QGIS 3

.gitattributes

@@ -0,0 +1 @@
+*.zip binary

scripts/qgis_fmask_burnMask.py

@@ -1,56 +1,130 @@
-# Definition of inputs and outputs
-# ==================================
-##Fmask=group
-##Burn cloud mask=name
-##ParameterRaster|dataFile|An image file to burn the cloud mask into|False
-##ParameterRaster|maskFile|Could mask from FMask|False
-##*ParameterBoolean|maskNull|Mask FMask null pixels|True
-##*ParameterBoolean|maskCloud|Mask FMask cloud pixels|True
-##*ParameterBoolean|maskShadow|Mask FMask shadow pixels|True
-##*ParameterBoolean|maskSnow|Mask FMask snow pixels|True
-##*ParameterBoolean|maskWater|Mask FMask water pixels|False
-##*ParameterBoolean|maskLand|Mask FMask land pixels|False
-##OutputRaster|outputFile|Maked output image
+# TODO yields Error1: PROJ...
+from qgis.processing import alg
+from processing.core.ProcessingConfig import ProcessingConfig
+from db_manager.db_plugins import data_model
+from processing.tools import system
+from qgis import processing
 
-from processing.tools import dataobjects, system
 
-# Run GDAL warp to make sure that the mask file exactly aligns with the image file
-progress.setText("Aligning mask raster to image raster...")
-dataRaster = dataobjects.getObject(dataFile)
-proj = dataRaster.crs().authid()
-resolution = dataRaster.rasterUnitsPerPixelX()
-bandCount = dataRaster.bandCount()
-extent = dataobjects.extent([dataRaster])
-warpMask = system.getTempFilename("tif")
-params = {
-    "INPUT": maskFile,
-    "DEST_SRS": proj,
-    "TR": resolution,
-    "USE_RASTER_EXTENT": True,
-    "RASTER_EXTENT": extent,
-    "EXTENT_CRS": proj,
-    "METHOD": 0,
-    "RTYPE": 0,
-    "OUTPUT": warpMask,
-}
-processing.runalg("gdalogr:warpreproject", params)
+@alg(
+    name="burncloudmask",
+    label=alg.tr("Burn cloud mask"),
+    group="fmask",
+    group_label=alg.tr("FMask"),
+)
+@alg.input(
+    type=alg.RASTER_LAYER,
+    name="dataFile",
+    label="An image file to burn the cloud mask into",
+    optional=False,
+)
+@alg.input(
+    type=alg.RASTER_LAYER,
+    name="maskFile",
+    label="Could mask from FMask",
+    optional=False,
+)
+@alg.input(
+    type=bool,
+    name="maskNull",
+    label="Mask FMask null pixels",
+    default=True,
+    advanced=True,
+)
+@alg.input(
+    type=bool,
+    name="maskCloud",
+    label="Mask FMask cloud pixels",
+    default=True,
+    advanced=True,
+)
+@alg.input(
+    type=bool,
+    name="maskShadow",
+    label="Mask FMask shadow pixels",
+    default=True,
+    advanced=True,
+)
+@alg.input(
+    type=bool,
+    name="maskSnow",
+    label="Mask FMask snow pixels",
+    default=True,
+    advanced=True,
+)
+@alg.input(
+    type=bool,
+    name="maskWater",
+    label="Mask FMask water pixels",
+    default=False,
+    advanced=True,
+)
+@alg.input(
+    type=bool,
+    name="maskLand",
+    label="Mask FMask land pixels",
+    default=False,
+    advanced=True,
+)
+@alg.input(type=alg.FILE_DEST, name="outputFile", label="Maked output image")
+def burncloudmask(instance, parameters, context, feedback, inputs):
+    """ burncloudmask """
 
-progress.setText("Applying mask to image...")
-# First reclassify fmask output into two classes
-flags = [maskNull, maskLand, maskCloud, maskShadow, maskSnow, maskWater]
-maskClass = [str(i) for i in range(len(flags)) if flags[i]]
-leaveClass = [str(i) for i in range(len(flags)) if not flags[i]]
-reclassString = " ".join(maskClass) + " = 0\n" + " ".join(leaveClass) + " = 1"
-reclassMask = system.getTempFilename("tif")
-params = {
-    "input": warpMask,
-    "txtrules": reclassString,
-    "output": reclassMask,
-    "GRASS_REGION_PARAMETER": extent,
-    "GRASS_REGION_CELLSIZE_PARAMETER": resolution,
-}
-processing.runalg("grass7:r.reclass", params)
+    dataRaster = instance.parameterAsRasterLayer(parameters, "dataFile", context)
+    # Run GDAL warp to make sure that the mask file exactly aligns with the image file
 
-# Then use OTB band maths on all bands
-params = {"-il": dataFile + ";" + reclassMask, "-exp": "im1*im2b1", "-out": outputFile}
-processing.runalg("otb:bandmathx", params)
+    feedback.setProgressText("Aligning mask raster to image raster...")
+    # feedback.setProgressText(str(dir(dataRaster)))
+
+    feedback.setProgressText(str(dir(parameters["dataFile"])))
+    extent = dataRaster.extent().asWktPolygon()
+    proj = dataRaster.crs().toWkt()
+    resolution = dataRaster.rasterUnitsPerPixelX()
+    bandCount = dataRaster.bandCount()
+    warpMask = system.getTempFilename("tif")
+    params = {
+        "INPUT": parameters["maskFile"],
+        "DEST_SRS": proj,
+        "TR": resolution,
+        "USE_RASTER_EXTENT": True,
+        "RASTER_EXTENT": extent,
+        "EXTENT_CRS": proj,
+        "METHOD": 0,
+        "RTYPE": 0,
+        "OUTPUT": warpMask,
+    }
+    processing.run("gdal:warpreproject", params, feedback=feedback, context=context)
+
+    feedback.setProgressText("Applying mask to image...")
+    # First reclassify fmask output into two classes
+    flags = [
+        parameters["maskNull"],
+        parameters["maskLand"],
+        parameters["maskCloud"],
+        parameters["maskShadow"],
+        parameters["maskSnow"],
+        parameters["maskWater"],
+    ]
+    maskClass = [str(i) for i in range(len(flags)) if flags[i]]
+    leaveClass = [str(i) for i in range(len(flags)) if not flags[i]]
+    reclassString = " ".join(maskClass) + " = 0\n" + " ".join(leaveClass) + " = 1"
+    reclassMask = system.getTempFilename("tif")
+    params = {
+        "input": warpMask,
+        "txtrules": reclassString,
+        "output": reclassMask,
+        "GRASS_REGION_PARAMETER": extent,
+        "GRASS_REGION_CELLSIZE_PARAMETER": resolution,
+    }
+    processing.run("grass7:r.reclass", params, feedback=feedback, context=context)
+
+    # Then use OTB band maths on all bands
+    params = {
+        "il": [
+            instance.parameterAsString(parameters, "dataFile", context),
+            reclassMask,
+        ],
+        "exp": "im1*im2b1",
+        "out": instance.parameterAsString(parameters, "outputFile", context),
+    }
+    processing.run("otb:BandMathX", params, feedback=feedback, context=context)

scripts/qgis_fmask_sentinel2Stacked.py

@@ -1,5 +1,5 @@
-# Definition of inputs and outputs
-# ==================================
+#Definition of inputs and outputs
+#==================================
 ##FMask=group
 ##FMask Sentinel 2=name
 ##ParameterFile|granuledir|Path to .SAFE or tile/granule directory|True|False
@@ -14,55 +14,56 @@
 ##*ParameterNumber|greensnowthreshold|Threshold for Green reflectance for snow detection (Eqn 20). Increase this to reduce snow commission errors|0|1|0.1
 
 from argparse import Namespace
+import sys
 import os.path
 import tempfile
 import shutil
 from processing.tools import dataobjects
 
+# here = os.path.dirname(scriptDescriptionFile)
+# if here not in sys.path:
+#     sys.path.append(here)
+
 from qgis_fmask.stacks.sentinel_stack import create_sentinel_stack
 from qgis_fmask.interfaces.fmask_sentinel2Stacked import mainRoutine
-from qgis_fmask.interfaces.fmask_sentinel2makeAnglesImage import (
-    mainRoutine as mainRoutine_angles,
-)
+from qgis_fmask.interfaces.fmask_sentinel2makeAnglesImage import mainRoutine as mainRoutine_angles
 from qgis_fmask.interfaces.redirect_print import redirect_print
 from qgis_fmask.interfaces.s2meta import find_xml_in_granule_dir
 
 
 tempdir = tempfile.mkdtemp()
 try:
-    progress.setConsoleInfo("Creating Sentinel 2 band stack VRT file ...")
-    tempvrt = os.path.join(tempdir, "temp.vrt")
+    feedback.pushConsoleInfo('Creating Sentinel 2 band stack VRT file ...')
+    tempvrt = os.path.join(tempdir, 'temp.vrt')
     create_sentinel_stack(granuledir, outfile=tempvrt)
-    progress.setConsoleInfo("Done.")
+    feedback.pushConsoleInfo('Done.')
 
     if not anglesfile:
-        progress.setConsoleInfo("Creating angles file ...")
-        anglesfile = os.path.join(tempdir, "angles.img")
+        feedback.pushConsoleInfo('Creating angles file ...')
+        anglesfile = os.path.join(tempdir, 'angles.img')
         cmdargs_angles = Namespace(
-            infile=find_xml_in_granule_dir(granuledir), outfile=anglesfile
-        )
+                infile=find_xml_in_granule_dir(granuledir),
+                outfile=anglesfile)
         import numpy as np
-
-        with np.errstate(invalid="ignore"):
+        with np.errstate(invalid='ignore'):
             mainRoutine_angles(cmdargs_angles)
-        progress.setConsoleInfo("Done.")
+        feedback.pushConsoleInfo('Done.')
 
     cmdargs = Namespace(
-        toa=tempvrt,
-        anglesfile=anglesfile,
-        output=output,
-        verbose=verbose,
-        tempdir=tempdir,
-        keepintermediates=False,
-        mincloudsize=mincloudsize,
-        cloudbufferdistance=cloudbufferdistance,
-        shadowbufferdistance=shadowbufferdistance,
-        cloudprobthreshold=cloudprobthreshold,
-        nirsnowthreshold=nirsnowthreshold,
-        greensnowthreshold=greensnowthreshold,
-    )
+            toa=tempvrt,
+            anglesfile=anglesfile,
+            output=output,
+            verbose=verbose,
+            tempdir=tempdir,
+            keepintermediates=False,
+            mincloudsize=mincloudsize,
+            cloudbufferdistance=cloudbufferdistance,
+            shadowbufferdistance=shadowbufferdistance,
+            cloudprobthreshold=cloudprobthreshold,
+            nirsnowthreshold=nirsnowthreshold,
+            greensnowthreshold=greensnowthreshold)
 
-    progress.setConsoleInfo("Running FMask (this may take a while) ...")
+    feedback.pushConsoleInfo('Running FMask (this may take a while) ...')
     with redirect_print(progress):
         mainRoutine(cmdargs)
 finally:
@@ -71,5 +72,5 @@
     except OSError:
         pass
 
-progress.setConsoleInfo("Done.")
+feedback.pushConsoleInfo('Done.')
 dataobjects.load(output, os.path.basename(output))

scripts/qgis_fmask_sentinel2makeAnglesImage.py

@@ -1,16 +1,24 @@
-# Definition of inputs and outputs
-# ==================================
+#Definition of inputs and outputs
+#==================================
 ##FMask=group
 ##Sentinel 2 Make Angles Image=name
 ##ParameterFile|infile|Input sentinel-2 tile metafile|False|False|xml
 ##OutputFile|outfile|Output angles image file|tif
 
 from argparse import Namespace
+import sys
+import os.path
 import numpy as np
 
+# here = os.path.dirname(scriptDescriptionFile)
+# if here not in sys.path:
+#     sys.path.append(here)
+
 from qgis_fmask.interfaces.fmask_sentinel2makeAnglesImage import mainRoutine
 
-cmdargs = Namespace(infile=infile, outfile=outfile)
+cmdargs = Namespace(
+        infile=infile,
+        outfile=outfile)
 
-with np.errstate(invalid="ignore"):
+with np.errstate(invalid='ignore'):
     mainRoutine(cmdargs)

scripts/qgis_fmask_usgsLandsatMakeAnglesImage.py

@@ -1,17 +1,26 @@
-# Definition of inputs and outputs
-# ==================================
+#Definition of inputs and outputs
+#==================================
 ##FMask=group
 ##Landsat Make Angles Image=name
 ##ParameterFile|mtl|MTL file|False|False|txt
 ##ParameterFile|templateimg|Image file name to use as template for output angles image|False|False|TIF
 ##OutputFile|outfile|Output angles image file|tif
 
 from argparse import Namespace
+import sys
+import os.path
 import numpy as np
 
+here = os.path.dirname(scriptDescriptionFile)
+if here not in sys.path:
+    sys.path.append(here)
+
 from qgis_fmask.interfaces.fmask_usgsLandsatMakeAnglesImage import mainRoutine
 
-cmdargs = Namespace(mtl=mtl, templateimg=templateimg, outfile=outfile)
+cmdargs = Namespace(
+        mtl=mtl,
+        templateimg=templateimg,
+        outfile=outfile)
 
-with np.errstate(invalid="ignore"):
+with np.errstate(invalid='ignore'):
     mainRoutine(cmdargs)

scripts/qgis_fmask_usgsLandsatSaturationMask.py

@@ -1,5 +1,5 @@
-# Definition of inputs and outputs
-# ==================================
+#Definition of inputs and outputs
+#==================================
 ##FMask=group
 ##Landsat Saturation Mask=name
 ##ParameterFile|infile|Input raw DN radiance image|False|False
@@ -8,11 +8,20 @@
 ##OutputFile|outfile|Output angles image file|tif
 
 from argparse import Namespace
+import sys
+import os.path
 import numpy as np
 
+here = os.path.dirname(scriptDescriptionFile)
+if here not in sys.path:
+    sys.path.append(here)
+
 from qgis_fmask.interfaces.fmask_usgsLandsatSaturationMask import mainRoutine
 
-cmdargs = Namespace(infile=infile, mtl=mtl, outfile=outfile)
+cmdargs = Namespace(
+        infile=infile,
+        mtl=mtl,
+        outfile=outfile)
 
-with np.errstate(invalid="ignore"):
+with np.errstate(invalid='ignore'):
     mainRoutine(cmdargs)