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Split scans between .comm/.incomm files on export

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For #21
This commit is contained in:
usov_i 2021-01-05 17:41:42 +01:00
parent b0a4e35d3d
commit c5ec09a5e3
4 changed files with 103 additions and 106 deletions
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2
pyzebra/__init__.py
View File

@ -1,6 +1,6 @@
from pyzebra.anatric import *
from pyzebra.ccl_findpeaks import ccl_findpeaks
from pyzebra.ccl_io import export_comm, load_1D, parse_1D
from pyzebra.ccl_io import export_1D, load_1D, parse_1D
from pyzebra.fit2 import fitccl
from pyzebra.h5 import *
from pyzebra.merge_function import add_dict, unified_merge

62
pyzebra/app/panel_ccl_integrate.py
View File

@ -68,7 +68,10 @@ def create():
det_data = {}
fit_params = {}
peak_pos_textinput_lock = False
js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
js_data = {
".comm": ColumnDataSource(data=dict(cont=[], ext=[])),
".incomm": ColumnDataSource(data=dict(cont=[], ext=[])),
}
def proposal_textinput_callback(_attr, _old, new):
ccl_path = os.path.join(PROPOSAL_PATH, new.strip())
@ -84,12 +87,7 @@ def create():
def _init_datatable():
scan_list = list(det_data["scan"].keys())
hkl = [
f'{int(m["h_index"])} {int(m["k_index"])} {int(m["l_index"])}'
if det_data["meta"]["indices"] == "hkl"
else f'{m["h_index"]} {m["k_index"]} {m["l_index"]}'
for m in det_data["scan"].values()
]
hkl = [f'{m["h_index"]} {m["k_index"]} {m["l_index"]}' for m in det_data["scan"].values()]
scan_table_source.data.update(
scan=scan_list,
hkl=hkl,
@ -511,26 +509,28 @@ def create():
preview_output_textinput = TextAreaInput(title="Export file preview:", width=500, height=400)
def preview_output_button_callback():
if det_data["meta"]["indices"] == "hkl":
ext = ".comm"
elif det_data["meta"]["indices"] == "real":
ext = ".incomm"
with tempfile.TemporaryDirectory() as temp_dir:
temp_file = temp_dir + "/temp"
export_data = deepcopy(det_data)
for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
if not export:
del export_data["scan"][s]
pyzebra.export_comm(
pyzebra.export_1D(
export_data,
temp_file,
lorentz=lorentz_toggle.active,
hkl_precision=int(hkl_precision_select.value),
)
with open(f"{temp_file}{ext}") as f:
preview_output_textinput.value = f.read()
exported_content = ""
for ext in (".comm", ".incomm"):
fname = temp_file + ext
if os.path.isfile(fname):
with open(fname) as f:
exported_content += f"{ext} file:\n" + f.read()
preview_output_textinput.value = exported_content
preview_output_button = Button(label="Preview file", default_size=200)
preview_output_button.on_click(preview_output_button_callback)
@ -539,37 +539,29 @@ def create():
title="hkl precision:", options=["2", "3", "4"], value="2", default_size=80
)
def export_results(det_data):
if det_data["meta"]["indices"] == "hkl":
ext = ".comm"
elif det_data["meta"]["indices"] == "real":
ext = ".incomm"
def save_button_callback():
with tempfile.TemporaryDirectory() as temp_dir:
temp_file = temp_dir + "/temp"
export_data = deepcopy(det_data)
for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
if not export:
del export_data["scan"][s]
pyzebra.export_comm(
export_data,
temp_file,
lorentz=lorentz_toggle.active,
hkl_precision=int(hkl_precision_select.value),
)
with open(f"{temp_file}{ext}") as f:
output_content = f.read()
pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
return output_content, ext
def save_button_callback():
cont, ext = export_results(det_data)
js_data.data.update(cont=[cont], ext=[ext])
for ext in (".comm", ".incomm"):
fname = temp_file + ext
if os.path.isfile(fname):
with open(fname) as f:
cont = f.read()
else:
cont = ""
js_data[ext].data.update(cont=[cont], ext=[ext])
save_button = Button(label="Download file", button_type="success", default_size=200)
save_button.on_click(save_button_callback)
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
save_button.js_on_click(CustomJS(args={"js_data": js_data[".comm"]}, code=javaScript))
save_button.js_on_click(CustomJS(args={"js_data": js_data[".incomm"]}, code=javaScript))
findpeak_controls = column(
row(peak_pos_textinput, column(Spacer(height=19), smooth_toggle)),

50
pyzebra/app/panel_param_study.py
View File

@ -77,7 +77,10 @@ def create():
det_data = {}
fit_params = {}
peak_pos_textinput_lock = False
js_data = ColumnDataSource(data=dict(cont=[], ext=[]))
js_data = {
".comm": ColumnDataSource(data=dict(cont=[], ext=[])),
".incomm": ColumnDataSource(data=dict(cont=[], ext=[])),
}
def proposal_textinput_callback(_attr, _old, new):
full_proposal_path = os.path.join(PROPOSAL_PATH, new.strip())
@ -612,51 +615,50 @@ def create():
preview_output_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
def preview_output_button_callback():
if det_data["meta"]["indices"] == "hkl":
ext = ".comm"
elif det_data["meta"]["indices"] == "real":
ext = ".incomm"
with tempfile.TemporaryDirectory() as temp_dir:
temp_file = temp_dir + "/temp"
export_data = deepcopy(det_data)
for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
if not export:
del export_data["scan"][s]
pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
with open(f"{temp_file}{ext}") as f:
preview_output_textinput.value = f.read()
pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
exported_content = ""
for ext in (".comm", ".incomm"):
fname = temp_file + ext
if os.path.isfile(fname):
with open(fname) as f:
exported_content += f"{ext} file:\n" + f.read()
preview_output_textinput.value = exported_content
preview_output_button = Button(label="Preview file", default_size=220)
preview_output_button.on_click(preview_output_button_callback)
def export_results(det_data):
if det_data["meta"]["indices"] == "hkl":
ext = ".comm"
elif det_data["meta"]["indices"] == "real":
ext = ".incomm"
def save_button_callback():
with tempfile.TemporaryDirectory() as temp_dir:
temp_file = temp_dir + "/temp"
export_data = deepcopy(det_data)
for s, export in zip(scan_table_source.data["scan"], scan_table_source.data["export"]):
if not export:
del export_data["scan"][s]
pyzebra.export_comm(export_data, temp_file, lorentz=lorentz_toggle.active)
with open(f"{temp_file}{ext}") as f:
output_content = f.read()
pyzebra.export_1D(export_data, temp_file, lorentz=lorentz_toggle.active)
return output_content, ext
def save_button_callback():
cont, ext = export_results(det_data)
js_data.data.update(cont=[cont], ext=[ext])
for ext in (".comm", ".incomm"):
fname = temp_file + ext
if os.path.isfile(fname):
with open(fname) as f:
cont = f.read()
else:
cont = ""
js_data[ext].data.update(cont=[cont], ext=[ext])
save_button = Button(label="Download file", button_type="success", default_size=220)
save_button.on_click(save_button_callback)
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
save_button.js_on_click(CustomJS(args={"js_data": js_data[".comm"]}, code=javaScript))
save_button.js_on_click(CustomJS(args={"js_data": js_data[".incomm"]}, code=javaScript))
findpeak_controls = column(
row(peak_pos_textinput, column(Spacer(height=19), smooth_toggle)),

95
pyzebra/ccl_io.py
View File

@ -208,13 +208,15 @@ def parse_1D(fileobj, data_type):
print("Unknown file extention")
# utility information
if all(
s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer()
for s in scan.values()
):
metadata["indices"] = "hkl"
else:
metadata["indices"] = "real"
metadata["indices"] = []
for s in scan.values():
if s["h_index"].is_integer() and s["k_index"].is_integer() and s["l_index"].is_integer():
s["h_index"] = int(s["h_index"])
s["k_index"] = int(s["k_index"])
s["l_index"] = int(s["l_index"])
metadata["indices"].append("hkl")
else:
metadata["indices"].append("real")
metadata["data_type"] = data_type
metadata["area_method"] = AREA_METHODS[0]
@ -222,54 +224,55 @@ def parse_1D(fileobj, data_type):
return {"meta": metadata, "scan": scan}
def export_comm(data, path, lorentz=False, hkl_precision=2):
"""exports data in the *.comm format
:param lorentz: perform Lorentz correction
:param path: path to file + name
:arg data - data to export, is dict after peak fitting
def export_1D(data, path, lorentz=False, hkl_precision=2):
"""Exports data in the .comm/.incomm format
Scans with integer/real hkl values are saved in .comm/.incomm files correspondingly. If no scans
are present for a particular output format, that file won't be created.
"""
zebra_mode = data["meta"]["zebra_mode"]
if data["meta"]["indices"] == "hkl":
extension = ".comm"
else: # data["meta"]["indices"] == "real":
extension = ".incomm"
file_content = {".comm": [], ".incomm": []}
with open(str(path + extension), "w") as out_file:
for key, scan in data["scan"].items():
if "fit" not in scan:
print("Scan skipped - no fit value for:", key)
continue
for (key, scan), indices in zip(data["scan"].items(), data["meta"]["indices"]):
if "fit" not in scan:
print("Scan skipped - no fit value for:", key)
continue
scan_str = f"{key:6}"
scan_str = f"{key:6}"
h, k, l = scan["h_index"], scan["k_index"], scan["l_index"]
if data["meta"]["indices"] == "hkl":
hkl_str = f"{int(h):6}{int(k):6}{int(l):6}"
else: # data["meta"]["indices"] == "real"
hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
h, k, l = scan["h_index"], scan["k_index"], scan["l_index"]
if indices == "hkl":
hkl_str = f"{h:6}{k:6}{l:6}"
else: # indices == "real"
hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
area_method = data["meta"]["area_method"]
area_n = scan["fit"][area_method].n
area_s = scan["fit"][area_method].s
area_method = data["meta"]["area_method"]
area_n = scan["fit"][area_method].n
area_s = scan["fit"][area_method].s
# apply lorentz correction to area
if lorentz:
if zebra_mode == "bi":
twotheta_angle = np.deg2rad(scan["twotheta_angle"])
corr_factor = np.sin(twotheta_angle)
else: # zebra_mode == "nb":
gamma_angle = np.deg2rad(scan["gamma_angle"])
nu_angle = np.deg2rad(scan["nu_angle"])
corr_factor = np.sin(gamma_angle) * np.cos(nu_angle)
# apply lorentz correction to area
if lorentz:
if zebra_mode == "bi":
twotheta_angle = np.deg2rad(scan["twotheta_angle"])
corr_factor = np.sin(twotheta_angle)
else: # zebra_mode == "nb":
gamma_angle = np.deg2rad(scan["gamma_angle"])
nu_angle = np.deg2rad(scan["nu_angle"])
corr_factor = np.sin(gamma_angle) * np.cos(nu_angle)
area_n = np.abs(area_n * corr_factor)
area_s = np.abs(area_s * corr_factor)
area_n = np.abs(area_n * corr_factor)
area_s = np.abs(area_s * corr_factor)
area_str = f"{area_n:10.2f}{area_s:10.2f}"
area_str = f"{area_n:10.2f}{area_s:10.2f}"
ang_str = ""
for angle, _ in CCL_ANGLES[zebra_mode]:
ang_str = ang_str + f"{scan[angle]:8}"
ang_str = ""
for angle, _ in CCL_ANGLES[zebra_mode]:
ang_str = ang_str + f"{scan[angle]:8}"
out_file.write(scan_str + hkl_str + area_str + ang_str + "\n")
file_content_ref = file_content[".comm"] if indices == "hkl" else file_content[".incomm"]
file_content_ref.append(scan_str + hkl_str + area_str + ang_str + "\n")
for ext, content in file_content.items():
if content:
with open(path + ext, "w") as out_file:
out_file.writelines(content)