pep8

eggshell/nc/nc_utils.py

@@ -629,7 +629,7 @@ def get_values(resource, variable=None):
 #         raise Exception(msg)
 #
 #
-#
+# #
 # def unrotate_pole(resource, write_to_file=False):
 #     """
 #     Calculates the unrotatated coordinates for a rotated pole grid
@@ -703,85 +703,85 @@ def get_values(resource, variable=None):
 #     ds.close()
 #
 #     return lats, lons
-
-
-def drs_filename(resource, skip_timestamp=False, skip_format=False,
-                 variable=None, rename_file=False, add_file_path=False):
-    """
-    generates filename according to the data reference syntax (DRS)
-    based on the metadata in the resource.
-    http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf
-    https://pypi.python.org/pypi/drslib
-    :param add_file_path: if add_file_path=True, path to file will be added (default=False)
-    :param resource: netcdf file
-    :param skip_timestamp: if True then from/to timestamp != added to the filename
-                           (default: False)
-    :param variable: appropriate variable for filename, if not set (default), variable will
-                      be determined. For files with more than one data variable,
-                      the variable parameter has to be defined (default: )
-                      example: variable='tas'
-    :param rename_file: rename the file. (default: False)
-    :returns str: DRS filename
-    """
-    from os import path, rename
-
-    try:
-        ds = Dataset(resource)
-        if variable is None:
-            variable = get_variable(resource)
-        # CORDEX example: EUR-11_ICHEC-EC-EARTH_historical_r3i1p1_DMI-HIRHAM5_v1_day
-        cordex_pattern = "{variable}_{domain}_{driving_model}_{experiment}_{ensemble}_{model}_{version}_{frequency}"
-        # CMIP5 example: tas_MPI-ESM-LR_historical_r1i1p1
-        cmip5_pattern = "{variable}_{model}_{experiment}_{ensemble}"
-        filename = resource
-        if ds.project_id == 'CORDEX' or ds.project_id == 'EOBS':
-            filename = cordex_pattern.format(
-                variable=variable,
-                domain=ds.CORDEX_domain,
-                driving_model=ds.driving_model_id,
-                experiment=ds.experiment_id,
-                ensemble=ds.driving_model_ensemble_member,
-                model=ds.model_id,
-                version=ds.rcm_version_id,
-                frequency=ds.frequency)
-        elif ds.project_id == 'CMIP5':
-            # TODO: attributes missing in netcdf file for name generation?
-            filename = cmip5_pattern.format(
-                variable=variable,
-                model=ds.model_id,
-                experiment=ds.experiment,
-                ensemble=ds.parent_experiment_rip
-            )
-        else:
-            raise Exception('unknown project %s' % ds.project_id)
-        ds.close()
-    except Exception:
-        LOGGER.exception('Could not read metadata %s', resource)
-    try:
-        # add from/to timestamp if not skipped
-        if skip_timestamp is False:
-            LOGGER.debug("add timestamp")
-            from_timestamp, to_timestamp = get_timerange(resource)
-            LOGGER.debug("from_timestamp %s", from_timestamp)
-            filename = "%s_%s-%s" % (filename, int(from_timestamp), int(to_timestamp))
-
-        # add format extension
-        if skip_format is False:
-            filename = filename + '.nc'
-
-        pf = path.dirname(resource)
-        # add file path
-        if add_file_path is True:
-            filename = path.join(pf, filename)
-
-        # rename the file
-        if rename_file is True:
-            if path.exists(path.join(resource)):
-                rename(resource, path.join(pf, filename))
-    except Exception:
-        LOGGER.exception('Could not generate DRS filename for %s', resource)
-
-    return filename
+#
+#
+# def drs_filename(resource, skip_timestamp=False, skip_format=False,
+#                  variable=None, rename_file=False, add_file_path=False):
+#     """
+#     generates filename according to the data reference syntax (DRS)
+#     based on the metadata in the resource.
+#     http://cmip-pcmdi.llnl.gov/cmip5/docs/cmip5_data_reference_syntax.pdf
+#     https://pypi.python.org/pypi/drslib
+#     :param add_file_path: if add_file_path=True, path to file will be added (default=False)
+#     :param resource: netcdf file
+#     :param skip_timestamp: if True then from/to timestamp != added to the filename
+#                            (default: False)
+#     :param variable: appropriate variable for filename, if not set (default), variable will
+#                       be determined. For files with more than one data variable,
+#                       the variable parameter has to be defined (default: )
+#                       example: variable='tas'
+#     :param rename_file: rename the file. (default: False)
+#     :returns str: DRS filename
+#     """
+#     from os import path, rename
+#
+#     try:
+#         ds = Dataset(resource)
+#         if variable is None:
+#             variable = get_variable(resource)
+#         # CORDEX example: EUR-11_ICHEC-EC-EARTH_historical_r3i1p1_DMI-HIRHAM5_v1_day
+#         cordex_pattern = "{variable}_{domain}_{driving_model}_{experiment}_{ensemble}_{model}_{version}_{frequency}"
+#         # CMIP5 example: tas_MPI-ESM-LR_historical_r1i1p1
+#         cmip5_pattern = "{variable}_{model}_{experiment}_{ensemble}"
+#         filename = resource
+#         if ds.project_id == 'CORDEX' or ds.project_id == 'EOBS':
+#             filename = cordex_pattern.format(
+#                 variable=variable,
+#                 domain=ds.CORDEX_domain,
+#                 driving_model=ds.driving_model_id,
+#                 experiment=ds.experiment_id,
+#                 ensemble=ds.driving_model_ensemble_member,
+#                 model=ds.model_id,
+#                 version=ds.rcm_version_id,
+#                 frequency=ds.frequency)
+#         elif ds.project_id == 'CMIP5':
+#             # TODO: attributes missing in netcdf file for name generation?
+#             filename = cmip5_pattern.format(
+#                 variable=variable,
+#                 model=ds.model_id,
+#                 experiment=ds.experiment,
+#                 ensemble=ds.parent_experiment_rip
+#             )
+#         else:
+#             raise Exception('unknown project %s' % ds.project_id)
+#         ds.close()
+#     except Exception:
+#         LOGGER.exception('Could not read metadata %s', resource)
+#     try:
+#         # add from/to timestamp if not skipped
+#         if skip_timestamp is False:
+#             LOGGER.debug("add timestamp")
+#             from_timestamp, to_timestamp = get_timerange(resource)
+#             LOGGER.debug("from_timestamp %s", from_timestamp)
+#             filename = "%s_%s-%s" % (filename, int(from_timestamp), int(to_timestamp))
+#
+#         # add format extension
+#         if skip_format is False:
+#             filename = filename + '.nc'
+#
+#         pf = path.dirname(resource)
+#         # add file path
+#         if add_file_path is True:
+#             filename = path.join(pf, filename)
+#
+#         # rename the file
+#         if rename_file is True:
+#             if path.exists(path.join(resource)):
+#                 rename(resource, path.join(pf, filename))
+#     except Exception:
+#         LOGGER.exception('Could not generate DRS filename for %s', resource)
+#
+#     return filename
 
 
 def sort_by_time(resource):

eggshell/plot/plt_eodata.py

@@ -195,7 +195,6 @@ def plot_products(products, extend=[10, 20, 5, 15], dir_output='.'):
 #     return imagefile
 
 
-
 # def plot_band(source, file_extension='PNG', colorscheem=None):
 #     """
 #     plots the first band of a geotif file

eggshell/plot/plt_ncdata.py

@@ -10,6 +10,7 @@
 from matplotlib import pyplot as plt
 from matplotlib.patches import Polygon
 import matplotlib.patches as mpatches
+import cartopy.crs as ccrs
 
 from cartopy.util import add_cyclic_point
 from eggshell.nc.calculation import fieldmean
@@ -30,7 +31,6 @@ def plot_extend(resource, file_extension='png'):
 
     :return graphic: graphic in specified format
     """
-    import matplotlib.patches as mpatches
     lats, lons = get_coordinates(resource, unrotate=True)
 
     # box_top = 45
@@ -51,7 +51,7 @@ def plot_extend(resource, file_extension='png'):
     ax = plt.axes(projection=projection)
     ax.stock_img()
     ax.coastlines()
-    ax.add_patch(mpatches.Polygon(xy, closed=True,  transform=ccrs.PlateCarree(), color='coral', alpha=0.6))
+    ax.add_patch(mpatches.Polygon(xy, closed=True, transform=ccrs.PlateCarree(), color='coral', alpha=0.6))
     # ccrs.Geodetic()
     ax.gridlines()
     plt.show()
@@ -90,8 +90,8 @@ def spaghetti(resouces, variable=None, title=None, file_extension='png'):
             title = "Field mean of %s " % variable
 
         LOGGER.info('plot values preparation done')
-    except:
-        msg = "plot values preparation failed"
+    except Exception as ex:
+        msg = "plot values preparation failed {}".format(ex)
         LOGGER.exception(msg)
         raise Exception(msg)
     try:
@@ -113,8 +113,8 @@ def spaghetti(resouces, variable=None, title=None, file_extension='png'):
 
         plt.close()
         LOGGER.info('timeseries spaghetti plot done for %s with %s lines.' % (variable, c))
-    except Exception as e:
-        msg = 'matplotlib spaghetti plot failed: {}'.format(e)
+    except Exception as ex:
+        msg = 'matplotlib spaghetti plot failed: {}'.format(ex)
         LOGGER.exception(msg)
     return output_png
 
@@ -149,7 +149,7 @@ def uncertainty(resouces, variable=None, ylim=None, title=None, file_extension='
         title = "Field mean of %s " % variable
 
     try:
-        fig = plt.figure(figsize=(20, 10), facecolor='w', edgecolor='k')  # dpi=600,
+        fig = plt.figure(figsize=(20, 10), facecolor='w', edgecolor='k')
         #  variable = get_variable(resouces[0])
         df = pd.DataFrame()
 
@@ -194,7 +194,8 @@ def uncertainty(resouces, variable=None, ylim=None, title=None, file_extension='
                      ha='right', va='bottom', alpha=0.5)
 
         try:
-            rmean = df_smooth.quantile([0.5], axis=1,)  # df_smooth.median(axis=1)
+            rmean = df_smooth.quantile([0.5], axis=1,)
+            # df_smooth.median(axis=1)
             # skipna=False  quantile([0.5], axis=1, numeric_only=False )
             q05 = df_smooth.quantile([0.10], axis=1,)  # numeric_only=False)
             q33 = df_smooth.quantile([0.33], axis=1,)  # numeric_only=False)

eggshell/plot/plt_utils.py

@@ -146,7 +146,7 @@ def concat_images(images, orientation='v'):
                     cw = oi.size[0]
                     ch = oi.size[1]
                     cp = h * i
-                    box = [0, cp, cw, ch+cp]
+                    box = [0, cp, cw, ch + cp]
                     result.paste(oi, box=box)
 
             if orientation == 'h':
@@ -158,7 +158,7 @@ def concat_images(images, orientation='v'):
                     cw = oi.size[0]
                     ch = oi.size[1]
                     cp = w * i
-                    box = [cp, 0, cw+cp, ch]
+                    box = [cp, 0, cw + cp, ch]
                     result.paste(oi, box=box)
 
             ip, image = mkstemp(dir=work_dir, suffix='.png')

eggshell/utils.py

@@ -15,6 +15,7 @@
 
 import eggshell as eg
 from eggshell.config import Paths
+from eggshell.nc.nc_utils import get_variable
 
 paths = Paths(eg)
 
@@ -163,45 +164,45 @@ def extract_archive(resources, output_dir=None):
     return files
 
 
-def get_coordinates(resource, variable=None, unrotate=False):
-    """
-    reads out the coordinates of a variable
-
-    :param resource: netCDF resource file
-    :param variable: variable name
-    :param unrotate: If True the coordinates will be returned for unrotated pole
-
-    :returns list, list: latitudes , longitudes
-    """
-    if type(resource) != list:
-        resource = [resource]
-
-    if variable is None:
-        variable = get_variable(resource)
-
-    if unrotate is False:
-        try:
-            if len(resource) > 1:
-                ds = MFDataset(resource)
-            else:
-                ds = Dataset(resource[0])
-
-            var = ds.variables[variable]
-            dims = list(var.dimensions)
-            if 'time' in dims:
-                dims.remove('time')
-            # TODO: find position of lat and long in list and replace dims[0] dims[1]
-            lats = ds.variables[dims[0]][:]
-            lons = ds.variables[dims[1]][:]
-            ds.close()
-            LOGGER.info('got coordinates without pole rotation')
-        except Exception as e:
-            msg = 'failed to extract coordinates: {}'.format(e)
-            raise Exception(msg)
-    else:
-        lats, lons = unrotate_pole(resource)
-        LOGGER.info('got coordinates with pole rotation')
-    return lats, lons
+# def get_coordinates(resource, variable=None, unrotate=False):
+#     """
+#     reads out the coordinates of a variable
+#
+#     :param resource: netCDF resource file
+#     :param variable: variable name
+#     :param unrotate: If True the coordinates will be returned for unrotated pole
+#
+#     :returns list, list: latitudes , longitudes
+#     """
+#     if type(resource) != list:
+#         resource = [resource]
+#
+#     if variable is None:
+#         variable = get_variable(resource)
+#
+#     if unrotate is False:
+#         try:
+#             if len(resource) > 1:
+#                 ds = MFDataset(resource)
+#             else:
+#                 ds = Dataset(resource[0])
+#
+#             var = ds.variables[variable]
+#             dims = list(var.dimensions)
+#             if 'time' in dims:
+#                 dims.remove('time')
+#             # TODO: find position of lat and long in list and replace dims[0] dims[1]
+#             lats = ds.variables[dims[0]][:]
+#             lons = ds.variables[dims[1]][:]
+#             ds.close()
+#             LOGGER.info('got coordinates without pole rotation')
+#         except Exception as e:
+#             msg = 'failed to extract coordinates: {}'.format(e)
+#             raise Exception(msg)
+#     else:
+#         lats, lons = unrotate_pole(resource)
+#         LOGGER.info('got coordinates with pole rotation')
+#     return lats, lons
 
 
 def rename_complexinputs(complexinputs):