: .ninja_log
1: BC
1: CMakeCache.txt
1: CMakeFiles
1: CMakeLibBuild.cmake
1: CMakeLibTests
1: CMakeServerLibTests
1: CPackConfig.cmake
1: CPackSourceConfig.cmake
1: CTestConfig.cmake
1: CTestLibBuild.cmake
1: CTestTestfile.cmake
1: LIBCURL
1: OSXScriptLauncher
1: build.ninja
1: cmake
1: cmake_install.cmake
1: cmakexbuild
1: cmsysTestProcess
1: cmsysTestSharedForward
1: cmsysTestsC
1: cmsysTestsCxx
1: cpack
1: ctest
1: exit_code
1: libCMakeLib.a
1: libCMakeServerLib.a
1: libCPackLib.a
1: libCTestLib.a
1: libcmbzip2.a
1: libcmcompress.a
1: libcmcurl.a
1: libcmexpat.a
1: libcmjsoncpp.a
1: libcmlibarchive.a
1: libcmliblzma.a
1: libcmlibrhash.a
1: libcmlibuv.a
1: libcmsys.a
1: libcmsysTestDynload.so
1: libcmsys_c.a
1: libcmzlib.a
1: memcheck_fail
1: pseudo_cppcheck
1: pseudo_cpplint
1: pseudo_emulator
1: pseudo_emulator_custom_command
1: pseudo_iwyu
1: pseudo_tidy
1: purify
1: pycmake.cpython-36m-darwin.so
1: pyctest.cbp
1: pyctest.cpython-36m-darwin.so
1: pyctestConfig.cmake
1: pyctestConfigVersion.cmake
1: rules.ninja
1: runcompilecommands
1: source
1: test-folder
1: test.py
1: testAffinity
1: testConsoleBufChild
1: testEncoding
1: test_output
1: valgrind
1/3 Test #1: dummy_a .......................... Passed 0.00 sec
test 2
Start 2: dummy_b
2: Test command: /bin/ls "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug"
2: Environment variables:
2: DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug
2: DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output
2: Test timeout computed to be: 10000000
2: .
2: ..
2: .ninja_deps
2: .ninja_log
2: BC
2: CMakeCache.txt
2: CMakeFiles
2: CMakeLibBuild.cmake
2: CMakeLibTests
2: CMakeServerLibTests
2: CPackConfig.cmake
2: CPackSourceConfig.cmake
2: CTestConfig.cmake
2: CTestLibBuild.cmake
2: CTestTestfile.cmake
2: LIBCURL
2: OSXScriptLauncher
2: build.ninja
2: cmake
2: cmake_install.cmake
2: cmakexbuild
2: cmsysTestProcess
2: cmsysTestSharedForward
2: cmsysTestsC
2: cmsysTestsCxx
2: cpack
2: ctest
2: exit_code
2: libCMakeLib.a
2: libCMakeServerLib.a
2: libCPackLib.a
2: libCTestLib.a
2: libcmbzip2.a
2: libcmcompress.a
2: libcmcurl.a
2: libcmexpat.a
2: libcmjsoncpp.a
2: libcmlibarchive.a
2: libcmliblzma.a
2: libcmlibrhash.a
2: libcmlibuv.a
2: libcmsys.a
2: libcmsysTestDynload.so
2: libcmsys_c.a
2: libcmzlib.a
2: memcheck_fail
2: pseudo_cppcheck
2: pseudo_cpplint
2: pseudo_emulator
2: pseudo_emulator_custom_command
2: pseudo_iwyu
2: pseudo_tidy
2: purify
2: pycmake.cpython-36m-darwin.so
2: pyctest.cbp
2: pyctest.cpython-36m-darwin.so
2: pyctestConfig.cmake
2: pyctestConfigVersion.cmake
2: rules.ninja
2: runcompilecommands
2: source
2: test-folder
2: test.py
2: testAffinity
2: testConsoleBufChild
2: testEncoding
2: test_output
2: valgrind
2/3 Test #2: dummy_b .......................... Passed 0.00 sec
test 3
Start 3: dummy_c
3: Test command: /bin/ls "-a" "/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug"
3: Environment variables:
3: DIR1=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug
3: DIR2=/Users/jrmadsen/devel/c++/qt-pyctest/clang-Debug/test_output
3: Test timeout computed to be: 10000000
3: .
3: ..
3: .ninja_deps
3: .ninja_log
3: BC
3: CMakeCache.txt
3: CMakeFiles
3: CMakeLibBuild.cmake
3: CMakeLibTests
3: CMakeServerLibTests
3: CPackConfig.cmake
3: CPackSourceConfig.cmake
3: CTestConfig.cmake
3: CTestLibBuild.cmake
3: CTestTestfile.cmake
3: LIBCURL
3: OSXScriptLauncher
3: build.ninja
3: cmake
3: cmake_install.cmake
3: cmakexbuild
3: cmsysTestProcess
3: cmsysTestSharedForward
3: cmsysTestsC
3: cmsysTestsCxx
3: cpack
3: ctest
3: exit_code
3: libCMakeLib.a
3: libCMakeServerLib.a
3: libCPackLib.a
3: libCTestLib.a
3: libcmbzip2.a
3: libcmcompress.a
3: libcmcurl.a
3: libcmexpat.a
3: libcmjsoncpp.a
3: libcmlibarchive.a
3: libcmliblzma.a
3: libcmlibrhash.a
3: libcmlibuv.a
3: libcmsys.a
3: libcmsysTestDynload.so
3: libcmsys_c.a
3: libcmzlib.a
3: memcheck_fail
3: pseudo_cppcheck
3: pseudo_cpplint
3: pseudo_emulator
3: pseudo_emulator_custom_command
3: pseudo_iwyu
3: pseudo_tidy
3: purify
3: pycmake.cpython-36m-darwin.so
3: pyctest.cbp
3: pyctest.cpython-36m-darwin.so
3: pyctestConfig.cmake
3: pyctestConfigVersion.cmake
3: rules.ninja
3: runcompilecommands
3: source
3: test-folder
3: test.py
3: testAffinity
3: testConsoleBufChild
3: testEncoding
3: test_output
3: valgrind
3/3 Test #3: dummy_c .......................... Passed 0.00 sec
100% tests passed, 0 tests failed out of 3
Total Test time (real) = 0.02 sec
Advanced Example
located in examples/TomoPy of source code
Downloads Miniconda in PyCTestPreInit.cmake
Installs conda packages in PyCTestPreInit.cmake
Checkouts source code of Python package via git clone ... in tomopy.py
Build source code via python setup.py install when running CTest
Generates a test around the nosetests unit testing
Generates tests around several algorithms by calling run_tomopy.py
Submits to CDash dashboard at cdash.nersc.gov
Timing and memory plots provided via TiMemory
Attaches CTest notes (e.g. ASCII results)
Attaches images from reconstruction (e.g. Dart measurement files)
PyCTestPreInit.cmake
message(STATUS "Including ${CMAKE_CURRENT_LIST_FILE}...")
find_program(DEFAULT_CONDA_EXE NAMES conda)
macro(SET_PYTHON_VERSION VAL)
if(NOT DEFINED PYTHON_VERSION OR "${PYTHON_VERSION}" STREQUAL "")
if(NOT "${VAL}" STREQUAL "")
set(PYTHON_VERSION "${VAL}")
endif(NOT "${VAL}" STREQUAL "")
endif(NOT DEFINED PYTHON_VERSION OR "${PYTHON_VERSION}" STREQUAL "")
endmacro(SET_PYTHON_VERSION VAL)
set_python_version("$ENV{PYTHON_VERSION}")
set_python_version("$ENV{TRAVIS_PYTHON_VERSION}")
set_python_version("2.7")
find_program(WGET_EXE NAMES wget)
find_program(BASH_EXE NAMES bash)
set(CONDA_PACKAGE_INSTALL OFF)
if(NOT "$ENV{CONDA_PACKAGE_INSTALL}" STREQUAL "")
set(CONDA_PACKAGE_INSTALL ON)
endif()
set(ENV{PYTHONPATH} "")
set(CONDA_PKGS nose six numpy h5py scipy scikit-image pywavelets mkl-devel
mkl_fft python-coveralls dxchange numexpr timemory scikit-image)
#set(PIP_PKGS timemory)
#------------------------------------------------------------------------------#
# local `miniconda` installation
#------------------------------------------------------------------------------#
# if not already installed
if(NOT EXISTS "${CMAKE_CURRENT_LIST_DIR}/miniconda/bin/conda")
set(CONDA_PACKAGE_INSTALL ON)
if("${PYTHON_VERSION}" VERSION_EQUAL "2.7")
set(MINICONDA_VER "Miniconda")
list(APPEND CONDA_PKGS "futures")
else()
set(MINICONDA_VER "Miniconda3")
endif()
if(APPLE)
set(_OS "MacOSX")
elseif(WIN32)
set(_OS "Windows")
else()
set(_OS "Linux")
endif(APPLE)
set(MINICONDA_URL "https://repo.continuum.io/miniconda/${MINICONDA_VER}-latest-${_OS}-x86_64.sh")
execute_process(COMMAND
${WGET_EXE} ${MINICONDA_URL} -O ${CMAKE_CURRENT_LIST_DIR}/miniconda.sh)
execute_process(COMMAND
${BASH_EXE} ${CMAKE_CURRENT_LIST_DIR}/miniconda.sh -b -p ${CMAKE_CURRENT_LIST_DIR}/miniconda)
endif(NOT EXISTS "${CMAKE_CURRENT_LIST_DIR}/miniconda/bin/conda")
# use miniconda
set(ENV{PATH} "${CMAKE_CURRENT_LIST_DIR}/miniconda/bin:$ENV{PATH}")
set(SEARCH_PATHS
${CMAKE_CURRENT_LIST_DIR}/miniconda
${CMAKE_CURRENT_LIST_DIR}/miniconda/bin)
#------------------------------------------------------------------------------#
# local `conda`
#------------------------------------------------------------------------------#
find_program(CONDA_EXE
NAMES conda
PATHS ${SEARCH_PATHS}
HINTS ${SEARCH_PATHS}
PATH_SUFFIXES bin
NO_DEFAULT_PATH)
if("${CONDA_EXE}" STREQUAL "${DEFAULT_CONDA_EXE}")
set(CONDA_EXE ${CMAKE_CURRENT_LIST_DIR}/miniconda/bin/conda CACHE
FILEPATH "Local conda installation" FORCE)
endif()
if(NOT CONDA_EXE OR NOT EXISTS "${CONDA_EXE}")
message(FATAL_ERROR "Error! Could not find 'conda' command in \"${SEARCH_PATHS}\"")
endif()
get_filename_component(CONDA_DIR "${CONDA_EXE}" PATH)
set(SEARCH_PATHS ${CONDA_DIR} ${SEARCH_PATHS})
#------------------------------------------------------------------------------#
# local `python`
#------------------------------------------------------------------------------#
find_program(PYTHON_EXE
NAMES python
PATHS ${SEARCH_PATHS}
HINTS ${SEARCH_PATHS}
PATH_SUFFIXES bin
NO_DEFAULT_PATH)
if(NOT PYTHON_EXE OR NOT EXISTS "${PYTHON_EXE}")
message(FATAL_ERROR "Error! Could not find 'python' command in \"${SEARCH_PATHS}\"")
endif()
#------------------------------------------------------------------------------#
# setup
#------------------------------------------------------------------------------#
if(CONDA_PACKAGE_INSTALL)
execute_process(COMMAND ${CONDA_EXE} config --add channels conda-forge)
execute_process(COMMAND ${CONDA_EXE} config --add channels jrmadsen)
execute_process(COMMAND ${CONDA_EXE} config --set always_yes yes --set changeps1 no)
execute_process(COMMAND ${CONDA_EXE} update conda)
execute_process(COMMAND ${CONDA_EXE} install python=${PYTHON_VERSION} ${CONDA_PKGS})
# update matplotlib and freetype due to MacOS issues with default
execute_process(COMMAND ${CONDA_EXE} update matplotlib)
execute_process(COMMAND ${CONDA_EXE} update freetype)
endif()tomopy.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
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
#------------------------------------------------------------------------------#
algorithms = [ 'gridrec', 'art', 'fbp', 'bart', 'mlem', 'osem', 'sirt',
'ospml_hybrid', 'ospml_quad', 'pml_hybrid', 'pml_quad' ]
#------------------------------------------------------------------------------#
def convert_image(fname, current_format, new_format):
_fext = new_format
_success = True
try:
from PIL import Image
_cur_img = "{}.{}".format(fname, current_format)
img = Image.open(_cur_img)
out = img.convert("RGB")
out.save(fname, "jpeg", quality=95)
print(" --> Converted '{}' to {} format...".format(fname, new_format.upper()))
except Exception as e:
print(" --> ##### {}...".format(e))
print(" --> ##### Exception occurred converting '{}' to {} format...".format(
fname, new_format.upper()))
_fext = current_format
_success = False
_fname = "{}.{}".format(fname, _fext)
return [ _fname, _success, _fext ]
#------------------------------------------------------------------------------#
def exit_action(errcode):
man = timemory.manager()
timemory.report(ign_cutoff=True)
fname = 'signal_error_{}.out'.format(errcode)
f = open(fname, 'w')
f.write('{}\n'.format(man))
f.close()
#------------------------------------------------------------------------------#
def output_image(image, fname):
img = pylab.imsave(fname, image, cmap='gray')
if os.path.exists(fname):
print(" --> Image file found @ '{}'...".format(fname))
else:
print(" ##################### WARNING #####################")
print(" --> No image file at @ '{}' (expected) ...".format(fname))
#------------------------------------------------------------------------------#
def rescale_image(rec, nimages, scale, transform=True):
rec_n = rec.copy()
try:
_min = np.amin(rec_n)
rec_n -= _min
_max = np.amax(rec_n)
if _max > 0.0:
rec_n /= 0.5 * _max
rec_n -= 1
import skimage.transform
if transform is True:
_nrows = rec[0].shape[0] * scale
_ncols = rec[0].shape[1] * scale
rec_tmp = np.ndarray([nimages, _nrows, _ncols])
for i in range(nimages):
rec_tmp[i] = skimage.transform.resize(rec_n[i],
(rec_n[i].shape[0] * scale, rec_n[i].shape[1] * scale))
rec_n = rec_tmp
except Exception as e:
print(" --> ##### {}...".format(e))
rec_n = rec.copy()
return rec_n
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def output_images(rec, nimages, full_basename, format="jpeg", scale=1, ncol=1):
imgs = []
nitr = 0
rec_i = None
fname = "{}".format(full_basename)
rec_n = rec.copy()
if scale > 1:
rescale_image(rec, nimages, scale)
print("Image size: {} x {} x {}".format(
rec[0].shape[0],
rec[0].shape[1],
rec.shape[0]))
print("Scaled Image size: {} x {} x {}".format(
rec_n[0].shape[0],
rec_n[0].shape[1],
rec_n.shape[0]))
for i in range(nimages):
nitr += 1;
_f = "{}{}".format(full_basename, i)
_fimg = "{}.{}".format(_f, format)
if rec_i is None:
rec_i = rec_n[i]
else:
rec_i = np.concatenate((rec_i, rec_n[i]), axis=1)
if nitr % ncol == 0 or i+1 == nimages:
fname = "{}{}.{}".format(fname, i, format)
output_image(rec_i, fname)
imgs.append(fname)
rec_i = None
fname = "{}".format(full_basename)
else:
fname = "{}{}_".format(fname, i)
return imgs
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def generate(nsize = 512, nangles = 360):
with timemory.util.auto_timer("[tomopy.shepp3d]"):
obj = tomopy.shepp3d(size=nsize)
with timemory.util.auto_timer("[tomopy.angles]"):
ang = tomopy.angles(nangles)
with timemory.util.auto_timer("[tomopy.project]"):
prj = tomopy.project(obj, ang)
np.save('projection.npy', prj)
np.save('angles.npy', ang)
return [ prj, ang, obj ]
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def run(algorithm, size, nangles, ncores, format, scale, ncol, get_recon = False):
nitr = size
ndigits = 6
imgs = []
bname = os.path.join(algorithm, "stack_{}_".format(algorithm))
bname = os.path.join(os.getcwd(), bname)
prj, ang, obj = generate(size, nangles)
with timemory.util.auto_timer("[tomopy.recon(algorithm='{}')]".format(algorithm)):
rec = tomopy.recon(prj, ang, algorithm=algorithm, ncore=ncores)
if get_recon is True:
return rec
imgs.extend(output_images(rec, nitr, bname, format, scale, ncol))
return imgs
#------------------------------------------------------------------------------#
def main(args):
manager = timemory.manager()
algorithm = args.algorithm
if len(args.compare) > 0:
algorithm = "comparison"
print('\nArguments:\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n'.format(
"\tAlgorithm", algorithm,
"\tSize", args.size,
"\tAngles", args.angles,
"\t# of cores", args.ncores,
"\tFormat", args.format,
"\tScale", args.scale,
"\t# of columns", args.ncol,
"\tcomparison", args.compare))
if len(args.compare) > 0:
args.ncol = 1
args.scale = 1
arr = None
_nrows = None
_ncols = None
_nitr = 0
seq = None
for alg in args.compare:
print("Reconstructing with {}...".format(alg))
if seq is None:
seq = "{}".format(alg)
else:
seq = "{}-{}".format(seq, alg)
tmp = run(alg, args.size, args.angles, args.ncores,
args.format, args.scale, args.ncol, get_recon=True)
tmp = rescale_image(tmp, args.size, args.scale, transform=False)
_nrow = tmp[0].shape[0]
_ncol = tmp[0].shape[1]
if arr is None:
_nrows = _nrow
_ncols = _ncol * len(args.compare)
arr = np.ndarray([args.size, _nrows, _ncols], dtype=float)
_b = (_ncol*_nitr)
_nitr += 1
_e = (_ncol*_nitr)
arr[:, :, _b:_e] = tmp[:,:,:]
#
print("Total array size: {} x {} x {}".format(
arr[0].shape[0],
arr[0].shape[1],
arr.shape[0]))
fname = os.path.join(algorithm, "stack_{}_".format(seq))
fname = os.path.join(os.getcwd(), fname)
imgs = output_images(arr, args.size, fname,
args.format, args.scale, args.ncol)
else:
print("Reconstructing with {}...".format(args.algorithm))
imgs = run(args.algorithm, args.size, args.angles, args.ncores,
args.format, args.scale, args.ncol)
# timing report to stdout
print('{}'.format(manager))
timemory.options.output_dir = "./{}".format(algorithm)
timemory.options.set_report("run_tomopy_{}.out".format(algorithm))
timemory.options.set_serial("run_tomopy_{}.json".format(algorithm))
manager.report()
#------------------------------------------------------------------#
# provide timing plots
try:
timemory.plotting.plot(files=[timemory.options.serial_filename], echo_dart=True)
except Exception as e:
print("Exception - {}".format(e))
#------------------------------------------------------------------#
# provide results to dashboard
try:
for i in range(0, len(imgs)):
img_base = "{}_stack_".format(algorithm, i)
img_name = os.path.basename(imgs[i]).replace(
".{}".format(args.format), "").replace(
"stack_{}_".format(algorithm), img_base)
img_type = args.format
img_path = imgs[i]
timemory.plotting.echo_dart_tag(img_name, img_path, img_type)
except Exception as e:
print("Exception - {}".format(e))
#------------------------------------------------------------------#
# provide ASCII results
try:
notes = manager.write_ctest_notes(directory="{}".format(algorithm))
print('"{}" wrote CTest notes file : {}'.format(__file__, notes))
except Exception as e:
print("Exception - {}".format(e))
modu_len = args.size % args.ncol
real_len = len(imgs)
if modu_len > 0:
expt_len = (args.size / args.ncol) + 1
else:
expt_len = (args.size / args.ncol)
if real_len != expt_len:
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type, exc_value, exc_traceback, limit=5)
msg = "Error! number of images ({}) does not match the expected total ({})!".format(
expt_len, real_len)
raise Exception(msg)
#------------------------------------------------------------------------------#
if __name__ == "__main__":
parser = argparse.ArgumentParser()
import multiprocessing as mp
ncores = mp.cpu_count()
parser.add_argument("-a", "--algorithm", help="Select the algorithm",
default="gridrec", choices=algorithms, type=str)
parser.add_argument("-A", "--angles", help="number of angles",
default=360, 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="jpeg", 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)
args = timemory.options.add_args_and_parse_known(parser)
if len(args.compare) == 1 and args.compare[0].lower() == "all":
args.compare = list(algorithms)
elif len(args.compare) == 1:
args.compare = []
if len(args.compare) == 0:
try:
import shutil
dir = os.path.join(os.getcwd(), args.algorithm)
shutil.rmtree(dir)
os.makedirs(dir)
except:
pass
else:
try:
import shutil
dir = os.path.join(os.getcwd(), "comparison")
shutil.rmtree(dir)
os.makedirs(dir)
except:
pass
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 = 2
os.kill(os.getpid(), signal.SIGHUP)
sys.exit(ret)run_tomopy.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
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
#------------------------------------------------------------------------------#
algorithms = [ 'gridrec', 'art', 'fbp', 'bart', 'mlem', 'osem', 'sirt',
'ospml_hybrid', 'ospml_quad', 'pml_hybrid', 'pml_quad' ]
#------------------------------------------------------------------------------#
def convert_image(fname, current_format, new_format):
_fext = new_format
_success = True
try:
from PIL import Image
_cur_img = "{}.{}".format(fname, current_format)
img = Image.open(_cur_img)
out = img.convert("RGB")
out.save(fname, "jpeg", quality=95)
print(" --> Converted '{}' to {} format...".format(fname, new_format.upper()))
except Exception as e:
print(" --> ##### {}...".format(e))
print(" --> ##### Exception occurred converting '{}' to {} format...".format(
fname, new_format.upper()))
_fext = current_format
_success = False
_fname = "{}.{}".format(fname, _fext)
return [ _fname, _success, _fext ]
#------------------------------------------------------------------------------#
def exit_action(errcode):
man = timemory.manager()
timemory.report(ign_cutoff=True)
fname = 'signal_error_{}.out'.format(errcode)
f = open(fname, 'w')
f.write('{}\n'.format(man))
f.close()
#------------------------------------------------------------------------------#
def output_image(image, fname):
img = pylab.imsave(fname, image, cmap='gray')
if os.path.exists(fname):
print(" --> Image file found @ '{}'...".format(fname))
else:
print(" ##################### WARNING #####################")
print(" --> No image file at @ '{}' (expected) ...".format(fname))
#------------------------------------------------------------------------------#
def rescale_image(rec, nimages, scale, transform=True):
rec_n = rec.copy()
try:
_min = np.amin(rec_n)
rec_n -= _min
_max = np.amax(rec_n)
if _max > 0.0:
rec_n /= 0.5 * _max
rec_n -= 1
import skimage.transform
if transform is True:
_nrows = rec[0].shape[0] * scale
_ncols = rec[0].shape[1] * scale
rec_tmp = np.ndarray([nimages, _nrows, _ncols])
for i in range(nimages):
rec_tmp[i] = skimage.transform.resize(rec_n[i],
(rec_n[i].shape[0] * scale, rec_n[i].shape[1] * scale))
rec_n = rec_tmp
except Exception as e:
print(" --> ##### {}...".format(e))
rec_n = rec.copy()
return rec_n
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def output_images(rec, nimages, full_basename, format="jpeg", scale=1, ncol=1):
imgs = []
nitr = 0
rec_i = None
fname = "{}".format(full_basename)
rec_n = rec.copy()
if scale > 1:
rescale_image(rec, nimages, scale)
print("Image size: {} x {} x {}".format(
rec[0].shape[0],
rec[0].shape[1],
rec.shape[0]))
print("Scaled Image size: {} x {} x {}".format(
rec_n[0].shape[0],
rec_n[0].shape[1],
rec_n.shape[0]))
for i in range(nimages):
nitr += 1;
_f = "{}{}".format(full_basename, i)
_fimg = "{}.{}".format(_f, format)
if rec_i is None:
rec_i = rec_n[i]
else:
rec_i = np.concatenate((rec_i, rec_n[i]), axis=1)
if nitr % ncol == 0 or i+1 == nimages:
fname = "{}{}.{}".format(fname, i, format)
output_image(rec_i, fname)
imgs.append(fname)
rec_i = None
fname = "{}".format(full_basename)
else:
fname = "{}{}_".format(fname, i)
return imgs
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def generate(nsize = 512, nangles = 360):
with timemory.util.auto_timer("[tomopy.shepp3d]"):
obj = tomopy.shepp3d(size=nsize)
with timemory.util.auto_timer("[tomopy.angles]"):
ang = tomopy.angles(nangles)
with timemory.util.auto_timer("[tomopy.project]"):
prj = tomopy.project(obj, ang)
np.save('projection.npy', prj)
np.save('angles.npy', ang)
return [ prj, ang, obj ]
#------------------------------------------------------------------------------#
@timemory.util.auto_timer()
def run(algorithm, size, nangles, ncores, format, scale, ncol, get_recon = False):
nitr = size
ndigits = 6
imgs = []
bname = os.path.join(algorithm, "stack_{}_".format(algorithm))
bname = os.path.join(os.getcwd(), bname)
prj, ang, obj = generate(size, nangles)
with timemory.util.auto_timer("[tomopy.recon(algorithm='{}')]".format(algorithm)):
rec = tomopy.recon(prj, ang, algorithm=algorithm, ncore=ncores)
if get_recon is True:
return rec
imgs.extend(output_images(rec, nitr, bname, format, scale, ncol))
return imgs
#------------------------------------------------------------------------------#
def main(args):
manager = timemory.manager()
algorithm = args.algorithm
if len(args.compare) > 0:
algorithm = "comparison"
print('\nArguments:\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n{} = {}\n'.format(
"\tAlgorithm", algorithm,
"\tSize", args.size,
"\tAngles", args.angles,
"\t# of cores", args.ncores,
"\tFormat", args.format,
"\tScale", args.scale,
"\t# of columns", args.ncol,
"\tcomparison", args.compare))
if len(args.compare) > 0:
args.ncol = 1
args.scale = 1
arr = None
_nrows = None
_ncols = None
_nitr = 0
seq = None
for alg in args.compare:
print("Reconstructing with {}...".format(alg))
if seq is None:
seq = "{}".format(alg)
else:
seq = "{}-{}".format(seq, alg)
tmp = run(alg, args.size, args.angles, args.ncores,
args.format, args.scale, args.ncol, get_recon=True)
tmp = rescale_image(tmp, args.size, args.scale, transform=False)
_nrow = tmp[0].shape[0]
_ncol = tmp[0].shape[1]
if arr is None:
_nrows = _nrow
_ncols = _ncol * len(args.compare)
arr = np.ndarray([args.size, _nrows, _ncols], dtype=float)
_b = (_ncol*_nitr)
_nitr += 1
_e = (_ncol*_nitr)
arr[:, :, _b:_e] = tmp[:,:,:]
#
print("Total array size: {} x {} x {}".format(
arr[0].shape[0],
arr[0].shape[1],
arr.shape[0]))
fname = os.path.join(algorithm, "stack_{}_".format(seq))
fname = os.path.join(os.getcwd(), fname)
imgs = output_images(arr, args.size, fname,
args.format, args.scale, args.ncol)
else:
print("Reconstructing with {}...".format(args.algorithm))
imgs = run(args.algorithm, args.size, args.angles, args.ncores,
args.format, args.scale, args.ncol)
# timing report to stdout
print('{}'.format(manager))
timemory.options.output_dir = "./{}".format(algorithm)
timemory.options.set_report("run_tomopy_{}.out".format(algorithm))
timemory.options.set_serial("run_tomopy_{}.json".format(algorithm))
manager.report()
#------------------------------------------------------------------#
# provide timing plots
try:
timemory.plotting.plot(files=[timemory.options.serial_filename], echo_dart=True)
except Exception as e:
print("Exception - {}".format(e))
#------------------------------------------------------------------#
# provide results to dashboard
try:
for i in range(0, len(imgs)):
img_base = "{}_stack_".format(algorithm, i)
img_name = os.path.basename(imgs[i]).replace(
".{}".format(args.format), "").replace(
"stack_{}_".format(algorithm), img_base)
img_type = args.format
img_path = imgs[i]
timemory.plotting.echo_dart_tag(img_name, img_path, img_type)
except Exception as e:
print("Exception - {}".format(e))
#------------------------------------------------------------------#
# provide ASCII results
try:
notes = manager.write_ctest_notes(directory="{}".format(algorithm))
print('"{}" wrote CTest notes file : {}'.format(__file__, notes))
except Exception as e:
print("Exception - {}".format(e))
modu_len = args.size % args.ncol
real_len = len(imgs)
if modu_len > 0:
expt_len = (args.size / args.ncol) + 1
else:
expt_len = (args.size / args.ncol)
if real_len != expt_len:
exc_type, exc_value, exc_traceback = sys.exc_info()
traceback.print_exception(exc_type, exc_value, exc_traceback, limit=5)
msg = "Error! number of images ({}) does not match the expected total ({})!".format(
expt_len, real_len)
raise Exception(msg)
#------------------------------------------------------------------------------#
if __name__ == "__main__":
parser = argparse.ArgumentParser()
import multiprocessing as mp
ncores = mp.cpu_count()
parser.add_argument("-a", "--algorithm", help="Select the algorithm",
default="gridrec", choices=algorithms, type=str)
parser.add_argument("-A", "--angles", help="number of angles",
default=360, 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="jpeg", 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)
args = timemory.options.add_args_and_parse_known(parser)
if len(args.compare) == 1 and args.compare[0].lower() == "all":
args.compare = list(algorithms)
elif len(args.compare) == 1:
args.compare = []
if len(args.compare) == 0:
try:
import shutil
dir = os.path.join(os.getcwd(), args.algorithm)
shutil.rmtree(dir)
os.makedirs(dir)
except:
pass
else:
try:
import shutil
dir = os.path.join(os.getcwd(), "comparison")
shutil.rmtree(dir)
os.makedirs(dir)
except:
pass
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 = 2
os.kill(os.getpid(), signal.SIGHUP)
sys.exit(ret)Release history Release notifications | RSS feed
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