def get_machine_centre_map():
config = st_config.get_config()
machine_centre_map = {}
for site in config["site"]:
for linac in site["linac"]:
machine_centre_map[linac["name"]] = site["name"]
return machine_centre_map
def advanced_debugging():
config = st_config.get_config()
st.sidebar.markdown("# Advanced Debugging")
if st.sidebar.button("Compare Baseline to Output Directory"):
"""
## Comparing Results to Baseline
"""
baseline_directory = pathlib.Path(
config["debug"]["baseline_directory"]).resolve()
png_baseline_directory = baseline_directory.joinpath("png")
baseline_png_paths = [
path for path in (png_baseline_directory.rglob("*"))
if path.is_file()
]
relative_png_paths = [
path.relative_to(png_baseline_directory)
for path in baseline_png_paths
]
output_dir = pathlib.Path(config["output"]["png_directory"]).resolve()
evaluation_png_paths = [
output_dir.joinpath(path) for path in relative_png_paths
]
for baseline, evaluation in zip(baseline_png_paths,
evaluation_png_paths):
f"### {baseline.parent.name}/{baseline.name}"
f"`{baseline}`\n\n**vs**\n\n`{evaluation}`"
baseline_image = imageio.imread(baseline)
try:
evaluation_image = imageio.imread(evaluation)
except FileNotFoundError as e:
"""
#### File was not found
"""
st.write(e)
f"""
For debugging purposes, here are all the files that
were found within {str(output_dir)}
"""
[str(path) for path in output_dir.rglob("*") if path.is_file()]
return
agree = np.allclose(baseline_image, evaluation_image)
f"Images Agree: `{agree}`"
def get_icom_live_stream_directories():
config = st_config.get_config()
icom_live_stream_directories = {}
for site in config["site"]:
icom_live_base_directory = pathlib.Path(
site["export-directories"]["icom_live"])
for linac in site["linac"]:
icom_live_stream_directories[linac["name"]] = str(
icom_live_base_directory.joinpath(linac["ip"]))
return icom_live_stream_directories
def get_mosaiq_details():
config = st_config.get_config()
mosaiq_details = {
site["name"]: {
"timezone": site["mosaiq"]["timezone"],
"server": f'{site["mosaiq"]["hostname"]}:{site["mosaiq"]["port"]}',
}
for site in config["site"]
}
return mosaiq_details
def get_default_gamma_options():
config = st_config.get_config()
default_gamma_options = config["gamma"]
return default_gamma_options
def get_default_icom_directories():
config = st_config.get_config()
default_icom_directory = config["icom"]["patient_directories"]
return default_icom_directory
def main():
config = st_config.get_config()
st.sidebar.markdown("""
# Overview
""")
st.sidebar.markdown("""
## Reference
""")
set_reference_overview = sidebar_overview()
st.sidebar.markdown("""
## Evaluation
""")
set_evaluation_overview = sidebar_overview()
overview_updater_map = {
"reference": set_reference_overview,
"evaluation": set_evaluation_overview,
}
st.sidebar.markdown("""
# Status indicators
""")
show_status_indicators()
st.sidebar.markdown("""
# Advanced options
Enable advanced functionality by ticking the below.
""")
advanced_mode = st.sidebar.checkbox("Run in Advanced Mode")
gamma_options = get_gamma_options(advanced_mode)
data_option_functions = {
"monaco": monaco_input_method,
"dicom": dicom_input_method,
"icom": icom_input_method,
"trf": trf_input_method,
"mosaiq": mosaiq_input_method,
}
default_reference_id = config["data_methods"]["default_reference"]
default_evaluation_id = config["data_methods"]["default_evaluation"]
available_data_methods = config["data_methods"]["available"]
default_reference = DATA_OPTION_LABELS[default_reference_id]
default_evaluation = DATA_OPTION_LABELS[default_evaluation_id]
data_method_map = {}
for method in available_data_methods:
data_method_map[
DATA_OPTION_LABELS[method]] = data_option_functions[method]
"""
### Reference
"""
reference_results = get_input_data_ui(
overview_updater_map,
data_method_map,
default_reference,
"reference",
advanced_mode,
)
"""
### Evaluation
"""
evaluation_results = get_input_data_ui(
overview_updater_map,
data_method_map,
default_evaluation,
"evaluation",
advanced_mode,
**reference_results,
)
"""
## Output Locations
"""
"""
### eSCAN Directory
The location to save the produced pdf report.
"""
default_site = evaluation_results.get("site", None)
if default_site is None:
default_site = reference_results.get("site", None)
_, escan_directory = st_misc.get_site_and_directory(
"eScan Site",
"escan",
default=default_site,
key="escan_export_site_picker")
if advanced_mode:
st.write(escan_directory.resolve())
default_png_output_directory = config["output"]["png_directory"]
if advanced_mode:
"""
### Image record
Path to save the image of the results for posterity
"""
png_output_directory = pathlib.Path(
st.text_input("png output directory",
default_png_output_directory))
st.write(png_output_directory.resolve())
else:
png_output_directory = pathlib.Path(default_png_output_directory)
"""
## Calculation
"""
if st.button("Run Calculation"):
"""
### MU Density usage warning
"""
st.warning(pymedphys.mudensity.WARNING_MESSAGE)
"""
### Calculation status
"""
run_calculation(
reference_results,
evaluation_results,
gamma_options,
escan_directory,
png_output_directory,
)
if advanced_mode:
advanced_debugging()
def get_logfile_root_dir():
config = st_config.get_config()
logfile_root_dir = pathlib.Path(config["trf_logfiles"]["root_directory"])
return logfile_root_dir