def _validateImages(self):
errors = []
ih = ImageHandler()
for imgFn, _ in self.iterFiles():
if isdir(imgFn):
errors.append("Folders can not be selected.")
errors.append(' %s' % imgFn)
else:
# Check if images are correct by reading the header of the
# imported files:
# Exceptions:
# - Compressed movies (bz2 or tbz extensions)
# - Importing in streaming, since files may be incomplete
# - Bad characters in path [':' ,'%', '#']
if (not self.dataStreaming and
not (imgFn.endswith('bz2') or
imgFn.endswith('tbz') or
ih.isImageFile(imgFn))):
if not errors: # if empty add the first line
errors.append("Error reading the following images:")
errors.append(' %s' % imgFn)
errors += ProtImportImages.validatePath(imgFn)
return errors
def _validateImages(self):
errors = []
ih = ImageHandler()
for imgFn, _ in self.iterFiles():
if isdir(imgFn):
errors.append("Folders can not be selected.")
errors.append(' %s' % imgFn)
else:
# Check if images are correct by reading the header of the
# imported files:
# Exceptions:
# - Compressed movies (bz2 or tbz extensions)
# - Importing in streaming, since files may be incomplete
# - Bad characters in path [':' ,'%', '#']
if (not self.dataStreaming
and not (imgFn.endswith('bz2') or imgFn.endswith('tbz')
or ih.isImageFile(imgFn))):
if not errors: # if empty add the first line
errors.append("Error reading the following images:")
errors.append(' %s' % imgFn)
errors += ProtImportImages.validatePath(imgFn)
return errors
def _validateImages(self):
errors = []
ih = ImageHandler()
for imgFn, _ in self.iterFiles():
if isdir(imgFn):
errors.append("Folders can not be selected.")
errors.append(' %s' % imgFn)
else:
# try to read the header of the imported images
# except for the special case of compressed movies (bz2 extension)
if not (imgFn.endswith('bz2') or imgFn.endswith('tbz') or ih.isImageFile(imgFn)):
if not errors: # if empty add the first line
errors.append("Error reading the following images:")
errors.append(' %s' % imgFn)
return errors
def _validate(self):
from pyworkflow.em.convert import ImageHandler
errors = []
if self.importFrom == self.IMPORT_FROM_FILES:
if not self.getPattern():
errors.append("The path and pattern can not be both empty!!!")
else:
# Just check the number of files matching the pattern
self.getMatchFiles()
if self.numberOfFiles == 0:
errors.append("There are no files matching the pattern " + "%s" % self.getPattern())
for imgFn, _ in self.iterFiles():
ih = ImageHandler()
if not ih.isImageFile(imgFn):
errors.append("The imported files must be images.")
break
return errors
def _validateImages(self):
errors = []
ih = ImageHandler()
for imgFn, _ in self.iterFiles():
if isdir(imgFn):
errors.append("Folders can not be selected.")
errors.append(' %s' % imgFn)
else:
# try to read the header of the imported images
# except for the special case of compressed movies (bz2 extension)
if not (imgFn.endswith('bz2') or imgFn.endswith('tbz')
or ih.isImageFile(imgFn)):
if not errors: # if empty add the first line
errors.append("Error reading the following images:")
errors.append(' %s' % imgFn)
return errors
def _validate(self):
from pyworkflow.em.convert import ImageHandler
ci = self.getImportClass()
if ci is None:
errors = ProtImportMicBase._validate(self)
for micFn, _ in self.iterFiles():
imgh = ImageHandler()
if imgh.isImageFile(micFn):
_, _, z, n = imgh.getDimensions(micFn)
if n > 1 or z > 1:
errors.append("The protocol not support micrographs stored in stacks. "
"If you want to obtain your micrographs individually, "
"you can run the following command:\n"
"scipion run scipion_directory/scripts/split_stacks.py --files *your files* --ext *extension*")
# JMRT: only check the first image, for large dataset
# even reading the header can take a while
break
return errors
else:
return ci.validateMicrographs()
def _validate(self):
from pyworkflow.em.convert import ImageHandler
ci = self.getImportClass()
if ci is None:
errors = ProtImportMicBase._validate(self)
for micFn, _ in self.iterFiles():
imgh = ImageHandler()
if imgh.isImageFile(micFn):
_, _, z, n = imgh.getDimensions(micFn)
if n > 1 or z > 1:
errors.append(
"The protocol not support micrographs stored in stacks. "
"If you want to obtain your micrographs individually, "
"you can run the following command:\n"
"scipion run scipion_directory/scripts/split_stacks.py --files *your files* --ext *extension*"
)
# JMRT: only check the first image, for large dataset
# even reading the header can take a while
break
return errors
else:
return ci.validateMicrographs()
