def run(password, admin_name, target, tag, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
updateService = conn.getUpdateService()
ds = conn.getObject("Dataset",
attributes={'name': target},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % target)
continue
params = omero.sys.ParametersI()
params.addString('username', admin_name)
query = "from TagAnnotation where textvalue='%s' \
AND details.owner.omeName=:username" % tag
query_service = conn.getQueryService()
tags = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(tags) == 0:
print("No tag with name %s found" % tag)
continue
tag_id = tags[0].id.getValue()
print(tag_id)
links = []
for image in ds.listChildren():
name = image.getName()
if name in images_to_tag:
# Check first that the image is not tagged
params = omero.sys.ParametersI()
params.addLong('parent', image.id)
params.addLong('child', tag_id)
query = "select link from ImageAnnotationLink as link \
where link.parent.id=:parent \
AND link.child.id=:child"
values = query_service.findAllByQuery(
query, params, conn.SERVICE_OPTS)
if len(values) == 0:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
link.child = TagAnnotationI(tag_id, False)
links.append(link)
else:
print("Tag %s already linked to %s" % (tag, name))
if len(links) > 0:
updateService.saveArray(links)
except Exception as exc:
print("Error when tagging the images: %s" % str(exc))
finally:
conn.close()
def link_tags(conn, datasetname, image_tag_links, image_ratings):
for i in range(1, 51):
username = "******" % i
print(username)
exp = conn.getAdminService().lookupExperimenter(username)
exp_id = exp.id.val
dataset = conn.getObject("Dataset",
attributes={'name': datasetname},
opts={'owner': exp_id})
if dataset is None:
print("Dataset not found")
continue
links = []
for image in dataset.listChildren():
name = image.name
if name in image_tag_links:
for tag_id in image_tag_links[name]:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
link.child = TagAnnotationI(tag_id, False)
link.details.owner = ExperimenterI(exp_id, False)
links.append(link)
if name in image_ratings:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
r = LongAnnotationI()
r.ns = rstring(RATING_NS)
r.longValue = rlong(image_ratings[name])
link.child = r
link.details.owner = ExperimenterI(exp_id, False)
links.append(link)
print('links', len(links))
group_id = dataset.getDetails().getGroup().id
conn.SERVICE_OPTS.setOmeroGroup(group_id)
try:
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
except ValidationException:
print("Failed to link for %s" % username)
def add_images_key_values(gateway, key_values, image_ids, group_id, description=None):
"""Adds some key:value pairs to a list of images"""
map_data = _dict_to_map_annotation(key_values, description)
data_manager, ctx = _data_manager_generator(gateway, group_id)
# Link the data to the image
if not hasattr(image_ids, '__iter__'):
image_ids = [image_ids]
for ID in image_ids:
link = ImageAnnotationLinkI()
link.setChild(map_data.asAnnotation())
link.setParent(ImageI(ID, False))
data_manager.saveAndReturnObject(ctx, link)
def add_image_tag(gateway, tag_text, image_id, description=None):
"""Adds a tag to an image"""
data_manager = gateway.getFacility(DataManagerFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
# Arrange the data
tag_data = TagAnnotationData(tag_text)
if description:
tag_data.setTagDescription(description)
# Link the data to the image
link = ImageAnnotationLinkI()
link.setChild(tag_data.asAnnotation())
link.setParent(ImageI(image_id, False))
return data_manager.saveAndReturnObject(ctx, link)
def link(self, obj1, obj2, client=None):
"""
Links two linkable model entities together by creating an instance of
the correct link entity (e.g. ProjectDatasetLinkI) and persisting it
in the DB. Accepts client instance to allow calls to happen in correct
user contexts. Currently support links are:
* project/dataset
* dataset/image
* image/annotation
:param obj1: parent object
:param obj2: child object
:param client: The client to use to create the link
"""
if client is None:
client = self.client
if isinstance(obj1, ProjectI):
if isinstance(obj2, DatasetI):
link = ProjectDatasetLinkI()
elif isinstance(obj1, DatasetI):
if isinstance(obj2, ImageI):
link = DatasetImageLinkI()
elif isinstance(obj1, ImageI):
if isinstance(obj2, Annotation):
link = ImageAnnotationLinkI()
else:
assert False, "Object type not supported."
"""check if object exist or not"""
if obj1.id is None:
link.setParent(obj1)
else:
link.setParent(obj1.proxy())
if obj2.id is None:
link.setChild(obj2)
else:
link.setChild(obj2.proxy())
return client.sf.getUpdateService().saveAndReturnObject(link)
def process_images(conn, script_params):
file_anns = []
message = ""
# Get the images
images, log_message = script_utils.get_objects(conn, script_params)
message += log_message
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [
image for image in images
if image.getROICount(["Polyline", "Line"]) > 0
]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
csv_data = []
for image in images:
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image," \
" not a kymograph." % (image.getName(), image.getId())
continue
roi_service = conn.getRoiService()
result = roi_service.findByImage(image.getId(), None)
secs_per_pixel_y = image.getPixelSizeY()
microns_per_pixel_x = image.getPixelSizeX()
if secs_per_pixel_y and microns_per_pixel_x:
microns_per_sec = microns_per_pixel_x / secs_per_pixel_y
else:
microns_per_sec = None
# for each line or polyline, create a row in csv table: y(t), x,
# dy(dt), dx, x/t (line), x/t (average)
col_names = "\nt_start (pixels), x_start (pixels), t_end (pixels)," \
" x_end (pixels), dt (pixels), dx (pixels), x/t, speed(um/sec)," \
"avg x/t, avg speed(um/sec)"
table_data = ""
for roi in result.rois:
for s in roi.copyShapes():
if s is None:
continue # seems possible in some situations
if type(s) == omero.model.LineI:
table_data += "\nLine ID: %s" % s.getId().getValue()
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dx_per_y = float(dx) / dy
speed = ""
if microns_per_sec:
speed = dx_per_y * microns_per_sec
table_data += "\n"
table_data += ",".join([
str(x)
for x in (y1, x1, y2, x2, dy, dx, dx_per_y, speed)
])
elif type(s) == omero.model.PolylineI:
table_data += "\nPolyline ID: %s" % s.getId().getValue()
v = s.getPoints().getValue()
points = roi_utils.points_string_to_xy_list(v)
x_start, y_start = points[0]
for i in range(1, len(points)):
x1, y1 = points[i - 1]
x2, y2 = points[i]
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dx_per_y = float(dx) / dy
av_x_per_y = abs(float(x2 - x_start) / (y2 - y_start))
speed = ""
avg_speed = ""
if microns_per_sec:
speed = dx_per_y * microns_per_sec
avg_speed = av_x_per_y * microns_per_sec
table_data += "\n"
table_data += ",".join([
str(x) for x in (y1, x1, y2, x2, dy, dx, dx_per_y,
speed, av_x_per_y, avg_speed)
])
# write table data to csv...
if len(table_data) > 0:
table_string = "Image ID:, %s," % image.getId()
table_string += "Name:, %s" % image.getName()
table_string += "\nsecsPerPixelY: %s" % secs_per_pixel_y
table_string += '\nmicronsPerPixelX: %s' % microns_per_pixel_x
table_string += "\n"
table_string += col_names
table_string += table_data
csv_data.append(table_string)
iids = [str(i.getId()) for i in images]
to_link_csv = [i.getId() for i in images if i.canAnnotate()]
csv_file_name = 'kymograph_velocities_%s.csv' % "-".join(iids)
with open(csv_file_name, 'w') as csv_file:
csv_file.write("\n \n".join(csv_data))
file_ann = conn.createFileAnnfromLocalFile(csv_file_name,
mimetype="text/csv")
fa_message = "Created Line Plot csv (Excel) file"
links = []
if len(to_link_csv) == 0:
fa_message += " but could not attach to images."
for iid in to_link_csv:
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = file_ann._obj
links.append(link)
if len(links) > 0:
links = conn.getUpdateService().saveAndReturnArray(links)
if file_ann:
file_anns.append(file_ann)
if not file_anns:
fa_message = "No Analysis files created. See 'Info' or 'Error'" \
" for more details"
elif len(file_anns) > 1:
fa_message = "Created %s csv (Excel) files" % len(file_anns)
message += fa_message
return file_anns, message
def buildFigure(self):
"""
The main building of the figure happens here, independently of format.
We set up directories as needed, call createFigure() to create
the PDF or TIFF then iterate through figure pages, adding panels
for each page.
Then we add an info page and create a zip of everything if needed.
Finally the created file or zip is uploaded to OMERO and attached
as a file annotation to all the images in the figure.
"""
# test to see if we've got multiple pages
page_count = 'page_count' in self.figure_json and self.figure_json[
'page_count'] or 1
self.page_count = int(page_count)
paper_spacing = 'paper_spacing' in self.figure_json and self.figure_json[
'paper_spacing'] or 50
page_col_count = 'page_col_count' in self.figure_json and self.figure_json[
'page_col_count'] or 1
# Create a zip if we have multiple TIFF pages or we're exporting Images
export_option = self.scriptParams['Export_Option']
createZip = False
if self.exportImages:
createZip = True
if (self.page_count > 1) and (export_option.startswith("TIFF")):
createZip = True
# somewhere to put PDF and images
self.zip_folder_name = None
if createZip:
self.zip_folder_name = "figure"
curr_dir = os.getcwd()
zipDir = os.path.join(curr_dir, self.zip_folder_name)
os.mkdir(zipDir)
if self.exportImages:
for d in (ORIGINAL_DIR, RESAMPLED_DIR, FINAL_DIR):
imgDir = os.path.join(zipDir, d)
os.mkdir(imgDir)
self.addReadMeFile()
# Create the figure file(s)
self.createFigure()
panels_json = self.figure_json['panels']
imageIds = set()
groupId = None
# We get our group from the first image
id1 = panels_json[0]['imageId']
groupId = self.conn.getObject("Image", id1).getDetails().group.id.val
# For each page, add panels...
col = 0
row = 0
for p in range(self.page_count):
print "\n------------------------- PAGE ", p + 1, "--------------------------"
px = col * (self.pageWidth + paper_spacing)
py = row * (self.pageHeight + paper_spacing)
page = {'x': px, 'y': py}
# if export_option == "TIFF":
# add_panels_to_tiff(conn, tiffFigure, panels_json, imageIds, page)
# elif export_option == "PDF":
self.add_panels_to_page(panels_json, imageIds, page)
# complete page and save
self.savePage()
col = col + 1
if col >= page_col_count:
col = 0
row = row + 1
# Add thumbnails and links page
self.addInfoPage(panels_json)
# Saves the completed figure file
self.saveFigure()
# PDF will get created in this group
if groupId is None:
groupId = self.conn.getEventContext().groupId
self.conn.SERVICE_OPTS.setOmeroGroup(groupId)
outputFile = self.figureFileName
ns = self.ns
mimetype = self.mimetype
if self.zip_folder_name is not None:
zipName = self.getZipName()
# Recursively zip everything up
compress(zipName, self.zip_folder_name)
outputFile = zipName
ns = "omero.web.figure.zip"
mimetype = "application/zip"
fileAnn = self.conn.createFileAnnfromLocalFile(outputFile,
mimetype=mimetype,
ns=ns)
links = []
for iid in list(imageIds):
print "linking to", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
# Don't want to fail at this point due to strange permissions combo
try:
links = self.conn.getUpdateService().saveAndReturnArray(
links, self.conn.SERVICE_OPTS)
except:
print "Failed to attach figure: %s to images %s" % (fileAnn,
imageIds)
return fileAnn
def processImages(conn, scriptParams):
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [image for image in images if
image.getROICount(["Polyline", "Line"]) > 0]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
csvData = []
for image in images:
print "\nAnalysing Image: %s ID: %s" \
% (image.getName(), image.getId())
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image," \
" not a kymograph." % (image.getName(), image.getId())
continue
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
secsPerPixelY = image.getPixelSizeY()
micronsPerPixelX = image.getPixelSizeX()
if secsPerPixelY and micronsPerPixelX:
micronsPerSec = micronsPerPixelX / secsPerPixelY
else:
micronsPerSec = None
# for each line or polyline, create a row in csv table: y(t), x,
# dy(dt), dx, x/t (line), x/t (average)
colNames = "\nt_start (pixels), x_start (pixels), t_end (pixels)," \
" x_end (pixels), dt (pixels), dx (pixels), x/t, speed(um/sec)," \
"avg x/t, avg speed(um/sec)"
tableData = ""
for roi in result.rois:
for s in roi.copyShapes():
if s is None:
continue # seems possible in some situations
if type(s) == omero.model.LineI:
tableData += "\nLine ID: %s" % s.getId().getValue()
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
speed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "\n"
tableData += ",".join(
[str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
speed)])
elif type(s) == omero.model.PolylineI:
tableData += "\nPolyline ID: %s" % s.getId().getValue()
points = pointsStringToXYlist(s.getPoints().getValue())
xStart, yStart = points[0]
for i in range(1, len(points)):
x1, y1 = points[i-1]
x2, y2 = points[i]
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
avXperY = abs(float(x2-xStart)/(y2-yStart))
speed = ""
avgSpeed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
avgSpeed = avXperY * micronsPerSec
tableData += "\n"
tableData += ",".join(
[str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
speed, avXperY, avgSpeed)])
# write table data to csv...
if len(tableData) > 0:
tableString = "Image ID:, %s," % image.getId()
tableString += "Name:, %s" % image.getName()
tableString += "\nsecsPerPixelY: %s" % secsPerPixelY
tableString += '\nmicronsPerPixelX: %s' % micronsPerPixelX
tableString += "\n"
tableString += colNames
tableString += tableData
print tableString
csvData.append(tableString)
else:
print "Found NO lines or polylines to analyze for Image"
iids = [str(i.getId()) for i in images]
toLinkCsv = [i.getId() for i in images if i.canAnnotate()]
csvFileName = 'kymograph_velocities_%s.csv' % "-".join(iids)
csvFile = open(csvFileName, 'w')
try:
csvFile.write("\n \n".join(csvData))
finally:
csvFile.close()
fileAnn = conn.createFileAnnfromLocalFile(csvFileName, mimetype="text/csv")
faMessage = "Created Line Plot csv (Excel) file"
links = []
if len(toLinkCsv) == 0:
faMessage += " but could not attach to images."
for iid in toLinkCsv:
print "linking csv to Image: ", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
links = conn.getUpdateService().saveAndReturnArray(links)
if fileAnn:
fileAnns.append(fileAnn)
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error'" \
" for more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, message
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]
def create_pdf(conn, scriptParams):
# make sure we can find all images
conn.SERVICE_OPTS.setOmeroGroup(-1)
figure_json_string = scriptParams['Figure_JSON']
figure_json = json.loads(figure_json_string)
n = datetime.now()
# time-stamp name by default: Figure_2013-10-29_22-43-53.pdf
figureName = "Figure_%s-%s-%s_%s-%s-%s." \
"pdf" % (n.year, n.month, n.day, n.hour, n.minute, n.second)
if 'figureName' in figure_json:
figureName = str(figure_json['figureName'])
# get Figure width & height...
pageWidth = figure_json['paper_width']
pageHeight = figure_json['paper_height']
# add to scriptParams for convenience
scriptParams['Page_Width'] = pageWidth
scriptParams['Page_Height'] = pageHeight
pdfName = figureName
if not pdfName.endswith('.pdf'):
pdfName = "%s.pdf" % pdfName
c = canvas.Canvas(pdfName, pagesize=(pageWidth, pageHeight))
panels_json = figure_json['panels']
imageIds = set()
groupId = None
for i, panel in enumerate(panels_json):
print "\n---------------- "
imageId = panel['imageId']
print "IMAGE", i, imageId
image = drawPanel(conn, c, panel, pageHeight, i)
if image.canAnnotate():
imageIds.add(imageId)
drawLabels(conn, c, panel, pageHeight)
# We get our group from the first image
if groupId is None:
groupId = image.getDetails().group.id.val
# complete page and save
c.showPage()
print panels_json
# Add thumbnails and links page
addInfoPage(conn, scriptParams, c, panels_json, figureName)
c.save()
# PDF will get created in this group
if groupId is None:
groupId = conn.getEventContext().groupId
conn.SERVICE_OPTS.setOmeroGroup(groupId)
ns = "omero.web.figure.pdf"
fileAnn = conn.createFileAnnfromLocalFile(
pdfName,
mimetype="application/pdf",
ns=ns)
links = []
for iid in list(imageIds):
print "linking to", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
# Don't want to fail at this point due to strange permissions combo
try:
links = conn.getUpdateService().saveAndReturnArray(
links, conn.SERVICE_OPTS)
except:
print "Failed to attach figure: %s to images %s" % (fileAnn, imageIds)
return fileAnn
def buildFigure(self):
"""
The main building of the figure happens here, independently of format.
We set up directories as needed, call createFigure() to create
the PDF or TIFF then iterate through figure pages, adding panels
for each page.
Then we add an info page and create a zip of everything if needed.
Finally the created file or zip is uploaded to OMERO and attached
as a file annotation to all the images in the figure.
"""
# test to see if we've got multiple pages
page_count = 'page_count' in self.figure_json and self.figure_json['page_count'] or 1
self.page_count = int(page_count)
paper_spacing = 'paper_spacing' in self.figure_json and self.figure_json['paper_spacing'] or 50
page_col_count = 'page_col_count' in self.figure_json and self.figure_json['page_col_count'] or 1
# Create a zip if we have multiple TIFF pages or we're exporting Images
export_option = self.scriptParams['Export_Option']
createZip = False
if self.exportImages:
createZip = True
if (self.page_count > 1) and (export_option.startswith("TIFF")):
createZip = True
# somewhere to put PDF and images
self.zip_folder_name = None
if createZip:
self.zip_folder_name = "figure"
curr_dir = os.getcwd()
zipDir = os.path.join(curr_dir, self.zip_folder_name)
os.mkdir(zipDir)
if self.exportImages:
for d in (ORIGINAL_DIR, RESAMPLED_DIR, FINAL_DIR):
imgDir = os.path.join(zipDir, d)
os.mkdir(imgDir)
self.addReadMeFile()
# Create the figure file(s)
self.createFigure()
panels_json = self.figure_json['panels']
imageIds = set()
groupId = None
# We get our group from the first image
id1 = panels_json[0]['imageId']
groupId = self.conn.getObject("Image", id1).getDetails().group.id.val
# For each page, add panels...
col = 0
row = 0
for p in range(self.page_count):
print "\n------------------------- PAGE ", p + 1, "--------------------------"
px = col * (self.pageWidth + paper_spacing)
py = row * (self.pageHeight + paper_spacing)
page = {'x': px, 'y': py}
# if export_option == "TIFF":
# add_panels_to_tiff(conn, tiffFigure, panels_json, imageIds, page)
# elif export_option == "PDF":
self.add_panels_to_page(panels_json, imageIds, page)
# complete page and save
self.savePage()
col = col + 1
if col >= page_col_count:
col = 0
row = row + 1
# Add thumbnails and links page
self.addInfoPage(panels_json)
# Saves the completed figure file
self.saveFigure()
# PDF will get created in this group
if groupId is None:
groupId = self.conn.getEventContext().groupId
self.conn.SERVICE_OPTS.setOmeroGroup(groupId)
outputFile = self.figureFileName
ns = self.ns
mimetype = self.mimetype
if self.zip_folder_name is not None:
zipName = self.getZipName()
# Recursively zip everything up
compress(zipName, self.zip_folder_name)
outputFile = zipName
ns = "omero.web.figure.zip"
mimetype = "application/zip"
fileAnn = self.conn.createFileAnnfromLocalFile(
outputFile,
mimetype=mimetype,
ns=ns)
links = []
for iid in list(imageIds):
print "linking to", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
# Don't want to fail at this point due to strange permissions combo
try:
links = self.conn.getUpdateService().saveAndReturnArray(
links, self.conn.SERVICE_OPTS)
except:
print "Failed to attach figure: %s to images %s" % (fileAnn, imageIds)
return fileAnn
def testQueryTaggedUnique(self):
# get group we're working on...
ctx = self.client.sf.getAdminService().getEventContext()
groupId = ctx.groupId
print 'groupId', groupId
# Admin sets permissions to read-ann
admin = self.root.sf.getAdminService()
rootUpdate = self.root.sf.getUpdateService()
gr = admin.getGroup(groupId)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupAnnotate(True)
p.setGroupWrite(False)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
gr.details.permissions = p
admin.updateGroup(gr)
# Update context for user
ctx = self.client.sf.getAdminService().getEventContext()
update = self.client.sf.getUpdateService()
queryService = self.client.sf.getQueryService()
tagCount = 5
# User creates tag linked to images
tag = TagAnnotationI()
tag.textValue = wrap("test_iQuerySpeed")
links = []
for i in range(tagCount):
iid = createImageWithPixels(self.client, self.uuid())
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = tag
links.append(link)
links = update.saveAndReturnArray(links)
tag = links[0].child
# check permissions
p = tag.getDetails().getPermissions()
assert p.isGroupRead()
assert p.isGroupAnnotate()
# Root also links user's tag to images
rootLinks = []
for l in links:
link = ImageAnnotationLinkI()
link.parent = ImageI(l.parent.id, False)
link.child = TagAnnotationI(l.child.id, False)
rootLinks.append(link)
rootUpdate.saveAndReturnArray(rootLinks, {'omero.group': str(groupId)})
q = """select distinct new map(obj.id as id,
obj.name as name,
obj.details.owner.id as ownerId,
obj as image_details_permissions,
obj.fileset.id as filesetId,
lower(obj.name) as n
,
pix.sizeX as sizeX,
pix.sizeY as sizeY,
pix.sizeZ as sizeZ
)
from Image obj left outer join obj.pixels pix
join obj.annotationLinks alink
where %s
order by lower(obj.name), obj.id """
params = ParametersI()
params.add('tid', tag.id)
# We can get all the tagged images like this.
# We use an additional select statement to give 'unique' results
uniqueClause = """alink.id = (select max(alink.id)
from ImageAnnotationLink alink
where alink.child.id=:tid and alink.parent.id=obj.id)"""
query = q % uniqueClause
result1 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result1) == tagCount
# Without the select statement, we get the same image returned
# multiple times if there is no 'distinct'
clause = "alink.child.id=:tid"
query = q % clause
result2 = queryService.projection(query, params,
{'omero.group': str(groupId)})
assert len(result2) == tagCount
for idx in range(len(result1)-1):
# Omit final since == isn't defined for Ice objects.
assert result1[idx] == result2[idx]
def create_pdf(conn, scriptParams):
figure_json_string = scriptParams['Figure_JSON']
figure_json = json.loads(figure_json_string)
n = datetime.now()
# time-stamp name by default: Figure_2013-10-29_22-43-53.pdf (tried : but they get replaced)
figureName = "Figure_%s-%s-%s_%s-%s-%s.pdf" % (n.year, n.month, n.day, n.hour, n.minute, n.second)
# get Figure width & height...
pageWidth = figure_json['paper_width']
pageHeight = figure_json['paper_height']
# add to scriptParams for convenience
scriptParams['Page_Width'] = pageWidth
scriptParams['Page_Height'] = pageHeight
if 'Figure_Name' in scriptParams:
figureName = scriptParams['Figure_Name']
if not figureName.endswith('.pdf'):
figureName = "%s.pdf" % figureName
c = canvas.Canvas(figureName, pagesize=(pageWidth, pageHeight))
panels_json = figure_json['panels']
imageIds = set()
for i, panel in enumerate(panels_json):
print "\n---------------- "
imageId = panel['imageId']
print "IMAGE", i, imageId
imageIds.add(imageId)
drawPanel(conn, c, panel, pageHeight, i)
drawLabels(conn, c, panel, pageHeight)
# complete page and save
c.showPage()
if True:
addInfoPage(conn, scriptParams, c, panels_json)
c.save()
ns = "omero.web.figure.pdf"
fileAnn = conn.createFileAnnfromLocalFile(
figureName,
mimetype="application/pdf",
ns=ns,
desc=figure_json_string)
links = []
for iid in list(imageIds):
print "linking to", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
print len(links)
if len(links) > 0:
links = conn.getUpdateService().saveAndReturnArray(links, conn.SERVICE_OPTS)
return fileAnn
