def main(configuration, gisPath, studyId, useCache):
# Parse the country prefix
prefix = cl.get_prefix(configuration)
if prefix is None:
sys.stderr.write(
"Invalid country code associated with configuration file: {}\n".
format(configuration))
sys.exit(1)
# Load the configuration
cfg = cl.load_configuration(configuration)
# Attempt to load the data from the database, if that fails, fall back to local file
try:
if not useCache:
cl.query_betas(cfg["connection_string"],
studyId,
filename=BETAVALUES)
else:
print("Using cached calibration values for map...")
except Exception as error:
if not os.path.exists(BETAVALUES):
sys.stderr.write(
"An unrecoverable error occurred: {}\n".format(error))
sys.exit(1)
else:
print(
"Unable to refresh calibration data from database, using previous copy..."
)
# Proceed with creating beta map
create_beta_map(cfg, gisPath, prefix)
def process(configuration, gisPath, prefix):
# Load the configuration
cfg = load_configuration(configuration)
# Load and bin the population
filename = "{}/{}_population.asc".format(gisPath, prefix)
[ascHeader, population] = load(filename, "population")
data = list(i for j in population for i in j)
data = list(i for i in data if i != ascHeader['nodata'])
populationBreaks = bin_data(data)
# Get the access to treatments rate and bin if need be
[treatments, needsBinning] = get_treatments_list(cfg, gisPath)
if treatments == -1:
print("Unable to load determine the treatments in the configuration.")
exit(1)
if needsBinning:
data = list(i for j in treatments for i in j)
data = list(i for i in data if i != ascHeader['nodata'])
treatments = bin_data(data)
# Load the PfPR data
filename = "{}/{}_pfpr2to10.asc".format(gisPath, prefix)
[_, pfpr] = load(filename, "PfPR")
# Load the climate and treatment rasters
climate = get_climate_zones(cfg, gisPath)
treatment = get_treatments_raster(cfg, gisPath)
# Prepare our results
pfprRanges = {}
zoneTreatments = {}
# Process the data
for row in range(0, ascHeader['nrows']):
for col in range(0, ascHeader['ncols']):
# Press on if there is nothing to do
zone = climate[row][col]
if zone == ascHeader['nodata']:
continue
# Note the bins
popBin = int(get_bin(population[row][col], populationBreaks))
treatBin = get_bin(treatment[row][col], treatments)
# Add to the dictionary as needed
if zone not in pfprRanges:
pfprRanges[zone] = {}
if popBin not in pfprRanges[zone]:
pfprRanges[zone][popBin] = []
if zone not in zoneTreatments:
zoneTreatments[zone] = []
# Add to our data sets
pfprRanges[zone][popBin].append(pfpr[row][col])
if treatBin not in zoneTreatments[zone]:
zoneTreatments[zone].append(treatBin)
return [pfprRanges, zoneTreatments, populationBreaks]
def main(configuration, studyId):
try:
# Load the configuration, query for the list of replicates
cfg = load_configuration(configuration)
replicates = select(cfg["connection_string"], SELECT_REPLICATES, {'studyId':studyId})
# Display list, prompt user
if len(replicates) == 0:
print("No studies returned!")
exit(0)
print("Studies returned: ")
for replicate in replicates:
print("{}\t{}\t{}\t{}".format(replicate[0], replicate[1], replicate[2], replicate[3]))
# Prompt for replicate id
replicateId = int(input("Replicate to retrive: "))
# Load the data set, exit if nothing is returned
rows = select(cfg["connection_string"], SELECT_DATASET, {'replicateId':replicateId})
if len(rows) == 0:
print("No data returned!")
exit(0)
# Save the replicate to disk
filename = "{}-verification-data.csv".format(replicateId)
print("Saving data set to: {}".format(filename))
with open(filename, "w") as csvfile:
for row in rows:
line = ','.join(str(row[ndx]) for ndx in range(0, len(row)))
csvfile.write("{}\n".format(line))
except DatabaseError:
sys.stderr.write("An unrecoverable database error occurred, exiting.\n")
sys.exit(1)
def main(configuration, gisPath, tolerance, step, username):
global parameters
# Determine the country prefix
prefix = cl.get_prefix(configuration)
if prefix is None:
sys.stderr.write("Invalid country code associated with configuration file: {}\n".format(configuration))
sys.exit(1)
# Load the configuration, and potentially raster data
cfg = cl.load_configuration(configuration)
climate = cl.get_climate_zones(cfg, gisPath)
treatment = cl.get_treatments_raster(cfg, gisPath)
# Load the relevent raster data
filename = os.path.join(gisPath, POPULATION_FILE.format(prefix))
[ascheader, population] = load_asc(filename)
lookup = cl.load_betas(CALIBRATION)
# Read the epsilons file in
[_, beta] = load_asc(BETAVALUES.format(prefix))
[_, epsilon] = load_asc(EPSILONVALUES.format(prefix))
print ("Evaluating epsilons for {} rows, {} columns".format(ascheader['nrows'], ascheader['ncols']))
# Scan each of the epsilons
for row in range(0, ascheader['nrows']):
for col in range(0, ascheader['ncols']):
# Pass on nodata
value = epsilon[row][col]
if value == ascheader['nodata']: continue
# Pass when value is less than maximum
if value < tolerance: continue
# Update the running list
addBeta(lookup, step, climate[row][col], beta[row][col], population[row][col], treatment[row][col])
# Note the progress
progressBar(row + 1, ascheader['nrows'])
# Check to see if we are done
if len(parameters) == 0:
print("Nothing to reduce!")
else:
writeBetas(lookup, prefix, username)
def main(args):
try:
cfg = load_configuration(args.configuration)
# Add the study if one was supplied
if args.add is not None:
studies = add_study(cfg["connection_string"], args.add)
print(f"Study Id: {studies}")
# Delete study
if args.remove is not None:
# delete
remove_study(cfg["connection_string"], args.remove)
# Rename study
if args.update:
id = args.update[0]
sname = str(args.update[1])
rename_studyname(cfg["connection_string"], id, sname)
# Display the formated list of studies in the database
if args.list:
rows = get_studies(cfg["connection_string"])
# Was nothing returned?
if len(rows) == 0:
print("No records returned")
return
# Display our resuts
layout = "{!s:32} {!s:10}"
print(layout.format("Study Name", "Study Id"))
print("-" * 42)
for row in rows:
print(layout.format(*(row[1], row[0])))
except database.DatabaseError:
# Defer to database library for error messages
sys.exit(1)
def main(configuration, studyId, burnIn, subset):
try:
# Load the configuration
cfg = load_configuration(configuration)
# Get the studies
print("Querying for studies...")
studies = get_studies(cfg["connection_string"], studyId)
if len(studies) == 0:
print("No studies to process!")
return
# Let the user know what is going on
if len(studies) == 1:
print("Processing study...")
else:
print("Processing {} studies...".format(len(studies)))
counter = 1
for study in studies:
# Process the replicates for this study
replicates = get_replicates(cfg["connection_string"], study[0],
study[1])
process_frequencies(cfg["connection_string"], replicates, subset)
process_summaries(cfg["connection_string"], replicates, burnIn)
# Update the status for the user
if len(studies) > 1:
print("{} of {} studies complete".format(
counter, len(studies)))
counter += 1
except database.DatabaseError:
sys.stderr.write(
"An unrecoverable database error occurred, exiting.\n")
sys.exit(1)