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@@ -23,6 +23,7 @@ if str(PROJECT_ROOT) not in sys.path:
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DATA_RAW = PROJECT_ROOT / "data" / "raw"
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DATA_GEN = PROJECT_ROOT / "data" / "gen"
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DEFAULT_METADATA_PATH = DATA_GEN / "metadata.pkl"
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+WWW_DIR = APP_DIR / "www"
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# -----------------------------------------------------------------------------
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# Local package imports
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@@ -67,7 +68,11 @@ def _empty_figure(message: str = "No plot available") -> go.Figure:
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def _load_metadata() -> pd.DataFrame:
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- """Load metadata table from disk or build it from DATA_RAW."""
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+ """Load metadata table from disk or build it from DATA_RAW.
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+
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+ If data/gen/metadata.pkl does not exist, the metadata table is recreated
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+ from data/raw and saved to data/gen/metadata.pkl.
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+ """
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if DEFAULT_METADATA_PATH.exists():
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df_meta = pd.read_pickle(DEFAULT_METADATA_PATH)
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else:
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@@ -100,10 +105,18 @@ DF_META = _load_metadata()
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def _metadata_for_display(df_meta: pd.DataFrame) -> pd.DataFrame:
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- """Return metadata with index columns exposed and an internal row_id."""
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+ """Return metadata for UI display.
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+
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+ Path-like columns are hidden from the table, but they remain available in
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+ DF_META for loading images.
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+ """
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df = df_meta.reset_index().copy()
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df.insert(0, "row_id", range(len(df)))
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+ # Hide all path-like columns from the UI table.
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+ df = df.loc[:, ~df.columns.str.contains("path", case=False)]
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+ df = df.loc[:, ~df.columns.str.contains("filename", case=False)]
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+
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preferred = [
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"row_id",
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"patient_id",
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@@ -113,8 +126,6 @@ def _metadata_for_display(df_meta: pd.DataFrame) -> pd.DataFrame:
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"is_corrupted",
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"PET_filename",
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"SEG_filename",
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- "PET_path",
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- "SEG_path",
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]
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cols = [c for c in preferred if c in df.columns] + [
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c for c in df.columns if c not in preferred
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@@ -124,6 +135,9 @@ def _metadata_for_display(df_meta: pd.DataFrame) -> pd.DataFrame:
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DF_DISPLAY = _metadata_for_display(DF_META)
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+ORGAN_CHOICES = ["All"] + sorted(DF_DISPLAY["organ"].dropna().astype(str).unique().tolist())
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+VISIT_CHOICES = ["All"] + [str(v) for v in sorted(DF_DISPLAY["visit"].dropna().unique().tolist())]
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+
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def _format_image_id(row: pd.Series) -> str:
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"""Create a readable image identifier from a selected metadata row."""
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@@ -166,11 +180,67 @@ def _safe_error_message(exc: BaseException) -> str:
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app_ui = ui.page_fluid(
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ui.head_content(
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- ui.tags.link(rel="shortcut icon", href="favicon.ico", type="image/x-icon")
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+ ui.tags.link(
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+ rel="shortcut icon",
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+ href="/favicon.ico?v=3",
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+ type="image/x-icon",
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+ )
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),
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ui.h2("Spatial SUV tail-feature explorer"),
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ui.layout_sidebar(
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ui.sidebar(
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+ ui.div(
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+ ui.h5("Run analysis"),
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+ ui.p("Select one row in the metadata table, then compute."),
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+ ui.input_action_button(
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+ "run",
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+ "Compute selected row",
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+ class_="btn-success btn-lg",
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+ width="100%",
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+ ),
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+ style="""
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+ position: sticky;
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+ top: 0;
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+ z-index: 1000;
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+ background: white;
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+ padding: 1rem 0 1rem 0;
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+ border-bottom: 1px solid #ddd;
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+ margin-bottom: 1rem;
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+ """,
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+ ),
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+ ui.h4("Metadata filters"),
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+ ui.input_text(
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+ "filter_patient",
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+ "Patient contains",
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+ value="",
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+ placeholder="e.g. A001",
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+ ),
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+ ui.input_select(
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+ "filter_organ",
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+ "Organ",
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+ choices=ORGAN_CHOICES,
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+ selected="All",
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+ ),
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+ ui.input_select(
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+ "filter_visit",
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+ "Visit",
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+ choices=VISIT_CHOICES,
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+ selected="All",
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+ ),
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+ ui.input_select(
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+ "filter_ae",
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+ "AE patient",
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+ choices=["All", "True", "False"],
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+ selected="All",
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+ ),
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+ ui.input_select(
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+ "filter_corrupted",
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+ "Corrupted",
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+ choices=["All", "True", "False"],
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+ selected="All",
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+ ),
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+ ui.hr(),
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+ ui.h4("Analysis settings"),
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ui.input_text(
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"probs",
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"Percentiles",
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@@ -204,14 +274,13 @@ app_ui = ui.page_fluid(
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ui.input_checkbox("compute_local_contrast", "Compute local contrast", value=True),
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ui.input_checkbox("compute_sphericity", "Compute sphericity", value=True),
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ui.input_checkbox("crop_to_roi", "Crop to ROI", value=True),
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- ui.hr(),
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- ui.input_action_button("run", "Compute selected row", class_="btn-primary"),
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- width=330,
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+ width=340,
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),
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ui.navset_tab(
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ui.nav_panel(
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"Metadata table",
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- ui.p("Select one row from the table, then click 'Compute selected row'."),
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+ ui.p("Filter and select one row, then click 'Compute selected row'."),
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+ ui.output_ui("filter_summary"),
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ui.output_data_frame("metadata_table"),
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),
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ui.nav_panel(
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@@ -246,12 +315,54 @@ app_ui = ui.page_fluid(
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def server(input: Inputs, output: Outputs, session: Session):
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+ @reactive.calc
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+ def filtered_metadata_display() -> pd.DataFrame:
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+ """Apply sidebar filters to the displayed metadata table."""
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+ df = DF_DISPLAY.copy()
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+
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+ patient_text = input.filter_patient().strip()
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+ organ = input.filter_organ()
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+ visit = input.filter_visit()
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+ ae = input.filter_ae()
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+ corrupted = input.filter_corrupted()
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+
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+ if patient_text:
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+ df = df[
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+ df["patient_id"]
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+ .astype(str)
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+ .str.contains(patient_text, case=False, na=False)
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+ ]
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+
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+ if organ != "All":
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+ df = df[df["organ"].astype(str) == organ]
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+
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+ if visit != "All":
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+ df = df[df["visit"].astype(str) == visit]
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+
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+ if ae != "All" and "is_AE_patient" in df.columns:
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+ df = df[df["is_AE_patient"].astype(bool) == (ae == "True")]
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+
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+ if corrupted != "All" and "is_corrupted" in df.columns:
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+ df = df[df["is_corrupted"].astype(bool) == (corrupted == "True")]
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+
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+ return df.reset_index(drop=True)
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+
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+ @render.ui
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+ def filter_summary():
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+ n_shown = len(filtered_metadata_display())
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+ n_total = len(DF_DISPLAY)
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+ return ui.div(
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+ ui.strong("Rows shown: "),
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+ f"{n_shown} / {n_total}",
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+ )
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+
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@render.data_frame
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def metadata_table():
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return render.DataGrid(
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- DF_DISPLAY,
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+ filtered_metadata_display(),
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selection_mode="row",
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- filters=True,
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+ filters=False,
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+ width="100%",
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height="650px",
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)
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@@ -260,7 +371,16 @@ def server(input: Inputs, output: Outputs, session: Session):
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selected = metadata_table.cell_selection()["rows"]
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if not selected:
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return None
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- return DF_DISPLAY.iloc[int(selected[0])]
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+
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+ df = filtered_metadata_display()
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+ if df.empty:
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+ return None
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+
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+ row_pos = int(selected[0])
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+ if row_pos >= len(df):
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+ return None
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+
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+ return df.iloc[row_pos]
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@reactive.calc
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@reactive.event(input.run)
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@@ -464,7 +584,7 @@ def server(input: Inputs, output: Outputs, session: Session):
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app = App(
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app_ui,
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server,
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- static_assets=Path(__file__).resolve().parent / "www",
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+ static_assets=WWW_DIR,
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)
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@@ -475,5 +595,3 @@ if __name__ == "__main__":
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# shiny run --reload shiny_app/app.py
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# Direct execution via `python shiny_app/app.py` works without auto-reload.
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run_app(app, host="127.0.0.1", port=8000, reload=False)
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-
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-
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