Issue875

hera/riskassessment/agents/Agents.py

@@ -1,4 +1,4 @@
-from hera.utils.unitHandler import ureg, Unum, Quantity, celsius, K
+from hera.utils.unitHandler import ureg, unumToPint, Quantity, celsius, K
 from hera.riskassessment.agents.effects import  injuryfactory
 import numpy
 import json
@@ -254,10 +254,7 @@ def getVolatility(self,temperature):
 		:return:
 			The vapor saturation as Unum.
 		"""
-		if isinstance(temperature, Unum):
-			temperature = temperature.asNumber(celsius)
-		elif isinstance(temperature, Quantity):
-			temperature = temperature.m_as(ureg.celsius)
+		temperature = unumToPint(temperature).m_as(ureg.celsius)
 		MW = self.getMolecularWeight().to(ureg.g/ureg.mol)
 
 		a,b,c,d = self._volatilityConst
@@ -277,10 +274,7 @@ def getDensity(self, temperature):
 			:return:
 				The density as Unum
 		"""
-		if isinstance(temperature, Unum):
-			temperature = temperature.asNumber(celsius)
-		elif isinstance(temperature, Quantity):
-			temperature = temperature.m_as(ureg.celsius)
+		temperature = unumToPint(temperature).m_as(ureg.celsius)
 		a,b,c = self._densityConst
 
 		return (a-b*(temperature-c))*ureg.g/ureg.cm**3
@@ -299,10 +293,7 @@ def vaporPressure(self, temperature):
 		float
 			Vapor pressure in bar.
 		"""
-		if isinstance(temperature, Unum):
-			temperature = temperature.asNumber(K)
-		elif isinstance(temperature, Quantity):
-			temperature = temperature.m_as(ureg.kelvin)
+		temperature = unumToPint(temperature).m_as(ureg.kelvin)
 		A = self._vaporConst["A"]
 		B = self._vaporConst["B"]
 		C = self._vaporConst["C"]

hera/riskassessment/agents/effects/Calculator.py

@@ -2,8 +2,10 @@
 import pandas
 from hera.utils import ureg
 import xarray
+from utils.unitHandler import unumToPint
 
-class AbstractCalculator(object): 
+
+class AbstractCalculator(object):
 	"""
 		Holds the abstract calculator. 
 	"""
@@ -88,11 +90,10 @@ def calculate(self,concentrationField,breathingRate=10*ureg.L/ureg.min,time="dat
 
 
 		"""
+		breathingRate = unumToPint(breathingRate)
 		breathingRatio = (breathingRate/self.injuryBreathingRate).magnitude
 		if inUnits is None:
-			if hasattr(concentrationField, "attrs"):
-				attrs_units = concentrationField.attrs.get("field", None)
-			inUnits = concentrationField.attrs[field] if attrs_units is not None  else ureg.mg / ureg.m ** 3
+			inUnits = concentrationField.attrs[field] if hasattr(concentrationField, "attrs") else 1*(ureg.mg / ureg.m ** 3)
 
 		CunitConversion = inUnits.m_as(ureg.mg / ureg.m ** 3)
 
@@ -165,12 +166,10 @@ def calculate(self,concentrationField,field,breathingRate=10*ureg.L/ureg.min,tim
 
 
         """
+		breathingRate = unumToPint(breathingRate)
 		breathingRatio = (breathingRate/self.injuryBreathingRate).magnitude
-
 		if inUnits is None:
-			if hasattr(concentrationField, "attrs"):
-				attrs_units = concentrationField.attrs.get("field", None)
-			inUnits = concentrationField.attrs[field] if attrs_units is not None  else ureg.mg / ureg.m ** 3
+			inUnits = concentrationField.attrs[field] if hasattr(concentrationField, "attrs") else 1*(ureg.mg / ureg.m ** 3)
 		CunitConversion = inUnits.m_as(ureg.mg / ureg.m ** 3)
 
 		if isinstance(concentrationField, xarray.Dataset):
@@ -236,12 +235,10 @@ def calculate(self,concentrationField,field,breathingRate=10*ureg.L/ureg.min,tim
 
 
         """
-		breathingRatio = (breathingRate / self.injuryBreathingRate).magnitude
-
+		breathingRate = unumToPint(breathingRate)
+		breathingRatio = (breathingRate/self.injuryBreathingRate).magnitude
 		if inUnits is None:
-			if hasattr(concentrationField, "attrs"):
-				attrs_units = concentrationField.attrs.get("field", None)
-			inUnits = attrs_units[field] if attrs_units is not None  else ureg.mg / ureg.m ** 3
+			inUnits = concentrationField.attrs[field] if hasattr(concentrationField, "attrs") else 1*(ureg.mg / ureg.m ** 3)
 		CunitConversion = inUnits.m_as(ureg.mg / ureg.m ** 3)
 
 		if isinstance(concentrationField, xarray.Dataset):

hera/riskassessment/agents/effects/Injury.py

@@ -195,7 +195,7 @@ def _postCalculatePointWise(self, retList):
 		pass
 
 	def calculate(self, concentrationField, field, time="datetime", x="x", y="y", breathingRate=10 * ureg.L / ureg.min,
-				  **parameters):
+				  sel={},isel={}):
 		"""Deprecated. Use ``calculateRegionOfInjured`` instead."""
 		import warnings
 		warnings.warn("This function is obselete. Use calculateRegionOfInjured instead")
@@ -205,9 +205,9 @@ def calculate(self, concentrationField, field, time="datetime", x="x", y="y", br
 											  x=x,
 											  y=y,
 											  breathingRate=breathingRate,
-											  **parameters)
+											  sel=sel,isel=isel)
 
-	def calculateRegionOfInjured(self,concentrationField,field,time="datetime",x="x",y="y",breathingRate=10*ureg.L / ureg.min,**parameters):
+	def calculateRegionOfInjured(self,concentrationField,field,time="datetime",x="x",y="y",breathingRate=10*ureg.L / ureg.min,sel={},isel={}):
 		"""
 			Calculates the fraction of the population that was effected in each point, and returns its contour.
 			The levels are determined by the injury type.
@@ -247,8 +247,7 @@ def calculateRegionOfInjured(self,concentrationField,field,time="datetime",x="x"
 		toxicLoads = self.calculateToxicLoads(concentrationField=concentrationField,
 											  time=time,
 											  breathingRate=breathingRate,
-											  field=field,
-											  **parameters).compute()
+											  field=field).sel(**sel).isel(**isel).compute()
 		for lvl in self.levels:
 			data = lvl.calculateContours(toxicLoads=toxicLoads,time=time,x=x,y=y)
 			if data is not None: 

hera/riskassessment/agents/effects/InjuryLevel.py

@@ -1,6 +1,7 @@
 import geopandas
 import pandas
 from hera.utils import tounit, ureg
+from hera.utils.unitHandler import unumToPint
 import numpy
 import json
 
@@ -338,7 +339,7 @@ def _getGeopandas(self,concentrationField,x,y,**parameters):
 		"""
 			Return the correct geopandas of the  Injury level
 		"""
-		level = self.threshold.asNumber()
+		level = unumToPint(self.threshold).magnitude
 		CS =  plt.contour(concentrationField[x],concentrationField[y],concentrationField.squeeze(),levels=numpy.atleast_1d(level))
 		if numpy.max(CS.levels) < level:
 			ret = geopandas.GeoDataFrame()

hera/riskassessment/presentation/casualtiesFigs.py

@@ -60,7 +60,7 @@ def plotCasualtiesRose(self,
 			projectedData.append(injuryareas)
 		projectedData = pandas.concat(projectedData)
 
-		pivotedData = projectedData.pivot("angle",'severity',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)
@@ -83,15 +83,15 @@ def plotCasualtiesRose(self,
 					cycler  += plt.cycler(width=[weights]*len(severityList))
 
 		bottom = numpy.zeros(pivotedData.shape[0])
+		pivotedData["total"] = 0
 		for severity,plotprops in zip(severityList,cycler):
 			if severity not in pivotedData.columns:
 				continue
 
 			ax.bar(pivotedData["angle"],pivotedData[severity],label=severity,bottom=bottom,**plotprops)
 			bottom += pivotedData[severity]
-		pivotedData["total"] = 0
-		for severity in severityList:
 			pivotedData["total"] += pivotedData[severity]
+
 		if windDistribution is not None:
 			windDist = windDistribution.copy()
 			windTicks = [25,50,75,100] if windTicks is None else sorted(windTicks)
@@ -175,7 +175,9 @@ def plotCasualtiesProjection(self,
 			:cycler: a property cycler for the polygons. 
 			:boundarycycler: a property cycler for the overall polygons.  
 		"""
-		if (ax is None): 
+		from hera.utils.matplotlibCountour import plot_polygons
+
+		if (ax is None):
 			fig = plt.gcf()
 			ax = fig.add_subplot(111) 
 		elif isinstance(ax,list): 
@@ -196,20 +198,15 @@ def plotCasualtiesProjection(self,
 		projected  	= retProj.dissolve("severity")
 
 		boundarycycler = plt.cycler(color=plt.rcParams['axes.prop_cycle'].by_key()['color']) if boundarycycler is None else boundarycycler		 		
-		cycler = plt.cycler(fc=plt.rcParams['axes.prop_cycle'].by_key()['color'])*plt.cycler(ec=['None']) if cycler is None else cycler		
+		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
-			if projected.loc[severity].geometry.filterType == 'GeometryCollection' or projected.loc[severity].geometry.filterType == 'MultiPolygon':
-				for pol in projected.loc[severity].geometry:
-					if pol.filterType == 'LineString':
-						ax.plot(*pol.xy,**lineprop)
-					else:
-						ax.add_patch(PolygonPatch(pol,**prop) )
-			else:
-				ax.add_patch(PolygonPatch(projected.loc[severity].geometry,**prop) )
+			geom =projected.loc[severity].geometry
+			plot_polygons(ax,geom,**prop)
+
 
 		for ((severity,severitydata),prop) in zip(results.shiftLocationAndAngle(loc,mathematical_angle=rotate_angle,geometry="TotalPolygon")
 								 .query("severity in %s" % numpy.atleast_1d(plumSeverity))

hera/simulations/LSM/singleSimulation.py

@@ -2,7 +2,7 @@
 import xarray
 import numpy
 import os
-from hera.utils.unitHandler import  *
+from hera.utils.unitHandler import ureg, unumToPint
 
 from ...utils import tounit,tonumber
 
@@ -67,10 +67,6 @@ def getDosage(self, Q=1 * ureg.kg, time_units=ureg.min, q_units=ureg.mg):
         final_xarray.attrs['dt'] = dt_minutes.to(time_units)
         final_xarray.attrs['Q']  = Q.to(q_units)
         final_xarray.attrs['C']  = q_units/ ureg.m ** 3
-        if not ret_pint:
-            final_xarray.attrs['dt'] = pintToUnum(final_xarray.attrs['dt']) 
-            final_xarray.attrs['Q']  = pintToUnum(final_xarray.attrs['Q'])
-            final_xarray.attrs['C']  = pintToUnum(final_xarray.attrs['C'])
 
         Qfactor = (Q.to(q_units) * ureg.min / ureg.m ** 3).m_as(q_units * time_units / ureg.m ** 3)
 
@@ -101,7 +97,7 @@ def getConcentration(self, Q=1*ureg.kg, time_units=ureg.min, q_units=ureg.mg):
         finalxarray = self.getDosage(Q=Q, time_units=time_units, q_units=q_units)
 
         dDosage = finalxarray['Dosage'].diff('datetime').to_dataset().rename({'Dosage': 'dDosage'})
-        dDosage['C'] = dDosage['dDosage'] / finalxarray.attrs['dt']
+        dDosage['C'] = dDosage['dDosage'] / finalxarray.attrs['dt'].m_as(time_units)
         dDosage.attrs = finalxarray.attrs
 
         return dDosage

hera/simulations/LSM/template.py

@@ -9,7 +9,7 @@
 from ..utils.inputForModelsCreation import InputForModelsCreator
 from hera.simulations.LSM.singleSimulation import SingleSimulation
 from hera.datalayer import datatypes
-from hera.utils.unitHandler import  Quantity, ureg, Unum
+from hera.utils.unitHandler import Quantity, ureg, unumToPint
 from hera import toolkit
 from hera.utils.jsonutils import JSONToConfiguration, stripConfigurationUnits
 from hera.utils import dictToMongoQuery, get_classMethod_logger
@@ -160,6 +160,11 @@ def run(self,topography=None, stations=None,canopy=None,params=dict(),deposition
                                      f"{toolkit.TOOLKIT_SAVEMODE_FILEANDDB_REPLACE} in order to replace it.")
                 if saveMode == toolkit.TOOLKIT_SAVEMODE_FILEANDDB_REPLACE:
                     docList.delete()
+
+            curr_counter = self.Toolkit.getCounterAndAdd(f"LSM_SIMULATION_{self.Toolkit.projectName}")
+            simulationName = simulationName if simulationName is not None else f"LSM_Simulation_{curr_counter}"
+            saveDir = os.path.join(saveDir, simulationName)
+
             doc = self.Toolkit.addSimulationsDocument(
                 type=self.doctype_simulation,
                 resource='None',
@@ -170,8 +175,7 @@ def run(self,topography=None, stations=None,canopy=None,params=dict(),deposition
                           simulationName=simulationName,
                           params=updated_params)
             )
-            curr_counter = self.Toolkit.getCounterAndAdd(f"LSM_SIMULATION_{self.Toolkit.projectName}")
-            saveDir = os.path.join(saveDir, f"LSM_Simulation_{curr_counter}")
+
             if self.to_xarray:
                 doc['resource'] = os.path.join(saveDir, 'netcdf', '*')
                 doc['dataFormat'] = datatypes.NETCDF_XARRAY
@@ -315,17 +319,19 @@ def run(self,topography=None, stations=None,canopy=None,params=dict(),deposition
     @staticmethod
     def prepareParams(desc, paramsToPrepare):
         logger = get_logger(instance=None, name="hera.simulations.LSM.prepareParams")
-        if desc is not None and 'units' in desc:
-            for key in desc["units"].keys():
-                param_item= paramsToPrepare[key]
-                if isinstance(param_item, Unum):
-                    paramsToPrepare[key] = param_item.asNumber(eval(desc["units"][key]))
-                elif isinstance(param_item, Quantity):
-                    paramsToPrepare[key] = param_item.m_as(desc["units"][key])
-                else:
-                    raise ValueError(f"parameters must use either pint or unum to specify units, currently type({param_item})={type(param_item)}")
-        if 'duration' in paramsToPrepare and isinstance(paramsToPrepare['duration'], Quantity):
-            paramsToPrepare['duration'] = paramsToPrepare['duration'].to(ureg.minutes)
+        try:
+            if desc is not None and 'units' in desc:
+                for key in 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]))
+                    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:
+            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"])
         for integer_field in ["TopoXn", "TopoYn"]:
             if not isinstance(paramsToPrepare[integer_field], int):
@@ -437,6 +443,15 @@ def getSimulationByID(self,id):
         """
         return SingleSimulation(self.getDocumentByID(id))
 
+    def getSimulationByName(self,simulationName):
+        """
+        get a simulation by document id
+
+        :param id:
+        :return:
+        """
+        return SingleSimulation(self.getSimulationsDocuments(type=self.doctype_simulation,templateName=self.templateName,simulationName=simulationName))
+
     def _getSimulationsList(self, **query):
         """
             List the Simulation parameters that fulfil the query
@@ -484,4 +499,4 @@ def getSimulationsTable(self,**query):
 
             return df
         except ValueError:
-            raise FileNotFoundError('No simulations.old found')
+            raise FileNotFoundError('No simulations found')

hera/simulations/LSM/toolkit.py

@@ -11,7 +11,7 @@
 from ... import datalayer
 from ... import toolkit
 from .singleSimulation import SingleSimulation
-from unum.units import *
+from hera.utils.unitHandler import ureg, unumToPint
 from ..utils.coordinateHandler import coordinateHandler
 from pathlib import Path
 
@@ -238,10 +238,10 @@ def getSimulations(self,simulationName=None,unitsTemplateVersion="v4-general", *
             for key in template._document['desc']["units"].keys():
                 if key in query.keys():
                     query_item= query[key]
-                    if isinstance(query_item, Unum):
-                        query[key] = query_item.asNumber(eval(template._document['desc']["units"][key]))
-                    elif isinstance(query_item, Quantity):
-                        query[key] = query_item.m_as(template._document['desc']["units"][key])
+                    if hasattr(query_item, 'asNumber') or hasattr(query_item, 'magnitude'):
+                        pint_item = unumToPint(query_item)
+                        unit_expr = template._document['desc']["units"][key]
+                        query[key] = pint_item.m_as(ureg.parse_expression(unit_expr))
                     else:
                         raise ValueError(f"query must use either pint or unum to specify units, currently type({query[key]})={type(query[key])}")
         else:

hera/simulations/deposition/models.py

@@ -1,7 +1,7 @@
 from ...datalayer import project
 from ...riskassessment import AgentHome
 from ..utils import tonumber, tounit
-from unum.units import *
+from hera.utils.unitHandler import ureg, unumToPint
 import numpy
 
 class depositionModels(object):
@@ -71,16 +71,23 @@ def depositionModel(self,newModel):
         self._depositionModel=newModel
 
     def __init__(self, projectName = "deposition", surface={"name":"Desert","zrough":0.04},
-                 ustar=1, density=1500, diameter = 1E-6*m,heatFlux=0.1*W/(m**2), temperature=293*K, depositionModel="Petroff"):
+                 ustar=1, density=1500, diameter=None, heatFlux=None, temperature=None, depositionModel="Petroff"):
+
+        if diameter is None:
+            diameter = 1E-6*ureg.m
+        if heatFlux is None:
+            heatFlux = 0.1*ureg.W/ureg.m**2
+        if temperature is None:
+            temperature = 293*ureg.K
 
         p = project.Project(projectName)
         self._depositionModel = depositionModel
         self._ustar = ustar
         self._density = density
-        self._temperature = tonumber(tounit(temperature,K),K)
+        self._temperature = tonumber(tounit(temperature, ureg.K), ureg.K)
         self._surface = surface if type(surface)==dict else p.getCacheDocuments(type="surface",surface=surface)[0].asDict()["desc"]
-        self._diameter = tonumber(tounit(diameter,m),m)
-        self._heatFlux = tonumber(tounit(heatFlux, W/(m**2)), W/(m**2))
+        self._diameter = tonumber(tounit(diameter, ureg.m), ureg.m)
+        self._heatFlux = tonumber(tounit(heatFlux, ureg.W/ureg.m**2), ureg.W/ureg.m**2)
 
     def depositionRate(self):
         return getattr(self, f"depositionRate_{self._depositionModel}")()