Commit adf85240 authored by Zhang, Yuanpeng's avatar Zhang, Yuanpeng ⭐
Browse files

updating

parent f7e07625

cal_config.json

+6 −6
Original line number Diff line number Diff line 
{

    "Diamond": "/SNS/NOM/IPTS-31346/nexus/NOM_193698.nxs.h5",

    "Diamond": "/SNS/NOM/IPTS-33585/nexus/NOM_198571.nxs.h5",

    "Instrument": "NOM",

    "Date": "2023-07-06",

    "SampleEnv": "furnace",

    "OutputDir": "/SNS/NOM/shared/CALIBRATION/autoreduce",

    "GenShadowMask": "shadow_mask_shifter_193698.in",

    "Date": "2024-08-13",

    "SampleEnv": "shifter",

    "OutputDir": "/SNS/NOM/shared/autoreduce/calibration",

    "GenShadowMask": "shadow_mask_shifter_198571.in",

    "DiaLattParam": 3.5671299351,

    "GroupMethod": "KMEANS_ED",

    "SaveInitCalTable": true,

nom_cal

+1 −0
Original line number Diff line number Diff line
@@ -33,6 +33,7 @@ echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- 


# Generate mask

if [ ! $gen_mask_file = "no" ]; then

    echo "Generating mask..."

    mantidpython $working_dir/inputs/mask_gen/nom_shadow_mask_gen.py $dia_file

    rm -rf $running_dir/manual_mask_cache/gen_mask/$gen_mask_file

    Rscript $working_dir/inputs/mask_gen/find_dip.R $gen_mask_file

utils/calib_diag.py

+17 −17
Original line number Diff line number Diff line
@@ -192,7 +192,7 @@ ax.set_xlabel('d-spacing') 
ax.set_ylabel('Detectors')



tmpfile = BytesIO()

fig.savefig(tmpfile, format='png')

fig.savefig(tmpfile, format='png', dpi=300)

encoded = base64.b64encode(tmpfile.getvalue()).decode('utf-8')



diag1_out = os.path.join(
@@ -209,22 +209,22 @@ html += "<div>{}</div>".format(html_tmp) 
#                      |||||      Diagnostics-2      |||||

#                      vvvvv  Calib versus Engineer  vvvvv

# +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

fig, ax = diagnostics.difc_plot2d("_cal", "_cal_eng", instr_ws="_group",

                                  mask="_mask", vrange=(0, 5))



tmpfile = BytesIO()

fig.savefig(tmpfile, format='png')

encoded = base64.b64encode(tmpfile.getvalue()).decode('utf-8')



diag2_out = os.path.join(

    out_cal_diag_dir,

    f"{diag_file_stem}_diag2.png"

)

fig.savefig(diag2_out, format='png', dpi=300)



html_tmp = '<h4>Calibrated vs. Engineering calibration constant</h4>'

html_tmp += '<img src=\'data:image/png;base64,{}\'>'.format(encoded)

html += "<div>{}</div>".format(html_tmp)

# fig, ax = diagnostics.difc_plot2d("_cal", "_cal_eng", instr_ws="_group",

#                                   mask="_mask", vrange=(0, 5))

# 

# tmpfile = BytesIO()

# fig.savefig(tmpfile, format='png')

# encoded = base64.b64encode(tmpfile.getvalue()).decode('utf-8')

# 

# diag2_out = os.path.join(

#     out_cal_diag_dir,

#     f"{diag_file_stem}_diag2.png"

# )

# fig.savefig(diag2_out, format='png', dpi=300)

# 

# html_tmp = '<h4>Calibrated vs. Engineering calibration constant</h4>'

# html_tmp += '<img src=\'data:image/png;base64,{}\'>'.format(encoded)

# html += "<div>{}</div>".format(html_tmp)



# +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

#                      |||||      Diagnostics-3     |||||

utils/nom_cal.py

+50 −30
Original line number Diff line number Diff line
@@ -226,6 +226,7 @@ for wksp_index in range(num_det): 
        # if the chi square is larger than the pre-set threshold.

        chi_s_min = 1.E5

        for sigma_trial in sigma_trials:

            try:

                FitPeak(InputWorkspace=wksp_check,

                        OutputWorkspace="dia_calibrant_d_fit",

                        ParameterTableWorkspace="dia_calibrant_d_table",
@@ -241,6 +242,22 @@ for wksp_index in range(num_det): 
                        FitBackgroundFirst=False,

                        RawParams=False,

                        CostFunction="Rwp")

            except:

                FitPeak(InputWorkspace=wksp_check,

                        OutputWorkspace="dia_calibrant_d_fit",

                        ParameterTableWorkspace="dia_calibrant_d_table",

                        WorkspaceIndex=wksp_index,

                        PeakFunctionType="Gaussian",

                        PeakParameterNames="Height, PeakCentre, Sigma",

                        PeakParameterValues=f"{height_init}, {c_est}, {sigma_trial}",

                        BackgroundType="Linear",

                        BackgroundParameterNames="A0, A1",

                        BackgroundParameterValues="10, 0",

                        FitWindow="1.2, 1.45",

                        PeakRange="1.2, 1.45",

                        FitBackgroundFirst=True,

                        RawParams=False,

                        CostFunction="Rwp")

            if mtd["dia_calibrant_d_table"].row(0)["Value"] < chi_s_min:

                chi_s_min = mtd["dia_calibrant_d_table"].row(0)["Value"]

                dia220_c_fitted = mtd["dia_calibrant_d_table"].row(2)["Value"]
@@ -678,6 +695,7 @@ for bank in range(mtd["dia_calibrant_d_cc_f_tof"].getNumberHistograms()): 
                tof_cent_trials = [tof_cent + item for item in np.arange(-5 , 6, 0.1)]

                chi2_min_tmp = 500.

                tof_cent_opt = tof_cent_trials[0]

                int_tmp = -1

                for tof_cent_trial in tof_cent_trials:

                    try:

                        FitPeak(InputWorkspace=f"dia_calibrant_d_cc_f_tof_{bank + 1}",
@@ -727,6 +745,8 @@ for bank in range(mtd["dia_calibrant_d_cc_f_tof"].getNumberHistograms()): 
                    d_tmp = mtd[f"dia_calibrant_d_cc_f_tof_{bank + 1}_{row_i}_table"].row(2)["Value"]

                    d_tmp /= difc_arb

                    d_fitted.append(d_tmp)

                else:

                    print(f"[Warning] dia_calibrant_d_cc_f_tof_{bank + 1}_{row_i} is failing the peak fitting.")

            else:

                d_norm.append(float(peak_list[row_i][0]))

                d_tmp = mtd[f"pdcal_diag_{bank + 1}_fitparam"].row(row_i)["centre"]
@@ -1119,21 +1139,21 @@ html += "<div>{}</div>".format(html_tmp) 
#                      vvvvv  Calib versus Engineer  vvvvv

# +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+



fig, ax = diagnostics.difc_plot2d("_cal", "_cal_eng", instr_ws="_group",

                                  mask="_mask", vrange=(0, 5))

tmpfile = BytesIO()

fig.savefig(tmpfile, format='png')

encoded = base64.b64encode(tmpfile.getvalue()).decode('utf-8')



diag_file_name = f"{diag_file_stem}_diag2.png"

diag_file_png = os.path.join(out_cal_diag_dir, diag_file_name)

fig.savefig(diag_file_png, format='png', dpi=300)

diag_file_png = os.path.join(out_cal_diag_dir_alt, diag_file_name)

fig.savefig(diag_file_png, format='png', dpi=300)



html_tmp = '<h4>Calibrated vs. Engineering calibration constant</h4>'

html_tmp += '<img src=\'data:image/png;base64,{}\'>'.format(encoded)

html += "<div>{}</div>".format(html_tmp)

# fig, ax = diagnostics.difc_plot2d("_cal", "_cal_eng", instr_ws="_group",

#                                   mask="_mask", vrange=(0, 5))

# tmpfile = BytesIO()

# fig.savefig(tmpfile, format='png')

# encoded = base64.b64encode(tmpfile.getvalue()).decode('utf-8')

# 

# diag_file_name = f"{diag_file_stem}_diag2.png"

# diag_file_png = os.path.join(out_cal_diag_dir, diag_file_name)

# fig.savefig(diag_file_png, format='png', dpi=300)

# diag_file_png = os.path.join(out_cal_diag_dir_alt, diag_file_name)

# fig.savefig(diag_file_png, format='png', dpi=300)

# 

# html_tmp = '<h4>Calibrated vs. Engineering calibration constant</h4>'

# html_tmp += '<img src=\'data:image/png;base64,{}\'>'.format(encoded)

# html += "<div>{}</div>".format(html_tmp)



# +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

#                      |||||      Diagnostics-3     |||||

utils/nom_cal_test.py

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