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 getProject(project_hash):
import cells.images
import cli.operations
project = get_project(project_hash)
project_name = get_project_name(project_hash)
project_dto = {"hash": project_hash, "name": project_name}
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)
# Get input image count
total_images = 0
stain_image_counts = {}
for image_data_row in image_data:
file_name = image_data_row["file_name"]
image_stain = None
for test_stain in variant.get("values", []):
if test_stain in file_name:
stain_image_counts[test_stain] = stain_image_counts.get(
test_stain, 0) + 1
image_stain = test_stain
break
if image_stain is None:
stain_image_counts["None"] = stain_image_counts.get("None", 0) + 1
total_images = total_images + 1
# Task Data
waypoint_tasks, waypoint_tasks_data = get_waypoint_tasks(project)
# Cell Data
cell_collection = cli.operations.get_cell_collection(project, image_data)
project_data_dto = {
"image_count": total_images,
"variant_data": stain_image_counts,
"task_data": waypoint_tasks_data,
"cell_count": len(cell_collection)
}
print project.get_project_hash()
return render_template('projects/overview.html',
project=project_dto,
project_data=project_data_dto)
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 createProjectConfigurationDimension(project_hash):
project = get_project(project_hash)
existing_dimensions = project.get_dimensions()
dimension_name = request.form.get("dimension_name")
dimension_type = request.form.get("dimension_type")
if (dimension_name is None or dimension_name in existing_dimensions.keys()
or len(dimension_name) < 4):
return redirect("/projects/" + project_hash + "/config")
else:
project.add_dimension(dimension_name, dimension_type)
return redirect("/projects/" + project_hash + "/dimensions/" +
dimension_name)
def getProjectConfigurationDimension(project_hash, dimension_name):
project = get_project(project_hash)
dimensions = project.get_dimensions()
dimension = dimensions.get(dimension_name)
project_dto = {"hash": project_hash, "name": project.get_project_name()}
dimension_dto = {
"name": dimension_name,
"type": dimension.get("type"),
"data": dimension.get("data", [])
}
page_data = {"title": "", "active_nav_tab": "config"}
return render_template('projects/dimension.html',
project=project_dto,
dimension=dimension_dto,
page_data=page_data)
def getProjectConfiguration(project_hash):
project = get_project(project_hash)
project_name = get_project_name(project_hash)
project_dto = {"hash": project_hash, "name": project_name}
project_configuration_dto = {
"variant":
project.get_variant(),
"dimensions":
project.get_dimensions(),
"parameters":
project.get_parameters(),
"dep": [{
"name": "Experiment Date",
"type": "function",
"data": "parse_date"
}, {
"name": "Experiment Name",
"type": "mapping",
"data": [
{
"tokens": [],
"value": ""
},
]
}]
}
page_data = {"title": "", "active_nav_tab": "config"}
return render_template('projects/config.html',
project=project_dto,
configuration=project_configuration_dto,
page_data=page_data)
def getProjectProblems(project_hash):
import cells.images
project = get_project(project_hash)
project_name = get_project_name(project_hash)
project_dto = {"hash": project_hash, "name": project_name}
problems = []
input_image_directory = project.get_input_image_directory()
variant = project.get_variant()
dimensions = project.get_dimensions()
if variant.get("name") is None or variant.get("name") == "":
problems.append({
"level":
"info",
"css":
"info",
"summary":
"You have not configured a variant (stain) and values for this project"
})
image_data = cells.images.get_image_collection(input_image_directory,
variant, dimensions)
# TODO: A variant value is not found in any images
stain_image_counts = {}
missing_variant_images = []
for image_data_row in image_data:
file_name = image_data_row["file_name"]
image_stain = None
for test_stain in variant.get("values", []):
if test_stain in file_name:
stain_image_counts[test_stain] = stain_image_counts.get(
test_stain, 0) + 1
image_stain = test_stain
break
if image_stain is None:
missing_variant_images.append(file_name)
for variant_value in variant.get("values", []):
if stain_image_counts.get(variant_value, 0) == 0:
problems.append({
"level":
"warning",
"css":
"warning",
"summary":
"The variant/stain '%s' did not match any images." %
variant_value
})
# Image has no variant
for missing_variant_image in missing_variant_images:
problems.append({
"level":
"warning",
"css":
"warning",
"summary":
"Image '%s' does not have a variant." % missing_variant_image
})
# Image has missing related variant image(s)
for image_data_row in image_data:
file_name = image_data_row["file_name"]
image_stain = None
for test_stain in variant.get("values", []):
if test_stain in file_name:
stain_image_counts[test_stain] = stain_image_counts.get(
test_stain, 0) + 1
image_stain = test_stain
break
missing_variants = []
if image_stain is not None:
for variant_value in variant.get("values", []):
related_file_name = file_name.replace(image_stain,
variant_value)
related_file = os.path.join(input_image_directory,
related_file_name)
if not os.path.isfile(related_file):
missing_variants.append(variant_value)
for missing_variant in missing_variants:
if missing_variant == variant.get("primary_value"):
problems.append({
"level":
"error",
"css":
"danger",
"summary":
"Missing variant with value '%s' for image '%s'. No output will be generated for this file."
% (missing_variant, file_name),
})
else:
problems.append({
"level":
"warning",
"css":
"warning",
"summary":
"Missing variant with value '%s' for image '%s'." %
(missing_variant, file_name)
})
page_data = {"title": "", "active_nav_tab": "problems"}
return render_template('projects/problems.html',
project=project_dto,
problems=problems,
page_data=page_data)
def getProjectDataSummary(project_hash):
import cells.images
import cli.operations
project = get_project(project_hash)
project_name = get_project_name(project_hash)
project_dto = {"hash": project_hash, "name": project_name}
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)
# Get input image count
total_images = 0
variant_counts = {}
for image_data_row in image_data:
file_name = image_data_row["file_name"]
image_stain = None
for test_stain in variant.get("values", []):
if test_stain in file_name:
variant_counts[test_stain] = variant_counts.get(test_stain,
0) + 1
image_stain = test_stain
break
if image_stain is None:
variant_counts["None"] = variant_counts.get("None", 0) + 1
total_images = total_images + 1
dimension_counts = {}
for key, value in dimensions.iteritems():
dimension_counts[key] = {}
for image_data_row in image_data:
for key in dimensions.keys():
dimension_value = image_data_row.get("dimensions", {}).get(key)
dimension_counts[key][dimension_value] = \
dimension_counts[key].get(dimension_value, 0) + 1
# Get counts for cells
cell_collection = cli.operations.get_cell_collection(project, image_data)
cell_variant_counts = {}
for key in variant_counts.keys():
cell_variant_counts[key] = 0
cell_dimension_counts = {}
for key, value in dimensions.iteritems():
cell_dimension_counts[key] = {}
for cell_data_row in cell_collection:
variant_value = cell_data_row.get("variant")
cell_variant_counts[variant_value] = cell_variant_counts.get(
variant_value, 0) + 1
for key in dimensions.keys():
dimension_value = cell_data_row.get("dimensions", {}).get(key)
cell_dimension_counts[key][dimension_value] = \
cell_dimension_counts[key].get(dimension_value, 0) + 1
variant_name = project.get_variant()["name"]
project_data_dto = {
"image_count": total_images,
"variant_name": variant_name,
"variant_data": variant_counts,
"cell_variant_data": cell_variant_counts,
"dimension_counts": dimension_counts,
"cell_dimension_counts": cell_dimension_counts
}
page_data = {"title": "", "active_nav_tab": "data"}
return render_template('projects/data.html',
project=project_dto,
project_data=project_data_dto,
page_data=page_data)