Merge pull request #73 from openearth/fix-logger

central logger

glofrim-py/glofrim/glofrim_cmf.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import logging
 import glob
 import shutil
 from os import mkdir, unlink
@@ -15,10 +14,6 @@
 from main import BMI_model_wrapper
 from utils import subcall
 
-log_fmt = '%(asctime)s - %(levelname)s - %(message)s'
-logging.basicConfig(level=logging.INFO, format=log_fmt, filemode='w')
-logger = logging.getLogger(__name__)
-
 class CMF_model(BMI_model_wrapper):
     def __init__(self, engine, config_fn,
                  model_data_dir, out_dir,
@@ -81,7 +76,7 @@ def set_model_input_files(self):
                         shutil.copy(src_fn, dst_path)
                         # remove *tmp.* files from data_dir
                         if 'tmp.' in  basename(src_fn):
-                            logger.info('removing tmp file {:s} from model data dir'.format(basename(src_fn)))
+                            self.logger.info('removing tmp file {:s} from model data dir'.format(basename(src_fn)))
                             unlink(src_fn)
                     # update config_fn
                     self.update_config(sec, opt, '"./{}/{}"'.format(folder, fn))
@@ -101,7 +96,7 @@ def set_inpmat_file(self, bounds, res, olat='NtoS'):
         # generate inpmat
         msg2 = './generate_inpmat {} {} {} {} {} {:s}'.format(
                         abs(res[0]), westin, eastin, northin, southin, olat)
-        logger.info(msg2)
+        self.logger.info(msg2)
         subcall(msg2, cwd=ddir)
         # set new inpmat and diminfo in config
         rel_path = relpath(dirname(self.config_fn), ddir)
@@ -132,7 +127,7 @@ def get_model_grid(self):
         """
         from nb.dd_ops import NextXY
 
-        logger.info('Getting CMF model grid parameters.')
+        self.logger.info('Getting CMF model grid parameters.')
         fn_lsmask = join(self.model_data_dir, 'lsmask.tif')
         if not isfile(fn_lsmask):
             raise IOError("lsmask.tif file not found at {}".format(fn_lsmask))
@@ -144,10 +139,10 @@ def get_model_grid(self):
             self.model_grid_transform = ds.transform
         self._fn_landmask = fn_lsmask
         msg = 'Model bounds {:s}; width {}, height {}'
-        logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
+        self.logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
 
         # read drainage direction data
-        logger.info('Getting CMF model drainage direction')
+        self.logger.info('Getting CMF model drainage direction')
         fn_nextxy = join(self.model_data_dir, 'nextxy.bin')
         if not isfile(fn_nextxy):
             raise IOError("nextxy.bin file not found at {}".format(fn_nextxy))
@@ -177,7 +172,7 @@ def model_2d_index(self, xy, **kwargs):
         indices : list of tuples
           list of (row, col) index tuples
         """
-        logger.info('Getting CMF model indices for xy coordinates.')
+        self.logger.info('Getting CMF model indices for xy coordinates.')
         fn_catmxy = join(self.model_data_dir, 'hires', 'reg.catmxy.tif')
         if not isfile(fn_catmxy):
             raise IOError("{} file not found".format(fn_catmxy))

glofrim-py/glofrim/glofrim_dfm.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import logging
 import glob
 import shutil
 from os import mkdir
@@ -13,11 +12,6 @@
 from main import BMI_model_wrapper
 from utils import ConfigParser
 
-log_fmt = '%(asctime)s - %(levelname)s - %(message)s'
-logging.basicConfig(level=logging.INFO, format=log_fmt, filemode='w')
-logger = logging.getLogger(__name__)
-
-
 class DFM_model(BMI_model_wrapper):
     def __init__(self, engine, config_fn,
                  model_data_dir, out_dir,
@@ -76,7 +70,7 @@ def get_model_coords(self):
         """Get DFM model coordinates for 1D and 2D mesh via BMI. The DFM model
         should be initialized first in order to access the variables."""
 
-        logger.info('Getting DFM model coordinates.')
+        self.logger.info('Getting DFM model coordinates.')
         # define separator between 2D and 1D parts of arrays == lenght of 2d cell points
         self._1d2d_idx = len(self.get_var('flowelemnode'))
         x_coords = self.get_var('xz') # x-coords of each cell centre point
@@ -96,12 +90,12 @@ def get_area_1d(self):
     def get_model_1d_index(self):
         """Creat a spatial index for the 1d coordinates. A model_1d_index
         attribute funtion is created to find the nearest 1d coordinate tuple"""
-        logger.info('Constructing spatial index for the 1D coordinates of the DFM model.')
+        self.logger.info('Constructing spatial index for the 1D coordinates of the DFM model.')
         # 1d coords
         n1d = len(self.model_1d_coords)
         self.model_1d_indices = np.arange(n1d, dtype=np.int32) + self._1d2d_idx
         # build spatial rtree index of points2
-        logger.info('Constructing spatial index for 1D vertices of DFM model')
+        self.logger.info('Constructing spatial index for 1D vertices of DFM model')
         self.model_1d_rtree = rtree.index.Index()
         for i, xy in enumerate(self.model_1d_coords):
             self.model_1d_rtree.insert(i+n1d, xy) # return index including 2d
@@ -117,7 +111,7 @@ def get_model_2d_index(self):
         A model_2d_index attribute funtion is created to find the nearest
         2d cell center"""
         # build spatial rtree index of 2d coords
-        logger.info('Constructing spatial index for the 2D mesh of the DFM model')
+        self.logger.info('Constructing spatial index for the 2D mesh of the DFM model')
         self.model_2d_rtree = rtree.index.Index()
         for i, xy in enumerate(self.model_2d_coords):
             self.model_2d_rtree.insert(i, xy)
@@ -130,3 +124,4 @@ def model_2d_index(self, xy, n=1):
         #TODO: assess validity based on e.g. max distance
         valid = np.ones(len(index), dtype=bool)
         return index, valid
+

glofrim-py/glofrim/glofrim_lfp.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import logging
 import glob
 import shutil
 import os
@@ -15,11 +14,6 @@
 from bmi.wrapper import BMIWrapper
 from main import BMI_model_wrapper
 
-log_fmt = '%(asctime)s - %(levelname)s - %(message)s'
-logging.basicConfig(level=logging.INFO, format=log_fmt, filemode='w')
-logger = logging.getLogger(__name__)
-
-
 class LFP_model(BMI_model_wrapper):
     def __init__(self, engine, config_fn,
                  model_data_dir, out_dir,
@@ -80,13 +74,14 @@ def get_model_coords(self):
         """Get LFP model coordinates for 1D and 2D mesh via BMI. The LFP model
         should be initialized first in order to access the variables."""
 
-        logger.info('Getting LFP model coordinates.')
+        self.logger.info('Getting LFP model coordinates.')
 
         i_ind, j_ind = np.where(np.logical_and(self.get_var('SGCwidth') > 0., self.get_var('DEM') != -9999))
-        print i_ind.shape, j_ind.shape
+        # print i_ind.shape, j_ind.shape
 
         fn_map = join(self.model_data_dir,
-                      self.model_config['dummysection']['DEMfile'])
+                      self.model_config['header1']['DEMfile'])
+
         if not isfile(fn_map):
             raise IOError('landmask file not found')
         self._fn_landmask = fn_map
@@ -97,22 +92,23 @@ def get_model_coords(self):
             self.model_grid_bounds = ds.bounds
             self.model_grid_shape = ds.shape
             self.model_grid_transform = ds.transform
-
-        list_x_coords, list_y_coords = self.model_grid_transform * (i_ind, j_ind)
+            list_x_coords, list_y_coords = ds.xy(i_ind, j_ind)
 
         self.model_1d_coords = zip(list_x_coords, list_y_coords)
-        self.model_1d_indices = zip(i_ind, j_ind)
+        self.model_1d_indices = np.arange(i_ind.size)
+        self.model_1d_rc = (i_ind, j_ind)
 
         pass
 
     def get_area_1d(self):
-        row, col = zip(*self.model_1d_indices)
+        row, col = self.model_1d_rc
         area_1D = self.get_var('dA')[row, col]
         return area_1D
 
 
 class ParConfigParser(ConfigParser):
     def __init__(self, **kwargs):
+        self.optionxform = lambda option:option # keep format with capital/lower letters
         defaults = dict(comment_prefixes=('!', '/', '#'),
                         inline_comment_prefixes=('!'),
                         delimiters=('='))
@@ -133,5 +129,5 @@ def _write_section(self, fp, section_name, section_items, delimiter):
         for key, value in section_items:
             value = self._interpolation.before_write(self, section_name, key, value)
             value = ' ' + str(value).replace('\n', '\n\t')
-            fp.write("{}{}\n".format(key.upper(), value))
-        fp.write("/\n")
+            fp.write("{}{}\n".format(key, value))
+        fp.write("\n")

glofrim-py/glofrim/glofrim_pcr.py

@@ -1,18 +1,11 @@
 # -*- coding: utf-8 -*-
 
-import logging
 from os.path import isdir, join, basename, dirname, abspath, isfile, isabs
 import numpy as np
 import rasterio
-
-from pcrglobwb_bmi_v203 import pcrglobwb_bmi
-
 from main import BMI_model_wrapper
 from utils import ConfigParser
 
-log_fmt = '%(asctime)s - %(levelname)s - %(message)s'
-logging.basicConfig(level=logging.INFO, format=log_fmt, filemode='w')
-logger = logging.getLogger(__name__)
 
 class PCR_model(BMI_model_wrapper):
     def __init__(self, config_fn,
@@ -21,6 +14,7 @@ def __init__(self, config_fn,
                  missing_value=-999, landmask_mv=255, forcing_data_dir=None,
                  **kwargs):
         """initialize the PCR-GLOBWB (PCR) model BMI class and model configuration file"""
+        from pcrglobwb_bmi_v203 import pcrglobwb_bmi
         # BMIWrapper for PCR model model
         pcr_bmi = pcrglobwb_bmi.pcrglobwbBMI()
         # set config parser
@@ -60,7 +54,7 @@ def get_model_grid(self):
         model_grid_shape : tuple
             model number of rows and cols
         """
-        logger.info('Getting PCR model grid parameters.')
+        self.logger.info('Getting PCR model grid parameters.')
         fn_map = join(self.model_config['globalOptions']['inputDir'],
                       self.model_config['globalOptions']['landmask'])
         if not isfile(fn_map):
@@ -73,14 +67,14 @@ def get_model_grid(self):
             self.model_grid_shape = ds.shape
             self.model_grid_transform = ds.transform
         msg = 'Model bounds {:s}; width {}, height {}'
-        logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
+        self.logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
         pass
 
     def get_drainage_direction(self):
         from nb.nb_io import read_dd_pcraster
         # read file with pcr readmap
         nodata = self.options.get('landmask_mv', 255)
-        logger.info('Getting PCR LDD map.')
+        self.logger.info('Getting PCR LDD map.')
         fn_ldd = self.model_config['routingOptions']['lddMap']
         if not isabs(fn_ldd):
             ddir = self.model_config['globalOptions']['inputDir']
@@ -105,14 +99,18 @@ def model_2d_index(self, xy, **kwargs):
         """
         import pcraster as pcr
         nodata = self.options.get('landmask_mv', 255)
-        logger.info('Getting PCR model indices of xy coordinates.')
+        self.logger.info('Getting PCR model indices of xy coordinates.')
         r, c = self.grid_index(*zip(*xy), **kwargs)
         r = np.array(r).astype(int)
         c = np.array(c).astype(int)
+        # check if inside domain
+        nrows, ncols = self.model_grid_shape
+        inside = np.logical_and.reduce((r>=0, r<nrows, c>=0, c<ncols))
         # get valid cells (inside landmask)
         lm_map = pcr.readmap(str(self._fn_landmask))
         lm_data = pcr.pcr2numpy(lm_map, nodata)
-        valid = lm_data[r, c] == 1
+        valid = np.zeros_like(inside, dtype=bool) 
+        valid[inside] = lm_data[r[inside], c[inside]] == 1
         return zip(r, c), valid
 
     # TODO: this should be in the setting file. not changing the actual ldd
@@ -139,7 +137,7 @@ def deactivate_routing(self, coupled_indices=None):
             msg = "Deactivating the LDD is only possible before the model is initialized"
             raise AssertionError(msg)
 
-        logger.info('Editing PCR ldd grid to deactivate routing in coupled cells.')
+        self.logger.info('Editing PCR ldd grid to deactivate routing in coupled cells.')
         # get ldd filename from config
         fn_ldd = self.model_config['routingOptions']['lddMap']
         if not isabs(fn_ldd):

glofrim-py/glofrim/glofrim_wfl.py

@@ -2,19 +2,12 @@
 
 #TODO: guess the input dir as in PCR has to be set up to work with path of the WFLOW ini-file instead
 
-import logging
 from os.path import isdir, join, basename, dirname, abspath, isfile, isabs
 import numpy as np
 import rasterio
-
-
-
 from main import BMI_model_wrapper
 from utils import ConfigParser
 
-log_fmt = '%(asctime)s - %(levelname)s - %(message)s'
-logging.basicConfig(level=logging.INFO, format=log_fmt, filemode='w')
-logger = logging.getLogger(__name__)
 
 class WFL_model(BMI_model_wrapper):
 
@@ -67,7 +60,7 @@ def get_model_grid(self):
         model_grid_shape : tuple
             model number of rows and cols
         """
-        logger.info('Getting WFLOW model grid parameters.')
+        self.logger.info('Getting WFLOW model grid parameters.')
         fn_map = getattr(self.model_config['model'], 'wflow_subcatch', 'staticmaps/wflow_subcatch.map')
         if not isabs(fn_map):
             ddir = self.model_data_dir
@@ -82,14 +75,14 @@ def get_model_grid(self):
             self.model_grid_shape = ds.shape
             self.model_grid_transform = ds.transform
         msg = 'Model bounds {:s}; width {}, height {}'
-        logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
+        self.logger.debug(msg.format(self.model_grid_bounds, *self.model_grid_shape))
         pass
 
     def get_drainage_direction(self):
         from nb.nb_io import read_dd_pcraster
         # read file with pcr readmap
         nodata = self.options.get('landmask_mv', 255)
-        logger.info('Getting WFLOW LDD map.')
+        self.logger.info('Getting WFLOW LDD map.')
         fn_ldd = getattr(self.model_config['model'], 'wflow_ldd', 'staticmaps/wflow_ldd.map')
         if not isabs(fn_ldd):
             ddir = self.model_data_dir
@@ -113,7 +106,7 @@ def model_2d_index(self, xy, **kwargs):
         indices : list of tuples
           list of (row, col) index tuples
         """
-        logger.info('Getting WFLOW model indices of xy coordinates.')
+        self.logger.info('Getting WFLOW model indices of xy coordinates.')
         r, c = self.grid_index(*zip(*xy), **kwargs)
         r = np.array(r).astype(int)
         c = np.array(c).astype(int)
@@ -163,11 +156,11 @@ def update(self, dt=None, **kwargs):
         state variables.
         """
         if dt is not None: # by default take internally set dt
-            logger.warning('dt is not used in the wflow bmi update function')
+            self.logger.warning('dt is not used in the wflow bmi update function')
         self.bmi.update()
         current_time = self.get_current_time()
         time_step = self.get_time_step()
-        logger.info(
+        self.logger.info(
             "%s -> start_time: %s, current_time %s, timestep %s",
             self.name,
             self.start_time,