Fixes from onperm

hera/riskassessment/__init__.py

@@ -4,3 +4,5 @@
 from .presentation.casualtiesFigs import casualtiesPlot
 from .protectionpolicy.ProtectionPolicy import ProtectionPolicy
 from .riskToolkit import RiskToolkit
+
+__all__ = ["Agent", "thresholdGeoDataFrame", "getRiskAreaAlgorithm", "casualtiesPlot", "ProtectionPolicy", "RiskToolkit"]

hera/riskassessment/presentation/casualtiesFigs.py

@@ -1,16 +1,35 @@
-import numpy 
 import matplotlib.pyplot as plt
 import mpl_toolkits.axisartist.floating_axes as floating_axes
-import mpl_toolkits.axisartist.angle_helper as angle_helper
-from matplotlib.projections import PolarAxes
-from mpl_toolkits.axisartist.grid_finder import (FixedLocator, MaxNLocator,
-                                                 DictFormatter)
-
+import numpy
 import pandas
-from ...utils import toMeteorologicalAngle,toMathematicalAngle, toAzimuthAngle
-
-from descartes import PolygonPatch 
-
+from matplotlib.patches import Polygon as MplPolygon
+from matplotlib.projections import PolarAxes
+from mpl_toolkits.axisartist.grid_finder import DictFormatter, FixedLocator
+from shapely.geometry import LineString, Point, Polygon
+
+from ...utils import toAzimuthAngle, toMathematicalAngle
+
+
+def plot_geom(ax, geom, patchProp, lineProp):
+    if geom.is_empty:
+        return
+    if isinstance(geom, Polygon):
+        patch=MplPolygon(list(geom.exterior.coords),
+        closed=True,
+        **patchProp)
+        ax.add_patch(patch)
+        for interior in geom.interiors:
+            x,y = interior.xy
+            ax.plot(x,y,**lineProp)
+    elif isinstance(geom, Point):
+        plt.plot(geom.x,geom.y, "o",**lineProp)
+    elif isinstance(geom, LineString):
+        x,y =geom.xy
+        plt.plot(x,y,**lineProp)
+    else:
+        for gg in geom.geoms:
+            plot_geom(ax,gg, patchProp, lineProp)
+
 class casualtiesPlot(object): 
 
 	"""
@@ -60,7 +79,7 @@ def plotCasualtiesRose(self,
 			projectedData.append(injuryareas)
 		projectedData = pandas.concat(projectedData)
 
-		pivotedData = projectedData.pivot(index="angle",columns='severity',values=effectedPopulation).reset_index().fillna(0)
+		pivotedData = projectedData.pivot(index="angle", columns='severity', values=effectedPopulation).reset_index().fillna(0)
 		if (ax is None):
 			fig = plt.gcf()
 			ax = fig.add_subplot(111,polar=True)
@@ -200,7 +219,6 @@ def plotCasualtiesProjection(self,
 		boundarycycler = plt.cycler(color=plt.rcParams['axes.prop_cycle'].by_key()['color']) if boundarycycler is None else boundarycycler		 		
 		cycler = plt.cycler(facecolor=plt.rcParams['axes.prop_cycle'].by_key()['color'])*plt.cycler(edgecolor=['None']) if cycler is None else cycler
 
-		patchList = []
 		for severity,prop,lineprop in zip(severityList,cycler,boundarycycler):
 			if severity not in projected.index:
 				continue

hera/simulations/LSM/singleSimulation.py

@@ -94,6 +94,9 @@ def getConcentration(self, Q=1*ureg.kg, time_units=ureg.min, q_units=ureg.mg):
         dDosage: xarray
             The calculated concentration in 'C' key
         """
+        time_units=unumToPint(time_units)
+        Q = unumToPint(Q)
+        q_units=unumToPint(q_units)
         finalxarray = self.getDosage(Q=Q, time_units=time_units, q_units=q_units)
 
         dDosage = finalxarray['Dosage'].diff('datetime').to_dataset().rename({'Dosage': 'dDosage'})

hera/simulations/LSM/template.py

@@ -1,18 +1,20 @@
-import os
 import glob
-from hera.utils.logging.helpers import get_logger
-import xarray
-import pandas
-import numpy
+import os
 from itertools import product
 
-from ..utils.inputForModelsCreation import InputForModelsCreator
-from hera.simulations.LSM.singleSimulation import SingleSimulation
-from hera.datalayer import datatypes
-from hera.utils.unitHandler import Quantity, ureg, unumToPint
+import numpy
+import pandas
+import xarray
+
 from hera import toolkit
-from hera.utils.jsonutils import JSONToConfiguration, stripConfigurationUnits
+from hera.datalayer import datatypes
+from hera.simulations.LSM.singleSimulation import SingleSimulation
 from hera.utils import dictToMongoQuery, get_classMethod_logger
+from hera.utils.jsonutils import JSONToConfiguration, stripConfigurationUnits
+from hera.utils.logging.helpers import get_logger
+from hera.utils.unitHandler import Quantity, unumToPint, ureg
+
+from ..utils.inputForModelsCreation import InputForModelsCreator
 
 
 class LSMTemplate:
@@ -119,7 +121,7 @@ def run(self,topography=None, stations=None,canopy=None,params=dict(),deposition
         updated_params.update(params)
         updated_params.update(descriptor)
         updated_params = JSONToConfiguration(updated_params)
-        updated_params = self.prepareParams(desc=self._document['desc'], paramsToPrepare=updated_params)
+        updated_params = self.prepareParams(template_desc=self._document['desc'], paramsToPrepare=updated_params)
         logger.info(f"Running simulation with the following parameters:\n{updated_params}")
         if topography is None:
             updated_params.update(homogeneousWind=".TRUE.")
@@ -317,19 +319,22 @@ def run(self,topography=None, stations=None,canopy=None,params=dict(),deposition
             return None
 
     @staticmethod
-    def prepareParams(desc, paramsToPrepare):
+    def prepareParams(template_desc, paramsToPrepare):
         logger = get_logger(instance=None, name="hera.simulations.LSM.prepareParams")
+        params = template_desc.get('params', {}) if template_desc is not None else {}
+        params.update(paramsToPrepare)
+        paramsToPrepare=params
         try:
-            if desc is not None and 'units' in desc:
-                for key in desc["units"].keys():
+            if template_desc is not None and 'units' in template_desc:
+                for key in template_desc["units"].keys():
                     param_item= paramsToPrepare[key]
                     if hasattr(param_item, 'asNumber') or hasattr(param_item, 'magnitude'):
-                        paramsToPrepare[key] = unumToPint(param_item).m_as(ureg.parse_expression(desc["units"][key]))
+                        paramsToPrepare[key] = unumToPint(param_item).m_as(ureg.parse_expression(template_desc["units"][key]))
                     elif key=='duration':
                         paramsToPrepare[key] = param_item*ureg.minutes
                     else:
-                        paramsToPrepare[key] = ureg.parse_expression(param_item).m_as(ureg.parse_expression(desc["units"][key]))
-        except:
+                        paramsToPrepare[key] = ureg.parse_expression(param_item).m_as(ureg.parse_expression(template_desc["units"][key]))
+        except Exception:
             raise ValueError(f"parameters must use either pint or unum to specify units, currently type({param_item})={type(param_item)}")
 
         paramsToPrepare = stripConfigurationUnits(paramsToPrepare, returnStandardize=True, ignoreStandardization=["duration"])
@@ -445,7 +450,7 @@ def getSimulationByID(self,id):
 
     def getSimulationByName(self,simulationName):
         """
-        get a simulation by document id
+        get a simulation by document name
 
         :param id:
         :return:

hera/utils/matplotlibCountour.py

@@ -31,7 +31,7 @@ def toGeopandas(ContourData, inunits=None):
         import geopandas
     except ImportError:
         print("gis support not installed. ")
-    inunits = inunits if inunits is not None else 1*ureg.m
+    inunits = unumToPint(inunits) if inunits is not None else 1*ureg.m
 
     units_conversion = unumToPint(inunits).m_as(ureg.m)
     polyList = []