Changes from main, and removal of output kalpana directory

Author: jmpmcmanus

kalpana/downscaling.py

@@ -656,7 +656,7 @@ def runStatic(ncFile, levels, epsgOut, pathOut,  grassVer, pathRasFiles, rasterF
                 same path of the extracted shape file (pathout).
             createGrassLocation: boolean. DEFAULT True
                 True for creating a new location and loading DEMs, false to use an existing location with DEMs already imported
-             createLocMethod: str. DEFAULT 'from_raster'
+            createLocMethod: str. DEFAULT 'from_raster'
                 Two options "from_epsg" (default) or "from_raster" otherwise an error will be thrown.
             attrCol: str. DEFAULT 'avgVal'
                 name of the attribute column
@@ -762,7 +762,7 @@ def runStatic(ncFile, levels, epsgOut, pathOut,  grassVer, pathRasFiles, rasterF
     logger.info(f'Output files saved on: {pathaux}') # Changed
 
 def meshRepLen2raster(fort14, epsgIn, epsgOut, pathOut, grassVer, pathRasFiles, rasterFiles, subDomain=None, 
-                      nameGrassLocation=None, createGrassLocation=True, createLocMethod='from_raster'):
+                      nameGrassLocation=None, createGrassLocation=True, createLocMethod='from_raster', exportDEM=False):
     ''' Function to rasterize mesh shapefile created from the fort.14 file
         Parameters
             fort14: str
@@ -786,10 +786,10 @@ def meshRepLen2raster(fort14, epsgIn, epsgOut, pathOut, grassVer, pathRasFiles,
                 same path of the extracted shape file (pathout).
             createGrassLocation: boolean. DEFAULT True
                 True for creating a new location and loading DEMs, false to use an existing location with DEMs already imported
-             createLocMethod: str. DEFAULT 'from_raster'
-                 Two options "from_epsg" (default) or "from_raster" otherwise an error will be thrown.
+            createLocMethod: str. DEFAULT 'from_raster'
+                Two options "from_epsg" (default) or "from_raster" otherwise an error will be thrown.
         Returns
-            NOne
+            None
     '''
     ## create gdf from fort14 file with elements as geometries
     t0 = time.time()
@@ -829,6 +829,9 @@ def meshRepLen2raster(fort14, epsgIn, epsgOut, pathOut, grassVer, pathRasFiles,
     ## setup grass env
     setGrassEnv(grassVer, pathGrassLocation, createGrassLocation, gs, gsetup,
                 pathRasFiles, rasterFiles, createLocMethod, epsgOut)
+    if exportDEM == True:
+        gs.run_command('r.out.gdal', input = 'dem', flags = 'cm', format = 'GTiff', nodata = -9999,
+               output = os.path.join(os.path.dirname(pathOut), 'downscaling_dem.tif'))
     ## get minimum area
     minArea = gdfMesh.elemArea.min()
     t0 = time.time()
@@ -907,3 +910,46 @@ def reprojectRas(filein, pathout, epsgOut=None, res='same'):
             rasOut.rio.to_raster(os.path.join(pathout, bname + f'_epsg{epsgOut}_res{res}.tif'), driver="COG") # Changed
             logger.info('Wrote '+bname+' to COG') # Changed
 
+def mergeDEMs(grassVer, pathRasFiles, rasterFiles, pathOut, epsgOut,
+              nameGrassLocation=None, createGrassLocation=True, createLocMethod='from_raster'):
+    ''' Function to rasterize mesh shapefile created from the fort.14 file
+        Parameters
+            grassVer: float
+                Version of the grass software (The code was writen for v8.0).
+            pathRasters: str
+                path of the raster files
+            rasterFiles: list or str
+                name(s) of the raster file(s). If 'all' is input, all files in pathRasters are used
+            pathOut: str
+                full path of the output DEM
+            nameGrassLocation: str. DEFAULT None
+                path and name of the grass location. If None the grass location will be called 'grassLoc' and save in the 
+                same path of the extracted shape file (pathout).
+            createGrassLocation: boolean. DEFAULT True
+                True for creating a new location and loading DEMs, false to use an existing location with DEMs already imported
+             createLocMethod: str. DEFAULT 'from_raster'
+                 Two options "from_epsg" (default) or "from_raster" otherwipathOut, epsgOut,se an error will be thrown.
+        Returns
+            None
+    '''
+    pathaux = os.path.dirname(pathOut)
+    ## add grass to the environment variables
+    grassEnvVar(grassVer)
+    ## import grass
+    import grass.script as gs
+    import grass.script.setup as gsetup
+    ## grass location path
+    if nameGrassLocation == None:
+        pathGrassLocation = os.path.join(pathaux, 'grassLoc')
+    else:
+        pathGrassLocation = os.path.join(pathaux, nameGrassLocation)
+
+    if rasterFiles == 'all':
+        rasterFiles = os.listdir(pathRasFiles)
+        
+    ## setup grass env
+    setGrassEnv(grassVer, pathGrassLocation, createGrassLocation, gs, gsetup,
+                pathRasFiles, rasterFiles, createLocMethod, epsgOut)
+        
+    gs.run_command('r.out.gdal', input = 'dem', flags = 'cm', format = 'GTiff', nodata = -9999, 
+           output = pathOut)

kalpana/kalpana.py

@@ -235,10 +235,16 @@ def main(args):
             if not os.path.exists(outputDir):
                 mode = 0o777
                 os.makedirs(outputDir, mode, exist_ok=True)
+                logger.info('Made directory '+outputDir)
+            else:
+                logger.info('Directory '+outputDir+' already made.')
+
+            if not os.path.exists(finalDir):
+                mode = 0o777
                 os.makedirs(finalDir, mode, exist_ok=True)
-                logger.info('Made directories '+outputDir+ ' and '+finalDir+'.')
+                logger.info('Made directory '+finalDir)
             else:
-                logger.info('Directories '+outputDir+' and '+finalDir+' already made.')
+                logger.info('Directory '+finalDir+' already made.')
 
             # log start of runStatic run
             logger.info('Start runScript with the following inputs: '+runScript+', '+str(epsgIn)+', '+str(epsgOut)+', '+pathOut+', '+grassVer+', '+ncFile+', '+meshFile+', '+conLevelsLog+', '+vUnitIn+', '+vUnitOut+', '+adcircVar+', '+conType+', '+str(subDomain)+', '+str(epsgSubDom)+', '+str(exportMesh)+', '+dzFile+', '+str(zeroDif)+', '+nameGrassLocation+', '+str(createGrassLocation)+', '+createLocMethod+', '+attrCol+', '+str(repLenGrowing)+', '+str(compAdcirc2dem)+', '+str(floodDepth)+', '+clumpThreshold+', '+str(perMinElemArea)+', '+str(ras2vec)+', '+str(exportOrg))
@@ -250,15 +256,16 @@ def main(args):
                  compAdcirc2dem, floodDepth, clumpThreshold, perMinElemArea, ras2vec, exportOrg)
 
             # move cog tiff to final directory
-            for finalPathFile in glob.glob(outputDir+'*_epsg4326.tif'):
-                try:
-                    shutil.move(finalPathFile, finalDir)
-                    logger.info('Moved cog file '+finalPathFile.split("/")[-1]+' to '+finalDir+' directory.')
-                    shutil.rmtree('/data/'+modelRunID+'/kalpana')
-                    logger.info('Removed TIFF file /data/'+modelRunID+'/kalpana.') 
-                except OSError as err:
-                    logger.error('Failed to move cog file '+finalPathFile.split("/")[-1]+' to '+finalDir+' directory.')
-                    sys.exit(1)
+            finalPathFile = glob.glob(outputDir+'*_epsg4326.tif')[0]
+            logger.info('The length of the finalPathFile is: '+str(len(finalPathFile)))
+            try:
+                shutil.move(finalPathFile, finalDir)
+                logger.info('Moved cog file '+finalPathFile+' to '+finalDir+' directory.')
+                shutil.rmtree('/data/'+modelRunID+'/kalpana', ignore_errors=True)
+                logger.info('Removed TIFF file /data/'+modelRunID+'/kalpana.') 
+            except OSError as err:
+                logger.error(err)
+                sys.exit(1)
         else:
             logger.info('ncFile '+ncFile+' does not use the NCSC_SAB_v1.22 grid or the hsofs grid, it uses the '+grid+' grid, so do not process')
 
@@ -374,13 +381,13 @@ def main(args):
 
         # create cog 
         # move cog tiff to final directory
-        for finalPathFile in glob.glob(outputDir+'*_epsg4326.tif'):
-            try:
-                shutil.move(finalPathFiles, finalDir)
-                logger.info('Created cog file '+finalPathFiles.split("/")[-1]+' and move to '+finalDir+' directory.')
-            except OSError as err:
-                logger.error('Failed to create cog file '+finalPathFiles.split("/")[-1]+' and move to '+finalDir+' directory.')
-                sys.exit(1)
+        finalPathFile = glob.glob(outputDir+'*_epsg4326.tif')[0]
+        try:
+            shutil.move(finalPathFile, finalDir)
+            logger.info('Created cog file '+finalPathFile+' and move to '+finalDir+' directory.')
+        except OSError as err:
+            logger.error(err)
+            sys.exit(1)
 
 if __name__ == "__main__":
     ''' Takes argparse inputs and passes theme to the main function