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Overall compliance heatmap: shows all dates for all participants (only supports last certain dates previously)

pull/95/head
Meng Li 2020-07-24 12:58:48 -04:00
parent 5f771618ae
commit b3aa4d82e1
6 changed files with 71 additions and 34 deletions
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7
Snakefile
View File

@ -22,7 +22,10 @@ if config["PHONE_VALID_SENSED_DAYS"]["COMPUTE"]:
if len(config["PHONE_VALID_SENSED_BINS"]["TABLES"]) == 0:
raise ValueError("If you want to compute PHONE_VALID_SENSED_DAYS, you need to add at least one table to [PHONE_VALID_SENSED_BINS][TABLES] in config.yaml")
files_to_compute.extend(expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv", pid=config["PIDS"], min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"]))
files_to_compute.extend(expand("data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv",
pid=config["PIDS"],
min_valid_hours_per_day=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_HOURS_PER_DAY"],
min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
if config["MESSAGES"]["COMPUTE"]:
files_to_compute.extend(expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["MESSAGES"]["DB_TABLE"]))
@ -143,7 +146,7 @@ if config["HEATMAP_SENSED_BINS"]["PLOT"]:
files_to_compute.extend(["reports/data_exploration/heatmap_sensed_bins_all_participants.html"])
if config["OVERALL_COMPLIANCE_HEATMAP"]["PLOT"]:
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}h/overall_compliance_heatmap.html", min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"]))
files_to_compute.extend(expand("reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html", min_valid_hours_per_day=config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_HOURS_PER_DAY"], min_valid_bins_per_hour=config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]))
# analysis example
if config["PARAMS_FOR_ANALYSIS"]["COMPUTE"]:

5
config.yaml
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@ -37,7 +37,7 @@ PHONE_VALID_SENSED_BINS:
PHONE_VALID_SENSED_DAYS:
COMPUTE: False
MIN_VALID_HOURS_PER_DAY: &min_valid_hours_per_day [16] # (out of 24) MIN_HOURS_PER_DAY
MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour 6 # (out of 60min/BIN_SIZE bins)
MIN_VALID_BINS_PER_HOUR: &min_valid_bins_per_hour [6] # (out of 60min/BIN_SIZE bins)
# Communication SMS features config, TYPES and FEATURES keys need to match
MESSAGES:
@ -229,8 +229,9 @@ HEATMAP_SENSED_BINS:
OVERALL_COMPLIANCE_HEATMAP:
PLOT: False
ONLY_SHOW_VALID_DAYS: False
EXPECTED_NUM_OF_DAYS: -1
BIN_SIZE: *bin_size
EXPECTED_NUM_OF_DAYS: 7
MIN_VALID_BINS_PER_HOUR: *min_valid_bins_per_hour
MIN_VALID_HOURS_PER_DAY: *min_valid_hours_per_day

4
rules/preprocessing.snakefile
View File

@ -52,9 +52,9 @@ rule phone_valid_sensed_days:
phone_sensed_bins = "data/interim/{pid}/phone_sensed_bins.csv"
params:
min_valid_hours_per_day = "{min_valid_hours_per_day}",
min_valid_bins_per_hour = config["PHONE_VALID_SENSED_DAYS"]["MIN_VALID_BINS_PER_HOUR"]
min_valid_bins_per_hour = "{min_valid_bins_per_hour}"
output:
"data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}h.csv"
"data/interim/{pid}/phone_valid_sensed_days_{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins.csv"
script:
"../src/data/phone_valid_sensed_days.R"

7
rules/reports.snakefile
View File

@ -62,15 +62,16 @@ rule heatmap_sensed_bins_all_participants:
rule overall_compliance_heatmap:
input:
phone_sensed_bins = expand("data/interim/{pid}/phone_sensed_bins.csv", pid=config["PIDS"]),
phone_valid_sensed_days = expand("data/interim/{pid}/phone_valid_sensed_days_{{min_valid_hours_per_day}}h.csv", pid=config["PIDS"]),
phone_valid_sensed_days = expand("data/interim/{pid}/phone_valid_sensed_days_{{min_valid_hours_per_day}}hours_{{min_valid_bins_per_hour}}bins.csv", pid=config["PIDS"]),
pid_files = expand("data/external/{pid}", pid=config["PIDS"])
params:
only_show_valid_days = config["OVERALL_COMPLIANCE_HEATMAP"]["ONLY_SHOW_VALID_DAYS"],
local_timezone = config["READABLE_DATETIME"]["FIXED_TIMEZONE"],
expected_num_of_days = config["OVERALL_COMPLIANCE_HEATMAP"]["EXPECTED_NUM_OF_DAYS"],
bin_size = config["OVERALL_COMPLIANCE_HEATMAP"]["BIN_SIZE"],
min_bins_per_hour = config["OVERALL_COMPLIANCE_HEATMAP"]["MIN_VALID_BINS_PER_HOUR"]
min_bins_per_hour = "{min_valid_bins_per_hour}"
output:
"reports/data_exploration/{min_valid_hours_per_day}h/overall_compliance_heatmap.html"
"reports/data_exploration/{min_valid_hours_per_day}hours_{min_valid_bins_per_hour}bins/overall_compliance_heatmap.html"
script:
"../src/visualization/overall_compliance_heatmap.py"

2
src/data/phone_valid_sensed_days.R
View File

@ -4,7 +4,7 @@ library("tidyr")
phone_sensed_bins <- read.csv(snakemake@input[["phone_sensed_bins"]])
min_valid_hours_per_day <- as.integer(snakemake@params[["min_valid_hours_per_day"]])
min_valid_bins_per_hour <- snakemake@params[["min_valid_bins_per_hour"]]
min_valid_bins_per_hour <- as.integer(snakemake@params[["min_valid_bins_per_hour"]])
output_file <- snakemake@output[[1]]
phone_valid_sensed_days <- phone_sensed_bins %>%

68
src/visualization/overall_compliance_heatmap.py
View File

@ -1,31 +1,54 @@
import pandas as pd
import numpy as np
import plotly.io as pio
import plotly.figure_factory as ff
import plotly.graph_objects as go
from dateutil import tz
import datetime
def getOneRow(data_per_participant, last_seven_dates, col_name, row):
def getOneRow(data_per_participant, last_certain_dates, col_name, row, expected_num_of_days, only_show_valid_days):
data = pd.read_csv(data_per_participant, index_col=["local_date"])
if col_name == "num_sensors":
data["num_sensors"] = data.max(axis=1)
for date in last_seven_dates:
if only_show_valid_days and col_name == "valid_sensed_hours":
# replace invalid days' valid sensed hours with np.nan to let our heatmap only shows valid days
data.loc[data[data["is_valid_sensed_day"] == False].index, "valid_sensed_hours"] = np.nan
if expected_num_of_days == -1:
# show all days
data.index = pd.to_datetime(data.index)
start_date = data.index.min()
# upsample data into one day bins
data = data.resample("1D").sum()
data["date_idx"] = (data.index - start_date).days
data.set_index("date_idx", inplace=True, drop=True)
row = row + data[col_name].tolist()
else:
# only show last certain days
for date in last_certain_dates:
if date in data.index:
row.append(data.loc[date][col_name])
else:
row.append(0)
return row
def getOverallComplianceHeatmap(sensors_with_data, valid_sensed_hours, last_seven_dates, bin_size, min_bins_per_hour, expected_num_of_days, output_path):
plot = ff.create_annotated_heatmap(z=sensors_with_data[last_seven_dates].values,
x=[date.replace("-", "/") for date in last_seven_dates],
def getOverallComplianceHeatmap(sensors_with_data, valid_sensed_hours, last_certain_dates, bin_size, min_bins_per_hour, expected_num_of_days, output_path):
plot = go.Figure(data=go.Heatmap(z=valid_sensed_hours[last_certain_dates].values,
x=[date.replace("-", "/") for date in last_certain_dates] if expected_num_of_days != -1 else last_certain_dates,
y=[pid + "." + label for pid, label in zip(sensors_with_data["pid"].to_list(), sensors_with_data["label"].to_list())],
annotation_text=valid_sensed_hours[last_seven_dates].values,
hovertemplate='Date: %{x}<br>Participant: %{y}<br>Number of sensors with data: %{z}<extra></extra>',
text=sensors_with_data[last_certain_dates].values,
hovertemplate="Date: %{x}<br>Participant: %{y}<br>Valid sensed hours: %{z}<br>Number of sensors with data: %{text}<extra></extra>" if expected_num_of_days != -1 else "Date_idx: %{x}<br>Participant: %{y}<br>Valid sensed hours: %{z}<br>Number of sensors with data: %{text}<extra></extra>",
colorscale="Viridis",
colorbar={"tick0": 0,"dtick": 1},
showscale=True)
plot.update_layout(title="Overall compliance heatmap for last " + str(expected_num_of_days) + " days.<br>Bin's color shows how many sensors logged at least one row of data for that day.<br>Bin's text shows the valid hours of that day.(A valid hour has at least one row of any sensor in "+ str(min_bins_per_hour) +" out of " + str(int(60 / bin_size)) + " bins of " + str(bin_size) + " minutes)")
showscale=True))
if expected_num_of_days != -1:
plot.update_layout(title="Overall compliance heatmap for last " + str(expected_num_of_days) + " days.<br>Bin's color shows valid sensed hours for that day.<br>A valid hour has at least one row of any sensor in "+ str(min_bins_per_hour) +" out of " + str(int(60 / bin_size)) + " bins of " + str(bin_size) + " minutes")
else:
plot.update_layout(title="Overall compliance heatmap for all days.<br>Bin's color shows valid sensed hours for that day.<br>A valid hour has at least one row of any sensor in "+ str(min_bins_per_hour) +" out of " + str(int(60 / bin_size)) + " bins of " + str(bin_size) + " minutes")
plot["layout"]["xaxis"].update(side="bottom")
pio.write_html(plot, file=output_path, auto_open=False, include_plotlyjs="cdn")
@ -33,17 +56,21 @@ def getOverallComplianceHeatmap(sensors_with_data, valid_sensed_hours, last_seve
phone_sensed_bins = snakemake.input["phone_sensed_bins"]
phone_valid_sensed_days = snakemake.input["phone_valid_sensed_days"]
pid_files = snakemake.input["pid_files"]
only_show_valid_days = snakemake.params["only_show_valid_days"]
local_timezone = snakemake.params["local_timezone"]
bin_size = snakemake.params["bin_size"]
min_bins_per_hour = snakemake.params["min_bins_per_hour"]
expected_num_of_days = int(snakemake.params["expected_num_of_days"])
if expected_num_of_days < -1:
raise ValueError("EXPECTED_NUM_OF_DAYS of OVERALL_COMPLIANCE_HEATMAP section in config.yaml must be larger or equal to -1.")
last_certain_dates = []
if expected_num_of_days != -1:
# get the list of dates to show
cur_date = datetime.datetime.now().astimezone(tz.gettz(local_timezone)).date()
last_seven_dates = []
for date_offset in range(expected_num_of_days-1, -1, -1):
last_seven_dates.append((cur_date - datetime.timedelta(days=date_offset)).strftime("%Y-%m-%d"))
last_certain_dates.append((cur_date - datetime.timedelta(days=date_offset)).strftime("%Y-%m-%d"))
sensors_with_data_records, valid_sensed_hours_records = [], []
for sensors_with_data_individual, valid_sensed_hours_individual, pid_file in zip(phone_sensed_bins, phone_valid_sensed_days, pid_files):
@ -54,15 +81,20 @@ for sensors_with_data_individual, valid_sensed_hours_individual, pid_file in zip
label = external_file_content[2].strip()
pid = pid_file.split("/")[-1]
sensors_with_data_records.append(getOneRow(sensors_with_data_individual, last_seven_dates, "num_sensors", [pid, label, device_id]))
valid_sensed_hours_records.append(getOneRow(valid_sensed_hours_individual, last_seven_dates, "valid_hours", [pid, label, device_id]))
sensors_with_data_records.append(getOneRow(sensors_with_data_individual, last_certain_dates, "num_sensors", [pid, label, device_id], expected_num_of_days, only_show_valid_days))
valid_sensed_hours_records.append(getOneRow(valid_sensed_hours_individual, last_certain_dates, "valid_sensed_hours", [pid, label, device_id], expected_num_of_days, only_show_valid_days))
sensors_with_data = pd.DataFrame(data=sensors_with_data_records, columns=["pid", "label", "device_id"] + last_seven_dates)
valid_sensed_hours = pd.DataFrame(data=valid_sensed_hours_records, columns=["pid", "label", "device_id"] + last_seven_dates)
if expected_num_of_days == -1:
# get the date_idx of all days
total_num_of_days = max([len(x) for x in sensors_with_data_records]) - 3
last_certain_dates = [date_idx for date_idx in range(total_num_of_days)]
sensors_with_data = pd.DataFrame(data=sensors_with_data_records, columns=["pid", "label", "device_id"] + last_certain_dates).replace(0, np.nan)
valid_sensed_hours = pd.DataFrame(data=valid_sensed_hours_records, columns=["pid", "label", "device_id"] + last_certain_dates).replace(0, np.nan)
if sensors_with_data.empty:
empty_html = open(snakemake.output[0], "w")
empty_html.write("There is no sensor data for all participants")
empty_html.close()
else:
getOverallComplianceHeatmap(sensors_with_data, valid_sensed_hours, last_seven_dates, bin_size, min_bins_per_hour, expected_num_of_days, snakemake.output[0])
getOverallComplianceHeatmap(sensors_with_data, valid_sensed_hours, last_certain_dates, bin_size, min_bins_per_hour, expected_num_of_days, snakemake.output[0])