Upload files to ''

Glavni_izdelava_IVP_modela.py

@@ -0,0 +1,119 @@
+import numpy
+import os
+import json
+import time
+import cModel
+import importlib
+import runSolver
+import numpy.linalg
+#Zalaufaj metodo solve_matrics namest IVP, method seperately.  Preverjas razlicne metode resevanja enega modela, pol ko bos pa naredi kopijo novega modela glede na članek kotinin
+importlib.reload(cModel)
+importlib.reload(runSolver)
+
+def getModel(solution, modelName):
+    Q = solution[modelName]
+    model = cModel.model()
+    setupFile = Q['setup']
+    modelFile = Q['model']
+    parameterFile = Q['parameters']
+    print('modelFile: {} {}'.format(modelFile, os.path.isfile(modelFile)))
+    print('parameterFile: {} {}'.format(parameterFile, os.path.isfile(parameterFile)))
+    model.parse(modelFile, parameterFile)
+    return model
+def getSum(data,modelName):
+    
+    model=getModel(data,modelName)
+    Q=data[modelName]['solution']
+    lut=Q['lut']
+    total=Q['sol'][-1,lut['total']]
+    #print(total)
+    fQ={}
+    for x in lut:
+        if x=='total':
+            continue
+        j=lut[x]
+        try:
+            v=model.get(model.mod['volumes'][x])['value']
+            fQ[x]=Q['sol'][-1,j]*v/total
+        except KeyError:
+            #print('{} {}'.format(x,x in model.mod['scaled']))
+            fQ[x]=Q['sol'][-1,j]
+    print(sum(list(fQ.values())))
+    print(sorted(fQ.items(), key=lambda item:item[1]))
+
+def mergeSolutions(seq):
+    out={}
+    #each element in sequence should have this components
+    for v in ['t','sol','se','qt','sOut']:
+        out[v]=numpy.concatenate([x[v] for x in seq])
+    #copy last for settings
+    for v in ['lut','lutSE','setup','model','parameters','qt','sOut']:
+        out[v]=seq[-1][v]
+    return out 
+
+def updateSetup(job):
+    setupFileSrc = job['setupFile']
+    setupFile = os.path.join(job['jobDir'], 'setupInput.json')
+    with open(setupFileSrc, 'r') as f:
+        setup = json.load(f)
+    try:
+        setup.update(job['setupUpdates'])
+    except KeyError:
+        pass
+    with open(setupFile, 'w+') as f:
+        f.write(json.dumps(setup))
+    return setupFile
+
+fh = os.path.expanduser('~')
+
+# Create job configurations
+job_configs = {
+    'cDiazepam': {
+        'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'cDiazepam_IVP'),
+        'modelFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam.json'),
+        'parameterFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam_parameters2.json'),
+        'setupFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'setup', 'setupMinute.json'),
+        'srcDir': 'NONE',
+        'doCalculate': True
+    },
+    'cDiazepam1': {
+        'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'cDiazepam1_IVP'),
+        'modelFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam.json'),
+        'parameterFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam_parameters2.json'),
+        'setupFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'setup', 'setupHours.json'),
+        'srcDir': 'NONE',
+        'doCalculate': True
+    },
+    'cDiazepamF': {
+        'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'cDiazepamF_IVP'),
+        'modelFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam.json'),
+        'parameterFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam_parameters1.json'),
+        'setupFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'setup', 'setupMinute.json'),
+        'srcDir': 'NONE',
+        'doCalculate': True
+    },
+    'cDiazepamB': {
+        'jobDir': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'cDiazepamB_IVP'),
+        'modelFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam.json'),
+        'parameterFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'models', 'cDiazepam_parameters1.json'),
+        'setupFile': os.path.join(fh, 'Documents', 'Sola', 'IJS', 'PBPK_public', 'setup', 'setupHours.json'),
+        'srcDir': 'NONE',
+        'doCalculate': True
+    }
+}
+
+# Execute jobs
+for job_name, job in job_configs.items():
+    if not job['doCalculate']:
+        continue
+
+    if not os.path.isdir(job['jobDir']):
+        os.mkdir(job['jobDir'])
+        
+    # Adjust local setup file with ad-hoc modifications
+    setupFile = updateSetup(job)
+#   t0,y0,S1,lut,lutSE=runSolver.getStartPoint(setupFile)               #Pridobivanje začetnih točk
+    runSolver.main([setupFile, job['modelFile'], job['parameterFile']], job['jobDir'], job['srcDir'])
+#(t0,y0,S1,lut,lutSE=runSolver.getStartPoint(setup)      )            #Pridobivanje začetnih točk
+#Zalaufaj metodo solve_matrics namest IVP, method seperately.  Preverjas razlicne metode resevanja enega modela, pol ko bos pa naredi kopijo novega modela glede na članek kotinin
+