Ejemplo n.º 1
0
def readDSPlateSetting(plateL, confDir, startAtZero = False,
                     dateFormat='%m%y%d', 
                     default={'Name':"A", 'Medium': "Complet", 'Serum':10},
                     addPlateWellsToDB=False, indices={'Xenobiotic':3, 'Dose':4}):
    '''
    Function to go from as many csv files as there are parameters describing plate setup, to a dictionary
    
    The csv file should not contain spaces in the cells
    
    The file 'wells' should contain the information on where physically on the plate the wells with the numbers
    are located. The numbers are the numbers as the images are saved.
    '''
    result = defaultdict(dict)
    idL = {}
    well_lines_dict = {}
    for plate in plateL:
        result[plate]={}         
        idL[plate]={}
        #getting where the existing wells are
        try:
            file_ =open(os.path.join(confDir,  "%s.csv" % plate))
            well_lines = file_.readlines(); file_.close()
        except OSError:
            raise OSError("can't find proper file")
        else:
            well_lines=np.array([line.strip("\n").strip('\t').split("-") for line in well_lines[1:]])
            print well_lines
            well_lines_dict[plate]=well_lines

        nb_col = 24; nb_row=16
        
        if addPlateWellsToDB:
            date = datetime.datetime.strptime(plate[2:6]+plate[-2:], dateFormat)
            p = Plate(name = plate, date = date, nb_col=nb_col, nb_row=nb_row)
            p.save()
        
#         current_parameters = defaultdict(list)
#         for parameter in WELL_PARAMETERS:
#             print 'Loading %s parameter'%parameter
#             try:
#                 f=open(os.path.join(confDir, "%s_%s.csv" % (plate, parameter)))
#                 current_lines=f.readlines()[1:]; f.close()
#             except IOError:
#                 pass
#             else:
#                 current_parameters[parameter]=np.array([line.strip("\n").split(",") for line in current_lines]).ravel()
#                 current_parameters[parameter] = np.delete(current_parameters[parameter], 
#                                         np.where(current_parameters[parameter]==''))
        for k, line in enumerate(well_lines):
            result[plate][k+1]=defaultdict(dict)
            for i,param in enumerate(WELL_PARAMETERS):
                try:
                    result[plate][k+1][param]=line[indices[param]].replace(' ', '')
                except KeyError:
                    result[plate][k+1][param]=default[param]
                    
            if addPlateWellsToDB:
                medium = result[plate][k+1]['Medium']
                serum = int(result[plate][k+1]['Serum'])
                
                conds = Cond.objects.filter(medium = medium)
                if len(conds)==0:
                    cond = addConds(medium, serum) 
                elif len(conds)==1:
                    if conds[0].serum!=serum:
                        cond =addConds(medium, serum)
                    else:
                        cond = conds[0]
                else:
                    conds = conds.filter(serum =serum)
                    if len(conds)==0:
                        cond =addConds(medium, serum)
                    elif len(conds)>1:
                        raise
                    else:
                        cond = conds[0]

            if addPlateWellsToDB and 'Xenobiotic' in WELL_PARAMETERS:
                xb = result[plate][k+1]['Xenobiotic']
                try:
                    dose = float(result[plate][k+1]['Dose'].replace(',', '.'))
                except ValueError:
                    #then it means there are letters in the field
                    try:
                        dose = float(result[plate][k+1]['Dose'].replace(',', '.')[:-2])
                    except ValueError:
                        #then it meants it's an empty field
                        dose=0
                    else:
                        unit = result[plate][k+1]['Dose'][-2:]
                        if unit=='uM':
                            dose*=10**(-6)
                        elif unit=='nM':
                            dose*=10**(-9)
                        elif unit=='pM':
                            dose*=10**(-12)
                
                treatments = Treatment.objects.filter(xb = xb)
                if len(treatments)==0:
                    treatment = addTreatment(xb, dose)
                elif len(treatments)==1:
                    if treatments[0].dose != dose:
                        treatment = addTreatment(xb, dose)
                    else:
                        treatment =treatments[0]
                else:
                    treatments = treatments.filter(dose =dose)
                    if len(treatments)==0:
                        treatment = addTreatment(xb, dose)
                    elif len(treatments)>1:
                        raise
                    else:
                        treatment =treatments[0]
                    
            if addPlateWellsToDB:
                clone = result[plate][k+1]['Name'].split("_")[0]
                w=Well(num=k+1, plate=p, treatment = treatment, clone = clone)
                w.save()
        #this is how to add many to many relations
                w.cond.add(cond); w.save()
                idL[plate][k+1]=w.id
                
    if addPlateWellsToDB:
        return result, {plate:np.reshape(range(1,nb_col*nb_row+1),(nb_row,nb_col))}, idL
    else:
        return result,{plate:np.reshape(range(1,nb_col*nb_row+1),(nb_row,nb_col))}, {}
Ejemplo n.º 2
0
def readXBPlateSetting(plateL, confDir, startAtZero = False,
                     plateName=None, dateFormat='%d%m%y', 
                     default={'Name':"Cl1", 'Medium': "Indtp", "Serum":10},
                     addPlateWellsToDB=False):
    '''
    Function to go from as many csv files as there are parameters describing plate setup, to a dictionary
    
    The csv file should not contain spaces in the cells
    
    The file 'wells' should contain the information on where physically on the plate the wells with the numbers
    are located. The numbers are the numbers as the images are saved.
    '''
    result = defaultdict(dict)
    idL = {}
    well_lines_dict = {}
    for plate in plateL:
        result[plate]={}         
        idL[plate]={}
        #getting where the existing wells are
        try:
            file_ =open(os.path.join(confDir,  "%s_Wells.csv" % plate))
            well_lines = file_.readlines(); file_.close()
        except OSError:
            nb_col = 12; nb_row=8
            well_lines = np.reshape(range(1,97),(8,12))
        else:
            well_lines=np.array([line.strip("\n").split(",") for line in well_lines[1:]], dtype=int)
            print well_lines
            well_lines_dict[plate]=well_lines
            
            try:
                a=int(well_lines[0][11])
            except:
                try:
                    a = int(well_lines[0][7])
                except:
                    raise AttributeError("Can't find the number of rows")
                else:
                    nb_col=8
            else:
                nb_col=12
            nb_row = len(well_lines) #dire le nb de lignes dans le fichier - mais en fait on a toujours huit colonnes

#        #opening file with well names (clone name usually)
#        filename = os.path.join(confDir, "%s_Name.csv" % plate)
#        
#        f=open(filename)
#        lines=f.readlines(); f.close()
#        
#        lines=np.array([line.strip("\n").split(",") for line in lines][1:]).ravel()
#        lines = np.delete(lines, np.where(lines==''))
        
        if addPlateWellsToDB:
            p = Plate(name = plateName, date = datetime.datetime.strptime(plate.split('_')[0], dateFormat), nb_col=nb_col, nb_row=nb_row)
            p.save()
        
        current_parameters = defaultdict(list)
        for parameter in WELL_PARAMETERS:
            print 'Loading %s parameter'%parameter
            try:
                f=open(os.path.join(confDir, "%s_%s.csv" % (plate, parameter)))
                current_lines=f.readlines()[1:]; f.close()
            except IOError:
                pass
            else:
                current_parameters[parameter]=np.array([line.strip("\n").split(",") for line in current_lines]).ravel()
                current_parameters[parameter] = np.delete(current_parameters[parameter], 
                                        np.where(current_parameters[parameter]==''))
        for k in well_lines.ravel():
            result[plate][k]=defaultdict(dict)
            for i,param in enumerate(WELL_PARAMETERS):
                try:
                    result[plate][k][param]=current_parameters[param][k-1]
                except IndexError:
                    result[plate][k][param]=default[param]
            if addPlateWellsToDB:
                medium = result[plate][k]['Medium']
                serum = int(result[plate][k]['Serum'])
                
                conds = Cond.objects.filter(medium = medium)
                if len(conds)==0:
                    cond = addConds(medium, serum) 
                elif len(conds)==1:
                    if conds[0].serum!=serum:
                        cond =addConds(medium, serum)
                    else:
                        cond = conds[0]
                else:
                    conds = conds.filter(serum =serum)
                    if len(conds)==0:
                        cond =addConds(medium, serum)
                    elif len(conds)>1:
                        raise
                    else:
                        cond = conds[0]

            if addPlateWellsToDB and 'Xenobiotic' in WELL_PARAMETERS:
                xb = result[plate][k]['Xenobiotic']
                dose = int(result[plate][k]['Dose'])
                
                treatments = Treatment.objects.filter(xb = xb)
                if len(treatments)==0:
                    treatment = addTreatment(xb, dose)
                elif len(treatments)==1:
                    if treatments[0].dose != dose:
                        treatment = addTreatment(xb, dose)
                    else:
                        treatment =treatments[0]
                else:
                    treatments = treatments.filter(dose =dose)
                    if len(treatments)==0:
                        treatment = addTreatment(xb, dose)
                    elif len(treatments)>1:
                        raise
                    else:
                        treatment =treatments[0]
                    
            if addPlateWellsToDB:
                clone = result[plate][k]['Name'].split("_")[0]
                w=Well(num=k, plate=p, treatment = treatment, clone = clone)
                w.save()
        #this is how to add many to many relations
                w.cond.add(cond); w.save()
                idL[plate][k]=w.id
                
    if addPlateWellsToDB:
        return result, well_lines_dict, idL
    else:
        return result,well_lines_dict, {}