def _validate(self):
errors = []
if not self.patternUntilted.get() or not self.patternTilted.get():
errors.append(pwutils.Message.ERROR_PATTERN_EMPTY)
else:
filePathsUntilted = glob(pwutils.expandPattern(self.patternUntilted.get()))
filePathsTilted = glob(pwutils.expandPattern(self.patternTilted.get()))
if len(filePathsUntilted) == 0 or len(filePathsTilted) == 0:
errors.append(pwutils.Message.ERROR_PATTERN_FILES)
return errors
class Config:
# scipion-pyworkflow will generate the path $SCIPION_HOME/software/bindings
# The path will be created in the working directory if SCIPION_HOME is not set
SCIPION_ED_HOME = os.environ.get(
'SCIPION_HOME', pwutils.expandPattern("~/.scipion-ed-home"))
# Allowing the user to set SCIPION_ED_USERDATA at installation is issue #8
SCIPION_ED_USERDATA = os.environ.get(
'SCIPION_ED_USERDATA', pwutils.expandPattern("~/ScipionEdUserData"))
# Location of the contents from scipion-ed-testdata
SCIPION_ED_TESTDATA = os.environ.get('SCIPION_ED_TESTDATA', None)
SCIPION_ED_TEST_OUTPUT = os.environ.get(
'SCIPION_ED_TEST_OUTPUT', os.path.join(SCIPION_ED_USERDATA, 'Tests'))
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmippLib
fn = xmippLib.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewers import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def getPattern(self):
""" Expand the pattern using environ vars or username
and also replacing special character # by digit matching.
"""
self._idRegex = None
filesPath = self.filesPath.get('').strip()
filesPattern = self.filesPattern.get('').strip()
if filesPattern:
fullPattern = join(filesPath, filesPattern)
else:
fullPattern = filesPath
pattern = pwutils.expandPattern(fullPattern.replace("$", ""))
match = re.match('[^#]*(#+)[^#]*', pattern)
if match is not None:
g = match.group(1)
n = len(g)
# prepare regex pattern - place ids, handle *, handle ?
idregex = pattern.replace(g, '(%s)' % ('[0-9]' * n))
idregex = idregex.replace('*', '.*')
idregex = idregex.replace('?', '.')
self._idRegex = re.compile(idregex)
pattern = pattern.replace(g, '[0-9]' * n)
return pattern
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen(['%s/scipion' % os.environ['SCIPION_HOME'],
'browser', 'dir', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path) else os.path.join(
os.getcwd(), path))
subprocess.Popen([
'%s/scipion' % os.environ['SCIPION_HOME'], 'browser', 'dir',
dpath
])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def openPath(self, path):
"Try to open the selected path"
path = expandPattern(path)
# If the path is a dir, open it with scipion browser dir <path>
if os.path.isdir(path):
dpath = (path if os.path.isabs(path)
else os.path.join(os.getcwd(), path))
subprocess.Popen([pw.getScipionScript(), 'view', dpath])
return
# If it is a file, interpret it correctly and open it with DataView
dirname = os.path.dirname(path)
fname = os.path.basename(path)
if '@' in fname:
path = os.path.join(dirname, fname.split('@', 1)[-1])
else:
path = os.path.join(dirname, fname)
if os.path.exists(path):
import xmipp
fn = xmipp.FileName(path)
if fn.isImage() or fn.isMetaData():
from pyworkflow.em.viewer import DataView
DataView(path).show()
else:
_open_cmd(path)
else:
# This is probably one special reference, like sci-open:... that
# can be interpreted with our handlers.
tag = path.split(':', 1)[0] if ':' in path else None
if tag in self.handlers:
self.handlers[tag](path.split(':', 1)[-1])
else:
print "Can't find %s" % path
def importMicrographs(self, pattern, suffix, voltage, sphericalAberration,
amplitudeContrast):
""" Copy images matching the filename pattern
Register other parameters.
"""
filePaths = glob(pwutils.expandPattern(pattern))
# imgSet = SetOfMicrographs(filename=self.micsPairsSqlite, prefix=suffix)
imgSet = self._createSetOfMicrographs(suffix=suffix)
acquisition = imgSet.getAcquisition()
# Setting Acquisition properties
acquisition.setVoltage(voltage)
acquisition.setSphericalAberration(sphericalAberration)
acquisition.setAmplitudeContrast(amplitudeContrast)
# Call a function that should be implemented by each subclass
self._setOtherPars(imgSet)
outFiles = [imgSet.getFileName()]
imgh = emlib.image.ImageHandler()
img = imgSet.ITEM_TYPE()
n = 1
size = len(filePaths)
filePaths.sort()
for i, fn in enumerate(filePaths):
# ext = os.path.splitext(basename(f))[1]
dst = self._getExtraPath(basename(fn))
if self.copyToProj:
pwutils.copyFile(fn, dst)
else:
pwutils.createLink(fn, dst)
if n > 1:
for index in range(1, n + 1):
img.cleanObjId()
img.setFileName(dst)
img.setIndex(index)
imgSet.append(img)
else:
img.cleanObjId()
img.setFileName(dst)
# Fill the micName if img is a Micrograph.
self._fillMicName(img, fn, pattern)
imgSet.append(img)
outFiles.append(dst)
sys.stdout.write("\rImported %d/%d" % (i + 1, size))
sys.stdout.flush()
print("\n")
imgSet.write()
return imgSet
def castConf(var, value):
""" Casting definitions for config parameters.
"""
value = pwutils.expandPattern(value)
castList = [c for k, c, d in formatConfParameters if k == var]
if castList:
cast = castList[0]
else:
cast = 'default'
if cast == 'splitTimesFloat':
if "*" in value:
newvar = reduce(lambda x, y: float(x) * float(y), value.split('*'))
elif "/" in value:
newvar = reduce(lambda x, y: float(x) / float(y), value.split('/'))
else:
newvar = float(value)
elif cast == bool:
try:
newvar = int(value) > 0
except:
newvar = False if value.lower() == 'false' else True
elif cast == 'path':
newvar = pwutils.expandPattern(value)
elif cast == 'default':
if value.lower() == 'true':
newvar = True
elif value.lower() == 'false':
newvar = False
else:
try: # to transform to int: '-1'.isdigit() = False...
newvar = int(value)
except:
try: # to transform to float (1.234, 1.32E-4...)
newvar = float(value)
except ValueError:
newvar = value
else:
newvar = cast(value)
return newvar
[DELAY, default 30]: delay in seconds between file appearance
""" % error
sys.exit(1)
if not len(sys.argv) in (3, 4):
usage("Incorrect number of input parameters")
inputPattern = sys.argv[1]
outputDir = sys.argv[2]
if len(sys.argv) == 4:
delay = sys.argv[3]
else:
delay = 30
inputFiles = glob(pwutils.expandPattern(inputPattern))
inputFiles.sort()
print "Input pattern: ", inputPattern
print "Input files: ", inputFiles
print "Delay: ", str(delay), " seconds."
print "Cleaning output directory: ", outputDir
pwutils.cleanPath(outputDir)
pwutils.makePath(outputDir)
aTime = int(delay)
n = 5
t = aTime / n
print "t=%s" % t
sys.exit(1)
if not len(sys.argv) in (3, 4, 5):
usage("Incorrect number of input parameters")
inputPattern = sys.argv[1]
outputDir = sys.argv[2]
gain = None
delay = 30
if len(sys.argv) == 4:
try:
delay = int(sys.argv[3])
gain = None
except Exception:
gain = pwutils.expandPattern(sys.argv[3])
delay = 30
elif len(sys.argv) == 5:
try:
delay = int(sys.argv[3])
gain = pwutils.expandPattern(sys.argv[4])
except Exception:
try:
gain = pwutils.expandPattern(sys.argv[3])
delay = int(sys.argv[4])
except:
usage("DELAY must be an integer.")
inputFiles = glob(pwutils.expandPattern(inputPattern))
inputFiles.sort()
if gain is not None:
def _iterFiles(self, pattern):
filePaths = glob(pwutils.expandPattern(pattern))
for fn in filePaths:
yield fn
def _onAction(self, e=None):
def is_running(process):
counter = 0
s = subprocess.Popen(["ps", "axw"], stdout=subprocess.PIPE)
for x in s.stdout:
if re.search(process, x):
counter = x.split()[0]
break
return counter
errors = []
doBackup = True
# Check the Data folder exists
dataFolder = pwutils.expandPattern(self._getValue(DATA_FOLDER))
if not os.path.exists(pwutils.expandPattern(dataFolder)):
errors.append("Data folder '%s' does not exists" % dataFolder)
# check errors
counter = is_running("mirror_directory.sh")
if counter > 0:
errors.append("There is a backup script running in the background")
errors.append("I cannot continue unless you stop it.")
errors.append('The command "kill -9 %s" will kill it.' % counter)
errors.append('Execute it at your own risk from a terminal')
backupFolder = pwutils.expandPattern(self._getValue(DATA_BACKUP))
if backupFolder == '':
doBackup = False
elif backupFolder.find("@") != -1: # if remote directory do not check
pass
elif not os.path.exists(pwutils.expandPattern(backupFolder)):
errors.append(
"""Backup folder '%s' already exists. If you want to use you must delete it first"""
% backupFolder)
userName = self._getValue(USER_NAME)
if self.re.match(userName.strip()) is None:
errors.append("Wrong username")
sampleName = self._getValue(SAMPLE_NAME)
if self.re.match(sampleName.strip()) is None:
errors.append("Wrong sample name")
projName = self._getProjectName()
projPath = os.path.join(dataFolder, projName)
scipionProj = self._getConfValue('SCIPION_PROJECT')
scipionProjPath = os.path.join(projPath, scipionProj)
# Do more checks only if there are not previous errors
if not errors:
if os.path.exists(projPath):
errors.append("Project path '%s' already exists." % projPath)
if not errors:
if not (self._getValue(MOTIONCORR) or self._getValue(MOTIONCOR2)
or self._getValue(OPTICAL_FLOW)):
errors.append("You should use at least one alignment method."
"(%s or %s)" % (MOTIONCORR, OPTICAL_FLOW))
if errors:
errors.insert(0, "*Errors*:")
self.windows.showError("\n - ".join(errors))
else:
self._createDataFolder(projPath, scipionProjPath)
command = os.path.join(os.getenv("SCIPION_HOME"),
"scripts/mirror_directory.sh")
if doBackup:
subprocess.Popen([command, dataFolder, projName, backupFolder],
stdout=open('logfile_out.log', 'w'),
stderr=open('logfile_err.log', 'w'))
print projName, projPath, scipionProjPath
self._createScipionProject(projName, projPath, scipionProjPath)
self.windows.close()
