Grass r.mfilter outputs empty file

Question

I have a problem with the grass function r.mfilter outputting an empty file. I'm running the tool from qgis processing standalone.

My system:

OS: Ubuntu 16.04.2 LTS
Saga: 2.2.3
Grass: 7.0.3
QGIS: 2.18.4

Saga installed as per instructions in this question

The script:

from qgis.core import *
from qgis.gui import *
import os
import sys
from PyQt4.QtGui import *
from PyQt4.QtCore import Qt

app = QgsApplication(sys.argv, True)
QgsApplication.initQgis();
QgsApplication.setPrefixPath('/usr', True)

sys.path.append('/usr/share/qgis/python/plugins')
from processing.core.Processing import Processing
import processing.tools.general as processing

Processing.initialize()

# Processing directory
cwd = os.getcwd()
procdir = cwd + '/LST-trad/hojd/'
tmpdir = cwd + '/LST-trad/Test2/'
outdir = cwd + '/LST-trad/treecover2/'
filter = cwd + "/LST-trad/qgis5x5filter_1or0_div1.txt"
files = os.listdir(procdir)
# Filter files
filefilt =[]
for f in files:
    if f.endswith(".tif"):
        filefilt.append(f)

print "help:"
#processing.alghelp("saga:rastercalculator")
processing.alghelp("grass:r.mfilter")

# Coordinates
arglist = []
for file in filefilt:
    x1 = int(file[7] + file[11:13]+"000")
    x2 = x1 + 25000
    y1 = int(file[4:6] + file[9:11] +"000")
    y2 = y1 + 25000
    coords =  str(x1) + "," + str(x2) + "," + str( y1) + "," + str(y2)
    outfile = "COV_" + file[4:]
    arglist.append([procdir+file, coords, outdir+outfile, outfile])

#print arglist

formula1 =('ifelse(a > 50, 1, 0)')
formula2 = ('a * 4')

for arg in arglist:
    tmp1 = tmpdir + "t1_" + arg[3]
    tmp2 = tmpdir + "t2_" + arg[3]
    print "saga"
    processing.runalg("saga:rastercalculator", arg[0], None, formula1, True, 1, tmp1)
    print "grass"
    processing.runalg("grass:r.mfilter", tmp1, filter,1,False,arg[1], 0, tmp2)
    print "rascal"
    processing.runalg("saga:rastercalculator", tmp2, None, formula2, True, 1, arg[2])

QgsApplication.exitQgis();

The filter file:

MATRIX    5
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
DIVISOR   1
TYPE      P 

output form alghelp(r.mfilter):

ALGORITHM: r.mfilter - Performs raster map matrix filter.
    input <ParameterRaster>
    filter <ParameterFile>
    repeat <ParameterNumber>
    -z <ParameterBoolean>
    GRASS_REGION_PARAMETER <ParameterExtent>
    GRASS_REGION_CELLSIZE_PARAMETER <ParameterNumber>
    output <OutputRaster>

One thing that confuses me is that the parameters listed here does not match the parameters listed in the grass documentation

Answer 1

I can't test your code, but you need to follow the syntax returned by processing.alghelp().

However, it's unclear which doesn't work with your code: maybe you need to add the outputs from the processing operations as objects (otherwise QGIS will interpret them as strings).

Try replacing the last for-loop of your code with something like this:

for arg in arglist:
    tmp1 = tmpdir + "t1_" + arg[3]
    tmp2 = tmpdir + "t2_" + arg[3]
    print "saga"
    first_op = processing.getObject(arg[0])
    processing.runalg("saga:rastercalculator", first_op, None, formula1, True, 1, tmp1)
    print "grass"
    second_op = processing.getObject(tmp1)
    processing.runalg("grass:r.mfilter", second_op, filter,1,False,arg[1], 0, tmp2)
    print "rascal"
    third_op = processing.getObject(tmp2)
    processing.runalg("saga:rastercalculator", third_op, None, formula2, True, 1, arg[2])

Note: I don't understand why you are running a loop without looping inside arglist: in fact, you directly call arg[0], arg[1] and arg[2] (I suppose you know what are you doing).

Answer 2

This question turned out to have the answer. It seems like the Grass tools are really picky about how you set the extent. It's somewhat annoying to not be able to set it to None, but at least this works.

I've also set the output type to None for the intermediate steps to avoid creating temporary middle-files as recommended in the comments.

from qgis.core import *
from qgis.gui import *
import os
import sys
from PyQt4.QtGui import *
from PyQt4.QtCore import Qt, QFileInfo

sys.path.append('/usr/share/qgis/python/plugins')
from processing.core.Processing import Processing
#import processing.tools.general as processing
from processing.tools.dataobjects import *
from processing.tools.general import *
from processing.tools.vector import *
from processing.tools.raster import *
from processing.tools.system import *

app = QgsApplication(sys.argv, True)
QgsApplication.initQgis();
QgsApplication.setPrefixPath('/usr', True)
Processing.initialize()

# Processing directory
cwd = os.getcwd()
procdir = cwd + '/LST-trad/hojd/'
outdir = cwd + '/LST-trad/treecover2/'
filterfile = cwd + "/LST-trad/qgis5x5filter_1or0_div1.txt"
files = os.listdir(procdir)
#files = [f for f in os.listdir(procdir) if os.path.isfile(f)]
# Filter files
#filefilt =[]
#for f in files:
    #if f.endswith(".tif"):
        #filefilt.append(f)

print "startar"

#print "help:"
#alghelp("saga:rastercalculator")
#alghelp("grass:r.mfilter")

inputraster = procdir + "/THL_66_6_0025.tif"
outputraster = outdir + "/uttest.tif"

fileInfo = QFileInfo(inputraster)
baseName = fileInfo.baseName()
rlayer = QgsRasterLayer(inputraster, baseName)

extent = rlayer.extent()
xmin = extent.xMinimum()
xmax = extent.xMaximum()
ymin = extent.yMinimum()
ymax = extent.yMaximum()

print "rascal 1"
outputs_SAGARASTERCALCULATOR_1=runalg('saga:rastercalculator', inputraster,[],'ifelse(a > 50, 1, 0)',True,1,None)

print "mfilter"
outputs_GRASS7R_MFILTER_1=runalg('grass7:r.mfilter', outputs_SAGARASTERCALCULATOR_1['RESULT'],filterfile,1.0,False,"%f,%f,%f,%f"% (xmin, xmax, ymin, ymax),0.0,None)

print "rascal 2"
outputs_SAGARASTERCALCULATOR_2=runalg('saga:rastercalculator', outputs_GRASS7R_MFILTER_1['output'],[],'a * 4',True,1,outputraster)

print "done"

QgsApplication.exitQgis();