From fbdeccd7c060ef926aba42e6a77749148d694c52 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 10 Jul 2024 15:58:40 +0200 Subject: [PATCH 01/14] added new inputs for dynamic occupancy --- caimira/src/caimira/calculator/validators/defaults.py | 2 ++ caimira/src/caimira/calculator/validators/form_validator.py | 2 ++ .../src/caimira/calculator/validators/virus/virus_validator.py | 2 ++ .../cern_caimira/apps/templates/base/calculator.form.html.j2 | 3 +++ 4 files changed, 9 insertions(+) diff --git a/caimira/src/caimira/calculator/validators/defaults.py b/caimira/src/caimira/calculator/validators/defaults.py index 30cb928f..3c8317ba 100644 --- a/caimira/src/caimira/calculator/validators/defaults.py +++ b/caimira/src/caimira/calculator/validators/defaults.py @@ -37,6 +37,7 @@ DEFAULTS = { 'infected_lunch_option': True, 'infected_lunch_start': '12:30', 'infected_people': 1, + 'dynamic_infected_occupancy': '[]', 'infected_start': '08:30', 'inside_temp': NO_DEFAULT, 'location_latitude': NO_DEFAULT, @@ -55,6 +56,7 @@ DEFAULTS = { 'room_volume': 0., 'simulation_name': NO_DEFAULT, 'total_people': NO_DEFAULT, + 'dynamic_exposed_occupancy': '[]', 'vaccine_option': False, 'vaccine_booster_option': False, 'vaccine_type': 'AZD1222_(AstraZeneca)', diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 233cdbf6..5a047e8d 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -37,9 +37,11 @@ class FormData: # Used if infected_dont_have_breaks_with_exposed infected_lunch_start: minutes_since_midnight infected_people: int + dynamic_infected_occupancy: list infected_start: minutes_since_midnight room_volume: float total_people: int + dynamic_exposed_occupancy: list data_registry: DataRegistry diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index 323c8106..9b68f460 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -549,6 +549,7 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'infected_lunch_option': '1', 'infected_lunch_start': '12:30', 'infected_people': '1', + 'dynamic_infected_occupancy': '[]', 'infected_start': '09:00', 'inside_temp': '293.', 'location_latitude': 46.20833, @@ -568,6 +569,7 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'room_volume': '75', 'simulation_name': 'Test', 'total_people': '10', + 'dynamic_exposed_occupancy': '[]', 'vaccine_option': '0', 'vaccine_booster_option': '0', 'vaccine_type': 'Ad26.COV2.S_(Janssen)', diff --git a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 index cabc5adf..45700ee5 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 @@ -447,6 +447,9 @@ ?
+ + +
From 527dd5ffa201f9a1f862ddf6850db17103f977f7 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 10 Jul 2024 15:59:54 +0200 Subject: [PATCH 02/14] added methods to read and parse dynamic occupancy. Probabilistic exposure and expected new cases were removed from results --- .../calculator/report/virus_report_data.py | 20 +++-- .../validators/virus/virus_validator.py | 85 ++++++++++++++++--- 2 files changed, 87 insertions(+), 18 deletions(-) diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index bf4f5733..b93bf7d4 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -171,13 +171,19 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable long_range_cumulative_doses = np.cumsum(long_range_deposited_exposures) prob = np.array(model.infection_probability()) - prob_dist_count, prob_dist_bins = np.histogram( - prob/100, bins=100, density=True) - prob_probabilistic_exposure = np.array( - model.total_probability_rule()).mean() - expected_new_cases = np.array(model.expected_new_cases()).mean() - exposed_presence_intervals = [ - list(interval) for interval in model.exposed.presence_interval().boundaries()] + prob_dist_count, prob_dist_bins = np.histogram(prob/100, bins=100, density=True) + + if form.exposure_option == "p_probabilistic_exposure": + prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() + else: prob_probabilistic_exposure = None + + if ((isinstance(form.dynamic_infected_occupancy, typing.List) and len(form.dynamic_infected_occupancy) > 0) or + (isinstance(form.dynamic_exposed_occupancy, typing.List) and len(form.dynamic_exposed_occupancy) > 0)): + expected_new_cases = None + else: + expected_new_cases = np.array(model.expected_new_cases()).mean() + + exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] conditional_probability_data = None uncertainties_plot_src = None diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index 9b68f460..513486de 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -439,6 +439,56 @@ class VirusFormData(FormData): ] = respiratory_activity['percentage'] return (self.precise_activity['physical_activity'], respiratory_dict) + + def generate_dynamic_occupancy(self, dynamic_occupancy: typing.List[typing.Dict[str, typing.Any]]): + ### Data format validation ### + for occupancy in dynamic_occupancy: + # Check if each occupancy entry is a dictionary + if not isinstance(occupancy, typing.Dict): + raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}."') + + # Check for required keys in each occupancy entry + dict_keys = list(occupancy.keys()) + if "total_people" not in dict_keys: + raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys[0]}".') + else: + value = occupancy["total_people"] + # Check if the total_people value is a non-negative integer + if not isinstance(value, int): + raise ValueError(f"Total number of people should be integer. Got {value}.") + elif not value >= 0: + raise ValueError(f"Total number of people should be non-negative. Got {value}.") + + if "start_time" not in dict_keys: + raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[1]}".') + if "finish_time" not in dict_keys: + raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[2]}".') + + # Validate time format for start_time and finish_time + for time_key in ["start_time", "finish_time"]: + time = occupancy[time_key] + if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): + raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') + + transition_times = [] + values = [] + for occupancy in dynamic_occupancy: + start_time = time_string_to_minutes(occupancy['start_time'])/60 + finish_time = time_string_to_minutes(occupancy['finish_time'])/60 + transition_times.extend([start_time, finish_time]) + values.append(occupancy['total_people']) + + unique_transition_times_sorted = np.array(sorted(set(transition_times))) + + if len(values) != len(unique_transition_times_sorted) - 1: + raise ValueError("Cannot compute dynamic occupancy with the inputs provided.") + + population_occupancy: models.IntPiecewiseConstant = models.IntPiecewiseConstant( + transition_times=tuple(unique_transition_times_sorted), + values=tuple(values) + ) + population_presence: typing.Union[None, models.Interval] = None + return population_occupancy, population_presence def infected_population(self) -> mc.InfectedPopulation: # Initializes the virus @@ -453,18 +503,26 @@ class VirusFormData(FormData): expiration_defn = {'Speaking': 1, 'Breathing': self.total_people - 1} elif (self.activity_type == 'precise'): - activity_defn, expiration_defn = self.generate_precise_activity_expiration() + activity_defn, expiration_defn = self.generate_precise_activity_expiration() # TODO: what to do here? activity = activity_distributions(self.data_registry)[activity_defn] expiration = build_expiration(self.data_registry, expiration_defn) - infected_occupants = self.infected_people + if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: + # If dynamic occupancy is defined, the generator will parse and validate the + # respective input to a format readable by the model - IntPiecewiseConstant. + infected_occupancy, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + else: + # The number of exposed occupants is the total number of occupants + # minus the number of infected occupants. + infected_occupancy = self.infected_people + infected_presence = self.infected_present_interval() infected = mc.InfectedPopulation( data_registry=self.data_registry, - number=infected_occupants, + number=infected_occupancy, + presence=infected_presence, virus=virus, - presence=self.infected_present_interval(), mask=self.mask(), activity=activity, expiration=expiration, @@ -478,11 +536,16 @@ class VirusFormData(FormData): if self.activity_type == 'precise' else str(self.data_registry.population_scenario_activity[self.activity_type]['activity'])) activity = activity_distributions(self.data_registry)[activity_defn] - - infected_occupants = self.infected_people - # The number of exposed occupants is the total number of occupants - # minus the number of infected occupants. - exposed_occupants = self.total_people - infected_occupants + + if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: + # If dynamic occupancy is defined, the generator will parse and validate the + # respective input to a format readable by the model - IntPiecewiseConstant. + exposed_occupancy, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + else: + # The number of exposed occupants is the total number of occupants + # minus the number of infected occupants. + exposed_occupancy = self.total_people - self.infected_people + exposed_presence = self.exposed_present_interval() if (self.vaccine_option): if (self.vaccine_booster_option and self.vaccine_booster_type != 'Other'): @@ -495,8 +558,8 @@ class VirusFormData(FormData): host_immunity = 0. exposed = mc.Population( - number=exposed_occupants, - presence=self.exposed_present_interval(), + number=exposed_occupancy, + presence=exposed_presence, activity=activity, mask=self.mask(), host_immunity=host_immunity, From ed354a1276f14ff31dc4388c1a5be3f781c343f6 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 10 Jul 2024 16:00:04 +0200 Subject: [PATCH 03/14] removed unused method --- .../src/caimira/calculator/validators/form_validator.py | 8 -------- 1 file changed, 8 deletions(-) diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 5a047e8d..2dd6cd12 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -371,14 +371,6 @@ class FormData: breaks=breaks, ) - def population_present_interval(self) -> models.Interval: - state_change_times = set( - self.infected_present_interval().transition_times()) - state_change_times.update( - self.exposed_present_interval().transition_times()) - all_state_changes = sorted(state_change_times) - return models.SpecificInterval(tuple(zip(all_state_changes[:-1], all_state_changes[1:]))) - def exposed_present_interval(self) -> models.Interval: if self.specific_breaks != {}: # It means the breaks are specific and not predefined breaks = self.generate_specific_break_times( From e3bd7148342f9db177d567ce196e018f409e8435 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Fri, 19 Jul 2024 10:43:47 +0200 Subject: [PATCH 04/14] added validation for dynamic infected population --- .../calculator/validators/virus/virus_validator.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index 513486de..ba63efe8 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -441,7 +441,7 @@ class VirusFormData(FormData): return (self.precise_activity['physical_activity'], respiratory_dict) def generate_dynamic_occupancy(self, dynamic_occupancy: typing.List[typing.Dict[str, typing.Any]]): - ### Data format validation ### + ##### Data format validation ##### for occupancy in dynamic_occupancy: # Check if each occupancy entry is a dictionary if not isinstance(occupancy, typing.Dict): @@ -453,7 +453,7 @@ class VirusFormData(FormData): raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys[0]}".') else: value = occupancy["total_people"] - # Check if the total_people value is a non-negative integer + # Check if the value is a non-negative integer if not isinstance(value, int): raise ValueError(f"Total number of people should be integer. Got {value}.") elif not value >= 0: @@ -481,7 +481,7 @@ class VirusFormData(FormData): unique_transition_times_sorted = np.array(sorted(set(transition_times))) if len(values) != len(unique_transition_times_sorted) - 1: - raise ValueError("Cannot compute dynamic occupancy with the inputs provided.") + raise ValueError("Cannot compute dynamic occupancy with the provided inputs.") population_occupancy: models.IntPiecewiseConstant = models.IntPiecewiseConstant( transition_times=tuple(unique_transition_times_sorted), @@ -512,6 +512,12 @@ class VirusFormData(FormData): # If dynamic occupancy is defined, the generator will parse and validate the # respective input to a format readable by the model - IntPiecewiseConstant. infected_occupancy, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + # If exposed population is static, defined from the "total_people" input, validate + # if every occurency of infected population is less or equal than it. + if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) == 0: + for infected_people in infected_occupancy.values: + if infected_people >= self.total_people: + raise ValueError('Number of infected people cannot be greater or equal to the number of total people.') else: # The number of exposed occupants is the total number of occupants # minus the number of infected occupants. From 2f8b053bb127240b15e81f7252ce81283f586819 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Fri, 19 Jul 2024 11:39:49 +0200 Subject: [PATCH 05/14] added "occupancy_format" input that controls the definition of dynamic activities --- .../calculator/report/virus_report_data.py | 30 ++++--- .../caimira/calculator/validators/defaults.py | 5 +- .../calculator/validators/form_validator.py | 11 +-- .../validators/virus/virus_validator.py | 88 ++++++++++--------- .../templates/base/calculator.form.html.j2 | 1 + 5 files changed, 73 insertions(+), 62 deletions(-) diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index b93bf7d4..4dbdbc54 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -173,15 +173,16 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable prob = np.array(model.infection_probability()) prob_dist_count, prob_dist_bins = np.histogram(prob/100, bins=100, density=True) - if form.exposure_option == "p_probabilistic_exposure": + # Probabilistic exposure + if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static": prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() - else: prob_probabilistic_exposure = None - - if ((isinstance(form.dynamic_infected_occupancy, typing.List) and len(form.dynamic_infected_occupancy) > 0) or - (isinstance(form.dynamic_exposed_occupancy, typing.List) and len(form.dynamic_exposed_occupancy) > 0)): - expected_new_cases = None - else: + else: prob_probabilistic_exposure = 0 + # Expected new cases + if (form.occupancy_format == "static"): expected_new_cases = np.array(model.expected_new_cases()).mean() + else: + # With dynamic occupancy, the expected number of new cases feature is disabled. + expected_new_cases = -1 exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] @@ -415,7 +416,8 @@ def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, m def scenario_statistics( mc_model: mc.ExposureModel, sample_times: typing.List[float], - compute_prob_exposure: bool + compute_prob_exposure: bool, + compute_expected_new_cases: bool, ): model = mc_model.build_model( size=mc_model.data_registry.monte_carlo['sample_size']) @@ -424,10 +426,15 @@ def scenario_statistics( prob_probabilistic_exposure = model.total_probability_rule() else: prob_probabilistic_exposure = 0. + + if (compute_expected_new_cases): + expected_new_cases = np.mean(model.expected_new_cases()) + else: + expected_new_cases = -1 return { 'probability_of_infection': np.mean(model.infection_probability()), - 'expected_new_cases': np.mean(model.expected_new_cases()), + 'expected_new_cases': expected_new_cases, 'concentrations': [ np.mean(model.concentration(time)) for time in sample_times @@ -453,17 +460,20 @@ def comparison_report( else: statistics = {} - if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure"): + if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static"): compute_prob_exposure = True else: compute_prob_exposure = False + compute_expected_new_cases = True if (form.occupancy_format == "static") else False + with executor_factory() as executor: results = executor.map( scenario_statistics, scenarios.values(), [report_data['times']] * len(scenarios), [compute_prob_exposure] * len(scenarios), + [compute_expected_new_cases] * len(scenarios), timeout=60, ) diff --git a/caimira/src/caimira/calculator/validators/defaults.py b/caimira/src/caimira/calculator/validators/defaults.py index 3c8317ba..8ef2d138 100644 --- a/caimira/src/caimira/calculator/validators/defaults.py +++ b/caimira/src/caimira/calculator/validators/defaults.py @@ -50,13 +50,14 @@ DEFAULTS = { 'mask_type': 'Type I', 'mask_wearing_option': 'mask_off', 'mechanical_ventilation_type': 'not-applicable', + 'occupancy_format': 'static', 'opening_distance': 0., 'room_heating_option': False, 'room_number': NO_DEFAULT, 'room_volume': 0., 'simulation_name': NO_DEFAULT, 'total_people': NO_DEFAULT, - 'dynamic_exposed_occupancy': '[]', + 'dynamic_exposed_occupancy': NO_DEFAULT, 'vaccine_option': False, 'vaccine_booster_option': False, 'vaccine_type': 'AZD1222_(AstraZeneca)', @@ -73,7 +74,7 @@ DEFAULTS = { 'window_opening_regime': 'windows_open_permanently', 'sensor_in_use': '', 'short_range_option': 'short_range_no', - 'short_range_interactions': '[]', + 'short_range_interactions': NO_DEFAULT, 'short_range_occupants': 0, } diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 2dd6cd12..0e5a6450 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -26,16 +26,13 @@ class FormData: exposed_lunch_option: bool exposed_lunch_start: minutes_since_midnight exposed_start: minutes_since_midnight - # Used if infected_dont_have_breaks_with_exposed infected_coffee_break_option: str - infected_coffee_duration: int # Used if infected_dont_have_breaks_with_exposed + infected_coffee_duration: int infected_dont_have_breaks_with_exposed: bool infected_finish: minutes_since_midnight - # Used if infected_dont_have_breaks_with_exposed - infected_lunch_finish: minutes_since_midnight - infected_lunch_option: bool # Used if infected_dont_have_breaks_with_exposed - # Used if infected_dont_have_breaks_with_exposed - infected_lunch_start: minutes_since_midnight + infected_lunch_finish: minutes_since_midnight # Used if infected_dont_have_breaks_with_exposed + infected_lunch_option: bool # Used if infected_dont_have_breaks_with_exposed + infected_lunch_start: minutes_since_midnight # Used if infected_dont_have_breaks_with_exposed infected_people: int dynamic_infected_occupancy: list infected_start: minutes_since_midnight diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index ba63efe8..99a00dce 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -202,7 +202,8 @@ class VirusFormData(FormData): f'The sum of all respiratory activities should be 100. Got {total_percentage}.') # Validate number of people with short-range interactions - max_occupants_for_sr = self.total_people - self.infected_people + if self.occupancy_format == "static": max_occupants_for_sr = self.total_people - self.infected_people + else: max_occupants_for_sr = np.max(np.array([entry["total_people"] for entry in self.dynamic_exposed_occupancy])) if self.short_range_occupants > max_occupants_for_sr: raise ValueError( f'The total number of occupants having short-range interactions ({self.short_range_occupants}) should be lower than the exposed population ({max_occupants_for_sr}).' @@ -494,36 +495,33 @@ class VirusFormData(FormData): # Initializes the virus virus = virus_distributions(self.data_registry)[self.virus_type] - activity_defn = self.data_registry.population_scenario_activity[ - self.activity_type]['activity'] - expiration_defn = self.data_registry.population_scenario_activity[ - self.activity_type]['expiration'] - if (self.activity_type == 'smallmeeting'): - # Conversation of N people is approximately 1/N% of the time speaking. - expiration_defn = {'Speaking': 1, - 'Breathing': self.total_people - 1} - elif (self.activity_type == 'precise'): - activity_defn, expiration_defn = self.generate_precise_activity_expiration() # TODO: what to do here? - - activity = activity_distributions(self.data_registry)[activity_defn] - expiration = build_expiration(self.data_registry, expiration_defn) - - if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: - # If dynamic occupancy is defined, the generator will parse and validate the - # respective input to a format readable by the model - IntPiecewiseConstant. - infected_occupancy, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) - # If exposed population is static, defined from the "total_people" input, validate - # if every occurency of infected population is less or equal than it. - if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) == 0: - for infected_people in infected_occupancy.values: - if infected_people >= self.total_people: - raise ValueError('Number of infected people cannot be greater or equal to the number of total people.') + # Occupancy + if self.occupancy_format == 'dynamic': + if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: + # If dynamic occupancy is defined, the generator will parse and validate the + # respective input to a format readable by the model - `IntPiecewiseConstant`. + infected_occupancy, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + else: + raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_infected_occupancy}".') else: # The number of exposed occupants is the total number of occupants # minus the number of infected occupants. infected_occupancy = self.infected_people infected_presence = self.infected_present_interval() + # Activity and expiration + activity_defn = self.data_registry.population_scenario_activity[self.activity_type]['activity'] + expiration_defn = self.data_registry.population_scenario_activity[self.activity_type]['expiration'] + if (self.activity_type == 'smallmeeting'): + # Conversation of N people is approximately 1/N% of the time speaking. + total_people: int = max(infected_occupancy.values) if self.occupancy_format == 'dynamic' else self.total_people + expiration_defn = {'Speaking': 1, 'Breathing': total_people - 1} + elif (self.activity_type == 'precise'): + activity_defn, expiration_defn = self.generate_precise_activity_expiration() + + activity = activity_distributions(self.data_registry)[activity_defn] + expiration = build_expiration(self.data_registry, expiration_defn) + infected = mc.InfectedPopulation( data_registry=self.data_registry, number=infected_occupancy, @@ -542,11 +540,14 @@ class VirusFormData(FormData): if self.activity_type == 'precise' else str(self.data_registry.population_scenario_activity[self.activity_type]['activity'])) activity = activity_distributions(self.data_registry)[activity_defn] - - if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: - # If dynamic occupancy is defined, the generator will parse and validate the - # respective input to a format readable by the model - IntPiecewiseConstant. - exposed_occupancy, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + + if self.occupancy_format == 'dynamic': + if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: + # If dynamic occupancy is defined, the generator will parse and validate the + # respective input to a format readable by the model - IntPiecewiseConstant. + exposed_occupancy, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + else: + raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_exposed_occupancy}".') else: # The number of exposed occupants is the total number of occupants # minus the number of infected occupants. @@ -597,8 +598,12 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'activity_type': 'office', 'air_changes': '', 'air_supply': '', + 'ascertainment_bias': 'confidence_low', 'ceiling_height': '', 'conditional_probability_viral_loads': '0', + 'dynamic_exposed_occupancy': '[]', + 'dynamic_infected_occupancy': '[]', + 'event_month': 'January', 'exposed_coffee_break_option': 'coffee_break_4', 'exposed_coffee_duration': '10', 'exposed_finish': '18:00', @@ -607,6 +612,8 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'exposed_lunch_start': '12:30', 'exposed_start': '09:00', 'floor_area': '', + 'geographic_cases': 0, + 'geographic_population': 0, 'hepa_amount': '250', 'hepa_option': '0', 'humidity': '0.5', @@ -618,43 +625,38 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'infected_lunch_option': '1', 'infected_lunch_start': '12:30', 'infected_people': '1', - 'dynamic_infected_occupancy': '[]', 'infected_start': '09:00', 'inside_temp': '293.', 'location_latitude': 46.20833, 'location_longitude': 6.14275, 'location_name': 'Geneva', - 'geographic_population': 0, - 'geographic_cases': 0, - 'ascertainment_bias': 'confidence_low', 'mask_type': 'Type I', 'mask_wearing_option': 'mask_off', 'mechanical_ventilation_type': '', 'calculator_version': calculator_version, 'opening_distance': '0.2', - 'event_month': 'January', + 'occupancy_format': 'static', 'room_heating_option': '0', 'room_number': '123', 'room_volume': '75', + 'short_range_interactions': '[]', + 'short_range_option': 'short_range_no', 'simulation_name': 'Test', 'total_people': '10', - 'dynamic_exposed_occupancy': '[]', - 'vaccine_option': '0', 'vaccine_booster_option': '0', - 'vaccine_type': 'Ad26.COV2.S_(Janssen)', 'vaccine_booster_type': 'AZD1222_(AstraZeneca)', + 'vaccine_option': '0', + 'vaccine_type': 'Ad26.COV2.S_(Janssen)', 'ventilation_type': 'natural_ventilation', 'virus_type': 'SARS_CoV_2', 'volume_type': 'room_volume_explicit', + 'window_height': '2', + 'window_opening_regime': 'windows_open_permanently', 'windows_duration': '10', 'windows_frequency': '60', - 'window_height': '2', + 'windows_number': '1', 'window_type': 'window_sliding', 'window_width': '2', - 'windows_number': '1', - 'window_opening_regime': 'windows_open_permanently', - 'short_range_option': 'short_range_no', - 'short_range_interactions': '[]', } diff --git a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 index 45700ee5..db159eb0 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 @@ -447,6 +447,7 @@ ?

+ {# "static" vs. "dynamic" #} From f4c9c5fa96340265ddf252caed8a097b3a13ec6d Mon Sep 17 00:00:00 2001 From: lrdossan Date: Fri, 19 Jul 2024 16:12:03 +0200 Subject: [PATCH 06/14] added test for dynamic occupancy from input form --- .../calculator/report/virus_report_data.py | 4 +- .../validators/co2/co2_validator.py | 6 +- .../caimira/calculator/validators/defaults.py | 2 +- .../validators/virus/virus_validator.py | 5 +- cern_caimira/tests/test_report_generator.py | 59 +++++++++++++++++++ 5 files changed, 70 insertions(+), 6 deletions(-) diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index 4dbdbc54..29fddac6 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -176,7 +176,7 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable # Probabilistic exposure if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static": prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() - else: prob_probabilistic_exposure = 0 + else: prob_probabilistic_exposure = -1 # Expected new cases if (form.occupancy_format == "static"): expected_new_cases = np.array(model.expected_new_cases()).mean() @@ -425,7 +425,7 @@ def scenario_statistics( # It means we have data to calculate the total_probability_rule prob_probabilistic_exposure = model.total_probability_rule() else: - prob_probabilistic_exposure = 0. + prob_probabilistic_exposure = -1 if (compute_expected_new_cases): expected_new_cases = np.mean(model.expected_new_cases()) diff --git a/caimira/src/caimira/calculator/validators/co2/co2_validator.py b/caimira/src/caimira/calculator/validators/co2/co2_validator.py index ba865a7c..7a41f6c6 100644 --- a/caimira/src/caimira/calculator/validators/co2/co2_validator.py +++ b/caimira/src/caimira/calculator/validators/co2/co2_validator.py @@ -60,8 +60,10 @@ class CO2FormData(FormData): self.data_registry = DataRegistry() def validate(self): - # Validate population parameters - self.validate_population_parameters() + # Validate population parameters when static occupancy is defined. + # Dynamic population is validated in the generate_dynamic_occupancy method. + if self.occupancy_format == 'static': + self.validate_population_parameters() # Validate room capacity if self.room_capacity: diff --git a/caimira/src/caimira/calculator/validators/defaults.py b/caimira/src/caimira/calculator/validators/defaults.py index 8ef2d138..bd14db38 100644 --- a/caimira/src/caimira/calculator/validators/defaults.py +++ b/caimira/src/caimira/calculator/validators/defaults.py @@ -37,7 +37,7 @@ DEFAULTS = { 'infected_lunch_option': True, 'infected_lunch_start': '12:30', 'infected_people': 1, - 'dynamic_infected_occupancy': '[]', + 'dynamic_infected_occupancy': NO_DEFAULT, 'infected_start': '08:30', 'inside_temp': NO_DEFAULT, 'location_latitude': NO_DEFAULT, diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index 99a00dce..c8230974 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -73,7 +73,10 @@ class VirusFormData(FormData): _DEFAULTS: typing.ClassVar[typing.Dict[str, typing.Any]] = DEFAULTS def validate(self): - self.validate_population_parameters() + # Validate population parameters when static occupancy is defined. + # Dynamic population is validated in the generate_dynamic_occupancy method. + if self.occupancy_format == 'static': + self.validate_population_parameters() validation_tuples = [('activity_type', self.data_registry.population_scenario_activity.keys()), ('mechanical_ventilation_type', diff --git a/cern_caimira/tests/test_report_generator.py b/cern_caimira/tests/test_report_generator.py index 6e257f61..3e9026b7 100644 --- a/cern_caimira/tests/test_report_generator.py +++ b/cern_caimira/tests/test_report_generator.py @@ -2,6 +2,7 @@ import concurrent.futures from functools import partial import os import time +import json import numpy as np import pytest @@ -123,4 +124,62 @@ def test_expected_new_cases(baseline_form_with_sr: VirusFormData): lr_expected_new_cases = alternative_statistics['stats']['Base scenario without short-range interactions']['expected_new_cases'] np.testing.assert_almost_equal(sr_lr_expected_new_cases, lr_expected_new_cases + sr_lr_prob_inf * baseline_form_with_sr.short_range_occupants, 2) + + +def test_static_vs_dynamic_occupancy_from_form(baseline_form_data, data_registry): + """ + Assert that the results between a static and dynamic occupancy model (from form inputs) are similar. + """ + executor_factory = partial( + concurrent.futures.ThreadPoolExecutor, 1, + ) + + # By default the baseline form accepts static occupancy + static_occupancy_baseline_form: VirusFormData = VirusFormData.from_dict(baseline_form_data, data_registry) + static_occupancy_model = static_occupancy_baseline_form.build_model() + static_occupancy_report_data = rep_gen.calculate_report_data(static_occupancy_baseline_form, executor_factory) + + # Update the initial form data to include dynamic occupancy (please note the 4 coffee and 1 lunch breaks) + baseline_form_data['occupancy_format'] = 'dynamic' + baseline_form_data['dynamic_infected_occupancy'] = json.dumps([ + {'total_people': 1, 'start_time': '09:00', 'finish_time': '10:03'}, + {'total_people': 0, 'start_time': '10:03', 'finish_time': '10:13'}, + {'total_people': 1, 'start_time': '10:13', 'finish_time': '11:16'}, + {'total_people': 0, 'start_time': '11:16', 'finish_time': '11:26'}, + {'total_people': 1, 'start_time': '11:26', 'finish_time': '12:30'}, + {'total_people': 0, 'start_time': '12:30', 'finish_time': '13:30'}, + {'total_people': 1, 'start_time': '13:30', 'finish_time': '14:53'}, + {'total_people': 0, 'start_time': '14:53', 'finish_time': '15:03'}, + {'total_people': 1, 'start_time': '15:03', 'finish_time': '16:26'}, + {'total_people': 0, 'start_time': '16:26', 'finish_time': '16:36'}, + {'total_people': 1, 'start_time': '16:36', 'finish_time': '18:00'}, + ]) + baseline_form_data['dynamic_exposed_occupancy'] = json.dumps([ + {'total_people': 9, 'start_time': '09:00', 'finish_time': '10:03'}, + {'total_people': 0, 'start_time': '10:03', 'finish_time': '10:13'}, + {'total_people': 9, 'start_time': '10:13', 'finish_time': '11:16'}, + {'total_people': 0, 'start_time': '11:16', 'finish_time': '11:26'}, + {'total_people': 9, 'start_time': '11:26', 'finish_time': '12:30'}, + {'total_people': 0, 'start_time': '12:30', 'finish_time': '13:30'}, + {'total_people': 9, 'start_time': '13:30', 'finish_time': '14:53'}, + {'total_people': 0, 'start_time': '14:53', 'finish_time': '15:03'}, + {'total_people': 9, 'start_time': '15:03', 'finish_time': '16:26'}, + {'total_people': 0, 'start_time': '16:26', 'finish_time': '16:36'}, + {'total_people': 9, 'start_time': '16:36', 'finish_time': '18:00'}, + ]) + baseline_form_data['total_people'] = 0 + baseline_form_data['infected_people'] = 0 + + dynamic_occupancy_baseline_form: VirusFormData = VirusFormData.from_dict(baseline_form_data, data_registry) + dynamic_occupancy_model = dynamic_occupancy_baseline_form.build_model() + dynamic_occupancy_report_data = rep_gen.calculate_report_data(dynamic_occupancy_baseline_form, executor_factory) + + assert (list(sorted(static_occupancy_model.concentration_model.infected.presence.transition_times())) == + list(dynamic_occupancy_model.concentration_model.infected.number.transition_times)) + assert (list(sorted(static_occupancy_model.exposed.presence.transition_times())) == + list(dynamic_occupancy_model.exposed.number.transition_times)) + + np.testing.assert_almost_equal(static_occupancy_report_data['prob_inf'], dynamic_occupancy_report_data['prob_inf'], 1) + assert dynamic_occupancy_report_data['expected_new_cases'] == -1 + assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == -1 \ No newline at end of file From a4be817c7276499883d03fd38a26bc6bd5a91083 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 22 Jul 2024 10:10:00 +0200 Subject: [PATCH 07/14] added dynamic occupancy possibility to co2 fitting algorithm --- .../validators/co2/co2_validator.py | 29 ++++++++--- .../calculator/validators/form_validator.py | 51 +++++++++++++++++++ .../validators/virus/virus_validator.py | 50 ------------------ .../apps/calculator/static/js/co2_form.js | 3 ++ .../templates/base/calculator.form.html.j2 | 4 +- 5 files changed, 79 insertions(+), 58 deletions(-) diff --git a/caimira/src/caimira/calculator/validators/co2/co2_validator.py b/caimira/src/caimira/calculator/validators/co2/co2_validator.py index 7a41f6c6..659bd27c 100644 --- a/caimira/src/caimira/calculator/validators/co2/co2_validator.py +++ b/caimira/src/caimira/calculator/validators/co2/co2_validator.py @@ -44,11 +44,14 @@ class CO2FormData(FormData): 'infected_lunch_option': True, 'infected_lunch_start': '12:30', 'infected_people': 1, + 'dynamic_infected_occupancy': '[]', 'infected_start': '08:30', 'room_capacity': None, 'room_volume': NO_DEFAULT, 'specific_breaks': '{}', 'total_people': NO_DEFAULT, + 'dynamic_exposed_occupancy': '[]', + 'occupancy_format': 'static', } def __init__(self, **kwargs): @@ -196,20 +199,34 @@ class CO2FormData(FormData): size = size or self.data_registry.monte_carlo['sample_size'] # Build a simple infected and exposed population for the case when presence # intervals and number of people are dynamic. Activity type is not needed. - infected_presence = self.infected_present_interval() + if self.occupancy_format == 'dynamic': + if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: + infected_people, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + else: + raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_infected_occupancy}".') + if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: + exposed_people, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + else: + raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_exposed_occupancy}".') + else: + infected_people = self.infected_people + exposed_people = self.total_people - self.infected_people + infected_presence = self.infected_present_interval() + exposed_presence = self.exposed_present_interval() + infected_population = models.SimplePopulation( - number=self.infected_people, + number=infected_people, presence=infected_presence, activity=None, # type: ignore ) - exposed_presence = self.exposed_present_interval() exposed_population=models.SimplePopulation( - number=self.total_people - self.infected_people, + number=exposed_people, presence=exposed_presence, activity=None, # type: ignore ) - - all_state_changes = self.population_present_changes(infected_presence, exposed_presence) + + all_state_changes=self.population_present_changes(infected_population.presence_interval(), + exposed_population.presence_interval()) total_people = [infected_population.people_present(stop) + exposed_population.people_present(stop) for _, stop in zip(all_state_changes[:-1], all_state_changes[1:])] diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 0e5a6450..281647b5 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -4,6 +4,7 @@ import logging import typing import ast import json +import re import numpy as np @@ -378,6 +379,56 @@ class FormData: self.exposed_start, self.exposed_finish, breaks=breaks, ) + + def generate_dynamic_occupancy(self, dynamic_occupancy: typing.List[typing.Dict[str, typing.Any]]): + ##### Data format validation ##### + for occupancy in dynamic_occupancy: + # Check if each occupancy entry is a dictionary + if not isinstance(occupancy, typing.Dict): + raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}."') + + # Check for required keys in each occupancy entry + dict_keys = list(occupancy.keys()) + if "total_people" not in dict_keys: + raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys[0]}".') + else: + value = occupancy["total_people"] + # Check if the value is a non-negative integer + if not isinstance(value, int): + raise ValueError(f"Total number of people should be integer. Got {value}.") + elif not value >= 0: + raise ValueError(f"Total number of people should be non-negative. Got {value}.") + + if "start_time" not in dict_keys: + raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[1]}".') + if "finish_time" not in dict_keys: + raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[2]}".') + + # Validate time format for start_time and finish_time + for time_key in ["start_time", "finish_time"]: + time = occupancy[time_key] + if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): + raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') + + transition_times = [] + values = [] + for occupancy in dynamic_occupancy: + start_time = time_string_to_minutes(occupancy['start_time'])/60 + finish_time = time_string_to_minutes(occupancy['finish_time'])/60 + transition_times.extend([start_time, finish_time]) + values.append(occupancy['total_people']) + + unique_transition_times_sorted = np.array(sorted(set(transition_times))) + + if len(values) != len(unique_transition_times_sorted) - 1: + raise ValueError("Cannot compute dynamic occupancy with the provided inputs.") + + population_occupancy: models.IntPiecewiseConstant = models.IntPiecewiseConstant( + transition_times=tuple(unique_transition_times_sorted), + values=tuple(values) + ) + population_presence: typing.Union[None, models.Interval] = None + return population_occupancy, population_presence def _hours2timestring(hours: float): diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index c8230974..60c4c52a 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -443,56 +443,6 @@ class VirusFormData(FormData): ] = respiratory_activity['percentage'] return (self.precise_activity['physical_activity'], respiratory_dict) - - def generate_dynamic_occupancy(self, dynamic_occupancy: typing.List[typing.Dict[str, typing.Any]]): - ##### Data format validation ##### - for occupancy in dynamic_occupancy: - # Check if each occupancy entry is a dictionary - if not isinstance(occupancy, typing.Dict): - raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}."') - - # Check for required keys in each occupancy entry - dict_keys = list(occupancy.keys()) - if "total_people" not in dict_keys: - raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys[0]}".') - else: - value = occupancy["total_people"] - # Check if the value is a non-negative integer - if not isinstance(value, int): - raise ValueError(f"Total number of people should be integer. Got {value}.") - elif not value >= 0: - raise ValueError(f"Total number of people should be non-negative. Got {value}.") - - if "start_time" not in dict_keys: - raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[1]}".') - if "finish_time" not in dict_keys: - raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[2]}".') - - # Validate time format for start_time and finish_time - for time_key in ["start_time", "finish_time"]: - time = occupancy[time_key] - if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): - raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') - - transition_times = [] - values = [] - for occupancy in dynamic_occupancy: - start_time = time_string_to_minutes(occupancy['start_time'])/60 - finish_time = time_string_to_minutes(occupancy['finish_time'])/60 - transition_times.extend([start_time, finish_time]) - values.append(occupancy['total_people']) - - unique_transition_times_sorted = np.array(sorted(set(transition_times))) - - if len(values) != len(unique_transition_times_sorted) - 1: - raise ValueError("Cannot compute dynamic occupancy with the provided inputs.") - - population_occupancy: models.IntPiecewiseConstant = models.IntPiecewiseConstant( - transition_times=tuple(unique_transition_times_sorted), - values=tuple(values) - ) - population_presence: typing.Union[None, models.Interval] = None - return population_occupancy, population_presence def infected_population(self) -> mc.InfectedPopulation: # Initializes the virus diff --git a/cern_caimira/src/cern_caimira/apps/calculator/static/js/co2_form.js b/cern_caimira/src/cern_caimira/apps/calculator/static/js/co2_form.js index 16df7060..9f491418 100644 --- a/cern_caimira/src/cern_caimira/apps/calculator/static/js/co2_form.js +++ b/cern_caimira/src/cern_caimira/apps/calculator/static/js/co2_form.js @@ -17,11 +17,14 @@ const CO2_data_form = [ "infected_lunch_option", "infected_lunch_start", "infected_people", + "dynamic_infected_occupancy", "infected_start", "room_capacity", "room_volume", "specific_breaks", "total_people", + "dynamic_exposed_occupancy", + "occupancy_format", ]; // Method to upload a valid data file (accepted formats: .xls and .xlsx) diff --git a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 index db159eb0..ed1e24ba 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.form.html.j2 @@ -448,8 +448,8 @@
{# "static" vs. "dynamic" #} - - + +
From 13c112b656bb77cf35dfa557ffeb8fd5497f26ea Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 22 Jul 2024 11:19:57 +0200 Subject: [PATCH 08/14] added validation for short range interactions --- .../validators/virus/virus_validator.py | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index 60c4c52a..bdea535f 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -211,6 +211,23 @@ class VirusFormData(FormData): raise ValueError( f'The total number of occupants having short-range interactions ({self.short_range_occupants}) should be lower than the exposed population ({max_occupants_for_sr}).' ) + + # Validate short-range interactions interval + if self.short_range_option == "short_range_yes": + for interaction in self.short_range_interactions: + # Check if presence is within long-range exposure + presence = self.short_range_interval(interaction) + if (self.occupancy_format == 'dynamic'): + long_range_start = min(time_string_to_minutes(self.dynamic_infected_occupancy[0]['start_time']), + time_string_to_minutes(self.dynamic_exposed_occupancy[0]['start_time'])) + long_range_stop = max(time_string_to_minutes(self.dynamic_infected_occupancy[-1]['finish_time']), + time_string_to_minutes(self.dynamic_exposed_occupancy[-1]['finish_time'])) + else: + long_range_start = min(self.infected_start, self.exposed_start) + long_range_stop = max(self.infected_finish, self.exposed_finish) + if not (long_range_start/60 <= presence.present_times[0][0] <= long_range_stop/60 and + long_range_start/60 <= presence.present_times[0][-1] <= long_range_stop/60): + raise ValueError(f"Short-range interactions should be defined during simulation time. Got {interaction}") def initialize_room(self) -> models.Room: # Initializes room with volume either given directly or as product of area and height @@ -234,7 +251,7 @@ class VirusFormData(FormData): def build_mc_model(self) -> mc.ExposureModel: room = self.initialize_room() ventilation: models._VentilationBase = self.ventilation() - infected_population = self.infected_population() + infected_population: models.InfectedPopulation = self.infected_population() short_range = [] if self.short_range_option == "short_range_yes": for interaction in self.short_range_interactions: From 3c20ed03068ed53688a7efe431436cc453e6ddb9 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 7 Aug 2024 14:34:22 +0100 Subject: [PATCH 09/14] handled expected number of new cases calculation (including tests) --- .../src/caimira/calculator/models/models.py | 53 ++++++++++++------- .../calculator/report/virus_report_data.py | 32 +++++------ .../tests/models/test_dynamic_population.py | 32 +++++------ cern_caimira/tests/test_report_generator.py | 2 +- 4 files changed, 59 insertions(+), 60 deletions(-) diff --git a/caimira/src/caimira/calculator/models/models.py b/caimira/src/caimira/calculator/models/models.py index 79577b67..64c566fd 100644 --- a/caimira/src/caimira/calculator/models/models.py +++ b/caimira/src/caimira/calculator/models/models.py @@ -1867,43 +1867,56 @@ class ExposureModel: return 0 def expected_new_cases(self) -> _VectorisedFloat: - if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or - isinstance(self.exposed.number, IntPiecewiseConstant)): - raise NotImplementedError("Cannot compute expected new cases " - "with dynamic occupancy") - """ The expected_new_cases may provide one or two different outputs: 1) Long-range exposure: take the infection_probability and multiply by the occupants exposed to long-range. 2) Short- and long-range exposure: take the infection_probability of long-range multiplied by the occupants exposed to long-range only, plus the infection_probability of short- and long-range multiplied by the occupants exposed to short-range only. + + In the case dynamic occupancy is defined, the maximum number of exposed occupants during the course of the simulation will be considered. """ + exposed_occ: int = max(self.exposed.number.values) if isinstance(self.exposed.number, IntPiecewiseConstant) else self.exposed.number if self.short_range != (): - new_cases_long_range = nested_replace(self, {'short_range': (),}).infection_probability() * (self.exposed.number - self.exposed_to_short_range) + new_cases_long_range = nested_replace(self, {'short_range': [],}).infection_probability() * (exposed_occ - self.exposed_to_short_range) return (new_cases_long_range + (self.infection_probability() * self.exposed_to_short_range)) / 100 - return self.infection_probability() * self.exposed.number / 100 + return self.infection_probability() * exposed_occ / 100 def reproduction_number(self) -> _VectorisedFloat: """ The reproduction number can be thought of as the expected number of cases directly generated by one infected case in a population. + It handles the cases when dynamic occupancy for the infected population is defined. """ - if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or - isinstance(self.exposed.number, IntPiecewiseConstant)): - raise NotImplementedError("Cannot compute reproduction number " - "with dynamic occupancy") - if self.concentration_model.infected.number == 1: - return self.expected_new_cases() + infected_number = self.concentration_model.infected.number + if isinstance(infected_number, IntPiecewiseConstant): + # Handle case when infected number is dynamic + max_occ = max(infected_number.values) + if max_occ == 1: + return self.expected_new_cases() + else: + # Adjust to treat dynamic occupancy, limiting infected to 1 when present + inf_occ_values = [1 if occ > 0 else occ for occ in infected_number.values] + single_exposure_model = nested_replace( + self, { + 'concentration_model.infected.number.values': inf_occ_values + } + ) + return single_exposure_model.expected_new_cases() + + elif isinstance(infected_number, int): + # Handle case when infected number is a single integer + if infected_number == 1: + return self.expected_new_cases() - # Create an equivalent exposure model but with precisely - # one infected case. - single_exposure_model = nested_replace( - self, { - 'concentration_model.infected.number': 1} - ) + # Create an equivalent exposure model but with precisely + # one infected case. + single_exposure_model = nested_replace( + self, { + 'concentration_model.infected.number': 1} + ) - return single_exposure_model.expected_new_cases() + return single_exposure_model.expected_new_cases() diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index 29fddac6..6b7633d8 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -177,12 +177,6 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static": prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() else: prob_probabilistic_exposure = -1 - # Expected new cases - if (form.occupancy_format == "static"): - expected_new_cases = np.array(model.expected_new_cases()).mean() - else: - # With dynamic occupancy, the expected number of new cases feature is disabled. - expected_new_cases = -1 exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] @@ -213,7 +207,8 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable "prob_hist_count": list(prob_dist_count), "prob_hist_bins": list(prob_dist_bins), "prob_probabilistic_exposure": prob_probabilistic_exposure, - "expected_new_cases": expected_new_cases, + "expected_new_cases": np.array(model.expected_new_cases()).mean(), + "uncertainties_plot_src": uncertainties_plot_src, "CO2_concentrations": CO2_concentrations, "conditional_probability_data": conditional_probability_data, "uncertainties_plot_src": uncertainties_plot_src, @@ -406,8 +401,14 @@ def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, m scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_mc_model() else: - no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], - total_people=form.total_people - form.short_range_occupants) + # When dynamic occupancy is defined, the replace of total people is useless - the expected number of new cases is not calculated. + if form.occupancy_format == 'static': + no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], total_people=form.total_people - form.short_range_occupants) + elif form.occupancy_format == 'dynamic': + for occ in form.dynamic_exposed_occupancy: # Update the number of exposed people with long-range exposure + if occ['total_people'] > form.short_range_occupants: occ['total_people'] = max(0, occ['total_people'] - form.short_range_occupants) + no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], dynamic_exposed_occupancy=form.dynamic_exposed_occupancy) + scenarios['Base scenario without short-range interactions'] = no_short_range_alternative.build_mc_model() return scenarios @@ -417,7 +418,6 @@ def scenario_statistics( mc_model: mc.ExposureModel, sample_times: typing.List[float], compute_prob_exposure: bool, - compute_expected_new_cases: bool, ): model = mc_model.build_model( size=mc_model.data_registry.monte_carlo['sample_size']) @@ -425,16 +425,11 @@ def scenario_statistics( # It means we have data to calculate the total_probability_rule prob_probabilistic_exposure = model.total_probability_rule() else: - prob_probabilistic_exposure = -1 - - if (compute_expected_new_cases): - expected_new_cases = np.mean(model.expected_new_cases()) - else: - expected_new_cases = -1 + prob_probabilistic_exposure = -1 return { 'probability_of_infection': np.mean(model.infection_probability()), - 'expected_new_cases': expected_new_cases, + 'expected_new_cases': np.mean(model.expected_new_cases()), 'concentrations': [ np.mean(model.concentration(time)) for time in sample_times @@ -464,8 +459,6 @@ def comparison_report( compute_prob_exposure = True else: compute_prob_exposure = False - - compute_expected_new_cases = True if (form.occupancy_format == "static") else False with executor_factory() as executor: results = executor.map( @@ -473,7 +466,6 @@ def comparison_report( scenarios.values(), [report_data['times']] * len(scenarios), [compute_prob_exposure] * len(scenarios), - [compute_expected_new_cases] * len(scenarios), timeout=60, ) diff --git a/caimira/tests/models/test_dynamic_population.py b/caimira/tests/models/test_dynamic_population.py index d7de725b..8a28f93b 100644 --- a/caimira/tests/models/test_dynamic_population.py +++ b/caimira/tests/models/test_dynamic_population.py @@ -230,32 +230,26 @@ def test_dynamic_total_probability_rule( "(including incidence rate) with dynamic occupancy")): dynamic_population_exposure_model.total_probability_rule() + def test_dynamic_expected_new_cases( + full_exposure_model: models.ExposureModel, dynamic_infected_single_exposure_model: models.ExposureModel, dynamic_exposed_single_exposure_model: models.ExposureModel, dynamic_population_exposure_model: models.ExposureModel): - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " - "with dynamic occupancy")): - dynamic_infected_single_exposure_model.expected_new_cases() - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " - "with dynamic occupancy")): - dynamic_exposed_single_exposure_model.expected_new_cases() - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " - "with dynamic occupancy")): - dynamic_population_exposure_model.expected_new_cases() + base_expected_new_cases = full_exposure_model.expected_new_cases() + npt.assert_almost_equal(base_expected_new_cases, dynamic_infected_single_exposure_model.expected_new_cases()) + npt.assert_almost_equal(base_expected_new_cases, dynamic_exposed_single_exposure_model.expected_new_cases()) + npt.assert_almost_equal(base_expected_new_cases, dynamic_population_exposure_model.expected_new_cases()) + def test_dynamic_reproduction_number( + full_exposure_model: models.ExposureModel, dynamic_infected_single_exposure_model: models.ExposureModel, dynamic_exposed_single_exposure_model: models.ExposureModel, dynamic_population_exposure_model: models.ExposureModel): - - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " - "with dynamic occupancy")): - dynamic_infected_single_exposure_model.reproduction_number() - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " - "with dynamic occupancy")): - dynamic_exposed_single_exposure_model.reproduction_number() - with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " - "with dynamic occupancy")): - dynamic_population_exposure_model.reproduction_number() + + base_reproduction_number = full_exposure_model.reproduction_number() + npt.assert_almost_equal(base_reproduction_number, dynamic_infected_single_exposure_model.reproduction_number()) + npt.assert_almost_equal(base_reproduction_number, dynamic_exposed_single_exposure_model.reproduction_number()) + npt.assert_almost_equal(base_reproduction_number, dynamic_population_exposure_model.reproduction_number()) diff --git a/cern_caimira/tests/test_report_generator.py b/cern_caimira/tests/test_report_generator.py index 3e9026b7..df49442e 100644 --- a/cern_caimira/tests/test_report_generator.py +++ b/cern_caimira/tests/test_report_generator.py @@ -180,6 +180,6 @@ def test_static_vs_dynamic_occupancy_from_form(baseline_form_data, data_registry list(dynamic_occupancy_model.exposed.number.transition_times)) np.testing.assert_almost_equal(static_occupancy_report_data['prob_inf'], dynamic_occupancy_report_data['prob_inf'], 1) - assert dynamic_occupancy_report_data['expected_new_cases'] == -1 + np.testing.assert_almost_equal(static_occupancy_report_data['expected_new_cases'], dynamic_occupancy_report_data['expected_new_cases'], 1) assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == -1 \ No newline at end of file From e545d99190b7210fb0169a125d43b9674683ee07 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Tue, 3 Sep 2024 14:32:27 +0200 Subject: [PATCH 10/14] handled probabilistic exposure from review --- .../calculator/report/virus_report_data.py | 2 +- .../templates/base/calculator.report.html.j2 | 28 +++++++++++-------- cern_caimira/tests/test_report_generator.py | 2 +- 3 files changed, 18 insertions(+), 14 deletions(-) diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index 6b7633d8..84f313e2 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -176,7 +176,7 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable # Probabilistic exposure if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static": prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() - else: prob_probabilistic_exposure = -1 + else: prob_probabilistic_exposure = None exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] diff --git a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 index 0868683e..88bdf0b2 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 @@ -145,19 +145,23 @@ {% if form.exposure_option == "p_probabilistic_exposure" %}
{% endif %} diff --git a/cern_caimira/tests/test_report_generator.py b/cern_caimira/tests/test_report_generator.py index df49442e..a6a5a031 100644 --- a/cern_caimira/tests/test_report_generator.py +++ b/cern_caimira/tests/test_report_generator.py @@ -181,5 +181,5 @@ def test_static_vs_dynamic_occupancy_from_form(baseline_form_data, data_registry np.testing.assert_almost_equal(static_occupancy_report_data['prob_inf'], dynamic_occupancy_report_data['prob_inf'], 1) np.testing.assert_almost_equal(static_occupancy_report_data['expected_new_cases'], dynamic_occupancy_report_data['expected_new_cases'], 1) - assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == -1 + assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == None \ No newline at end of file From b92bbb6334d22bbef629c660a7c6868205e4e1a4 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 16 Sep 2024 14:48:46 +0200 Subject: [PATCH 11/14] changes after rebase from master --- .../src/caimira/calculator/models/models.py | 56 ++++++++----------- .../calculator/report/virus_report_data.py | 31 +++++----- .../validators/co2/co2_validator.py | 6 +- .../calculator/validators/form_validator.py | 35 ++++++------ .../validators/virus/virus_validator.py | 6 +- .../apps/calculator/test_model_generator.py | 32 ++++++++++- .../test_specific_model_generator.py | 2 - .../tests/models/test_dynamic_population.py | 28 ++++++---- .../templates/base/calculator.report.html.j2 | 30 ++++++---- .../templates/cern/calculator.report.html.j2 | 20 ++++--- cern_caimira/tests/test_report_generator.py | 2 +- 11 files changed, 147 insertions(+), 101 deletions(-) diff --git a/caimira/src/caimira/calculator/models/models.py b/caimira/src/caimira/calculator/models/models.py index 64c566fd..9af2a8cf 100644 --- a/caimira/src/caimira/calculator/models/models.py +++ b/caimira/src/caimira/calculator/models/models.py @@ -1873,50 +1873,42 @@ class ExposureModel: 2) Short- and long-range exposure: take the infection_probability of long-range multiplied by the occupants exposed to long-range only, plus the infection_probability of short- and long-range multiplied by the occupants exposed to short-range only. - In the case dynamic occupancy is defined, the maximum number of exposed occupants during the course of the simulation will be considered. + Currently disabled when dynamic occupancy is defined for the exposed population. """ - exposed_occ: int = max(self.exposed.number.values) if isinstance(self.exposed.number, IntPiecewiseConstant) else self.exposed.number + + if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or + isinstance(self.exposed.number, IntPiecewiseConstant)): + raise NotImplementedError("Cannot compute expected new cases " + "with dynamic occupancy") if self.short_range != (): - new_cases_long_range = nested_replace(self, {'short_range': [],}).infection_probability() * (exposed_occ - self.exposed_to_short_range) + new_cases_long_range = nested_replace(self, {'short_range': [],}).infection_probability() * (self.exposed.number - self.exposed_to_short_range) return (new_cases_long_range + (self.infection_probability() * self.exposed_to_short_range)) / 100 - return self.infection_probability() * exposed_occ / 100 + return self.infection_probability() * self.exposed.number / 100 def reproduction_number(self) -> _VectorisedFloat: """ The reproduction number can be thought of as the expected number of cases directly generated by one infected case in a population. - It handles the cases when dynamic occupancy for the infected population is defined. + Currently disabled when dynamic occupancy is defined for both the infected and exposed population. """ - infected_number = self.concentration_model.infected.number - if isinstance(infected_number, IntPiecewiseConstant): - # Handle case when infected number is dynamic - max_occ = max(infected_number.values) - if max_occ == 1: - return self.expected_new_cases() - else: - # Adjust to treat dynamic occupancy, limiting infected to 1 when present - inf_occ_values = [1 if occ > 0 else occ for occ in infected_number.values] - single_exposure_model = nested_replace( - self, { - 'concentration_model.infected.number.values': inf_occ_values - } - ) - return single_exposure_model.expected_new_cases() - - elif isinstance(infected_number, int): - # Handle case when infected number is a single integer - if infected_number == 1: - return self.expected_new_cases() + if (isinstance(self.concentration_model.infected.number, IntPiecewiseConstant) or + isinstance(self.exposed.number, IntPiecewiseConstant)): + raise NotImplementedError("Cannot compute reproduction number " + "with dynamic occupancy") - # Create an equivalent exposure model but with precisely - # one infected case. - single_exposure_model = nested_replace( - self, { - 'concentration_model.infected.number': 1} - ) + if self.concentration_model.infected.number == 1: + return self.expected_new_cases() - return single_exposure_model.expected_new_cases() + # Create an equivalent exposure model but with precisely + # one infected case. + single_exposure_model = nested_replace( + self, { + 'concentration_model.infected.number': 1} + ) + + return single_exposure_model.expected_new_cases() + \ No newline at end of file diff --git a/caimira/src/caimira/calculator/report/virus_report_data.py b/caimira/src/caimira/calculator/report/virus_report_data.py index 84f313e2..6c4d62e6 100644 --- a/caimira/src/caimira/calculator/report/virus_report_data.py +++ b/caimira/src/caimira/calculator/report/virus_report_data.py @@ -173,10 +173,13 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable prob = np.array(model.infection_probability()) prob_dist_count, prob_dist_bins = np.histogram(prob/100, bins=100, density=True) - # Probabilistic exposure - if form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static": - prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() - else: prob_probabilistic_exposure = None + # Probabilistic exposure and expected new cases (only for static occupancy) + prob_probabilistic_exposure = None + expected_new_cases = None + if form.occupancy_format == "static": + if form.exposure_option == "p_probabilistic_exposure": + prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean() + expected_new_cases = np.array(model.expected_new_cases()).mean() exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] @@ -207,11 +210,10 @@ def calculate_report_data(form: VirusFormData, executor_factory: typing.Callable "prob_hist_count": list(prob_dist_count), "prob_hist_bins": list(prob_dist_bins), "prob_probabilistic_exposure": prob_probabilistic_exposure, - "expected_new_cases": np.array(model.expected_new_cases()).mean(), + "expected_new_cases": expected_new_cases, "uncertainties_plot_src": uncertainties_plot_src, "CO2_concentrations": CO2_concentrations, "conditional_probability_data": conditional_probability_data, - "uncertainties_plot_src": uncertainties_plot_src, } @@ -417,24 +419,20 @@ def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, m def scenario_statistics( mc_model: mc.ExposureModel, sample_times: typing.List[float], + static_occupancy: bool, compute_prob_exposure: bool, ): model = mc_model.build_model( size=mc_model.data_registry.monte_carlo['sample_size']) - if (compute_prob_exposure): - # It means we have data to calculate the total_probability_rule - prob_probabilistic_exposure = model.total_probability_rule() - else: - prob_probabilistic_exposure = -1 return { 'probability_of_infection': np.mean(model.infection_probability()), - 'expected_new_cases': np.mean(model.expected_new_cases()), + 'expected_new_cases': np.mean(model.expected_new_cases()) if static_occupancy else None, 'concentrations': [ np.mean(model.concentration(time)) for time in sample_times ], - 'prob_probabilistic_exposure': prob_probabilistic_exposure, + 'prob_probabilistic_exposure': model.total_probability_rule() if compute_prob_exposure else None, } @@ -455,16 +453,15 @@ def comparison_report( else: statistics = {} - if (form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure" and form.occupancy_format == "static"): - compute_prob_exposure = True - else: - compute_prob_exposure = False + static_occupancy = form.occupancy_format == "static" + compute_prob_exposure = form.short_range_option == "short_range_yes" and form.exposure_option == "p_probabilistic_exposure" and static_occupancy with executor_factory() as executor: results = executor.map( scenario_statistics, scenarios.values(), [report_data['times']] * len(scenarios), + [static_occupancy] * len(scenarios), [compute_prob_exposure] * len(scenarios), timeout=60, ) diff --git a/caimira/src/caimira/calculator/validators/co2/co2_validator.py b/caimira/src/caimira/calculator/validators/co2/co2_validator.py index 659bd27c..941f8b75 100644 --- a/caimira/src/caimira/calculator/validators/co2/co2_validator.py +++ b/caimira/src/caimira/calculator/validators/co2/co2_validator.py @@ -201,11 +201,13 @@ class CO2FormData(FormData): # intervals and number of people are dynamic. Activity type is not needed. if self.occupancy_format == 'dynamic': if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: - infected_people, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + infected_people = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + infected_presence = None else: raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_infected_occupancy}".') if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: - exposed_people, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + exposed_people = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + exposed_presence = None else: raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_exposed_occupancy}".') else: diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 281647b5..70e89e58 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -19,7 +19,7 @@ minutes_since_midnight = typing.NewType('minutes_since_midnight', int) @dataclasses.dataclass class FormData: - specific_breaks: dict + # Static occupancy inputs exposed_coffee_break_option: str exposed_coffee_duration: int exposed_finish: minutes_since_midnight @@ -27,19 +27,23 @@ class FormData: exposed_lunch_option: bool exposed_lunch_start: minutes_since_midnight exposed_start: minutes_since_midnight - infected_coffee_break_option: str - infected_coffee_duration: int + infected_coffee_break_option: str #Used if infected_dont_have_breaks_with_exposed + infected_coffee_duration: int #Used if infected_dont_have_breaks_with_exposed infected_dont_have_breaks_with_exposed: bool infected_finish: minutes_since_midnight - infected_lunch_finish: minutes_since_midnight # Used if infected_dont_have_breaks_with_exposed - infected_lunch_option: bool # Used if infected_dont_have_breaks_with_exposed - infected_lunch_start: minutes_since_midnight # Used if infected_dont_have_breaks_with_exposed - infected_people: int - dynamic_infected_occupancy: list + infected_lunch_finish: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed + infected_lunch_option: bool #Used if infected_dont_have_breaks_with_exposed + infected_lunch_start: minutes_since_midnight #Used if infected_dont_have_breaks_with_exposed infected_start: minutes_since_midnight + infected_people: int + occupancy_format: str room_volume: float + specific_breaks: dict total_people: int + + # Dynamic occupancy inputs dynamic_exposed_occupancy: list + dynamic_infected_occupancy: list data_registry: DataRegistry @@ -385,24 +389,24 @@ class FormData: for occupancy in dynamic_occupancy: # Check if each occupancy entry is a dictionary if not isinstance(occupancy, typing.Dict): - raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}."') + raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}".') # Check for required keys in each occupancy entry dict_keys = list(occupancy.keys()) if "total_people" not in dict_keys: - raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys[0]}".') + raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys}".') else: value = occupancy["total_people"] # Check if the value is a non-negative integer if not isinstance(value, int): - raise ValueError(f"Total number of people should be integer. Got {value}.") + raise ValueError(f'Total number of people should be integer. Got "{type(value)}".') elif not value >= 0: - raise ValueError(f"Total number of people should be non-negative. Got {value}.") + raise ValueError(f'Total number of people should be non-negative. Got "{value}".') if "start_time" not in dict_keys: - raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys[1]}".') + raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys}".') if "finish_time" not in dict_keys: - raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys[2]}".') + raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys}".') # Validate time format for start_time and finish_time for time_key in ["start_time", "finish_time"]: @@ -427,8 +431,7 @@ class FormData: transition_times=tuple(unique_transition_times_sorted), values=tuple(values) ) - population_presence: typing.Union[None, models.Interval] = None - return population_occupancy, population_presence + return population_occupancy def _hours2timestring(hours: float): diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index bdea535f..ea3642c8 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -470,7 +470,8 @@ class VirusFormData(FormData): if isinstance(self.dynamic_infected_occupancy, typing.List) and len(self.dynamic_infected_occupancy) > 0: # If dynamic occupancy is defined, the generator will parse and validate the # respective input to a format readable by the model - `IntPiecewiseConstant`. - infected_occupancy, infected_presence = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + infected_occupancy = self.generate_dynamic_occupancy(self.dynamic_infected_occupancy) + infected_presence = None else: raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_infected_occupancy}".') else: @@ -515,7 +516,8 @@ class VirusFormData(FormData): if isinstance(self.dynamic_exposed_occupancy, typing.List) and len(self.dynamic_exposed_occupancy) > 0: # If dynamic occupancy is defined, the generator will parse and validate the # respective input to a format readable by the model - IntPiecewiseConstant. - exposed_occupancy, exposed_presence = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + exposed_occupancy = self.generate_dynamic_occupancy(self.dynamic_exposed_occupancy) + exposed_presence = None else: raise TypeError(f'If dynamic occupancy is selected, a populated list of occupancy intervals is expected. Got "{self.dynamic_exposed_occupancy}".') else: diff --git a/caimira/tests/apps/calculator/test_model_generator.py b/caimira/tests/apps/calculator/test_model_generator.py index 435ecd39..2aca9c3e 100644 --- a/caimira/tests/apps/calculator/test_model_generator.py +++ b/caimira/tests/apps/calculator/test_model_generator.py @@ -1,5 +1,5 @@ import dataclasses -import typing +import re import numpy as np import numpy.testing as npt @@ -588,3 +588,33 @@ def test_form_timezone(baseline_form_data, data_registry, longitude, latitude, m name, offset = form.tz_name_and_utc_offset() assert name == expected_tz_name assert offset == expected_offset + + +@pytest.mark.parametrize( + ["dynamic_occupancy_input", "error"], + [ + [[["total_people", 10, "start_time", "10:00", "finish_time", "11:00"]], "Each occupancy entry should be in a dictionary format. Got \"\"."], + [[{"tal_people": 10, "start_time": "10:00", "finish_time": "11:00"}], "Unable to fetch \"total_people\" key. Got \"['tal_people', 'start_time', 'finish_time']\"."], + [[{"total_people": 10, "art_time": "10:00", "finish_time": "11:00"}], "Unable to fetch \"start_time\" key. Got \"['total_people', 'art_time', 'finish_time']\"."], + [[{"total_people": 10, "start_time": "10:00", "ish_time": "11:00"}], "Unable to fetch \"finish_time\" key. Got \"['total_people', 'start_time', 'ish_time']\"."], + [[{"total_people": 10, "start_time": "10", "finish_time": "11:00"}], "Wrong time format - \"HH:MM\". Got \"10\"."], + [[{"total_people": 10, "start_time": "10:00", "finish_time": "11"}], "Wrong time format - \"HH:MM\". Got \"11\"."], + ] +) +def test_dynamic_occupancy_structure(dynamic_occupancy_input, error, baseline_form: virus_validator.VirusFormData): + with pytest.raises(TypeError, match=re.escape(error)): + baseline_form.generate_dynamic_occupancy(dynamic_occupancy_input) + + +@pytest.mark.parametrize( + ["dynamic_occupancy_input", "error"], + [ + [[{"total_people": "10", "start_time": "10:00", "finish_time": "11:00"}], "Total number of people should be integer. Got \"\"."], + [[{"total_people": 9.8, "start_time": "10:00", "finish_time": "11:00"}], "Total number of people should be integer. Got \"\"."], + [[{"total_people": [10], "start_time": "10:00", "finish_time": "11:00"}], "Total number of people should be integer. Got \"\"."], + [[{"total_people": -1, "start_time": "10:00", "finish_time": "11:00"}], "Total number of people should be non-negative. Got \"-1\"."], + ] +) +def test_dynamic_occupancy_total_people(dynamic_occupancy_input, error, baseline_form: virus_validator.VirusFormData): + with pytest.raises(ValueError, match=re.escape(error)): + baseline_form.generate_dynamic_occupancy(dynamic_occupancy_input) diff --git a/caimira/tests/apps/calculator/test_specific_model_generator.py b/caimira/tests/apps/calculator/test_specific_model_generator.py index 6945a2c1..513d908c 100644 --- a/caimira/tests/apps/calculator/test_specific_model_generator.py +++ b/caimira/tests/apps/calculator/test_specific_model_generator.py @@ -1,5 +1,3 @@ -from typing import Type -import numpy as np import pytest from caimira.calculator.validators.virus import virus_validator diff --git a/caimira/tests/models/test_dynamic_population.py b/caimira/tests/models/test_dynamic_population.py index 8a28f93b..a6377094 100644 --- a/caimira/tests/models/test_dynamic_population.py +++ b/caimira/tests/models/test_dynamic_population.py @@ -232,24 +232,32 @@ def test_dynamic_total_probability_rule( def test_dynamic_expected_new_cases( - full_exposure_model: models.ExposureModel, dynamic_infected_single_exposure_model: models.ExposureModel, dynamic_exposed_single_exposure_model: models.ExposureModel, dynamic_population_exposure_model: models.ExposureModel): - base_expected_new_cases = full_exposure_model.expected_new_cases() - npt.assert_almost_equal(base_expected_new_cases, dynamic_infected_single_exposure_model.expected_new_cases()) - npt.assert_almost_equal(base_expected_new_cases, dynamic_exposed_single_exposure_model.expected_new_cases()) - npt.assert_almost_equal(base_expected_new_cases, dynamic_population_exposure_model.expected_new_cases()) + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " + "with dynamic occupancy")): + dynamic_infected_single_exposure_model.expected_new_cases() + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " + "with dynamic occupancy")): + dynamic_exposed_single_exposure_model.expected_new_cases() + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute expected new cases " + "with dynamic occupancy")): + dynamic_population_exposure_model.expected_new_cases() def test_dynamic_reproduction_number( - full_exposure_model: models.ExposureModel, dynamic_infected_single_exposure_model: models.ExposureModel, dynamic_exposed_single_exposure_model: models.ExposureModel, dynamic_population_exposure_model: models.ExposureModel): - base_reproduction_number = full_exposure_model.reproduction_number() - npt.assert_almost_equal(base_reproduction_number, dynamic_infected_single_exposure_model.reproduction_number()) - npt.assert_almost_equal(base_reproduction_number, dynamic_exposed_single_exposure_model.reproduction_number()) - npt.assert_almost_equal(base_reproduction_number, dynamic_population_exposure_model.reproduction_number()) + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " + "with dynamic occupancy")): + dynamic_infected_single_exposure_model.reproduction_number() + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " + "with dynamic occupancy")): + dynamic_exposed_single_exposure_model.reproduction_number() + with pytest.raises(NotImplementedError, match=re.escape("Cannot compute reproduction number " + "with dynamic occupancy")): + dynamic_population_exposure_model.reproduction_number() diff --git a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 index 88bdf0b2..fadd5e79 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/base/calculator.report.html.j2 @@ -104,7 +104,7 @@
{% endblock long_range_warning_animation %} -
Expected new cases: {{ long_range_expected_cases | float_format }}
+ {% if form.occupancy_format == "static" %}
Expected new cases: {{ long_range_expected_cases | float_format }}
{% endif %}
{% if form.short_range_option == "short_range_yes" %} @@ -126,19 +126,27 @@ {% endblock warning_animation %} -
Expected new cases: {{ expected_new_cases | float_format }}
+ {% if form.occupancy_format == "static" %} +
Expected new cases: {{ expected_new_cases | float_format }}
+ {% endif %} {% endif %}
{% block report_summary %}
{% if form.short_range_option == "short_range_yes" %}
{% endif %} {% block probabilistic_exposure_probability %} @@ -302,7 +310,7 @@ Scenario P(I) - Expected new cases + {% if form.occupancy_format == "static" %}Expected new cases{% endif %} @@ -310,7 +318,7 @@ {{ scenario_name }} {{ scenario_stats.probability_of_infection | non_zero_percentage }} - {{ scenario_stats.expected_new_cases | float_format }} + {% if form.occupancy_format == "static" %}{{ scenario_stats.expected_new_cases | float_format }}{% endif %} {% endfor %} @@ -630,11 +638,11 @@
    {% for interaction in form.short_range_interactions %}
  • Interaction no. {{ loop.index }}: -
      -
    • Expiratory activity: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }}
      • -
    • Start time: {{ interaction.start_time }}
      • -
    • Duration: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}
      • -
    +
      +
    • Expiratory activity: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }}
      • +
    • Start time: {{ interaction.start_time }}
      • +
    • Duration: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}
      • +
    • {% endfor %}
diff --git a/cern_caimira/src/cern_caimira/apps/templates/cern/calculator.report.html.j2 b/cern_caimira/src/cern_caimira/apps/templates/cern/calculator.report.html.j2 index 701c2ab0..4248b65b 100644 --- a/cern_caimira/src/cern_caimira/apps/templates/cern/calculator.report.html.j2 +++ b/cern_caimira/src/cern_caimira/apps/templates/cern/calculator.report.html.j2 @@ -11,7 +11,7 @@ {% set long_range_prob_inf = prob_inf %} {% endif %} -{% if ((long_range_prob_inf > red_prob_lim) or (expected_new_cases >= 1)) %} +{% if ((long_range_prob_inf > red_prob_lim) or (form.occupancy_format == "static" and expected_new_cases >= 1)) %} {% set long_range_scale_warning = 'red' %} {% set long_range_warning_color= 'bg-danger' %} {% elif (orange_prob_lim <= long_range_prob_inf <= red_prob_lim) %} @@ -22,7 +22,7 @@ {% set long_range_warning_color = 'bg-success' %} {% endif %} -{% if ((prob_inf > red_prob_lim) or (expected_new_cases >= 1)) %} {% set scale_warning = 'red' %} +{% if ((prob_inf > red_prob_lim) or (form.occupancy_format == "static" and expected_new_cases >= 1)) %} {% set scale_warning = 'red' %} {% elif (orange_prob_lim <= prob_inf <= red_prob_lim) %} {% set scale_warning = 'orange' %} {% else %} {% set scale_warning = 'green' %} {% endif %} @@ -70,7 +70,10 @@ {% if form.short_range_option == "short_range_yes" %}
@@ -84,7 +87,10 @@ {% endif %} @@ -137,12 +143,12 @@ Scenario P(i) - Expected new cases + {% if form.occupancy_format == "static" %}Expected new cases{% endif %} {% for scenario_name, scenario_stats in alternative_scenarios.stats.items() %} - {%if (( scenario_stats.probability_of_infection > red_prob_lim) or (scenario_stats.expected_new_cases >= 1)) %} + {%if (( scenario_stats.probability_of_infection > red_prob_lim) or (form.occupancy_format == "static" and scenario_stats.expected_new_cases >= 1)) %} {% elif (orange_prob_lim <= scenario_stats.probability_of_infection <= red_prob_lim) %} @@ -151,7 +157,7 @@ {% endif%} {{ scenario_name }} {{ scenario_stats.probability_of_infection | non_zero_percentage }} - {{ scenario_stats.expected_new_cases | float_format }} + {% if form.occupancy_format == "static" %}{{ scenario_stats.expected_new_cases | float_format }}{% endif %} {% endfor %} diff --git a/cern_caimira/tests/test_report_generator.py b/cern_caimira/tests/test_report_generator.py index a6a5a031..f15833a2 100644 --- a/cern_caimira/tests/test_report_generator.py +++ b/cern_caimira/tests/test_report_generator.py @@ -180,6 +180,6 @@ def test_static_vs_dynamic_occupancy_from_form(baseline_form_data, data_registry list(dynamic_occupancy_model.exposed.number.transition_times)) np.testing.assert_almost_equal(static_occupancy_report_data['prob_inf'], dynamic_occupancy_report_data['prob_inf'], 1) - np.testing.assert_almost_equal(static_occupancy_report_data['expected_new_cases'], dynamic_occupancy_report_data['expected_new_cases'], 1) + assert dynamic_occupancy_report_data['expected_new_cases'] == None assert dynamic_occupancy_report_data['prob_probabilistic_exposure'] == None \ No newline at end of file From bfa20d5e06734b2d06b284a0ef119c980d0b6e0f Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 16 Sep 2024 16:22:54 +0200 Subject: [PATCH 12/14] updated validation method (and extra test) --- .../validators/co2/co2_validator.py | 6 +- .../calculator/validators/form_validator.py | 195 +++++++++--------- .../validators/virus/virus_validator.py | 6 +- .../apps/calculator/test_model_generator.py | 24 ++- 4 files changed, 126 insertions(+), 105 deletions(-) diff --git a/caimira/src/caimira/calculator/validators/co2/co2_validator.py b/caimira/src/caimira/calculator/validators/co2/co2_validator.py index 941f8b75..36ed80fa 100644 --- a/caimira/src/caimira/calculator/validators/co2/co2_validator.py +++ b/caimira/src/caimira/calculator/validators/co2/co2_validator.py @@ -63,10 +63,8 @@ class CO2FormData(FormData): self.data_registry = DataRegistry() def validate(self): - # Validate population parameters when static occupancy is defined. - # Dynamic population is validated in the generate_dynamic_occupancy method. - if self.occupancy_format == 'static': - self.validate_population_parameters() + # Validate population parameters + self.validate_population_parameters() # Validate room capacity if self.room_capacity: diff --git a/caimira/src/caimira/calculator/validators/form_validator.py b/caimira/src/caimira/calculator/validators/form_validator.py index 70e89e58..074ebf20 100644 --- a/caimira/src/caimira/calculator/validators/form_validator.py +++ b/caimira/src/caimira/calculator/validators/form_validator.py @@ -98,76 +98,110 @@ class FormData: return form_dict def validate_population_parameters(self): - # Validate number of infected <= number of total people - if self.infected_people >= self.total_people: - raise ValueError( - 'Number of infected people cannot be greater or equal to the number of total people.') - - # Validate time intervals selected by user - time_intervals = [ - ['exposed_start', 'exposed_finish'], - ['infected_start', 'infected_finish'], - ] - if self.exposed_lunch_option: - time_intervals.append( - ['exposed_lunch_start', 'exposed_lunch_finish']) - if self.infected_dont_have_breaks_with_exposed and self.infected_lunch_option: - time_intervals.append( - ['infected_lunch_start', 'infected_lunch_finish']) - - for start_name, end_name in time_intervals: - start = getattr(self, start_name) - end = getattr(self, end_name) - if start > end: + # Static occupancy is defined. + if self.occupancy_format == 'static': + # Validate number of infected <= number of total people + if self.infected_people >= self.total_people: raise ValueError( - f"{start_name} must be less than {end_name}. Got {start} and {end}.") + 'Number of infected people cannot be greater or equal to the number of total people.') - def validate_lunch(start, finish): - lunch_start = getattr(self, f'{population}_lunch_start') - lunch_finish = getattr(self, f'{population}_lunch_finish') - return (start <= lunch_start <= finish and - start <= lunch_finish <= finish) + # Validate time intervals selected by user + time_intervals = [ + ['exposed_start', 'exposed_finish'], + ['infected_start', 'infected_finish'], + ] + if self.exposed_lunch_option: + time_intervals.append( + ['exposed_lunch_start', 'exposed_lunch_finish']) + if self.infected_dont_have_breaks_with_exposed and self.infected_lunch_option: + time_intervals.append( + ['infected_lunch_start', 'infected_lunch_finish']) - def get_lunch_mins(population): - lunch_mins = 0 - if getattr(self, f'{population}_lunch_option'): - lunch_mins = getattr( - self, f'{population}_lunch_finish') - getattr(self, f'{population}_lunch_start') - return lunch_mins - - def get_coffee_mins(population): - coffee_mins = 0 - if getattr(self, f'{population}_coffee_break_option') != 'coffee_break_0': - coffee_mins = COFFEE_OPTIONS_INT[getattr( - self, f'{population}_coffee_break_option')] * getattr(self, f'{population}_coffee_duration') - return coffee_mins - - def get_activity_mins(population): - return getattr(self, f'{population}_finish') - getattr(self, f'{population}_start') - - populations = [ - 'exposed', 'infected'] if self.infected_dont_have_breaks_with_exposed else ['exposed'] - for population in populations: - # Validate lunch time within the activity times. - if (getattr(self, f'{population}_lunch_option') and - not validate_lunch(getattr(self, f'{population}_start'), getattr( - self, f'{population}_finish')) - ): - raise ValueError( - f"{population} lunch break must be within presence times." - ) - - # Length of breaks < length of activity - if (get_lunch_mins(population) + get_coffee_mins(population)) >= get_activity_mins(population): - raise ValueError( - f"Length of breaks >= Length of {population} presence." - ) - - for attr_name, valid_set in [('exposed_coffee_break_option', COFFEE_OPTIONS_INT), - ('infected_coffee_break_option', COFFEE_OPTIONS_INT)]: - if getattr(self, attr_name) not in valid_set: + for start_name, end_name in time_intervals: + start = getattr(self, start_name) + end = getattr(self, end_name) + if start > end: raise ValueError( - f"{getattr(self, attr_name)} is not a valid value for {attr_name}") + f"{start_name} must be less than {end_name}. Got {start} and {end}.") + + def validate_lunch(start, finish): + lunch_start = getattr(self, f'{population}_lunch_start') + lunch_finish = getattr(self, f'{population}_lunch_finish') + return (start <= lunch_start <= finish and + start <= lunch_finish <= finish) + + def get_lunch_mins(population): + lunch_mins = 0 + if getattr(self, f'{population}_lunch_option'): + lunch_mins = getattr( + self, f'{population}_lunch_finish') - getattr(self, f'{population}_lunch_start') + return lunch_mins + + def get_coffee_mins(population): + coffee_mins = 0 + if getattr(self, f'{population}_coffee_break_option') != 'coffee_break_0': + coffee_mins = COFFEE_OPTIONS_INT[getattr( + self, f'{population}_coffee_break_option')] * getattr(self, f'{population}_coffee_duration') + return coffee_mins + + def get_activity_mins(population): + return getattr(self, f'{population}_finish') - getattr(self, f'{population}_start') + + populations = [ + 'exposed', 'infected'] if self.infected_dont_have_breaks_with_exposed else ['exposed'] + for population in populations: + # Validate lunch time within the activity times. + if (getattr(self, f'{population}_lunch_option') and + not validate_lunch(getattr(self, f'{population}_start'), getattr( + self, f'{population}_finish')) + ): + raise ValueError( + f"{population} lunch break must be within presence times." + ) + + # Length of breaks < length of activity + if (get_lunch_mins(population) + get_coffee_mins(population)) >= get_activity_mins(population): + raise ValueError( + f"Length of breaks >= Length of {population} presence." + ) + + for attr_name, valid_set in [('exposed_coffee_break_option', COFFEE_OPTIONS_INT), + ('infected_coffee_break_option', COFFEE_OPTIONS_INT)]: + if getattr(self, attr_name) not in valid_set: + raise ValueError( + f"{getattr(self, attr_name)} is not a valid value for {attr_name}") + # Dynamic occupancy is defined. + elif self.occupancy_format == 'dynamic': + for dynamic_format in (self.dynamic_infected_occupancy, self.dynamic_exposed_occupancy): + for occupancy in dynamic_format: + # Check if each occupancy entry is a dictionary + if not isinstance(occupancy, typing.Dict): + raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}".') + + # Check for required keys in each occupancy entry + dict_keys = list(occupancy.keys()) + if "total_people" not in dict_keys: + raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys}".') + else: + value = occupancy["total_people"] + # Check if the value is a non-negative integer + if not isinstance(value, int): + raise ValueError(f'Total number of people should be integer. Got "{type(value)}".') + elif not value >= 0: + raise ValueError(f'Total number of people should be non-negative. Got "{value}".') + + if "start_time" not in dict_keys: + raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys}".') + if "finish_time" not in dict_keys: + raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys}".') + + # Validate time format for start_time and finish_time + for time_key in ["start_time", "finish_time"]: + time = occupancy[time_key] + if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): + raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') + else: + raise ValueError(f"'{self.occupancy_format}' is not a valid value for 'self.occupancy_format'. Accepted values are 'static' or 'dynamic'.") def validate(self): raise NotImplementedError("Subclass must implement") @@ -385,35 +419,6 @@ class FormData: ) def generate_dynamic_occupancy(self, dynamic_occupancy: typing.List[typing.Dict[str, typing.Any]]): - ##### Data format validation ##### - for occupancy in dynamic_occupancy: - # Check if each occupancy entry is a dictionary - if not isinstance(occupancy, typing.Dict): - raise TypeError(f'Each occupancy entry should be in a dictionary format. Got "{type(occupancy)}".') - - # Check for required keys in each occupancy entry - dict_keys = list(occupancy.keys()) - if "total_people" not in dict_keys: - raise TypeError(f'Unable to fetch "total_people" key. Got "{dict_keys}".') - else: - value = occupancy["total_people"] - # Check if the value is a non-negative integer - if not isinstance(value, int): - raise ValueError(f'Total number of people should be integer. Got "{type(value)}".') - elif not value >= 0: - raise ValueError(f'Total number of people should be non-negative. Got "{value}".') - - if "start_time" not in dict_keys: - raise TypeError(f'Unable to fetch "start_time" key. Got "{dict_keys}".') - if "finish_time" not in dict_keys: - raise TypeError(f'Unable to fetch "finish_time" key. Got "{dict_keys}".') - - # Validate time format for start_time and finish_time - for time_key in ["start_time", "finish_time"]: - time = occupancy[time_key] - if not re.compile("^(2[0-3]|[01]?[0-9]):([0-5]?[0-9])$").match(time): - raise TypeError(f'Wrong time format - "HH:MM". Got "{time}".') - transition_times = [] values = [] for occupancy in dynamic_occupancy: diff --git a/caimira/src/caimira/calculator/validators/virus/virus_validator.py b/caimira/src/caimira/calculator/validators/virus/virus_validator.py index ea3642c8..ca491b7f 100644 --- a/caimira/src/caimira/calculator/validators/virus/virus_validator.py +++ b/caimira/src/caimira/calculator/validators/virus/virus_validator.py @@ -73,10 +73,8 @@ class VirusFormData(FormData): _DEFAULTS: typing.ClassVar[typing.Dict[str, typing.Any]] = DEFAULTS def validate(self): - # Validate population parameters when static occupancy is defined. - # Dynamic population is validated in the generate_dynamic_occupancy method. - if self.occupancy_format == 'static': - self.validate_population_parameters() + # Validate population parameters + self.validate_population_parameters() validation_tuples = [('activity_type', self.data_registry.population_scenario_activity.keys()), ('mechanical_ventilation_type', diff --git a/caimira/tests/apps/calculator/test_model_generator.py b/caimira/tests/apps/calculator/test_model_generator.py index 2aca9c3e..5feb19ef 100644 --- a/caimira/tests/apps/calculator/test_model_generator.py +++ b/caimira/tests/apps/calculator/test_model_generator.py @@ -590,6 +590,20 @@ def test_form_timezone(baseline_form_data, data_registry, longitude, latitude, m assert offset == expected_offset +@pytest.mark.parametrize( + ["occupancy_format_input", "error"], + [ + ['dynamc', "'dynamc' is not a valid value for 'self.occupancy_format'. Accepted values are 'static' or 'dynamic'.",], + ['stact', "'stact' is not a valid value for 'self.occupancy_format'. Accepted values are 'static' or 'dynamic'.",], + ['random', "'random' is not a valid value for 'self.occupancy_format'. Accepted values are 'static' or 'dynamic'.",] + ] +) +def test_dynamic_format_input(occupancy_format_input, error, baseline_form: virus_validator.VirusFormData): + baseline_form.occupancy_format = occupancy_format_input + with pytest.raises(ValueError, match=re.escape(error)): + baseline_form.validate() + + @pytest.mark.parametrize( ["dynamic_occupancy_input", "error"], [ @@ -602,8 +616,11 @@ def test_form_timezone(baseline_form_data, data_registry, longitude, latitude, m ] ) def test_dynamic_occupancy_structure(dynamic_occupancy_input, error, baseline_form: virus_validator.VirusFormData): + baseline_form.occupancy_format = "dynamic" + baseline_form.dynamic_infected_occupancy = dynamic_occupancy_input + baseline_form.dynamic_exposed_occupancy = dynamic_occupancy_input with pytest.raises(TypeError, match=re.escape(error)): - baseline_form.generate_dynamic_occupancy(dynamic_occupancy_input) + baseline_form.validate() @pytest.mark.parametrize( @@ -616,5 +633,8 @@ def test_dynamic_occupancy_structure(dynamic_occupancy_input, error, baseline_fo ] ) def test_dynamic_occupancy_total_people(dynamic_occupancy_input, error, baseline_form: virus_validator.VirusFormData): + baseline_form.occupancy_format = "dynamic" + baseline_form.dynamic_infected_occupancy = dynamic_occupancy_input + baseline_form.dynamic_exposed_occupancy = dynamic_occupancy_input with pytest.raises(ValueError, match=re.escape(error)): - baseline_form.generate_dynamic_occupancy(dynamic_occupancy_input) + baseline_form.validate() From f7a4b32da199671edfc71c420e13c00d249c26e9 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Mon, 16 Sep 2024 16:23:05 +0200 Subject: [PATCH 13/14] version update --- caimira/pyproject.toml | 2 +- cern_caimira/pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/caimira/pyproject.toml b/caimira/pyproject.toml index b442e11f..bd15d9da 100644 --- a/caimira/pyproject.toml +++ b/caimira/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "caimira" -version = "4.17.0a1" +version = "4.17.1a1" description = "CAiMIRA - CERN Airborne Model for Indoor Risk Assessment" license = { text = "Apache-2.0" } authors = [ diff --git a/cern_caimira/pyproject.toml b/cern_caimira/pyproject.toml index 98d101bd..8eedd26d 100644 --- a/cern_caimira/pyproject.toml +++ b/cern_caimira/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "cern-caimira" -version = "4.17.0a1" +version = "4.17.1a1" description = "CAiMIRA - CERN Airborne Model for Indoor Risk Assessment" license = { text = "Apache-2.0" } authors = [ From 492587b8b339d6ff92d66a2ee113b6e5d0c94ea6 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Thu, 19 Sep 2024 10:44:19 +0200 Subject: [PATCH 14/14] updated version to 4.17.0a2 --- caimira/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/caimira/pyproject.toml b/caimira/pyproject.toml index bd15d9da..93d1f1e4 100644 --- a/caimira/pyproject.toml +++ b/caimira/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "caimira" -version = "4.17.1a1" +version = "4.17.0a2" description = "CAiMIRA - CERN Airborne Model for Indoor Risk Assessment" license = { text = "Apache-2.0" } authors = [