sector integration using azimuthalIntegrator.integrate_1d doesn't work

[y-hhung]

Dear all,

I have been using the azimuthal integrator module for some GIWAXS data, where I am interested in studying the integrated data within a certain azimuthal range instead of the whole range. I find that whatever azimuthal range I use, the output data is the same, suggesting that it isn't correctly doing the azimuthal integration.

Below are the functions I use. I would like to be able to integrate the data properly for certain values of chi_pos and chi_width.

If anyone has any advice this would be much appreciated!

Thanks,

Esthy

def pyfai_1D(df, filename, qbins, chi_pos = 0, chi_width = 180, diagnostics=False,mask=False,maskfile='',rotate=False) :
    filedf = df.loc[[filename]]
    
    if diagnostics == True : print(filedf)
    
    detector  = pyFAI.detectors.Detector(
        filedf.pixel_size[0], # pixel dimension x in m
        filedf.pixel_size[0], # pixel dimension y in m
        max_shape=(filedf.shape_x[0],filedf.shape_y[0]) # array size in pixels
    )
    
    ai = pyFAI.azimuthalIntegrator.AzimuthalIntegrator(
     
        poni1 = (filedf.shape_y[0]-filedf.beam_center_y[0])*filedf.pixel_size[0], # factoring in rotation
        poni2 = (filedf.shape_x[0]-filedf.beam_center_x[0])*filedf.pixel_size[0], # factoring in rotation                
        detector = detector,
        rot2 = np.deg2rad(filedf.twothet[0]),
        wavelength = filedf.wavelength[0],
        dist = filedf.distance[0]
    )
           
    pg = pygix.Transform()
    pg.load(ai)
    pg.incident_angle = filedf.incident_angle[0]
    
    if mask == True:
        pg.maskfile = maskfile    
    
    if diagnostics == True :
        print(ai)

    sample_orientation = 3 

    pg.sample_orientation = sample_orientation   
    img = np.rot90(np.rot90(fabio.open(filedf.fileloc[0]).data))
    
    qmin = 0 # minimum Q # 0.01 to 2.5
    qmax = 2 # maximum Q
    
    q, intensity = ai.integrate1d(img, npt=qbins, unit="q_A^-1", radial_range=(qmin, qmax), azimuth_range=(chi_pos-chi_width/2, chi_pos+chi_width/2), correctSolidAngle=True)

    return intensity,q

def mass_convert_1D_combine_pyfai(filedir, label ='',chi_pos = 0, chi_width = 180, qbins = 800, vmin = 0, vmax = 100, ymax = 2, sqrt = False, combining = False, plotting=False) :      
    dtrek_files = glob.glob(filedir+'\*.img')
    dtrek_files = sorted(dtrek_files)

    vals = dtrek_vals(dtrek_files[0])
    df = pd.DataFrame.from_dict(vals)
    df = df.drop(0)
    
    for dtrek_file in dtrek_files :    
        vals = dtrek_vals(dtrek_file)
        df = df._append(pd.DataFrame.from_dict(vals)) #, index = 0, orient='columns', dtype=None
    df = df.set_index('filename')
    
    df_1D = pd.DataFrame()
    if combining:
        intensities = []

    if combining == False:
        for dtrek_file in dtrek_files :       
            
            filename = os.path.split(dtrek_file)[1]        
            print(f'Processing: {filename}\r', end="")
            intensity, q = pyfai_1D(df, filename, qbins, diagnostics=False,mask=False,maskfile='',rotate=False)

            df_1D["Q_"+filename] = q # /10 to angstrom if not in function
            df_1D["I_"+filename] = intensity
            plt.plot(q, intensity)
            plt.xlabel('q (A^-1)')
            plt.xlim(0.1,2.5)
            plt.xticks(np.arange(0, 2.5, step=0.25)) 
            plt.ylabel('Intensity')
            plt.title(f'1D Integration for {filename}')
            plt.show()
        
            df_1D.to_csv(os.path.join(filedir,'1Dintegrations.csv'), index=False)
        
    else:
        for dtrek_file in dtrek_files :       
            
            filename = os.path.split(dtrek_file)[1]        
            print(f'Processing: {filename}\r', end="")
            intensity,q = pyfai_1D(df, filename, qbins,diagnostics=False,mask=False,maskfile='',rotate=False)

            df_1D["Q"] = q # /10 to angstrom if not in function
            intensities.append(intensity)
        GIarray = np.sum(intensities, axis=0)    
        df_1D["I"] = GIarray
        
        fig,ax = plt.subplots(figsize=(10,6))  
        ax.plot(q, GIarray)
        #ax.set_xscale('log')
        ax.xaxis.set_minor_formatter(ScalarFormatter())    
        ax.xaxis.set_major_formatter(ScalarFormatter())
        plt.xlim(0.1,2)
        #plt.xticks(np.arange(0, 2.5, step=0.25)) 
        plt.xlabel('q (A$^{-1}$)')
        plt.ylabel('Intensity')
        plt.title(f'1D Integration for {filename}')
        plt.show()
        
        df_1D.to_csv(os.path.join(filedir,label+'1Dintegrations_combined.csv'), index=False)

[kif]

Hi Esthy, pygix did not receive much update for several years, thus Edgar ported most of its features directly into pyFAI. Beside this, I see no issue. Could you please print your "azimuth_range" and validate that it is correct ?