def __init__(self, project):
self.__project_variant = project.get_variant()
self.__project_dimensions = project.get_dimensions()
self.__images_directory = project.get_input_image_directory()
self.__waypoints_directory = project.get_artifacts_directory(
"waypoints")
self.jobs = cli.jobs.get_job_types()
#{
# "trace": cli.jobs.trace.Trace(project),
# "imdata": cli.jobs.imdata.ImageData(project),
# "shapes": cli.jobs.shapes.Shapes(project),
# "classedge": cli.jobs.classify.ClassifyEdges(project),
# "jclass": cli.jobs.jclass.JunctionClassify(project),
# "jclasssum": cli.jobs.jclasssum.JunctionClassSummarize(project),
# "fastclass": cli.jobs.edgeseg.FastSegClassify(project),
#}
# Use this for an ordered list of the jobs in the chain
job_keys = []
priortized_jobs = sorted(self.jobs.values(), key=lambda x: x.priority)
for pj in priortized_jobs:
job_keys.append(pj.job_name)
self.job_types = job_keys
def get_waypoint_tasks(project):
import cells.waypoints.seeding
import cells.images
input_image_directory = project.get_input_image_directory()
variant = project.get_variant()
dimensions = project.get_dimensions()
image_data = cells.images.get_image_collection(input_image_directory,
variant, dimensions)
counter = 0
for image_data_row in image_data:
if image_data_row.get("stain") == "TxRed":
# print image_data_row
counter += 1
if counter > 5:
break
input_waypoints_directory = project.get_artifacts_directory("waypoints")
waypoint_files = glob.glob(input_waypoints_directory + os.sep + "*")
waypoint_tasks = cells.waypoints.seeding.get_waypoints_tasks(
waypoint_files, image_data)
# Calculate task status data
waypoint_tasks_data = {}
tasks_total = 0
tasks_done = 0
tasks_wip = 0
tasks_open = 0
tasks_progress = 0.0
tasks_total = len(waypoint_tasks)
for waypoint_task in waypoint_tasks:
if waypoint_task.get("status") == "open":
tasks_open = tasks_open + 1
elif waypoint_task.get("status") == "in-progress":
tasks_wip = tasks_wip + 1
elif waypoint_task.get("status") == "complete":
tasks_done = tasks_done + 1
if tasks_total > 0:
tasks_progress = round(100.0 * float(tasks_done) / tasks_total, 2)
waypoint_tasks_data["total"] = tasks_total
waypoint_tasks_data["done"] = tasks_done
waypoint_tasks_data["wip"] = tasks_wip
waypoint_tasks_data["open"] = tasks_open
waypoint_tasks_data["progress"] = tasks_progress
return waypoint_tasks, waypoint_tasks_data
def getCachedWaypointImage(project, image_name):
import cv2
import cells.waypoints.seeding
cache_root = os.path.join(app.static_folder, "tmp")
image_cache = os.path.join(cache_root, "images")
if not os.path.isdir(cache_root):
os.makedirs(cache_root)
if not os.path.isdir(image_cache):
os.makedirs(image_cache)
input_waypoints_directory = project.get_artifacts_directory("waypoints")
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory, working_file_name)
if not os.path.isfile(working_file):
return getCachedImage(project, image_name)
image_file = os.path.join(project.get_input_image_directory(), image_name)
task_image_name = "task-wp-" + image_name + ".png"
working_temp_image_name = "temp-" + image_name
working_temp_file = os.path.join(image_cache, working_temp_image_name)
image = cv2.imread(image_file)
image_waypoints = cells.waypoints.seeding.load_waypoints(working_file)
for waypoints_row in image_waypoints:
waypoints = waypoints_row.get("waypoints")
for idx in range(0, len(waypoints)):
r, c = waypoints[idx]
r_next, c_next = waypoints[(idx + 1) % len(waypoints)]
x, y = c, r
x_next, y_next = c_next, r_next
cv2.line(image, (x, y), (x_next, y_next), (244, 238, 66), 1)
cv2.imwrite(working_temp_file, image)
image = Image.open(working_temp_file)
output_image = image.convert("RGB")
output_image.save(image_cache + os.sep + task_image_name, "PNG")
image_relative_url = "/static/tmp/images/" + task_image_name
# Cache bust
image_relative_url = image_relative_url + "?cachev=" + str(time.time())
return image_relative_url
def getTask(project_hash, task_hash):
if request.method == 'POST':
return postTask(project_hash, task_hash)
else:
import cells.waypoints.seeding
import cli.project
import cv2
project = get_project(project_hash)
# waypoint_tasks, waypoint_tasks_data = getWaypointTasks(project)
project_header = {"hash": project_hash}
task_hash_decoded = base64.urlsafe_b64decode(task_hash.encode("ascii"))
task_type = task_hash_decoded.split("::")[0]
task_key = task_hash_decoded.split("::")[1]
image_name = task_key
# Load Image Data
image_file = os.path.join(project.get_input_image_directory(),
image_name)
input_image = cv2.imread(image_file)
height, width, channels = input_image.shape
input_waypoints_directory = project.get_artifacts_directory(
"waypoints")
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory,
working_file_name)
completed_file_name = image_name + ".tsv"
completed_file = os.path.join(input_waypoints_directory,
completed_file_name)
task_status = "open"
if os.path.isfile(working_file):
task_status = "in-progress"
elif os.path.isfile(completed_file):
task_status = "complete"
# Load waypoints
if task_status == "complete":
image_waypoints = cells.waypoints.seeding.load_waypoints(
completed_file)
elif task_status == "in-progress":
image_waypoints = cells.waypoints.seeding.load_waypoints(
working_file)
else:
image_waypoints = []
row = 1
for waypoints_row in image_waypoints:
waypoints_row["row"] = row
row += 1
# Get png versions of images
working_image_wp_url = getCachedWaypointImage_v2(
input_image, image_waypoints, image_name)
working_image_url = getCachedImage(project, image_name)
view_type_parameter = request.args.get('vt')
if view_type_parameter == "review":
view_type = "review"
else:
view_type = "waypoints"
task_data = {
"hash": task_hash,
"status": task_status,
"image_name": task_key,
"image_width": height,
"image_height": width,
"image_wp_url": working_image_wp_url,
"image_url": working_image_url
}
return render_template('tasks/task.html',
project=project_header,
task=task_data,
image_url=working_image_url,
image_waypoints=image_waypoints,
view_type=view_type)
def postTask(project_hash, task_hash):
import cells.waypoints.seeding
import cells.images
if request.form["task_action"] == "save":
project = get_project(project_hash)
input_waypoints_directory = project.get_artifacts_directory(
"waypoints")
task_hash_decoded = base64.urlsafe_b64decode(task_hash.encode("ascii"))
task_type = task_hash_decoded.split("::")[0]
image_name = task_hash_decoded.split("::")[1]
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory,
working_file_name)
waypoints = []
waypoints_raw = json.loads(request.form["waypoints"])
for point in waypoints_raw:
waypoints.append([point.get("y"), point.get("x")])
cells.waypoints.seeding.append_waypoints(working_file,
waypoints,
created_from=image_name)
elif request.form["task_action"] == "done":
project = get_project(project_hash)
input_waypoints_directory = project.get_artifacts_directory(
"waypoints")
task_hash_decoded = base64.urlsafe_b64decode(task_hash.encode("ascii"))
task_type = task_hash_decoded.split("::")[0]
image_name = task_hash_decoded.split("::")[1]
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory,
working_file_name)
finished_file = working_file.replace(".tsv-working", ".tsv")
if not os.path.isfile(working_file):
raise Exception("Tried to save a working file that didn't exist.")
if os.path.isfile(finished_file):
raise Exception("Tried to overwrite a finished waypoints file.")
shutil.move(working_file, finished_file)
elif request.form["task_action"] == "reopen":
project = get_project(project_hash)
input_waypoints_directory = project.get_artifacts_directory(
"waypoints")
task_hash_decoded = base64.urlsafe_b64decode(task_hash.encode("ascii"))
task_type = task_hash_decoded.split("::")[0]
image_name = task_hash_decoded.split("::")[1]
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory,
working_file_name)
finished_file = working_file.replace(".tsv-working", ".tsv")
if not os.path.isfile(finished_file):
raise Exception("Tried to save a finished file that didn't exist.")
if os.path.isfile(working_file):
raise Exception(
"Tried to overwrite an existing working waypoints file.")
shutil.move(finished_file, working_file)
elif request.form["task_action"] == "delete":
project = get_project(project_hash)
input_waypoints_directory = project.get_artifacts_directory(
"waypoints")
task_hash_decoded = base64.urlsafe_b64decode(task_hash.encode("ascii"))
task_type = task_hash_decoded.split("::")[0]
image_name = task_hash_decoded.split("::")[1]
working_file_name = image_name + ".tsv-working"
working_file = os.path.join(input_waypoints_directory,
working_file_name)
wp_row_raw = request.form["wp_row"]
if wp_row_raw is not None:
wp_row = int(wp_row_raw)
if wp_row > 0:
cells.waypoints.seeding.delete_waypoints(working_file, wp_row)
return redirect("/projects/" + project_hash + "/tasks/" + task_hash)