avaframe/log2Report/generateReport.py
"""
Generate a markdown report for data provided in dictionary
"""
# Load modules
import logging
import pathlib
import shutil
import pandas as pd
from tabulate import tabulate
from datetime import datetime
# create local logger
# change log level in calling module to DEBUG to see log messages
log = logging.getLogger(__name__)
def copyPlots2ReportDir(reportDir, plotDict):
""" copy the plots to report directory
The plots are in a dictionary:
plotDict = {'plot1': PurePath to plot1, 'plot2': PurePath to plot2...}
Parameters
-----------
reportDir: pathlib path
path to directory where to copy the plots to
plotDict: dict
dict of the location of the plots to copy
"""
if not isinstance(reportDir, pathlib.PurePath):
reportDir = pathlib.Path(reportDir)
for key in plotDict:
if key != 'type':
if isinstance(plotDict[key], pathlib.PurePath):
plotPath = plotDict[key]
plotName = reportDir / plotPath.name
shutil.copy2(plotPath, plotName)
log.debug('Copied: %s to %s' % (plotPath, plotName))
def addLineBlock(titleString, reportDKey, pfile, italicFont=False, onlyFirstLine=False):
""" add lineblock to report
Parameters
-----------
titleString: str
string that shall be added
reportDKey: dict
dictionary with info for string
pfile: file
italicFont: bool
if True write value in italic
onlyFirstLine: bool
if first item in reportDKey is added to pfile - break
"""
for value in reportDKey:
if value != 'type':
if italicFont:
pfile.write('%s *%s* \n' % (titleString, reportDKey[value]))
else:
pfile.write('%s %s \n' % (titleString, reportDKey[value]))
pfile.write(' \n')
if onlyFirstLine:
break
def writeReportFile(reportD, pfile):
""" Create markdown report with blocks, tables, list according to type key
Parameters
----------
reportD : dict
report dictionary
pfile : file object
file where markdown format report is written to
"""
# Loop through keys and perform action according to value found in type
for key in reportD:
subKey = 'type'
# HEADER BLOCK
# Title
if reportD[key][subKey] == 'title':
addLineBlock('#', reportD[key], pfile, onlyFirstLine=True)
# Avalanche name
if reportD[key][subKey] == 'avaName':
addLineBlock('### Avalanche directory:', reportD[key], pfile, italicFont=True)
# Simulation name
if reportD[key][subKey] == 'simName':
addLineBlock('### Simulation name:', reportD[key], pfile, italicFont=True)
# Time info
if reportD[key][subKey] == 'time':
addLineBlock('### Date:', reportD[key], pfile, onlyFirstLine=True)
# PARAMETER BLOCK
# Table listing all the key : value pairs in rows
if reportD[key][subKey] == 'list':
pfile.write('### %s \n' % key)
pfile.write(' \n')
pfile.write('| Parameters | Values | \n')
pfile.write('| ---------- | ------ | \n')
for value in reportD[key]:
if value != 'type':
pfile.write('| %s | %s | \n' % (value, reportD[key][value]))
pfile.write(' \n')
# Table listing the key : value pairs in columns
if reportD[key][subKey] == 'columns':
pfile.write('### %s \n' % key)
pfile.write(' \n')
for value in reportD[key]:
if value != 'type':
pfile.write('| %s ' % value)
pfile.write('| \n')
for value in reportD[key]:
if value != 'type':
pfile.write('| ----------')
pfile.write('| \n')
for value in reportD[key]:
if value != 'type':
pfile.write('| %s ' % reportD[key][value])
pfile.write('| \n')
pfile.write(' \n')
# Multiline, multicolumn table from pandas Dataframe
if reportD[key][subKey] == 'pandasDF':
pfile.write('### %s \n' % key)
pfile.write(' \n')
df = reportD[key]['dataDF']
# only keep necessary columns
colNames = list(reportD[key]['column names'].keys())
df = df[colNames]
# format floats
dataType = df.dtypes
for col in colNames:
if 'float' in str(dataType[col]):
df[col] = df[col].map(lambda x: '{0:.4f}'.format(x))
# rename columns
df = df.rename(columns=reportD[key]['column names'])
df = df.transpose()
nCols = len(reportD[key]['column names'])
df.to_markdown(buf=pfile, tablefmt="github", headers=["<!-- -->"]*nCols)
pfile.write(' \n')
pfile.write(' \n')
# IMAGE BLOCK
if reportD[key][subKey] == 'image':
pfile.write('### %s \n' % key)
pfile.write(' \n')
for value in reportD[key]:
if value != 'type' and isinstance(reportD[key][value], pathlib.Path):
pfile.write('##### Figure: %s \n' % value)
pfile.write(' \n')
pfile.write(' \n' % (value, reportD[key][value].name))
pfile.write(' \n')
pfile.write(' \n')
# TEXT BLOCK
if reportD[key][subKey] == 'text':
pfile.write('### %s \n' % key)
pfile.write(' \n')
for value in reportD[key]:
if value != 'type':
pfile.write('##### Topic: %s \n' % value)
pfile.write(' \n')
pfile.write('%s \n' % (reportD[key][value]))
pfile.write(' \n')
def writeReport(outDir, reportDictList, reportOneFile, plotDict='', standaloneReport=False,
reportName='fullSimulationReport'):
""" Write a report in markdown format for simulations, saved to outDir
Parameters
----------
outDir : str
path to output directory
reportDictList : list
list of report dictionaries from simulations
reportOneFile : boolean
True to write all info in the same file
plotDict : dict
optional dictionary with info on plots that shall be included in report
standaloneReport: bool
if True copy plots to reportDir
reportName: str
report file name, fullSimulationReport is the default value
"""
if reportOneFile:
now = datetime.now()
dtString = now.strftime("%Y%m%d_%Hh%Mm%Ss")
# Start writing markdown style report
reportPath = pathlib.Path(outDir, (reportName + '_' + dtString + '.md'))
with open(reportPath, 'w') as pfile:
# Loop through all simulations
for reportD in reportDictList:
if plotDict != '' and ('simName' in reportD):
# add plot info to general report Dict
reportD['Simulation Results'] = plotDict[reportD['simName']['name']]
reportD['Simulation Results'].update({'type': 'image'})
# copy plots to reportDir
if standaloneReport:
for key in reportD:
subKey = 'type'
if reportD[key][subKey] == 'image':
copyPlots2ReportDir(outDir, reportD[key])
# Write report file
writeReportFile(reportD, pfile)
else:
# Loop through all simulations
for reportD in reportDictList:
if plotDict != '':
# add plot info to general report Dict
reportD['Simulation Results'] = plotDict[reportD['simName']['name']]
reportD['Simulation Results'].update({'type': 'image'})
# Start writing markdown style report
reportPath = pathlib.Path(outDir, ('%s.md' % reportD['simName']['name']))
with open(reportPath, 'w') as pfile:
# Write report file
writeReportFile(reportD, pfile)