def create():
doc = curdoc()
def events_list_callback(_attr, _old, new):
doc.events_list_hdf_viewer.value = new
events_list = TextAreaInput(title="Spind events:", rows=7, width=1500)
events_list.on_change("value", events_list_callback)
doc.events_list_spind = events_list
lattice_const_textinput = TextInput(
title="Lattice constants:",
value="8.3211,8.3211,8.3211,90.00,90.00,90.00")
max_res_spinner = Spinner(title="max-res:", value=2, step=0.01, width=145)
seed_pool_size_spinner = Spinner(title="seed-pool-size:",
value=5,
step=0.01,
width=145)
seed_len_tol_spinner = Spinner(title="seed-len-tol:",
value=0.02,
step=0.01,
width=145)
seed_angle_tol_spinner = Spinner(title="seed-angle-tol:",
value=1,
step=0.01,
width=145)
eval_hkl_tol_spinner = Spinner(title="eval-hkl-tol:",
value=0.15,
step=0.01,
width=145)
diff_vec = []
ub_matrices = []
def process_button_callback():
# drop table selection to clear result fields
results_table_source.selected.indices = []
nonlocal diff_vec
with tempfile.TemporaryDirectory() as temp_dir:
temp_peak_list_dir = os.path.join(temp_dir, "peak_list")
os.mkdir(temp_peak_list_dir)
temp_event_file = os.path.join(temp_peak_list_dir, "event-0.txt")
temp_hkl_file = os.path.join(temp_dir, "hkl.h5")
comp_proc = subprocess.run(
[
"mpiexec",
"-n",
"2",
"python",
os.path.join(doc.spind_path, "gen_hkl_table.py"),
lattice_const_textinput.value,
"--max-res",
str(max_res_spinner.value),
"-o",
temp_hkl_file,
],
check=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
text=True,
)
print(" ".join(comp_proc.args))
print(comp_proc.stdout)
# prepare an event file
diff_vec = []
with open(temp_event_file, "w") as f:
for event in events_list.value.splitlines():
diff_vec.append(np.array(event.split()[4:7], dtype=float))
f.write(event + "\n")
print(f"Content of {temp_event_file}:")
with open(temp_event_file) as f:
print(f.read())
comp_proc = subprocess.run(
[
"mpiexec",
"-n",
"2",
"python",
os.path.join(doc.spind_path, "SPIND.py"),
temp_peak_list_dir,
temp_hkl_file,
"-o",
temp_dir,
"--seed-pool-size",
str(seed_pool_size_spinner.value),
"--seed-len-tol",
str(seed_len_tol_spinner.value),
"--seed-angle-tol",
str(seed_angle_tol_spinner.value),
"--eval-hkl-tol",
str(eval_hkl_tol_spinner.value),
],
check=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
text=True,
)
print(" ".join(comp_proc.args))
print(comp_proc.stdout)
spind_out_file = os.path.join(temp_dir, "spind.txt")
spind_res = dict(
label=[],
crystal_id=[],
match_rate=[],
matched_peaks=[],
column_5=[],
ub_matrix=[],
)
try:
with open(spind_out_file) as f_out:
for line in f_out:
c1, c2, c3, c4, c5, *c_rest = line.split()
spind_res["label"].append(c1)
spind_res["crystal_id"].append(c2)
spind_res["match_rate"].append(c3)
spind_res["matched_peaks"].append(c4)
spind_res["column_5"].append(c5)
# last digits are spind UB matrix
vals = list(map(float, c_rest))
ub_matrix_spind = np.transpose(
np.array(vals).reshape(3, 3))
ub_matrix = np.linalg.inv(ub_matrix_spind)
ub_matrices.append(ub_matrix)
spind_res["ub_matrix"].append(
str(ub_matrix_spind * 1e-10))
print(f"Content of {spind_out_file}:")
with open(spind_out_file) as f:
print(f.read())
except FileNotFoundError:
print("No results from spind")
results_table_source.data.update(spind_res)
process_button = Button(label="Process", button_type="primary")
process_button.on_click(process_button_callback)
if doc.spind_path is None:
process_button.disabled = True
ub_matrix_textareainput = TextAreaInput(title="UB matrix:",
rows=7,
width=400)
hkl_textareainput = TextAreaInput(title="hkl values:", rows=7, width=400)
def results_table_select_callback(_attr, old, new):
if new:
ind = new[0]
ub_matrix = ub_matrices[ind]
res = ""
for vec in diff_vec:
res += f"{ub_matrix @ vec}\n"
ub_matrix_textareainput.value = str(ub_matrix * 1e10)
hkl_textareainput.value = res
else:
ub_matrix_textareainput.value = ""
hkl_textareainput.value = ""
results_table_source = ColumnDataSource(
dict(label=[],
crystal_id=[],
match_rate=[],
matched_peaks=[],
column_5=[],
ub_matrix=[]))
results_table = DataTable(
source=results_table_source,
columns=[
TableColumn(field="label", title="Label", width=50),
TableColumn(field="crystal_id", title="Crystal ID", width=100),
TableColumn(field="match_rate", title="Match Rate", width=100),
TableColumn(field="matched_peaks",
title="Matched Peaks",
width=100),
TableColumn(field="column_5", title="", width=100),
TableColumn(field="ub_matrix", title="UB Matrix", width=700),
],
height=300,
width=1200,
autosize_mode="none",
index_position=None,
)
results_table_source.selected.on_change("indices",
results_table_select_callback)
tab_layout = column(
events_list,
row(
column(
lattice_const_textinput,
row(max_res_spinner, seed_pool_size_spinner),
row(seed_len_tol_spinner, seed_angle_tol_spinner),
row(eval_hkl_tol_spinner),
process_button,
),
column(results_table,
row(ub_matrix_textareainput, hkl_textareainput)),
),
)
return Panel(child=tab_layout, title="spind")
console.log(events);
for (event of events) {
console.log(event);
var url = `${app}/waveform/${run}/${event}`;
console.log(url);
window.open(url)
}
"""
# create a Javascript callback that will open an URL to view waveform
callback_btn_waveform = CustomJS(args=dict(ms=multi_select,
run=run_id,
app=APP_URL),
code=code)
btn_waveform = Button(label="View Waveform for Chosen Events")
btn_waveform.js_on_click(callback_btn_waveform)
btn_waveform.disabled = True
btn_waveform.align = "center"
btn_waveform.height = 30
btn_waveform.margin = (20, 0, 0, 0)
# add a btn to clear all options in multi select
def callback_btn_clear():
"""
Clears all optiosn in the multi select and disables buttons
"""
doc.add_next_tick_callback(partial(disable_btn, btn=btn_clear))
doc.add_next_tick_callback(partial(disable_btn, btn=btn_waveform))
doc.add_next_tick_callback(
partial(clear_options, multi_select=multi_select))
