Add equipment to copd, epilepsy and cancer modules (#1706)

* Add comprehensive equipment to disease modules with facility-level dependencies

- Cancer modules (breast, prostate, bladder, oesophageal, other adult cancers):
  * Added facility-level dependent equipment based on column H specifications
  * Equipment includes imaging (X-ray, ultrasound), laboratory analysis, and cancer-specific tools
  * Probabilities vary by facility level (1a=community, 1b+=hospitals)

- COPD module:
  * Added moderate exacerbation treatment HSI with respiratory equipment
  * Incentive spirometers (100% availability) and blood gas analyzers (facility-dependent)
  * Enhanced severe exacerbation equipment with respiratory support tools

- Epilepsy module:
  * Added comprehensive rehabilitation equipment for severe epilepsy cases
  * Pediatric-specific equipment for children with epilepsy
  * Assessment tools, mobility aids, and physiotherapy equipment

- Fixed equipment codes:
  * 454  202 (X-ray machine)
  * 453  161 (Ultrasound scanning machine)

All equipment codes validated against ResourceFile_EquipmentCatalogue.csv

* Simplify equipment allocation across cancer treatment modules

- Remove probability-based equipment allocation conditions
- Convert equipment codes to descriptive names
- Consolidate multiple add_equipment() calls into single calls
- Focus on 'ever use' approach for facility planning
- Applies to: bladder_cancer, breast_cancer, copd, epilepsy, oesophagealcancer, other_adult_cancers, prostate_cancer

Addresses PR feedback to eliminate hard-coded probability parameters.

* Remove unnecessary random number generation and magic number probabilities

- Remove all instances of 'if self.module.rng.random() < 1.0:' (100% probability)
- Combine multiple equipment additions into single calls for efficiency
- Simplify equipment allocation by removing always-true conditional checks
- Addresses PR reviewer feedback about magic numbers and random generation

Files updated:
- prostate_cancer.py: Fixed 4 instances of unnecessary random checks
- oesophagealcancer.py: Fixed 1 instance for safety equipment
- other_adult_cancers.py: Fixed 1 instance for safety equipment

* Address reviewer feedback: use equipment names, combine add_equipment calls, remove random probabilities

- Replace numeric equipment codes with descriptive names (e.g., {50} -> 'Safety Goggles')
- Combine multiple add_equipment() calls into single statements for better readability
- Remove all random number generation and magic number probabilities from HSI equipment allocation
- Maintain 'if equipment is ever used, it should be available' philosophy per reviewer guidance

Fixes issues in:
- other_adult_cancers.py: Combined equipment calls in palliative care HSI
- prostate_cancer.py: Removed random probabilities, combined equipment statements, used names
- oesophagealcancer.py: Removed all random equipment allocation, used equipment names

---------

Co-authored-by: Tim Hallett <[email protected]>

Author: andrew-phillips-1

src/tlo/methods/bladder_cancer.py

@@ -733,7 +733,16 @@ def apply(self, person_id, squeeze_factor):
         if cons_avail:
             # Use a biopsy to diagnose whether the person has bladder Cancer
             # If consumables are available update the use of equipment and run the dx_test representing the biopsy
-            self.add_equipment({'Cystoscope', 'Ordinary Microscope', 'Ultrasound scanning machine'})
+            self.add_equipment({
+                'Cystoscope',
+                'Ordinary Microscope',
+                'Ultrasound scanning machine',
+                'Analyser, Haematology',
+                'Analyser, Chemistry',
+                'X-ray machine',
+                'Sample Rack',
+                'Safety Goggles'
+            })
 
             # Use a cystoscope to diagnose whether the person has bladder Cancer:
             dx_result = hs.dx_manager.run_dx_test(
@@ -806,7 +815,16 @@ def apply(self, person_id, squeeze_factor):
         if cons_avail:
             # Use a biopsy to diagnose whether the person has bladder Cancer
             # If consumables are available log the use of equipment and run the dx_test representing the biopsy
-            self.add_equipment({'Cystoscope', 'Ordinary Microscope', 'Ultrasound scanning machine'})
+            self.add_equipment({
+                'Cystoscope',
+                'Ordinary Microscope',
+                'Ultrasound scanning machine',
+                'Analyser, Haematology',
+                'Analyser, Chemistry',
+                'X-ray machine',
+                'Sample Rack',
+                'Safety Goggles'
+            })
 
             # Use a cystoscope to diagnose whether the person has bladder Cancer:
             dx_result = hs.dx_manager.run_dx_test(
@@ -899,6 +917,19 @@ def apply(self, person_id, squeeze_factor):
             # If consumables are available and the treatment will go ahead - update the equipment
             self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
+            # Additional cancer treatment equipment for bladder cancer surgery
+            self.add_equipment({
+                'Analyser, Haematology',
+                'Analyser, Chemistry',
+                'Analyser, Hormones',
+                'X-ray machine',
+                'Ultrasound scanning machine',
+                'Cystoscope',
+                'Sample Rack',
+                'Ordinary Microscope',
+                'Safety Goggles'
+            })
+
             # Record date and stage of starting treatment
             df.at[person_id, "bc_date_treatment"] = self.sim.date
             df.at[person_id, "bc_stage_at_which_treatment_given"] = df.at[person_id, "bc_status"]
@@ -942,6 +973,17 @@ def apply(self, person_id, squeeze_factor):
         assert not pd.isnull(df.at[person_id, "bc_date_diagnosis"])
         assert not pd.isnull(df.at[person_id, "bc_date_treatment"])
 
+        # Equipment for post-treatment monitoring and follow-up
+        self.add_equipment({
+            'Analyser, Haematology',
+            'Analyser, Chemistry',
+            'X-ray machine',
+            'Ultrasound scanning machine',
+            'Cystoscope',
+            'Sample Rack',
+            'Safety Goggles'
+        })
+
         if df.at[person_id, 'bc_status'] == 'metastatic':
             # If has progressed to metastatic, then start Palliative Care immediately:
             hs.schedule_hsi_event(
@@ -1002,7 +1044,16 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - update the equipment
-            self.add_equipment({'Infusion pump', 'Drip stand'})
+            self.add_equipment({
+                'Infusion pump',
+                'Drip stand',
+                'Analyser, Haematology',
+                'Analyser, Chemistry',
+                'X-ray machine',
+                'Ultrasound scanning machine',
+                'Sample Rack',
+                'Safety Goggles'
+            })
 
             # Record the start of palliative care if this is first appointment
             if pd.isnull(df.at[person_id, "bc_date_palliative_care"]):

src/tlo/methods/breast_cancer.py

@@ -704,7 +704,26 @@ def apply(self, person_id, squeeze_factor):
         if cons_avail:
             # Use a biopsy to diagnose whether the person has breast Cancer
             # If consumables are available, add the used equipment and run the dx_test representing the biopsy
-            self.add_equipment({'Ultrasound scanning machine', 'Ordinary Microscope'})
+
+            # Equipment for breast cancer biopsy and diagnosis
+            self.add_equipment({
+                'Ultrasound scanning machine',
+                'Ordinary Microscope',
+                'Cusco\'s/ bivalved Speculum',
+                'Biological Microscopes',
+                'Examination couch',
+                'Lamp, Anglepoise',
+                'Analyser, Haematology',
+                'Analyzer, Clinical immunoassay',
+                'Anatomical marker L-R',
+                'Analyser, Hormones',
+                'Apron protective x-ray lead',
+                'Safety Goggles',
+                'Magnetic resonance imaging (MRI)',
+                'Manual Rotary Microtome',
+                'Sample Rack',
+                'Shaker'
+            })
 
             dx_result = hs.dx_manager.run_dx_test(
                 dx_tests_to_run='biopsy_for_breast_cancer_given_breast_lump_discernible',
@@ -802,8 +821,32 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - add the used equipment
+            # Major surgery equipment package (already includes core surgical equipment)
             self.add_equipment(self.healthcare_system.equipment.from_pkg_names('Major Surgery'))
 
+            # Additional breast cancer treatment equipment
+            self.add_equipment({
+                'Infusion pump',
+                'Drip stand',
+                'Pulse oximeter',
+                'Blood pressure machine',
+                'Laparotomy Set',
+                'Examination couch',
+                'Light, operating, mobile',
+                'Trolley, emergency',
+                'Analyser, Haematology',
+                'Analyzer, Clinical immunoassay',
+                'Automatic Cell washer',
+                'Backsplit cotton gown',
+                'Coagulation machine',
+                'Sterilizing unit, steam, medium, 240 litre',
+                'Magnetic Stirrer',
+                'Micropipettes 10 - 100ul',
+                'Flow Cytometer',
+                'Bone Densitometry',
+                'Automatic staining machine'
+            })
+
             # Log the use of adjuvant chemotherapy
             self.get_consumables(
                 item_codes=self.module.item_codes_breast_can['treatment_chemotherapy'],
@@ -852,6 +895,25 @@ def apply(self, person_id, squeeze_factor):
         assert not pd.isnull(df.at[person_id, "brc_date_diagnosis"])
         assert not pd.isnull(df.at[person_id, "brc_date_treatment"])
 
+        # Equipment for breast cancer follow-up monitoring
+        self.add_equipment({
+            'Ultrasound scanning machine',
+            'Examination couch',
+            'Lamp, Anglepoise',
+            'Ordinary Microscope',
+            'Blood pressure machine',
+            'Pulse oximeter',
+            'Computed Tomography',
+            'Analyser, Haematology',
+            'Analyzer, Clinical immunoassay',
+            'Analyser, Hormones',
+            'Coagulation machine',
+            'Bone Densitometry',
+            'Backsplit cotton gown',
+            'Safety Goggles',
+            'Sample Rack'
+        })
+
         if df.at[person_id, 'brc_status'] == 'stage4':
             # If has progressed to stage4, then start Palliative Care immediately:
             hs.schedule_hsi_event(
@@ -913,7 +975,26 @@ def apply(self, person_id, squeeze_factor):
 
         if cons_available:
             # If consumables are available and the treatment will go ahead - add the used equipment
-            self.add_equipment({'Infusion pump', 'Drip stand'})
+            # Equipment for palliative care
+            self.add_equipment({
+                'Infusion pump',
+                'Drip stand',
+                'Bed, adult',
+                'Mattress for hospital bed',
+                'Blood pressure machine',
+                'Pulse oximeter',
+                'Trolley, emergency',
+                'Examination couch',
+                'Stethoscope',
+                'Analyser, Haematology',
+                'Analyzer, Clinical immunoassay',
+                'Backsplit cotton gown',
+                'Coagulation machine',
+                'Automatic Cell washer',
+                'Sterilizing unit, steam, 39 ltr',
+                'Safety Goggles',
+                'Sample Rack'
+            })
 
             # Record the start of palliative care if this is first appointment
             if pd.isnull(df.at[person_id, "brc_date_palliative_care"]):

src/tlo/methods/copd.py

@@ -229,6 +229,16 @@ def _common_first_appt(
                 {self.item_codes["bronchodilater_inhaler"]: 1}
             ):
                 individual_properties["ch_has_inhaler"] = True
+
+            # Schedule moderate COPD treatment for moderate cases (to handle equipment)
+            if "breathless_moderate" in symptoms:
+                event = HSI_Copd_TreatmentOnModerateExacerbation(
+                    module=self, person_id=person_id
+                )
+                schedule_hsi_event(
+                    event, topen=self.sim.date, priority=0
+                )
+
             if "breathless_severe" in symptoms:
                 event = HSI_Copd_TreatmentOnSevereExacerbation(
                     module=self, person_id=person_id
@@ -541,8 +551,9 @@ def __init__(self, module, person_id):
         super().__init__(module, person_id=person_id)
 
     def apply(self, person_id):
-        df = self.sim.population.props
-        person = df.loc[person_id, ['is_alive', 'age_years', 'ch_will_die_this_episode', 'ch_lungfunction']]
+        person = self.sim.population.props.loc[
+            person_id, ['is_alive', 'age_years', 'ch_will_die_this_episode', 'ch_lungfunction']
+        ]
         # Check if an individual should still die and, if so, cause the death
         if person.is_alive and person.ch_will_die_this_episode:
             self.sim.modules['Demography'].do_death(
@@ -552,6 +563,30 @@ def apply(self, person_id):
             )
 
 
+class HSI_Copd_TreatmentOnModerateExacerbation(HSI_Event, IndividualScopeEventMixin):
+    """HSI event for issuing treatment to individuals with moderate COPD exacerbation.
+    This represents community-based care for non-severe breathlessness."""
+
+    def __init__(self, module, person_id):
+        super().__init__(module, person_id=person_id)
+
+        self.TREATMENT_ID = "Copd_Treatment_Moderate"
+        self.ACCEPTED_FACILITY_LEVEL = "1a"
+        self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({"Over5OPD": 1})
+
+    def apply(self, person_id, squeeze_factor):
+        """Treatment for moderate COPD exacerbation - community-based care."""
+
+        # Equipment for moderate COPD cases
+        self.add_equipment({
+            'Incentive spirometers',
+            'Analyser, Blood Gas'
+        })
+
+        # Give bronchodilator treatment if available
+        self.get_consumables({self.module.item_codes['bronchodilater_inhaler']: 1})
+
+
 class HSI_Copd_TreatmentOnSevereExacerbation(HSI_Event, IndividualScopeEventMixin):
     """ HSI event for issuing treatment to all individuals with severe exacerbation. We first check the availability of
     oxygen at the default facility(1a). If no oxygen is found we refer individuals to the next higher level facility
@@ -590,7 +625,19 @@ def apply(self, person_id, squeeze_factor):
                 oxygen=self.get_consumables({self.module.item_codes['oxygen']: 23_040}),
                 aminophylline=self.get_consumables({self.module.item_codes['aminophylline']: 600})
             )
-            self.add_equipment({'Oxygen cylinder, with regulator', 'Nasal Prongs', 'Drip stand', 'Infusion pump'})
+
+            # Equipment for severe COPD exacerbations
+            self.add_equipment({
+                'Oxygen cylinder, with regulator',
+                'Nasal Prongs',
+                'Drip stand',
+                'Infusion pump',
+                'Incentive spirometers',
+                'Analyser, Blood Gas',
+                'Ambu bag, adult with mask',
+                'Postural Drainage Couch',
+                'Resuscitator'
+            })
 
             if prob_treatment_success:
                 df.at[person_id, 'ch_will_die_this_episode'] = False

src/tlo/methods/epilepsy.py

@@ -637,6 +637,21 @@ def apply(self, person_id, squeeze_factor):
         df = self.sim.population.props
         hs = self.sim.modules["HealthSystem"]
 
+        # Add equipment for severe epilepsy cases
+        if df.at[person_id, 'ep_seiz_stat'] == '3':  # Frequent seizures
+            # Assessment and mobility equipment for severe epilepsy
+            self.add_equipment({'Wheelchair'})
+
+            # Pediatric equipment for children with severe epilepsy
+            if df.at[person_id, 'age_years'] < 18:
+                self.add_equipment({
+                    'Paediatric Corner sit',
+                    'Paediatric CP Chair',
+                    'Paediatric mat',
+                    'Paediatric rollator',
+                    'Paediatric Standing frame'
+                })
+
         # Check what drugs are available
         best_available_medicine = self.module.get_best_available_medicine(self)
 
@@ -703,6 +718,51 @@ def apply(self, person_id, squeeze_factor):
         if not df.at[person_id, 'ep_antiep']:
             return hs.get_blank_appt_footprint()
 
+        # Add equipment for severe epilepsy cases at follow-up visits
+        if df.at[person_id, 'ep_seiz_stat'] == '3':  # Frequent seizures
+            # Equipment for severe epilepsy rehabilitation and support
+            self.add_equipment({
+                'Adaptive communication switches (Infrared switches)',
+                'Speech therapy kit',
+                'Bobath bed',
+                'Box and Block Test',
+                'Built Up (adapted) Utensils',
+                'Goniometer',
+                'Grasp Dynamometer',
+                'Hand function kits',
+                'Hot Pack Therapy Units',
+                'Interferential therapy machine',
+                'Muscle stimulator',
+                'TENs Unit',
+                'Transcutaneous electrical neuromuscular stimulation',
+                'Exercise Mats',
+                'Gym mat',
+                'Parallel Bars',
+                'Pulley System',
+                'Suspension Slings',
+                'Rehabilitation wall bars',
+                'Rollators',
+                'Walking Frame',
+                'Walking Cane',
+                'Overhead pulley',
+                'Training stairs',
+                'Stress Ball',
+                'Wheelchair',
+                'Ordinary balls',
+                'Medicinal Balls (Sets of 0.5kgs, 1kg, 2kgs, 3kgs, 4kgs, 5kgs)',
+                'Exercise ball'
+            })
+
+            # Pediatric equipment for children with severe epilepsy
+            if df.at[person_id, 'age_years'] < 18:
+                self.add_equipment({
+                    'Paediatric Corner sit',
+                    'Paediatric CP Chair',
+                    'Paediatric mat',
+                    'Paediatric rollator',
+                    'Paediatric Standing frame'
+                })
+
         # Request the medicine
         best_available_medicine = self.module.get_best_available_medicine(self)
         if best_available_medicine is not None: