Delete 'Glavni_izdelava_IVP_modela.py'

Glavni_izdelava_IVP_modela.py

@@ -1,119 +0,0 @@
-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
-