def dzi_get_project_ref(project):
if current_app.config['HISTOANNOT_SERVER_MODE'] != 'dzi_node':
# TODO: Check permission!
return ProjectRef(project)
else:
pdata = json.loads(request.form.get('project_data'))
return ProjectRef(project, pdata)
def block_detail_by_name(task_id, specimen_name, block_name):
# Get the current task data
project,task = get_task_data(task_id)
pr = ProjectRef(project)
return render_template('slide/task_detail.html',
project=project, project_name=pr.disp_name, task=task, task_id=task_id,
specimen_name=specimen_name, block_name=block_name)
def wrapped_view(**kwargs):
# Find or allocate an assigned worker for this slide
worker_url = find_delegate_for_slide(project=kwargs['project'],
slide_name=kwargs['slide_name'])
# If no worker, just call the method
if worker_url is None:
return view(**kwargs)
# Call the worker's method
full_url = '%s/%s' % (worker_url, request.full_path)
# Take the project information and embed it in the call as a POST parameter
pr = ProjectRef(kwargs['project'])
post_data = urllib.urlencode(
{'project_data': json.dumps(pr.get_dict())})
return urllib2.urlopen(full_url, post_data).read()
def do_preload_file(project, proj_dict, specimen, block, resource, slide_name,
slide_ext):
sr = SlideRef(ProjectRef(project, proj_dict), specimen, block, slide_name,
slide_ext)
print('Fetching %s %s %s %s.%s' %
(project, specimen, block, slide_name, slide_ext))
tiff_file = sr.get_local_copy(resource, check_hash=True)
print('Fetched to %s' % tiff_file)
return tiff_file
def labelset_editor(project):
# Read the project ref
pr = ProjectRef(project)
# Render the entry page
return render_template('dbtrain/labelset_editor.html',
project=project,
disp_name=pr.disp_name,
labelset=None)
def get_slide_ref(slice_id, project=None):
"""
Create a slide reference from a database slide ID
:param slice_id: database ID of a slide
:type slide_id: int
:param project: optional project reference to associate with
:type project: ProjectRef
:return:
"""
db = get_db()
# Load slide from database
row = db.execute('SELECT * from slide_info WHERE id = ?', (slice_id,)).fetchone()
# Handle missing data
if row is None:
return None
# Create a project reference
if project is None:
project = ProjectRef(row['project'])
# Create a slide reference
return SlideRef(project, row['specimen_name'], row['block_name'], row['slide_name'], row['slide_ext'])
def slide_view(task_id, slide_id, resolution, affine_mode):
# Get the current task data
project, task = get_task_data(task_id)
# Get the next/previous slides for this task
si, prev_slide, next_slide, stain_list, user_prefs = get_slide_info(
task_id, slide_id)
# Check that the affine mode and resolution requested are available
pr = ProjectRef(project)
sr = SlideRef(pr, si['specimen_name'], si['block_name'], si['slide_name'],
si['slide_ext'])
have_affine = sr.resource_exists('affine', True) or sr.resource_exists(
'affine', False)
have_x16 = sr.resource_exists('x16', True) or sr.resource_exists(
'x16', False)
# If one is missing, we need a redirect
rd_affine_mode = affine_mode if have_affine else 'raw'
rd_resolution = resolution if have_x16 else 'raw'
# Get the list of available overlays and jsonify
overlays = sr.get_available_overlays(local=False)
if (affine_mode == 'affine' and not have_affine) or (resolution == 'x16'
and not have_x16):
return redirect(
url_for('slide.slide_view',
task_id=task_id,
slide_id=slide_id,
resolution=rd_resolution,
affine_mode=rd_affine_mode))
# Get additional project info
pr = ProjectRef(project)
# Form the URL templates for preloading and actual dzi access, so that in JS we
# can just do a quick substitution
url_ctx = {
'project': project,
'specimen': si['specimen_name'],
'block': si['block_name'],
'slide_name': si['slide_name'],
'slide_ext': si['slide_ext'],
'mode': affine_mode,
'resource': 'XXXXX'
}
url_tmpl_preload = url_for('dzi.dzi_preload_endpoint', **url_ctx)
url_tmpl_dzi = url_for('dzi.dzi', **url_ctx)
url_tmpl_download = url_for('dzi.dzi_download', **url_ctx)
# Build a dictionary to call
context = {
'slide_id': slide_id,
'slide_info': si,
'next_slide': next_slide,
'prev_slide': prev_slide,
'stain_list': stain_list,
'affine_mode': affine_mode,
'have_affine': have_affine,
'have_x16': have_x16,
'resolution': resolution,
'seg_mode': task['mode'],
'task_id': task_id,
'project': si['project'],
'project_name': pr.disp_name,
'block_id': si['block_id'],
'url_tmpl_preload': url_tmpl_preload,
'url_tmpl_dzi': url_tmpl_dzi,
'url_tmpl_download': url_tmpl_download,
'task': task,
'fixed_box_size': get_dltrain_fixed_box_size(task),
'user_prefs': user_prefs,
'overlays': overlays
}
# Add optional fields to context
for field in ('sample_id', 'sample_cx', 'sample_cy'):
if field in request.form:
context[field] = request.form[field]
# Render the template
return render_template('slide/slide_view.html', **context)