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xmipp_old
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#!/usr/bin/env python3
# ***************************************************************************
# * Authors: Carlos Oscar S. Sorzano (coss@cnb.csic.es)
# * David Maluenda (dmaluenda@cnb.csic.es)
# *
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# ***************************************************************************/
import os
import re
import shutil
import sys
from datetime import datetime
import json
from scripts import *
from scripts.utils import checkCMakeVersion
# ----K-E-E-P----U-P-D-A-T-E-D---- #
####################################
XMIPP_VERSION = '3.23.11.0' #
XMIPP_VERNAME = 'devel' #
RELEASE_DATE = '28/11/2023' #
CMAKE_VERSION_REQUIRED = '3.16' #
####################################
XMIPP = 'xmipp'
XMIPP_CORE = 'xmippCore'
XMIPP_VIZ = 'xmippViz'
SCIPION_EM_XMIPP = 'scipion-em-xmipp'
CUFFTADVISOR = 'cuFFTAdvisor'
CTPL = 'CTPL'
GTEST = 'googletest'
LIBSVM = 'libsvm'
LIBCIFPP = 'libcifpp'
VERSION_FILE = 'xmipp_version.txt'
COMPILE_LOG = 'compileLOG.txt'
CONFIG_FILE = 'xmipp.conf'
COMPRESED_REPORT = 'reportInstallation.tar.gz'
REPOSITORIES = {XMIPP: 'https://github.com/I2PC/xmipp.git',
XMIPP_CORE: 'https://github.com/I2PC/xmippCore.git',
XMIPP_VIZ: 'https://github.com/I2PC/xmippViz.git',
SCIPION_EM_XMIPP: 'https://github.com/I2PC/scipion-em-xmipp.git',
CUFFTADVISOR: 'https://github.com/DStrelak/cuFFTAdvisor.git',
CTPL: 'https://github.com/vit-vit/CTPL.git',
GTEST: 'https://github.com/google/googletest',
LIBSVM: 'https://github.com/cossorzano/libsvm.git',
LIBCIFPP: 'https://github.com/MartinSalinas98/libcifpp'}
# {dep-repo: (branch, check-conf)}
DEPENDENCIES = {CUFFTADVISOR: ('master', 'CUDA'),
CTPL: ('master', None),
GTEST: ('v1.13.x', None),
LIBSVM: ('master', None),
LIBCIFPP: ('ms_feature_ciflibrary', None)}
# if a skippable compilation fails (if 'key' found in the failed code),
# a hint is printed in order to export 'value' or edit the config file
SKIPPABLE_BINS = {"optical_alignment": "OPENCV=False",
"volume_homogenizer": "OPENCV=False",
"cuda": "CUDA=False"}
XMIPP_ENV = {}
def checkGithubConnection():
from http.client import HTTPConnection
from socket import gaierror
conn = HTTPConnection("www.github.com", timeout=3)
try:
conn.request("HEAD", "/")
return True
except gaierror:
return False
finally:
conn.close()
def stampVersion():
LAST_COMPILATION = datetime.now().strftime("%d/%m/%Y")
def getCommit(repo):
""" In devel mode 'commit.info' should not exist.
In production mode 'commit.info' is added by tar.py
"""
commitFn = os.path.join('src', repo, 'commit.info')
notFoundInfo = "(no git repo detected)"
if os.path.isfile(commitFn):
with open(commitFn, 'r') as file:
commitInfo = file.readline()
elif ensureGit(False)[0]:
found, br, hsh = getCurrentBranch(os.path.join('src', repo),
getHash=True)
commitInfo = "%s (%s)" % (br, hsh) if found else notFoundInfo
else:
commitInfo = notFoundInfo
return commitInfo
compilingInfo = {'XMIPP_VERSION': XMIPP_VERSION,
'RELEASE_DATE': RELEASE_DATE,
'XMIPP_BRANCH': getCommit(XMIPP),
'PLUGIN_BRANCH': getCommit(SCIPION_EM_XMIPP),
'CORE_BRANCH': getCommit(XMIPP_CORE),
'VIZ_BRANCH': getCommit(XMIPP_VIZ),
'LAST_COMPILATION': LAST_COMPILATION,
'XMIPP_VERNAME': XMIPP_VERNAME
}
versionBinFn = os.path.join('src', 'xmipp', 'applications', 'programs',
'version', 'version.cpp')
createDir(os.path.dirname(versionBinFn))
with open(versionBinFn, 'w') as f:
f.write("""// Auto-generated code to get compilation Info
#include <sys/utsname.h>
#include <iostream>
#include <string.h>
using namespace std;
int main(int argc, char** argv){
if (argc>2)
{
std::cout << "Incorrect parameter" << std::endl;
return 1;
}
int shrt = 0;
if (argc>1)
{
if((strcmp(argv[1], "--short") == 0))
{
shrt = 1;
}else{
std::cout << "Incorrect parameter: " << argv[1] << std::endl;
return 2;
}
}
if (shrt==1)
{
std::cout << "%(XMIPP_VERSION)s" << std::endl;
}else{
struct utsname utsname; // stores the data returned by uname()
struct utsname *utsname_ptr = &utsname; // pointer to the struct holding the data returned by uname()
int ret;
ret = uname(utsname_ptr);
std::cout << std::endl;
std::cout << " \033[4mXmipp version\033[24m: \033[1m%(XMIPP_VERSION)s (%(XMIPP_VERNAME)s)\033[0m" << std::endl;
std::cout << std::endl;
std::cout << " Release date: %(RELEASE_DATE)s" << std::endl;
std::cout << " Xmipp branch: %(XMIPP_BRANCH)s" << std::endl;
std::cout << " Plugin branch: %(PLUGIN_BRANCH)s" << std::endl;
std::cout << " Core branch: %(CORE_BRANCH)s" << std::endl;
std::cout << " Viz branch: %(VIZ_BRANCH)s" << std::endl;
std::cout << " Compilation date: %(LAST_COMPILATION)s" << std::endl;
std::cout << " System compiler: g++ " << __VERSION__ << std::endl;
std::cout << " System: " << utsname.machine << " " << utsname.sysname
<< " " << utsname.release << std::endl
<< " " << utsname.version << std::endl;
std::cout;
}
return 0;
}
""" % compilingInfo)
def createDir(dirname):
if not os.path.exists(dirname):
os.makedirs(dirname)
def cleanSources():
for dep in DEPENDENCIES.keys():
runJob("rm -rf src/%s" % dep)
runJob("rm -rf src/scipion-em-xmipp")
runJob("rm -rf src/xmippCore")
runJob("rm -rf src/xmippViz")
runJob("rm -rf src/xmipp/bin")
runJob("rm -rf src/xmipp/lib")
runJob("rm -rf src/xmipp/.sconsign.dblite")
if ensureGit(False)[0]:
runJob("git stash") # to get exactly like in repo
def cleanBinaries():
for ext in ['so', 'os', 'o']:
runJob('find src/* -name "*.%s" -exec rm -rf {} \;' % ext, showWithReturn=False)
runJob('find . -iname "*.pyc" -delete', showWithReturn=False)
runJob("rm -rf %s build" % Config.FILE_NAME, showWithReturn=False)
# I'm getting ValueError : unsupported pickle protocol: 5' when switching from one python version to another
# This seems to be cached at dblite file.
runJob('find . -iname "*.dblite" -delete', showWithReturn=False)
cleanEmptyFolders()
def cleanDeprecated():
listCurrentPrograms = []
listFilesXmipp = []
runJob('find src/xmipp/bin/*', log=listFilesXmipp,
show_command=False, show_output=False)
listFilesXmipp = [os.path.basename(x).replace('xmipp_', '') for x in listFilesXmipp]
listCurrentFolders = [x[0] for x in os.walk('src/xmipp/applications/programs/')]
for folder in listCurrentFolders[1:]:
for file in os.listdir(folder):
if '.cpp' in file:
listCurrentPrograms.append(os.path.basename(folder))
listCurrentScripts = [os.path.basename(x[0]) for x in os.walk('src/xmipp/applications/scripts/')]
listCurrentPrograms = listCurrentPrograms + listCurrentScripts[1:]
list2RemoveXmipp = [x for x in listFilesXmipp if (x not in listCurrentPrograms and 'test_' not in x)]
for x in list2RemoveXmipp:
runJob('rm src/xmipp/bin/xmipp_{}'.format(x))
if len(list2RemoveXmipp) > 0:
print('Deprecated programs removed')
def cleanEmptyFolders():
log = []
path = "src/xmipp/applications/programs/"
runJob("find {} –type d -empty".format(path), log=log, show_output=False,
showWithReturn=False)
for folder in log:
if os.path.isdir(folder):
runJob("rm -rf {}".format(folder))
def checkout(branch):
log = []
r, currentBranch = getCurrentBranch()
if currentBranch == branch:
return True
isRepositoryClean()
if runJob("git checkout %s" % branch, log=log, show_command=False, show_output=False):
return True
else:
print(yellow("Cannot checkout branch '%s'. Remaining on the branch '%s'." % (branch, currentBranch)))
return True
def isRepositoryClean(showError=True):
log = []
runJob('git diff --name-only', show_output=False, show_command=False, log=log)
if showError and log: # non-empty log means there are uncommited changes
print(red('Repository contains uncommitted changes.'))
print(red("Use 'compileAndInstall' mode to keep developing."))
return not log
def pull():
log=[]
isRemoteBranch = runJob('git rev-parse HEAD@{upstream}', show_command=False, show_output=False, log=log)
if not isRemoteBranch:
print(yellow(str('Git info: ' + log[0])))
if checkGithubConnection() and isRemoteBranch:
return runJob("git pull", show_command=False, show_output=False)
print(yellow('Local branch, no upstream for this'))
return True # meaning that this is a local branch or we are offline, so pull doesn't make sense
def cloneOrCheckout(repo, branch):
branchName = branch
repo_dir = os.path.join('src', repo) if repo != XMIPP else '.'
if not os.path.exists(repo_dir):
if branch not in getAllBranchesAndTags(repo):
branchName = 'HEAD'
branch = None
print('Cloning repository: {}/{}'.format(repo, branchName))
print(yellow('Working...'), end='\r')
# If the repo doesn't exist, just clone the whole repo
log = []
if branch is None:
# let the git client to decide what is the default branch
status = runJob("git clone %s %s" % (REPOSITORIES[repo], repo_dir),
show_output=False, show_command=False, log=log)
if status == False:
exitProgram(1, [False, 1, ''.join(log), "Please review the conexion to the repository"])
else:
status = runJob("git clone -b %s %s %s" % (branch, REPOSITORIES[repo], repo_dir),
show_output=False, show_command=False, log=log)
if status == False:
exitProgram(1, [False, 1, ''.join(log), "Please review the conexion to the repository"])
return True
else:
print('Checkouting and pull repository: {}/{}'.format(repo, branch))
print(yellow('Working...'), end='\r')
workDir = os.getcwd()
os.chdir(repo_dir)
checkout(branch)
pull()
os.chdir(workDir)
return True
def removePrefix(text, prefix):
if text.startswith(prefix):
return text[len(prefix):]
return text
def getCurrentCIBranch():
# see https://docs.travis-ci.com/user/environment-variables/
# see https://docs.github.com/en/actions/reference/environment-variables#default-environment-variables
# On Travis, PR will have the TRAVIS_PULL_REQUEST_BRANCH variable non-empty
# otherwise the TRAVIS_BRANCH will hold the name of the current branch
# On Github Actions, GITHUB_REF will hold either the tag or branch (including prefix) to the branch which triggered
# the workflow
# For pull request, GITHUB_HEAD_REF will be set (no prefix)
current_branch = (
os.environ.get('TRAVIS_PULL_REQUEST_BRANCH') or
os.environ.get('TRAVIS_BRANCH') or
os.environ.get('GITHUB_HEAD_REF') or
os.environ.get('GITHUB_REF'))
current_branch = removePrefix(current_branch, 'refs/heads/')
current_branch = removePrefix(current_branch, 'refs/tags/')
print(green("Detected branch: " + current_branch))
return current_branch is not None, current_branch
def getCurrentBranch(cwd='./', getHash=False):
""" If getHash=True: return (success, branch, hash)
If getHash=False: return (success, branch)
"""
outBranchArgs = 2 if getHash else 1
log = []
commit = []
if not os.path.exists(cwd) or not runJob('git rev-parse --short HEAD',
cwd=cwd, show_output=False,
show_command=False, log=commit):
return (False,) + (None,)*outBranchArgs
result = runJob('git name-rev ' + commit[0], cwd=cwd, show_output=False,
show_command=False, log=log)
if result: # log contains commit_space_branchName
return (True,) + tuple(log[0].split()[::-1][0:outBranchArgs])
print(yellow('Cannot list branches for ' + ''.join(log)))
return (False,) + (None,)*outBranchArgs
def getAllBranchesAndTags(repo):
log = []
result = runJob('git ls-remote -t -h %s' % REPOSITORIES[repo],
show_output=False, log=log, show_command=False)
if result:
branchesAndTags = [l.split('/')[-1] for l in log]
return branchesAndTags
strError = 'Cannot list branches for ' + repo + ' ' + ''.join(log)
status = [False, 1, strError, "Please review the connetion to the repository"]
exitProgram(1, status)
def getDefaultBranch(repo):
log = []
key = 'HEAD branch:'
# this might not work for git < 1.8.5,
# see https://stackoverflow.com/a/32503667/5484355
# and https://stackoverflow.com/questions/2832269/git-remote-head-is-ambiguous
# In such a case we return None (and during e.g. clone the client should
# decide what is the default branch)
result = runJob('git remote show %s' % REPOSITORIES[repo],
show_output=False, log=log, show_command=False)
if result:
for l in log:
if key in l:
branch = l.split(key)[1] # HEAD branch: devel
return (True, branch.strip())
exitProgram(1, [False, 1, 'Cannot auto-detect default branch for ' + repo +
'. Maybe git version < 1.8.5?\n' + ''.join(log),
'Check the git version, the languaje must be english, check also '
'the internet connetion'])
def getSources(branch):
print("\nGetting Xmipp sources ------------------------------------")
if ensureGit(True)[0] == False:
exitProgram(status[1])
createDir("src")
repos = [XMIPP_CORE, XMIPP_VIZ, SCIPION_EM_XMIPP]
if not isCIBuild():
# do not change current commit
repos.append(XMIPP)
for r in repos:
if cloneOrCheckout(r, branch):
print(green('Done '))
return True
def getDependencies():
print("\nGetting external dependencies ----------------------------")
status = ensureGit(True)
if status[0] == False:
exitProgram(status[1], status)
createDir("src")
for dep, args in DEPENDENCIES.items():
branch = args[0]
configChecked = not args[1] or buildConfig.is_true(args[1])
if configChecked:
cloneOrCheckout(dep, branch)
print(green('Done '))
return True
def printVersion():
buildDir = 'build'
shortFlag = ''
log = []
for arg in sys.argv[2:]:
if arg == '--short':
shortFlag = '--short'
elif arg.startswith('dir='):
buildDir = arg[4:]
versionBin = "%s/bin/xmipp_version" % buildDir
envSetting = "%s/xmipp.bashrc" % buildDir
if not (os.path.isfile(versionBin) and os.path.isfile(envSetting)):
print("Build not found...")
else:
runJob(". %s ; %s %s" % (envSetting, versionBin, shortFlag),
show_command=False, log=log)
if not log:
log = 'System information not available'
else:
log = '\n'.join(log)
log = log.replace('\x1b[4m', '')
log = log.replace('\x1b[24m', '')
log = log.replace('\x1b[1m', '')
log = log.replace('\x1b[0m', '')
logCmake = []
runJob('cmake --version', log=logCmake, show_command=False, show_output=False)
if not logCmake:
logCmake = 'cmake information not available'
else:
logCmake = logCmake[0]
print(' {}'.format(logCmake))
logNvcc = []
runJob('nvcc --version', log=logNvcc, show_command=False, show_output=False)
if not logNvcc:
logNvcc = 'nvcc information not available'
else:
logNvcc = ''.join(logNvcc)
logNvcc = logNvcc[logNvcc.find('release'):logNvcc.find('release') + 12]
print(' nvcc version: {}'.format(logNvcc))
with open(VERSION_FILE, 'w') as f:
if log:
f.write(log)
f.write('\n nvcc version: ')
f.write(logNvcc)
f.write('\n ')
f.write(logCmake)
def getScipionHome():
""" Returns SCIPION_HOME, the directory for scipion3 or EMPTY str. """
return os.environ.get("SCIPION_HOME", whereis("scipion3")) or ''
def compileModule(Nproc,module):
sconsProgress = True
printProgress = False
progresLines = 1
progresLinesPrecompiled = 1
print(yellow('Working... Visit compileLOG.txt for details'), end='\r')
if module == "xmipp":
write_compileLog('\n\n' + '#' * 27 + '\nCompiling Xmipp------------\n',
COMPILE_LOG=COMPILE_LOG)
printProgress = True
progresLines = 780 #773
progresLinesPrecompiled = 235 #232
if module == "xmippCore":
write_compileLog('\n\n' + '#' * 27 + '\nCompiling XmippCore--------\n',
COMPILE_LOG=COMPILE_LOG)
if module == "xmippViz":
write_compileLog('\n\n' + '#' * 27 + '\nCompiling XmippViz---------\n',
COMPILE_LOG=COMPILE_LOG)
log = []
ok = runJob("/usr/bin/env python3 -u $(which scons) -j%s" % Nproc, "src/%s" % module, log=log,
show_command=False, sconsProgress=sconsProgress, progresLines=progresLines,
progresLinesPrecompiled=progresLinesPrecompiled, printProgress=printProgress,
COMPILE_LOG=COMPILE_LOG)
lastError= ''
#print(yellow('len log scons module: {}: {}'.format(module, len(log))))
if not ok:
failingBin = None
for l in log[-30:]: # inspecting last 30 lines
# expected error: 'scons: *** [some/program/to/compile] Error 1'
errorRegex = re.match("scons: \*\*\* \[(.*)\] (.*Error) ([0-9]*)[: ]*(.*)", l)
if errorRegex:
failingBin = errorRegex.group(1)
errorType = errorRegex.group(2)
errorNum = errorRegex.group(3)
errorMsg = errorRegex.group(4)
for k, v in SKIPPABLE_BINS.items():
if k in failingBin:
exitProgram(1, [False, 1,
"\nSome error found compiling '%s' program."
% failingBin.split('/')[-1],
"You can skip this program by including '%s' "
"in the config file." % (v)])
if 'unsupported pickle protocol' in errorMsg:
exitProgram(1, [False, 1, 'Unsupported pickle protocol',
"\nThis error might be because you changed the python "
"version. If so, please run './xmipp cleanBin' to "
"clean up the installation and, then re-compile Xmipp."])
errorRegex = re.match(".*: fatal error: (.*): No such file or directory", l)
if errorRegex:
missingPath = errorRegex.group(1)
if lastError != missingPath:
lastError = missingPath
missingDir = missingPath.split(os.path.sep)[0]
missingFile = os.path.join(*missingPath.split(os.path.sep))
if len(missingFile) > 1:
missingFile = missingFile[1:]
if missingDir in DEPENDENCIES.keys():
depDir = os.path.join('src', missingDir)
hint = ('cd %s ; git checkout -- %s ; cd -' % (depDir, missingFile)
if os.path.isdir(depDir) else './xmipp get_dependencies')
strSupport = "This file belongs to %s dependency. Please, " \
"try '%s' and re-compile." % (missingDir, hint)
else: strSupport = 'Run /xmipp cleanAll to remove all repositories ' \
'(local changes will be removed) and compile Xmipp from scrach'
exitProgram(1, [False, 1, "\n'%s' file not found." % missingPath, strSupport])
exitProgram(1, [False, 1, "Some error occurred during the compilation of %s %s" %
(module, (" ('%s')" % failingBin) if failingBin else ''),
''])
print(green('Done. Visit compileLOG.txt for details' + (' ' * 70)))
return ok
def compile_cuFFTAdvisor():
print("Building cuFFTAdvisor...")
print(yellow('Working...'), end='\r')
log = []
advisorDir = "src/cuFFTAdvisor/"
currDir = os.getcwd()
libDir = "src/xmipp/lib/"
createDir(libDir)
os.chdir(advisorDir)
if runJob("make all", show_command=False, show_output=False, log=log):
log2 = []
os.chdir(currDir)
if runJob("cp " + advisorDir + "build/libcuFFTAdvisor.so" + " " + libDir, log=log2, show_output=False, show_command=False):
print(green("Done "))
os.chdir(currDir)
return True, log + log2
else:
os.chdir(currDir)
print(red(log[0]))
return False, log + log2
else:
os.chdir(currDir)
print(red(log[0]))
return False, log
def compile_googletest():
print("Building googletest...")
print(yellow('Working...'), end='\r')
log = []
currDir = os.getcwd()
buildDir = os.path.join("src", "googletest", "build")
createDir(buildDir)
os.chdir(buildDir)
if runJob("cmake ..", show_output=False, show_command=False, log=log):
log2 = []
if runJob("make gtest gtest_main", show_output=False,
show_command=False, log=log2):
os.chdir(currDir)
print(green("Done "))
return True, log + log2
else:
os.chdir(currDir)
print(red(str(log + log2)))
return False, log + log2
else:
os.chdir(currDir)
print(red(str(log)))
return False, log
def compile_libsvm():
print("Building libsvm...")
print(yellow('Working...'), end='\r')
log = []
#if the libsvm repo is updated, remember that the repoFork/Makefile was edited to remove references to libsvm-so.2
currDir = os.getcwd()
libsvmDir = os.path.join("src", "libsvm")
os.chdir(libsvmDir)
if runJob("make lib", show_output=False, show_command=False, log=log):
log2 = []
libDir = "src/xmipp/lib"
os.chdir(currDir)
createDir(libDir)
if runJob("cp " + libsvmDir + "/libsvm.so" + " " + libDir, log=log2, show_command=False, show_output=False):
os.chdir(currDir)
print(green("Done "))
return True, log + log2
else:
os.chdir(currDir)
print(red(log[0]))
return False, log + log2
else:
os.chdir(currDir)
print(red(log[0]))
return False, log
def compile_libcifpp(Nproc):
print("Building libcifpp...")
print(yellow('Working...'), end='\r')
log = []
# Check if CMake version is up to date
error = checkCMakeVersion(CMAKE_VERSION_REQUIRED)
if error[0] == False:
exitProgram(1, error[1])
return False, log
currDir = os.getcwd()
# Moving to library directory
libcifppDir = os.path.join("src", "libcifpp")
os.chdir(libcifppDir)
# Installing
fullDir = os.path.join(currDir, libcifppDir, '')
if runJob("cmake -S . -B build -DCMAKE_INSTALL_PREFIX=" + fullDir + " -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DCIFPP_DOWNLOAD_CCD=OFF -DCIFPP_INSTALL_UPDATE_SCRIPT=OFF",
show_output=False, show_command=False, log=log):
log1 = []
if runJob(f"cmake --build build -j {Nproc}", show_output=False, show_command=False, log=log1):
log2 = []
if runJob("cmake --install build", show_output=False, show_command=False, log=log2):
# Check if libcifpp created up on compiling lib or lib64 directory
libcifppLibDir = "lib64" if os.path.exists("lib64") else "lib"
# Copying .so file
os.chdir(currDir)
libDir = "src/xmipp/lib"
createDir(libDir)
log3 = []
if runJob("cp " + os.path.join(libcifppDir, libcifppLibDir, "libcifpp.so*") + " " + libDir, log=log3, show_output=False, show_command=False):
print(green("Done" + (' ' * 70)))
return True, log + log1 + log2 + log3
else:
print(red(log[0]))
return False, log + log1 + log2 + log3
else:
os.chdir(currDir)
print(red(log[0]))
return False, log + log1 + log2
else:
os.chdir(currDir)
print(red(log[0]))
return False, log + log1
else:
os.chdir(currDir)
print(red(log[0]))
return False, log
def checkScons():
return runJob("scons --version", show_output=False, show_command=False)
def compile(Nproc):
if checkScons():
if isinstance(Nproc, str) and Nproc.startswith('N='):
Nproc = int(Nproc.split('N=')[1])
buildConfig.check_version(XMIPP_VERNAME)
todayDate = 'Compilation Date: {}\n'.format(datetime.today())
write_compileLog(todayDate, append=False, COMPILE_LOG=COMPILE_LOG)
if not compileDependencies(Nproc):
return False
return compileXmipp(Nproc)
else:
exitProgram(15)
def compileDependencies(Nproc):
print("\nBuilding Dependencies ------------------------------------")
if buildConfig.is_true('CUDA'):
cudaBinDir, nvccBaseName = os.path.split(buildConfig.get()['NVCC'])
# cuFFTAdvisor compilation needs 'nvcc' accessible through the PATH
if not checkProgram(nvccBaseName)[0] and checkProgram(buildConfig.get()['NVCC'])[0]:
# if nvcc basename is not found but absolute path yes, adding the dir to the path.
os.environ['PATH'] = os.pathsep.join([cudaBinDir, os.environ['PATH']])
if (checkProgram('make') or installDepConda('make')):
write_compileLog('\n\n' + '#' * 27 + '\nCompiling cuFFTAdvisor--------\n',
COMPILE_LOG=COMPILE_LOG)
result, log = compile_cuFFTAdvisor()
write_compileLog('\n'.join(log), COMPILE_LOG=COMPILE_LOG)
if not result:
exitProgram(16)
write_compileLog('\n\n' + '#' * 27 + '\nCompiling googletest--------\n',
COMPILE_LOG=COMPILE_LOG)
result, log = compile_googletest()
write_compileLog('\n'.join(log), COMPILE_LOG=COMPILE_LOG)
if not result:
exitProgram(17)
write_compileLog('\n\n' + '#' * 27 + '\nCompiling libsvm--------\n',
COMPILE_LOG=COMPILE_LOG)
result, log = compile_libsvm()
write_compileLog('\n'.join(log), COMPILE_LOG=COMPILE_LOG)
if not result:
exitProgram(18)
write_compileLog('\n\n' + '#' * 27 + '\nCompiling libcifpp--------\n',
COMPILE_LOG=COMPILE_LOG)
result, log = compile_libcifpp(Nproc)
write_compileLog('\n'.join(log), COMPILE_LOG=COMPILE_LOG)
if not result:
exitProgram(19)
return True
def compileXmipp(Nproc):
stampVersion()
print("\nCompiling xmippCore---------------------------------------")
if not compileModule(Nproc,"xmippCore"):
return False
print("\nCompiling xmipp-------------------------------------------")
if not compileModule(Nproc,"xmipp"):
return False
print("\nCompiling xmippViz----------------------------------------")
if not compileModule(Nproc,"xmippViz"):
return False
# Merge Xmipp and XmippCore compiled databases
cdb_list = ["compile_commands.json", "compile_commands_2.json"]
merged = list()
for cdb in cdb_list:
if os.path.exists(cdb):
with open(cdb, 'r') as cdb_id:
merged.extend(json.load(cdb_id))
with open("compile_commands.json", 'w') as cdb_id:
json.dump(merged, cdb_id)
if os.path.exists("compile_commands_2.json"):
os.remove("compile_commands_2.json")
return True
def runTests(testNames):
if len(testNames)==0 or 'help' in testNames or '--help' in testNames:
print("Usage: xmipp test op\n"
"\n"
" op = --show: Show how to invoke all available tests\n"
" --allPrograms: Run all program tests\n"
" --allFuncs: Run all function tests\n"
" 'testName': Run certain test (more than one is available)."
"\n")
return
print("Testing ---------------------------------------------")
xmippSrc = os.environ.get('XMIPP_SRC', None)
if xmippSrc and os.path.isdir(xmippSrc):
os.environ['PYTHONPATH'] = ':'.join([
os.path.join(os.environ['XMIPP_SRC'], XMIPP),
os.environ.get('PYTHONPATH', '')])
testsPath = os.path.join(os.environ['XMIPP_SRC'], XMIPP, 'tests')
else:
print(red('XMIPP_SRC is not in the enviroment.') +
'\nTo run the tests you need to run: ' +
blue('source build/xmipp.bashrc'))
exitProgram(0)
dataSetPath = os.path.join(testsPath, 'data')
# if not os.path.isdir(dataSetPath):
# createDir(dataSetPath)
os.environ["XMIPP_TEST_DATA"] = dataSetPath
# downloading/updating the dataset
url = "http://scipion.cnb.csic.es/downloads/scipion/data/tests"
dataset = 'xmipp_programs'
if os.path.isdir(dataSetPath):
print(blue("Updating the test files"))
task = "update"
else:
print(blue("Downloading the test files"))
task = "download"
args = "%s %s %s" % ("tests/data", url, dataset)
runJob("bin/xmipp_sync_data %s %s" % (task, args), cwd='src/xmipp')
noCudaStr = '--noCuda' if not buildConfig.is_true('CUDA') else ''
print(" Tests to do: %s" % ', '.join(testNames))
if not runJob("(cd src/xmipp/tests; %s test.py %s %s)"
% (getPython(), ' '.join(testNames), noCudaStr)):
sys.exit(-1)
def getPython():
if checkProgram("scipion3")[0]:
return "scipion3 python"
else:
return 'python3'
def addDeepLearninModel(login, modelPath='', update=None):
""" Takes the folder name modelName from models dir and
makes a .tgz, uploads the .tgz to scipion web.
"""
def usageDL():
print("""
XMIPP addModel help:
This mode is used to upload a model folder to the Scipion/Xmipp server.
Usually the model folder contains big files used to fed deep learning procedures
with pretrained data. All the models stored in the server will be downloads
using the 'get_models' mode or during the compilation/installation time
if 'USE_DL=True' in the config file. [or with 'scipion3 installb deepLearningToolkit']
modelsPath must be the absolute path
Usage: -> ./xmipp addModel <usr@server> <modelsPath> [--update]
Behaviour: 0. modelName = basename(modelsPath) <- Please, check the folder's name!
1. Packing in 'xmipp_model_modelName.tgz'
2. Check if that model already exists (use --update to override an existing model)
3. Upload the model to the server.
4. Update the MANIFEST file.
The model name will be the folder name in <modelsPath>
""")
sys.exit(0)
if login == '--help':
usageDL()
modelPath = modelPath.rstrip("/")
if not os.path.isdir(modelPath):
print("<modelsPath> is not a directory. Please, check the path. \n"
"The name of the model will be the name of that folder.\n")
usageDL()
modelName = os.path.basename(modelPath)
modelsDir = os.path.dirname(modelPath)
tgzFn = "xmipp_model_%s.tgz" % modelName
localFn = os.path.join(modelsDir, tgzFn)
print("Creating the '%s' model." % tgzFn)
runJob("tar czf %s %s" % (tgzFn, modelName), cwd=modelsDir)
remotePath = "scipionfiles/downloads/scipion/software/em"
print("Warning: Uploading, please BE CAREFUL! This can be dangerous.")
print('You are going to be connected to "%s" to write in folder '
'"%s".' % (login, remotePath))
if input("Continue? YES/no\n").lower() == 'no':
sys.exit()
print("Trying to upload the model using '%s' as login" % login)
args = "%s %s %s %s" % (login, os.path.abspath(localFn), remotePath, update)
if runJob("src/xmipp/bin/xmipp_sync_data upload %s" % args):
print("'%s' model successfully uploaded! Removing the local .tgz"
% modelName)
runJob("rm %s" % localFn)
pDLdownload = None
def downloadDeepLearningModels(dest, dedicatedMode=False):
if not buildConfig.is_true('USE_DL') and not dedicatedMode:
return True
url = "http://scipion.cnb.csic.es/downloads/scipion/software/em"
if not os.path.exists('build/bin/xmipp_sync_data'):
print(red('Xmipp has not been installed. Please, first install it '))
return False
if dest == 'build':
modelsPath = os.path.join(dest, 'models')
else:
modelsPath = dest
dataSet = "DLmodels"
# downloading/updating the DLmodels
if os.path.isdir(modelsPath):
print("Updating the Deep Learning models (in backgound)")
task = "update"
else:
print("Downloading Deep Learning models (in backgound)")
task = "download"
global pDLdownload
# using Popen instead of runJob in order to download in parallel
pDLdownload = runJob("bin/xmipp_sync_data %s %s %s %s"
% (task, dest, url, dataSet),
cwd='build', show_command=False,
in_parallel=not dedicatedMode)
if dedicatedMode:
ok = pDLdownload
else: # in parallel poll() is None untill finished
ok = pDLdownload.poll() is None or pDLdownload.poll() == 0
return ok
def linkToScipion(dirname):
scipionSoftware = os.environ.get('SCIPION_SOFTWARE',
os.path.join(getScipionHome(), 'software'))
scipionLibs = os.path.join(scipionSoftware, 'lib')
scipionBindings = os.path.join(scipionSoftware, 'bindings')
scipionSoftwareEM = os.path.join(scipionSoftware, 'em')
xmippHomeLink = os.path.join(scipionSoftwareEM, 'xmipp')
currentDir = os.getcwd()
dirnameAbs = os.path.join(currentDir,dirname)
if os.path.isdir(scipionLibs) and os.path.isdir(scipionBindings):
print("\nLinking to Scipion ---------------------------------------")
print(yellow('Working...'), end='\r')
if os.path.isdir(xmippHomeLink):
runJob("rm %s" %xmippHomeLink)
runJob("ln -srf %s %s" % (dirnameAbs, xmippHomeLink))
xmippLink = os.readlink(xmippHomeLink)
coreLib = os.path.join(xmippLink, "lib", "libXmippCore.so")
xmippLib = os.path.join(xmippLink, "lib", "libXmipp.so")
SVMLib = os.path.join(xmippLink, "lib", "libsvm.so")
CIFPPLib = os.path.join(xmippLink, "lib", "libcifpp.so*")
bindings = os.path.join(xmippLink, "bindings", "python", "*")
os.chdir(scipionSoftwareEM)
runJob("ln -srf %s %s" % (coreLib, scipionLibs))
runJob("ln -srf %s %s" % (SVMLib, scipionLibs))
runJob("ln -srf %s %s" % (CIFPPLib, scipionLibs))
runJob("ln -srf %s %s" % (xmippLib, scipionLibs))
runJob("ln -srf %s %s" % (bindings, scipionBindings))
os.chdir(currentDir)
print(green(str("Xmipp linked to Scipion on " + xmippHomeLink) + (' ' * 150)))
else:
print(yellow("No scipion3 found. If you intended to use Xmipp in "
"the Scipion framework:\ncompile Xmipp "
"with Scipion './scipion3 run ./xmipp' or check the binding at "
"SCIPION_HOME/software/bindings..."))
def install(dirname):
print("\nInstalling -----------------------------------------------")
print(yellow('Working...'), end='\r')
if XMIPP_VERNAME =='devel': show_command = True
else: show_command = False
cleanDeprecated()
cpCmd = "rsync -LptgoD " if checkProgram("rsync") else "cp"
ok = True
createDir(dirname)
createDir(dirname+"/lib")
ok = ok and runJob(cpCmd+" src/*/lib/lib* "+dirname+"/lib/", show_command=show_command)
if os.path.exists(dirname + "/bin"):
shutil.rmtree(dirname + "/bin")
createDir(dirname+"/bin")
dirBin = os.path.join(os.getcwd(), "src/xmipp/bin/")
filenames = os.listdir(dirBin)
for f in filenames:
if os.path.islink(os.path.join(dirBin, f)):
ok = ok and runJob('ln -s ' + os.path.join(dirBin, f) + ' ' + os.path.join(dirname, 'bin', f), show_command=show_command, show_output=False)
else:
ok = ok and runJob(cpCmd + os.path.join(dirBin, f) + ' ' + os.path.join(dirname, 'bin', f), show_command=show_command)
destPathPyModule = os.path.expanduser(os.path.abspath(os.path.join(dirname, "pylib", "xmippPyModules")))
createDir(destPathPyModule)
initFn = destPathPyModule + "/__init__.py"
if not os.path.isfile(initFn):
with open(initFn, 'w') as f:
pass # just to create a init file to be able to import it as module
dirBin = os.path.join(os.getcwd(), 'src/xmipp/libraries/py_xmipp')
folders = list(os.walk(dirBin))
for folderPath, _, folderFiles in folders:
folderName = os.path.relpath(folderPath, dirBin)
createDir(os.path.join(destPathPyModule, folderName))
for file in folderFiles:
runJob("ln -s " + os.path.join(folderPath, file) + ' ' + os.path.join(destPathPyModule, folderName, file),
show_output=False, show_command=show_command, log=[])
createDir(dirname+"/bindings")
createDir(dirname+"/bindings/matlab")
ok = ok and runJob(cpCmd+" src/xmipp/bindings/matlab/*.m* "+dirname+"/bindings/matlab/", show_command=show_command)
createDir(dirname+"/bindings/python")