def edit(self, args, config, edit_path=edit_path):
from omero.util.temp_files import create_path, remove_path
start_text = "# Edit your preferences below. Comments are ignored\n"
for k in sorted(config.keys()):
start_text += ("%s=%s\n" % (k, config[k]))
temp_file = create_path()
try:
edit_path(temp_file, start_text)
except RuntimeError as re:
self.ctx.dbg(traceback.format_exc())
self.ctx.die(
954, "%s: Failed to edit %s" %
(getattr(re, "pid", "Unknown"), temp_file))
args.NAME = config.default()
old_config = dict(config)
self.drop(args, config)
args.file = [open(str(temp_file), "r")]
args.q = True
try:
self.load(args, config)
except Exception as e:
for key, value in list(old_config.items()):
config[key] = value
raise e
finally:
remove_path(temp_file)
def cleanup_tmpdir(self):
"""
Remove all known files and finally the temporary directory.
If other files exist, an exception will be raised.
"""
try:
remove_path(self.dir)
except:
self.logger.error("Failed to remove dir %s" % self.dir, exc_info = True)
def cleanup_tmpdir(self):
"""
Remove all known files and finally the temporary directory.
If other files exist, an exception will be raised.
"""
try:
remove_path(self.dir)
except:
self.logger.error("Failed to remove dir %s" % self.dir,
exc_info=True)
def as_dictionary(path, readers="", extra_args=None):
"""Run as_stdout, parses the output and returns a dictionary of the form::
{
some_file_in_group :
[
some_file_in_group
some_other_file_in_group
...
last_file_in_group
],
some_file_in_second_group : ...
}
you can pass more arguments to the `import` command through the
extra_args argument in the form of a list.
to_import = as_dictionary("/my/dir/with_tifs", extra_args=["--depth", "6"])
will go through the directories with a depth level of 6 instead of
the default 4. Arguments of interest might be: `debugging`,
`report`, `logback`. Note that the command runs locally so options
such as `--exclude` will not work as they need information from the server.
"""
t = create_path("candidates", "err")
path = _to_list(path)
path.insert(0, "---file=%s" % t)
try:
as_stdout(path, readers=readers, extra_args=extra_args)
f = open(str(t), "r")
output = f.readlines()
f.close()
finally:
remove_path(t)
gline = -1
key = None
groups = {}
for line in output:
line = line.strip()
if len(line) == 0:
continue
if line.startswith("#"):
gline = -1
else:
if gline == -1:
gline = 1
key = line
groups[key] = [line]
else:
groups[key].append(line)
return groups
def _checkstd(self, output, which):
rfile = output.val[which]
ofile = rfile.val
assert ofile
tmppath = create_path("pingtest")
try:
self.client.download(ofile, str(tmppath))
assert os.path.getsize(str(tmppath))
return tmppath.text()
finally:
remove_path(tmppath)
def _checkstd(self, output, which):
rfile = output.val[which]
ofile = rfile.val
assert ofile
tmppath = create_path("clitest")
try:
self.client.download(ofile, str(tmppath))
assert os.path.getsize(str(tmppath))
return tmppath.text()
finally:
remove_path(tmppath)
def as_dictionary(path, readers=""):
"""
Run as_stdout, parses the output and returns a dictionary of the form::
{
some_file_in_group :
[
some_file_in_group
some_other_file_in_group
...
last_file_in_group
],
some_file_in_second_group : ...
}
"""
t = create_path("candidates", "err")
path = _to_list(path)
path.insert(0, "---file=%s" % t)
try:
as_stdout(path, readers=readers)
f = open(str(t), "r")
output = f.readlines()
f.close()
finally:
remove_path(t)
gline = -1
key = None
groups = {}
for line in output:
line = line.strip()
if len(line) == 0:
continue
if line.startswith("#"):
gline = -1
else:
if gline == -1:
gline = 1
key = line
groups[key] = [line]
else:
groups[key].append(line)
return groups
def as_dictionary(path, readers=""):
"""
Run as_stdout, parses the output and returns a dictionary of the form::
{
some_file_in_group :
[
some_file_in_group
some_other_file_in_group
...
last_file_in_group
],
some_file_in_second_group : ...
}
"""
t = create_path("candidates", "err")
path = _to_list(path)
path.insert(0, "---file=%s" % t)
try:
as_stdout(path, readers=readers)
f = open(str(t), "r")
output = f.readlines()
f.close()
finally:
remove_path(t)
gline = -1
key = None
groups = {}
for line in output:
line = line.strip()
if len(line) == 0:
continue
if line.startswith("#"):
gline = -1
else:
if gline == -1:
gline = 1
key = line
groups[key] = [line]
else:
groups[key].append(line)
return groups
def testBasicUsagePassString(self):
p = t_f.create_path("foo", ".bar")
self.assertTrue(p.exists())
t_f.remove_path(str(p))
self.assertFalse(p.exists())
def testBasicUsagePassString(self):
p = t_f.create_path("foo",".bar")
self.assertTrue(p.exists())
t_f.remove_path(str(p))
self.assertFalse(p.exists())
def importFile(self, fileName, exName):
"""
Import file or directory using 'bin/omero importer'
This method is solely responsible for logging the user in,
attempting (possibly multiply) an import, logging and
throwing an exception if necessary.
"""
key = self.loginUser(exName)
if not key:
self.log.info("File not imported: %s", fileName)
return
try:
self.state.appropriateWait(self.throttleImport) # See ticket:5739
self.log.info("Importing %s (session=%s)", fileName, key)
imageId = []
t = create_path("dropbox", "err")
to = create_path("dropbox", "out")
cli = omero.cli.CLI()
cli.loadplugins()
cmd = ["-s", self.host, "-p", str(self.port), "-k", key, "import"]
cmd.extend([str("---errs=%s"%t), str("---file=%s"%to), "--", "--agent=dropbox"])
cmd.extend(shlex.split(self.importArgs))
cmd.append(fileName)
logging.debug("cli.invoke(%s)" % cmd)
cli.invoke(cmd)
retCode = cli.rv
if retCode == 0:
self.log.info("Import of %s completed (session=%s)", fileName, key)
if to.exists():
f = open(str(to),"r")
lines = f.readlines()
f.close()
if len(lines) > 0:
for line in lines:
imageId.append(line.strip())
else:
self.log.error("No lines in output file. No image ID.")
else:
self.log.error("%s not found !" % to)
else:
self.log.error("Import of %s failed=%s (session=%s)", fileName, str(retCode), key)
self.log.error("***** start of output from importer-cli to stderr *****")
if t.exists():
f = open(str(t),"r")
lines = f.readlines()
f.close()
for line in lines:
self.log.error(line.strip())
else:
self.log.error("%s not found !" % t)
self.log.error("***** end of output from importer-cli *****")
finally:
remove_path(t)
remove_path(to)
return imageId
self.ctx.dbg(traceback.format_exc())
self.ctx.die(954, "%s: Failed to edit %s"
% (getattr(re, "pid", "Unknown"), temp_file))
args.NAME = config.default()
old_config = dict(config)
self.drop(args, config)
args.file = [open(str(temp_file), "r")]
args.q = True
try:
self.load(args, config)
except Exception as e:
for key, value in old_config.items():
config[key] = value
raise e
finally:
remove_path(temp_file)
@with_config
def version(self, args, config):
self.ctx.out(config.version(config.default()))
@with_config
def path(self, args, config):
self.ctx.out(config.filename)
@with_rw_config
def lock(self, args, config):
self.ctx.input("Press enter to unlock")
@with_rw_config
def upgrade(self, args, config):
start_text = "# Edit your preferences below. Comments are ignored\n"
for k in sorted(config.keys()):
start_text += ("%s=%s\n" % (k, config[k]))
temp_file = create_path()
try:
edit_path(temp_file, start_text)
except RuntimeError, re:
self.ctx.dbg(traceback.format_exc())
self.ctx.die(954, "%s: Failed to edit %s"
% (getattr(re, "pid", "Unknown"), temp_file))
args.NAME = config.default()
self.drop(args, config)
args.file = [open(str(temp_file), "r")]
args.q = True
self.load(args, config)
remove_path(temp_file)
@with_config
def version(self, args, config):
self.ctx.out(config.version(config.default()))
@with_config
def path(self, args, config):
self.ctx.out(config.filename)
@with_rw_config
def lock(self, args, config):
self.ctx.input("Press enter to unlock")
@with_rw_config
def upgrade(self, args, config):
def process_image(conn, imageId, parameterMap):
"""
Process an image.
Create a 5D image representing the ROI "cropping" the
original image
Image is put in a dataset if specified.
"""
image = conn.getObject("Image", imageId)
if image is None:
print "No image found for ID: %s" % imageId
return
parentDataset = image.getParent()
parentProject = parentDataset.getParent()
imageName = image.getName()
updateService = conn.getUpdateService()
print image.countImportedImageFiles()
# specifically count Fileset files
fileCount = image.countFilesetFiles()
fileset = image.getFileset() # will be None for pre-FS images
fsId = fileset.getId()
# list files
if fileCount > 0:
for origFile in image.getImportedImageFiles():
name = origFile.getName()
path = REPO + origFile.getPath()
slide_name,slide_ext = os.path.splitext(name)
slide_path = os.path.abspath(path+name)
print slide_path
slide = SlideImage(slide_path)
# x, y, w, h, zStart, zEnd, tStart, tEnd
rois = getRectangles(conn, imageId)
imgW = image.getSizeX()
imgH = image.getSizeY()
for index, r in enumerate(rois):
x, y, w, h, z1, z2, t1, t2 = r
# Bounding box
X = max(x, 0)
Y = max(y, 0)
X2 = min(x + w, imgW)
Y2 = min(y + h, imgH)
W = X2 - X
H = Y2 - Y
if (x, y, w, h) != (X, Y, W, H):
print "\nCropping ROI (x, y, w, h) %s to be within image."\
" New ROI: %s" % ((x, y, w, h), (X, Y, W, H))
rois[index] = (X, Y, W, H, z1, z2, t1, t2)
print "rois"
print rois
if len(rois) == 0:
print "No rectangular ROIs found for image ID: %s" % imageId
return
#make a new 5D image per ROI
images = []
iIds = []
for i,r in enumerate(rois):
x, y, w, h, z1, z2, t1, t2 = r
print " ROI x: %s y: %s w: %s h: %s z1: %s z2: %s t1: %s t2: %s"\
% (x, y, w, h, z1, z2, t1, t2)
description = "Image from ROIS on parent Image:\n Name: %s\n"\
" Image ID: %d" % (imageName, imageId)
print description
tmp_path = create_path('omero','.tmp', folder=True)
if (i + 1) < 10:
new_image_name = slide_name + '_' + '00' + str(i + 1) + '.ome.tif'
outfilepath = tmp_path + '/' + new_image_name
elif (i + 1) >= 10:
new_image_name = slide_name + '_' + '0' + str(i + 1) + '.ome.tif'
outfilepath = tmp_path + '/' + new_image_name
print 'new image path', outfilepath
s = time.time()
OMETIFF(None, name, outfilepath, imageId, len(rois), slide, r, 0).process()
print 'pylibtiff took:',time.time()-s,'seconds'
p = time.time()
newImg = create_image_from_tiles(conn,image,new_image_name,outfilepath,description,r)
print 'tile uploading creation took:',time.time()-p,'seconds'
# delete_roi_image(outfilepath)
remove_path(outfilepath)
images.append(newImg)
iIds.append(newImg.getId())
if slide:
slide.close_slide()
if len(iIds) == 0:
print "No new images created."
return
if 'Container_Name' in parameterMap and \
len(parameterMap['Container_Name'].strip()) > 0:
# create a new dataset for new images
datasetName = parameterMap['Container_Name']
dataset = omero.model.DatasetI()
dataset.name = rstring(datasetName)
desc = "Images in this Dataset are from ROIs of parent Image:\n"\
" Name: %s\n Image ID: %d" % (imageName, imageId)
dataset.description = rstring(desc)
dataset = updateService.saveAndReturnObject(dataset)
parentDataset = dataset
else:
# put new images in existing dataset
dataset = None
if parentDataset is not None and parentDataset.canLink():
parentDataset = parentDataset._obj
else:
parentDataset = None
parentProject = None # don't add Dataset to parent.
if parentDataset is None:
link = None
print "No dataset created or found for new images."\
" Images will be orphans."
else:
link = []
for iid in iIds:
dsLink = omero.model.DatasetImageLinkI()
dsLink.parent = omero.model.DatasetI(
parentDataset.id.val, False)
dsLink.child = omero.model.ImageI(iid, False)
updateService.saveObject(dsLink)
link.append(dsLink)
if parentProject and parentProject.canLink():
# and put it in the current project
projectLink = omero.model.ProjectDatasetLinkI()
projectLink.parent = omero.model.ProjectI(
parentProject.getId(), False)
projectLink.child = omero.model.DatasetI(
dataset.id.val, False)
updateService.saveAndReturnObject(projectLink)
return images, dataset, link, iIds
def testBasicUsage(self):
p = t_f.create_path("foo", ".bar")
assert p.exists()
t_f.remove_path(p)
assert not p.exists()
def importFile(self, fileName, exName):
"""
Import file or directory using 'bin/omero importer'
This method is solely responsible for logging the user in,
attempting (possibly multiply) an import, logging and
throwing an exception if necessary.
"""
try:
self.state.appropriateWait(self.throttleImport) # See ticket:5739
key = self.loginUser(exName)
if not key:
self.log.info("File not imported: %s", fileName)
return
self.log.info("Importing %s (session=%s)", fileName, key)
imageId = []
t = create_path("dropbox", "err")
to = create_path("dropbox", "out")
cli = omero.cli.CLI()
cli.loadplugins()
cmd = ["-s", self.host, "-p", str(self.port), "-k", key, "import"]
cmd.extend(
[str("---errs=%s" % t),
str("---file=%s" % to), "--", "--agent=dropbox"])
cmd.extend(shlex.split(self.importArgs))
cmd.append(fileName)
logging.debug("cli.invoke(%s)" % cmd)
cli.invoke(cmd)
retCode = cli.rv
if retCode == 0:
self.log.info(
"Import of %s completed (session=%s)", fileName, key)
if to.exists():
f = open(str(to), "r")
lines = f.readlines()
f.close()
if len(lines) > 0:
for line in lines:
imageId.append(line.strip())
else:
self.log.error("No lines in output file. No image ID.")
else:
self.log.error("%s not found !" % to)
else:
self.log.error(
"Import of %s failed=%s (session=%s)",
fileName, str(retCode), key)
self.log.error(
"***** start of output from importer-cli to stderr *****")
if t.exists():
f = open(str(t), "r")
lines = f.readlines()
f.close()
for line in lines:
self.log.error(line.strip())
else:
self.log.error("%s not found !" % t)
self.log.error("***** end of output from importer-cli *****")
finally:
remove_path(t)
remove_path(to)
return imageId
def testBasicUsagePassString(self):
p = t_f.create_path("foo", ".bar")
assert p.exists()
t_f.remove_path(str(p))
assert not p.exists()
def testBasicUsage(self):
p = t_f.create_path("foo", ".bar")
assert p.exists()
t_f.remove_path(p)
assert not p.exists()
def testBasicUsagePassString(self):
p = t_f.create_path("foo", ".bar")
assert p.exists()
t_f.remove_path(str(p))
assert not p.exists()
