def _attempt_patient_name_from_mosaiq(headers):
UNKNOWN_PATIENT_NAME = "Unknown"
st.write("""
#### Corresponding Mosaiq SQL Details
""")
try:
(
machine_centre_map,
mosaiq_details,
mosaiq_servers,
) = _get_mosaiq_configuration(headers)
except KeyError:
st.warning("Need Mosaiq access to determine patient name. "
f"Patient name set to '{UNKNOWN_PATIENT_NAME}'.")
patient_name = UNKNOWN_PATIENT_NAME
return patient_name
try:
mosaiq_details = get_logfile_mosaiq_info(headers, machine_centre_map,
mosaiq_details,
mosaiq_servers)
except _NoMosaiqEntries:
st.warning(
"Searched Mosaiq for an entry corresponding to this logfile. "
"No entry was found. As such, for now, patient name has been "
f"set to '{UNKNOWN_PATIENT_NAME}'.")
patient_name = UNKNOWN_PATIENT_NAME
return patient_name
mosaiq_details = mosaiq_details.drop("beam_completed", axis=1)
st.write(mosaiq_details)
patient_names = set()
for _, row in mosaiq_details.iterrows():
st.write(row)
patient_name = utl_patient.convert_patient_name_from_split(
row["last_name"], row["first_name"])
patient_names.add(patient_name)
patient_name = _utilities.filter_patient_names(patient_names)
return patient_name
def trf_input_method(patient_id="", key_namespace="", **_):
indexed_trf_directory = get_indexed_trf_directory()
patient_id = st.text_input("Patient ID",
patient_id,
key=f"{key_namespace}_patient_id")
patient_id
filepaths = list(
indexed_trf_directory.glob(f"*/{patient_id}_*/*/*/*/*.trf"))
raw_timestamps = [
"_".join(path.parent.name.split("_")[0:2]) for path in filepaths
]
timestamps = list(
pd.to_datetime(raw_timestamps, format="%Y-%m-%d_%H%M%S").astype(str))
timestamp_filepath_map = dict(zip(timestamps, filepaths))
timestamps = sorted(timestamps, reverse=True)
if len(timestamps) == 0:
if patient_id != "":
st.write(
NoRecordsFound(
f"No TRF log file found for patient ID {patient_id}"))
return {"patient_id": patient_id}
if len(timestamps) == 1:
default_timestamp = timestamps[0]
else:
default_timestamp = []
selected_trf_deliveries = st.multiselect(
"Select TRF delivery timestamp(s)",
timestamps,
default=default_timestamp,
key=f"{key_namespace}_trf_deliveries",
)
if not selected_trf_deliveries:
return {}
"""
#### TRF filepath(s)
"""
selected_filepaths = [
timestamp_filepath_map[timestamp]
for timestamp in selected_trf_deliveries
]
[str(path.resolve()) for path in selected_filepaths]
"""
#### Log file header(s)
"""
headers = []
tables = []
for path in selected_filepaths:
header, table = read_trf(path)
headers.append(header)
tables.append(table)
headers = pd.concat(headers)
headers.reset_index(inplace=True)
headers.drop("index", axis=1, inplace=True)
headers
"""
#### Corresponding Mosaiq SQL Details
"""
mosaiq_details = get_logfile_mosaiq_info(headers)
mosaiq_details = mosaiq_details.drop("beam_completed", axis=1)
mosaiq_details
patient_names = set()
for _, row in mosaiq_details.iterrows():
row
patient_name = utl_patient.convert_patient_name_from_split(
row["last_name"], row["first_name"])
patient_names.add(patient_name)
patient_name = filter_patient_names(patient_names)
deliveries = cached_deliveries_loading(tables, delivery_from_trf)
individual_identifiers = [
f"{path.parent.parent.parent.parent.name} {path.parent.name}"
for path in selected_filepaths
]
identifier = f"TRF ({individual_identifiers[0]})"
return {
"patient_id": patient_id,
"patient_name": patient_name,
"data_paths": selected_filepaths,
"identifier": identifier,
"deliveries": deliveries,
}
def icom_input_method(patient_id="",
icom_directory=None,
key_namespace="",
advanced_mode_local=False,
**_):
if icom_directory is None:
icom_directory = get_default_icom_directory()
if advanced_mode_local:
icom_directory = st.text_input(
"iCOM Patient Directory",
str(icom_directory),
key=f"{key_namespace}_icom_directory",
)
icom_directory = pathlib.Path(icom_directory)
if advanced_mode_local:
patient_id = st.text_input("Patient ID",
patient_id,
key=f"{key_namespace}_patient_id")
patient_id
icom_deliveries = list(icom_directory.glob(f"{patient_id}_*/*.xz"))
icom_deliveries = sorted(icom_deliveries)
icom_files_to_choose_from = [path.stem for path in icom_deliveries]
timestamps = list(
pd.to_datetime(icom_files_to_choose_from,
format="%Y%m%d_%H%M%S").astype(str))
"""
Here you need to select the timestamps that correspond to a single
fraction of the plan selected above. Most of the time
you will only need to select one timestamp here, however in some
cases you may need to select multiple timestamps.
This can occur if for example a single fraction was delivered in separate
beams due to either a beam interupt, or the fraction being spread
over multiple energies
"""
if len(timestamps) == 0:
if patient_id != "":
st.write(
NoRecordsFound(
f"No iCOM delivery record found for patient ID {patient_id}"
))
return {"patient_id": patient_id}
if len(timestamps) == 1:
default_timestamp = timestamps[0]
else:
default_timestamp = []
timestamps = sorted(timestamps, reverse=True)
selected_icom_deliveries = st.multiselect(
"Select iCOM delivery timestamp(s)",
timestamps,
default=default_timestamp,
key=f"{key_namespace}_icom_deliveries",
)
icom_filenames = [
path.replace(" ", "_").replace("-", "").replace(":", "")
for path in selected_icom_deliveries
]
icom_paths = []
for icom_filename in icom_filenames:
icom_paths += list(
icom_directory.glob(f"{patient_id}_*/{icom_filename}.xz"))
if advanced_mode_local:
[str(path.resolve()) for path in icom_paths]
patient_names = set()
for icom_path in icom_paths:
patient_name = str(icom_path.parent.name).split("_")[-1]
try:
patient_name = utl_patient.convert_patient_name_from_split(
*patient_name.split(", "))
except: # pylint: disable = bare-except
pass
patient_names.add(patient_name)
patient_name = filter_patient_names(patient_names)
icom_streams = load_icom_streams(icom_paths)
deliveries = cached_deliveries_loading(icom_streams, delivery_from_icom)
if selected_icom_deliveries:
identifier = f"iCOM ({icom_filenames[0]})"
else:
identifier = None
if len(deliveries) == 0:
st.write(InputRequired("Please select at least one iCOM delivery"))
results = {
"patient_id": patient_id,
"patient_name": patient_name,
"icom_directory": str(icom_directory),
"selected_icom_deliveries": selected_icom_deliveries,
"data_paths": icom_paths,
"identifier": identifier,
"deliveries": deliveries,
}
return results
def icom_input_method(patient_id="",
key_namespace="",
advanced_mode_local=False,
**_):
icom_directories = _config.get_default_icom_directories()
if advanced_mode_local:
st.write("iCOM patient directories", icom_directories)
icom_directories = [pathlib.Path(path) for path in icom_directories]
if advanced_mode_local:
patient_id = st.text_input("Patient ID",
patient_id,
key=f"{key_namespace}_patient_id")
st.write(patient_id)
icom_deliveries = []
for path in icom_directories:
icom_deliveries += list(path.glob(f"{patient_id}_*/*.xz"))
icom_deliveries = sorted(icom_deliveries)
icom_files_to_choose_from = [path.stem for path in icom_deliveries]
timestamps = list(
pd.to_datetime(icom_files_to_choose_from,
format="%Y%m%d_%H%M%S").astype(str))
choice_path_map = dict(zip(timestamps, icom_deliveries))
st.write("""
Here you need to select the timestamps that correspond to a single
fraction of the plan selected above. Most of the time
you will only need to select one timestamp here, however in some
cases you may need to select multiple timestamps.
This can occur if for example a single fraction was delivered in separate
beams due to either a beam interrupt, or the fraction being spread
over multiple energies
""")
if len(timestamps) == 0:
if patient_id != "":
st.write(
_exceptions.NoRecordsFound(
f"No iCOM delivery record found for patient ID {patient_id}"
))
return {"patient_id": patient_id}
if len(timestamps) == 1:
default_timestamp = [timestamps[0]]
else:
default_timestamp = []
timestamps = sorted(timestamps, reverse=True)
try:
selected_icom_deliveries = st.multiselect(
"Select iCOM delivery timestamp(s)",
timestamps,
default=default_timestamp,
key=f"{key_namespace}_icom_deliveries",
)
except st.errors.StreamlitAPIException:
st.write(f"Default timestamp = `{default_timestamp}`")
st.write(f"All timestamps = `{timestamps}`")
raise
icom_filenames = [
path.replace(" ", "_").replace("-", "").replace(":", "")
for path in selected_icom_deliveries
]
icom_paths = []
for selected in selected_icom_deliveries:
icom_paths.append(choice_path_map[selected])
if advanced_mode_local:
st.write([str(path.resolve()) for path in icom_paths])
patient_names = set()
for icom_path in icom_paths:
patient_name = str(icom_path.parent.name).split("_")[-1]
try:
patient_name = utl_patient.convert_patient_name_from_split(
*patient_name.split(", "))
except: # pylint: disable = bare-except
pass
patient_names.add(patient_name)
patient_name = _utilities.filter_patient_names(patient_names)
icom_streams = load_icom_streams(icom_paths)
deliveries = _deliveries.cached_deliveries_loading(
icom_streams, _deliveries.delivery_from_icom)
if selected_icom_deliveries:
identifier = f"iCOM ({icom_filenames[0]})"
else:
identifier = None
if len(deliveries) == 0:
st.write(
_exceptions.InputRequired(
"Please select at least one iCOM delivery"))
st.stop()
results = {
"site": None,
"patient_id": patient_id,
"patient_name": patient_name,
"selected_icom_deliveries": selected_icom_deliveries,
"data_paths": icom_paths,
"identifier": identifier,
"deliveries": deliveries,
}
return results
