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CircuitscapeUtils.py
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CircuitscapeUtils.py
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# -*- coding: utf-8 -*-
"""
***************************************************************************
CircuitscapeUtils.py
---------------------
Date : June 2018
Copyright : (C) 2018 by Guillem Domingo Ribas
Email : guillem.dri@gmail.com
***************************************************************************
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 3 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************
"""
__author__ = 'Guillem Domingo Ribas'
__date__ = 'June 2018'
__copyright__ = '(C) 2018, Guillem Domingo Ribas'
# This will get replaced with a git SHA1 when you do a git archive
__revision__ = '$Format:%H$'
import os
import stat
import subprocess
import ConfigParser
from processing.core.ProcessingLog import ProcessingLog
from processing.core.ProcessingConfig import ProcessingConfig
from processing.tools.system import getTempFilename, isWindows, userFolder
class CircuitscapeUtils:
LOG_COMMANDS = 'LOG_COMMANDS'
LOG_CONSOLE = 'LOG_CONSOLE'
CIRCUITSCAPE_FOLDER = 'CIRCUITSCAPE_FOLDER'
FOUR_NEIGHBOURS = 'FOUR_NEIGHBOURS'
AVERAGE_CONDUCTANCE = 'AVERAGE_CONDUCTANCE'
PREEMPT_MEMORY = 'PREEMPT_MEMORY'
MAX_CURRENT_MAPS = 'MAX_CURRENT_MAPS'
CUM_MAX_MAPS = 'CUM_MAX_MAPS'
ZERO_FOCAL = 'ZERO_FOCAL'
COMPRESS_OUTPUT = 'COMPRESS_OUTPUT'
LOG_TRANSFORM = 'LOG_TRANSFORM'
@staticmethod
def circuitscapePath():
folder = ProcessingConfig.getSetting(
CircuitscapeUtils.CIRCUITSCAPE_FOLDER)
if folder is None or folder == '':
folder = ''
if isWindows():
testPath = 'C:/Program Files/Circuitscape'
if os.path.exists(os.path.join(testPath, 'cs_run.exe')):
folder = testPath
return folder
@staticmethod
def writeConfiguration():
cfg = ConfigParser.SafeConfigParser()
cfg.add_section('Options for advanced mode')
cfg.set(
'Options for advanced mode', 'ground_file_is_resistances', 'True')
cfg.set('Options for advanced mode', 'remove_src_or_gnd', 'keepall')
cfg.set('Options for advanced mode', 'ground_file', '')
cfg.set('Options for advanced mode', 'use_unit_currents', 'False')
cfg.set('Options for advanced mode', 'source_file', '')
cfg.set('Options for advanced mode', 'use_direct_grounds', 'False')
cfg.add_section('Mask file')
cfg.set('Mask file', 'mask_file', '')
cfg.set('Mask file', 'use_mask', 'False')
cfg.add_section('Calculation options')
cfg.set('Calculation options', 'low_memory_mode', 'False')
cfg.set('Calculation options', 'parallelize', 'False')
cfg.set('Calculation options', 'solver', 'cg+amg')
cfg.set('Calculation options', 'print_timings', 'True')
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.PREEMPT_MEMORY))
cfg.set('Calculation options', 'preemptive_memory_release', value)
cfg.set('Calculation options', 'print_rusages', 'False')
cfg.set('Calculation options', 'max_parallel', '0')
cfg.add_section('Short circuit regions (aka polygons)')
cfg.set('Short circuit regions (aka polygons)', 'polygon_file', '')
cfg.set('Short circuit regions (aka polygons)',
'use_polygons', 'False')
cfg.add_section('Options for one-to-all and all-to-one modes')
cfg.set('Options for one-to-all and all-to-one modes',
'use_variable_source_strengths', 'False')
cfg.set('Options for one-to-all and all-to-one modes',
'variable_source_file', '')
cfg.add_section('Output options')
cfg.set('Output options', 'set_null_currents_to_nodata', 'False')
value = str(ProcessingConfig.getSetting(CircuitscapeUtils.ZERO_FOCAL))
cfg.set('Output options', 'set_focal_node_currents_to_zero', value)
cfg.set('Output options', 'set_null_voltages_to_nodata', 'False')
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.COMPRESS_OUTPUT))
cfg.set('Output options', 'compress_grids', value)
cfg.set('Output options', 'write_cur_maps', 'True')
cfg.set('Output options', 'write_volt_maps', 'True')
cfg.set('Output options', 'output_file', '')
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.CUM_MAX_MAPS))
cfg.set('Output options', 'write_cum_cur_map_only', value)
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.LOG_TRANSFORM))
cfg.set('Output options', 'log_transform_maps', value)
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.MAX_CURRENT_MAPS))
cfg.set('Output options', 'write_max_cur_maps', value)
cfg.add_section('Options for reclassification of habitat data')
cfg.set('Options for reclassification of habitat data',
'reclass_file', '')
cfg.set('Options for reclassification of habitat data',
'use_reclass_table', 'False')
cfg.add_section('Logging Options')
cfg.set('Logging Options', 'log_level', 'INFO')
cfg.set('Logging Options', 'log_file', 'None')
cfg.set('Logging Options', 'profiler_log_file', 'None')
cfg.set('Logging Options', 'screenprint_log', 'False')
cfg.add_section(
'Options for pairwise and one-to-all and all-to-one modes')
cfg.set('Options for pairwise and one-to-all and all-to-one modes',
'included_pairs_file', '')
cfg.set('Options for pairwise and one-to-all and all-to-one modes',
'use_included_pairs', 'False')
cfg.set('Options for pairwise and one-to-all and all-to-one modes',
'point_file', '')
cfg.add_section('Connection scheme for raster habitat data')
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.AVERAGE_CONDUCTANCE))
cfg.set('Connection scheme for raster habitat data',
'connect_using_avg_resistances', value)
value = str(
ProcessingConfig.getSetting(CircuitscapeUtils.FOUR_NEIGHBOURS))
cfg.set('Connection scheme for raster habitat data',
'connect_four_neighbors_only', value)
cfg.add_section('Habitat raster or graph')
cfg.set('Habitat raster or graph',
'habitat_map_is_resistances', 'True')
cfg.set('Habitat raster or graph', 'habitat_file', '')
cfg.add_section('Circuitscape mode')
cfg.set('Circuitscape mode', 'data_type', 'raster')
cfg.set('Circuitscape mode', 'scenario', '')
iniPath = getTempFilename('.ini')
with open(iniPath, 'wb') as f:
cfg.write(f)
return iniPath
@staticmethod
def batchJobFilename():
if isWindows():
fileName = 'circuitscape_batch_job.bat'
else:
fileName = 'circuitscape_batch_job.sh'
batchFile = userFolder() + os.sep + fileName
return batchFile
@staticmethod
def createBatchJobFileFromCommands(commands):
batchFile = open(CircuitscapeUtils.batchJobFilename(), 'w')
for command in commands:
batchFile.write(command.encode('utf8') + '\n')
batchFile.write('exit')
batchFile.close()
@staticmethod
def executeCircuitscape(command, progress):
if isWindows():
command = ['cmd.exe', '/C ', CircuitscapeUtils.batchJobFilename()]
else:
os.chmod(CircuitscapeUtils.batchJobFilename(), stat.S_IEXEC
| stat.S_IREAD | stat.S_IWRITE)
command = [CircuitscapeUtils.batchJobFilename()]
fused_command = ''.join(['"%s" ' % c for c in command])
loglines = []
loglines.append('Circuitscape execution console output')
proc = subprocess.Popen(
fused_command,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT,
universal_newlines=True,
).stdout
for line in iter(proc.readline, ''):
loglines.append(line)
if ProcessingConfig.getSetting(CircuitscapeUtils.LOG_CONSOLE):
ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)