def update_project(project_id):
new_project = request.get_json()
try:
project = Project.get(Project.id == project_id)
except models.DoesNotExist:
return jsonify({ 'message': 'Project not found' }), 400
if new_project['id'] != project.id:
return jsonify({ 'message': 'Cannot update project at this url' }), 400
try:
if new_project['markerOptions']:
marker_options = new_project['markerOptions']
for marker_name in marker_options:
try:
marker_option = MarkerOption.get(MarkerOption.name == marker_name)
ProjectMarkerOption.get(ProjectMarkerOption.project == project.id,
ProjectMarkerOption.marker_option == marker_option.id)
except models.DoesNotExist:
ProjectMarkerOption.create(project = project, marker_option = marker_option)
if new_project['users']:
users = new_project['users']
for user in users:
try:
project_user = ProjectUser.get(ProjectUser.app_user == user['id'],
ProjectUser.project == project)
except models.DoesNotExist:
ProjectUser.create(app_user = user['id'], project = project)
if new_project['stacks']:
stacks = new_project['stacks']
with db.atomic():
for stack in stacks:
try:
project_stack = ProjectStack.get(ProjectStack.stack == stack['id'],
ProjectStack.project == project)
except models.DoesNotExist:
project_stack = ProjectStack.create(project=project, stack = stack['id'])
probe_setting = stack['probeSettings']
probe_position = json.loads(probe_setting['position'])
ProbeSetting.create(x_offset=int(probe_position['xOffset']),
y_offset=int(probe_position['yOffset']),
project_stack=project_stack,
label=probe_position['label']
)
message = "Project updated"
except Exception as ex:
print ex
project = Project.get(Project.id == project_id)
return jsonify({ 'message': 'Project updated', 'project': project.deep_serialized() }), 200
def project_stack_images(project_id, stack_id):
first_image = Image.select().join(StackImage).where(StackImage.stack == stack_id).get().key
last_underscore = first_image.rfind('_')
stack_title = first_image[:last_underscore]
project_stack = ProjectStack.get(ProjectStack.project == project_id, ProjectStack.stack == stack_id)
project_stack_user_data = project_stack.project_stack_data.where(ProjectStackDatum.user == g.user_id)
probe_type = project_stack.project.probe_type
probe_settings = project_stack.probe_setting.get()
images = (Image.select().join(StackImage).where(StackImage.stack == stack_id)
.order_by(Image.name))
project_stacks = Stack.select().join(ProjectStack).where(ProjectStack.project == project_id).order_by(Stack.id)
marker_options = MarkerOption.select().join(ProjectMarkerOption).where(ProjectMarkerOption.project == project_id)
return jsonify({ 'images': [image.stack_image_serialized for image in images],
'data': [d.serialized for d in project_stack_user_data],
'probeSettings': probe_settings.serialized,
'stackTitle': stack_title,
'probeType': probe_type,
'markerOptions': [marker_option.name for marker_option in marker_options],
'projectStackIds': [stack.id for stack in project_stacks]
})
def projects():
req = request.get_json()
message = ""
try:
page = req['page']
page_size = req['pageSize']
except (TypeError, KeyError):
page = 1
page_size = 20
if request.method == 'POST':
try:
request_error = False
title = req['title']
comments = req['comments']
stacks = req['stacks']
probe_type = req['probeType']
except KeyError:
request_error = True
if request_error:
return jsonify({ 'message': 'Insufficient information to create project' }), 400
try:
project = Project.create(title=title, comments=comments, probe_type=probe_type)
if req['markerOptions']:
marker_options = req['markerOptions']
for marker_name in marker_options:
try:
marker_option = MarkerOption.get(MarkerOption.name == marker_name)
ProjectMarkerOption.create(project = project, marker_option = marker_option)
except Exception as ex:
print("line 74")
print ex
if req['users']:
users = req['users']
for user in users:
try:
ProjectUser.create(app_user = user['id'], project = project)
except Exception as ex:
print ex
for stack in stacks:
try:
project_stack = ProjectStack.create(project=project, stack = stack['stackId'])
probe_setting = stack['probeSettings']
probe_position = json.loads(probe_setting['position'])
ProbeSetting.create(x_offset=int(probe_position['xOffset']),
y_offset=int(probe_position['yOffset']),
project_stack=project_stack,
label=probe_position['label']
)
except Exception as ex:
print ex
message = "Project created"
except Exception as ex:
print ex
projects = (Project.select()
.order_by(Project.created_date.desc()))
# .paginate(page, page_size))
return jsonify({
'message': message,
'projects': [project.serialized for project in projects],
'projectCount': SelectQuery(models.Project).count()
}), 201
def get_marker_options():
marker_options = MarkerOption.select().order_by(MarkerOption.name)
return jsonify({ 'markerOptions': [marker_option.name for marker_option in marker_options] })
def json_to_excel_neuron_dimensions(report, project_id):
xlsx_file = Workbook()
ws = xlsx_file.active
ws['A1'] = 'User'
ws['B1'] = 'Case'
ws['C1'] = 'Hemisphere'
ws['D1'] = 'Stain'
ws['E1'] = 'Region'
ws['F1'] = 'Section'
ws['G1'] = 'Probe'
ws['H1'] = 'Z Value'
ws['I1'] = 'Neuron Height'
ws['J1'] = 'Neuron Width'
micrometer_scale_length = 10 # will this ever change?
row = 1
column = 'K'
marker_columns = {}
marker_mappings = {
'Neuron': 'neuron',
'Oligodendrocyte': 'oligodendrocyte',
'Astrocyte': 'astrocyte',
'Pericyte': 'pericyte',
'Marker 1': 'markerone',
'Marker 2': 'markertwo',
'Out of Focus': 'out-of-focus',
'Length': 'length',
'Blood Cell(s)': 'blood-cell',
'Guard Zone': 'guard-zone'
}
marker_types = (MarkerOption.select()
.join(ProjectMarkerOption)
.where(ProjectMarkerOption.project == project_id)
.order_by(MarkerOption.name))
for marker in marker_types:
ws['{0}{1}'.format(column, row)] = marker.name
marker_columns[marker_mappings[marker.name]] = column
column = chr(ord(column) + 1)
for project_stack in report:
stack_info = project_stack.split('_')
if len(stack_info) != 6:
stack_info = ['a', 'b', 'c', 'd', 'e', 'f']
for stack_image in report[project_stack]:
for user in report[project_stack][stack_image]:
for marker in report[project_stack][stack_image][user]:
if marker['markerType'] == 'neuron':
row += 1
ws['A{}'.format(row)] = user
ws['B{}'.format(row)] = stack_info[0]
ws['C{}'.format(row)] = stack_info[1]
ws['D{}'.format(row)] = stack_info[2]
ws['E{}'.format(row)] = stack_info[3]
ws['F{}'.format(row)] = stack_info[4]
ws['G{}'.format(row)] = stack_info[5]
ws['H{}'.format(row)] = stack_image
ws['I{}'.format(row)] = (float(marker['yCrosshairPercent']) / 100) * micrometer_scale_length * 2 # see Marker model
ws['J{}'.format(row)] = (float(marker['xCrosshairPercent']) / 100)* micrometer_scale_length * 2 # "
return xlsx_file
def json_to_excel_stack_counts(report, project_id):
xlsx_file = Workbook()
ws = xlsx_file.active
ws['A1'] = 'User'
ws['B1'] = 'Case'
ws['C1'] = 'Hemisphere'
ws['D1'] = 'Stain'
ws['E1'] = 'Region'
ws['F1'] = 'Section'
ws['G1'] = 'Probe'
ws['H1'] = 'Z Value'
row = 1
column = 'I'
marker_columns = {}
marker_mappings = {
'Neuron': 'neuron',
'Oligodendrocyte': 'oligodendrocyte',
'Astrocyte': 'astrocyte',
'Pericyte': 'pericyte',
'Marker 1': 'markerone',
'Marker 2': 'markertwo',
'Out of Focus': 'out-of-focus',
'Length': 'length',
'Blood Cell(s)': 'blood-cell',
'Guard Zone': 'guard-zone'
}
marker_types = (MarkerOption.select()
.join(ProjectMarkerOption)
.where(ProjectMarkerOption.project == project_id)
.order_by(MarkerOption.name))
for marker in marker_types:
ws['{0}{1}'.format(column, row)] = marker.name
marker_columns[marker_mappings[marker.name]] = column
column = chr(ord(column) + 1)
for project_stack in report:
stack_info = project_stack.split('_')
if len(stack_info) != 6:
stack_info = ['a', 'b', 'c', 'd', 'e', 'f']
for stack_image in report[project_stack]:
for user in report[project_stack][stack_image]:
row += 1
ws['A{}'.format(row)] = user
ws['B{}'.format(row)] = stack_info[0]
ws['C{}'.format(row)] = stack_info[1]
ws['D{}'.format(row)] = stack_info[2]
ws['E{}'.format(row)] = stack_info[3]
ws['F{}'.format(row)] = stack_info[4]
ws['G{}'.format(row)] = stack_info[5]
ws['H{}'.format(row)] = stack_image
user_markers = {}
for m in report[project_stack][stack_image][user]:
try:
user_markers[m['markerType']] = user_markers[m['markerType']] + 1
except KeyError:
user_markers[m['markerType']] = 1
if user_markers:
for marker in user_markers:
ws['{0}{1}'.format(marker_columns[marker], row)] = user_markers[marker]
return xlsx_file