def load_existing_ekgAnnotations(startTime, endTime, ekgNote):
"""Loads existing annotations from file.
Parameters -- from column file headers
----------
startTime:str
Timestamp marking beginning of annotation, preferably in ISO format.
endTime:str
Timestamp marking end of annotation, preferably in ISO format.
ekgNote:str
Annotation code for EKG (e.g. "EKG Interpretable")
Returns
-------
"""
ekgIdx = annotatorSettings.ekgCodes.index(ekgNote)
ekgComments = BoxAnnotation(
fill_color=annotatorSettings.ekgColorSelector[ekgIdx])
views.ekgViewer.add_layout(ekgComments)
# FIXME: Timestamp issue likely in the future.
# I honestly do not know why these values work...but there is a current issue with Bokeh datetime.
# I subtracted the timestamp provided by x1 and the known epoch UTC timestamp of 1/1/2020 to get 18000000000000.
# I divided by various magnitudes of 10 until timestamp on bokeh was correct.
ekgComments.left = pd.to_datetime(str(startTime)).tz_localize('Etc/GMT+4')
ekgComments.right = pd.to_datetime(str(endTime)).tz_localize('Etc/GMT+4')
def load_existing_ekgAnnotations(startTime, endTime, ekgNote):
"""Loads existing annotations from file.
Parameters -- from column file headers
----------
startTime:str
Timestamp marking beginning of annotation, preferably in ISO format.
endTime:str
Timestamp marking end of annotation, preferably in ISO format.
ekgNote:str
Annotation code for EKG (e.g. "EKG Interpretable")
Returns
-------
"""
global ekgColorSelector
ekgIdx = annotatorSettings.ekgCodes.index(ekgNote)
ekgComments = BoxAnnotation(fill_color=ekgColorSelector[ekgIdx])
ekgViewer.add_layout(ekgComments)
# FIXME: Timestamp issue likely in the future.
# I honestly do not know why these values work...but there is a current issue with Bokeh datetime.
# I subtracted the timestamp provided by x1 and the known epoch UTC timestamp of 1/1/2020 to get 18000000000000.
# I divided by various magnitudes of 10 until timestamp on bokeh was correct.
ekgComments.left = pd.to_datetime(str(startTime)).tz_localize('Etc/GMT+4')
ekgComments.right = pd.to_datetime(str(endTime)).tz_localize('Etc/GMT+4')
def load_existing_ppgQos_annotations(startTime, endTime, ppgNote, qosNote):
"""Loads existing annotations from file.
Parameters -- from file column headers
----------
startTime:str
Timestamp marking beginning of annotation, preferably in ISO format.
endTime:str
Timestamp marking end of annotation, preferably in ISO format.
ppgNote:str
Annotation code for PPG (e.g. "PPG Interpretable")
qosNote:str
Annotation code for QoS (e.g. "QoS Correct")
Returns
-------
"""
global ppgColorSelector, ppgViewer
ppgIdx = annotatorSettings.ppgCodes.index(ppgNote)
qosIdx = annotatorSettings.qosCodes.index(qosNote)
# Use ppgNote and qosNote to determine color of loaded annotation to add to plot.
ppgComments = BoxAnnotation(fill_color=ppgColorSelector[ppgIdx])
ppgViewer.add_layout(ppgComments)
# FIXME: Timestamp issue likely in the future.
# I honestly do not know why these values work...but there is a current issue with Bokeh datetime.
# I subtracted the timestamp provided by x1 and the known epoch UTC timestamp of 1/1/2020 to get 18000000000000.
# I divided by various magnitudes of 10 until timestamp on bokeh was correct.
ppgComments.left = (pd.to_datetime(str(startTime)).value +
18000000000000) / 1000000
ppgComments.right = (pd.to_datetime(str(endTime)).value +
18000000000000) / 1000000
qosComments = BoxAnnotation(fill_color=qosColorSelector[qosIdx],
fill_alpha=1)
ppgViewer.add_layout(qosComments)
qosComments.top = annotatorSettings.ppgYRange[1]
qosComments.bottom = annotatorSettings.ppgYRange[1] - 100
qosComments.left = (pd.to_datetime(str(startTime)).value +
18000000000000) / 1000000
qosComments.right = (pd.to_datetime(str(endTime)).value +
18000000000000) / 1000000
def ppgViewerSelectionCallback(attr, old, new):
"""Create an annotation based on the geometry of the box select tool.
Parameters
----------
attr:str
'geometries'
old:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
new:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
Returns
-------
"""
# Provide globals to help reader know what is local and global
global ppgViewer, ppgDataFrame, args, ppgColorSelector, qosColorSelector, ppgButtonGroup, qosButtonGroup
# Edge case. Make sure minimum x value for annotation is 0.
if new[0]['x0'] < 0:
x0 = 0
else:
x0 = abs(int(new[0]['x0']))
x1 = abs(int(new[0]['x1']))
# Create box annotation. Color of annotation depends on which button in a group is selected (active).
ppgComments = BoxAnnotation(
fill_color=ppgColorSelector[ppgButtonGroup.active])
ppgViewer.add_layout(ppgComments)
ppgComments.left = x0
ppgComments.right = x1
# Create box annotation. Color of annotation depends on which button in a group is selected (active).
qosComments = BoxAnnotation(
fill_color=qosColorSelector[qosButtonGroup.active], fill_alpha=1)
ppgViewer.add_layout(qosComments)
qosComments.top = annotatorSettings.ppgYRange[1]
qosComments.bottom = annotatorSettings.ppgYRange[1] - 100
qosComments.left = x0
qosComments.right = x1
save_annotation_dimensions(x0, x1, args.spo2QosAnnotatedFile)
def ppgViewerSelectionCallback(attr, old, new):
"""Create an annotation based on the geometry of the box select tool.
Parameters
----------
attr:str
'geometries'
old:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
new:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
Returns
-------
"""
# Provide globals to help reader know what is local and global
global ppgViewer, ppgDataFrame, args, ppgColorSelector, qosColorSelector, ppgButtonGroup, qosButtonGroup
# Edge case. Make sure minimum x value for annotation is 0.
if new[0]['x0'] < 0:
x0 = 0
else:
x0 = abs(int(new[0]['x0']))
x1 = abs(int(new[0]['x1']))
# Create box annotation. Color of annotation depends on which button in a group is selected (active).
ppgComments = BoxAnnotation(fill_color=ppgColorSelector[ppgButtonGroup.active])
ppgViewer.add_layout(ppgComments)
ppgComments.left = x0
ppgComments.right = x1
# # Create box annotation. Color of annotation depends on which button in a group is selected (active).
# qosComments = BoxAnnotation(fill_color=qosColorSelector[qosButtonGroup.active], fill_alpha=1)
# ppgViewer.add_layout(qosComments)
#
# qosComments.top = annotatorSettings.ppgYRange[1]
# qosComments.bottom = annotatorSettings.ppgYRange[1] - 100
# qosComments.left = x0
# qosComments.right = x1
save_annotation_dimensions(x0,x1,args.spo2QosAnnotatedFile)
def ekgViewerSelectionCallback(attr, old, new):
"""Create an annotation based on the geometry of the box select tool.
Parameters
----------
attr:str
'geometries'
old:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
new:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
Returns
-------
"""
# Provide globals to help reader know what is local and global
global ekgViewer, args, ekgColorSelector, ekgButtonGroup
# Edge case. Make sure minimum x value for annotation is 0.
if new[0]['x0'] < 0:
x0 = 0
else:
x0 = abs(int(new[0]['x0']))
x1 = abs(int(new[0]['x1']))
# Create box annotation. Color of annotation depends on which button in a group is selected (active).
ekgComments = BoxAnnotation(
fill_color=ekgColorSelector[ekgButtonGroup.active])
ekgComments.left = x0
ekgComments.right = x1
ekgViewer.add_layout(ekgComments)
save_annotation_dimensions(x0, x1, args.ekgAnnotatedFile)
def ekgViewerSelectionCallback(attr, old, new):
"""Create an annotation based on the geometry of the box select tool.
Parameters
----------
attr:str
'geometries'
old:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
new:list
e.g. [{'vx0': 464, 'vy0': 23.7869873046875, 'y0': 0, 'y1': 4503.400000000001, 'type': 'rect', 'x0': 1481149362095.9377, 'vx1': 552, 'x1': 1481149364565.3564, 'vy1': 341.03603515625}]
Returns
-------
"""
# Provide globals to help reader know what is local and global
global ekgViewer, args, ekgColorSelector, ekgButtonGroup
# Edge case. Make sure minimum x value for annotation is 0.
if new[0]['x0'] < 0:
x0 = 0
else:
x0 = abs(int(new[0]['x0']))
x1 = abs(int(new[0]['x1']))
# Create box annotation. Color of annotation depends on which button in a group is selected (active).
ekgComments = BoxAnnotation(fill_color=ekgColorSelector[ekgButtonGroup.active])
ekgComments.left = x0
ekgComments.right = x1
ekgViewer.add_layout(ekgComments)
save_annotation_dimensions(x0,x1,args.ekgAnnotatedFile)
def load_existing_ppgQos_annotations(startTime, endTime, ppgNote, qosNote):
"""Loads existing annotations from file.
Parameters -- from file column headers
----------
startTime:str
Timestamp marking beginning of annotation, preferably in ISO format.
endTime:str
Timestamp marking end of annotation, preferably in ISO format.
ppgNote:str
Annotation code for PPG (e.g. "PPG Interpretable")
qosNote:str
Annotation code for QoS (e.g. "QoS Correct")
Returns
-------
"""
global ppgColorSelector, ppgViewer
if ppgNote != '':
ppgIdx = annotatorSettings.ppgCodes.index(ppgNote)
# Use ppgNote and qosNote to determine color of loaded annotation to add to plot.
ppgComments = BoxAnnotation(fill_color=ppgColorSelector[ppgIdx])
ppgViewer.add_layout(ppgComments)
# FIXME: Timestamp issue likely in the future.
# I honestly do not know why these values work...but there is a current issue with Bokeh datetime.
# I subtracted the timestamp provided by x1 and the known epoch UTC timestamp of 1/1/2020 to get 18000000000000.
# I divided by various magnitudes of 10 until timestamp on bokeh was correct.
ppgComments.left = pd.to_datetime(str(startTime)).tz_localize('Etc/GMT+4')
ppgComments.right = pd.to_datetime(str(endTime)).tz_localize('Etc/GMT+4')
if qosNote != '':
qosIdx = annotatorSettings.qosCodes.index(qosNote)
qosComments = BoxAnnotation(fill_color=qosColorSelector[qosIdx],fill_alpha=0.5)
ppgViewer2.add_layout(qosComments)
# qosComments.top = annotatorSettings.ppgYRange[1]
# qosComments.bottom = annotatorSettings.ppgYRange[1] - 100
qosComments.left = pd.to_datetime(str(startTime)).tz_localize('Etc/GMT+4')
qosComments.right = pd.to_datetime(str(endTime)).tz_localize('Etc/GMT+4')
def add_anno():
alarm = alarms.alarms[alarmNumber]
ala = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala2 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala3 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala5 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala6 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala7 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
views.ekgViewer.add_layout(ala)
views.ppgViewer.add_layout(ala2)
views.hrViewer.add_layout(ala3)
views.bpViewer.add_layout(ala5)
views.spo2Viewer.add_layout(ala6)
views.ppgViewer2.add_layout(ala7)
ala.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
ala2.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala2.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
ala3.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala3.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
ala5.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala5.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
ala6.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala6.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
ala7.left = pd.to_datetime(str(alarm)) - pd.Timedelta('0.25 seconds')
ala7.right = pd.to_datetime(str(alarm)) + pd.Timedelta('0.25 seconds')
# Availability: https://github.com/bokeh/bokeh #
#################################################
from bokeh.core.properties import Bool, List, Instance, String, Enum, Int
from bokeh.models.annotations import Label
from bokeh.models.tools import Drag, BoxAnnotation
from bokeh.models.renderers import Renderer
from bokeh.models.callbacks import Callback
from bokeh.core.enums import Dimensions
_DEFAULT_BOX_ANNOTATION = lambda: BoxAnnotation(level="overlay",
render_mode="css",
top_units="screen",
left_units="screen",
bottom_units="screen",
right_units="screen",
fill_color="#ff3333",
fill_alpha=0.3,
line_color="red",
line_alpha=1.0,
line_width=2,
line_dash=[4, 4])
class MeasureJTool(Drag):
__implementation__ = "measureJTool.ts"
names = List(String)
renderers = List(Instance(Renderer))
with open(spo2QosAnnotatedFile, 'r') as readfile:
reader = csv.reader(readfile)
next(reader)
for row in reader:
load_existing_ppgQos_annotations(row[0], row[1], row[2], row[3])
with open(ekgAnnotatedFile, 'r') as readfile:
reader = csv.reader(readfile)
next(reader)
for row in reader:
load_existing_ekgAnnotations(row[0], row[1], row[2])
for alarm in alarms:
ala = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala2 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala3 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala4 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala5 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ala6 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,
fill_alpha=0.5)
ekgViewer.add_layout(ala)
ppgViewer.add_layout(ala2)
hrViewer.add_layout(ala3)
ekgViewer.add_layout(ala4)
with open(spo2QosAnnotatedFile,'r') as readfile:
reader = csv.reader(readfile)
next(reader)
for row in reader:
load_existing_ppgQos_annotations(row[0], row[1], row[2], row[3])
with open(ekgAnnotatedFile,'r') as readfile:
reader = csv.reader(readfile)
next(reader)
for row in reader:
load_existing_ekgAnnotations(row[0], row[1], row[2])
for alarm in alarms:
ala = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ala2 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ala3 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ala4 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ala5 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ala6 = BoxAnnotation(fill_color=annotatorSettings.alarmColor,fill_alpha=0.5)
ekgViewer.add_layout(ala)
ppgViewer.add_layout(ala2)
hrViewer.add_layout(ala3)
ekgViewer.add_layout(ala4)
bpViewer.add_layout(ala5)
spo2Viewer.add_layout(ala6)
ala.left = pd.to_datetime(str(alarm))-pd.Timedelta('0.25 seconds')