Skip to content

Commit

Permalink
Merge pull request #417 from neutrons/pdffit_output
Browse files Browse the repository at this point in the history 
add in pdffit format output
  • Loading branch information
@Kvieta1990
Kvieta1990 authored Nov 23, 2023
2 parents fb2c069 + cc9c193 commit 645b882
Show file tree
Hide file tree
Showing 3 changed files with 306 additions and 18 deletions.
2 changes: 2 additions & 0 deletions addie/initialization/widgets/postprocessing_tab_m.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@ def run(main_window=None):
main_window.postprocessing_ui_m.pushButton_savesc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_loadmc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_loadsc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_mergeBanks.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_StoG.setEnabled(False)
main_window.postprocessing_ui_m.comboBox_pdfform.addItems(['g(r)', 'G(r)'])

# setup the plot view
Expand Down
261 changes: 243 additions & 18 deletions addie/post_process_m/event_handler.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,17 @@
DeleteWorkspace
import numpy as np
from scipy.signal import argrelextrema
from datetime import datetime

weekdays = [
'Mon',
'Tue',
'Wed',
'Thu',
'Fri',
'Sat',
'Sun'
]


def open_workspaces(main_window):
Expand Down Expand Up @@ -231,6 +242,8 @@ def open_and_load_workspaces(main_window):
main_window.postprocessing_ui_m.pushButton_loadsc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_savemc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_savesc.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_mergeBanks.setEnabled(False)
main_window.postprocessing_ui_m.pushButton_StoG.setEnabled(False)
if main_window.postprocessing_ui_m.checkBox_defaultWorkspace.isChecked():
main_window.postprocessing_ui_m.pushButton_extract.setEnabled(True)
main_window.postprocessing_ui_m.frame_workspaces_table.cur_wks = 'SQ_banks_normalized'
Expand Down Expand Up @@ -264,6 +277,7 @@ def extract_button(main_window):

main_window.postprocessing_ui_m.pushButton_loadmc.setEnabled(True)
main_window.postprocessing_ui_m.pushButton_savemc.setEnabled(True)
main_window.postprocessing_ui_m.pushButton_mergeBanks.setEnabled(True)

main_window.ui.statusbar.setStyleSheet("color: blue")
main_window.ui.statusbar.showMessage("Workspace successfully extracted!",
Expand Down Expand Up @@ -697,6 +711,7 @@ def merge_banks(main_window):

main_window.postprocessing_ui_m.pushButton_savesc.setEnabled(True)
main_window.postprocessing_ui_m.pushButton_loadsc.setEnabled(True)
main_window.postprocessing_ui_m.pushButton_StoG.setEnabled(True)

print("[Info] Banks successfully merged")

Expand Down Expand Up @@ -791,6 +806,10 @@ def save_file_merged(main_window, file_name, auto=False):


def save_file_stog(main_window, file_name):
rc = main_window._pystog_inputs_collect["RippleParams"][0]
rx = main_window._pystog_inputs_collect["RippleParams"][2]
rn = main_window._pystog_inputs_collect["RippleParams"][1]

if isinstance(file_name, list):
save_directory = QFileDialog.getExistingDirectory(main_window,
'Save StoG Files',
Expand All @@ -803,11 +822,43 @@ def save_file_stog(main_window, file_name):
x_stog = main_window._pystog_output_files[item]["xlist"]
y_stog = main_window._pystog_output_files[item]["ylist"]

with open(os.path.join(save_directory, item), 'w') as new_file:
new_file.write(str(len(x_stog)) + '\n')
new_file.write('#\n')
for i in range(len(x_stog)):
new_file.write(str(x_stog[i]) + ' ' + str(y_stog[i]) + '\n')
if "pdffit.gr" in item:
current_time = datetime.now()
current_timezone = datetime.now().astimezone().strftime("%Z")
current_weekday = current_time.weekday()
time_stamp = weekdays[current_weekday] + " "
time_stamp += current_time.strftime("%m-%d-%Y %H:%M:%S") + " "
time_stamp += current_timezone
kt = "Qmax"
ts_qmax = float(main_window._pystog_inputs_collect[kt])
with open(os.path.join(save_directory, item), 'w') as f:
f.write(f"# {len(x_stog)}\n")
f.write("# Pair Distribution Function (PDF)\n")
f.write(f"# created: {time_stamp}\n")
str_tmp = f"# comment: neutron, Qmax={ts_qmax}, "
str_tmp += "Qdamp=0.017659, Qbroad=0.0191822\n"
kt = "FourierFilter"
ft_sel = main_window._pystog_inputs_collect[kt]
if ft_sel:
kt = "Rmin"
ft_rmin = float(main_window._pystog_inputs_collect[kt])
str_tmp += f"# comment: Fourier filtered, rcut={ft_rmin} \n"
str_tmp += "# comment: Ripple removed, "
str_tmp += f"Rcutoff, 1st peak min, max = {rc}, {rn}, {rx}\n"
f.write(str_tmp)
for count, r_val in enumerate(x_stog):
if count == len(x_stog) - 1:
f.write("{0:16.12F}{1:18.12F}".format(r_val,
y_stog[count]))
else:
f.write("{0:16.12F}{1:18.12F}\n".format(r_val,
y_stog[count]))
else:
with open(os.path.join(save_directory, item), 'w') as new_file:
new_file.write(str(len(x_stog)) + '\n')
new_file.write('#\n')
for i in range(len(x_stog)):
new_file.write(str(x_stog[i]) + ' ' + str(y_stog[i]) + '\n')
main_window.ui.statusbar.setStyleSheet("color: blue")
main_window.ui.statusbar.showMessage("Files saved successfully!",
main_window.statusbar_display_time)
Expand All @@ -834,11 +885,44 @@ def save_file_stog(main_window, file_name):
x_stog = main_window._pystog_output_files[file_name]["xlist"]
y_stog = main_window._pystog_output_files[file_name]["ylist"]

with open(save_file, 'w') as new_file:
new_file.write(str(len(x_stog)) + '\n')
new_file.write('#\n')
for i in range(len(x_stog)):
new_file.write(str(x_stog[i]) + ' ' + str(y_stog[i]) + '\n')
if "pdffit.gr" in file_name:
current_time = datetime.now()
current_timezone = datetime.now().astimezone().strftime("%Z")
current_weekday = current_time.weekday()
time_stamp = weekdays[current_weekday] + " "
time_stamp += current_time.strftime("%m-%d-%Y %H:%M:%S") + " "
time_stamp += current_timezone
kt = "Qmax"
ts_qmax = float(main_window._pystog_inputs_collect[kt])
with open(save_file, 'w') as f:
f.write(f"# {len(x_stog)}\n")
f.write("# Pair Distribution Function (PDF)\n")
f.write(f"# created: {time_stamp}\n")
str_tmp = f"# comment: neutron, Qmax={ts_qmax}, "
str_tmp += "Qdamp=0.017659, Qbroad=0.0191822\n"
kt = "FourierFilter"
ft_sel = main_window._pystog_inputs_collect[kt]
if ft_sel:
kt = "Rmin"
ft_rmin = float(main_window._pystog_inputs_collect[kt])
str_tmp += f"# comment: Fourier filtered, rcut={ft_rmin} \n"
str_tmp += "# comment: Ripple removed, "
str_tmp += f"Rcutoff, 1st peak min, max = {rc}, {rn}, {rx}\n"
f.write(str_tmp)
for count, r_val in enumerate(x_stog):
if count == len(x_stog) - 1:
f.write("{0:16.12F}{1:18.12F}".format(r_val,
y_stog[count]))
else:
f.write("{0:16.12F}{1:18.12F}\n".format(r_val,
y_stog[count]))
else:
with open(save_file, 'w') as new_file:
new_file.write(str(len(x_stog)) + '\n')
new_file.write('#\n')
for i in range(len(x_stog)):
new_file.write(str(x_stog[i]) + ' ' + str(y_stog[i]) + '\n')

main_window.ui.statusbar.setStyleSheet("color: blue")
main_window.ui.statusbar.showMessage("File saved successfully!",
main_window.statusbar_display_time)
Expand Down Expand Up @@ -981,7 +1065,7 @@ def execute_stog(main_window):
os.chdir(path)
with open('pystog_input.json', 'w') as pystog_file:
json.dump(json_format, pystog_file, indent=2)
subprocess.run(["pystog_cli", "--json", "pystog_input.json"])
subprocess.check_call(["pystog_cli", "--json", "pystog_input.json"])
os.chdir(cwd)
print("[Info] PyStoG successfully executed")

Expand Down Expand Up @@ -1133,21 +1217,106 @@ def add_stog_data(main_window):
data_ft_gr = stem + "_ft.gr"
data_rmc_fq = stem + "_rmc.fq"
data_rmc_gr = stem + "_rmc.gr"

data_list = [data_sq, data_gr, data_ft_sq, data_ft_gr, data_rmc_fq, data_rmc_gr]
data_pdffit_gr = stem + "_pdffit.gr"

data_list = [
data_sq,
data_gr,
data_ft_sq,
data_ft_gr,
data_rmc_fq,
data_rmc_gr,
data_pdffit_gr
]

for file_name in data_list:
if file_name == data_pdffit_gr:
file_tmp = os.path.join(
main_window.output_folder,
"StoG",
data_rmc_gr
)
file_out_tmp = os.path.join(
main_window.output_folder,
"StoG",
data_pdffit_gr
)
try:
file_in = open(file_tmp, "r")
except FileNotFoundError:
err_msg = f"[Error] S(Q) data file {file_tmp} not found. "
err_msg += "Please check the output dir setting."
print(err_msg)
main_window.ui.statusbar.setStyleSheet("color: red")
main_window.ui.statusbar.showMessage(
"S(Q) file loading error, see the terminal for more info!",
main_window.statusbar_display_time
)
return

line = file_in.readline()
line = file_in.readline()
x_list = []
y_list = []
while line:
line = file_in.readline()
if line:
if line.split()[1] != "nan":
x_val = float(line.split()[0])
x_list.append(x_val)
y_val = float(line.split()[1])
kt = "NumberDensity"
rho_val = float(main_window._pystog_inputs_collect[kt])
kt = "FaberZiman"
fz_val = float(main_window._pystog_inputs_collect[kt])
y_val *= (4. * np.pi * x_val * rho_val / fz_val)
y_list.append(y_val)
file_in.close()

with open(file_out_tmp, "w") as f:
current_time = datetime.now()
current_timezone = datetime.now().astimezone().strftime("%Z")
current_weekday = current_time.weekday()
time_stamp = weekdays[current_weekday] + " "
time_stamp += current_time.strftime("%m-%d-%Y %H:%M:%S") + " "
time_stamp += current_timezone
kt = "Qmax"
ts_qmax = float(main_window._pystog_inputs_collect[kt])
f.write(f"# {len(x_list)}\n")
f.write("# Pair Distribution Function (PDF)\n")
f.write(f"# created: {time_stamp}\n")
str_tmp = f"# comment: neutron, Qmax={ts_qmax}, "
str_tmp += "Qdamp=0.017659, Qbroad=0.0191822\n"
f.write(str_tmp)
for count, r_val in enumerate(x_list):
if count == len(x_list) - 1:
f.write("{0:16.12F}{1:18.12F}".format(r_val,
y_list[count]))
else:
f.write("{0:16.12F}{1:18.12F}\n".format(r_val,
y_list[count]))

main_window._pystog_output_files[file_name] = {"xlist": x_list, "ylist": y_list}
file_list_tree.add_stog_data(file_name)

continue

file_tmp = os.path.join(main_window.output_folder,
"StoG",
file_name)
try:
file_in = open(file_tmp, "r")
except FileNotFoundError:
print(f"[Error] S(Q) data file {file_tmp} not found. Please check the output dir setting.")
err_msg = f"[Error] S(Q) data file {file_tmp} not found. "
err_msg += "Please check the output dir setting."
print(err_msg)
main_window.ui.statusbar.setStyleSheet("color: red")
main_window.ui.statusbar.showMessage("S(Q) file loading error, see the terminal for more info!",
main_window.statusbar_display_time)
main_window.ui.statusbar.showMessage(
"S(Q) file loading error, see the terminal for more info!",
main_window.statusbar_display_time
)
return

line = file_in.readline()
line = file_in.readline()
x_list = []
Expand All @@ -1163,6 +1332,8 @@ def add_stog_data(main_window):
main_window._pystog_output_files[file_name] = {"xlist": x_list, "ylist": y_list}
file_list_tree.add_stog_data(file_name)

return True


def generate_final(main_window):
x_vals_final = main_window._pystog_output_files[main_window._stem + "_rmc.gr"]["xlist"]
Expand All @@ -1175,7 +1346,7 @@ def generate_final(main_window):
faber_ziman = float(main_window._pystog_inputs_collect["FaberZiman"])
for count, item in enumerate(x_vals_final):
if (item <= rcut_final) and (item >= rmax_final or item <= rmin_final):
y_vals_final.append(faber_ziman)
y_vals_final.append(-faber_ziman)
else:
y_vals_final.append(y_vals_init[count])
final_file_name = main_window._stem + "_rmc_rr.gr"
Expand All @@ -1189,5 +1360,59 @@ def generate_final(main_window):
file_final_out.write("{0:10.4F}{1:15.6F}\n".format(item, y_vals_final[count]))
file_final_out.close()

main_window._pystog_output_files[final_file_name] = {"xlist": x_vals_final, "ylist": y_vals_final}
main_window._pystog_output_files[final_file_name] = {
"xlist": x_vals_final,
"ylist": y_vals_final
}
main_window.postprocessing_ui_m.frame_filelist_tree.add_stog_data(final_file_name)

final_file_pdffit = main_window._stem + "_rr_pdffit.gr"
kt = "NumberDensity"
rho_val = float(main_window._pystog_inputs_collect[kt])
x_final_pdffit = x_vals_final
y_final_pdffit = list()
for count, item in enumerate(x_final_pdffit):
yt = y_vals_final[count] * 4. * np.pi * item * rho_val / faber_ziman
y_final_pdffit.append(yt)

out_file = os.path.join(
main_window.output_folder,
"StoG",
final_file_pdffit
)
with open(out_file, "w") as f:
current_time = datetime.now()
current_timezone = datetime.now().astimezone().strftime("%Z")
current_weekday = current_time.weekday()
time_stamp = weekdays[current_weekday] + " "
time_stamp += current_time.strftime("%m-%d-%Y %H:%M:%S") + " "
time_stamp += current_timezone
kt = "Qmax"
ts_qmax = float(main_window._pystog_inputs_collect[kt])
f.write(f"# {len(x_final_pdffit)}\n")
f.write("# Pair Distribution Function (PDF)\n")
f.write(f"# created: {time_stamp}\n")
str_tmp = f"# comment: neutron, Qmax={ts_qmax}, "
str_tmp += "Qdamp=0.017659, Qbroad=0.0191822\n"
kt = "FourierFilter"
ft_sel = main_window._pystog_inputs_collect[kt]
if ft_sel:
kt = "Rmin"
ft_rmin = float(main_window._pystog_inputs_collect[kt])
str_tmp += f"# comment: Fourier filtered, rcut={ft_rmin} \n"
str_tmp += "# comment: Ripple removed, "
str_tmp += f"Rcutoff, 1st peak min, max = {rcut_final}, {rmin_final}, {rmax_final}\n"
f.write(str_tmp)
for count, r_val in enumerate(x_final_pdffit):
if count == len(x_final_pdffit) - 1:
f.write("{0:16.12F}{1:18.12F}".format(r_val,
y_final_pdffit[count]))
else:
f.write("{0:16.12F}{1:18.12F}\n".format(r_val,
y_final_pdffit[count]))

main_window._pystog_output_files[final_file_pdffit] = {
"xlist": x_final_pdffit,
"ylist": y_final_pdffit
}
main_window.postprocessing_ui_m.frame_filelist_tree.add_stog_data(final_file_pdffit)
Loading

5 comments on commit 645b882

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

GitLab pipeline for addie-dev has been submitted for this commit: "https://code.ornl.gov/sns-hfir-scse/deployments/addie-deploy/-/pipelines/487603"

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

GitLab pipeline for addie-qa has been submitted for this commit: "https://code.ornl.gov/sns-hfir-scse/deployments/addie-deploy/-/pipelines/487605"

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

GitLab pipeline for addie has been submitted for this commit: "https://code.ornl.gov/sns-hfir-scse/deployments/addie-deploy/-/pipelines/487753"

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

GitLab pipeline for addie-dev has been submitted for this commit: "https://code.ornl.gov/sns-hfir-scse/deployments/addie-deploy/-/pipelines/500949"

@github-actions
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

GitLab pipeline for addie-dev has been submitted for this commit: "https://code.ornl.gov/sns-hfir-scse/deployments/addie-deploy/-/pipelines/500950"

Please sign in to comment.